Client Resources

Getting Started

Getting Started icon

What can OSC do for you? OSC's high performance computing, secure data storage and technical expertise can help advance research, accelerate business innovation and support classroom instruction.  

Our comprehensive services guide provides an overview of our resources and how you can use them.

  1. Cluster computing: OSC offers three supercomputer clusters – Pitzer, Owens and Ascend – that all support GPU computing.
     
  2. Research data storage: Clients can make use of work-area and supplemental storage during projects as well as long-term storage of data. Transfer files through our OnDemand platform or Globus subscription.
     
  3. Software: We provide a variety of software applications to support all aspects of scientific research. Ohio researchers may access licenses for some software packages through our statewide software program.
     
  4. Research software engineering: Our staff members can provide expert consultation on topics such as computing languages, programming models, numerical libraries and development tools for parallel/threaded computing and data analysis. 
     
  5. Data analytics and machine learning: Our hardware and software offerings can accommodate the intensive workloads of data analytics and machine learning work.
     
  6. Dependability: The State of Ohio Computer Center, home of our computing clusters, provides security, climate control and fully redundant systems designed to keep OSC online at all times.
     
  7. Education: Faculty and students can learn about high performance computing through our webinars, workshops and how-to guides. Classroom accounts are available to instructors seeking to incorporate HPC work into courses.

How does the academic community use OSC?

Faculty at Ohio higher education institutions use OSC to conduct original research in fields ranging from engineering and medicine to plant biology and political science. Our extensive collection of case studies shows the breadth of research work underway, how graduate and undergraduate students are gaining critical HPC experience, and how academic clients make use of the wide variety of services and expert support that OSC provides.

How does the commercial and nonprofit community use OSC?

Commercial and nonprofit clients across the United States use OSC for research, simulations, development and testing of products. Our extensive collection of case studies offers examples of this work, including clients involved with pharmaceutical drug development, the simulation of how fluid dynamics impact vehicle performance, the study of factors impacting oil and gas pipeline corrosion, and the advancement of weather-forecasting technology.

What does it cost to use OSC?

As an academic computing resource for the State of Ohio, OSC is always free for Ohio classroom usage, and academic researchers in Ohio qualify for credits that largely or completely offset fees. Commercial and nonprofit clients purchase services at set rates.  Find more details about our cost structure.  

What training or client support does OSC offer?

OSC provides a variety of training and support options for clients:

Ready to take the next step?

Interested in arranging a presentation for your group about OSC’s resources and services? Please contact us at oschelp@osc.edu.

Ready to get started now?

Request a new login ID for an existing project

Request a new project

 

New User Resource Guide

Getting Started at OSC

This guide was created for new users of OSC.

It explains how to use OSC from the very beginning of the process, from creating an account right up to using resources at OSC.

OSC account setup

The first step is to make sure that you have an OSC username.

There are multiple ways to start this process.

You can sign up at MyOSC or be invited to use OSC via email.

Make sure to select the PI checkbox if you are a PI at your institution and want to start your own project at OSC.

After creating an account at MyOSC, you may not be able to log into OSC using OnDemand or an SSH client. If you do not have access to a project, you would get an "invalid credentials" message, although the credentials are correct. Sometimes OSC administrators need to approve your username if your institution is not recognized in our database. 

Contact OSC Help with questions.

Email notifications from OSC

As soon as you register for an account with OSC, you will start receiving automated emails from MyOSC. These include password expiration emails, access to project(s), etc. These are sent from "no-reply@osc.edu."  All folders should be checked, including spam/junk. If you did not receive this email, please contact OSC Help.

OSC will also add you to our mailing list within a month of your account being opened. Emails will be sent from  oschelp@osc.edu for system notices, monthly newsletters, event updates, etc. This information can also be found on our events page and known issues page.

Finally, we may notify clients through ServiceNow, our internal ticketing and monitoring system. These notices will come from the OH-TECH Service Desk, support@oh-tech.org.

Project and user management

Creating a project

Only users with PI status are able to create a project. See how to request PI status in manage profile information. Follow the instructions in creating projects and budgets to create a new project.

Adding new or existing users to a project

Once a project is created, the PI should add themselves to it and any others that they want to permit to use OSC resources under their project.

Refer to adding/inviting users to a project for details on how to do this.

Reuse an existing project

If there was already a project that you would like to reuse, follow the same instructions as found in creating projects and budget, but skip to the budget creation section.

These instructions are the same for projects which are restricted. Creating a new budget and getting it activated or approved will set the project to active.

Costs of OSC resources

If there are questions about the cost, refer to service costs.

Generally, an Ohio academic PI can create a budget for $1,000 on a project and use the annual $1,000 credit offered to Ohio academic PIs. Review service cost terms for explanations of budgets and credits at OSC.

See the complete MyOSC documentation in our Client Portal here. The OSCusage command can also provide useful details. 

Classroom project support

OSC supports classrooms by making it simpler for students to use OSC resources through a customizable OnDemand interface at class.osc.edu

Visit the OSC classroom resource guide and contact oschelp@osc.edu if you want to discuss the options there.

There will be no charges for classroom projects.

Transfer files to/from OSC systems

There are a few options for transferring files between OSC and other systems.

OnDemand file explorer

Using the OnDemand file explorer is the quickest option to get started. Just log into ondemand.osc.edu and click "File Explorer" from the navigation bar at the top of the page. From there you can upload/download files and directories.

Users cannot access ondemand.osc.edu unless they have an active OSC account and have been added to at least one project. Refer to the above sections which cover this.

This is a simple option, but for files or directories that are very large, it may not be best. See other options below in this case.

SFTP client software

Local software can be used to connect to OSC for downloading and uploading files.

There are quite a few options for this, and OSC does not have a preference for which one you use.

The general guidance for all of them is to connect to host sftp.osc.edu using port 22.

Globus

Using Globus is recommended for users that frequently need to transfer many large files/dirs.

We have documentation detailing how to connect to our OSC endpoint in Globus and how to set up a local endpoint on your machine with Globus.

Request extra storage for a project

Storage can be requested for a project that is larger than the standard offered by home directories.

On the project details page, submit a "Request Storage Change" and a ticket will be created for OSC staff to create the project space quota. 

Make sure that the cost of storage is understood prior to sending the request.
See service costs for details.

Getting started using OSC

Finally, after the above setup, you can start using OSC resources. Usually you have some setup that needs to be performed before you can really start using OSC, like creating a custom environment, gaining access to preinstalled software or installing software to your home directory that is not already available.

Interactive desktop session

The best place to start is by visiting ondemand.osc.edu, logging in and starting an interactive desktop session.

Look for the navigation bar at the top of the page and select Interactive Apps, then Owens Desktop.

Notice that there are a lot of fields, but the most important ones, for now, are cores and the number of hours.

Try using only a single core at first, until you are more familiar with the system and can decide when more cores will be needed.

Other interactive apps

If there is specific software in the Interactive Apps list that you want to use, then go ahead and start a session with it. Just remember to change the cores to one until you understand what you need.

Getting to a terminal without starting a desktop session

A terminal session can also be started in OnDemand by clicking Clusters then Owens Shell Access.

In this terminal you can perform the needed commands in the below sections on environment setup and software use/installation.

You can choose to log into OSC with any ssh client available. Make sure to use either owens.osc.edu or pitzer.osc.edu as the hostname to connect to.

Environment setup to install packages for different programming languages

Some of the common programming languages for which users need an environment set up are python and R.

See add python packages with conda or R software for details.

There are other options, so please browse the OSC software listing.

OSC managed software

All the software already available at OSC can be found in the software listing.

Each page has some information on how to use the software from a command line. If you are unfamiliar with the command line in Linux, then try reviewing some Linux tutorials.

For now, try to get comfortable with moving to different directories on the filesystem, creating and editing files, and using the module commands from the software pages.

Install software not provided by OSC

Software not already installed on OSC systems can be installed locally to one's home directory without admin privileges. Try reviewing locally installing software at OSC.

This may be difficult for new users to accomplish; please contact OSC Help with questions.

Batch system basics

After getting set up at OSC and understanding the use of interactive sessions, you should start looking into how to utilize the batch system to have your software run programmatically.

The benefits of the batch system are that a user can submit what we call a job (a request to reserve resources) and have the job execute from start to finish without any interaction by the user.

A good place to start is by reviewing job scripts.

OnDemand job composer

OnDemand provides a convenient method for editing and submitting jobs in the job composer.

It can be used by logging into ondemand.osc.edu and clicking Jobs at the top and then Job Composer. A short help message should be shown on basic usage.

Training

OSC offers periodic training both at our facility and at universities across the state on a variety of topics. Additionally, we will partner with other organizations to enable our users to access additional training resources. 

We are currently in the process of updating our training strategy and documents. If you are interested in having us come to your campus to provide training, please contact OSC Help. You can also contact us if there is a specific training need you would like to see us address.

To get an introduction to HPC, see our HPC Basics page.

To learn more about using the command line, see our UNIX Basics page.

For detailed instructions on how to perform tasks on our systems, check out HOWTO articles

Still Need Help?

Before contacting OSC Help, please check to see if your question is answered in either the FAQ or the Knowledge Base. Many of the questions asked by both new and experienced OSC users are answered on these web pages.

If you still cannot solve your problem, please do not hesitate to contact OSC Help:

Phone: (614) 292-1800
Email: oschelp@osc.edu
Submit your issue online
Schedule virtual consultation

Basic and advanced support is available Monday through Friday, 9 a.m.– 5 p.m., except for these listed holidays.

We recommend following HPCNotices on X to get up-to-the-minute information on system outages and important operations-related updates.

Supercomputer: 

HPC Basics

New! Online Training Courses

Check out our new online training courses for an introduction to OSC services. You can get more information on the OSC Training page.

Overview

HPC, or High Performance Computing, generally refers to aggregating computing resources together in order to perform more computing operations at once.

Basic definitions

  • Core (processor) - A single unit that executes a single chain of instructions.
  • Node - a single computer or server.
  • Cluster - many nodes connected together which are able to coordinate between themselves.

HPC Workflow

Using HPC is a little different from running programs on your desktop. When you login you’ll be connected to one of the system’s “login nodes”. These nodes serve as a staging area for you to marshal your data and submit jobs to the batch scheduler. Your job will then wait in a queue along with other researchers' jobs. Once the resources it requires become available, the batch scheduler will then run your job on a subset of our hundreds of “compute nodes”. You can see the overall structure in the diagram below.

 

Diagram: Several connected parts illustrating the layout of an OSC cluster. Users connect to one of a few "login nodes", which in turn connect to the "batch system", which runs jobs on a subset of the "compute nodes". The "shared filesystem" is connected to both the login nodes and the compute nodes.

 

HPC Citizenship

An important point about the diagram above is that OSC clusters are a collection of shared, finite resources. When you connect to the login nodes, you are sharing their resources (CPU cycles, memory, disk space, network bandwidth, etc.) with a few dozen other researchers. The same is true of the file servers when you access your home or project directories, and can even be true of the compute nodes.

For most day-to-day activities you should not have to worry about this, and we take precautions to limit the impact that others might have on your experience. That said, there are a few use cases that are worth watching out for:

  • The login nodes should only be used for light computation; any CPU- or memory-intensive operations should be done using the batch system. A good rule of thumb is that if you wouldn't want to run a task on your personal desktop because it would slow down other applications, you shouldn't run it on the login nodes. (See also: Interactive Jobs.)

  • I/O-intensive jobs should copy their files to fast, temporary storage, such as the local storage allocated to jobs or the Scratch parallel filesystem.

  • When running memory-intensive or potentially unstable jobs, we highly recommend requesting whole nodes.  By doing so you prevent other users jobs from being impacted by your job.

  • If you request partial nodes, be sure to consider the amount of memory available per core. (See: HPC Hardware.) If you need more memory, request more cores. It is perfectly acceptable to leave cores idle in this situation; memory is just as valuable a resource as processors.

In general, we just encourage our users to remember that what you do may affect other researchers on the system. If you think something you want to do or try might interfere with the work of others, we highly recommend that you contact us at oschelp@osc.edu.

Getting Connected

There are two ways to connect to our systems. The traditional way will require you to install some software locally on your machine, including an SSH client, SFTP client, and optionally an X Windows server. The alternative is to use our zero-client web portal, OnDemand.

OnDemand Web Portal

OnDemand is our "one stop shop" for access to our High Performance Computing resources. With OnDemand, you can upload and download files, create, edit, submit, and monitor jobs, run GUI applications, and connect via SSH, all via a web broswer, with no client software to install and configure.

You can access OnDemand by pointing a web browser to ondemand.osc.edu. Documentation is available here. Any newer version of a common web brower should be sufficient to connect.

Using Traditional Clients

Required Software

In order to use our systems, you'll need two main pieces of software: an SFTP client and an SSH client.

SFTP ("SSH File Transfer Protocol") clients allow you transfer files between your workstation and our shared filesystem in a secure manner. We recommend the following applications:

  • FileZilla: A high-performance open-source client for Windows, Linux, and OS X. A guide to using FileZilla is available here (external).
  • CyberDuck: A high quality free client for Windows and OS X.
  • sftp: The command-line utility sftp comes pre-installed on OS X and most Linux systems.

SSH ("Secure Shell") clients allow you to open a command-line-based "terminal session" with our clusters. We recommend the following options:

  • PuTTY: A simple, open-source client for Windows.
  • Secure Shell for Google Chrome: A free, HTML5-based SSH client for Google Chrome.
  • ssh: The command-line utility ssh comes pre-installed on OS X and most Linux systems.

A third, optional piece of software you might want to install is an X Windows server, which will be necessary if you want to run graphical, windowed applications like MATLAB. We recommend the following X Windows servers:

  • Xming: Xming offers a free version of their X Windows server for Microsoft Windows systems.
  • X-Win32: StarNet's X-Win32 is a commercial X Windows server for Microsoft Windows systems. They offer a free, thirty-day trial.
  • X11.app/XQuartz: X11.app, an Apple-supported version of the open-source XQuartz project, is freely available for OS X. 

In addition, for Windows users, you can use OSC Connectwhich is a native windows application developed by OSC to provide a launcher for secure file transfer, VNC, terminal, and web based services, as well as preconfigured management of secure tunnel connections. See this page for more information on OSC Connect. 

Connecting via SSH

The primary way you'll interact with the OSC clusters is through the SSH terminal. See our supercomputing environments for the hostnames of our current clusters. You should not need to do anything special beyond entering the hostname.

Once you've established an SSH connection, you will be presented with some informational text about the cluster you've connected to followed by a UNIX command prompt. For a brief discussion of UNIX command prompts and what you can do with them, see the next section of this guide.

Transferring Files

To transfer files, use your preferred SFTP client to connect to:

sftp.osc.edu

You may see warning message including SSH key fingerprint. Verify that the fingerprint in the message matches one of the SSH key fingerprint listed here, then type yes.

Since process times are limited on the login nodes, trying to transfer large files directly to pitzer.osc.edu or other login nodes may terminate partway through. The sftp.osc.edu is specially configured to avoid this issue, and so we recommend it for all your file transfers.

Note: The sftp.osc.edu host is not connected to the scheduler, so you cannot submit jobs from this host. Use of this host for any purpose other than file transfer is not permitted.

Firewall Configuration 

See our Firewall and Proxy Settings page for information on how to configure your firewall to allow connection to and from OSC.

Setting up X Windows (Optional)

With an X Windows server you will be able to run graphical applications on our clusters that display on your workstation. To do this, you will need to launch your X Windows server before connecting to our systems. Then, when setting up your SSH connection, you will need to be sure to enable "X11 Forwarding".

For users of the command-line ssh client, you can do this by adding the "-X" option. For example, the below will connect to the Pitzer cluster with X11 forwarding:

$ ssh -X username@pitzer.osc.edu

If you are connecting with PuTTY, the checkbox to enable X11 forwarding can be found in the connections pane under "Connections → SSH → X11".

For other SSH clients, consult their documentation to determine how to enable X11 forwarding.

NOTE: The X-Windows protocol is not a high-performance one. Depending on your system and Internet connection, X Windows applications may run very slowly, even to the point of being unusable. If you find this to be the case and graphical applications are a necessity for your work, please contact OSC Help to discuss alternatives.
Supercomputer: 
Service: 

Budgets and Accounts

The Ohio Supercomputer Center provides services to clients from a variety of types of organizations. The methods for gaining access to the systems are different between Ohio academic institutions and everyone else.

Ohio academic clients

Primarily, our users are Ohio-based and academic, and the vast majority of our resources will continue to be consumed by Ohio-based academic users. See the "Ohio Academic Fee Model FAQ" section on our service costs webpage.

Other clients

Other users (business, non-Ohio academic, nonprofit, hospital, etc.) interested in using Center resources may purchase services at a set rate available on our price list. Expert consulting support is also available.

Other computing centers

For users interested in gaining access to larger resources, please contact OSC Help. We can assist you in applying for resources at an NSF or XSEDE site.

Managing an OSC project

Once a project has been created, the PI can create accounts for users by adding them through the client portal. Existing users can also be added. More information can be found on the Project Menu documentation page.

I need additional resources for my existing project and/or I received an email my allocation is exhausted

If an academic PI wants a new project or to update the budget balance on an existing project(s), please see our creating projects and budget documentation

I wish to use OSC to support teaching a class

We provide special classroom projects for this purpose and at no cost. You may use the client portal after creating an account. The request will need to include a syllabus or a similar document. 

I don't think I fit in the above categories

Please contact us in order to discuss options for using OSC resources.

Project Applications

Application if you are employed by an Ohio Academic Institution

Please contact OSC Help with questions and see the fee structure FAQ

Use of computing resources and services at OSC is subject to the Ohio Supercomputer Center (OSC) Code of Ethics for Academic Users.  Ohio Academic Clients are eligible for highly subsidized access to OSC resources, with fees only accruing after a credit provided is exhausted. Clients from an Ohio academic institution that expect to use more than the credit should consult with their institution on the proper guidance for requesting approval to be charged for usage. See the academic fee structure FAQ page for more information.

Eligible principal investigators (PIs) at Ohio academic institutions are able to request projects at OSC, but should also consult with their institution before incurring charges. In order to be an eligible PI at OSC, you must be eligible to hold PI status at your college, university, or research organization administered by an Ohio academic institution (i.e., be a full-time, permanent academic researcher or tenure-track faculty member at an Ohio college or university). Students, post-doctoral fellows, visiting scientists, and others who wish to use the facilities may be authorized users on projects headed by an eligible PI. Once a PI has received their project information, he/she can manage users for the project. Principal Investigators of OSC projects are responsible for updating their authorized user list, their outside funding sources, and their publications and presentations that cite OSC. All of these tasks can be accomplished by contacting using the client portal. Please review the documentation for more information. PIs are also responsible for monitoring their project's budget (balance) and for requesting a new budget (balance) before going negative, as projects with negative balances are restricted.

OSC's online project requests through our Client Portal is part of an electronic system that leads you through the process step by step. Before you begin to fill in the application form, especially if you are new to the process, look at the academic fee structure page.  You can save a partially completed project request for later use.

If you need assistance, please contact OSC Help.

Application if you are NOT employed by an Ohio Academic Institution

Researchers from businesses, non-Ohio academic, nonprofits, hospitals or other organizations (which do not need to be based in Ohio) who wish to use the OSC's resources should complete the Other Client request form available here. All clients not affiliated with and approved by an Ohio academic institution must sign a service agreement, provide a $500 deposit, and pay for resource usage per a standard price list.

Letter of Commitment for Outside Funding Proposals

OSC will provide a letter of commitment users can include with their account proposals for outside funding, such as from the Department of Energy, National Institutes of Health, National Science Foundation (limited to standard text, per NSF policy), etc. This letter details OSC's commitment to supporting research efforts of its users and the facilities and platforms we provide our users. [Note: This letter does not waive the normal OSC budget process; it merely states that OSC is willing to support such research.] The information users must provide for the letter is:

  • address to which the letter should be directed (e.g. NSF, Department, mailing address)
  • name of funding agency's representative
  • name of the proposal, as well as names and home institutions of the Co-PIs
  • budget amount per year you would apply for if you were to receive funding
  • number of years of proposed research
  • solicitation number

Send e-mail with your request for the commitment letter to OSC Help or submit online. We will prepare a draft for your approval and then we will send you the final PDF for your proposal submission. Please allow at least two working days for this service.

Letter of Support for Outside Funding Proposals

Letters of support may be subject to strict and specific guidelines, and may not be accepted by your funding agency.

If you need a letter of support, please see above "Letter of Commitment for Outside Funding Proposals". 

Applying at NSF Centers

Researchers requiring additional computing resources should consider applying for allocations at National Science Foundation Centers. For more information, please write to oschelp@osc.edu, and your inquiry will be directed to the appropriate staff member.:

We require you cite OSC in any publications or reports that result from projects supported by our services.

UNIX Basics

OSC HPC resources use an operating system called "Linux", which is a UNIX-based operating system, first released on 5 October 1991. Linux is by a wide margin the most popular operating system choice for supercomputing, with over 90% of the Top 500 list running some variant of it. In fact, many common devices run Linux variant operating systems, including game consoles, tablets, routers, and even Android-based smartphones.

While Linux supports desktop graphical user interface configurations (as does OSC) in most cases, file manipulation will be done via the command line. Since all jobs run in batch will be non-interactive, they by definition will not allow the use of GUIs. Thus, we strongly suggest new users become comfortable with basic command-line operations, so that they can learn to write scripts to submit to the scheduler that will behave as intended. We have provided some tutorials explaining basics from moving about the file system, to extracting archives, to modifying your environment, that are available for self-paced learning.

Linux Command Line Fundamentals

This tutorial teaches you about the linux command line and shows you some useful commands. It also shows you how to get help in linux by using the man and apropos commands.


Linux Tutorial

This tutorial guides you through the process of creating and submitting a batch script on one of our compute clusters. This is a linux tutorial which uses batch scripting as an example, not a tutorial on writing batch scripts. The primary goal is not to teach you about batch scripting, but for you to become familiar with certain linux commands that can be used either in a batch script or at the command line. There are other pages on the OSC web site that go into the details of submitting a job with a batch script.


Linux Shortcuts

This tutorial shows you some handy time-saving shortcuts in linux. Once you have a good understanding of how the command line works, you will want to learn how to work more efficiently.


Tar Tutorial

This tutorial shows you how to download tar (tape archive) files from the internet and how to deal with large directory trees of files.


Service: 

Linux Command Line Fundamentals

 

Description

This tutorial teaches you about the linux command line and shows you some useful commands. It also shows you how to get help in linux by using the man and apropos commands.

For more training and practice using the command line, you can find many great tutorials. Here are a few:

https://www.learnenough.com/command-line-tutorial

https://cvw.cac.cornell.edu/Linux/

http://www.ee.surrey.ac.uk/Teaching/Unix/

https://www.udacity.com/course/linux-command-line-basics--ud595

 

More Advanced:

http://moo.nac.uci.edu/~hjm/How_Programs_Work_On_Linux.html

Prerequisites

None.

Introduction

Unix is an operating system that comes with several application programs. Other examples of operating systems are Microsoft Windows, Apple OS and Google's Android. An operating system is the program running on a computer (or a smartphone) that allows the user to interact with the machine -- to manage files and folders, perform queries and launch applications. In graphical operating systems, like Windows, you interact with the machine mainly with the mouse. You click on icons or make selections from the menus. The Unix that runs on OSC clusters gives you a command line interface. That is, the way you tell the operating system what you want to do is by typing a command at the prompt and hitting return. To create a new folder you type mkdir. To copy a file from one folder to another, you type cp. And to launch an application program, say the editor emacs, you type the name of the application. While this may seem old-fashioned, you will find that once you master some simple concepts and commands you are able to do what you need to do efficiently and that you have enough flexibility to customize the processes that you use on OSC clusters to suit your needs.

Common Tasks on OSC Clusters

What are some common tasks you will perform on OSC clusters? Probably the most common scenario is that you want to run some of the software we have installed on our clusters. You may have your own input files that will be processed by an application program. The application may generate output files which you need to organize. You will probably have to create a job script so that you can execute the application in batch mode. To perform these tasks, you need to develop a few different skills. Another possibility is that you are not just a user of the software installed on our clusters but a developer of your own software -- or maybe you are making some modifications to an application program so you need to be able to build the modified version and run it. In this scenario you need many of the same skills plus some others. This tutorial shows you the basics of working with the Unix command line. Other tutorials go into more depth to help you learn more advanced skills.

The Kernel and the Shell

You can think of Unix as consisting of two parts -- the kernel and the shell. The kernel is the guts of the Unix operating system -- the core software running on a machine that performs the infrastructure tasks like making sure multiple users can work at the same time. You don't need to know anything about the kernel for the purposes of this tutorial. The shell is the program that interprets the commands you enter at the command prompt. There are several different flavors of Unix shells -- Bourne, Korn, Cshell, TCshell and Bash. There are some differences in how you do things in the different shells, but they are not major and they shouldn't show up in this tutorial. However, in the interest of simplicity, this tutorial will assume you are using the Bash shell. This is the default shell for OSC users. Unless you do something to change that, you will be running the Bash shell when you log onto Owens or Pitzer.

The Command Prompt

The first thing you need to do is log onto one of the OSC clusters, Owens or Pitzer. If you do not know how to do this, you can find help at the OSC home page. If you are connecting from a Windows system, you need to download and setup the OSC Starter Kit which you can find here. If you are connecting from a Mac or Linux system, you will use ssh. To get more information about using ssh, go to the OSC home page, hold your cursor over the "Supercomputing" menu in the main blue menu bar and select "FAQ." This should help you get started. Once you are logged in look for the last thing displayed in the terminal window. It should be something like

-bash-3.2$

with a block cursor after it. This is the command prompt -- it's where you will see the commands you type in echoed to the screen. In this tutorial, we will abbreviate the command prompt with just the dollar sign - $. The first thing you will want to know is how to log off. You can log off of the cluster by typing "exit" then typing the <Enter> key at the command prompt:

$ exit <Enter>

For the rest of this tutorial, when commands are shown, the <Enter> will be omitted, but you must always enter <Enter> to tell the shell to execute the command you just typed.

First Simple Commands

So let's try typing a few commands at the prompt (remember to type the <Enter> key after the command):

$ date

$ cal

$ finger

$ who

$ whoami

$ finger -l

That last command is finger followed by a space then a minus sign then the lower case L. Is it obvious what these commands do? Shortly you will learn how to get information about what each command does and how you can make it behave in different ways. You should notice the difference between "finger" and "finger -l" -- these two commands seem to do similar things (they give information about the users who are logged in to the system) but they print the information in different formats. try the two commands again and examine the output. Note that you can use the scroll bar on your terminal window to look at text that has scrolled off the screen.

man

The "man" command is how you find out information about what a command does. Type the following command:

$ man

It's kind of a smart-alecky answer you get back, but at least you learn that "man" is short for "manual" and that the purpose is to print the manual page for a command. Before we start looking at manual pages, you need to know something about the way Unix displays them. It does not just print the manual page and return you to the command prompt -- it puts you into a mode where you are interactively viewing the manual page. At the bottom of the page you should see a colon (:) instead of the usual command prompt (-bash-3.2$). You can move around in the man page by typing things at the colon. To exit the man page, you need to type a "q" followed by <Enter>. So try that first. Type

$ man finger

then at the colon of the man page type

: q

You do not have to type <Enter> after the "q" (this is different from the shell prompt.) You should be back at the shell prompt now. Now let's go through the man page a bit. Once again, type

$ man finger

Now instead of just quitting, let's look at the contents of the man page. The entire man page is probably not displayed in your terminal. To scroll up or down, use the arrow keys or the <Page Up> and <Page Down> keys of the keyboard. The <Enter> and <Space> keys also scroll. Remember that "q" will quit out of the man page and get you back to the shell prompt.

The first thing you see is a section with the heading "NAME" which displays the name of the command and a short summary of what it does. Then there is a section called "SYNOPSIS" which shows the syntax of the command. In this case you should see

SYNOPSIS

     finger [-lmsp] [user ...] [user@host ...]

Remember how "finger" and "finger -l" gave different output? The [-lmsp] tells you that you can use one of those four letters as a command option -- i.e., a way of modifying the way the command works. In the "DESCRIPTION" section of the man page you will see a longer description of the command and an explanation of the options. Anything shown in the command synopsis which is contained within square brackets ([ ]) is optional. That's why it is ok to type "finger" with no options and no user. What about "user" -- what is that? To see what that means, quit out of the man page and type the following at the command prompt:

$ whoami

Let's say your username is osu0000. Then the result of the "whoami" command is osu0000. Now enter the following command (but replace osu0000 with your username):

$ finger osu0000

You should get information about yourself and no other users. You can also enter any of the usernames that are output when you enter the "finger" command by itself. The user names are in the leftmost column of output. Now try

 

$ finger -l osu0000

$ finger -lp osu0000

$ finger -s osu0000 osu0001

For the last command, use your username and the username of some other username that shows up in the output of the "finger" command with no arguments.

Note that a unix command consists of three parts:

  • command
  • option(s)
  • argument(s)

You don't necessarily have to enter an argument (as you saw with the "finger" command) but sometimes a command makes no sense without an argument so you must enter one -- you saw this with the "man" command. Try typing

$ man man

and looking briefly at the output. One thing to notice is the synopsis -- there are a lot of possible options for the "man" command, but the last thing shown in the command synopsis is "name ..." -- notice that "name" is not contained in square brackets. This is because it is not optional -- you must enter at least one name. What happens if you enter two names?

$ man man finger

The first thing that happens is you get the man page for the "man" command. What happens when you quit out of the man page? You should now get the man page for the "finger" command. If you quit out of this one you will be back at the shell prompt.

Combining Commands

You can "pipe" the output of one command to another. First, let's learn about the "more" command:

$ man more

Read the "DESCRIPTION" section -- it says that more is used to page through text that doesn't fit on one screen. It also recommends that the "less" command is more powerful. Ok, so let's learn about the "less" command:

$ man less

You see from the description that "less" also allows you to examine text one screenful at a time. Does this sound familiar? The "man" command actually uses the "less" command to display its output. But you can use the "less" command yourself. If you have a long text file named "foo.txt" you could type

$ less foo.txt

and you would be able to examine the contents of the file one screen at a time. But you can also use "less" to help you look at the output of a command that prints more than one screenful of output. Try this:

$ finger | less

That's "finger" followed by a space followed by the vertical bar (shifted backslash on most keyboards) followed by a space followed by "less" followed by <Enter>. You should now be looking at the output of the "finger" command in an interactive fashion, just as you were looking at man pages. Remember, to scroll use the arrow keys, the <Page Up> and <Page Down> keys, the <Enter> key or the space bar; and to quit, type "q".

Now try the following (but remember to replace "osu0000" with your actual username):

$ finger | grep osu0000

The "grep" command is Unix's command for searching. Here you are telling Unix to search the output of the "finger" command for the text "osu0000" (or whatever your username is.)

If you try to pipe the output of one command to a second command and the second is a command which works with no arguments, you won't get what you expect. Try

$ whoami | finger

You see that it does not give the same output as

$ finger osu0000

(assuming "whoami" returns osu0000.)

In this case what you can do is the following:

$ finger `whoami`

That's "finger" space backquote "whoami" backquote. The backquote key is to the left of the number 1 key on a standard keyboard.

apropos

Enter the following command:

$ man apropos

As you can see, the apropos searches descriptions of commands and finds commands whose descriptions match the keyword you entered as the argument. That means it outputs a list of commands that have something to do with the keyword you entered. Try this

$ apropos

Ok, you need to enter an argument for the "apropos" command.

So try

$ apropos calendar

Now you see that among the results are two commands -- "cal" and "difftime" that have something to do with the keyword "calendar."

Linux Tutorial

 

Description

This tutorial guides you through the process of creating and submitting a batch script on one of our compute clusters. This is a linux tutorial which uses batch scripting as an example, not a tutorial on writing batch scripts. The primary goal is not to teach you about batch scripting, but for you to become familiar with certain linux commands. There are other pages on the OSC web site that go into the details of submitting a job with a batch script.

Prerequisites

Goals

  • Create subdirectories to organize information
  • Create a batch script with a text editor
  • Submit a job
  • Check on the progress of the job
  • Change the permissions of the output files
  • Get familiar with some common unix commands

Step 1 - Organize your directories

When you first log in to our clusters, you are in your home directory. For the purposes of this illustration, we will pretend you are user osu0001 and your project code is PRJ0001, but when you try out commands you must use your own username and project code.

$ pwd
/users/PRJ0001/osu0001
 
Note: you will see your user name and a different number after the /users.
 
It's a good idea to organize your work into separate directories. If you have used Windows or the Mac operating system, you may think of these as folders. Each folder may contain files and subfolders. The subfolders may contain other files and subfolders of their own. In linux we use the term "directory" instead of "folder." Use directories to organize your work.
 
Type the following four lines and take note of the output after each one:
 
$ touch foo1
$ touch foo2
$ ls
$ ls -l
$ ls -lt
$ ls -ltr
 
The "touch" command just creates an empty file with the name you give it.
You probably already know that the ls command shows the contents of the current working directory; that is, the directory you see when you type pwd. But what is the point of the "-l", "-lt" or "-ltr"? You noticed the difference in the output between just the "ls" command and the "ls -l" command.
Most unix commands have options you can specify that change the way the command works. The options can be specified by the "-" (minus sign) followed by a single letter. "ls -ltr" is actually specifying three options to the ls command.
l: I want to see the output in long format -- one file per line with some interesting information about each file
t: sort the display of files by when they were last modified, most-recently modified first
r: reverse the order of display (combined with -t this displays the most-recently modified file last -- it should be BatchTutorial in this case.)
 
I like using "ls -ltr" because I find it convenient to see the most recently modified file at the end of the list.
 
Now try this:
$ mkdir BatchTutorial
$ ls -ltr
 
The "mkdir" command makes a new directory with the name you give it. This is a subfolder of the current working directory. The current working directory is where your current focus is in the hierarchy of directories. The 'pwd' command shows you are in your home directory:
 
$ pwd
/users/PRJ0001/osu0001
 
Now try this:
$ cd BatchTutorial
$ pwd
 
What is the output of 'pwd' now? "cd" is short for "change directory" -- think of it as moving you into a different place in the hierarchy of directories. Now do
$ cd ..
$ pwd
Where are you now?

Step 2 -- Get familiar with some more unix commands

Try the following:

$ echo where am I?
$ echo I am in `pwd`
$ echo my home directory is $HOME
$ echo HOME
$ echo this directory contains `ls -l`

These examples show what the echo command does and how to do some interesting things with it. The `pwd` means the result of issuing the command pwd. HOME is an example of an environment variable. These are strings that stand for other strings. HOME is defined when you log in to a unix system. $HOME means the string the variable HOME stands for. Notice that the result of "echo HOME" does not do the substitution. Also notice that the last example shows things don't always get formatted the way you would like.

Some more commands to try:

$ cal
$ cal > foo3
$ cat foo3
$ whoami
$ date

Using the ">" after a command puts the output of the command into a file with the name you specify. The "cat" command prints the contents of a file to the screen.

Two very important UNIX commands are the cp and mv commands. Assume you have a file called foo3 in your current directory created by the "cal > foo3" command. Suppose you want to make a copy of foo3 called foo4. You would do this with the following command:

$ cp foo3 foo4
$ ls -ltr

Now suppose you want to rename the file 'foo4' to 'foo5'. You do this with:

$ mv foo4 foo5
$ ls -ltr

'mv' is short for 'move' and it is used for renaming files. It can also be used to move a file to a different directory.

$ mkdir CalDir
$ mv foo5 CalDir
$ ls
$ ls CalDir

Notice that if you give a directory with the "ls" command is shows you what is in that directory rather than the current working directory.

Now try the following:

$ ls CalDir
$ cd CalDir
$ ls
$ cd ..
$ cp foo3 CalDir
$ ls CalDir

Notice that you can use the "cp" command to copy a file to a different directory -- the copy will have the same name as the original file. What if you forget to do the mkdir first?

$ cp foo3 FooDir

Now what happens when you do the following:

$ ls FooDir
$ cd FooDir
$ cat CalDir
$ cat FooDir
$ ls -ltr

CalDir is a directory, but FooDir is a regular file. You can tell this by the "d" that shows up in the string of letters when you do the "ls -ltr". That's what happens when you try to cp or mv a file to a directory that doesn't exist -- a file gets created with the target name. You can imagine a scenario in which you run a program and want to copy the resulting files to a directory called Output but you forget to create the directory first -- this is a fairly common mistake.

Step 3 -- Environment Variables

Before we move on to creating a batch script, you need to know more about environment variables. An environment variable is a word that stands for some other text. We have already seen an example of this with the variable HOME. Try this:

$ MY_ENV_VAR="something I would rather not type over and over"
$ echo MY_ENV_VAR
$ echo $MY_ENV_VAR
$ echo "MY_ENV_VAR stands for $MY_ENV_VAR"

You define an environment variable by assigning some text to it with the equals sign. That's what the first line above does. When you use '$' followed by the name of your environment variable in a command line, UNIX makes the substitution. If you forget the '$' the substitution will not be made.

There are some environment variables that come pre-defined when you log in. Try using 'echo' to see the values of the following variables: HOME, HOSTNAME, SHELL, TERM, PATH.

Now you are ready to use some of this unix knowledge to create and run a script.

Step 4 -- Create and run a script

Before we create a batch script and submit it to a compute node, we will do something a bit simpler. We will create a regular script file that will be run on the login node. A script is just a file that consists of unix commands that will run when you execute the script file. It is a way of gathering together a bunch of commands that you want to execute all at once. You can do some very powerful things with scripting to automate tasks that are tedious to do by hand, but we are just going to create a script that contains a few commands we could easily type in. This is to help you understand what is happening when you submit a batch script to run on a compute node.

Use a text editor to create a file named "tutorial.sh" which contains the following text (note that with emacs or nano you can use the mouse to select text and then paste it into the editor with the middle mouse button):

$ nano tutorial.sh

 

echo ----
echo Job started at `date`
echo ----
echo This job is working on node `hostname`

SH_WORKDIR=`pwd`
echo working directory is $SH_WORKDIR
echo ----
echo The contents of $SH_WORKDIR
ls -ltr
echo
echo ----
echo
echo creating a file in SH_WORKDIR
whoami > whoami-sh-workdir

SH_TMPDIR=${SH_WORKDIR}/sh-temp
mkdir $SH_TMPDIR
cd $SH_TMPDIR
echo ----
echo TMPDIR IS `pwd`
echo ----
echo wait for 12 seconds
sleep 12
echo ----
echo creating a file in SH_TMPDIR
whoami > whoami-sh-tmpdir

# copy the file back to the output subdirectory
cp ${SH_TMPDIR}/whoami-sh-tmpdir ${SH_WORKDIR}/output

cd $SH_WORKDIR

echo ----
echo Job ended at `date`

To run it:

$ chmod u+x tutorial.sh
$ ./tutorial.sh

Look at the output created on the screen and the changes in your directory to see what the script did.

Step 5 -- Create and run a batch job

Use your favorite text editor to create a file called tutorial.pbs in the BatchTutorial directory which has the following contents (remember, you can use the mouse to cut and paste text):

#PBS -l walltime=00:02:00
#PBS -l nodes=1:ppn=1
#PBS -N foobar
#PBS -j oe
#PBS -r n

echo ----
echo Job started at `date`
echo ----
echo This job is working on compute node `cat $PBS_NODEFILE`

cd $PBS_O_WORKDIR
echo show what PBS_O_WORKDIR is
echo PBS_O_WORKDIR IS `pwd`
echo ----
echo The contents of PBS_O_WORKDIR:
ls -ltr
echo
echo ----
echo
echo creating a file in PBS_O_WORKDIR
whoami > whoami-pbs-o-workdir

cd $TMPDIR
echo ----
echo TMPDIR IS `pwd`
echo ----
echo wait for 42 seconds
sleep 42
echo ----
echo creating a file in TMPDIR
whoami > whoami-tmpdir

# copy the file back to the output subdirectory
pbsdcp -g $TMPDIR/whoami-tmpdir $PBS_O_WORKDIR/output

echo ----
echo Job ended at `date`
 
To submit the batch script, type
$ qsub tutorial.pbs
Use qstat -u [username] to check on the progress of your job. If you see something like this
$ qstat -u osu0001

                                                                             Req'd  Req'd   Elap
Job ID             Username    Queue    Jobname          SessID NDS   TSK    Memory Time  S Time
------------------ ----------- -------- ---------------- ------ ----- ------ ------ ----- - -----
458842.oak-batch   osu0001     serial   foobar              --      1      1    --  00:02 Q   --
 
this means the job is in the queue -- it hasn't started yet. That is what the "Q" under the S column means.
 
If you see something like this:
                                                                             Req'd  Req'd   Elap
Job ID             Username    Queue    Jobname          SessID NDS   TSK    Memory Time  S Time
------------------ ----------- -------- ---------------- ------ ----- ------ ------ ----- - -----
458842.oak-batch   osu0001     serial   foobar            26276     1      1    --  00:02 R   --
this means the job is running and has job id 458842.
 
When the output of the qstat command is empty, the job is done.
 
After it is done, there should be a file called "foobar.o458842" in the directory.
Note that your file will end with a different number -- namely the job id number assigned to your job.
Check this with
$ ls -ltr
$ cat foobar.oNNNNNN

Where (NNNNNN is your job id).

The name of this file is determined by two things:
  1. The name you give the job in the script file with the header line #PBS -N foobar
  2. The job id number assigned to the job.

The name of the script file (tutorial.pbs) has nothing to do with the name of the output file.

Examine the contents of the output file foobar.oNNNNNN carefully. You should be able to see the results of some of the commands you put in tutorial.pbs. It also shows you the values of the variables PBS_NODEFILE, PBS_O_WORKDIR and TMPDIR. These variables exist only while your job is running. Try

$ echo $PBS_O_WORKDIR

and you will see it is no longer defined. $PBS_NODEFILE is a file which contains a list of all the nodes your job is running on. Because this script has the line

#PBS -l nodes=1:ppn=1

the contents of $PBS_NODEFILE is the name of a single compute node.

Notice that $TMPDIR is /tmp/pbstmp.NNNNNN (again, NNNNNN is the id number for this job.) Try

$ ls /tmp/pbstmp.NNNNNN

Why doesn't this directory exist? Because it is a directory on the compute node, not on the login node. Each machine in the cluster has its own /tmp directory and they do not contain the same files and subdirectories. The /users directories are shared by all the nodes (login or compute) but each node has its own /tmp directory (as well as other unshared directories.)

Tar Tutorial

 

Prerequisites

Step 1 -- Create a directory to work with and download a "tarball"

Start off with the following:

$ mkdir TarTutorial
$ cd TarTutorial
$ wget http://www.mmm.ucar.edu/wrf/src/WRFDAV3.1.tar.gz
$ ls -ltr

The third command will take a while because it is downloading a file from the internet. The file is call a "tarball" or a "gzipped tarball". TAR is an old unix short name for "tape archive" but a tar file is a file that contains a bunch of other files. If you have to move a bunch of files from one place to another, a good way to do it is to pack them into a tar file, move the tar file where you want it then unpack the files at the destination. A tar file usually has the extension ".tar". What about the ".gz"? This means the tar file has been further compressed with the program gzip -- this makes it a lot smaller.

Step 2 -- Unpack the "tarball" and check out the contents

After step 1 your working directory should be ~/TarTutorial and there should be a file called WRFDAV3.1.tar.gz in it.

Now do this:

$ gunzip WRFDAV3.1.tar.gz
$ ls -ltr

You should now have a file called WRFDAV3.1.tar which should be quite a bit larger in size than WRFDAV3.1.tar.gz -- this is because it has been uncompressed by the "gunzip" command which is the opposite of the "gzip" command.

Now do this:

$ tar -xvf WRFDAV3.1.tar
$ ls -ltr

You should see a lot of filenames go by on the screen and when the first command is done and you issue the ls command you should see two things -- WRFDAV3.1.tar is still there but there is also a directory called WRFDA. You can look at the contents of this directory and navigate around in the directory tree to see what is in there. The options on the "tar" command have the following meanings (you can do a "man tar" to get all the options):

x: extract the contents of the tar file

v: be verbose, i.e. show what is happening on the screen

f: the name of the file which follows the "f" option is the tar file to expand.

Another thing you can do is see how much space is being taken up by the files. Make sure TarTutorial is your working directory then issue the following command:

$ du .

Remember that "." (dot) means the current working directory. The "du" command means "disk usage" -- it shows you how much space is being used by every file and directory in the directory tree. It ends up with the highest level files and directories. You might prefer to do

$ du -h .
$ ls -ltrh

Adding the "-h" option to these commands puts the file sizes in human-readable format -- you should get a size of 66M for the tar file -- that's 66 megabytes -- and "du" should print a size of 77M next to ./WRFDA.

Step 3 -- create your own "tarball"

Now, make your own tar file from the WRFDA directory tree:

$ tar -cf mywrf.tar WRFDA
$ ls -ltrh

You have created a tar from all the files in the WRFDA directory. The options given to the "tar" command have the following meanings:

c: create a tar file

f: give it the name which follows the "f" option

The files WRFDAV3.1.tar and mywrf.tar are identical. Now compress the tar file you made:

$ gzip mywrf.tar
$ ls -ltrh

You should see a file called mywrf.tar.gz which is smaller than WRFDAV3.1.tar.

Step 4 -- Clean up!

You don't want to leave all these files lying around. So delete them

$ rm WRFDAV3.1.tar
$ rm mywrf.tar
$ rm WRFDA

Oops! You can't remove the directory. You need to use the "rmdir" command:

$ rmdir WRFDA

Oh no! That doesn't work on a directory that's not empty. So are you stuck with all those files? Maybe you can do this:

$ cd WRFDA
$ rm *
$ cd ..
$ rmdir WRFDA

That won't work either because there are some subdirectories in WRFDA and "rm *" won't remove them. Do you have to work your way to the all the leaves at the bottom of the directory tree and remove files then come back up and remove directories? No, there is a simpler way:

$ rm -Rf WRFDA

This will get rid of the entire directory tree. The options have the following meanings:

R: recursively remove all files and directories

f: force; i.e., just remove everything without asking for confirmation

I encourage you to do

$ man rm

and check out all the options. Or some of them -- there are quite a few.

 

Unix Shortcuts

 

Description

This tutorial shows you some handy time-saving shortcuts in linux. Once you have a good understanding of how the command line works, you will want to learn how to work more efficiently.

Prerequisites

Linux command line fundamentals.

Goals

  • Save you time when working on a linux system
  • Increase your appreciation of the power of linux

Step 1 -- The Arrow Keys

Note: even if you know how to use the up arrow in linux, you need to enter the commands in this section because they are used in the following sections. So to begin this tutorial, go to your home directory and create a new directory called ShortCuts:

$ cd
$ mkdir Shortcuts
$ cd Shortcuts

(If a directory or file named "Shortcuts" already exists, name it something else.)

Imagine typing in a long linux command and making a typo. This is one of the frustrating things about a command line interface -- you have to retype the command, correcting the typo this time. Or what if you have to type several similar commands -- wouldn't it be nice to have a way to recall a previous command, make a few changes, and enter the new command? This is what the up arrow is for.

Try the following:

$ cd ..
$ cd ShortCuts (type a capital C)

Linux should tell you there is no directory with that name.

Now type the up arrow key -- the previous command you entered shows up on the command line, and you can use the left arrow to move the cursor just after the capital C, hit Backspace, and type a lower case c. Note you can also position the cursor before the capital C and hit Delete to get rid of it.

Once you have changed the capital C to a lower case c you can hit Return to enter the command -- you do not have to move the cursor to the end of the line.

Now hit the up arrow key a few times, then hit the down arrow key and notice what happens. Play around with this until you get a good feel for what is happening.

Linux maintains a history of commands you have entered. Using the up and down arrow keys, you can recall previously-entered commands to the command line, edit them and re-issue them.

Note that in addition to the left and right arrow keys you can use the Home and End keys to move to the beginning or end of the command line. Also, if you hold down the Ctrl key when you type an arrow key, the cursor will move by an entire word instead of a single character -- this is useful is many situations and works in many editors.

Let's use this to create a directory hierarchy and a few files. Start in the Shortcuts directory and enter the following commands, using the arrow keys to simplify your job:

$ mkdir directory1
$ mkdir directory1/directory2
$ mkdir directory1/directory2/directory3
$ cd directory1/directory2/diectoryr3  (remember the Home key and the Ctrl key with left and right arrows)
$ hostname > file1
$ whoami > file2
$ mkdir directory4
$ cal > directory4/file3

Step 2 -- Using the TAB key

Linux has short, cryptic command names to save you typing -- but it is still a command line interface, and that means you interact with the operating system by typing in commands. File names can be long, directory hierarchies can be deep, and this can mean you have to type a lot to specify the file you want or change to current working directory. Not only that, but you have to remember the names of files and directories you type in. The TAB key gives you a way to enter with commands with less typing and less memorization.

Go back to the Shortcuts directory:

$ cd
$ cd Shortcuts

Now enter the following:

$ hostname > file1
$ cal > file2
$ whoami > different-file
$ date > other-file
$ cal > folio5

Now type the following, without hitting the Return key:

$ cat oth <Tab>

What happened? Linux completed the name "other-file" for you! The Tab key is your way of telling Linux to finish the current word you are typing, if possible. Because there is only one file in the directory whose name begins with "oth", when you hit the Tab key Linux is able to complete the name.

Hit Return (if you haven't already) to enter the cat command. Now try

$ cat d <Tab>

As you would expect, Linux completes the name "different-file"

What if you enter

$ cat fi <Tab>

Notice Linux completes as much of the name as possible. You can now enter a "1" or a "2" to finish it off.

But what if you forget what the options are? What if you can't remember if you created "file1" and "file2" or if you created "fileA" and fileB"?

With the comman line showing this:

$ cat file

hit the Tab key twice. Aha! Linux shows you the possible choices for completing the word.

Try

$ cat f <Tab>

The Tab will not add anything -- the command line will still read

$ cat f

Now type the letter o followed by a Tab -- once you add the o there is only one possible completion -- "folio".

Now enter the following:

$ cat directory1/directory2/directory3/directory4/file3

That's kind of a painful to type.

Now type the following without entering Return:

$ ls dir <Tab>

Nice! As you would expect, Linux completes the name of the directory for you. This is because there is only one file in the Shortcuts directory whose name begins with "dir"

Hit Return and Linux will tell you that directory1 contains directory2.

Now type this:

$ ls dir <Tab>

and before you hit return type another d followed by another Tab. Your command line should now look like this:

$ ls directory1/directory2/

If you hit Return, Linux will tell you that directory2 contains directory3.

Now try this:

$ ls dir <Tab>

then type another d followed by <Tab> then another d followed by tab. Don't hit Return yet. Your command line should look like this:

$ ls directory1/directory2/directory3/

Don't hit Return yet. Now type the letter f followed by a Tab. What do you think should happen?

Step 3 -- The Exclamation Point

Hitting the up arrow key is a nice way to recall previously-used commands, but it can get tedious if you are trying to recall a command you entered a while ago -- hitting the same key 30 times is a good way to make yourself feel like an automaton. Fortunately, linux offers a couple of other ways to recall previous commands that can be useful.

Go back to the Shortcuts directory

$ cd ~/Shortcuts

and enter the following:

$ hostname
$ cal
$ date
$ whoami

Now enter this:

$ !c

and hit return.

What happened? Now try

$ !h

and hit return.

The exclamation point ("bang" to Americans, "shriek" to some Englishmen I've worked with) is a way of telling linux you want to recall the last command which matches the text you type after it. So "!c" means recall the last command that starts with the letter c, the "cal" command in this case. You can enter more than one character after the exclamation point in order to distinguish between commands. For example if you enter

$ cd ~/Shortcuts
$ cat file1
$ cal
$ !c

the last command will redo the "cal" command. But if you enter

$ cat file1
$ cal
$ !cat

the last command re-executes the "cat" command.

Step 4 -- Ctrl-r

One problem with using the exclamation point to recall a previous command is that you can feel blind -- you don't get any confirmation about exactly which command you are recalling until it has executed. Sometimes you just aren't sure what you need to type after the exclamation point to get the command you want.

Typing Ctrl-r (that's holding down the Ctrl key and typing a lower case r) is another way to repeat previous commands without having to type the whole command, and it's much more flexible than the bang. The "r" is for "reverse search" and what happens is this. After you type Ctrl-r, start typing the beginning of a previously entered command -- linux will search, in reverse order, for commands that match what you type. To see it in action, type in the following commands (but don't hit <Enter> after the last one):

$ cd ~/Shortcuts
$ cat file1
$ cat folio5
$ cal
$ Ctrl-r cat

You should see the following on your command line:

(reverse-i-search)`cat': cat folio5

Try playing with this now. Type in " fi" (that's a space, an "f" and an "i") -- did the command shown at the prompt change? Now hit backspace four times.

Now enter a right or left arrow key and you will find yourself editing the matching command. This is one you have to play around with a bit before you understand exactly what it is doing. So go ahead and play with it.

Step 5 -- history

Now type

$ history

and hit return.

Cool, huh? You get to see all the commands you have entered (probably a maximum of 1000.) You can also do something like

$ history | grep cal

to get all the commands with the word "cal" in them. You can use the mouse to cut and paste a previous command, or you can recall it by number with the exclamation point:

$ !874

re-executes the command number 874 in your history.

For more information about what you can do to recall previous commands, check out http://www.thegeekstuff.com/2011/08/bash-history-expansion/

Step 6 -- Ctrl-t

I am just including this because to me it is a fun piece of linux trivia. I don't find it particularly useful. Type

$ cat file1

and hit <Return>. Now hit the up arrow key to recall this command and hist the left arrow key twice so the cursor is on the "e" of "file1". Now hit Ctrl-t (again, hold down the control key and type a lower case t.) What just happened? Try hitting Ctrl-t a couple more times. That's right -- it transposes two characters in the command line -- the one the cursor is on and the one to its left. Also, it moves the cursor to the right. Frankly, it takes me more time to think about what is going to happen if I type Ctrl-t than it takes me to delete some characters and retype them in the correct order. But somewhere out there is a linux black belt who gets extra productivity out of this shortcut.

Step 7 -- The alias command

Another nice feature of linux is the alias command. If there is a command you enter a lot you can define a short name for it. For example, we have been typing "cat folio5" a lot in this tutorial. You must be getting sick of typing "cat folio5". So enter the following:

$ alias cf5='cat folio5'

Now type

$ cf5

and hit return. Nice -- you now have a personal shortcut for "cat folio5". I use this for the ssh commands:

$ alias gogl='ssh -Y jeisenl@pitzer.osc.edu'

I put this in the .bash_aliases file on my laptop so that it is always available to me.

Classroom Project Resource Guide

This document includes information on utilizing OSC resources in your classroom effectively.


Request a Classroom Project

Classroom projects will not be billed under the Ohio academic fee structure; all fees will be fully discounted at the time of billing.

Please submit a new project request for a classroom project. You will request a $500 budget. If an additional budget is needed or you want to re-use your project code, you can apply through MyOSC or contact us at OSCHelp. We require a class syllabus; this will be uploaded on the last screen before you submit the request. 

During setup, OSC staff test accounts may be added to the project for troubleshooting purposes.

Access

We suggest that students consider connecting to our OnDemand portal to access the HPC resources. All production supercomputing resources can be accessed via that website without having to worry about client configuration. We have a guide for new students to help them figure out the basics of using OSC.

If your class has set up a custom R or Jupyter environment at OSC, please ask the students to connect to class.osc.edu

Resources

We currently have two production clusters, Pitzer and Owens, with Nvidia GPUs available that may be used for classroom purposes. All systems have "debug" queues that, during typical business hours, allow small jobs of less than one hour to start much quicker than they might otherwise.

If you need to reserve access to particular resources, please contact OSC Help, preferably with at least two weeks lead time, so that we can put in the required reservations to ensure resources are available during lab or class times.

Software

We have a list of supported software, including sample batch scripts, in our documentation. If you have specific needs that we can help with, let OSC Help know.

If you are using Rstudio, please see this webpage

If you are using Jupyter, please see the page Using Jupyter for Classroom.

Account Maintenance

Our classroom project information guide will instruct you on how to get students added to your project using our client portal. For more information, see the documentation. You must also add your username as an authorized user

Homework Submissions

We can provide you with project space to have students submit assignments through our systems. Please ask about this service and see our how-to. We typically grant 1-5 TB for classroom projects. 

Support

Help can be found by contacting OSC Help weekdays, 9 a.m. to 5 p.m. (614-292-1800).
Fill out a request online. 

We update our web pages to show relevant events at the center (including training) and system notices on our main page (osc.edu). We also provide important information in the “message of the day” (visible when you log in). You also can receive notices by following @HPCNotices on X. 

Helpful Links

FAQ: http://www.osc.edu/supercomputing/faq

Main supercomputing pages: http://www.osc.edu/supercomputing/

 

 

 

Documentation Attachment: 
Supercomputer: 

Classroom Guide for Students

Join a Classroom Project

Your classroom instructor will provide you with a project and access code that will allow you to join the classroom project. Visit our user management page for more information. 

Ohio State users only: osu.edu and buckeyemail.osu.edu are treated as two separate emails in our system. Please provide your professor the appropriate email address. 

All emails will be sent from "no-reply@osc.edu" - all folders should be checked, including spam/junk. If they did not receive this email, please contact OSC Help.

Review our classroom project info guide for detailed informatoin.

Account Management

You can manage your OSC account via MyOSC, our client porta. This includes:

Access

If your class uses a custom R or Jupyter environment at OSC, please connect to class.osc.edu

If you do not see your class there, we suggest connecting to ondemand.osc.edu

You can log into class.osc.edu or ondemand.osc.edu either using your OSC HPC Credentials or Third-Party Credentials. See this OnDemand page for more information. 

File Transfer

There are a few different ways of transferring files between OSC storage and your local computer. We suggest using OnDemand File App if you are new to Linux and looking to transfer smaller-sized files - measured in MB to several hundred MB. For larger files, please use an SFTP client to connect to  sftp.osc.edu  or Globus.

More Information for New Users

We have a guide for new users to help them figure out the basics of using OSC; included are basics on getting connected, HPC system structure, file transfers, and batch systems.

FAQ: http://www.osc.edu/supercomputing/faq

Main Supercomputing pages: http://www.osc.edu/supercomputing/

Support

Help can be found by contacting OSC Help weekdays, 9AM to 5PM (614-292-1800).
Fill out a request online. 

 

 

 

 

Documentation Attachment: 
Supercomputer: 

Using Jupyter for Classroom

OSC provide an isolated and custom Jupyter environment for each classroom project that requires Jupyter Notebook or JupyterLab. 

The instructor must apply for a classroom project that is unique for the course. More details on the classroom project can be found in our classroom project guide. Once we get the information, we will provide you a project ID and a course ID (which is commonly the course ID provided by instructor + school code, e.g. MATH_2530_OU).  The instructor can set up a Jupyter environment for the course using the information (see below). The Jupyter environment will be tied to the project ID.

Set up a Jupyter environment

The instructor can set up a Jupyter environment for the course once the project space is initialized:

  1. Login to Owens or Pitzer as PI account of the classroom project.
  2. Run setup script with the project ID and course ID:
~support/classroom/tools/setup_jupyter_classroom  /fs/ess/project_ID  course_ID

If the Jupyter environment is created successfully, please inform us so we can update you when your class is ready at class.osc.edu.

Upgrade a Jupyter environment

You may need to upgrade Jupyter kernels to the latest stable version for a security vulnerability or trying out new features. Please run upgrade script with the project ID and course ID:

~support/classroom/tools/upgrade_jupyter_classroom /fs/ess/project_ID course_ID

Manage the Jupyter environment

Install packages

When your class is ready, launch your class session at class.osc.edu. Then, open a notebook and use the following command to install packages:

pip install --no-cache-dir --ignore-installed [package-name]

Please note that using the --no-cache-dir and --ignore-installed flags can skip using the caches in the home directory, which may cause conflicts when installing classroom packages if you have previously used pip to install packages in multiple Python environments.

Install extensions

Jupyter Notebook

To enable or install nbextension, please use --sys-prefix to install into the classroom Jupyter environment, e.g.

!jupyter contrib nbextension install --sys-prefix

Please do not use --user, which install to your home directory and could mess up the Jupyter environment.

JupyterLab

To install labextension, simply click Extension Manager icon at the side bar

Screen Shot 2021-07-27 at 1.30.45 PM.png

Enable local package access (optional)

By default this Jupyter environment is an isolated Python environment. Anyone launches python from this environment can only access packages installed inside unless PYTHONPATH is used. The instructor can change it by setting include-system-site-packages = true in /fs/ess/project_ID/course_ID/jupyter/pyvenv.cfg. This will allows students to access packages in home directory ~/.local/lib/pythonX.X/site-packages ,and install packages via pip install –user

Workspace

When a class session starts, we create a classroom workspace under the instructor's and students' home space: $HOME/osc_classes/course_ID, and launch Jupyter at the workspace. The root /  will appear in the landing page (Files) but everything can be found in $HOME/osc_classes/course_ID on OSC system.

Shared Access

Share class material

The instructor can upload class material to /fs/ess/project_ID/course_ID/materials . When a student launch a Jupyter session, the diretory will be copied to the student's worksapce $HOME/osc_classes/course_ID . The student will see the directory materials on the landing page. PI can add files to the material source directory. New files will be copied to the destination every time when a new Jupyter session starts. But If PI modifies existing files, the changes won't be copied as the files were copied before. Therefore we recommend renaming the file after the update so that it will be copied

If a large amount of data is added to /materials dir, then students may experience job failures. This is because there is not enough time for the data to be copied to their home dir.

Use data dir for large files

For large files, create a data dir to the classroom and place the large files there.

mkdir /fs/ess/project_ID/course_ID/data

Now the large data will not be copied to each user's home dir when they start a classroom job session. Make sure to reference this data properly in notebooks that will be copied to students home dirs from the /materials dir.

Access student workspace

The instructor and TAs can access a student's workspace with limited permissions. First, the instructor sends us a request with the information including the instructor's and TAs' OSC accounts. After a student launches a class session, you can access known files and directories in the student's workspace. For example, you cannot explore the student's workspace

ls /users/PZS1234/student1/osc_classes/course_ID
ls: cannot open directory /users/PZS1234/student1/osc_classes/course_ID: Permission denied

but you can access a known file or directory in the workspace

ls /users/PZS1234/student1/osc_classes/course_ID/homework

    Using Rstudio for classroom

    OSC provides an isolated and custom R environment for each classroom project that requires Rstudio. The interface can be accessed at class.osc.edu. Before using this interface, please apply for a classroom project account that is unique for the course.  More details on the classroom project can be found here. The custom R environment for the course will be tied to this project ID. Please inform us if you have additional requirements for the class. Once we get the information, we will provide you a course_ID (which is commonly the course ID provided by instructor + school code, e.g. MATH2530_OU)and add your course to the server with the class module created using the course_ID. After login to the class.osc.edu server, you will see several Apps listed. Pick Rstudio server and that will take you to the Rstudio Job submission page. Please pick your course from the drop-down menu under the Class materials and the number of hours needed. 

    final-copy.jpg

    Clicking on the Launch will submit the Rstudio job to the scheduler and you will see Connect to Rstudio server option when the resource is ready for the job. Each Rstudio launch will run on 1 core on Owens machine with 4GB of memory. 

     

    final-copy22.jpg

    Rstudio will open up in a new tab with a custom and isolated environment that is set through a container-based solution. This will create a folder under $HOME/osc_classes/course_ID for each user. Please note that inside the Rstudio, you won't be able to access any files other than class materials. However, you can access the class directory outside of Rstudio to upload or download files.

    Screen Shot 2020-07-21 at 11.32.42 PM.png

    You can quit a Rstudio session by clicking on File from the top tabs then on the Quit. This will only quit the session, but the resource you requested is still held until walltime limit is reached. To release the resource, please click on DELETE in the Rstudio launch page.

    Shared Access

    PI can store and share materials like data, scripts, etc, and R packages with the class. We will set up a  project space for the project ID of the course. This project space will be created under /fs/ess/project_ID. Once the project space is ready, please login to Owens or Pitzer as PI account of the classroom project. Run the following script with the project ID and course ID. This will create a folder with the course_ID  under the project space and then two subfolders 1) Rpkgs 2) materials under it.

    ~support/classroom/tools/setup_rstudio_classroom /fs/ess/project_ID course_ID
    
    

    Shared R packages

    Once the class module is ready, PI can access the course at class.osc.edu under the Rstudio job submission page. PI can launch the course environment and install R packages for the class. 

    It is important to install R packages for the class only in the class R environment after launching the Rstudio interface for the course. If you install R packages without launching class Rstudio, R will have access to your personnel R libraries at $HOME and could affect the installation process. 

    After launching Rstudio, please run the .libPaths() as follows

    > .libPaths()
    [1] "/users/PZS0680/soottikkal/osc_classes/OSCWORKSHOP/R" "/fs/ess/PZS0687/OSCWORKSHOP/Rpkgs"                  
    [3] "/usr/local/R/gnu/9.1/3.6.3/site/pkgs"                "/usr/local/R/gnu/9.1/3.6.3/lib64/R/library" 

    Here you will see four R library paths. The last two are system R library paths and are accessible for all OSC users. OSC installs a number of popular R packages at the site location. You can check available packages with library() command. The first path is a personal R library of each user in the course environment and is not shared with students. The second lib path is accessible to all students of the course(Eg: /fs/ess/PZS0687/OSCWORKSHOP/Rpkgs). PI should install R packages in this library to share with the class. As a precaution, it is a good idea to eliminate PI's personal R library from .libPaths() before R package installation as follows. Please note that this step is needed to be done only when preparing course materials by PI.

    > .libPaths(.libPaths()[-1])
    > .libPaths()
    [1] "/fs/ess/PZS0687/OSCWORKSHOP/Rpkgs"          "/usr/local/R/gnu/9.1/3.6.3/site/pkgs"      
    [3] "/usr/local/R/gnu/9.1/3.6.3/lib64/R/library"

    Now there is only one writable R library path such that all packages will be installed into this library path and shared for all users.

    PI can install all packages required for the class using install.packages() function. Once the installation is complete, students will have access to all those packages. 

    Please note that students can also install their own packages. Those packages will be installed into their personable library in the class environment i.e., the first path listed under .libPaths()

    Shared materials

    PI can share materials like data, scripts, and rmd files stored in /fs/ess/project_ID/course_ID/materials with students. When a student launch a Rstduio session, the directory will be copied to the student's workspace $HOME/osc_classes/courseID (destination). Please inform us if you want to use a source directory other than  /fs/ess/project_ID/course_ID/materials. The student will see the directory materials on the landing page. PI can add files to the material source directory. New files will be copied to the destination every time when a new Rstudio session starts.  But If PI modifies existing files, the changes won't be copied as the files were copied before. Therefore we recommend renaming the file after the update so that it will be copied. 

    There are several different ways to copy materials manually from a directory to students' workspace. T

    1. On class.osc.edu server, click on Files from the top tabs, then on $HOME directory. From the top right, click on Go to and enter the storage path (Eg: /fs/ess/PZS0687/) in the box and press OK. This will open up storage path and users can copy files. Open the class folder from the $HOME tree shown on left and paste files there. All files copied to  $HOME/osc_classes/course_ID will appear in the Rstudio FIle browser.

      Screen Shot 2020-07-21 at 11.38.18 PM.png
    2. On class.osc.edu server, Click on Clusters from the top tabs, then on Owens Shell Access. This will open up a terminal on Owens where students can enter Unix command for copying. Eg: 

      cp -r /fs/ess/PZS0687/OSCWORKSHOP/materials $HOME/osc_classes/course_ID

      Please note that $HOME/osc_classes/course_ID will be created only after launching Rstudio instance at least once.
    3. Students can also upload material directly to Rstudio using the upload tab located in the File browser of Rstudio from their local computer. This assumes they have already downloaded materials to their computers.

      arrow_1.png

    Checklist for PIs

    • Apply for a classroom project ID that is unique to the course
    • Add yourself, PI, to the project as an authorized user.
    • Inform us about additional requirements such as R version or other software
    • Once the class module is ready, create class materials under the storage path, and install R packages in the class environment.
    • Make a reservation on OSC cluster for the class schedule.
    • Invite students to the project at my.osc.edu to give them access to the project ID.

    Please reach out to oschelp@osc.edu if you have any questions. 
     

    Using nbgrader for Classroom

    Using ngbrader in Jupyter

    Install nbgrader

    You can install nbgrader in a notebook:

    1. Launch a Juypter session from class.osc.edu
    2. Open a new notebook 
    3. To Install nbgrader, run:
    !pip install nbgrader
    !jupyter nbextension install --sys-prefix --py nbgrader --overwrite 
    !jupyter nbextension enable --sys-prefix --py nbgrader 
    !jupyter serverextension enable --sys-prefix --py nbgrader
    

    To check the installed extensions, run

    !jupyter nbextension list
    

    There are six enabled extensionsScreen Shot 2020-08-21 at 11.31.36 PM.png

    Configure nbgrader

    In order to upload and collect assignments, nbgrader requires a exchange directory with write permissions for everyone. For example, to create a directory in project space, run:

    %%bash
    mkdir -p /fs/ess/projectID/courseID/exchange
    chmod a+wx /fs/ess/projectID/courseID/exchange

    Then get your cousre ID for configuratin. In a notebook, run:

    %%bash
    echo $OSC_CLASS_ID
    

    Finally create the nbgrader configuration at the root of the workspace. In a notebook, run 

    %%file nbgrader_config.py
    c = get_config()
    c.CourseDirectory.course_id = "courseID"     # it must be the value of $OSC_CLASS_ID
    c.Exchange.root = "/fs/ess/projectID/courseID/exchange"
    c.Exchange.timezone = 'EST'
    

    Once the file is created, you can launch a new Jupyter session then start creating assignments. For using nbgrader, please refer the nbgrader documents.

    Access assignments

    To let students access the assignments, students need to have the following configuration file in the root of their workspace:

    %%file nbgrader_config.py
    c = get_config()
    c.Exchange.root = "/fs/ess/projectID/courseID/exchange"
    
       

      HOWTO

      Our HOWTO collection contains short tutorials that help you step through some of the common (but potentially confusing) tasks users may need to accomplish, that do not quite rise to the level of requiring more structured training materials. Items here may explain a procedure to follow, or present a "best practices" formula that we think may be helpful.

      Service: 

      HOW TO: Look at requested time accuracy using XDMoD

      The XDMoD tool at xdmod.osc.edu can be used to get an overview of how accurate the requested time of jobs are with the elapsed time of jobs.

      One way of specifying a time request is:

      #SBATCH --time=xx:xx:xx

      The elapsed time is how long the job ran for before completing. This can be obtained using the  sacct command.

      $ sacct -u <username> --format=jobid,account,elapsed

      It is important to understand that the requested time is used when scheduling a submitted job. If a job requests a time that is much more than the expected elapsed time, then it may take longer to start because the resources need to be allocated for the time that the job requests even if the job only uses a small portion of that requested time.

      This allows one to view the requested time accuracy for an individual job, but XDMoD can be used to do this for jobs submitted in over a time range.

      First, login to xdmod.osc.edu, see this page for more instructions.

      https://www.osc.edu/supercomputing/knowledge-base/xdmod_tool

      Then, navigate to the Metric Explorer tab.

      Look for the Metric Catalog on the left side of the page and expand the SUPREMM options. Select Wall Hours: Requested: Per Job and group by None.

      walltime_acc_metric_tab.png

      This will now show the average time requested.

      The actual time data can be added by navigating to Add Data -> SUPREMM -> Wall Hours: Per Job.

      walltime_acc_add_data.png

      walltime_acc_select_walltime.png

      This will open a new window titled Data Series Definition, to change some parameters before showing the new data. In order to easily distinguish between elapsed and requested time, change the Display Type to Bar, then click add to view the new data.

      walltime_add_data_settings.png

      Now there is a line which shows the average requested time of jobs, and bars which depict the average elapsed time of jobs. Essentialy, the closer the bar is to the line, without intersecting the line, the more accurate the time predicition. If the bar intersects the line, then it may indicate the there was not enough time requested for a job to complete, but remember that these values are averages.

      walltime_acc_final_zoom.png

      One can also view more detailed information about these jobs by clicking a data point and using the Show raw data option.

      wall_acc_select_datapoint.png

      In order to have the Show raw data option, one may need to use the Drilldown option first to sort the jobs in that list by use or another metric.

      wall_acc_show_raw_data.png

      Supercomputer: 

      HOWTO: Collect performance data for your program

      This page outlines ways to generate and view performance data for your program using tools available at OSC.

      Intel Tools

      This section describes how to use performance tools from Intel. Make sure that you have an Intel module loaded to use these tools.

      Intel VTune

      Intel VTune is a tool to generate profile data for your application. Generating profile data with Intel VTune typically involves three steps:

      1. Prepare the executable for profiling.

      You need executables with debugging information to view source code line detail: re-compile your code with a -g  option added among the other appropriate compiler options. For example:

      mpicc wave.c -o wave -g -O3
      

      2. Run your code to produce the profile data.

      Profiles are normally generated in a batch job. To generate a VTune profile for an MPI program:

      mpiexec <mpi args> amplxe-cl <vtune args> <program> <program args>

      where <mpi args> represents arguments to be passed to mpiexec, <program> is the executable to be run, <vtune args> represents arguments to be passed to the VTune executable amplxe-cl, and <program args> represents arguments passed to your program.

      For example, if you normally run your program with mpiexec -n 12 wave_c, you would use

      mpiexec -n 12 amplxe-cl -collect hotspots -result-dir r001hs wave_c

      To profile a non-MPI program:

      amplxe-cl <vtune args> <program> <program args>

      The profile data is saved in a .map file in your current directory.

      As a result of this step, a subdirectory that contains the profile data files is created in your current directory. The  subdirectory name is based on the -result-dir argument and the node id, for example, r001hs.o0674.ten.osc.edu.

      3. Analyze your profile data.

      You can open the profile data using the VTune GUI in interactive mode. For example:

      amplxe-gui r001hs.o0674.ten.osc.edu

      One should use an OnDemand VDI (Virtual Desktop Interface) or have X11 forwarding enabled (see Setting up X Windows). Note that X11 forwarding can be distractingly slow for interactive applications.

      Intel ITAC

      Intel Trace Analyzer and Collector (ITAC) is a tool to generate trace data for your application. Generating trace data with Intel ITAC typically involves three steps:

      1. Prepare the executable for tracing.

      You need to compile your executbale with -tcollect  option added among the other appropriate compiler options to insert instrumentation probes calling the ITAC API. For example:

      mpicc wave.c -o wave -tcollect -O3
      

      2. Run your code to produce the trace data.

      mpiexec -trace <mpi args> <program> <program args>

      For example, if you normally run your program with mpiexec -n 12 wave_c, you would use

      mpiexec -trace -n 12 wave_c

      As a result of this step, .anc, .f, .msg, .dcl, .stf, and .proc files will be generated in your current directory.

      3. Analyze the trace data files using Trace Analyzer

      You will need to use traceanalyzer to view the trace data. To open Trace Analyzer:

      traceanalyzer /path/to/<stf file>

      where the base name of the .stf file will be the name of your executable.

      One should use an OnDemand VDI (Virtual Desktop Interface) or have X11 forwarding enabled (see Setting up X Windows) to view the trace data. Note that X11 forwarding can be distractingly slow for interactive applications.

      Intel APS

      Intel's Application Performance Snapshot (APS) is a tool that provides a summary of your application's performance . Profiling HPC software with Intel APS typically involves four steps:

      1. Prepare the executable for profiling.

      Regular executables can be profiled with Intel APS. but source code line detail will not be available. You need executables with debugging information to view source code line detail: re-compile your code with a -g  option added among the other approriate compiler options. For example:

      mpicc wave.c -o wave -tcollect -O3
      

      2. Run your code to produce the profile data directory.

      Profiles are normally generated in a batch job. To generate profile data for an MPI program:

      mpiexec -trace <mpi args> <program> <program args>

      where <mpi args> represents arguments to be passed to mpiexec, <program> is the executable to be run and <program args> represents arguments passed to your program.

      For example, if you normally run your program with mpiexec -n 12 wave_c, you would use

      mpiexec -n 12 wave_c

      To profile a non-MPI program:

      aps <program> <program args>

      The profile data is saved in a subdirectory in your current directory. The directory name is based on the date and time, for example, aps_result_YYYYMMDD/

      3. Generate the profile file from the directory.

      To generate the html profile file from the result subdirectory:

      aps --report=./aps_result_YYYYMMDD
      

      to create the file aps_report_YYYYMMDD_HHMMSS.html.

      4. Analyze the profile data file.

      You can open the profile data file using a web browswer on your local desktop computer. This option typically offers the best performance.

      ARM Tools

      This section describes how to use performance tools from ARM.

      ARM MAP

      Instructions for how to use MAP is available here.

      ARM DDT

      Instructions for how to use DDT is available here.

      ARM Performance Reports

      Instructions for how to use Performance Reports is available here.

      Other Tools

      This section describes how to use other performance tools.

      HPC Toolkit

      Rice University's HPC Toolkit is a collection of performance tools. Instructions for how to use it at OSC is available here.

      TAU Commander

      TAU Commander is a user interface for University of Oregon's TAU Performance System. Instructions for how to use it at OSC is available here.

      Supercomputer: 
      Service: 

      HOWTO: Create and Manage Python Environments

      While our Python installations come with many popular packages installed, you may come upon a case in which you need an additional package that is not installed. If the specific package you are looking for is available from anaconda.org (formerlly binstar.org), you can easily install it and required dependencies by using the conda package manager.

      Procedure

      The following steps are an example of how to set up a Python environment and install packages to a local directory using conda. We use the name  local for the environment, but you may use any other name.

      Load proper Python module

      We have python and miniconda3 modules. python modules are based on Anaconda package manager, and miniconda3 module is based on Miniconda package manager. python modules are typically recommended when you use Python in a standard environment that we provide. However, if you want to create your own python environment, we recommend using miniconda3 module, since you can start with minimal configurations.

      module load miniconda3
      

      Create Python installation to local directory

      Three alternative create commands are listed. These cover the most common cases.

      CREATE NEW ENVIRONMENT

      The following will create a minimal Python installation without any extraneous packages:

      conda create -n local
      
      CLONE BASE ENVIRONMENT

      If you want to clone the full base Python environment from the system, you may use the following create command:

      conda create -n local --clone base
      
      CREATE NEW ENVIRONMENT WITH SPECIFIC PACKAGES

      You can augment the command above by listing specific packages you would like installed into the environment. For example, the following will create a minimal Python installation with only the specified packages (in this case, numpy and babel):

      conda create -n local numpy babel
      

      By default, conda will install the newest versions of the packages it can find. Specific versions can be specified by adding =<version> after the package name. For example, the following will create a Python installation with Python version 2.7 and NumPy version 1.16:

      conda create -n local python=2.7 numpy=1.16
      

      To verify that a clone has been created, use the command

      conda info -e

      For additional conda command documentation see https://docs.conda.io/projects/conda/en/latest/commands.html#conda-general-commands

      Activate environment

      Before the created environment can be used, it must be activated.

      For the bash shell:

      source activate local
      

      At the end of the conda create step, you may saw a message from the installer that you can use conda activate command for activating environment. But, please don't use conda activate command, because it will try to update your shell configuration file and it may cause other issues. So, please use source activate command as we suggest above.

      On newer versions of Anaconda on the Owens cluster you may also need to perform the removal of the following packages before trying to install your specific packages:

      conda remove conda-build
      conda remove conda-env
      

      Install packages

      To install additional packages, use the conda install command. For example, to install the yt package:

      conda install yt
      

      By default, conda will install the newest version if the package that it can find. Specific versions can be specified by adding =<version> after the package name. For example, to install version 1.16 of the NumPy package:

      conda install numpy=1.16
      

      If you need to install packages with pip, then you can install pip in your virtual environment by

      conda install pip

      Then, you can install packages with pip as

      pip install PACKAGE

      Please make sure that you have installed pip in your enviroment not using one from the miniconda module. The pip from the miniconda module will give access to the pacakges from the module to your environemt which may or may not be desired. Also set export PYTHONNOUSERSITE=True to prevent packages from user's .local path.

      Test Python package

      Now we will test our installed Python package by loading it in Python and checking its location to ensure we are using the correct version. For example, to test that NumPy is installed correctly, run

      python -c "from __future__ import print_function; import numpy; print(numpy.__file__)"
      

      and verify that the output generally matches

      $HOME/.conda/envs/local/lib/python3.6/site-packages/numpy/__init__.py
      

      To test installations of other packages, replace all instances of numpy with the name of the package you installed.

      Remember, you will need to load the proper version of Python before you go to use your newly installed package. Packages are only installed to one version of Python.

      Install your own Python packages

      If the method using conda above is not working, or if you prefer, you can consider installing Python packages from the source. Please read HOWTO: install your own Python packages.

      But I use virtualenv and/or pip!

      See the comparison to these package management tools here:

      https://docs.conda.io/projects/conda/en/latest/commands.html#conda-vs-pip-vs-virtualenv-commands

      Use pip only without conda package manager

      pip installations are supported:

      module load python
      module list                            # check which python you just loaded
      pip install --user --upgrade PACKAGE   # where PACKAGE is a valid package name
      

      Note the default installation prefix is set to the system path where OSC users cannot install the package. With the option --user, the prefix is set to $HOME/.local where lib, bin, and other top-level folders for the installed packages are placed. Finally, the option --upgrade will upgrade the existing packages to the newest available version.

      The one issue with this approach is portability with multiple Python modules. If you plan to stick with a single Python module, then this should not be an issue. However, if you commonly switch between different Python versions, then be aware of the potential trouble in using the same installation location for all Python versions.

      Use pip in a Python virtual environment (Python 3 only)

      Typically, you can install packages with the methods shown in Install packages section above, but in some cases where the conda package installations have no source from conda channels or have dependency issues, you may consider using pip in an isolated Python virtual environment. 

      To create an isolated virtual environment:

      module reset
      python3 -m venv --without-pip $HOME/venv/mytest --prompt "local"
      source $HOME/venv/mytest/bin/activate
      (local) curl https://bootstrap.pypa.io/get-pip.py |python     # get the newest version of pip
      (local) deactivate
      

      where we use the path $HOME/venv/mytest and the name local for the environment, but you may use any other path and name. 

      To activate and deactivate the virtual environment:

      source $HOME/venv/mytest/bin/activate
      (local) deactivate 
      

      To install packages:

      source $HOME/venv/mytest/bin/activate
      (local) pip install PACKAGE 
      

      You don't need the --user option within the virtual environment.  

      Further Reading

      Conda Test Drive: https://conda.io/docs/test-drive.html 

       

       

      Supercomputer: 

      HOWTO: Install Tensorflow locally

      This documentation describes how to install tensorflow package locally in your $HOME space. For more details on Tensorflow see the software page.

      Load python module

      module load python/3.7-2019.10
      
      We already provide some versions of tensorflow centrally installed on our clusters. To see the available versions, run conda list tensorflow. See software page for software details and usage instructions on the clusters.

      If you need to install tensorflow versions not already provided or would like to use tensorflow in a conda environment proceed with the tutorial below.

      Create Python Environment

      First we will create a conda environment which we will later install tensorflow into. See HOWTO: Create and Manage Python Environments for details on how to create and setup your environemnt.

      Make sure you activate your environment before proceeding:

      source activate MY_ENV
      

      Install package

      Install the latest version of tensorflow.

      conda install tensorflow
      

      You can see all available version for download on conda with conda search tensorflow

      There is also a gpu compatable version called tensorflow-gpu

      If there are errors on this step you will need to resolve them before continuing.

      Test python package

      Now we will test tensorflow package by loading it in python and checking its location to ensure we are using the correct version.

      python -c "import tensorflow;print (tensorflow.__file__)"
      

      Output:

      $HOME/.conda/envs/MY_ENV/lib/python3.9/site-packages/tensorflow/__init__.py
      

      Remember, you will need to load the proper version of python before you go to use your newly installed package.  Packages are only installed to one version of python.

      Please refer HOWTO: Use GPU with Tensorflow and PyTorch if you would like to use tenorflow with Gpus.

      Supercomputer: 

      HOWTO: Install Python packages from source

      While we provide a number of Python packages, you may need a package we do not provide. If it is a commonly used package or one that is particularly difficult to compile, you can contact OSC Help for assistance. We also have provided an example below showing how to build and install your own Python packages and make them available inside of Python. These instructions use "bash" shell syntax, which is our default shell. If you are using something else (csh, tcsh, etc), some of the syntax may be different.

      Please consider using conda Python package manager before you try to build Python using the method explained here. We have instructions on conda here.

      Gather your materials

      First, you need to collect what you need in order to perform the installation. We will do all of our work in $HOME/local/src. You should make this directory now.

      mkdir -p $HOME/local/src
      

      Next, we will need to download the source code for the package we want to install. In our example, we will use NumExpr. (NumExpr is already available through conda, so it is recommended you use conda to install it: tutorial here. The following steps are simply an example of the procedure you would follow to perform an installation of software unavailable in conda or pip). You can either download the file to your desktop and then upload it to OSC, or directly download it using the wget utility (if you know the URL for the file).

      cd ~/local/src
      wget https://github.com/pydata/numexpr/releases/download/v2.8.4/numexpr-2.8.4.tar.gz
      

      Next, extract the downloaded file. In this case, since it's a "tar.gz" format, we can use tar to decompress and extract the contents.

      tar xvfz numexpr-2.8.4.tar.gz
      

      You can delete the downloaded archive now or keep it should you want to start the installation from scratch.

      Build it!

      Environment

      To build the package, we will want to first create a temporary environment variable to aid in installation. We'll call INSTALL_DIR.

      export INSTALL_DIR=${HOME}/local/numexpr/2.8.4
      

      We are roughly following the convention we use at the system level. This allows us to easily install new versions of software without risking breaking anything that uses older versions. We have specified a folder for the program (numexpr), and for the version (2.8.4). To be consistent with Python installations, we will create a second temporary environment variable that will contain the actual installation location.

      export TREE=${INSTALL_DIR}/lib/python3.6/site-packages
      

      Next, make the directory tree.

      mkdir -p $TREE
      

      Compile

      To compile the package, we should switch to the GNU compilers. The system installation of Python was compiled with the GNU compilers, and this will help avoid any unnecessary complications. We will also load the Python package, if it hasn't already been loaded.

      module swap intel gnu
      module load python/3.6-conda5.2
      

      Next, build it. This step may vary a bit, depending on the package you are compiling. You can execute python setup.py --help to see what options are available. Since we are overriding the install path to one that we can write to and that fits our management plan, we need to use the --prefix option.

      NumExpr build also requires us to set the PYTHONPATH variable before building:

      export PYTHONPATH=$PYTHONPATH:~/local/numexpr/2.8.4/lib/python3.6/site-packages

      Find the setup.py file:

      cd numexpr-2.8.4

      Now to build:

      python setup.py install --prefix=$INSTALL_DIR
      

      Make it usable

      At this point, the package is compiled and installed in ~/local/numexpr/2.8.4/lib/python3.6/site-packages. Occasionally, some files will be installed in ~/local/numexpr/2.8.4/bin as well. To ensure Python can locate these files, we need to modify our environment.

      Manual

      The most immediate way -- but the one that must be repeated every time you wish to use the package -- is to manually modify your environment. If files are installed in the "bin" directory, you'll need to add it to your path. As before, these examples are for bash, and may have to be modified for other shells. Also, you will have to modify the directories to match your install location.

      export PATH=$PATH:~/local/numexpr/2.8.4/bin
      

      And for the Python libraries:

      export PYTHONPATH=$PYTHONPATH:~/local/numexpr/2.8.4/lib/python3.6/site-packages
      

      Hardcode it

      We don't recommend this option, as it is less flexible and can cause conflicts with system software. But if you want, you can modify your .bashrc (or similar file, depending on your shell) to set these environment variables automatically. Be extra careful; making a mistake in .bashrc (or similar) can destroy your login environment in a way that will require a system administrator to fix. To do this, you can copy the lines above modifying $PATH and $PYTHONPATH into .bashrc. Remember to test them interactively first. If you destroy your shell interactively, the fix is as simple as logging out and then logging back in. If you break your login environment, you'll have to get our help to fix it.

      Make a module (recommended!)

      This is the most complicated option, but it is also the most flexible, as you can have multiple versions of this particular software installed and specify at run-time which one to use. This is incredibly useful if a major feature changes that would break old code, for example. You can see our tutorial on writing modules here, but the important variables to modify are, again, $PATH and $PYTHONPATH. You should specify the complete path to your home directory here and not rely on any shortcuts like ~ or $HOME.  Below is a modulefile written in Lua:

      If you are following the tutorial on writing modules, you will want to place this file in $HOME/local/share/lmodfiles/numexpr/2.8.4.lua:

      -- This is a Lua modulefile, this file 2.8.4.lua can be located anywhere
      -- But if you are following a local modulefile location convention, we place them in
      -- $HOME/local/share/lmodfiles/
      -- For numexpr we place it in $HOME/local/share/lmodfiles/numexpr/2.8.4.lua
      -- This finds your home directory
      local homedir = os.getenv("HOME")
      prepend_path("PYTHONPATH", 
      pathJoin(homedir, "/local/numexpr/2.8.4/lib/python3.6/site-packages"))
      prepend_path(homedir, "local/numexpr/2.8.4/bin")
      

      Once your module is created (again, see the guide), you can use your Python package simply by loading the software module you created.

      module use $HOME/local/share/lmodfiles/
      module load numexpr/2.8.4
      Supercomputer: 
      Service: 

      HOWTO: Use GPU with Tensorflow and PyTorch

      GPU Usage on Tensorflow

      Environment Setup

      To begin, you need to first create and new conda environment or use an already existing one. See HOWTO: Create  Python Environment for more details. In this example we are using python/3.6-conda5.2

      Once you have a conda environment created and activated we will now install tensorflow-gpu into the environment (In this example we will be using version 2.4.1 of tensorflow-gpu:

      conda install tensorflow-gpu=2.4.1
      

       

      Verify GPU accessability (Optional):

      Now that we have the environment set up we can check if tensorflow can access the gpus.

      To test the gpu access we will submit the following job onto a compute node with a gpu:

      #!/bin/bash
      #SBATCH --account <Project-Id>
      #SBATCH --job-name Python_ExampleJob
      #SBATCH --nodes=1
      #SBATCH --time=00:10:00
      #SBATCH --gpus-per-node=1
      
      
      ml python
      
      source activate tensorflow_env
      
      
      # run either of the following commands
      
      python << EOF 
      import tensorflow as tf 
      print(tf.test.is_built_with_cuda()) 
      EOF
      
      python << EOF
      from tensorflow.python.client import device_lib
      print(device_lib.list_local_devices())
      EOF
      
      
      

      You will know tensorflow is able to successfully access the gpu if tf.test.is_built_with_cuda() returns True and device_lib.list_local_devices() returns an object with /device:GPU:0 as a listed device.

      At this point tensorflow-gpu should be setup to utilize a GPU for its computations.

       

      GPU vs CPU

      A GPU can provide signifcant performace imporvements to many machine learnings models. Here is an example python script demonstrating the performace improvements. This is ran on the same environment  created in the above section.

      from timeit import default_timer as timer
      import tensorflow as tf
      from tensorflow import keras
      import numpy as np
      
      
      (X_train, y_train), (X_test, y_test) = keras.datasets.cifar10.load_data()
      
      
      # scaling image values between 0-1
      X_train_scaled = X_train/255
      X_test_scaled = X_test/255
      
      # one hot encoding labels
      y_train_encoded = keras.utils.to_categorical(y_train, num_classes = 10)
      y_test_encoded = keras.utils.to_categorical(y_test, num_classes = 10)
      
      def get_model():
          model = keras.Sequential([
              keras.layers.Flatten(input_shape=(32,32,3)),
              keras.layers.Dense(3000, activation='relu'),
              keras.layers.Dense(1000, activation='relu'),
              keras.layers.Dense(10, activation='sigmoid')    
          ])
      
          model.compile(optimizer='SGD',
                    loss='categorical_crossentropy',
                    metrics=['accuracy'])
          return model
      
      # GPU
      with tf.device('/GPU:0'):
          start = timer()
          model_cpu = get_model()
          model_cpu.fit(X_train_scaled, y_train_encoded, epochs = 1)
          end = timer()
      
      
      print("GPU time: ", end - start)
      
      # CPU
      with tf.device('/CPU:0'):
          start = timer()
          model_gpu = get_model()
          model_gpu.fit(X_train_scaled, y_train_encoded, epochs = 1)
          end = timer()
      
      print("CPU time: ", end - start)

      Example code sampled from here

      The above code was then submitted in a job with the following script:

      #!/bin/bash 
      #SBATCH --account <Project-Id> 
      #SBATCH --job-name Python_ExampleJob 
      #SBATCH --nodes=1 
      #SBATCH --time=00:10:00 
      #SBATCH --gpus-per-node=1 
      
      ml python/3.6-conda5.2 
      
      source activate tensorflow_env
      
      python tensorflow_example.py
      Make sure you request a gpu! For more information see GPU Computing

      As we can see from the output, the GPU provided a signifcant performace improvement.

      GPU time:  3.7491355929996644
      
      CPU time:  78.8043485119997

       

      Usage on Jupyter

      If you would like to use a gpu for your tensorflow project in a jupyter notebook follow the below commands to set up your environment.

      To begin, you need to first create and new conda environment or use an already existing one. See HOWTO: Create  Python Environment for more details. In this example we are using python/3.6-conda5.2

      Once you have a conda environment created and activated we will now install tensorflow-gpu into the environment (In this example we will be using version 2.4.1 of tensorflow-gpu:

      conda install tensorflow-gpu=2.4.1

      Now we will setup a jupyter kernel. See HOWTO: Use a Conda/Virtual Environment With Jupyter for details on how to create a jupyter kernel with your conda environment.

      Once you have the kernel created see Usage section of Python page for more details on accessing the Jupyter app from OnDemand. 

      When configuring your notebook make sure to select a GPU enabled node and a cuda version.

      Screenshot 2023-08-22 at 11.30.53 AM.jpeg

      Now you are all setup to use a gpu with tensorflow on a juptyer notebook.

       

      GPU Usage on PyTorch

      Environment Setup

      To begin, you need to first create and new conda environment or use an already existing one. See HOWTO: Create  Python Environment for more details. In this example we are using python/3.6-conda5.2

      Once you have a conda environment created and activated we will now install pytorch into the environment (In the example we will be using version 1.3.1 of pytorch:

      conda install pytorch=1.3.1
      

       

      Verify GPU accessability (Optional):

      Now that we have the environment set up we can check if pytorch can access the gpus.

      To test the gpu access we will submit the following job onto a compute node with a gpu:

      #!/bin/bash
      #SBATCH --account <Project-Id>
      #SBATCH --job-name Python_ExampleJob
      #SBATCH --nodes=1
      #SBATCH --time=00:10:00
      #SBATCH --gpus-per-node=1
      
      
      ml python/3.6-conda5.2
      
      source activate pytorch_env
      
      
      python << EOF
      import torch
      print(torch.cuda.is_available())
      device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
      print(device)
      EOF

      You will know pytorch is able to successfully access the gpu if torch.cuda.is_available() returns True and torch.device("cuda:0" if torch.cuda.is_available() else "cpu") returns cuda:0 .

      At this point PyTorch should be setup to utilize a GPU for its computations.

       

      GPU vs CPU

      Here is an example pytorch script demonstrating the performace improvements from GPUs

      import torch
      from timeit import default_timer as timer
      
      
      # check for cuda availability
      print("Cuda: ", torch.cuda.is_available())
      device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
      print("Device: ", device)
      
      
      #GPU 
      b = torch.ones(4000,4000).cuda() # Create matrix on GPU memory
      start_time = timer() 
      for _ in range(1000): 
          b += b 
      elapsed_time = timer() - start_time 
      
      print('GPU time = ',elapsed_time)
      
      
      #CPU
      a = torch.ones(4000,4000) # Create matrix on CPU memory
      start_time = timer()
      for _ in range(1000):
          a += a
      elapsed_time = timer() - start_time
      
      print('CPU time = ',elapsed_time)
      
      
      

       

      The above code was then submitted in a job with the following script:

      #!/bin/bash 
      #SBATCH --account <Project-Id> 
      #SBATCH --job-name Python_ExampleJob 
      #SBATCH --nodes=1 
      #SBATCH --time=00:10:00 
      #SBATCH --gpus-per-node=1 
      
      ml python/3.6-conda5.2 
      
      source activate pytorch_env
      
      python pytorch_example.py
      Make sure you request a gpu! For more information see GPU Computing

      As we can see from the output, the GPU provided a signifcant performace improvement.

      GPU time =  0.0053490259997488465
      
      CPU time =  4.232843188998231

       

      Usage on Jupyter

      If you would like to use a gpu for your PyTorch project in a jupyter notebook follow the below commands to set up your environment.

      To begin, you need to first create and new conda environment or use an already existing one. See HOWTO: Create  Python Environment for more details. In this example we are using python/3.6-conda5.2

      Once you have a conda environment created and activated we will now install pytorch into the environment (In the example we will be using version 1.3.1 of pytorch:

      conda install pytorch=1.3.1

      You also may need to install numba for PyTorch to access a gpu from the jupter notebook.

      conda install numba=0.54.1

       

      Now we will setup a jupyter kernel. See HOWTO: Use a Conda/Virtual Environment With Jupyter for details on how to create a jupyter kernel with your conda environment.

      Once you have the kernel created see Usage section of Python page for more details on accessing the Jupyter app from OnDemand. 

      When configuring your notebook make sure to select a GPU enabled node and a cuda version.

      Screenshot 2023-08-22 at 11.30.53 AM.jpeg

      Now you are all setup to use a gpu with PyTorch on a juptyer notebook.

      Horovod

      If you are using Tensorflow or PyTorch you may want to also consider using Horovod. Horovod will take single-GPU training scripts and scale it to train across many GPUs in parallel.

       

      Supercomputer: 

      HOWTO: Debugging Tips

      This article focuses on debugging strategies for C/C++ codes, but many are applicable to other languages as well.

      Rubber Duck Debugging

      This approach is a great starting point. Say you have written some code, and it does not do what you expect it to do. You have stared at it for a few minutes, but you cannot seem to spot the problem.

      Try explaining what the problem is to a rubber duck. Then, walk the rubber duck through your code, line by line, telling it what it does. Don’t have a rubber duck? Any inanimate object will do (or even an animate one if you can grab a friend).

      It sounds silly, but rubber duck debugging helps you to get out of your head, and hopefully look at your code from a new perspective. Saying what your code does (or is supposed to do) out loud has a good chance of revealing where your understanding might not be as good as you think it is.

      Printf() Debugging

      You’ve written a whole bunch of new code. It takes some inputs, chugs along for a while, and then creates some outputs. Somewhere along this process, something goes wrong. You know this because the output is not at all what you expected. Unfortunately, you have no idea where things are going wrong in the code.

      This might be a good time to try out printf() debugging. It’s as simple as its name implies: simply add (more) printf() statements to your code. You’ve likely seen this being used. It’s the name given to the infamous ‘printf(“here”);’ calls used to verify that a particular codepath is indeed taken.

      Consider printing out arguments and return values to key functions. Or, the results or summary statistics from large calculations. These values can be used as “sanity checks” to ensure that up until that point in the code, everything is going as expected.

      Assertion calls, such as "assert(...)", can also be used for a similar purpose. However, often the positive feedback you get from print statements is helpful in when you’re debugging. Seeing a valid result printed in standard out or a log file tells you positively that at least something is working correctly.

      Debuggers

      Debuggers are tools that can be used to interactively (or with scripts) debug your code. A fairly common debugger for C and C++ codes is gdb. Many guides exist online for using gdb with your code.

      OSC systems also provide the ARM DDT debugger. This debugger is designed for use with HPC codes and is arguably easier to use than gdb. It can be used to debug MPI programs as well.

      Debuggers allow you to interact with the program while it is running. You can do things like read and write variable values, or check to see if/when certain functions are called.

      Testing

      Okay, this one isn’t exactly a debugging strategy. It’s a method to catch bugs early, and even prevent the addition of bugs. Writing a test suite for your code that’s easy to run (and ideally fast) lets you test new changes to ensure they don’t break existing functionality.

      There are lots of different philosophies on testing software. Too many to cover here. Here’s two concepts that are worth looking into: unit testing and system testing.

      The idea behind unit testing is writing tests for small “units” of code. These are often functions or classes. If you know that the small pieces that make up your code work, then you’ll have more confidence in the overall assembled program. There’s an added architecture benefit here too. Writing code that is testable in the first place often results in code that’s broken up into separate logical pieces (google “separation of concerns”). This makes your code more modular and less “spaghetti-like”. Your code will be easier to modify and understand.

      The second concept – system testing – involves writing tests that run your entire program. These often take longer than unit tests, but have the added benefit that they’ll let you know whether or not your entire program still works after introducing a new change.

      When writing tests (both system and unit tests), it’s often helpful to include a couple different inputs. Occasionally a program may work just fine for one input, but fail horribly with another input.

      Minimal, Reproducible Example

      Maybe your code takes a couple hours (or longer…) to run. There’s a bug in it, but every time you try to fix it, you have to wait a few hours to see if the fix worked. This is driving you crazy.

      A possible approach to make your life easier is to try to make a Minimal, Reproducible Example (see this stackoverflow page for information).

      Try to extract just the code that fails, from your program, and also its inputs. Wrap this up into a separate program. This allows you to run just the code that failed, hopefully greatly reducing the time it takes to test out fixes to the problem.

      Once you have this example, can you make it smaller? Maybe take out some code that’s not needed to reproduce the bug, or shrink the input even further? Doing this might help you solve the problem.

      Tools and other resources

      • Compiler warnings – compilers are your friend. Chances are your compiler has a flag that can be used to enable more warnings than are on by default. GNU tools have “-Wall” and “-Wextra”. These can be used to instruct the compiler to tell you about places in the code where bugs may exist.
      • The Practice of Programming by Brian Kernighan and Rob Pike contains a very good chapter on debugging C and C++ programs.
      • Valgrind is a tool that can be used for many types of debugging including looking for memory corruptions and leaks. However, it slows down your code a very sizeable amount. This might not be feasible for HPC codes
      • ASAN (address sanitizer) is another tool that can be used for memory debugging. It is less featureful than Valgrind, but runs much quicker, and so will likely work with your HPC code.

       

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      HOWTO: Establish durable SSH connections

      In December 2021 OSC updated its firewall to enhance security. As a result, SSH sessions are being closed more quickly than they used to be. It is very easy to modify your SSH options in the client you use to connect to OSC to keep your connection open.

      In ~/.ssh/config (use the command touch ~/.ssh/config to create it if there is no exisitng one), you can set 3 options:

      TCPKeepAlive=no
      ServerAliveInterval=60
      ServerAliveCountMax=5

      Please refer to your SSH client documentation for how to set these options in your client.

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      HOWTO: Identify users on a project account and check status

      An eligible principal investigator (PI) heads a project account and can authorize/remove user accounts under the project account (please check our Allocations and Accounts documentation for more details). This document shows you how to identify users on a project account and check the status of each user. 

      Identify Users on a Project Account

      If you know the project acccount

      If the project account (projectID) is known, the OSCgetent command will list all users on the project:

      $ OSCgetent group projectID
      

      The returned information is in the format of:

      projectID:*:gid: list of user IDs
      

      gid is the group identifier number unique for the project account projectID. 

      For example, the command OSCgetent group PZS0712 lists all users on the project account PZS0712 as below:

      $ OSCgetent group PZS0712
      PZS0712:*:5513:amarcum,guilfoos,hhamblin,kcahill,xwang
      

      Multiple groups can also be queried at once.

      For Example, the command OSCgetent group PZS0712 PZS0726 lists all users on both PZS0712 and PZS0726:

      PZS0712:*:5513:amarcum,guilfoos,hhamblin,kcahill,xwang
      PZS0726:*:6129:amarcum,kkappel
      

      Details on a project can also be obtained along with the user list using the OSCfinger command.

      $ OSCfinger -g projectID 
      

      This returns:

      Group: projectID                                  GID: XXXX
      Status: 'active/restricted/etc'                   Type: XX
      Principal Investigator: 'PI email'                Admins: NA
      Members: 'list of users'
      Category: NA
      Institution: 'affliated institution'
      Description: 'short description'
      ---
      

      If you don't know the project acccount, but know the username

      If the project account is not known, but the username is known, use the  OSCfinger command to list all of the groups the user belongs to:

      OSCfinger username
      

      The returned information is in the format of:

      Login: username                                   Name: First Last
      Directory: home directory path                    Shell: /bin/bash
      E-mail: user's email address
      Primary Group: user's primary project
      Groups: list of projects and other groups user is in
      Password Changed: date password was last changed  Password Expires: date password expires
      Login Disabled: TRUE/FALSE                             Password Expired: TRUE/FALSE
      Current Logins:
      Displays if user is currently logged in and from where/when
      

      For example, with the username as amarcum, the command OSCfinger amarcum returns the information as below:

      $ OSCfinger amarcum
      Login: amarcum                                    Name: Antonio Marcum
      Directory: /users/PZS0712/amarcum                 Shell: /bin/bash
      E-mail: amarcum@osc.edu
      Primary Group: PZS0712
      Groups: sts,ruby,l2supprt,oscall,clntstf,oscstaff,clntall,PZS0712,PZS0726
      Password Changed: May 12 2019 15:47 (calculated)  Password Expires: Aug 11 2019 12:05 AM
      Login Disabled: FALSE                             Password Expired: FALSE
      Current Logins:
      On since Mar 07 2019 12:12 on pts/14 from pitzer-login01.hpc.osc.edu
      ----
      

      If you don't know either the project account or user account

      If the project account or username is not known, use the OSCfinger -e command with the '-e' flag to get the user account based on the user's name.

      Use the following command to list all of the user accounts associated with a First and Last name:

      $ OSCfinger -e 'First Last'
      

      For example, with user's first name as Summer and last name as Wang, the command

      OSCfinger -e 'Summer Wang' returns the information as below:

      $ OSCfinger -e 'Summer Wang'
      Login: xwang                                      Name: Summer Wang
      Directory: /users/oscgen/xwang                    Shell: /bin/bash
      E-mail: xwang@osc.edu
      Primary Group: PZS0712
      Groups: amber,abaqus,GaussC,comsol,foampro,sts,awsmdev,awesim,ruby,matlab,aasheats,mars,ansysflu,wrigley,lgfuel,l2supprt,fsl,oscall,clntstf,oscstaff,singadm,clntall,dhgremot,fsurfer,PZS0530,PCON0003,PZS0680,PMIU0149,PZS0712,PAS1448
      Password Changed: Jan 08 2019 11:41               Password Expires: Jul 08 2019 12:05 AM
      Login Disabled: FALSE                             Password Expired: FALSE
      ---
      

      Once you know the user account username, follow the discussions in the previous section identify users on a project to get all user accounts on the project. Please contact OSC Help if you have any questions. 

      Check the Status of a User

      Use the OSCfinger command to check the status of a user account as below:

      OSCfinger username
      

      For example, if the username is xwang, the command  OSCfinger xwang will return:

      $ OSCfinger xwang
      Login: xwang                                      Name: Summer Wang
      Directory: /users/oscgen/xwang                    Shell: /bin/bash
      E-mail: xwang@osc.edu
      Primary Group: PZS0712
      Groups: amber,abaqus,GaussC,comsol,foampro,sts,awsmdev,awesim,ruby,matlab,aasheats,mars,ansysflu,wrigley,lgfuel,l2supprt,fsl,oscall,clntstf,oscstaff,singadm,clntall,dhgremot,fsurfer,PZS0530,PCON0003,PZS0680,PMIU0149,PZS0712,PAS1448
      Password Changed: Jan 08 2019 11:41               Password Expires: Jul 08 2019 12:05 AM
      Login Disabled: FALSE                             Password Expired: FALSE
      ---
      
      • The home directory of xwang is   Directory: /users/oscgen/xwang
      • The shell of xwang is bash (Shell: /bin/bash). If the information is Shell:/access/denied, it means this user account has been either archived or restricted. Please contact OSC Help if you'd like to reactivate this user account.
      • xwang@osc.edu is the associated email with the user account xwang; that is, all OSC emails related to the account xwang will be sent to xwang@osc.edu (Mail forwarded to xwang@osc.edu). Please contact OSC Help if the email address associated with this user account has been changed to ensure important notifications/messages/reminders from OSC may be received in a timely manner.

      Check the Usage and Quota of a User's Home Directory/Project Space

      All users see their file system usage statistics when logging in, like so:

      As of 2018-01-25T04:02:23.749853 userid userID on /users/projectID used XGB of quota 500GB and Y files of quota 1000000 files
      

      The information is from the file /users/reporting/storage/quota/*_quota.txt , which is updated twice a day. Some users may see multiple lines associated with a username, as well as information on project space usage and quota of their Primary project, if there is one. The usage and quota of the home directory of a username is provided by the line including the file server your home directory is on (for more information, please visit Home Directories), while others (generated due to file copy) can be safely ignored. 

      You can check any user's home directory or a project's project space usage and quota by running:

      grep -h 'userID' OR 'projectID' /users/reporting/storage/quota/*_quota.txt
      
      

      Here is an example of project PZS0712:

      $ grep -h PZS0712 /users/reporting/storage/quota/*_quota.txt
      As of 2019-03-07T13:55:01.000000 project/group PZS0712 on /fs/project used 262 GiB of quota 2048 GiB and 166987 files of quota 200000 files
      As of 2019-03-07T13:55:01.000000 userid xwang on /fs/project/PZS0712 used 0 GiB of quota 0 GiB and 21 files of quota 0 files
      As of 2019-03-07T13:55:01.000000 userid dheisterberg on /fs/project/PZS0712 used 262 GiB of quota 0 GiB and 166961 files of quota 0 files
      As of 2019-03-07T13:55:01.000000 userid amarcum on /fs/project/PZS0712 used 0 GiB of quota 0 GiB and 2 files of quota 0 files
      As of 2019-03-07T13:55:01.000000 userid root on /fs/project/PZS0712 used 0 GiB of quota 0 GiB and 2 files of quota 0 files
      As of 2019-03-07T13:55:01.000000 userid guilfoos on /fs/project/PZS0712 used 0 GiB of quota 0 GiB and 1 files of quota 0 files
      As of 2019-03-07T13:51:23.000000 userid amarcum on /users/PZS0712 used 399.86 MiB of quota 500 GiB and 8710 files of quota 1000000 files
      

      Here is an example for username amarcum:

      $ grep -h amarcum /users/reporting/storage/quota/*_quota.txt
      As of 2019-03-07T13:55:01.000000 userid amarcum on /fs/project/PZS0712 used 0 GiB of quota 0 GiB and 2 files of quota 0 files
      As of 2019-03-07T13:56:39.000000 userid amarcum on /users/PZS0645 used 4.00 KiB of quota 500 GiB and 1 files of quota 1000000 files
      As of 2019-03-07T13:56:39.000000 userid amarcum on /users/PZS0712 used 399.86 MiB of quota 500 GiB and 8710 files of quota 1000000 files
      

      Check the RU Usage for Projects and Users

      The OSCusage commnad can provide detailed information about computational usage for a given project and user.

      See the OSCusage command page for details.

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      HOWTO: Install a MATLAB toolbox

      If you need to use a MATLAB toolbox that is not provided through our installations. You can follow these instructions, and if you have any difficulties you can contact OSC Help for assistance.

      A reminder: It is your responsibility to verify that your use of software packages on OSC’s systems including any 3rd party toolboxes (whether installed by OSC staff or by yourself)  complies with the packages’ license terms.

      Gather your materials

      First, we recommend making a new directory within your home directory in order to keep everything organized. You can use the unix command to make a new directory: "mkdir"

      Now you can download the toolbox either to your desktop, and then upload it to OSC, or directly download it using the "wget" utility (if you know the URL for the file).

      Now you can extract the downloaded file.

      Adding the path

      There are two methods on how to add the MATLAB toolbox path.

      Method 1: Load up the Matlab GUI and click on "Set Path" and "Add folder"

      Method 2: Use the "addpath" fuction in your script. More information on the function can be found here: https://www.mathworks.com/help/matlab/ref/addpath.html

      Running the toolbox

      Please refer to the instructions given alongside the toolbox. They should contain instructions on how to run the toolbox.

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      HOWTO: Install your own Perl modules

      While we provide a number of Perl modules, you may need a module we do not provide. If it is a commonly used module, or one that is particularly difficult to compile, you can contact OSC Help for assistance, but we have provided an example below showing how to build and install your own Perl modules. Note, these instructions use "bash" shell syntax; this is our default shell, but if you are using something else (csh, tcsh, etc), some of the syntax may be different.

      CPAN Minus

      CPAN, the Comprehensive Perl Achive Network, is the primary source for publishing and fetching the latest modules and libraries for the Perl programming language. The default method for installing Perl modules using the "CPAN Shell", provides users with a great deal of power and flexibility but at the cost of a complex configuration and inelegant default setup.

      Setting Up CPAN Minus

      To use CPAN Minus with the system Perl (version 5.16.3), we need to ensure that the "cpanminus" module is loaded, if it hasn't been loaded already.

      module load cpanminus
      

      Please note that this step is not required if you have already loaded a version of Perl using the module load command.

      Next, in order to use cpanminus, you will need to run the following command only ONCE:

      perl -I $CPANMINUS_INC -Mlocal::lib
      

      Using CPAN Minus

      In most cases, using CPAN Minus to install modules is as simple as issuing a command in the following form:

      cpanm [Module::Name]
      

      For example, below are three examples of installing perl modules:

      cpanm Math::CDF
      cpanm SET::IntervalTree
      cpanm DB_File
      
      

      Testing Perl Modules

      To test a perl module import, here are some examples below:

      perl -e "require Math::CDF"
      perl -e "require Set::IntervallTree"
      perl -e "require DB_File"
      

      The modules are installed correctly if no output is printed.

      What Local Modules are Installed in my Account?

      To show the local modules you have installed in your user account:

      perldoc perllocal
      

      Reseting Module Collection

      If you should ever want to start over with your perl module collection, delete the following folders:

      rm -r ~/perl5 
      rm -r ~/.cpanm
      

       

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      HOWTO: Locally Installing Software

      Sometimes the best way to get access to a piece of software on the HPC systems is to install it yourself as a "local install". This document will walk you through the OSC-recommended procedure for maintaining local installs in your home directory or project space. The majority of this document describes the process of "manually" building and installing your software. We also show a partially automated approach through the use of a bash script in the Install Script section near the end.

      NOTE: Throughout this document we'll assume you're installing into your home directory, but you can follow the steps below in any directory for which you have read/write permissions.
      This document assumes you are familiar with the process of building software using "configure" or via editing makefiles, and only provides best practices for installing in your home directory.

      Getting Started

      Before installing your software, you should first prepare a place for it to live. We recommend the following directory structure, which you should create in the top-level of your home directory:

          local
          |-- src
          |-- share
              `-- lmodfiles
      

      This structure is analogous to how OSC organizes the software we provide. Each directory serves a specific purpose:

      • local - Gathers all the files related to your local installs into one directory, rather than cluttering your home directory. Applications will be installed into this directory with the format "appname/version". This allows you to easily store multiple versions of a particular software install if necessary.
      • local/src - Stores the installers -- generally source directories -- for your software. Also, stores the compressed archives ("tarballs") of your installers; useful if you want to reinstall later using different build options.
      • local/share/lmodfiles - The standard place to store module files, which will allow you to dynamically add or remove locally installed applications from your environment.

      You can create this structure with one command:

          mkdir -p $HOME/local/src $HOME/local/share/lmodfiles
      

      (NOTE:  $HOME is defined by the shell as the full path of your home directory. You can view it from the command line with the command echo $HOME.)

      Installing Software

      Now that you have your directory structure created, you can install your software. For demonstration purposes, we will install a local copy of Git.

      First, we need to get the source code onto the HPC filesystem. The easiest thing to do is find a download link, copy it, and use the wget tool to download it on the HPC. We'll download this into $HOME/local/src:

          cd $HOME/local/src
          wget https://github.com/git/git/archive/v2.9.0.tar.gz
      

      Now extract the tar file:

          tar zxvf v2.9.0.tar.gz
      

      Next, we'll go into the source directory and build the program. Consult your application's documentation to determine how to install into $HOME/local/"software_name"/"version". Replace "software_name" with the software's name and "version" with the version you are installing, as demonstrated below. In this case, we'll use the configure tool's --prefix option to specify the install location.

      You'll also want to specify a few variables to help make your application more compatible with our systems. We recommend specifying that you wish to use the Intel compilers and that you want to link the Intel libraries statically. This will prevent you from having to have the Intel module loaded in order to use your program. To accomplish this, add CC=icc CFLAGS=-static-intel to the end of your invocation of configure. If your application does not use configure, you can generally still set these variables somewhere in its Makefile or build script.

      Then, we can build Git using the following commands:

          cd git-2.9.0
          autoconf # this creates the configure file
          ./configure --prefix=$HOME/local/git/2.9.0 CC=icc CFLAGS=-static-intel
          make && make install
      

      Your application should now be fully installed. However, before you can use it you will need to add the installation's directories to your path. To do this, you will need to create a module.

      Creating a Module

      Modules allow you to dynamically alter your environment to define environment variables and bring executables, libraries, and other features into your shell's search paths.


      Automatically create a module

      We can use the mkmod script to create a simple Lua module for the Git installation:

      module load mkmod
      create_module.sh git 2.9.0 $HOME/local/git/2.9.0
      

      It will create the module $HOME/local/share/lmodfiles/git/2.9.0.lua. Please note that by default our mkmod script only creates module files that define some basic environment variables PATHLD_LIBRARY_PATH, MANPATH, and GIT_HOME. These default variables may not cover all paths desired. We can overwrite these defaults in this way:

      module load mkmod
      TOPDIR_LDPATH_LIST="lib:lib64" \
      TOPDIR_PATH_LIST="bin:exe" \
      create_module.sh git 2.9.0 $HOME/local/git/2.9.0
      

      This adds $GIT_HOME/bin, $GIT_HOME/exe to PATH and $GIT_HOME/lib , $GIT_HOME/lib64 to LD_LIBRARY_PATH.

      We can also add other variables by using ENV1, ENV2, and more. For example, suppose we want to change the default editor to vim for Git:

      module load mkmod
      ENV1="GIT_EDITOR=vim" \
      create_module.sh git 2.9.0 $HOME/local/git/2.9.0

      Manually create a module 

      We will be using the filename 2.9.0.lua ("version".lua). A simple Lua module for our Git installation would be:

      -- Local Variables
      local name = "git"
      local version = "2.9.0"
      
      -- Locate Home Directory
      local homedir = os.getenv("HOME")
      local root = pathJoin(homedir, "local", name, version)
      
      -- Set Basic Paths
      prepend_path("PATH", pathJoin(root, "bin"))
      prepend_path("LD_LIBRARY_PATH", root .. "/lib")
      prepend_path("LIBRARY_PATH", root .. "/lib")
      prepend_path("INCLUDE", root .. "/include")
      prepend_path("CPATH", root .. "/include")
      prepend_path("PKG_CONFIG_PATH", root .. "/lib/pkgconfig")
      prepend_path("MANPATH", root .. "/share/man")
      

      NOTE: For future module files, copy our sample modulefile from ~support/doc/modules/sample_module.lua. This module file follows the recommended design patterns laid out above and includes samples of many common module operations

      Our clusters use a Lua based module system. However, there is another module system based in TCL that will not be discussed in this HOWTO.
      NOTE: TCL is cross-compatible and is converted to Lua when loaded. More documentation is available at https://www.tacc.utexas.edu/research-development/tacc-projects/lmod/ or by executing module help.

      Initializing Modules

      Any module file you create should be saved into your local lmodfiles directory ($HOME/local/share/lmodfiles). To prepare for future software installations, create a subdirectory within lmodfiles named after your software and add one module file to that directory for each version of the software installed.

      In the case of our Git example, you should create the directory $HOME/local/share/lmodfiles/git and create a module file within that directory named 2.9.0.lua.

      To make this module usable, you need to tell lmod where to look for it. You can do this by issuing the command module use $HOME/local/share/lmodfiles in our example. You can see this change by performing module avail. This will allow you to load your software using either module load git or module load git/2.9.0

      NOTE: module use$HOME/local/share/lmodfiles and module load "software_name" need to be entered into the command line every time you enter a new session on the system.

      If you install another version later on (lets say version 2.9.1) and want to create a module file for it, you need to make sure you call it 2.9.1.lua. When loading Git, lmod will automatically load the newer version. If you need to go back to an older version, you can do so by specifying the version you want: module load git/2.9.0.

      To make sure you have the correct module file loaded, type which git which should emit "~/local/git/2.9.0/bin/git" (NOTE: ~ is equivalent to $HOME). 

      To make sure the software was installed correctly and that the module is working, type git --version which should emit "git version 2.9.0".

      Automating With Install Script

      Simplified versions of the scripts used to manage the central OSC software installations are provided at ~support/share/install-script. The idea is that you provide the minimal commands needed to obtain, compile, and install the software (usually some variation on wget, tar, ./configure, make, and make install) in a script, which then sources an OSC-maintained template that provides all of the "boilerplate" commands to create and manage a directory structure similar to that outlined in the Getting Started section above. You can copy an example install script from ~support/share/install-script/install-osc_sample.sh and follow the notes in that script, as well as in ~support/share/install-script/README.md, to modify it to install software of your choosing.

      NOTE: By default, the install script puts the module files in $HOME/osc_apps/lmodfiles, so you will need to run module use $HOME/osc_apps/lmodfiles and module load [software-name] every time you enter a new session on the system and want to use the software that you have installed.

      Further Reading

      For more information about modules, be sure to read the webpage indicated at the end of module help. If you have any questions about modules or local installations, feel free to contact the OSC Help Desk and oschelp@osc.edu.

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      HOWTO: Manage Access Control List (ACLs)

      An ACL (access control list) is a list of permissions associated with a file or directory. These permissions allow you to restrict access to a certain file or directory by user or group. 

      OSC supports NFSv4 ACL on our home directory and POSIX ACL on our project and scratch file systems. Please see the how to use NFSv4 ACL for home directory ACL management and how to use POSIX ACL for managing ACLs in project and scratch file systems. 

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      HOWTO: Use NFSv4 ACL

      This document shows you how to use the NFSv4 ACL permissions system. An ACL (access control list) is a list of permissions associated with a file or directory. These permissions allow you to restrict access to a certian file or directory by user or group. NFSv4 ACLs provide more specific options than typical POSIX read/write/execute permissions used in most systems.

      These commands are useful for managing ACLs in the dir locations of /users/<project-code>.

      Understanding NFSv4 ACL

      This is an example of an NFSv4 ACL

      A::user@nfsdomain.org:rxtncy
      
      A::alice@nfsdomain.org:rxtncy
      
      A::alice@nfsdomain.org:rxtncy
      
      A::alice@nfsdomain.org:rxtncy
      

      The following sections will break down this example from left to right and provide more usage options

       

      ACE Type

      The 'A' in the example is known as the ACE (access control entry) type. The 'A' denotes "Allow" meaning this ACL is allowing the user or group to perform actions requiring permissions. Anything that is not explicitly allowed is denied by default.

      Note: 'D' can denote a Deny ACE. While this is a valid option, this ACE type is not reccomended since any permission that is not explicity granted is automatically denied meaning Deny ACE's can be redundant and complicated.

       

      ACE Flags

      The above example could have a distinction known as a flag shown below

      A:d:user@osc.edu:rxtncy
      

      The 'd' used above is called an inheritence flag. This makes it so the ACL set on this directory will be automatically established on any new subdirectories. Inheritence flags only work on directories and not files. Multiple inheritence flags can be used in combonation or omitted entirely. Examples of inheritence flags are listed below:

      Flag Name Function
      d directory-inherit New subdirectories will have the same ACE
      f file-inherit New files will have the same ACE minus the inheritence flags 
      n no-propogate inherit New subdirectories will inherit the ACE minus the inheritence flags
      i inherit-only New files and subdirectories will have this ACE but the ACE for the directory with the flag is null

       

      ACE Principal

      The 'user@nfsdomain.org' is a principal. The principle denotes the people the ACL is allowing access to. Principals can be the following:

      • A named user
      • Special principals
        • OWNER@
        • GROUP@
        • EVERYONE@
      • A group
        • Note: When the principal is a group, you need to add a group flag, 'g', as shown in the below example
        • A:g:group@osc.edu:rxtncy
          

       

      ACE Permissions

      The 'rxtncy' are the permissions the ACE is allowing. Permissions can be used in combonation with each other. A list of permissions and what they do can be found below:

      Permission Function
      r read-data (files) / list-directory (directories)
      w write-data (files) / create-file (directories)
      a append-data (files) / create-subdirectory (directories)
      x execute (files) / change-directory (directories)
      d delete the file/directory
      D delete-child : remove a file or subdirectory from the given directory (directories only)
      t read the attributes of the file/directory
      T write the attribute of the file/directory
      n read the named attributes of the file/directory
      N write the named attributes of the file/directory
      c read the file/directory ACL
      C write the file/directory ACL
      o change ownership of the file/directory

       

      Note: Aliases such as 'R', 'W', and 'X' can be used as permissions. These work simlarly to POSIX Read/Write/Execute. More detail can be found below.

      Alias Name Expansion
      R Read rntcy
      W Write watTNcCy (with D added to directory ACE's)
      X Execute xtcy

       

      Using NFSv4 ACL

      This section will show you how to set, modify, and view ACLs

       

      Set and Modify ACLs

      To set an ACE use this command:

      nfs4_setfacl [OPTIONS] COMMAND file
      

      To modify an ACE, use this command:

      nfs4_editfacl [OPTIONS] file
      

      Where file is the name of your file or directory. More information on Options and Commands can be found below.

       

      Commands

      Commands are only used when first setting an ACE. Commands and their uses are listed below.

      COMMAND FUNCTION
      -a acl_spec [index] add ACL entries in acl_spec at index (DEFAULT: 1)
      -x acl_spec | index remove ACL entries or entry-at-index from ACL
      -A file [index] read ACL entries to add from file
      -X file  read ACL entries to remove from file
      -s acl_spec set ACL to acl_spec (replaces existing ACL)
      -S file read ACL entries to set from file
      -m from_ace to_ace modify in-place: replace 'from_ace' with 'to_ace'

       

      Options

      Options can be used in combination or ommitted entirely. A list of options is shown below:

      OPTION NAME FUNCTION
      -R recursive Applies ACE to a directory's files and subdirectories
      -L logical Used with -R, follows symbolic links
      -P physical Used with -R, skips symbolic links
       

       

      View ACLs

      To view ACLs, use the following command:

      nfs4_getfacl file
      

      Where file is your file or directory

      Use cases

      Create a share folder for a specific group

      First, make the top-level of home dir group executable.

      nfs4_setfacl -a A:g:<group>@osc.edu:X $HOME
      We make $HOME only executable so that the group can only traverse to the share folder which is created in the next steps, and view other folders in your home dir. Providing executable access lets one (user/group) go to that dir, but not read it's contents.

      Next create a new folder to store shared data

      mkdir share_group

      Move all data to be shared that already exists to this folder

      mv <src> ~/share_group

      Apply the acl for all current files and dirs under ~/share_group, and set acl so that new files created there will automatically have proper group permissions

      nfs4_setfacl -R -a A:dfg:<group>@osc.edu:RX ~/share_group

      using an acl file

      One can also specify the acl to be used in a single file, then apply that acl to avoid duplicate entries and keep the acl entries consistent.

      $ cat << EOF > ~/group_acl.txt
      
      A:fdg:clntstf@osc.edu:rxtncy
      A::OWNER@:rwaDxtTnNcCy
      A:g:GROUP@:tcy
      A::EVERYONE@:rxtncy
      EOF
      $ nfs4_setfacl -R -S ~/group_acl.txt ~/share_group
      
      Remember that any existing data moved into the share folder will retain its original permissions/acl.
      That data will need to be set with a new acl manually to allow group read permissions.

      Share data in your home directory with other users

      Assume that you want to share a directory (e.g data) and its files and subdirectories, but it is not readable by other users,

      > ls -ld /users/PAA1234/john/data
      drwxr-x--- 3 john PAA1234 4096 Nov 21 11:59 /users/PAA1234/john/data
      

      Like before, allow the user execute permissions to $HOME.

      > nfs4_setfacl -a A::userid@osc.edu:X $HOME

      set an ACL to the directory 'data'  to allow specific user access:

      > cd /users/PAA1234/john
      > nfs4_setfacl -R -a A:df:userid@osc.edu:RX data
      

      or  to to allow a specific group access:

      > cd /users/PAA1234/john
      > nfs4_setfacl -R -a A:dfg:groupname@osc.edu:RX data

      You can repeat the above commands to add more users or groups.

      Share entire home dir with a group

      Sometimes one wishes to share their entire home dir with a particular group. Care should be taken to only share folders with data and not any hidden dirs.

      Some folders in a home dir should retain permissions to only allow the user which owns them to read them. An example is the ~/.ssh dir, which should always have read permissions only for the user that owns it.

      Use the below command to only assign group read permissions only non-hidden dirs.

      for dir in $(ls $HOME); do nfs4_setfacl -R -a A:dfg:<group>@osc.edu:RX $dir; done

      After sharing an entire home dir with a group, you can still create a single share folder with the previous instructions to share different data with a different group only. So, all non-hidden dirs in your home dir would be readable by group_a, but a new folder named 'group_b_share' can be created and its acl altered to only share its contents with group_b.

      Please contact oschelp@osc.edu if there are any questions.

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      HOWTO: Use POSIX ACL

      This document shows you how to use the POSIX ACL permissions system. An ACL (access control list) is a list of permissions associated with a file or directory. These permissions allow you to restrict access to a certian file or directory by user or group.

      These commands are useful for project and scratch dirs located in /fs/ess.

      Understanding POSIX ACL

      An example of a basic POSIX ACL would look like this:

      # file: foo.txt 
      # owner: tellison 
      # group: PZSXXXX 
      user::rw- 
      group::r-- 
      other::r--

      The first three lines list basic information about the file/directory in question: the file name, the primary owner/creator of the file, and the primary group that has permissions on the file. The following three lines show the file access permissions for the primary user, the primary group, and any other users. POSIX ACLs use the basic rwx permissions, explaned in the following table:

      Permission Explanation
      r Read-Only Permissions
      w Write-Only Permissions
      x

      Execute-Only Permissions

       

      Using POSIX ACL

      This section will show you how to set and view ACLs, using the setfacl and getfacl commands

      Viewing ACLs with getfacl

      The getfacl command displays a file or directory's ACL. This command is used as the following

      $ getfacl [OPTION] file

      Where file is the file or directory you are trying to view. Common options include:

      Flag Description
      -a/--access Display file access control list only
      -d/--default Display default access control list only (only primary access), which determines the default permissions of any files/directories created in this directory
      -R/--recursive Display ACLs for subdirectories
      -p/--absolute-names Don't strip leading '/' in pathnames

      Examples:

      A simple getfacl call would look like the following:

      $ getfacl foo.txt 
      # file: foo.txt
      # owner: user
      # group: PZSXXXX
      user::rw-
      group::r--
      other::r--

      A recursive getfacl call through subdirectories will list each subdirectories ACL separately

      $ getfacl -R foo/
      # file: foo/
      # owner: user
      # group: PZSXXXX
      user::rwx
      group::r-x
      other::r-x
      
      # file: foo//foo.txt
      # owner: user
      # group: PZSXXXX
      user::rwx
      group::---
      other::---
      
      # file: foo//bar
      # owner: user
      # group: PZSXXXX
      user::rwx
      group::---
      other::---
      
      # file: foo//bar/foobar.py
      # owner: user
      # group: PZSXXXX
      user::rwx
      group::---
      other::---
      

      Setting ACLs with setfacl

      The setfacl command allows you to set a file or directory's ACL. This command is used as the following

      $ setfacl [OPTION] COMMAND file

      Where file is the file or directory you are trying to modify. 

      Commands and Options

      setfacl takes several commands to modify a file or directory's ACL

      Command Function
      -m/--modify=acl

      modify the current ACL(s) of files. Use as the following

      setfacl -m u/g:user/group:r/w/x file

      -M/--modify-file=file

      read ACL entries to modify from a file. Use as the following

      setfaclt -M file_with_acl_permissions file_to_modify

      -x/--remove=acl

      remove entries from ACL(s) from files. Use as the following

      setfaclt -x u/g:user/group:r/w/x file

      -X/--remove-file=file

      read ACL entries to remove from a file. Use as the following

      setfaclt -X file_with_acl_permissions file_to_modify

      -b/--remove-all Remove all extended ACL permissions

      Common option flags for setfacl are as follows:

      Option Function
      -R/--recursive Recurse through subdirectories
      -d/--default Apply modifications to default ACLs
      --test test ACL modifications (ACLs are not modified

      Examples

      You can set a specific user's access priviledges using the following

      setfacl -m u:username:-wx foo.txt

      Similarly, a group's access priviledges can be set using the following

      setfacl -m g:PZSXXXX:rw- foo.txt

      You can remove a specific user's access using the following

      setfacl -x user:username foo.txt

      Grant a user recursive read access to a dir and all files/dirs under it (notice that the capital 'X' is used to provide execute permissions only to dirs and not files):

      setfacl -R -m u:username:r-X shared-dir

      Set a dir so that any newly created files or dirs under will inherit the parent dirs facl:

      setfacl -d -m u:username:r-X shared-dir

      HOWTO: Reduce Disk Space Usage

      This HOWTO will demonstrate how to lower ones' disk space usage. The following procedures can be applied to all of OSC's file systems.

      We recommend users regularly check their data usage and clean out old data that is no longer needed.

      Users who need assistance lowering their data usage can contact OSC Help.

      Preventing Excessive Data Usage Before It Starts

      Users should ensure that their jobs are written in such a way that temporary data is not saved to permanent file systems, such as the project space file system or their home directory.

      If your job copies data from the scratch file system or its node's local disk ($TMPDIR) back to a permanent file system, such as the project space file system or a home directory ( /users/PXX####/xxx####/), you should ensure you are only copying the files you will need later.

      Identifying Old and Large Data

      The following commands will help you identify old data using the find command.

      find commands may produce an excessive amount of output. To terminate the command while it is running, click CTRL + C.

      Find all files in a directory that have not been accessed in the past 100 days:

      This command will recursively search the users home directory and give a detailed listing of all files not accessed in the past 100 days.

      The last access time atime is updated when a file is opened by any operation, including grep, cat, head, sort, etc.

      find ~ -atime +100 -exec ls -l {} \;
      
      • To search a different directory replace ~ with the path you wish to search. A period . can be used to search the current directory.
      • To view files not accessed over a different time span, replace 100 with your desired number of days.
      • To view the total size in bytes of all the files found by find, you can add | awk '{s+=$5} END {print "Total SIZE (bytes): " s}' to the end of the command:
      find ~ -atime +100 -exec ls -l {} \;| awk '{s+=$5} END {print "Total SIZE (bytes): " s}'
      

      Find all files in a directory that have not been modified in the past 100 days:

      This command will recursively search the users home directory and give a detailed listing of all files not modified in the past 100 days.

      The last modified time mtime is updated when a file's contents are updated or saved. Viewing a file will not update the last modified time.

      find ~ -mtime +100 -exec ls -l {} \; 
      
      • To search a different directory replace ~ with the path you wish to search. A period . can be used to search the current directory.
      • To view files not modified over a different time span, replace 100 with your desired number of days.
      • To view the total size in bytes of all the files found by find, you can add | awk '{s+=$5} END {print "Total SIZE (bytes): " s}' to the end of the command:
      find ~ -mtime +100 -exec ls -l {} \;| awk '{s+=$5} END {print "Total SIZE (bytes): " s}'
      

      List files larger than a specified size:

      Adding the -size <size> option and argument to the find command allows you to only view files larger than a certain size. This option and argument can be added to any other find command.

      For example, to view all files in a users home directory that are larger than 1GB:

      find ~ -size +1G -exec ls -l {} \;
      

      List number of files in directories

      Use the following command to view list dirs under <target-dir> and number of files contained in the dirs.

      du --inodes -d 1 <target-dir>
      

      Deleting Identified Data

      CAUTION: Be careful when deleting files. Be sure your command will do what you want before running it. Extra caution should be used when deleting files from a file system that is not backed up, such as the scratch file system.

      If you no longer need the old data, you can delete it using the rm command.

      If you need to delete a whole directory tree (a directory and all of its subcontents, including other directories), you can use the rm -R command.

      For example, the following command will delete the data directory in a users home directory:

      rm -R ~/data
      

      If you would like to be prompted for confirmation before deleting every file, use the -i option.

      rm -Ri ~/data 
      

      Enter y or n when prompted. Simply pressing the enter button will default to n.

      Deleting files found by find

      The rm command can be combined with any find command to delete the files found. The syntax for doing so is:

      find <location> <other find options> -exec rm -i {} \;
      

      Where <other find options> can include one or more of the options -atime <time>, -mtime <time>, and -size <size>.

      The following command would find all files in the ~/data directory 1G or larger that have not been accessed in the past 100 days, and then prompt for confirmation to delete each file:

      find ~/data -atime +100 -size 1G -exec rm -i {} \;
      

      If you are absolutely sure the files identified by find are okay to delete you can remove the -i option to rm and you will not be prompted. Extreme caution should be used when doing so!

      Archiving Data

      If you still need the data but do not plan on needing the data in the immediate future, contact OSC Help to discuss moving the data to an archive file system. Requests for data to be moved to the archive file system should be larger than 1TB.

      Compressing

      If you need the data but do not access the data frequently, you should compress the data using tar or gzip.

      Moving Data to a Local File System

      If you have the space available locally you can transfer your data there using sftp or Globus.

      Globus is recommended for large transfers.

      The OnDemand File application should not be used for transfers larger than 1GB.

      Supercomputer: 
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      HOWTO: Run Python in Parallel

      We can improve performace of python calculation by running python in parallel. In this turtorial we will be making use of the multithreading library to run python code in parallel.

      Multiprocessing is part of the standard python library distribution on versions python/2.6 and above so no additonal instalation is required (Owens and Pitzer both offer 2.7 and above so this should not be an issue). However, we do recommend you use python environments when using multiple libraries to avoid version conflicts with different projects you may have. See here for more information.

      Pool

      One way to parallelizing is by created a parallel pool. This can be done by using the Pool method:

      p = Pool(10)

      This will create a pool of 10 worker processes.

      Once you have a pool of worker processes created you can then use the map method to assign tasks to each worker.

      p.map(my_function, something_iterable)

      Here is an example python code:

      from multiprocessing import Pool
      from timeit import default_timer as timer
      import time
      
      
      def sleep_func(x):
              time.sleep(x)
      
      
      if __name__ == '__main__':
      
              arr = [1,1,1,1,1]
      
              # create a pool of 5 worker processes
              p = Pool(5)
      
              start = timer()
      
              # assign sleep_func to a worker for each entry in arr.
              # each array entry is passed as an argument to sleep_func
              p.map(sleep_func, arr)
      
              print("parallel time: ", timer() - start)
      
      
              start = timer()
              # run the functions again but in serial
              for a in arr:
                  sleep_func(a)
              print("serial time: ", timer() - start)

      The above code was then submitted using the below job script:

      #!/bin/bash
      
      #SBATCH --account <your-project-id>
      #SBATCH --job-name Python_ExampleJob
      #SBATCH --nodes=1
      #SBATCH --time=00:10:00
      
      module load python
      
      python example_pool.py

      After submitting the above job, the following was the output:

      parallel time:  1.003282466903329
      serial time:  5.005984931252897

      See the documenation for more details and examples on using Pool.

      Process

      The mutiprocessing library also provides the Process method to run functions asynchronously.

       

      To create a Process object you can simply make a call to: 

      proc = Process(target=my_function, args=[my_function, arguments, go, here])

      The target is set equal to the name of your function which you want to run asynchronously and args is a list of arguement for your function.

      Start running a process asynchronously by:

      proc.start()

      Doing so will begin running the function in another process and the main parent process will continue in its execution.

      You can make the parent process wait for a child process to finish with:

      proc.join()

       

      If you use proc.run() it will run your process and wait for it to finish before continuing on in executing the parent process. 

      Note: The below code will start proc2 only after proc1 has finshed. If you want to start multiple processes and wait for them use start() and join() instead of run.

      proc1.run()
      proc2.run()

      Examples

      Here some example code:

      from multiprocessing import Process
      from timeit import default_timer as timer
      import time
      
      def sleep_func(x):
              print(f'Sleeping for {x} sec')
              time.sleep(x)
      
      if __name__ == '__main__':
              
              # initialize process objects
              proc1 = Process(target=sleep_func, args=[1])
              proc2 = Process(target=sleep_func, args=[1])
              
              # begin timer
              start = timer()
              
              # start processes
              proc1.start()
              proc2.start()
              
              # wait for both process to finish
              proc1.join()
              proc2.join()
              
              print('Time: ', timer() - start)
              

      Running this code give the following output:

      Sleeping for 1 sec
      Sleeping for 1 sec
      Time:  1.0275288447737694

       

      You can create a many process easily in loop aswell:

      from multiprocessing import Process
      from timeit import default_timer as timer
      import time
      
      def sleep_func(x):
              print(f'Sleeping for {x} sec')
              time.sleep(x)
      
      if __name__ == '__main__':
              
              # empty list to later store processes 
              processes = []
              
              # start timer
              start = timer()
              
             
              for i in range(10):
                  # initialize and start processes
                  p = Process(target=sleep_func, args=[5])
                  p.start()
        
                  # add the processes to list for later reference
                  processes.append(p)
              
              # wait for processes to finish.
              # we cannot join() them within the same loop above because it would 
              # wait for the process to finish before looping and creating the next one. 
              # So it would be the same as running them sequentially.
              for p in processes:
                  p.join()
              
              print('Time: ', timer() - start)
              
        

      Output:

      Sleeping for 5 sec
      Sleeping for 5 sec
      Sleeping for 5 sec
      Sleeping for 5 sec
      Sleeping for 5 sec
      Sleeping for 5 sec
      Sleeping for 5 sec
      Sleeping for 5 sec
      Sleeping for 5 sec
      Sleeping for 5 sec
      Time:  5.069192241877317

      See documentation for more information and example on using Process.

      Shared States

      When running process in parallel it is generally best to avoid sharing states between processes. However, if data must be shared see documentation for more information and examples on how to safely share data.

      Other Resources

      • Spark:You can also drastically improve preformance of your python code by using Apache Spark. See Spark for more details.
      • Horovod: If you are using Tensorflow, PyTorch or other python machine learning packages you may want to also consider using Horovod. Horovod will take single-GPU training scripts and scale it to train across many GPUs in parallel.
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      HOWTO: Submit Homework to Repository at OSC

      This page outlines a way a professor can set up a file submission system at OSC for his/her classroom project.

      Usage for Professor

      After connecting to OSC system, professor runs submit_prepare as

      $ /users/PZS0645/support/bin/submit_prepare

      Follow the instruction and provided the needed information (name of the assignment, TA username if appropriate, a size limit if not the default 1000MB per student, and whether or not you want the email notification of a submit). It will create a designated directory where students submit their assignments, as well as generate submit for students used to submit homework to OSC, both of which are located in the directory specified by the professor.

      If you want to create multiple directories for different assignments, simply run the following command again with specifying the different assignment number:

      $ /users/PZS0645/support/bin/submit_prepare

      Note:

      The PI can also enforce the deadline by simply changing the permission of the submission directory or renaming the submission directory at the deadline.

      (Only works on Owens): One way is to use at command following the steps below:

      • Use at command to specify the deadline:
      at [TIME]

      where TIME is formatted HH:MM AM/PM MM/DD/YY. For example:

      at 2:30 PM 08/21/2017
      • After running this command, run:
      $ chmod 700 [DIRECTORY]

      where DIRECTORY is the assignment folder to be closed off.

      • Enter [ctrl+D] to submit this command.

      The permission of DIRECTORY will be changed to 700 at 2:30PM, August 21, 2018. After that, the student will get an error message when he/she tries to submit an assignment to this directory.

      Usage for Students

      A student should create one directory which includes all the files he/she wants to submit before running this script to submit his/her assignment. Also, the previous submission of the same assignment from the student will be replaced by the new submission. 

      To submit the assignment, the student runs submit after connecting to OSC system as

      $ /path/to/directory/from/professor/submit

      Follow the instructions. It will allow students to submit an assignment to the designated directory specified by the professor and send a confirmation email, or return an error message.

      Supercomputer: 
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      HOWTO: Submit multiple jobs using parameters

      Often users want to submit a large number of jobs all at once, with each using different parameters for each job. These parameters could be anything, including the path of a data file or different input values for a program. This how-to will show you how you can do this using a simple python script, a CSV file, and a template script. You will need to adapt this advice for your own situation.

      Consider the following batch script:

      #!/bin/bash
      #SBATCH --ntasks-per-node=2
      #SBATCH --time=1:00:00
      #SBATCH --job-name=week42_data8
      
      # Copy input data to the nodes fast local disk
      cp ~/week42/data/source1/data8.in $TMPDIR
      
      cd $TMPDIR
      
      # Run the analysis
      full_analysis data8.in data8.out
      
      # Copy results to proper folder
      cp  data8.out ~/week42/results

      Let's say you need to submit 100 of these jobs on a weekly basis. Each job uses a different data file as input. You recieve data from two different sources, and so your data is located within two different folders. All of the jobs from one week need to store their results in a single weekly results folder. The output file name is based upon the input file name.

      Creating a Template Script

      As you can see, this job follows a general template.  There are three main parameters that change in each job:

      1. The week 
        • Used as part of the job name
        • Used to find the proper data file to copy to the nodes local disk
        • Used to copy the results to the correct folder
      2. The data source
        • Used to find the proper data file to copy to the nodes local disk
      3. The data file's name
        • Used as part of the job name
        • Used to find the proper data file to copy to the nodes local disk
        • Used to specify both the input and output file to the program full_analysis
        • Used to copy the results to the correct folder

      If we replace these parameters with variables, prefixed by the dollar sign $and surrounded by curly braces { }, we get the following template script:

      Slurm does not support using variables in the #SBATCH section, so we need to set the job name in the submit command.
      #!/bin/bash
      #SBATCH --ntasks-per-node=2
      #SBATCH --time=1:00:00
      
      # Copy input data to the nodes fast local disk 
      cp ~/${WEEK}/data/${SOURCE}/${DATA}.in $TMPDIR
      cd $TMPDIR
      
      # Run the analysis 
      full_analysis ${DATA}.in ${DATA}.out
      
      # Copy results to proper folder
      cp  ${DATA}.out ~/${WEEK}/results
      

      Automating Job Submission

      We can now use the sbatch --exportoption to pass parameters to our template script. The format for passing parameters is:

      sbatch --job-name=name --export=var_name=value[,var_name=value...]

      Submitting 100 jobs using the sbatch --export option manually does not make our task much easier than modifying and submitting each job one by one. To complete our task we need to automate the submission of our jobs. We will do this by using a python script that submits our jobs using parameters it reads from a CSV file.  

      Note that python was chosen for this task for its general ease of use and understandability -- if you feel more comfortable using another scripting language feel free to interpret/translate this python code for your own use.

      The script for submitting multiple jobs using parameters can be found at ~support/share/misc/submit_jobs.py

      Use the following command to run a test with the examples already created:

      Make sure to replace <your-proj-code> with a project you are a member of to charge jobs to.
      ~support/share/misc/submit_jobs.py -t ~support/share/misc/submit_jobs_examples/job_template2.sh WEEK,SOURCE,DATA ~support/share/misc/submit_jobs_examples/parameters_example2.csv <your-proj-code>

      This script will open the CSV file and step through the file line by line, submitting a job for each line using the line's values. If the submit command returns a non-zero exit code, usually indicating it was not submitted, we will print this out to the display. The jobs will be submitted using the general format (using the example WEEK,SOURCE,DATA environment variables):

      sbatch -A <project-account> -o ~/x/job_logs/x_y_z.job_log --job-name=x_y_z --export=WEEK=x,SOURCE=y,DATA=z job.sh

      Where x, y and z are determined by the values in the CSV parameter file. Below we relate x to week, y to source and z to data.

      Creating a CSV File

      We now need to create a CSV file with parameters for each job. This can be done with a regular text editor or using a spreadsheet editor such as Excel. By default you should use commas as your delimiter.  

      Here is our CSV file with parameters:

      week42,source1,data1
      week42,source1,data2
      week42,source1,data3
      ...
      week42,source2,data98
      week42,source2,data99
      week42,source2,data100
      

      The submit script would read in the first row of this CSV file and form and execute the command:

      sbatch -A <project-account> -o week42/job_logs/week42_source1_data1.job_log --job-name=week42_source1_data1 --export=WEEK=week42,SOURCE=source1,DATA=data1 job.sh

      Submitting Jobs

      Once all the above is done, all you need to do to submit your jobs is to make sure the CSV file is populated with the proper parameters and run the automatic submission script with the right flags.

      Try using submit_jobs.py --help for an explanation:

      $ ~support/share/misc/submit_jobs.py --help
      usage: submit_jobs.py [-h] [-t]
                            jobscript parameter_names job_parameters_file account
      
      Automatically submit jobs using a csv file; examples in
      ~support/share/misc/submit_jobs_examples/
      
      positional arguments:
        jobscript            job script to use
        parameter_names      comma separated list of names for each parameter
        job_parameters_file  csv parameter file to use
        account              project account to charge jobs to
      
      optional arguments:
        -h, --help           show this help message and exit
        -t, --test           test script without submitting jobs
      Before submitting a large number of jobs for the first time using this method it is recommended you test with a small number of jobs and using the -t flag as well to check the submit commands.

      Modifying for unique uses

      It is a good idea to copy the ~support/share/misc/submit_jobs.py file and modify for unique use cases.

      Contact oschelp@osc.edu and OSC staff can assist if there are questions using the default script or adjusting the script for unique use cases.

      HOWTO: Tune Performance

      Table of Contents

      Introduction

      Setup

      Debugging

      Hardware

      Performance Measurement

      Timing

      Profiling

      Help From the Compiler

      Compiler Optimization Reports

      Memory Optimizations

      Vectorization/Streaming

      OpenMP

      MPI

      GPU Accelerated Computing

      Summary

       

      Introduction

      This tutorial presents techniques to tune the performance of an application. Keep in mind that correctness of results, code readability/maintainability, and portability to future systems are more important than performance. For a big picture view, you can check the status of a node while a job is running by visiting the OSC grafana page and using the "cluster metrics" report, and you can use the online interactive tool XDMoD to look at resource usage information for a job.

      Some application software specific factors that can affect performance are

      • Effective use of processor features for a high degree of internal concurrency in a single core
      • Memory access patterns (memory access is slow compared to computation)
      • Use of an appropriate file system for file I/O
      • Scalability of algorithms
      • Compiler optimizations
      • Explicit parallelism

      We will be using this code based on the HPCCD miniapp from Mantevo. It performs the Conjugate Gradient (CG) on a 3D chimney domain. CG is an iterative algorithm to numerically approximate the solution to a system of linear equations.

      Run code with:

      srun -n <numprocs> ./test_HPCCG nx ny nz
      

      where nx, ny, nz are the number of nodes in the x, y, and z dimension on each processor.

       

      Setup

      First start an interactive Pitzer Desktop session with OnDemand.

      You need to load intel 19.0.5 and mvapich2 2.3.3:

      module load intel/19.0.5 mvapich2/2.3.3
      

      Then clone the repository:

      git clone https://code.osu.edu/khuvis.1/performance_handson.git

       

      Debugging

      Debuggers let you execute your program one line at a time, inspect variable values, stop your programming at a particular line, and open a core file after the program crashes.

      For debugging, use the -g flag and remove optimzation or set to -O0. For example:

      icc -g -o mycode.c
      gcc -g -O0 -o mycode mycode.c

      To see compiler warnings and diagnostic options:

      icc -help diag
      man gcc
      

      ARM DDT

      ARM DDT is a commercial debugger produced by ARM. It can be loaded on all OSC clusters:

      module load arm-ddt
      

      To run a non-MPI program from the command line:

      ddt --offline --no-mpi ./mycode [args]
      

      To run an MPI program from the command line:

      ddt --offline -np num.procs ./mycode [args]
      Hands On

      Compile and run the code:

      make
      srun -n 2 ./test_HPCCG 150 150 150

      You should have received the following error message at the end of the program output:

      ===================================================================================
      =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
      =   PID 308893 RUNNING AT p0200
      =   EXIT CODE: 11
      =   CLEANING UP REMAINING PROCESSES
      =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
      ===================================================================================
      YOUR APPPLICATIN TERMINATED WITH EXIT STRING: Segmentation fault (signal 11)
      This typically referes to a problem with your application.
      Please see tthe FAQ page for debugging suggestions
      

      Set compiler flags -O0 -g  to CPP_OPT_FLAGS in Makefile. Then recompile and run with ARM DDT:

      make clean; make
      module load arm-ddt
      ddt -np 2 ./test_HPCCG 150 150 150
      

       

      Solution

      ddt_handson.png

      When DDT stops on the segmentation fault, the stack is in the YAML_Element::~YAML_Element function of YAML_Element.cpp. Looking at this function, we see that the loop stops at children.size() instead of children.size()-1. So, line 13 should be changed from

      for(size_t i=0; i<=children.size(); i++) {
      

      to

      for(size_t i=0; i<children.size(); i++) {
      

       

      Hardware

      On Pitzer, there are 40 cores per node (20 cores per socket and 2 sockets per node). There is support for AVX512, vector length 8 double or 16 single precision values and fused multiply-add. (There is hardware support for 4 thread per core, but it is currently not enabled on OSC systems.)

      There are three cache levels on Pitzer, and the statistics are shown in the table below:

      Pitzer Cache Statistics
      Cache level Size (KB) Latency (cycles) Max BW (bytes/cycle) Sustained BW (bytes/cycle)
      L1 DCU 32 4-6 192 133
      L2 MLC 1024 14 64 52
      L3 LLC 28160 50-70 16 15

      Never do heavy I/O in your home directory. Home directories are for long-term storage, not scratch files.

      One option for I/O intensive jobs is to use the local disk on a compute node. Stage files to and from your home directory into $TMPDIR using the pbsdcp command (e.g. pbsdcp file1 file2 $TMPDIR), and execute the program in $TMPDIR.

      Another option is to use the scratch file system ($PFSDIR). This is faster than other file systems, good for parallel jobs, and may be faster than local disk.

      For more information about OSC's file system, click here.

      For example batch scripts showing the use of $TMPDIR and $PFSDIR, click here.

      For more information about Pitzer, click here.

       

      Performance Measurement

      FLOPS stands for "floating point operations per second." Pitzer has a theoretical maximum of 720 teraflops. With the LINPACK benchmark of solving a dense system of linear equations, 543 teraflops. With the STREAM benchmark, which measures sustainable memory bandwidth and the corresponding computation rate for vector kernels, copy: 299095.01 MB/s, scale: 298741.01 MB/s, add: 331719.18 MB/s, and traid: 331712.19 MB/s. Application performance is typically much less than peak/sustained performance since applications usually do not take full advantage of all hardware features.

       

      Timing

      You can time a program using the /usr/bin/time command. It gives results for user time (CPU time spent running your program), system time (CPU time spent by your program in system calls), and elapsed time (wallclock). It also shows % CPU, which is (user + system) / elapsed, as well as memory, pagefault, swap, and I/O statistics.

      /usr/bin/time j3
      5415.03user 13.75system 1:30:29elapsed 99%CPU \
      (0avgtext+0avgdata 0maxresident)k \
      0inputs+0outputs (255major+509333minor)pagefaults 0 swaps
      

      You can also time portions of your code:

        C/C++ Fortran 77/90 MPI (C/C++/Fortran)
      Wallclock

      time(2), difftime(3),

      getrusage(2)

      SYSTEM_CLOCK(2) MPI_Wtime(3)
      CPU times(2) DTIME(3), ETIME(3) X

       

      Profiling

      A profiler can show you whether code is compute-bound, memory-bound, or communication bound. Also, it shows how well the code uses available resources and how much time is spent in different parts of your code. OSC has the following profiling tools: ARM Performance Reports, ARM MAP, Intel VTune, Intel Trace Analyzer and Collector (ITAC), Intel Advisor, TAU Commander, and HPCToolkit.

      For profiling, use the -g flag and specify the same optimization level that you normally would normally use with -On. For example:

      icc -g -O3 -o mycode mycode.c

      Look for

      • Hot spots (where most of the time is spent)
      • Excessive number of calls to short functions (use inlining!)
      • Memory usage (swapping and thrashing are not allowed at OSC)
      • % CPU (low CPU utilization may mean excessive I/O delays).

      ARM Performance Reports

      ARM PR works on precompiled binaries, so the -g flag is not needed. It gives a summary of your code's performance that you can view with a browser.

      For a non-MPI program:

      module load arm-pr
      perf-report --no-mpi ./mycode [args]
      

      For an MPI program:

      module load arm-pr
      perf-report --np num_procs ./mycode [args]

      ARM MAP

      Interpreting this profile requires some expertise. It gives details about your code's performance. You can view and explore the resulting profile using an ARM client.

      For a non-MPI program:

      module load arm-map
      map --no-mpi ./mycode [args]
      

      For an MPI program:

      module load arm-pr
      map --np num_procs ./mycode [args]

      For more information about ARM Tools, view OSC resources or visit ARM's website.

      Intel Trace Analyzer and Collector (ITAC)

      ITAC is a graphical tool for profiling MPI code (Intel MPI).

      To use:

      module load intelmpi # then compile (-g) code
      mpiexec -trace ./mycode
      

      View and explore the results using a GUI with traceanalyzer:

      traceanalyzer <mycode>.stf

       

      Help From the Compiler

      HPC software is traditionally written in Fortran or C/C++. OSC supports several compiler families. Intel (icc, icpc, ifort) usually gives fastest code on Intel architecture). Portland Group (PGI - pgcc, pgc++, pgf90) is good for GPU programming, OpenACC. GNU (gcc, g++, gfortran) is open source and universally available.

      Compiler options are easy to use and let you control aspects of the optimization. Keep in mind that different compilers have different values for options.  For all compilers, any highly optimized builds, such as those employing the options herein, should be thoroughly validated for correctness.

      Some examples of optimization include:

      • Function inlining (eliminating function calls)
      • Interprocedural optimization/analysis (ipo/ipa)
      • Loop transformations (unrolling, interchange, splitting, tiling)
      • Vectorization (operate on arrays of operands)
      • Automatic parallization of loops (very conservative multithreading)

      Compiler flags to try first are:

      • General optimization flags (-O2, -O3, -fast)
      • Fast math
      • Interprocedural optimization/analysis

      Faster operations are sometimes less accurate. For Intel compilers, fast math is default with -O2 and -O3. If you have a problem, use -fp-model precise. For GNU compilers, precise math is default with -O2 and -O3. If you want faster performance, use -ffast-math.

      Inlining is replacing a subroutine or function call with the actual body of the subprogram. It eliminates overhead of calling the subprogram and allows for more loop optimizations. Inlining for one source file is typically automatic with -O2 and -O3.

      Optimization Compiler Options

      Options for Intel compilers are shown below. Don't use -fast for MPI programs with Intel compilers. Use the same compiler command to link for -ipo with separate compilation. Many other optimization options can be found in the man pages. The recommended options are -O3 -xHost. An example is ifort -O3 program.f90.

      -fast Common optimizations
      -On

      Set optimization level (0, 1, 2, 3)

      -ipo Interprocedural optimization, multiple files
      -O3 Loop transforms
      -xHost Use highest instruction set available
      -parallel Loop auto-parallelization

      Options for PGI compilers are shown below. Use the same compiler command to link for -Mipa with separate compilation. Many other optimization options can be found in the man pages. The recommended option is -fast. An example is pgf90 -fast program.f90.

      -fast Common optimizations
      -On

      Set optimization level (0, 1, 2, 3, 4)

      -Mipa Interprocedural optimization
      -Mconcur Loop auto-parallelization

      Options for GNU compilers are shown below. Use the same compiler command to link for -Mipa with separate compilation. Many other optimization options can be found in the man pages. The recommended options are -O3 -ffast-math. An example is gfortran -O3 program.f90.

      -On Set optimization level (0, 1, 2, 3)
      N/A for separate compilation Interprocedural optimization
      -O3 Loop transforms
      -ffast-math Possibly unsafe floating point optimizations
      -march=native Use highest instruction set available

      Hands On

      Compile and run with different compiler options:

      time srun -n 2 ./test_HPCCG 150 150 150

      Using the optimal compiler flags, get an overview of the bottlenecks in the code with the ARM performance report:

      module load arm-pr
      perf-report -np 2 ./test_HPCCG 150 150 150
      
      Solution

       

      On Pitzer, sample times were:

      Compiler Option Runtime (seconds)
      -g 129
      -O0 -g 129
      -O1 -g 74
      -O2 -g 74
      -O3 -g

      74

      The performance report shows that the code is compute-bound.

      pr_handson.png

       

      Compiler Optimization Reports

      Compiler optimization reports let you understand how well the compiler is doing at optimizing your code and what parts of your code need work. They are generated at compile time and describe what optimizations were applied at various points in the source code. The report may tell you why optimizations could not be performed.

      For Intel compilers, -qopt-report and outputs to a file.

      For Portland Group compilers, -Minfo and outputs to stderr.

      For GNU compilers, -fopt-info and ouputs to stderr by default.

      A sample output is:

      LOOP BEGIN at laplace-good.f(10,7)
         remark #15542: loop was not vectorized: inner loop was already vectorized
      
         LOOP BEGIN at laplace-good.f(11,10)
         <Peeled loop for vectorization>
         LOOP END
      
         LOOP BEGIN at laplace-good.f(11,10)
            remark #15300: LOOP WAS VECTORIZED
         LOOP END
      
         LOOP BEGIN at laplace-good.f(11,10)
         <Remainder loop for vectorization>
            remark #15301: REMAINDER LOOP WAS VECTORIZED
         LOOP END
      
         LOOP BEGIN at laplace-good.f(11,10)
         <Remainder loop for vectorization>
         LOOP END
      LOOP END
      

      Hands On

      Add the compiler flag -qopt-report=5 and recompile to view an optimization report.

      Vectorization/Streaming

      Code is structured to operate on arrays of operands. Vector instructions are built into the processor. On Pitzer, the vector length is 16 single or 8 double precision. The following is a vectorizable loop:

      do i = 1,N
        a(i) = b(i) + x(1) * c(i)
      end do
      

      Some things that can inhibit vectorization are:

      • Loops being in the wrong order (usually fixed by compiler)
      • Loops over derived types
      • Function calls (can sometimes be fixed by inlining)
      • Too many conditionals
      • Indexed array accesses

      Hands On

      Use ARM MAP to identify the most expensive parts of the code.

      module load arm-map
      map -np 2 ./test_HPCCG 150 150 150
      

      Check the optimization report previously generated by the compiler (with -qopt-report=5) to see if any of the loops in the regions of the code are not being vectorized. Modify the code to enable vectorization and rerun the code.

      Solution

      vec_handson.pngMap shows that the most expensive segment of the code is lines 83-84 of HPC_sparsemv.cpp:

      for (int j=0; j< cur_nnz; j++)
        y[i] += cur_vals[j]*x[cur_inds[j]];
      

      The optimization report confirms that the loop was not vectorized due to a dependence on y.

      optreport_handson.png

      Incrementing a temporary variable instead of y[i], should enable vectorization:

      for (int j=0; j< cur_nnz; j++)
        sum += cur_vals[j]*x[cur_inds[j]];
      y[i] = sum;

      Recompiling and rerunning with change reduces runtime from 74 seconds to 63 seconds.​​

      Memory Optimizations

      Memory access is often the most important factor in your code's performance. Loops that work with arrays should use a stride of one whenever possible. C and C++ are row-major (store elements consecutively by row in 2D arrays), so the first array index should be the outermost loop and the last array index should be the innermost loop. Fortran is column-major, so the reverse is true. You can get factor of 3 or 4 speedup just by using unit stride. Avoid using arrays of derived data types, structs, or classes. For example, use structs of arrays instead of arrays of structures.

      Efficient cache usage is important. Cache lines are 8 words (64 bytes) of consecutive memory. The entire cache line is loaded when a piece of data is fetched.

      The code below is a good example. 2 cache lines are used for every 8 loop iterations, and it is unit stride:

      real*8 a(N), b(N)
      do i = 1,N
        a(i) = a(i) + b(i)
      end do
      
      ! 2 cache lines:
      ! a(1), a(2), a(3) ... a(8)
      ! b(1), b(2), b(3) ... b(8)
      

      The code below is a bad example. 1 cache line is loaded for each loop iteration, and it is not unit stride:

      TYPE :: node
        real*8 a, b, c, d, w, x, y, z
      END TYPE node
      TYPE(node) :: s(N)
      do i = 1, N
        s(i)%a = s(i)%a + s(i)%b
      end do
      
      ! cache line:
      ! a(1), b(1), c(1), d(1), w(1), x(1), y(1), z(1)
      

      Hands On

      Look again at the most expensive parts of the code using ARM MAP:

      module load arm-map
      map -np 2 ./test_HPCCG 150 150 150
      

      Look for any inefficient memory access patterns. Modify the code to improve memory access patterns and rerun the code. Do these changes improve performance?

      Solution

      Lines 110-148 of generate_matrix.cpp are nested loops:

      for (int ix=0; ix<nx; ix++) {
        for (int iy=0; iy<ny; iy++) {
          for (int iz=0; iz<nz; iz++) {
            int curlocalrow = iz*nx*ny+iy*nx+ix;
            int currow = start_row+iz*nx*ny+iy*nx+ix;
            int nnzrow = 0;
            (*A)->ptr_to_vals_in_row[curlocalrow] = curvalptr;
            (*A)->ptr_to_inds_in_row[curlocalrow] = curindptr;
            .
            .
            .
          }
        }
      }

      The arrays are accessed in a manner so that consecutive values of ix are accesssed in order. However, our loops are ordered so that the ix is the outer loop. We can reorder the loops so that ix is iterated in the inner loop:

      for (int iz=0; iz<nz; iz++) {
        for (int iy=0; iy<ny; iy++) {
          for (int ix=0; ix<nx; ix++) {
            .
            .
            .
          }
        }
      }

       This reduces the runtime from 63 seconds to 22 seconds.

      OpenMP

      OpenMP is a shared-memory, threaded parallel programming model. It is a portable standard with a set of compiler directives and a library of support functions. It is supported in compilers by Intel, Portland Group, GNU, and Cray.

      The following are parallel loop execution examples in Fortran and C. The inner loop vectorizes while the outer loop executes on multiple threads:

      PROGRAM omploop
      INTEGER, PARAMETER :: N = 1000
      INTEGER i, j
      REAL, DIMENSION(N, N) :: a, b, c, x
      ... ! Initialize arrays
      !$OMP PARALLEL DO
      do j = 1, N
        do i = 1, N
          a(i, j) = b(i, j) + x(i, j) * c(i, j)
        end do
      end do
      !$OMP END PARALLEL DO
      END PROGRAM omploop
      
      int main() {
        int N = 1000;
        float *a, *b, *c, *x;
      ... // Allocate and initialize arrays
      #pragma omp parallel for
        for (int i = 0; i < N; i++) {
          for (int j = 0; j < N; j++) {
            a[i*N+j] = b[i*N+j] + x[i*N+j] * c[i*N+j]
          }
        }
      }
      

      You can add an option to compile a program with OpenMP.

      For Intel compilers, add the -qopenmp option. For example, ifort -qopenmp ompex.f90 -o ompex.

      For GNU compilers, add the -fopenmp option. For example, gcc -fopenmp ompex.c -o ompex.

      For Portland group compilers, add the -mp option. For example, pgf90 -mp ompex.f90 -o ompex.

      To run an OpenMP program, requires multiple processors through Slurm (--N 1 -n 40) and set the OMP_NUM_THREADS environment variable (default is use all available cores). For the best performance, run at most one thread per core.

      An example script is:

      #!/bin/bash
      #SBATCH -J omploop
      #SBATCH -N 1
      #SBATCH -n 40
      #SBATCH -t 1:00
      
      export OMP_NUM_THREADS=40
      /usr/bin/time ./omploop
      

      For more information, visit http://www.openmp.org, OpenMP Application Program Interface, and self-paced turorials. OSC will host an XSEDE OpenMP workshop on November 5, 2019.

       

      MPI

      MPI stands for message passing interface for when multiple processes run on one or more nodes. MPI has functions for point-to-point communication (e.g. MPI_Send, MPI_Recv). It also provides a number of functions for typical collective communication patterns, including MPI_Bcast (broadcasts value from root process to all other processes), MPI_Reduce (reduces values on all processes to a single value on a root process), MPI_Allreduce (reduces value on all processes to a single value and distributes the result back to all processes), MPI_Gather (gathers together values from a group of processes to a root process), and MPI_Alltoall (sends data from all processes to all processes).

      A simple MPI program is:

      #include <mpi.h>
      #include <stdio.h>
      
      int main(int argc, char *argv[]) {
        int rank, size;
        MPI_INIT(&argc, &argv);
        MPI_Comm_rank(MPI_COMM_WORLD, &rank);
        MPI_COMM_size(MPI_COMM_WORLD, &size);
        printf("Hello from node %d of %d\n", rank size);
        MPI_Finalize();
        return(0);
      }
      

      MPI implementations available at OSC are mvapich2, Intel MPI (only for Intel compilers), and OpenMPI.

      MPI programs can be compiled with MPI compiler wrappers (mpicc, mpicxx, mpif90). They accept the same arguments as the compilers they wrap. For example, mpicc -o hello hello.c.

      MPI programs must run in batch only. Debugging runs may be done with interactive batch jobs. srun automatically determines exectuion nodes from PBS:

      #!/bin/bash
      #SBATCH -J mpi_hello
      #SBATCH -N 2
      #SBATCH --ntasks-per-node=40
      #SBATCH -t 1:00
      
      cd $PBS_O_WORKDIR
      srun ./hello
      

      For more information about MPI, visit MPI Forum and MPI: A Message-Passing Interface Standard. OSC will host an XSEDE MPI workshop on September 3-4, 2019. Self-paced tutorials are available here.

      Hands On

      Use ITAC to get a timeline of the run of the code.

      module load intelmpi
      LD_PRELOAD=libVT.so \
      mpiexec -trace -np 40 ./test_HPCCG 150 150 150
      traceanalyzer <stf_file>
      

      Look at the Event Timeline (under Charts). Do you see any communication patterns that could be replaced by a single MPI command?

      Solution

      Looking at the Event Timeline, we see that a large part of runtime is spent in the following communication pattern: MPI_Barrier, MPI_Send/MPI_Recv, MPI_Barrier. We also see that during this communication rank 0 is sending data to all other rank. We should be able to replace all of these MPI calls with a single call to MPI_Bcast.

      The relavent code is in lines 82-89 of ddot.cpp: 

        MPI_Barrier(MPI_COMM_WORLD);
        if(rank == 0) {
          for(int dst_rank=1; dst_rank < size; dst_rank++) {
            MPI_Send(&global_result, 1, MPI_DOUBLE, dst_rank, 1, MPI_COMM_WORLD);
          }
        }
        if(rank != 0) MPI_Recv(&global_result, 1, MPI_DOUBLE, 0, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
        MPI_Barrier(MPI_COMM_WORLD);

      and can be replaced with:

      MPI_Bcast(&global_result, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
      

       

      Interpreted Languages

      Although many of the tools we already mentioned can also be used with interpreted languages, most interpreted languages such as Python and R have their own profiling tools.

      Since they are still running on th same hardware, the performance considerations are very similar for interpreted languages as they are for compiled languages:

      • Vectorization
      • Efficient memory utilization
      • Use built-in and library functions where possible
      • Use appropriate data structures
      • Understand and use best practices for the language

      One of Python's most common profiling tools is cProfile. The simplest way to use cProfile is to add several arguments to your Python call so that an ordered list of the time spent in all functions called during executation. For instance, if a program is typically run with the command:

      python ./mycode.py

      replace that with

      python -m cProfile -s time ./mycode.py
      

      Here is a sample output from this profiler:python_profile.png

      See Python's documentation for more details on how to use cProfile.

      One of the most popular profilers for R is profvis. It is not available by default with R so it will need to be installed locally before its first use and loaded into your environment prior to each use. To profile your code, just put how you would usually call your code as the argument into profvis:

      $ R
      > install.packages('profvis')
      > library('profvis')
      > profvis({source('mycode.R')}
      

      Here is a sample output from profvis:
      r_profile.png
      For more information on profvis is available here.

      Hands On

      Python

      First, enter the Python/ subdirectory of the code containing the python script ns.py. Profile this code with cProfile to determine the most expensive functions of the code. Next, rerun and profile with the array as an argument to ns.py. Which versions runs faster? Can you determine why it runs faster?

      Solution

      Execute the following commands:

      python -m cProfile -s time ./ns.py
      python -m cProfile -s time ./ns.py array
      

      In the original code, 66 seconds out 68 seconds are spent in presPoissPeriodic. When the array argument is passed, the time spent in this function is approximately 1 second and the total runtime goes down to about 2 seconds.

      The speedup comes from the vectorization of the main computation in the body of presPoissPeriodic by replacing nester for loops with a single like operation on arrays.

      R

      Now, enter the R/ subdirectory of the code containing the R script lu.R. Make sure that you have the R module loaded. First, run the code with profvis without any additional arguments and then again with frmt="matrix".
      Which version of the code runs faster? Can you tell why it runs faster based on the profile?

      Solution

      Runtime for the default version is 28 seconds while the runtime when frmt="matrix" is 20 seconds.
      Here is the profile with default arguments:rprof_df_trace.png

      And here is the profile with frmt="matrix":
      rprof_mat_trace.png

      We can see that most of the time is being spent in lu_decomposition. The difference, however, is that the dataframe version seems to have a much higher overhead associated with accessing elements of the dataframe. On the other hand, the profile of the matrix version seems to be much flatter with fewer functions being called during LU decomposition. This reduction in overhead by using a matrix instead of a dataframe results in the better performance.

      Supercomputer: 
      Service: 
      Technologies: 

      HOWTO: Tune VASP Memory Usage

      This article discusses memory tuning strategies for VASP.

      Data Distribution

      Typically the first approach for memory sensitive VASP issues is to tweak the data distribution (via NCORE or NPAR). The information at https://www.vasp.at/wiki/index.php/NPAR covers a variety of machines. OSC has fast communications via Infiniband. 

      Performance and memory consumption are dependent on the simulation model.  So we recommend a series of benchmarks varying the number of nodes and NCORE. The recommended initial value for NCORE is the processor count per node which is the ntasks-per-node value in Slurm (the ppn value in PBS). Of course, if this benchmarking is intractable then one must reexamine the model. For general points see:  https://www.vasp.at/wiki/index.php/Memory_requirements and https://www.vasp.at/wiki/index.php/Not_enough_memory  And of course one should start small and incrementally improve or scale up one's model.

      Rationalization

      Using the key parameters with respect to memory scaling listed at the VASP memory requirements page one can rationalize VASP memory usage.  The general approach is to study working calculations and then apply that understanding to scaled up or failing calculations.  This might help one identify if a calculation is close to a node's memory limit and happens to cross over the limit for reasons that might be out of ones control, in which case one might need to switch to higher memory nodes.

      Here is an example of rationalizing memory consumption.  Extract from a simulation output the key parameters:

      Dimension of arrays:
      k-points NKPTS = 18 k-points in BZ NKDIM = 18 number of bands NBANDS= 1344
      total plane-waves NPLWV = 752640
      ...
      dimension x,y,z NGXF= 160 NGYF= 168 NGZF= 224
      support grid NGXF= 320 NGYF= 336 NGZF= 448

      This yields 273 GB of memory, NKDIM*NBANDS*NPLWV*16 + 4*(NGXF/2+1)*NGYF*NGZF*16, according to
      https://www.vasp.at/wiki/index.php/Memory_requirements

      This estimate should be compared to actual memory reports.  See for example XDModD and grafana.  Note that most application software has an overhead in the ballpack of ten to twenty percent.  In addition, disk caching can consume significant memory.  Thus, one must adjust the memory estimate upward.  It can then be comapred to the available memory per cluster and per cluster node type.

      Miscellaneous

      • OSC sets the default resource limits for shells, except for core dump file size, to unlimited; see the limit/ulimit/unlimit commands depending on your shell.
      • In the INCAR input file NWRITE=3 is for verbose output and NWRITE=4 is for debugging output.
      • OSC does not have a VASP license and our staff has limited experience with it.  So investigate alternate forms of help:  ask within your research group and  post on the VASP mailing list.
      • Valgrind is a tool that can be used for many types of debugging including looking for memory corruptions and leaks. However, it slows down your code a very sizeable amount. This might not be feasible for HPC codes
      • ASAN (address sanitizer) is another tool that can be used for memory debugging. It is less featureful than Valgrind, but runs much quicker, and so will likely work with your HPC code.

       

      Supercomputer: 
      Service: 

      HOWTO: Use 'rclone' to Upload Data

      rclone is a tool that can be used to upload and download files to a cloud storage (like Microsoft OneDrive, BuckeyeBox) from the command line. It's shipped as a standalone binary, but requires some user configuration before using. In this page, we will provide instructions on how to use rclone to upload data to OneDrive. For instructions with other cloud storage, check rclone Online documentation.

      You can use "Globus" feature of OnDemand to perform data transfer between OneDrive and other storage. See this File Transfer and Management page for more information. 

      Setup

      Before configuration, please first log into OSC OnDemand and request a Pitzer Lightweight Desktop session. Walltime of 1 hour should be sufficient to finish the configuration.  

      Note: this does not work with the 'konqueror' browser present on OSC Systems. Please set default to Firefox first before you do the setup following the instructions below:
      * xfce: Applications (Top left corner) -> Settings -> Preferred Applications
      * mate: System (top bar towards the left) -> Preferences -> Preferred Applications

      Once the session is ready, open a terminal. In the terminal, run the command

      rclone config

      It prompts you with a bunch of questions:

      • It shows "No remotes found -- make a new one" or list available remotes you made before
        •  Answer "n" for "New remote"
      • "name>" (the name for the new remote)
        • Type "OneDrive" (or whatever else you want to call this remote)
      • "Storage>" (the storage type of the new remote)
        • This should display a list to choose from. Enter the number corresponding to the "Microsoft OneDrive" storage type, which is "26".
        • (It is "6" for BuckeyeBox)
      • "client_id>"
        • Leave this blank (just press enter).
      • "client_secret>"
        • Leave this blank (just press enter).
      • "Edit advanced config?"
        • Type "n" for no
      • "Use auto config?"
        • Answer "y" for yes
      • A web browser window should pop up allowing you to log into box. It is a good idea at this point to verify that the url is actually OneDrive before entering any credentials 
        • Enter your OSU email
        • This should take you to the OSU login page. Login with your OSU credentials 
        • Go back to the terminal once "Success" is displayed.
      • "Your choice>"
        • One of five options to locate the drive you wish to use.
        • Type "1" to use your personal or business OneDrive
      • "Choose drive to use"
        • Type "0"
      • "Is this Okay? y/n>"
        • Type "y" to confirm the drive you wish to use is correct.
      • "y/e/d>"
        • Type "y" to confirm you wish to add this remote to rclone.

      Testing rclone

      Note: you do not need to use Pitzer Lightweight Desktop when you run 'rclone'. You can test the data transfer with a small file using login nodes (either Pitzer or Owens), or request a regular compute node to do the data transfer with large files. 

      Create an empty hello.txt file and upload it to OneDrive using 'rclone copy' as below in a terminal:

      touch hello.txt
      rclone copy hello.txt OneDrive:/test

      This creates a toplevel directory in OneDrive called 'test' if it does not already exist, and uploads the file hello.txt to it.

      To verify the uploading is successful, you can either login to OneDrive in a web browser to check the file, or use rclone ls command in the terminal as:

      rclone ls OneDrive:/test
      Note: be careful when using ls on a large directory, because it's recursive. You can add a '--max-depth 1' flag to stop the recursion. 

      Downloading from OneDrive to OSC

      Copy the contents of a source directory from a configured OneDrive remote, OneDrive:/src/dir/path, into a destination directory in your OSC session, /dest/dir/path, using the code below:

      rclone copy OneDrive:/src/dir/path /dest/dir/path

      Identical files on the source and destination directories are not transferred. Only the contents of the provided source directory are copied, not the directory name and contents.

      copy does not delete files from the destination. To delete files from the destination directory in order to match the source directory, use the sync command instead.

      If only one file is being transferred, use the copyto command instead.

      Note: The --no-traverse option can be used to increase efficiency by stopping rclone from listing the destination. It should be used when copying a small number of files and/or have a large number of files on the destination, but not when a large number of files are being copied.
      Note: Shared folders will not appear when listing a directory they are filed in. They are still accessible and data can be move to/from them. For example, the commands rclone ls OneDrive:/path/to/shared_folder and rclone copy OneDrive:/path/to/shared_folder /dest/dir/path will work normally even though the shared folder does not appear when listing their source directory.

      Limitations

      If rclone remains unused for 90 days, the refresh token will expire, leading to issues with authorization. This can be easily resolved by executing the rclone config reconnect remote: command, which generates a fresh token and refresh token.

      Naming

      It's important to note OneDrive is case insensitive which prohibits the coexistence files such as "Hello.doc" and "hello.doc". Certain characters are prohibited from being in OneDrive filenames and are commonly encountered on non-Windows platforms. Rclone addresses this by converting these filenames to their visually equivalent Unicode alternatives.

      File Sizes

      The largest allowed file size is 250 GiB for both OneDrive Personal and OneDrive for Business (Updated 13 Jan 2021).

      Path Length

      The entire path, including the file name, must contain fewer than 400 characters for OneDrive, OneDrive for Business and SharePoint Online. It is important to know the limitation when encrypting file and folder names with rclone, as the encrypted names are typically longer than the original ones.

      Number of Files

      OneDrive seems to be OK with at least 50,000 files in a folder, but at 100,000 rclone will get errors listing the directory like couldn’t list files: UnknownError:.

      Reference

       

      Supercomputer: 

      HOWTO: Use Address Sanitizer

      Address Sanitizer is a tool developed by Google detect memory access error such as use-after-free and memory leaks. It is built into GCC versions >= 4.8 and can be used on both C and C++ codes. Address Sanitizer uses runtime instrumentation to track memory allocations, which mean you must build your code with Address Sanitizer to take advantage of it's features.

      There is extensive documentation on the AddressSanitizer Github Wiki.

      Memory leaks can increase the total memory used by your program. It's important to properly free memory when it's no longer required. For small programs, loosing a few bytes here and there may not seem like a big deal. However, for long running programs that use gigabytes of memory, avoiding memory leaks becomes increasingly vital. If your program fails to free the memory it uses when it no longer needs it, it can run out of memory, resulting in early termination of the application. AddressSanitizer can help detect these memory leaks.

      Additionally, AddressSanitizer can detect use-after-free bugs. A use-after-free bug occurs when a program tries to read or write to memory that has already been freed. This is undefined behavior and can lead to corrupted data, incorrect results, and even program crashes.

      Building With Address Sanitzer

      We need to use gcc to build our code, so we'll load the gcc module:

      module load gnu/9.1.0

      The "-fsanitize=address" flag is used to tell the compiler to add AddressSanitizer.

      Additionally, due to some environmental configuration settings on OSC systems, we must also statically link against Asan. This is done using the "-static-libasan" flag.

      It's helpful to compile the code with debug symbols. AddressSanitizer will print line numbers if debug symbols are present. To do this, add the "-g" flag. Additionally, the "-fno-omit-frame-pointer" flag may be helpful if you find that your stack traces do not look quite correct.

      In one command, this looks like:

      gcc main.c -o main -fsanitize=address -static-libasan -g

      Or, splitting into separate compiling and linking stages:

      gcc -c main.c -fsanitize=address -g
      gcc main.o -o main -fsanitize=address -static-libasan

      Notice that both the compilation and linking steps require the "-fsanitize-address" flag, but only the linking step requires "-static-libasan". If your build system is more complex, it might make sense to put these flags in CFLAGS and LDFLAGS environment variables.

      And that's it!

      Examples

      No Leak

      First, let's look at a program that has no memory leaks (noleak.c):

      #include <stdio.h>
      #include <stdlib.h>
      #include <string.h>
      
      int main(int argc, const char *argv[]) {
          char *s = malloc(100);
          strcpy(s, "Hello world!");
          printf("string is: %s\n", s);
          free(s);
          return 0; 
      }

      To build this we run:

      gcc noleak.c -o noleak -fsanitize=address -static-libasan -g

      And, the output we get after running it:

      string is: Hello world!

      That looks correct! Since there are no memory leaks in this program, AddressSanitizer did not print anything. But, what happens if there are leaks?

      Missing free

      Let's look at the above program again, but this time, remove the free call (leak.c):

      #include <stdio.h>
      #include <stdlib.h>
      #include <string.h>
      
      int main(int argc, const char *argv[]) {
          char *s = malloc(100);
          strcpy(s, "Hello world!");
          printf("string is: %s\n", s);
          return 0;
      }

      Then, to build:

      gcc leak.c -o leak -fsanitize=address -static-libasan

      And the output:

      string is: Hello world!
      
      =================================================================
      ==235624==ERROR: LeakSanitizer: detected memory leaks
      
      Direct leak of 100 byte(s) in 1 object(s) allocated from:
          #0 0x4eaaa8 in __interceptor_malloc ../../.././libsanitizer/asan/asan_malloc_linux.cc:144
          #1 0x5283dd in main /users/PZS0710/edanish/test/asan/leak.c:6
          #2 0x2b0c29909544 in __libc_start_main (/lib64/libc.so.6+0x22544)
      
      SUMMARY: AddressSanitizer: 100 byte(s) leaked in 1 allocation(s).

      This is a leak report from AddressSanitizer. It detected that 100 bytes were allocated, but never freed. Looking at the stack trace that it provides, we can see that the memory was allocated on line 6 in leak.c

      Use After Free

      Say we found the above leak in our code, and we wanted to fix it. We need to add a call to free. But, what if we add it in the wrong spot?

      #include <stdio.h>
      #include <stdlib.h>
      #include <string.h>
      
      int main(int argc, const char *argv[]) {
          char *s = malloc(100);
          free(s);
          strcpy(s, "Hello world!");
          printf("string is: %s\n", s);
          return 0;
      }
      

      The above (uaf.c) is clearly wrong. Albiet a contrived example, the allocated memory, pointed to by "s", was written to and read from after it was freed.

      To Build:

      gcc uaf.c -o uaf -fsanitize=address -static-libasan

      Building it and running it, we get the following report from AddressSanitizer:

      =================================================================
      ==244157==ERROR: AddressSanitizer: heap-use-after-free on address 0x60b0000000f0 at pc 0x00000047a560 bp 0x7ffcdf0d59f0 sp 0x7ffcdf0d51a0
      WRITE of size 13 at 0x60b0000000f0 thread T0
          #0 0x47a55f in __interceptor_memcpy ../../.././libsanitizer/sanitizer_common/sanitizer_common_interceptors.inc:790
          #1 0x528403 in main /users/PZS0710/edanish/test/asan/uaf.c:8
          #2 0x2b47dd204544 in __libc_start_main (/lib64/libc.so.6+0x22544)
          #3 0x405f5c  (/users/PZS0710/edanish/test/asan/uaf+0x405f5c)
      
      0x60b0000000f0 is located 0 bytes inside of 100-byte region [0x60b0000000f0,0x60b000000154)
      freed by thread T0 here:
          #0 0x4ea6f7 in __interceptor_free ../../.././libsanitizer/asan/asan_malloc_linux.cc:122
          #1 0x5283ed in main /users/PZS0710/edanish/test/asan/uaf.c:7
          #2 0x2b47dd204544 in __libc_start_main (/lib64/libc.so.6+0x22544)
      
      previously allocated by thread T0 here:
          #0 0x4eaaa8 in __interceptor_malloc ../../.././libsanitizer/asan/asan_malloc_linux.cc:144
          #1 0x5283dd in main /users/PZS0710/edanish/test/asan/uaf.c:6
          #2 0x2b47dd204544 in __libc_start_main (/lib64/libc.so.6+0x22544)
      
      SUMMARY: AddressSanitizer: heap-use-after-free ../../.././libsanitizer/sanitizer_common/sanitizer_common_interceptors.inc:790 in __interceptor_memcpy
      Shadow bytes around the buggy address:
        0x0c167fff7fc0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
        0x0c167fff7fd0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
        0x0c167fff7fe0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
        0x0c167fff7ff0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
        0x0c167fff8000: fa fa fa fa fa fa fa fa fd fd fd fd fd fd fd fd
      =>0x0c167fff8010: fd fd fd fd fd fa fa fa fa fa fa fa fa fa[fd]fd
        0x0c167fff8020: fd fd fd fd fd fd fd fd fd fd fd fa fa fa fa fa
        0x0c167fff8030: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
        0x0c167fff8040: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
        0x0c167fff8050: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
        0x0c167fff8060: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
      Shadow byte legend (one shadow byte represents 8 application bytes):
        Addressable:           00
        Partially addressable: 01 02 03 04 05 06 07 
        Heap left redzone:       fa
        Freed heap region:       fd
        Stack left redzone:      f1
        Stack mid redzone:       f2
        Stack right redzone:     f3
        Stack after return:      f5
        Stack use after scope:   f8
        Global redzone:          f9
        Global init order:       f6
        Poisoned by user:        f7
        Container overflow:      fc
        Array cookie:            ac
        Intra object redzone:    bb
        ASan internal:           fe
        Left alloca redzone:     ca
        Right alloca redzone:    cb
        Shadow gap:              cc
      ==244157==ABORTING
      

      This is a bit intimidating. It looks like there's alot going on here, but it's not as bad as it looks. Starting at the top, we see what AddressSanitizer detected. In this case, a "WRITE" of 13 bytes (from our strcpy). Immediately below that, we get a stack trace of where the write occured. This tells us that the write occured on line 8 in uaf.c in the function called "main".

      Next, AddressSanitizer reports where the memory was located. We can ignore this for now, but depending on your use case, it could be helpful information.

      Two key pieces of information follow. AddressSanitizer tells us where the memory was freed (the "freed by thread T0 here" section), giving us another stack trace indicating the memory was freed on line 7. Then, it reports where it was originally allocated ("previously allocated by thread T0 here:"), line 6 in uaf.c.

      This is likely enough information to start to debug the issue. The rest of the report provides details about how the memory is laid out, and exactly which addresses were accessed/written to. You probably won't need to pay too much attention to this section. It's a bit "down in the weeds" for most use cases.

      Heap Overflow

      AddresssSanitizer can also detect heap overflows. Consider the following code (overflow.c):

      #include <stdio.h>
      #include <stdlib.h>
      #include <string.h>
      int main(int argc, const char *argv[]) {
          // whoops, forgot c strings are null-terminated
          // and not enough memory was allocated for the copy
          char *s = malloc(12);
          strcpy(s, "Hello world!");
          printf("string is: %s\n", s);
          free(s);
          return 0;
      }

      The "Hello world!" string is 13 characters long including the null terminator, but we've only allocated 12 bytes, so the strcpy above will overflow the buffer that was allocated. To build this:

      gcc overflow.c -o overflow -fsanitize=address -static-libasan -g -Wall

      Then, running it, we get the following report from AddressSanitizer:

      ==168232==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x60200000003c at pc 0x000000423454 bp 0x7ffdd58700e0 sp 0x7ffdd586f890
      WRITE of size 13 at 0x60200000003c thread T0
          #0 0x423453 in __interceptor_memcpy /apps_src/gnu/8.4.0/src/libsanitizer/sanitizer_common/sanitizer_common_interceptors.inc:737
          #1 0x5097c9 in main /users/PZS0710/edanish/test/asan/overflow.c:8
          #2 0x2ad93cbd7544 in __libc_start_main (/lib64/libc.so.6+0x22544)
          #3 0x405d7b  (/users/PZS0710/edanish/test/asan/overflow+0x405d7b)
      
      0x60200000003c is located 0 bytes to the right of 12-byte region [0x602000000030,0x60200000003c)
      allocated by thread T0 here:
          #0 0x4cd5d0 in __interceptor_malloc /apps_src/gnu/8.4.0/src/libsanitizer/asan/asan_malloc_linux.cc:86
          #1 0x5097af in main /users/PZS0710/edanish/test/asan/overflow.c:7
          #2 0x2ad93cbd7544 in __libc_start_main (/lib64/libc.so.6+0x22544)
      
      SUMMARY: AddressSanitizer: heap-buffer-overflow /apps_src/gnu/8.4.0/src/libsanitizer/sanitizer_common/sanitizer_common_interceptors.inc:737 in __interceptor_memcpy
      Shadow bytes around the buggy address:
        0x0c047fff7fb0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
        0x0c047fff7fc0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
        0x0c047fff7fd0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
        0x0c047fff7fe0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
        0x0c047fff7ff0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
      =>0x0c047fff8000: fa fa 00 fa fa fa 00[04]fa fa fa fa fa fa fa fa
        0x0c047fff8010: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
        0x0c047fff8020: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
        0x0c047fff8030: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
        0x0c047fff8040: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
        0x0c047fff8050: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
      Shadow byte legend (one shadow byte represents 8 application bytes):
        Addressable:           00
        Partially addressable: 01 02 03 04 05 06 07 
        Heap left redzone:       fa
        Freed heap region:       fd
        Stack left redzone:      f1
        Stack mid redzone:       f2
        Stack right redzone:     f3
        Stack after return:      f5
        Stack use after scope:   f8
        Global redzone:          f9
        Global init order:       f6
        Poisoned by user:        f7
        Container overflow:      fc
        Array cookie:            ac
        Intra object redzone:    bb
        ASan internal:           fe
        Left alloca redzone:     ca
        Right alloca redzone:    cb
      ==168232==ABORTING

      This is similar to the use-after-free report we looked at above. It tells us that a heap buffer overflow occured, then goes on to report where the write happened and where the memory was originally allocated. Again, the rest of this report describes the layout of the heap, and probably isn't too important for your use case.

      C++ Delete Mismatch

      AddressSanitizer can be used on C++ codes as well. Consider the following (bad_delete.cxx):

      #include <iostream>
      #include <cstring>
      
      int main(int argc, const char *argv[]) {
          char *cstr = new char[100];
          strcpy(cstr, "Hello World");
          std::cout << cstr << std::endl;
      
          delete cstr;
          return 0;
      }

      What's the problem here? The memory pointed to by "cstr" was allocated with new[]. An array allocation must be deleted with the delete[] operator, not "delete".

      To build this code, just use g++ instead of gcc:

      g++ bad_delete.cxx -o bad_delete -fsanitize=address -static-libasan -g

      And running it, we get the following output:

      Hello World
      =================================================================
      ==257438==ERROR: AddressSanitizer: alloc-dealloc-mismatch (operator new [] vs operator delete) on 0x60b000000040
          #0 0x4d0a78 in operator delete(void*, unsigned long) /apps_src/gnu/8.4.0/src/libsanitizer/asan/asan_new_delete.cc:151
          #1 0x509ea8 in main /users/PZS0710/edanish/test/asan/bad_delete.cxx:9
          #2 0x2b8232878544 in __libc_start_main (/lib64/libc.so.6+0x22544)
          #3 0x40642b  (/users/PZS0710/edanish/test/asan/bad_delete+0x40642b)
      
      0x60b000000040 is located 0 bytes inside of 100-byte region [0x60b000000040,0x60b0000000a4)
      allocated by thread T0 here:
          #0 0x4cf840 in operator new[](unsigned long) /apps_src/gnu/8.4.0/src/libsanitizer/asan/asan_new_delete.cc:93
          #1 0x509e5f in main /users/PZS0710/edanish/test/asan/bad_delete.cxx:5
          #2 0x2b8232878544 in __libc_start_main (/lib64/libc.so.6+0x22544)
      
      SUMMARY: AddressSanitizer: alloc-dealloc-mismatch /apps_src/gnu/8.4.0/src/libsanitizer/asan/asan_new_delete.cc:151 in operator delete(void*, unsigned long)
      ==257438==HINT: if you don't care about these errors you may set ASAN_OPTIONS=alloc_dealloc_mismatch=0
      ==257438==ABORTING
      

      This is similar to the other AddressSanitizer outputs we've looked at. This time, it tells us there's a mismatch between new and delete. It prints a stack trace for where the delete occured (line 9) and also a stack trace for where to allocation occured (line 5).

      Performance

      The documentation states:

      This tool is very fast. The average slowdown of the instrumented program is ~2x

      AddressSanitizer is much faster than tools that do similar analysis such as valgrind. This allows for usage on HPC codes.

      However, if you find that AddressSanitizer is too slow for your code, there are compiler flags that can be used to disable it for specific functions. This way, you can use address sanitizer on cooler parts of your code, while manually auditing the hot paths.

      The compiler directive to skip analyzing functions is:

      __attribute__((no_sanitize_address)

       

      Supercomputer: 
      Technologies: 

      HOWTO: Use Cron and OSCusage for Regular Emailed Reports

      It is possible to utilize Cron and the OSCusage command to send regular usage reports via email

      Cron

      It is easy to create Cron jobs on the Owens and Pitzer clusters at OSC. Cron is a Linux utility which allows the user to schedule a command or script to run automatically at a specific date and time. A cron job is the task that is scheduled.

      Shell scripts run as a cron job are usually used to update and modify files or databases; however, they can perform other tasks, for example a cron job can send an email notification.

      Getting Help

      In order to use what cron has to offer, here is a list of the command name and options that can be used

      Usage: 
      crontab [options] file 
      crontab [options] 
      crontab -n [hostname] 
      Options: 
      -u  define user 
      -e edit user's crontab 
      -l list user's crontab 
      -r delete user's crontab 
      -i prompt before deleting 
      -n  set host in cluster to run users' crontabs 
      -c get host in cluster to run users' crontabs 
      -s selinux context 
      -x  enable debugging 

      Also, if this is your first time using cron, you will be asked to choose an editor for setting your cron job. Choose whatever you find to be easiest for you.

      Running a Cron Job

      To check for any running cron jobs on the server, use the command (As shown above)

      crontab -l 

      and to create and edit your cron job use the following command,

      crontab -e 

      Now, in order to write you first cron job, you need to be familiar with the formatting system that cron follows.

      Linux Crontab Format

      The formatting system has 6 fields, each field from 1-5 is used to define the date and time of the execution. The 6th field is used for the command or script to be executed. The format is the following,

      MIN HOUR DOM MON DOW CMD 

      where,

      figure 1: Cron’s formatting syntax

      Getting Notified by Email Using a Cron Job

      You can get an email notification using a cron job as mentioned earlier. The following is an example of a cron job that runs every minute and sends an email notification every minute,

      * * * * * {cmd} | mail -s "title of the email notification" {your email} 

      A user can also set up email notifications regarding usage by using the OSCusage cmd,

      12 15 * * * /opt/osc/bin/OSCusage | mail -s "OSC usage on $(date)" {your email} 2> /path/to/file/for/stdout/and/stderr 2>&1 

      This cron job will run every day at (15:12 or 3:12 PM).

      Using OSCusage

      The OSCusage command offers many options, the following is a list that pertains to that,

      $ /opt/osc/bin/OSCusage --help 
      usage: OSCusage.py [-h] [-u USER] 
      [-s {opt,pitzer,glenn,bale,oak,oakley,owens,ruby}] [-A] 
      [-P PROJECT] [-q] [-H] [-r] [-n] [-v] 
      [start_date] [end_date] 
      
      positional arguments: 
      start_date start date (default: 2020-04-23) 
      end_date end date (default: 2020-04-24) 
      
      optional arguments: 
      -h, --help show this help message and exit 
      -u USER, --user USER username to run as. Be sure to include -P or -A. (default: kalattar) 
      -s {opt,pitzer,glenn,bale,oak,oakley,owens,ruby}, --system {opt,pitzer,glenn,bale,oak,oakle 
      -A Show all 
      -P PROJECT, --project PROJECT project to query (default: PZS0715) 
      -q show user data 
      -H show hours 
      -r show raw 
      -n show job ID 
      -v do not summarize 

      As it can be seen, one could for example use OSCusage to receive information regarding another user’s usage with the -u option and write a cron script that is set up with email notification.

      Some other usage examples,

       OSCusage 2018-01-24 

      where the command specifies the usage’s start time. The end time could also be specified with,

      OSCusage 2018-01-24 2018-01-25 

      Terminating a Cron Job

      To terminate a cron job, you need to first determine the process id,

      ps aux | grep crontab 

      and then use,

      kill {PID}

      A user can also just clear out the cron script with,

      crontab -e 
      Supercomputer: 

      HOWTO: Use Docker and Apptainer/Singularity Containers at OSC

      It is now possible to run Docker and Apptainer/Singularity containers on the Owens and Pitzer clusters at OSC. Single-node jobs are currently supported, including GPU jobs; MPI jobs are planned for the future.

      From the Docker website:  "A container image is a lightweight, stand-alone, executable package of a piece of software that includes everything needed to run it: code, runtime, system tools, system libraries, settings."

      As of June 21st, 2022, Singularity is replaced with Apptainer, which is just a renamed open-source project. For more information visit the Apptainer/Singularity page

      This document will describe how to run Docker and Apptainer/Singularity containers on the Owens and Pitzer. You can use containers from Docker Hub, Sylabs Cloud, or any other source. As examples we will use hello-world from Singularity Hub and ubuntu from Docker Hub.

      If you encounter any error, check out Known Issues on using Apptainer/Singularity at OSC. If the issue can not be resolved, please contact OSC help

      Contents

      1. Getting help
      2. Setting up your environment
      3. Access a container
      4. Run a container
      5. File system access
      6. GPU usage within a container
      7. Build a container
      8. References

      Getting help

      The most up-to-date help on Apptainer/Singularity comes from the command itself.

      apptainer help
      

      User guides and examples can be found in Apptainer documents.

      Setting up your environment for Apptainer/Singularity usage

      No setup is required. You can use Apptainer/Singularity directly on all clusters.

      Accessing a container

      An Apptainer/Singularity container is a single file with a .sif  extension.

      You can simply download ("pull") a container from a hub. Popular hubs are Docker Hub and Singularity Hub. You can go there and search if they have a container that meets your needs. Docker Hub has more containers and may be more up to date but supports a much wider community than just HPC. Singularity Hub is for HPC, but the number of available containers are fewer. Additionally there are domain and vendor repositories such as biocontainers and NVIDIA HPC containers that may have relevant containers.

      Pull a container from hubs

      Docker Hub

      Pull from the 7.2.0 branch of the gcc repository on Docker Hub. The 7.2.0 is called a tag.

      apptainer pull docker://gcc:7.2.0
      

      Filename:  gcc_7.2.0.sif

      Pull an Ubuntu container from Docker Hub.

      apptainer pull docker://ubuntu:18.04
      

      Filename:  ubuntu_18.04.sif

      Singularity Hub

      Pull the singularityhub/hello-world container from the Singularity hub. Since no tag is specified it pulls from the master branch of the repository.

      apptainer pull shub://singularityhub/hello-world
      

      Filename:  hello-world_latest.sif

      Downloading containers from the hubs is not the only way to get one. You can, for example get a copy from your colleague's computer or directory. If you would like to create your own container you can start from the user guide below. If you have any questions, please contact OSC Help.

      Running a container

      There are four ways to run a container under Apptainer/Singularity.

      You can do this either in a batch job or on a login node.

      Don’t run on a login node if the container will be performing heavy computation, of course.
      If unsure about the amount of memory that a singularity process will require, then be sure to request an entire node for the job. It is common for singularity jobs to be killed by the OOM killer because of using too much RAM.

      We note that the operating system on Owens is Red Hat:

      [owens-login01]$ cat /etc/os-release
      NAME="Red Hat Enterprise Linux Server"
      VERSION="7.5 (Maipo)"
      ID="rhel"
      [..more..]

      In the examples below we will often check the operating system to show that we are really inside a container.

      Run container like a native command

      If you simply run the container image it will execute the container’s runscript.

      Example:  Run singularityhub/hello-world

      Note that this container returns you to your native OS after you run it.

      [owens-login01]$ ./hello-world_latest.sif
      Tacotacotaco
      

      Use the “run” sub-command

      The Apptainer “run” sub-command does the same thing as running a container directly as described above. That is, it executes the container’s runscript.

      Example:  Run a container from a local file

      [owens-login01]$ apptainer run hello-world_latest.sif
      Tacotacotaco
      

      Example:  Run a container from a hub without explicitly downloading it

      [owens-login01]$ apptainer run shub://singularityhub/hello-world
      INFO: Downloading shub image
      Progress |===================================| 100.0%
      Tacotacotaco
      

      Use the “exec” sub-command

      The Apptainer “exec” sub-command lets you execute an arbitrary command within your container instead of just the runscript.

      Example:  Find out what operating system the singularityhub/hello-world container uses

      [owens-login01]$ apptainer exec hello-world_latest.sif cat /etc/os-release
      NAME="Ubuntu"
      VERSION="14.04.5 LTS, Trusty Tahr"
      ID=ubuntu
      [..more..] 
      

      Use the “shell” sub-command

      The Apptainer “shell” sub-command invokes an interactive shell within a container.

      Example:  Run an Ubuntu shell. Note the “Apptainer” prompt within the shell.

      [owens-login01 ~]$ apptainer shell ubuntu_18.04.sif
      Singularity ubuntu_18.04.sif:~> cat /etc/os-release
      NAME="Ubuntu"
      VERSION="18.04 LTS (Bionic Beaver)"
      ID=ubuntu
      [.. more ..] 
      Singularity ubuntu_18.04.sif:~> exit
      exit
      

      File system access

      When you use a container you run within the container’s environment.  The directories available to you by default from the host environment are

      • your home directory
      • working directory (directory you were in when you ran the container)
      • /fs/ess
      • /tmp

      You can review our Available File Systems page for more details about our file system access policy.

      If you run the container within a job you will have the usual access to the $PFSDIR environment variable with adding node attribute "pfsdir" in the job request (--gres=pfsdir). You can access most of our file systems from a container without any special treatment.

      GPU usage within a container

      If you have a GPU-enabled container you can easily run it on Owens or Pitzer just by adding the --nv flag to the apptainer exec or run command.  The example below comes from the "exec" command section of Apptainer User Guide.  It runs a TensorFlow example using a GPU on Owens.  (Output has been omitted from the example for brevity.)

      [owens-login01]$ sinteractive -n 28 -g 1
      ...
      [o0756]$ git clone https://github.com/tensorflow/models.git
      [o0756]$ apptainer exec --nv docker://tensorflow/tensorflow:latest-gpu \
      python ./models/tutorials/image/mnist/convolutional.py
      

      In some cases it may be necessary to bind the CUDA_HOME path and add $CUDA_HOME/lib64 to the shared library search path:

      [owens-login01]$ sinteractive -n 28 -g 1
      ...
      [o0756]$ module load cuda
      [o0756]$ export APPTAINER_BINDPATH=$CUDA_HOME
      [o0756]$ export APPTAINERENV_LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib64
      [o0756]$ apptainer exec --nv my_container mycmd
      

      Build a container

      It is possible to build or create a custom container, but it will require additional setup. Please contact OSC support for more details.

      References

       

       
      Supercomputer: 

      HOWTO: Use Extensions with JupyterLab

      JupyterLab stores the main build of JupyterLab with associated data, including extensions in Application Directory. The default Application Directory is the JupyterLab installation directory where is read-only for OSC users. Unlike Jupyter Notebook, JupyterLab cannot accommodate multiple paths for extensions management. Therefore we set the user's home directory for Application Directory so as to allow user to manage extensions.

      NOTE: The extension management is only available for JupyterLab 2 or later.

      Manage and install extensions

      After launching a JupyterLab session, open a notebook and run

      !jupyter lab path

      Check if home directory is set for to the Application Directory

      Application directory:   /users/PXX1234/user/.jupyter/lab/3.0
      User Settings directory: /users/PXX1234/user/.jupyter/lab/user-settings
      Workspaces directory: /users/PXX1234/user/ondemand/data/sys/dashboard/batch_connect/dev/bc_osc_jupyter/output/f2a4f918-b18c-4d2a-88bc-4f4e1bdfe03e

      If home directory is NOT set, try removing the corresonding directory, e.g. if you are using JupyterLab 2.2, remove the entire directory $HOME/.jupyter/lab/2.2 and re-launch JupyterLab 2.2.

      If this is the first time to use extension or use extensions that are installed with different Jupyter version or on different cluster, you will need to run

      !jupyter lab build

      to initialize the JupyterLab application.

      To manage and install extensions, simply click Extension Manager icon at the side bar:

      Screen Shot 2021-07-27 at 1.30.45 PM.png

      Please note that OSC Jupyter app is a portal to launch JupyterLab installed on OSC. It does not act the same as the standalone Jupyter installed on your computer. Some extensions that work on your computer might not work with OSC Jupyter. If you experience any issue, please contact OSC help

       

       
      Supercomputer: 
      Service: 

      HOWTO: Use GPU in Python

      If you plan on using GPUs in tensorflow or pytorch see HOWTO: Use GPU with Tensorflow and PyTorch

      This is an exmaple to utilize a GPU to improve performace in our python computations. We will make use of the Numba python library. Numba provides numerious tools to improve perfromace of your python code including GPU support.

      This tutorial is only a high level overview of the basics of running python on a gpu. For more detailed documentation and instructions refer to the official numba document: https://numba.pydata.org/numba-doc/latest/cuda/index.html

      Environment Setup

      To begin, you need to first create and new conda environment or use an already existing one. See HOWTO: Create  Python Environment for more details. 

      Once you have an environment created and activated run the following command to install the latest version of Numba into the environment. 

      conda install numba
      conda install cudatoolkit

      You can specify a specific version by replacing numba with number={version}. In this turtorial we will be using numba version 0.57.0 and cudatoolkit version 11.8.0.

      Write Code

      Now we can use numba to write a kernel function. (a kernel function is a GPU function that is called from CPU code).

      To invoke a kernel, you need to include the @cuda.jit decorator above your gpu function as such:

      @cuda.jit
      def my_funtion(array):
           # function code

      Next to invoke a kernel you must first specify the thread heirachy with the number of blocks per grid and threads per block you want on your gpu:

      threadsperblock = 32
      blockspergrid = (an_array.size + (threadsperblock - 1))

      For more details on thread heirachy see: https://numba.pydata.org/numba-doc/latest/cuda/kernels.html

       

      Now you can call you kernel as such:

      my_function[blockspergrid, threadsperblock](an_array)

      Kernel instantiation is done by taking the compiled kernel function (here my_function) and indexing it with a tuple of integers.

      Run the kernel, by passing it the input array (and any separate output arrays if necessary). By default, running a kernel is synchronous: the function returns when the kernel has finished executing and the data is synchronized back.

      Note: Kernels cannot explicitly return a value, as a result, all returned results should be written to a reference. For example, you can write your output data to an array which was passed in as an argument (for scalars you can use a one-element array) 

      Memory Transfer

      Before we can use a kernel on an array of data we need to transfer the data from host memory to gpu memory. 

      This can be done by (assume arr is already created and filled with the data):

      d_arr = cuda.to_device(arr)

      d_arr is a reference to the data stored in the gpu memory. 

      Now to get the gpu data back into host memory we can run (assume gpu_arr has already been initialized ot an empty array):

      d_arr.copy_to_host(gpu_arr)

       

      Example Code:

      from numba import cuda
      import numpy as np
      from timeit import default_timer as timer
      
      # gpu kernel function
      @cuda.jit
      def increment_by_one_gpu(an_array):
          #get the absolute position of the current thread in out 1 dimentional grid
          pos = cuda.grid(1) 
      
          #increment the entry in the array based on its thread position
          if pos < an_array.size:
              an_array[pos] += 1
      
      
      # cpu function
      def increment_by_one_nogpu(an_array):
          # increment each position using standard iterative approach
          pos = 0
          while pos < an_array.size:
              an_array[pos] += 1
              pos += 1
      
      if __name__ == "__main__":
      
          # create numpy array of 10 million 1s
          n = 10_000_000
          arr = np.ones(n)
      
          # copy the array to gpu memory
          d_arr = cuda.to_device(arr)
      
          # print inital array values
          print("GPU Array: ", arr)
          print("NON-GPU Array: ", arr)
      
          #specify threads
          threadsperblock = 32
          blockspergrid = (len(arr) + (threadsperblock - 1)) // threadsperblock
      
          # start timer
          start = timer()
          # run gpu kernel
          increment_by_one_gpu[blockspergrid, threadsperblock](d_arr)
          # get time elapsed for gpu
          dt = timer() - start
      
          print("Time With GPU: ", dt)
          
          # restart timer
          start = timer()
          # run cpu function
          increment_by_one_nogpu(arr)
          # get time elapsed for cpu
          dt = timer() - start
      
          print("Time Without GPU: ", dt)
      
          # create empty array
          gpu_arr = np.empty(shape=d_arr.shape, dtype=d_arr.dtype)
      
          # move data back to host memory
          d_arr.copy_to_host(gpu_arr)
      
          print("GPU Array: ", gpu_arr)
          print("NON-GPU Array: ", arr)
      

       

      Now we need to write a job script to submit the python code. 

      Make sure you request a gpu for your job! See GPU Computing for more details.
      #!/bin/bash
      
      #SBATCH --account <project-id>
      #SBATCH --job-name Python_ExampleJob
      #SBATCH --nodes=1
      #SBATCH --time=00:10:00
      #SBATCH --gpus-per-node=1
      
      
      module load miniconda3
      module list
      
      source activate gpu_env
      
      python gpu_test.py
      
      conda deactivate

       

      Running the above job returns the following output:

      GPU Array:  [1. 1. 1. ... 1. 1. 1.]
      NON-GPU Array:  [1. 1. 1. ... 1. 1. 1.]
      Time With GPU:  0.34201269410550594
      Time Without GPU:  2.2052815910428762
      GPU Array:  [2. 2. 2. ... 2. 2. 2.]
      NON-GPU Array:  [2. 2. 2. ... 2. 2. 2.]

      As we can see, running the function on a gpu resulted in a signifcant speed increase. 

       

      Usage on Jupyter

      see HOWTO: Use a Conda/Virtual Environment With Jupyter for more information on how to setup jupyter kernels.

      One you have your jupyter kernel created, activate your python environment in the command line (source activate ENV).

      Install numba and cudatoolkit the same as was done above:

      conda install numba
      conda install cudatoolkit

      Now you should have numba installed into your jupyter kernel.

      See Python page for more information on how to access your jupyter notebook on OnDemand.

       

      Make sure you select a node with a gpu before laucnhing your jupyter app:

      On_Demand_GPU.jpeg

       

      Additional Resources

      If you are using Tensorflow, PyTorch or other machine learning frameworks you may want to also consider using Horovod. Horovod will take single-GPU training scripts and scale it to train across many GPUs in parallel.

       

      Supercomputer: 

      HOWTO: Use Globus (Overview)

       

      GlobusOnline-265x258.jpg

      Globus is a cloud-based service designed to let users move, share, and discover research data via a single interface, regardless of its location or number of files or size.

      Globus was developed and is maintained at the University of Chicago and is used extensively at supercomputer centers and major research facilities.

      Globus is available as a free service that any user can access. More on how Globus works can be found on the Globus "How It Works" page.

      Data Transfer

      Globus can be used to transfer data between source and destination systems including OSC storage, cloud storage, storage at other HPC centers with Globus support, laptops, desktops. 

      If you would like to transfer data between OSC storage and your own laptop/desktop which has not installed Globus Connect Personal yet, please go to 'Globus Connect Personal Installation' first

      Step 1: Log into Globus

      Log into https://www.globus.org/

      When prompted to login, select "Ohio Supercomputer Center (OSC)" from the drop-down list of organizations and then click Continue. This will redirect you to the Ohio Supercomputer Center login page where you can log in with your OSC username and password.

      Step 2: Locate collections of your data

      Click 'File Manager' on the left of the page. Switch to 'two panel' view by click icons next to 'Panels'. One panel will act as the source while the other is the destination. 

      Click 'Collection' to search the collection of your data.

      For OSC storage, use 'OSC endpoints' information to locate the collection. 

      Step 3: Transfer the file

      Select the file(s) or directory that you would like to transfer between collections. You can now select the "Transfer or Sync to..." and hit the blue "Start" icon above the file selector.

      Step 4: Verfiy the transfer 

      Click Activity in the command menu on the left of the page to go to the Activity page.

      Globus Connect Personal Installation

      Globus Installation on Windows

      1. Download Globus Connect Personal.

      2. Launch the application installer.

      3. If you have local administrator permissions on your machine, and will be the only user, click on 'Install'.

        • If you do not have local administrator permissions or wish to specify a non-default destination directory for installation, or will have multiple GCP users, click on the 'Browse' button and select a directory which you have read/write access to.
           
      4. After installation has completed GCP will launch. Click on 'Log In' in order to authenticate with Globus and begin the Collection Setup process.

      5. Grant the required consents to GCP Setup.

      6. Enter the details for your GCP Collection.

      7. Exit the Setup process or open the Globus web app to view collection details or move data to or from your collection.

      8. At the end of the installation, you will see an icon in the menu bar at the bottom of your screen, indicating that Globus Connect Personal is running and your new collection is ready to be used.

      OSC endpoints

      • Enter 'OSC Globus Connect Server' in the endpoint search box to find all the endpointss managed by OSC as below:
        Endpoint
      OSC's home directory OSC $HOME
      OSC's project directory OSC /fs/project
      OSC's scratch directory OSC /fs/scratch
      OSC's ess storage OSC /fs/ess
      AWS S3 storage OSC S3
      OSC high assurance

      OSC /fs/ess/ High Assurance for project storage

      OSC /fs/scratch/ High Assurance for scratch storage

      Note: the default path will be $HOME for home directory, /fs/ess for project storage, /fs/scratch for scratch filesystem. You can change to a more specific directory by providing the path in ‘Directory’. The location for project/scratch data would be under /fs/ess/<project-code> or /fs/scratch/<project-code>.

      Data Sharing

      With Globus, you can easily share research data with your collaborators. You don’t need to create accounts on the server(s) where your data is stored. You can share data with anyone using their identity or their email address.

      To share data, you’ll create a guest collection and grant your collaborators access as described in the instructions below. If you like, you can designate other Globus users as "access managers" for the guest collection, allowing them to grant or revoke access privileges for other Globus users.

      1. Log into Globus and navigate to the File Manager.

      2. Select the collection that has the files/folders you wish to share and, if necessary, activate the collection.

      3. Highlight the folder that you would like to share and Click Share in the right command pane.

        Note: Sharing is available for folders. Individual files can only be shared by sharing the folder that contains them. If you are using an ad blocker plugin in your browser, the share button may be unavailable. We recommend users whitelist app.globus.org, docs.globus.org, and globus.org within the plugin to circumvent this issue.

        If Share is not available, contact the endpoint’s administrator or refer to Globus Connect Server Installation Guide for instructions on enabling sharing. If you’re a using a Globus Connect Personal endpoint and you’re a Globus Plus user, enable sharing by opening the Preferences for Globus Connect Personal, clicking the Access tab, and checking the Sharable box.

      4. Provide a name for the guest collection, and click Create Share. If this is the first time you are accessing the collection, you may need to authenticate and consent to allow Globus services to manage your collections on your behalf.

      5. When your collection is created, you’ll be taken to the Sharing tab, where you can set permissions. The starting permissions give read and write access (and the Administrator role) to the person who created the collection.

        Click the Add Permissions button or icon to share access with others. You can add permissions for an individual user, for a group, or for all logged-in users. In the Identity/E-mail field, type a person’s name or username (if user is selected) or a group name (if group is selected) and press Enter. Globus will display matching identities. Pick from the list. If the user hasn’t used Globus before or you only have an email address, enter the email address and click Add.

        Note: Granting write access to a folder allows users to modify and delete files and folders within the folder.

        You can add permissions to subfolders by entering a path in the Path field.

      6. After receiving the email notification, your colleague can click on the link to log into Globus and access the guest collection.

      7. You can allow others to manage the permissions for a collection you create. Use the Roles tab to manage roles for other users. You can assign roles to individual users or to groups. The default is for the person who created the collection to have the Administrator role.

        The Access Manager role grants the ability to manage permissions for a collection. (Users with this role automatically have read/write access for the collection.) 

        When a role is assigned to a group, all members of the group have the assigned role.

      Data Sharing with Service Account

      Sometimes, a group may need to share data uploaded by several OSC users with external entities using Globus. To simplify this process OSC can help set up a service account that owns the data and create a Globus share that makes the data accessible to individuals. Contact OSC Help for this service. 

      Further Reading

      HOWTO: Use AWS S3 in Globus

      Beofre creating a new collection, please set up a S3 bucket and configure the IAM access permissions to that bucket. If you need more information on how to do that, see the AWS S3 documentation and Amazon Web Services S3 Connector pages.

      Create a New Collection

      • Login to Globus. If your institution does not have an organizational login, you may choose to either Sign in with Google or Sign in with ORCiD iD
      • Navigate to the 'COLLECTIONS' on the sidebar and search 'OSC S3'. Click 'OSC S3' to go to this gateway
      • Click on the “Credentials” tab of the “OSC S3” page. Register your AWS IAM access key ID and AWS IAM Secret Key with Globus. Click the “Continue” button, and you will return to the full “Credentials” tab where you can see your saved AWS access credentials.
      • Click on the 'Collections' tab. You will see all of the collections added by you before. To add a new collection, click 'Add Guest Collection'. Click the “Browse” button to get a directory view and select the bucket or subfolder folder you want. Provide the name of the collection in 'Display Name” field
      • Click 'Create Collection' to finish the creation
      • Click 'COLLECTIONS' on the sidebar. Click the 'Administered by You' and then you can locate the new collection you just created. 

       

      HOWTO: User OneDrive in Globus

      Accessing User OneDrive in Globus

      Globus is a cloud-based service designed to let users move, share, and discover research data via a single interface, regardless of its location or number of files or size.

      This makes Globus incredibly useful for transferring large files for users. This service is also able to work alongside OneDrive, making your this storage even more attainable.

      Data Transfer with OneDrive

      Step 1: Log into Globus

      Log into https://www.globus.org/

      When prompted to login, select "Ohio Supercomputer Center (OSC)" from the drop-down list of organizations and then click Continue. This will redirect you to the Ohio Supercomputer Center login page where you can log in with your OSC username and password.

      Step 2: Choose the Appropriate Collections

      Select the File Manager tab on the left hand toolbar. You will be introduced to the file exchange function in the two-panel format.

      Globus File Manager.png

      In the left panel, select the collection that you would like to import the data to. In the right panel, you can simply type "OSU OneDrive" and the collection should appear.

      OSU OneDrive.png

      The first time that you access this collection, you will be prompted for some initial account setup.

      Authentication Required.png

      Complete the Authentication Request and, if prompted, verify that you wish to grant access to the Collection.

      Once opened, the default location will be My Files. Click the "up one folder" icon to see the other locations.

      Up One Folder.png

      Step 3: Transfer the Files

      Select the file(s) or directory that you would like to transfer between collections. You can now select the "Transfer or Sync to..." and hit the blue "Start" icon above the file selector.

      Step 4: Verify the transfer 

      Click Activity in the command menu on the left of the page to go to the Activity page. You will now be able to monitor the processing of the request and the confirmation receipt will appear here.

      Following Sites in SharePoint

      To follow a SharePoint site, log into the OSU SharePoint service with your OSC name.# credentials. Next, navigate to the site you would like to connect to via Globus and click the star icon on the site to follow:

      Sharepoint.png

      Finally, return to Globus and click the "up one folder" button until you see the "Shared libraries" and the SharePoint site will now be available.

      HOWTO: Deploy your own endpoint on a server

      OSC clients who are affiliated with Ohio State can deploy their own endpoint on a server using OSU subscriptions. Please follow the steps below:

      1. Send a request to OSC Help the following information:
        • Name of organization that will be running the endpoint, ie: OSU Arts and Sciences
          • NOTE: if the name already exists, they will have to coordinate with the existing Admin for that project
        • OSU affiliated email address associated with the Globus account, ie: name.#@osu.edu
      2. OSC will create a new project at https://developers.globus.org, make the user provided in #1 the administrator, and inform the user to set up the endpoint credentials
      3. The user goes to https://developers.globus.org/ and chooses “Register a new Globus Connect Server v5”. Under the project, the user chooses Add dropdown and chooses Add new Globus Connect Server. Provide a display name for the endpoint, ie: datamover02.hpc.osc.edu. Select “Generate New Client Secret” and save that value and Client ID and use those values when configuring the Globus Connect Server install on their local system
      4. The user finishes configuring Globus Connect Server and runs the necessary commands to register the new endpoint with Globus. Once the new endpoint is registered, please email OSC Help the endpoint name so we can mark the endpoint as managed under the OSU subscription

       

      Supercomputer: 

      HOWTO: Use VNC in a batch job

      SSHing directly to a compute node at OSC - even if that node has been assigned to you in a current batch job - and starting VNC is an "unsafe" thing to do. When your batch job ends (and the node is assigned to other users), stray processes will be left behind and negatively impact other users. However, it is possible to use VNC on compute nodes safely.

      You can use OnDemand, which is a much easier way to access desktops. If your work is not a very large, very intensive computation (for example, you do not expect to saturate all of the cores on a machine for a significant portion of the time you have the application you require open - e.g., you are using the GUI to set up a problem for a longer non-interactive compute job), you can choose one VDI under "Virtual Desktop Interface" from "Desktops" menu. Otherwise, please use "Interactive HPC" from Desktops" menu.

      The examples below are for Pitzer. If you use other systems, please see this page for supported versions of TurboVNC on our systems.

      Starting your VNC server

      Step one is to create your VNC server inside a batch job.

      Option 1: Interactive

      The preferred method is to start an interactive job, requesting an gpu node, and then once your job starts, you can start the VNC server.

      salloc --nodes=1 --ntasks-per-node=40 --gpus-per-node=1 --gres=vis --constraint=40core srun --pty /bin/bash
      

      This command requests an entire GPU node, and tells the batch system you wish to use the GPUs for visualization. This will ensure that the X11 server can access the GPU for acceleration. In this example, I have not specified a duration, which will then default to 1 hour.

      module load virtualgl
      module load turbovnc
      

      Then start your VNC server. (The first time you run this command, it may ask you for a password - this is to secure your VNC session from unauthorized connections. Set it to whatever password you desire. We recommend a strong password.)

      vncserver
      
      To set the vnc password again use the vncpasswd command.

      The output of this command is important: it tells you where to point your client to access your desktop. Specifically, we need both the host name (before the :), and the screen (after the :).

      New 'X' desktop is p0302.ten.osc.edu:1
      

      Connecting to your VNC server

      Because the compute nodes of our clusters are not directly accessible, you must log in to one of the login nodes and allow your VNC client to "tunnel" through SSH to the compute node. The specific method of doing so may vary depending on your client software.

      The port assigned to the vncserver will be needed. It is usually 5900 + <display_number>. e.g.

      New 'X' desktop is p0302.ten.osc.edu:1

      would use port 5901.

      Linux/MacOS

      Option 1: Manually create an SSH tunnel 

      I will be providing the basic command line syntax, which works on Linux and MacOS. You would issue this in a new terminal window on your local machine, creating a new connection to Pitzer.

      ssh -L <port>:<node_hostname>.ten.osc.edu:<port> <username>@pitzer.osc.edu
      

      The above command establishes a proper ssh connection for the vnc client to use for tunneling to the node.

      Open your VNC client, and connect to localhost:<screen_number>, which will tunnel to the correct node on Pitzer.

      Option 2: Use your VNC software to tunnel 

      This example uses Chicken of the VNC, a MacOS VNC client. It is a vncserver started on host n0302 with port 5901 and display 1.

      The default window that comes up for Chicken requires the host to connect to, the screen (or port) number, and optionally allows you to specify a host to tunnel through via SSH. This screenshot shows a proper configuration for the output of vncserver shown above. Substitute your host, screen, and username as appropriate.

      When you click [Connect], you will be prompted for your HPC password (to establish the tunnel, provided you did not input it into the "password" box on this dialog), and then (if you set one), for your VNC password. If your passwords are correct, the desktop will display in your client.

      Windows

      This example shows how to create a SSH tunnel through your ssh client.  We will be using Putty in this example, but these steps are applicable to most SSH clients.

      First, make sure you have x11 forwarding enabled in your SSH client.

      Next, open up the port forwarding/tunnels settings and enter the hostname and port you got earlier in the destination field.  You will need to add 5900 to the port number when specifiying it here.  Some clients may have separate boxes for the desination hostname and port.  

      For source port, pick a number between 11-99 and add 5900 to it.  This number between 11-99 will be the port you connect to in your VNC client.

      Make sure to add the forwaded port, and save the changes you've made before exiting the configutations window.

      PuTTY Tunnel Configuration Settings

      Now start a SSH session to the respective cluster your vncserver is running on.  The port forwarding will automatically happen in the background.  Closing this SSH session will close the forwarded port; leave the session open as long as you want to use VNC.

      Now start a VNC client.  TurboVNC has been tested with our systems and is recommended.  Enter localhost:[port], replacing [port] with the port between 11-99 you chose earlier.

      New TurboVNC Connection

      If you've set up a VNC password you will be prompted for it now.  A desktop display should pop up now if everything is configured correctly.

      How to Kill a VNC session?

      Occasionally you may make a mistake and start a VNC server on a login node or somewhere else you did not want to.  In this case it is important to know how to properly kill your VNC server so no processes are left behind.

      The command syntax to kill a VNC session is:

      vncserver -kill :[screen]
      

      In the example above, screen would be 1.

      You need to make sure you are on the same node you spawned the VNC server on when running this command.

      Supercomputer: 
      Service: 
      Fields of Science: 

      HOWTO: Use a Conda/Virtual Environment With Jupyter

      The IPython kernel for a Conda/virtual environment must be installed on Jupyter prior to use. This tutorial will walk you though the installation and setup procedure.

      First you must create a conda/virtual environment. See create conda/virtual environment if there is not already an environment that has been created.

      Install kernel

      Load the preferred version of Python or Miniconda3 using the command:

      module load python
      

      or

      module load miniconda3

      Replace "python" or "miniconda3" with the appropriate version, which could be the version you used to create your Conda/venv environment. You can check available Python versions by using the command:

      module spider python

      Run one of the following commands based on how your Conda/virtual environment was created. Replace "MYENV" with the name of your Conda environment or the path to the environment.

      • If the Conda environment was created via conda create -n MYENV command, use the following command:

            ~support/classroom/tools/create_jupyter_kernel conda MYENV
      • If the Conda environment was created via conda create -p /path/to/MYENV command, use the following command:

            ~support/classroom/tools/create_jupyter_kernel conda /path/to/MYENV
      • If the Python virtual environment was created via python3 -m venv /path/to/MYENV command, use the following command

            ~support/classroom/tools/create_jupyter_kernel venv /path/to/MYENV

       

      The resulting kernel name appears as "MYENV [/path/to/MYENV]" in the Jupyter kernel list. You can change the display name by appending a preferred name in the above commands. For example:

      ~support/classroom/tools/create_jupyter_kernel conda MYENV "My Research Project"

      This results in the kernel name "My Research Project" in the Jupyter kernel list.

       

      You should now be able to access the new Jupyter kernel on OnDemand in a jupyter session. See Usage section of Python page for more details on accessing the Jupyter app.

       

      Install Jupyterlab Debugger kernel

      According to Jupyterlab page, debugger requires ipykernel >= 6. Please create your own kernel with conda using the following commands:

      module load miniconda
      conda create -n jupyterlab-debugger -c conda-forge "ipykernel>=6" xeus-python
      ~support/classroom/tools/create_jupyter_kernel conda jupyterlab-debugger

      You should see a kernelspec 'conda_jupyterlab-debugger' created in home directory. Once the debugger kernel is done, you can use it:
      1. go to OnDemand
      2. request a JupyterLab app with kernel 3
      3. open a notebook with the debugger kernel.
      4. you can enable debug mode at upper-right kernel of the notebook

       

      Manually install kernel

      If the create_jupyter_kernel script does not work for you, try the following steps to manually install kernel:

      # change to the proper version of python
      module load python  
          
      # replace with the name of conda env           
      MYENV=useful-project-name
          
      # create the cpnda enironment
      conda create -n $MYENV
          
      # Activate your conda/virtual environment
      ## For Conda environment
      source activate $MYENV
          
      # ONLY if you created venv instead of conda env
      ## For Python Virtual environment
      source /path/to/$MYENV/bin/activate
          
      # Install Jupyter kernel 
      python -m ipykernel install --user --name $MYENV --display-name "Python ($MYENV)"

       

      Remove kernel

      If the envirnoment is rebuilt or renamed, users may want to erase any custom jupyter kernel installations.

      Be careful! This command will erase entire directories and all files within them.
      rm -rf ~/.local/share/jupyter/kernels/${MYENV}
      

       

       

      Supercomputer: 
      Service: 
      Fields of Science: 

      HOWTO: Use an Externally Hosted License

      Many software packages require a license.  These licenses are usually made available via a license server, which allows software to check out necessary licenses.  In this document external refers to a license server that is not hosted inside OSC.

      If you have such a software license server set up using a license manager, such as FlexNet, this guide will instruct you on the necessary steps to connect to and use the licenses at OSC.

      Users who wish to host their software licenses inside OSC should consult OSC Help.

       

      You are responsible for ensuring you are following your software license terms.  Please ensure your terms allow you to use the license at OSC before beginning this process!

      Introduction

      Broadly speaking, there are two different ways in which the external license server's network may be configured.  These differ by whether the license server is directly externally reachable or if it sits behind a private internal network with a port forwarding firewall.  

      If your license server sits behind a private internal network with a port forwarding firewall you will need to take additional steps to allow the connection from our systems to the license server to be properly routed. 

      License Server is Directly Externally Reachable

      Figure depicting a License Server with firewall connected to the internet, and an outbound compute node whose traffic is routed through NAT to the internet

      License Server is Behind Port Forwarding Firewall

      Figure depicting a License Server with a Full Port Forwarding Firefall inside a Private Internal Nework connected to the internet, and an outbound compute node whose traffic is routed through NAT to the internet

      Unsure?

      If you are unsure about which category your situation falls under contact your local IT administrator.

      Configure Remote Firewall

       OSC changed NAT IP addresses on December 14, 2021. Please update the IP addresses of license server configured for the firewall to allow the connections from nat.osc.edu (192.148.249.248 to 192.148.249.251). 

      In order for connections from OSC to reach the license server, the license server's firewall will need to be configured.  All outbound network traffic from all of OSC's compute nodes are routed through a network address translation host (NAT).

      The license server should be configured to allow connections from nat.osc.edu including the following IP addresses to the SERVER:PORT where the license server is running:

      • 192.148.249.248
      • 192.148.249.249
      • 192.148.249.250
      • 192.148.249.251

      A typical FlexNet-based license server uses two ports: one is server port and the other is daemon port, and the firewall should be configured for the both ports. A typical license file looks, for example,

      SERVER licXXX.osc.edu 0050XXXXX5C 28000
      VENDOR {license name} port=28001
      

      In this example, "28000" is the server port, and "28001" is the daemon port. The daemon port is not mandatory if you use it on a local network, however it becomes necessary if you want to use it outside of your local network. So, please make sure you declared the daemon port in the license file and configured the firewall for the port.

      Confirm Configuration

      The firewall settings should be verified by attempting to connect to the license server from the compute environment using telenet.

      Get on to a compute node by requesting a short, small, interactive job and test the connection using telenet:

      telnet <License Server IP Address> <Port#>
      

      (Recommended) Restrict Access to IPs/Usernames

      It is also recommended to restrict accessibility using the remote license server's access control mechanisms, such as limiting access to particular usernames in the options.dat file used with FlexNet-based license servers.

      For FlexNet tools, you can add the following line to your options.dat file, one for each user.

      INCLUDEALL USER <OSC username>
      

      If you have a large number of users to give access to you may want to define a group using GROUP within the options.dat file and give access to that whole group using INCLUDEALL GROUP <group name> .

      Users who use other license managers should consult the license manager's documentation.

      Modify Job Environment to Point at License Server

      The software must now be told to contact the license server for it's licenses.  The exact method of doing so can vary between each software package, but most use an environment variable that specifies the license server IP address and port number to use.

      For example LS DYNA uses the environment variable LSTC_LICENSE and LSTC_LICENSE_SERVER to know where to look for the license.  The following lines would be added to a job script to tell LS-DYNA to use licenses from port 2345 on server 1.2.3.4, if you use bash:

      export LSTC_LICENSE=network
      export LSTC_LICENSE_SERVER=2345@1.2.3.4
      

      or, if you use csh:

      setenv LSTC_LICENSE network
      setenv LSTC_LICENSE_SERVER 2345@1.2.3.4
      

      License Server is Behind Port Forwarding Firewall

      If the license server is behind a port forwarding firewall, and has a different IP address from the IP address of the firewall, additional steps must be taken to allow connections to be properly routed within the license server's internal network.  

      1. Use the license server's fully qualified domain name in SERVER line in the license file instead of the IP address.
      2. Contact your IT team to have the firewall IP address mapped to the fully qualified domain name.

       

      Software Specific Details

      The following outlines details particular to a specific software package.  

      ANSYS

      Uses the following environment variables:

      
      ANSYSLI_SERVERS=<port>@<IP>
      ANSYSLMD_LICENSE_FILE=<port>@<IP>
      

      If your license server is behind a port forwarding firewall and you cannot use a fully qualified domain name in the license file, you can add ANSYSLI_EXTERNAL_IP={external IP address} to ansyslmd.ini on the license server.

       

       

      HOWTO: Use ulimit command to set soft limits

      This document shows you how to set soft limits using the ulimit command.

      The ulimit command sets or reports user process resource limits. The default limits are defined and applied when a new user is added to the system. Limits are categorized as either soft or hard. With the ulimit command, you can change your soft limits for the current shell environment, up to the maximum set by the hard limits. You must have root user authority to change resource hard limits.

      Syntax

      ulimit [-HSTabcdefilmnpqrstuvx [Limit]]
      flags description
      -H Specifies that the hard limit for the given resource is set. If you have root user authority, you can increase the hard limit. Anyone can decrease it
      -S Specifies that the soft limit for the given resource is set. A soft limit can be increased up to the value of the hard limit. If neither the -H nor -S flags are specified, the limit applies to both
      -a Lists all of the current resource limits
      -b The maximum socket buffer size
      -c The maximum size of core files created
      -d The maximum size of a process's data segment
      -e The maximum scheduling priority ("nice")
      -f The maximum size of files written by the shell and its children
      -i The maximum number of pending signals
      -l The maximum size that may be locked into memory
      -m The maximum resident set size (many systems do not honor this limit)
      -n The maximum number of open file descriptors (most systems do not allow this value to be set)
      -p The pipe size in 512-byte blocks (this may not be set)
      -q The maximum number of bytes in POSIX message queues
      -r The maximum real-time scheduling priority
      -s The maximum stack size
      -t The maximum amount of cpu time in seconds
      -u The maximum number of processes available to a single user
      -v The maximum amount of virtual memory available to the shell and, on some systems, to its children
      -x The maximum number of file locks
      -T The maximum number of threads

      The limit for a specified resource is set when the Limit parameter is specified. The value of the Limit parameter can be a number in the unit specified with each resource, or the value "unlimited." For example, to set the file size limit to 51,200 bytes, use:

      ulimit -f 100

      To set the size of core dumps to unlimited, use:

      ulimit –c unlimited

      How to change ulimit for a MPI program

      The ulimit command affects the current shell environment. When a MPI program is started, it does not spawn in the current shell. You have to use srun to start a wrapper script that sets the limit if you want to set the limit for each process. Below is how you set the limit for each shell (We use  ulimit –c unlimited to allow unlimited core dumps, as an example): 

      1. Prepare your batch job script named "myjob" as below (Here, we request a job with 5-hour 2-cores):
      #!/bin/bash
      #SBATCH --ntasks=2
      #SBATCH --time=5:00:00
      #SBATCH ...
      
      
      ...
      srun ./test1
      ...
      1. Prepare the wrapper script named "test1" as below:
      #!/bin/bash
      ulimit –c unlimited
      .....(your own program)
      1. sbatch myjob
      Supercomputer: 
      Service: 

      HOWTO: test data transfer speed

      The data transfer speed between OSC and another network can be tested.

      Test data transfer speed with iperf3 tool

      Connect to a data mover host at osc and note the hostname.

      $ ssh sftp.osc.edu
      # login
      $ hostname
      datamover02.hpc.osc.edu
      # the hostname may also be datamover01.hpc.osc.edu
      

      From there, an iperf3 server process can be started. Note the port used.

      iperf3 -s -p 5201
      Server listening on 5201
      # the above port number could be different
      

      Next, on your local machine, try to connect to the iperf3 server process

      iperf3 -c datamover02.hpc.osc.edu -p 5201

      If it connects sucessfully, then it will start testing and then finish with a summary

      Connecting to host datamover02.hpc.osc.edu, port 5201
      ...
      - - - - - - - - - - - - - - - - - - - - - - - - -
      [ ID] Interval           Transfer     Bitrate
      [  7]   0.00-10.00  sec  13.8 MBytes  11.6 Mbits/sec                  sender
      [  7]   0.00-10.00  sec  13.8 MBytes  11.6 Mbits/sec                  receiver

      Run iperf3 using docker (alternative)

      Docker can be used if iperf3 is not installed on client machine, but docker is.

      $ docker run --rm -it networkstatic/iperf3 -c datamover02.hpc.osc.edu -p 5201
      
      Make sure iperf3 server process is running on OSC datamover host or client iperf3 will fail with error.

      Citation

      The Ohio Supercomputer Center provides High Performance Computing resources and expertise to academic researchers across the State of Ohio. Any paper citing this document has utilized OSC to conduct research on our production services. OSC is a member of the Ohio Technology Consortium, a division of the Ohio Department of Higher Education.

      Hardware

      OSC services can be cited by visiting the documentation for the service in question and finding the "Citation" page (located in the menu to the side).

      HPC systems currently in production use can be found here: https://www.osc.edu/supercomputing/hpc

      Decommissioned HPC systems can be found here: https://www.osc.edu/supercomputing/hpc/decommissioned.

      Logos

      Please refer to our branding webpage

      Citing OSC

      We prefer that you cite OSC when using our services, using the following information, taking into account the appropriate citation style guidelines. For your convenience, we have included the citation information in BibTeX and EndNote formats.

      Ohio Supercomputer Center. 1987. Ohio Supercomputer Center. Columbus OH: Ohio Supercomputer Center. http://osc.edu/ark:/19495/f5s1ph73.

      BibTeX:

      @misc{OhioSupercomputerCenter1987,
      ark = {ark:/19495/f5s1ph73},
      url = {http://osc.edu/ark:/19495/f5s1ph73},
      year  = {1987},
      author = {Ohio Supercomputer Center},
      title = {Ohio Supercomputer Center}
      }
      

      EndNote:

      %0 Generic
      %T Ohio Supercomputer Center
      %A Ohio Supercomputer Center
      %R ark:/19495/f5s1ph73
      %U http://osc.edu/ark:/19495/f5s1ph73
      %D 1987

      Here is an .ris file to better suit your needs. Please change the import option to .ris

      Documentation Attachment: 

      New User Training

      Recorded on March 15, 2023.

      Transcript: 

      Kate Cahill

      [Slide: “An Introduction to OSC Resources and Services”]

      All right, so thank you again for everyone for joining and we'll get started. So today I'm going to give you an introduction to OSC resources and services. So, talking about our systems, and how you can get to use them as a researcher.  

       

      [Slide: “Kate Cahill Education & Training Specialist”]

      As I said, my name is Kate and I do education and training for OSC.  

       

      [Slide: “Outline”]  

      So today we're going to cover just general, you know, intro to OSC Intro to high performance, computing so some concepts and definitions that are useful to know if you're new to using HPC systems. I'll talk about the hardware that we have at OSC, and then some details on how to get a new account or a new project, if you're starting a new research project with us. We'll take a short break, and then the latter part of the presentation will be about using the system. So, the user environment, how to work with software on the clusters and an intro to batch processing and running jobs on the systems. And then we'll finish. I'll just do a demonstration of our OnDemand web portal, so you can see what that looks like if you haven't logged into it already, and I’ll highlight the features of that, and how that makes it easy to get started. So like I said, you can put questions in the chat. Let me know if you can't hear me, or if something's not clear, and you can also ask questions as we go. I'll pause between our sections.

       

      [Slide: “What is the Ohio Supercomputer Center?”]

      So what is the Ohio supercomputer center?

       

      [Slide: “About OSC”]

      We are a part of the Ohio Department of Higher Education and we’re part of a group that's called OH-TECH, which is a statewide consortium for technology support services. So OH-TECH is comprised of OSC, OhioLINK, which is the digital library services, and OARnet, which is the the statewide network system that we have. And so, we are a statewide resource for all higher education institutions in Ohio, and we provide, you know, different types of high performance computing services and computational science expertise. And we, you know, are meant to serve the whole State.

       

      [Slide: “Service Catalog”]

      So here is some details about the services that we have at OSC. So I’m sure you’re aware that we have, you know, HPC clusters. So, that's the main reason people come to OSC is to use our large-scale computing resources. But we also have other services, such as data storage for different research needs, education activities. So you know, training events like this one, you know we can do training, you know, at your institution or for your department or group. We also partner with people on education projects to use HPC in classes and develop curriculum for computational science of different kinds. And we do a lot of web software development. So we have a team that's focused on developing different types of software and tools to use HPC resources on the web. And that's where we get our OnDemand portal. So that's their main focus. And then scientific software development as well. So, we manage the software that we have on our clusters. But we also partner with people to develop new software optimize existing things to make software run better on HPC systems.

       

      [Slide: “Client Services”]

      So, here's just an overview of kind of the activities that OSC was involved in, and this is fiscal year, 22. So this is the end of 2021, and the first half of 2022. So we had 55 active Ohio universities, with projects, 68, Ohio, or 68 companies or industry, part, you know people that were active doing research on our systems, 54 nonprofits and government agencies had active users and then we had other educational institutions with active accounts at OSC. And we have almost 8,500 active clients at this point, so people with accounts who are using our systems. And a 1,000 of those a little more than a 1,000 of those are PIs, so those are people that that run projects and lead research. And you can see the breakdown of roles, you know, for the people that we have accounts for. So about a quarter of them or faculty or staff, and the bulk of them are students. And we had a 127 college courses that used OSC so we have classroom projects that are separate from our research projects, and you can, you know, use those to have your students access OSC and do course work and homework for your courses. Twenty-nine training opportunities such as this one with the over 700 trainees.

       

      [Slide: “HPC Concepts”]

      And so that's just a general overview of OSC. Let me know if you have any questions about what we do or any of our services. But now I want to talk about HPC concepts. So, a lot of people who use OSC are new to HPC in general. So I’m just going to talk with generally about some concepts and define some terms.

       

      [Slide: “Why Use HPC?”]

      So, there's a lot of reasons why people need to use high performance computing resources. You know, typically people have some analysis or simulation that they want to run, that, you know, if they want to run it at a larger scale, it's just going to take days or weeks on a typical desktop computer. And so, they just need more computing power, so more cores, more ability to parallelize other types of acceleration, like using GPUs, or just using distributed computing tools like Spark. Or it may be that you're working with data sets, or you're collecting data, and it's just a very large volume of data, and it's really hard to work with that, you know, given the storage, or the memory that you have on your own systems. So, we have large memory nodes for that purpose. And then you know, more storage in general so you can work with larger data sets. Or it could be that there's a particular software package that just works best on HPC systems, and you can't access it otherwise.

       

      [Slide: “What is the difference between your laptop and a supercomputer?”]

      So here are three general points that it's good to keep in mind about what's the difference between your laptop or desktop and a supercomputer. So one way to think about a supercomputer is thinking about you know thousands or tens of thousands of individual computers that are linked together through a high, a very high-speed network, and so that you know, so you can, you know, link them all together so they can work together to do larger scale computing. That's really how we get the supercomputers. Another thing to keep in mind is that nobody is going to the computer itself. No one is standing in front of the supercomputer and working with it directly through a you know, a monitor and a keyboard. Everybody is remotely connecting to these systems. So they're all you know in in a in a separate, a separate area, you know, and we're all logging into them remotely. And so it's just important to keep in mind that your activity on the system is kind of moderated by the network that you're using. So if you're on a fast network, you know, you're going to get really good integration with what you're doing and really good response rates. If you're on a slower network, if you're, you know, somewhere with a slow wi-fi connection, you're going to see a slower response. So just keep that in mind when you're working with the systems. And then the third point is that these systems are shared. So you saw that, I said we have over almost 8,500 clients active on our systems this past year, and so at any given time hundreds of people are logged on and using the system or running jobs. So there's just some things that we ask you to do, so that we can all use the system, and everyone can have their jobs completed and their research move forward as efficiently as possible. So there's certain things that that the system we have, the system set up in a certain way, so that it can be shared effectively.

       

      [Slide: “HPC Terminology”]

      So here's some terminology that's good to know for using HPC systems. So we talk a lot about a node or a compute node. And so a node is sort of the unit of a cluster, and it's it's kind of equivalent to a high end desktop. It has its own memory, it has its own storage, it has its own processors. And so you know, each of those nodes is sort of like a desktop computer, and then they're all linked together, and they create the cluster. And so the compute cluster is that group of nodes that are connected by a high-speed network, and that forms the supercomputer. So, a supercomputer and a cluster, or a about synonymous. And a core we often talk about a core that usually is, relates to a processor or a CPU, and so you'll see I'll explain our hardware in a minute, and I’ll talk about cores per node. So that's really processors CPUs per node. And so, there's usually multiple cores per processor, chip and per node. And so you need to know that architecture when you make a request to the system. And then, finally, we refer a lot to GPUs, and those are graphical processing units. So, this is a separate type of processor that does much more kind of very parallel work. We refer to it often as an accelerator because it it's really good at doing some, you know, a lot of small calculations really, quickly, and so depending on the type of work you have to do, if it can be broken up effectively to use a GPU, it can speed up your work a lot. So GPUs have become very popular in lots of different workflows. So they're a big part of super computers now.

       

      [Slide: “Memory”]

      And some of the things to keep in mind memory is the really fast storage that holds the data that is being calculated on. So in an active an active job or simulation or analysis, memory is holding the data that's being used for that analysis. And so in a supercomputer we have memory, that is, you can have shared memory, some memory that's shared across all of your processors on a single node. The memory will be shared for all the processors on that node. If you use more than one node in your calculations then you're going to have distributed memory where the know the memory on one node won't be the same as the memory on the on another node, and you have to make sure that your calculation has all the information it needs. So, there's different types of decisions you have to make about how to use the system to, you know, speed up your code as much as much as possible, taking into account the different memory that's available to you. And each core has an associated amount of memory. So, we don't require that you tell us how much memory you need you just make a node and core request, and then we give you a relative amount of memory associated with that number, of course. But I'll go into more detail with the hardware.

       

      [Slide: “Storage”]

      And for storage. So, storage is where you're, you're keeping things for a longer term. Then you would keep you keep data in memory. And so you can have storage that is, you know, active in a in an active job holding, you know, data that's already been created, or it's already been analyzed. And you just need that for your output. And then there's longer term storage, for you know different purposes as well, and I’ll go over our data storage options at OSC.

       

      [Slide: “Structure of a Supercomputer”]

      And so here is just a way to look at the supercomputer kind of covering all these concepts. So you can see the compute nodes are labeled at the bottom, and so those are the individual nodes that are network together to form the cluster. So that's the main part of the supercomputer. We have a separate type of node called the login node. That's for just kind of setting up jobs and reviewing output, but not for your main compute. And then you, as the researcher, are accessing this through some kind of network, either using a terminal program or a web portal. And then every and then the data storage options are available, you know, to access through the login nodes and the compute nodes as well.

       

      [Slide: “Hardware Overview”]

      So, any questions about general HPC things or General OSC surfaces. So, I'll go on to talk about the hardware that we have at OSC.  

       

      [Slide: “System Status”]

      So at this point, so right now we have three systems that are currently active, and that's Owens, Pitzer and Ascend, and Pitzer is really divided into two sections. The original Pitzer and Pitzer expansion. So that's what you see here. So, Owens has been around the longest, Ascend just came online at the end of last year. And so, the larger systems are Owens and Pitzer. You can see if you look at the node, count that Ascend is a lot smaller. It's more specialized. So, it's a GPU focused system. So, unless you have work that is really GPU heavy that you need, GPUs, you may not, and you may not Ascend at all. Owens and Pitzer are still our main systems. And then, so yeah, that kind of gives you the general sense of the systems. But now I’m going to talk more specifically about each of them.

       

      [Slide: “Owens Compute Nodes”]

      So on Owens, Owens has 648 standard nodes. Those are standard compute nodes, and each of those has 28 cores or processors per node, and 128 GB of memory. So that's a standard compute node on Owens

       

      [Slide: “Owens Data Analytics Nodes”]

      Owens also has 16 large memory nodes. Each of those nodes has 48 cores per node and one and a half terabytes of memory, as well as 12 TB of local disk, space or storage. And so those are, for you know the types of jobs that need just a lot of memory to, you know hold all the data that's being, you know, calculated, or to do all the analytics that needs to be done.

       

      [Slide: “Owens GPU Nodes”]

      And Owens also, in addition to the regular compute nodes, has a 160 GPU nodes. And so, these are the same as the standard compute nodes so 28 cores per node, but they also have one NVIDIA P100 GPUs on them. So, each node has one GPU.

       

      [Slide: “Owens Cluster Specifications”]

      And so here is kind of all those parts of Owens put together. And this may be hard to read. It's not very large. But you can definitely look at all of these details and more specifications on Owens on our main website. If you just go under cluster computing, and you can choose Owens. You can see all these details.

       

      [Slide: “Pitzer Cluster Specifications Original”]

      And so here is the overview for Pitzer. So this is the original part of Pitzer. And so this has 224 standard nodes, with 40 cores per node. And 192 GB of memory, and a terabyte of local storage per node. There's also 32 GPU nodes on Pitzer with the same 40 cores per node.  

      There's more memory, and there's two GPUs per node on Pitzer. So it's depending on the workload you need to you need to run. You might need, you know, two GPUs per note instead of one. And then there are four huge memory notes on Pitzer as well. Those are 80 cores per node and 3 TB of memory. So again, you know, these are for jobs that need a lot of single node parallelization. So you can use a lot of cores on one node, and you need a lot of memory.  

       

      [Slide: “Pitzer Cluster Specifications”]

      Here we go, and so Pitzer, so the expansion of Pitzer, in addition to the original Pitzer, the expansion has 340 standard nodes, and those each have 48 cores per node. And then 42 GPU nodes as well. And again, those are two GPUs per node. And there's also 12 large memory nodes on the Pitzer expansion as well. And for dense GPU nodes so for jobs that that can take advantage of, for you can use four GPUs per node we have a couple of nodes for that as well. And again, the details of this are on our website. That's where you can see all of the technical specifications for our clusters.

       

      [Slide: “Ascend Cluster Specifications”]

      And so Ascend like I said, it's the newest system. It's much smaller in in sort of node counts than Owens or Pitzer and so it's mainly focused on GPU nodes. So Ascend has 24 GPU nodes, with 88 total cores per node and 4 GPUs per node as well. So yeah, like, I said, this is GPU focused system. So, if your if your work is going to be, you know, very GPU heavy you can request access to the system, but we didn't give general access to everyone because it's not very large, and it's kind of specialized.

       

      [Slide: “Login Nodes - Usage”]

      And just to reiterate the login nodes. So, each of the systems has login nodes, and so that's when you first log into the system you're on the login nodes. And so, this is where you will set up your files, edit files, you know, get your input data and everything together to submit a job to the batch system so that you can access the compute nodes. This is not where you're going to run your jobs. There's very small limits on the login nodes as to how long any process can run, so if you start a process of some kind, it'll get stopped after 20 min. And you only have access to 1 GB of memory on the login nodes. So, they're really not for compute that you can do some small scale work, you know, like opening a graphical interface, or compiling like a very small code as long as it's really, you know not very compute intensive and won't take very long. But you don't want to use it too much, because it can slow down the login notes for everybody else. So the login nodes are mainly for setting up your jobs and looking at output, not for actually computing. And that's why we want you to use the batch system to use the compute nodes.

       

      [Slide: “Data Storage Systems”]

      So now I’m going to talk about our data storage systems. Any questions?

       

      [Slide: “File Systems at OSC”]

      So we have several file systems that OSC for different purposes. I'm going to talk about four of them. So, you can see them here on the data storage on the left. We have the home file system, the project file system, the scratch file system, and then the compute nodes. So, the storage that's available on the compute nodes. Those are the ones that I’m going to focus on.

       

      [Slide: “Research Data Storage”]

      And so the some of the features of these different file systems, the home location. So every account, so if you have an account at OSC, you'll have a location that that's your home directory, and that'll be on the home file system. And most accounts will have 500 GB storage available in the home directory. There might be some accounts that that have less, but almost all of them will have the 500 GB, and this is the main place that we expect that you can use to store your files, and we back this up regularly. So if you happen to lose something, or accidentally delete something vital, you can let us know, and we can help you restore it. So, we consider this kind of permanent protected storage. And then but if your group or your project needs more storage, then is available in each of the user accounts, then the project PI can request access to the project file system. And so this is just like a supplemental storage to the home directories. Most PIs or most groups need about one to 5 TB of storage on the project file system, and it's accessible to everybody in that project. And then there's also the scratch file system available. And this is available to everyone, you don't have to request access, so you can access it directly, and this is, we consider temporary storage. So we don't back up the scratch file system so you can use it, for you know large files that you might not want to fill your home directory up with. You can put them there if you're going to be actively using them, for you know, a couple of weeks or months, and you just want to keep them, you know, somewhere else than your Home Directory. That's what the scratch file system is for. And then on the compute nodes each compute node that you'll have access to will have its own storage. And so it's for use during your job. And so ideally, all of your compute. And you know, file creation, file, generation output, creation will happen on the compute node, and then at the end of the job you'll just copy everything back to your home directory. So you're not, you know, using the network to during your job to read and write. It just makes your job more efficient kind of reduces the overhead of that of that network usage, but you only have access to it while your job is running. So at the end of the job, you all that information is removed. So you said to make sure to copy back your results at the end of your job. We also have archive storage. So if you have some data set or database that you want to have, you know, stored for a longer period of time. They're not going to access regularly. You can talk to us. You can email OSC help and ask about that as well.

       

      [Screen: Table showing Filesystem, Quota, Network, Backed-Up?, Purged]

      And so here's just kind of an overview of the different features of the file systems. So, and I've included on the on the left. So the name of the file, the file system is home. You can use the variable dollar sign home as a reference to your home directory for the project file system. It's FSESS or FS Project, I think it's just FSESS. And then your project code to reach your project files. If you have that as a separate request the scratch file system you can reach by FS scratch, and then your project code, and then you can reference the location of the compute. Compute node storage with the TMPDIR and you can see the quotas so generally the quota for the home directory is a half terabyte. The project file system is you know amount that you choose. That's by request. We have a nominal quota of a 100 TB on the scratch file system and the compute. The compute file system varies, but it's usually at least 1 TB per node. You can see the different network speeds for the file system. So like I said, the home and the project or not very fast, the scratch file system has a faster network. So that is, you know, if you wanted to keep a large data set on the scratch file system and use it during a job. The scratch file system is more optimized for that. The home and project are backed up, scratch and compute are not. And we do have a purge on the scratch file system about every 90 days, so that is, if you have some files out there that you haven't used in a while, you know if they're you know. If they get old, they haven’t been they haven't been access for 90 days, they might be purged. We don't always purge, but when it gets full, we do, and then the compute node file system is removed when your job ends, so you only have access to it while your job is running. And again, there's links here on the bottom about where you can get more details about the file systems.

       

      [Slide: “Getting Started at OSC”]

      And I see information question in the chat. But sounds like you got the information you needed. So any other question, any questions about file systems or hardware?

       

      Olamide E Opadokun:

      Yeah. So the other file types that are backed up, for how long are they kept on the system?

       

      Kate Cahill:

      So you mean, like in the Home Directory?  

       

      Olamide E Opadokun:

      Yeah.

       

      Kate Cahill:

      So there's a couple of layers to that. So Wilbur, do you know what our current scheme is for that? I know we back it up like multiple times a day, but then we have offsite backups as well. So I think it might be up to two weeks, or maybe further.

       

      Wilbur Ouma:  

      Yeah, I don't have the correct, all the information on that. Yeah. But I know we do back up almost several times per day. Yeah, but we've had some requests people coming back that maybe they inadvertently deleted some files or data, maybe the last, you know a month or several weeks, and we've been able to recover those.  

       

      Kate Cahill:  

      Yeah, so I would certainly say that if you, if you do find that something has been deleted that you want recovered to let us know as soon as possible, because, you know, we don't keep them, you know, for months back, or anything. So you don't want it to wait too long. But at least couple of weeks, I believe.

       

      Olamide E Opadokun:  

      Okay. So they kept on the system for a couple of weeks and then deleted?

       

      Kate Cahill:  

      So the backups. So it's, you know we take. We take backups of the home directories, and we can restore things that have been deleted from a from an earlier version. And then we have offsite backups as well. So if we, if we happen to have some problem with our system and we lose power, we have versions that are stored off site as well. It's just a question of kind of like, how long those like you how far back those backups go. But yeah, so it's more about, you know. If you if you remove something and then you want it back, we can restore an earlier version of it. Once you let us know that you need it again. But on the home directory and the project directory we don't remove anything, so it's entirely up to you what's on those.

       

      Olamide E Opadokun:  

      Oh, okay, so that that's not what subjected to the long-term storage, the archive storage, because that's just always going to be available right?

       

      Kate Cahill:  

      Yeah. So the archive storage is a separate storage. So it's not like we automatically archive your home directory. That would be, you’d have to ask us to put something on the archive storage. It would be separate.

       

      Olamide E Opadokun:  

      Okay, thank you.

       

      Michael Broe:  

      So the issue, I often I advise graduate students who are working with PIs, who have. So the PI has the OSC account, and then they move away. They go to different jobs that if they go. And so then they ask me, can I get access to my data again? And I'm just would like to clarify if the PI doesn't keep this under control. How long will the data hang around, or how can they access it. If and so they've moved on from the OSU. And so, they no longer have an OSU account and they're trying to get access to data from, maybe several years ago, because their papers just been published. I know it's a big issue, a difficult issue. But I just like to clarify what is going on there.

       

      Kate Cahill:  

      Yeah. So when someone leaves OSU and is no longer active their account. So I mean, if like, if they're not, if they're not part of your group anymore, and you're not working with them. And you don't, you know you're not going to have them on your OSC account. You know their OSC account will kind of just sort of age. It doesn't get automatically removed, but it goes into a restricted state, and then it goes into an archive state, and we remove that home directory. So it's always a good idea when somebody is leaving, so like, you know, for the PI to make a backup of that of that students' information at OSC so they have access to it if they need something from an earlier project. But yeah, certainly, after a couple of years, and I don't think that we could, that we would still have the student’s home directory data available unless there was some, you know, archive process that we actually said, “Put this on an archive.” I think from our perspective it's up to the PI, the person that runs the project to, you know, make a backup of that information. So, they have it like, make it back up way from OSC.

       

      Michael Broe:  

      Yeah, or the if they believe the project is going to continue it, it's on the project. It's going to be backed up in, as long as the project exists.  

       

      Kate Cahill:  

      Right, so, if so, yeah, if the student has data in their home directory that everybody else wants to have access to for the project to continue, they should move it to the project directory. That's the shared space between all of the accounts that will stay as long as long as the OSC, the overall project is still there. So, if you have that project that shared project space for everybody in your in your group. You can, you can use that as another way to keep that that information available to everybody else. But yeah, it's definitely something that has to be kind of, there has to be a procedure when somebody leaves to make sure that that data isn't lost.

       

      Michael Broe:  

      Yes, great, that's the perfect answer. Thank you.

       

      Kate Cahill:  

      Alright great, so I’m going to start to talk about how to get started at OSC. So, this is more about getting an account and getting a project, and how we manage those things here.  

       

      [Slide: “Who can get an OSC Project?”]  

      So we have different types of projects that are available. So our main type of project is the academic project. And so that's generally led by a PI, and that person is generally a full-time faculty, member or research scientist at an Ohio academic institution. They could also. That's the main type of PI that we have at OSC for academic projects. And so the PI can request a project, and once they have that project, they can put anybody on it that they want, so they can authorize accounts for, you know, students post docs, other faculty, other their staff collectors, people from out of state people from out of the country. Anybody can have an account. But the PI has to have a certain role at an Ohio institution. Another type of project that we have is the classroom project, and so those are for specific courses. So, they're shorter-term projects that are kind of you know, specialized for giving students in a class access to OSC. We also have commercial projects available as well, so commercial organizations can purchase time at OSC as well.

       

      [Slide: “Accounts and Projects at OSC”]

      So a project we define a project code. So when you request a new project we'll define a code it becomes with a P, usually has three letters and four numbers, and that is like, I said, headed by a PI and includes any number of other users that the PI authorizes. And this is, and the project is the is how we account for computing resources. An account is a specific user so that will have a specific username and password. And that's how that that person will access OSC systems and the HPC systems. And so, an account is one person. So every person should have a unique account. You can work on more than one project, but you'll just have the one account to access all of them.  

       

      [Slide: “Usage Charges”]  

      And so we do charge for usage of our systems, and those charges are in terms of core hours, GPU hours, and terabyte months. And so, a project will have a dollar balance and any services that you use like compute and storage are charged to that balance and you know we are still subsidized by the state, so our charges are still partially subsidized, and so they're cheaper than your, you know commercial cloud resources. You can see more details on the link here. And yeah. So, if you're interested in in sort of the charges, the specific charges.

       

      [Slide: “Ohio Academic Projects”]

      So for academic projects annually, each project can receive a $1,000 grant so that can be your budget for the year, and so that that rolls over every fiscal year. So it'll be the beginning of July. You know, all academic projects will be eligible for a new $1,000 grant and so that's a way to kind of, you know, have a starting budget, and you know, get to use OSC resources, fully subsidized. If you think you're going to need more than that, then you have to add money to that budget. And so we do it this way, so that there are no unexpected charges. So you don't have some, you know, jobs that are over running, you know, or you know that somebody submits too many jobs or they're too big, and they end up charging more. The budget is a hard limit, and we also don't do proposal submissions anymore. We used to have an Allocations Committee that would review proposals, but we don't have that now, since we have this this fee model. The classroom projects that I mentioned before are fully subsidized, so they will have a budget as well. But it is not a budget that will be charged to anyone. And all of these the projects and getting an account are all available at our client portal site which is my.osc.edu.

       

      [Slide: “Client Portal- my.osc.edu”]

      And so the client portal, like I said, is mainly for project, management and account management. It's really useful for PIs to kind of oversee the projects, the activity on their projects, so you can. When you log into the client portal. If you're on a project, you'll see some statement about the usage on your projects. So, you can see it broken down by project, by type and system, by usage per day, and then below you'll see your active projects, and then you'll see your budget balance and your usage. So, it's just a way to see that information at a glance, and then you can, you know using the client portal, you can create an account. Keep your email and your password updated. Recover access to your account, if it's restricted, change your shell if you don't want to use the standard batch shell you can change to a different shell, and then you can do things like, manage your users, and request services and resources like storage and software.

       

      [Slide: “Statewide Users Group (SUG)”]  

      And so OSC, you know, has a statewide users group. So that's you know everybody that uses OSC to give you a chance to provide advice to OSC. So we can hear from the OSC community about. You know what they would like to see OSC do in future kind of where you want to see us go as far as resources or services. So this this group meets twice a year, and there's a chairperson elected yearly from the you know, Ohio Academic community generally, and we have some standing committees that meet as part of this group. So there's Software and Activities Committee and the Hardware and Operations Committee. And this is usually a day long sort of symposium that happens at OSC. But it's also a hybrid event where you can also share your research in poster sessions and Flash talks and meet other OSC researchers. And this happens twice a year, generally April and October. And you can check the OSC calendar to find out information about the next one, which is on April 20th. You can register, you know, present a poster send a flash talk, or just, you know, come and meet OSC staff and other researchers.

       

      [Slide: “Communications & Citing OSC”]

      So as far as communications we do send regular user emails, information about downtimes and any other unplanned maintenance events. We do have quarterly downtimes. We just had a downtime yesterday, so we're good for a quarter now. But we want to keep you updated. So make sure your email is is correct so you can receive those. And there's also information on our main website about citation. So if you are gone publish any work you've done with OSC resources, you can. You can cite the resource that you use

       

      [Slide: “Short Break”]

      All right, so we're going to take just like a five min break right here, so everybody can get up and move around a little bit, and we'll be back at 1:50. But does anybody have any questions? All right so I’ll be back in five minutes.  

       

      [Slide: “Short Break” beginning at about 41:35]

      All right, so I’m going to get started again. Does anybody have any questions?

       

      [Slide: “User Environment”]

      So now we're going to talk about what it's like to use the systems and some information about HPC systems and software batch system environment.

       

      [Slide: “Linux Operating System”]

      So the user environment we use. We have a Linux operating system which is the most widely used in HPC so that's really common. If you have use HPC systems before you've probably interacted with the Linux system. It generally has been a command line based. So you need to have, you know some sense of the commands that you need to enter, to do things like, you know, refiles or move files. There is a choice of shells I mentioned. So bash is the default shell. But there are other shells available. If you you know, want to work at a different shell, you have to change your shell in the client portal. And so then you'll have that environment. And this is open-source software and there's a lot of tutorials available online. We have a couple linked here under the command-line fundamentals page on our website, just as suggestions potential tutorials. It's good to have some command line, comfort like. Just know a couple of standard commands to navigate the file system, for example. Just so you're comfortable in it, but you don't necessarily need to use the command line for most of your work anymore.

       

      [Slide: “Connecting to an OSC Cluster”]

      So to connect to an OSC cluster you have a couple of options like I said, everybody connects over a network. So you're going to use some kind of, you know. But you know, network connection tool. The historical way to connect to a system is using ssh through a terminal window. So in a Mac or Linux system you'd open the terminal program, and at the prompt enter ssh and then your user ID and @.  And then the name of the sort of address of the system that you want to access. So you could access Owens it'd be owens.osc.edu and SSH. Is the command for secure shell. So you're connecting, you know, to the system through a secure shell. If you have a windows system, I believe there's a terminal program on there now, or you can download some free versions like putty is a terminal program you could use other options for connecting. So the main way that most of OSC clients, the connections, clusters these days is our on Demand portal. So that's our web portal. So you just need a you know you have a browser, and you just need to go to ondemand.osc.edu and enter your OSC user name and password, and then you have access to all the compute resources at OSC. Through the through the browser.  

       

      [Slide: “Transferring Files to and from the Cluster”]

      Another key step you generally have to take with transferring files. You know you have to take in your set up. Your research is to transfer files to and from the cluster. And so again, you have several options with the command Line tools. You can use sftp or scp, you know, in a terminal window. And so you would, you know. copy either from your local system to the cluster or the other way for smaller files. You can do that right through the login nodes so same kind of connection as the ssh, you can do owens.osc.edu. If your network is slow or your files are larger. You have another option called the file transfer server. So, instead of connecting to Owens or Pitzer directly, you would connect to sftp.osc.edu, and that just gives you access to the same file systems. But you're over a file transfer network that gives you a longer time to transfer file, so there's no time out on there. And so that helps with large files for slow networks. On the OnDemand portal. We have file management tools that include file transfer tools, so you can do a drag and drop to transfer files or use the upload and download buttons and the limit on that. It can be up to 10 GB. That's for very fast networks, so you can get, you know, fairly good size files to transfer again. It's network dependent. So you may see different outcomes depending on where you're connecting to the systems. We also have a tool called globus, and that is for large files or for large file trees. So if you want to transfer a bunch of structure, you know file structure all at once. Globus is another tool for that, and that is a web-based tool as well. It's a not an OSC tool it's a separate tool that we have an account with and you have to set it up once hyou have that it'll transfer files in the background for you and there's how to here Link on the bottom to show you how to get started using globus.

       

      [Slide: “OSC OnDemand”]

      So I see a question. Can you access the HPC resources through a terminal? If you don't have an OSU account. So you don't have to have anything to. You know we we're not. We're not a high of state focus, so it's not OSU account. You do have to have an OSC account. So you have to have an account with us at OSC, and you have to have access, you have to have a project, you know that you're a part of that will give you access to the clusters, so you can go to our client Portal, which is my.osc.edu, and you know, get, you know, just create your own OSC account. But until you're on a project you're part of a project, or you've created a project that you're a part of. You won't have cluster access until then. So those are the things you need. And so here's some more details about our on demand portal. So like I said, it's ondemand.osc.edu and you can just open a browser window, and then you just need your OSC username and password to log in you can. You can do a kind of a connection, and then use a different credential. But you still need an OSC account, so you need to know an OSC username and password. And so, once you connect through the OnDemand portal you'll see tools like file management and job management, visualization tools and virtual desktop tools and interactive job apps for different types of things like MATLAB and R and Ansys, so it's pretty comprehensive. It's also a shell window, so you can open a shell and work at the command line as well.

       

      [Slide: “Using and Running Software at OSC”]

      So now I want to talk about using software at OSC. And how you get information about it, and how you get started working with it. So any question, any other questions about environment getting logged in? All right so software at OSC.

       

      [Slide: “Software Maintained by OSC”]

      Last time I checked which maybe out of date now we had over 235 software. Packages that we maintain at OSC for for our clients. And so there's a lot of lot of options out there. And so, if there's software that you're interested in, you can always so that the first thing you should do is check if we already have it on OSC. So you can check on our main site. You can look under resources and look at available software. And you can browse just a list of all the software or the list by, you know, by cluster or by software type. Or you can just do a search for the software package you're interested in. If we have it, if we support it, we'll have a software page on it, and the software page is really going to give you all the information you need about how you know what you need to know to use the software at OSC. So this will include version information, license information, and some usage examples. So it's really key for forgetting the information to get started.

       

      [Slide: “Third party applications”]

      We have, you know, the general programming software tools, various compilers. We have some parallel profilers and debuggers. So if you're writing your own code, you can use these tools to kind of optimize it, Ansys, we have MPI libraries, we have Java, Python, R. These are some of our most popular software packages. We also have parallel specific programming software. So the MPI libraries, OpenMP, CUDA, OpenCL and OpenACC for different types of parallelism for GPU computing and things like that.

       

      [Slide: “Access to Licensed Software”]

      So what software licensing is really complicated. But we try, when we support software at OSC to get statewide licenses for academic users as kind of our you know, base level of software access. And so we try and make that, you know, kind of the goal for all of our software, some software, even with that, as the license requires that individual people who are going to use it sign a license agreement. So check the software page it will tell you the details about what the license is, and if you have to take any steps because if you have to sign a license agreement, you can use the software until you've done that and we've added you to the software group. So check the software, page to get information about the license licensing, and if there's any requests you have to make of us. And also, like I said, the software page will have details about how to use the software. So some software also requires that you like put it into your batch script that you are like checking out a license. So you know, specifics like that, you'll see on the software page

       

      [Slide: “OSC doesn’t have the software you need?”]

      If we don't support the software that you need. So if you want to use software that that we don't have installed, and we don't maintain. If it's a commercial software package, you can make a request to OSC that you think it this should be included, because you think there's a group of researchers who would use it. So it's about kind of how important it would be to you know a certain number of researchers. We can consider it and add it if it if it seems reasonable. If it's open source, software you know something that you can download yourself. You can install it in your home directory. So that's something that that you can do, so that you and your group members can use that software and we have a how to on kind of the steps that you would take to install as to in software locally, and certainly the you know, whatever software you'd want to install would probably have details that you'd have to read up on to see, you know what the steps are for installing it. And then, if you have a license to, you know, for a commercial software that we support, or you know we can install. We can help you use that license at OSC as well. So there's several options for, software and we can definitely answer any questions about. You know software usage as you as you're trying things.

       

      [Slide: “Loading Software Environment”]

      So once you know the software that you want to use. We use software modules to manage the software environments so that we can maintain the software, you know, in a specific location, make updates, add new versions without you having to change all of your paths for the you know location of that software. You can just load the software module into your environment, and then you have access to all the software executables and libraries and things. So you need to use commands like module list. We'll give you the list of software modules that you have loaded already in your environment. So there are some default ones that everybody gets to begin with, and you can always change those. But we kind of have a standard environment that works for most people. So these are like these are command line tools. But you also are going to use these in in the batch scripts that you are going to create. So you should know these. If you want to search for modules, you can do module spider, and then a keyword or module avail. And then, when you want to add software to your environment, you do module load, and then the name of the software, and if there's multiple versions, you may have to be more specific about the version of the module that you want. And you can unload. You can remove things with the module unload, and you can swap versions of software with the module swap command.

       

      [Slide: “Batch Processing”]

       So now we can talk about batch processing. Now that we have kind of all the all the pieces.  

       

      [Slide: “Why do supercomputers use queuing?”]  

      So the batch system is the main way to access the compute nodes on the clusters. And so that's kind of the main, I mean part of the system. So you need to know about the batch system so that you can get access to that computing ability. And so supercomputers use queuing so that you can provide all the information to the scheduler and the resource manager, and say, “I need this much of the system. So I need five nodes for six hours, and you know, and here's all the information about my job.” And so the system can take that information, and you know, with everybody else's requests. You end up in a queue, and once the resources are available, then your job will get access to the compute resources, and then it can run all the commands that you've included and do your analysis, and then you get your output. And OSC uses Slurm for scheduler and resource manager. If you're familiar with those so that's the tool that you should become comfortable with.  

       

      [Slide: “Steps for Running a Job on the Compute Nodes”]  

      And that's what we'll see. I'll show you an example batch script using the Slurm commands. And so here's just the steps that you'll go through to run a job to access. The compute nodes. You're going to create a batch script. You're going to prepare and gather your input files in in your home directory or your project directory. But wherever you are with your batch script, that's where your input files will be. You'll submit the job to the to the scheduler. The job will be queued. Once the resources are available, your job will run, and then your results will be copied back into your home directory when your job finishes.

       

      [Slide: “Specifying Resources in a Job Script”]

      And so the resources that you have to specify in a job script. I've mentioned them, you know, a couple of times. You need to and specify a number of nodes number of cores per node. Request GPUs, if you want GPUs, you don't have to specify memory, so memory will be relative to the number of cores your request, so it's about 4 GB of memory per core. On the standard nodes. It's different on the on the large memory nodes. But there's still a relative amount. So you don't have to request memory while time is. How long you want to have access to those compute nodes. And so you want to have enough time for your job to complete, but not too much more than that, just because you're when you're requesting more resources than you need, and it will take longer for your job to start. So you do want to overestimate slightly. So you know, if your job is going to take 12 hours. You might want to request, you know, 14 or 16, just to make sure that your job is, you know, fully completed before the wall time ends. And this is something you get used to, you know. You just keep making requests and seeing how long your job really takes, and you get better at getting that wall time, you know. Request to be pretty close to your job needs. You include your project code. So that's how we account for usage. So we need to have that project code in there. And then if there are any software licenses that you have to request. You'll see on the software page. If the license, if the software you want to use has a license request, you have to include that'll be in your job script, too.

       

      [Slide: “Sample Slurm Batch Script”]

      And so here is what a sample batch script looks like. So the lines on the top are all are all directly, you know, information to the scheduler, so Slurm has to run in in the batch shell. So we put that bash call in there at the beginning and then all the S batch lines are lines to the schedule, or, you know, these are our specific comments that are directed at the scheduler. And so this includes the wall time. So this is a one hour request number of nodes is two, and n tasks per node is 40. So Slurm uses in tasks per node for cores. So this is two nodes, 40 cores. We give the job a name so that you can recognize it in the in the queue. The account is your project code. So Slurm calls project account, and so you put your project code there and then the rest of the job script are all the commands to run your job. So we just say, you know, make sure that we're starting in the in the directory where our job was submitted. Just so, because that's where our input files should be. So that that line CD Slurm: submit the IR that's just saying, make sure I’m in this directory and then we're going to set up the software environment. So we have a module load command. Then we're going to copy our input files over to the compute node. So the copies CP is copy, hello.c is our code, and we're copying it over to the compute node. And then we're going to so then we're going to run that. We're going to compile our code and then run that that job, get our results and then copy those results. The last line is a copy results, and then back to your working directory. So these are all the commands that we go into a batch script. And so this would be, you, you know, create this as a text file and give it a name and save it.

       

      [Slide: “Submit & Manage Batch Jobs”]

      And so, once you have that ready and your input, files are ready. You're going to use this command on the top S batch, and then the name of that job script to submit. If it works and it submits correctly, then you'll see a response, and it's right here, submitted job response,  

      Slurm response, submitted batch job and you'll get a code. And that is your job ID and that's a way you can reference that job in to the queue. So if you find that you made a mistake in your job script or something, you want to cancel that job you do S cancel and then that job ID so this code here if you wanted to pause your job or hold it before it starts to wait for something else to finish you can use S control hold in the job ID, S control release job ID will release the job from hold. And then if you just want to look at the all the jobs you've submitted. You can do the SQ Command dash you, and then your user ID and that'll just show you what jobs you have in the queue at this point, and what their status is. You want to do that because that that the queue will be very, very long, and if you look at the whole thing, it won't really normally get much information out of it. So this is just kind of the very simple, simple information to get started submitting back jobs to a lot more information you could use to kind of make your jobs more complex or do more things with the batch system. We have several pages on our main website under batch processing at OSC. That have more details about all the different ways. You can use the batch jobs, and Wilbur teaches a training that is the batch system training to have more practice with the batch jobs so you can do some hands-on activities. And so that's another good option.

       

      [Slide: “Scheduling Policies and Limits”]  

      And so we do have scheduling policies and limits for our systems. And so this is just so that you know jobs don't take over the whole system, or you know. So we have limits both on wall time. So we have for a single node job a wall time limit of 168 hours. For more than one to node jobs. We have a limit of 96 hour, and then we have per user and per group limits. So with number of concurrently running jobs is limited, and the number of processor cores is limited. So if you have many, you know so several large jobs you're limited in the total number of cores you can have in use. And so we have per user and per group. This is the, these are the current limits for Owens. They're not the same from system to system. So if you are curious, you can see those details in the cluster technical specification documents. You'll see a batch limit page that'll kind of give you these details, but you shouldn't unless you or your group are running many, many jobs you probably won't hit these limits.

       

      [Slide: “Waiting for Your Job To Run”]

      So how long it takes your job to run is based on how busy the system is, and what kind of resources you request. So if the system is really busy, it'll take longer for your job to start if you request resources that are more limited, like large memory nodes or GPUs, or particular software licenses that are popular. It'll just take longer for those resources to become available. And so I’ll show you on OnDemand how you can see what the system load looks like, so you can kind of if you, if you can, you know, choose which system to use. You can look at the system, load and see which one might start sooner.

       

      [Slide: “Interactive Batch Jobs”]

      You can also do batch jobs, interactive batch jobs, where you make a request. You get access to a compute node, and you use it. Live so you can do this from the command line. You can do this through OnDemand. And so this is useful for kind of small scale testing or you know, kind of work flow development, type activities where you want to kind of do things live and see how it goes before you, you know, submit a batch job that runs on its own. And so it's the same kind of you still have to use the batch system so you're still making a request to the resource manager and scheduler number of nodes, number, of course, wall time and then you get access to a compute. No, directly you want to, you know, keep in mind that a large request will take some time to start, and you have to be there when the job starts to use the compute node, because the wall time will start running as soon as the job begins. So this is a useful tool, and OnDemand a lot of interactive tools you can use with different software packages. But this isn't really where you should be doing most of your production work. This is more for testing and trying things out.

       

      [Slide: “Batch Queues”]

      Customers have separate batch systems. So if you submit a job to Pitzer, you can't see it in the queue for Owens. So just make sure that you know which system you're submitting to. We do have some debug, some debug reservations on our clusters as well. So if you run a very short job that you just want to test some part of your work.  You can use the debug queue to run that quickly.

       

      [Slide: “Parallel Computing”]

      To use, you know the systems to get the most you know out of using the systems. You want to use multiple processors. You want to take advantage of the compute resources available. And so you know, that could be multiple cores and a single node. So you know, we have a lot of single notes that are 40 cores, 48 cores, that's a lot of processing just on a single node. That's a good place to start with parallelism to make sure that your job can take advantage of multiple cores and then you can, if you want, you can expand beyond a single core to multiple nodes. And you you're going to use, you know, different types of parallel tools for that to work. So, you have to learn more about MPI. And so, it depends on the type of work you're doing, you know, if you could take advantage of the different types of parallelism.

       

      Michael Broe:  

      [Slide: “To Take Advantage of Parallel Computing”]  

      Can I just jump in here? Go ahead. This is Michael Broe. So use showed in a Slurm script before, like number of nodes. Let's say it's one, and then in tasks equals one.

       

      [Slide: “Sample Slurm Batch Script”]

      Yeah. Those two in tasks per node equals 50. But there's another Slum option which is CPUs per task. And I don't understand how that interact with tasks per node, and what your recommended procedure is with that.

       

      Kate Cahill:  

      So I have not used that variation in Slurm. So CPUs per tasks, have you done that Wilbur?

       

      Wilbur Ouma:  

      No, I haven't, but I have an idea of what it could be doing. So by default, Slurm doesn't equate the number of tasks to be same as the number of CPU cost that we using. So there's some pipeline in which you assign one task. So in Slurm the one tasks actually changes a lot. You could be doing, if you doing an MPI process, it could be the parent task, and then you have like the child tasks, you can have one parent Slurm task that it's running other child tasks that you can say, you know, that will be using different CPUs. So, to simplify things. What you've been like always see is to equate one Slurm task by default to be like one process right? But Slurm still comes with the option of specifying CPUs. Right so, and the reason is because Slurm differentiates CPU calls or processes from tasks like being one. But you just try to simplify that and make sure that okay to make it simple. You will put one processor or one process to be equivalent to one Slurm task. So for most of the analysis that that I do carry out. I don't need to specify the number of CPU, so the like the CPU option for Slurm. I just specify the number of tasks per node or number of tasks, if I'm requesting for one node. And that will by default translate to the number of process that I want for that particular analysis. Does that answer your question, Michael?

       

      Michael Broe:  

      Yes, it does. I mean if I can ignore CPUs per task completely, I will. I just wanted to know if I was missing something. But if that's if it's a refinement, and it sounds like it's a very great refinement. It's not for this webinar, but it's good to know that what your default take on it is. So that's great. Thank you.

       

      Kate Cahill:

      [Slide: “To Take Advantage of Parallel Computing”]  

      And so yeah, when you're thinking about your parallelism. Make sure that the software you're using, or the code that you're writing is going to take advantage of multiple cores and or multiple nodes. So you want to make sure that that you know you have something that can run in parallel and that you learn about the parallel versions of software that you may already use. We have a tool called mpiexec. That's when you want to use multiple nodes and divide the work across them we use, for you know, so you can use the mpi tools it won't, miss, you know it's not necessarily going to work to just request more. No nodes or cores and it and your job will instantly run faster. You know, if you if it doesn't take advantage of those resources, it's not going to improve anything. So just keep that in mind and do some research on the tools you want to use, and how they work in parallel. So what information you need to know, to provide them so that they can work in parallel.

       

      [Slide: “New – Online Training Available!”]

      And so that is kind of everything I wanted to cover about the details about, you know, using OSC resources and then in a minute I'll switch over to a web browser and just show you OnDemand, so you can see what it looks like, but wanted to highlight a couple of things about how to get help and more information. We have some new online training resources available. So this is on ScarletCanvas. So we've got a version of ScarletCanvas from Ohio State. That is an OSC you know version of ScarletCanvas and so this is a free and available to everyone, not OSU, not Ohio State related and all you need to do is create a ScarletCanvas account, and then you can register. You can self register and go through these training courses. And so these are, you know, covers a lot of the material that I covered today, you know, in the OSC Intro, and then the batch system at OSC course we'll cover a lot of but Wilbur covers in his intro to OSC Batch. And so you can look, watch videos go through activities, do quizzes. Do some hands on, just to give you more practice, or a way to give you a reference for these services kind of get comfortable with some of the things, some of the concepts that we've talked about. And you can let us know if there's a certain, you know, certain type of training you'd like to see that we could develop for this as well. So we want to add some new things to this as we go and you can find that if you go to osc.edu, search for training. You get our training page, and you'll get the link for these courses.

       

      [Slide: “Resources to get your questions answered”]

      Other resources to get your questions answered. We have a getting started guide, so that I’ll just kind of give you information about different parts of the OSC resources that you can, you know, find information on our website. We have an FAQ that's useful to kind of check into before you, you know. Look for help elsewhere. See if see if that's already included in there. We have a lot of how to's. So these are sort of step by step, guides for doing different activities that people tend to need to do on OSC systems like installing software or installing R or Python packages or using Globus. So there's a lot of those. And then we do have office hours. So there every other Tuesday, and they're virtual so anybody can attend. We do ask you sign up in advance, so you can see them on our website on the event page. There's you know, an event for each one, but make sure you sign up in advance to reserve a time and then we do provide to some updates through the message of the day, which is when you log into our systems, you'll see a big statement, and that's the message of the day, and then we have a twitter feed called HPC notices, and that's just for system updates. So if you follow that you can get any updates we want to share about the systems.

       

      [Slide: “Key OSC Website”]

      And these are the main websites that I've talked about today. Our main page is OSC.EDU, our client Portal is MY.OSC.EDU and our web portal to access the clusters is ONDEMAND.OSC.EDU. And so any questions I’m going to switch over to the browser and open OnDemand.

       

      [Switching to Browser]

      But thank you for attending. If you, if you want to go before I start the demo go right ahead.

       

      [ondemand.osc.edu browser]

      And so I was already logged in. But you just have to log in with your you with your OSC username and password. And then you reach the OnDemand dashboard, and you can see here, here's the message of the day and so you can see some information about, you know updates on Pitzer and general updates about classroom support. Over on the right, you can see we have a separate version of OnDemand that's specific for classroom projects, and that's class.osc.edu. So if you wanted to use OSC for a class you would, we could set up that environment for your class, so it'll so little more simplified and a little more targeted to classroom type users. But also you see some efficiency reports here. So we have some monitoring tools that we use that can tell you kind of how efficient your jobs are, so you can get a sense of sort of when you run a job. Are you using all the resources that you requested, or how efficient is your request? It's just a reference, just so. You kind of have an idea and then on the top here all the different menus for OnDemand. So we have our file manager. And so this will have the different locations that you have access to, so everybody will have a home directory. And then, if you have a scratch location for one, for a project that you'll see that or a project location and you can see the different project codes. So if you have multiple projects, you'll see different locations. If you click on any of your locations and you'll see this sort of file manager open up, and so then you can navigate into your folders. You can create directories or folders.

       

      [Open OnDemand Browser showing File Page then File Example then File Page]

      You can create files. You can upload and download and just manage your files. And you can also edit files here so pick one that might be good, so you can, you know, just view the contents of a file. You can edit a file so it can open it as a file editor and make changes to the file and then save them. And then, you know work with files, you know, through this. So you don't, you don't have to go to the command line. You can use this to manage and update and edit files. And so the jobs menu. This is where the job composer is a tool for submitting jobs. So it kind of helps you manage all the parts of creating a job like getting your input files together, creating a job, a job script. The active jobs are, that's just the queue. So once you submitted a job, you can look at jobs that are running. And so over. Here are some filter options, so you can look at your jobs, you can look at all jobs and you can focus on a particular cluster.

       

      [Open OnDemand Browser Active Jobs Page]

      So if I look at all jobs on Owens, I can filter this, you know, so I have running jobs. I can look at. I can't spell. I can look at. You know jobs that are in a cued status. But one thing I wanted to show you is when your job is running, you'll be able to get some information about it while it's running. So if you click on the little arrow on the side. You'll get information about the job, so you'll see kind of the job ID. You'll see the requests this is one node 28 cores, the time limit, how long it's been running. But you also see these sort of detailed information about CPU and memory usage, so this can be useful to somebody trying out some new jobs to see, you know, if I make a request of a certain number of cores, is my job actually using all that resource. And so you can see this job is using, you know, about 20 of its CPU usage. And you know not much memory here, but you can get a sense of what your job is doing when it's using the resources. So that's a useful tool. Under the clusters menu, this is where you can open a shell window as a shell, you know terminal window, so you can, you know, use this to work in the command line. There's also a system status tool here, and this is what I mentioned.  

       

      [Open OnDemand Browser Cluster Status Page]

      If you were, you know, wanted to choose which system to use. The system status can kind of give you a sense of how busy the different clusters are, so that this one is Ascend. And so you may not, you may not have access to a send or may not need to use it, but you can see on Owens. It's about, you know, 70% full. And there's 164 jobs queued. Pitzer is partially offline right now, so even though it says it's not full. It's actually you know at full as far as what's available, so you can see that a lot more jobs are queued on Pitzer right now. So if you wanted to start a job now Owens might be a good option if you can use Owens.

       

      [Open OnDemand Browser Active Jobs Page]

      And so that's just the system status, and then the interactive apps are here. And so these are all tools that we've developed at OSC to use these different software packages for data analysis, visualization. You got Jupiter notebooks, Jupiter Lab, Jupiter with Spark and R studio.

       

      [Open OnDemand Browser RStudio Server]

      And so each of these are interactive jobs. So you're going to get access to a compute node. And so then you can, you know, use a tool that you may already be familiar with, to run on the compute nodes. Still, these are going to be fairly small scale, but it's a good way to get started. And so you just need to have information like what cluster you want to use, what version of our you want to work with. You have to put in your project code and you tell it how long you want your job to go, and then, if you want to use a specific node type, you can use a GPU node or a large memory node. But just remember, these are interactive job requests, so it's going to wait in the batch until these resources are ready. So if you, if you make a specialized request, it'll take longer, and then you can tell it number, of cores. And so when you launch this, it will once it once the job starts. So I've submitted this and so it's queued in the, you know it's waiting in the queue right now. And so once it starts I’ll open it, and it'll look like our studio, and I’ll have access to my files that are on the system, and I can, just, you know, run, run in R like I would if I was, you know, running on my laptop. But I’m using the compute resources at OSC. So this might take a while to start, because I choose Pitzer. Oh, it looks like it's starting. So it takes a minute to get started. And so now it's running, so I’ll click, connect to R studio and so that it'll just run R studio for me on Pitzer.

       

      [Webpage running R studio via Pitzer]

      And so then I, you know. So this is a good way to use the system to kind of get comfortable with running things. But again, this is not necessarily the best choice for production running. You still want to submit, you know, a job to run on the batch system kind of on its own. So you don't have to manage it directly.

       

      [Previous Open OnDemand and R Studio Browser]

      And so yeah, you can see other options over here. These are virtual desktops. So just another way to work in the system. You get a virtual Linux desktop, and then these are different graphical interfaces for different visualization and analysis tools. And Jupiter notebooks, like I said, is here. So that's really popular for classroom purposes. And that's those are the main features of OnDemand. So any questions?

       

      Michael Broe:  

      Thank you very much. That's fantastic introduction. I have a question, but it's not a newbie question. It's about quarto and python. But if I can, you know, explain why you here? I will. But I don't want to get in the way of anything you want to finish up now.

       

      Kate Cahill:  

      Sure. So I see a question. Do we have to be proficient in R to use OSC system or is the code generated automatically. So you do. I mean, if you want to use R you have to, you know, use some existing R code, or write your own. Wilbur is actually, you know, kind of one of our key R experts. But yeah, the code doesn't get generated automatically. You'd have to create some or use some existing code to do some to do some analysis with R. We do have some R tutorials in here as well. So, I don't know if you saw that when I was doing the interactive app. There is access to OSC tutorial workshop materials. And so that's just, it just gets copied into your home directory, and you can look at some R tutorial tools, so it's just example R code that you can work with. But it's pretty, general. It's just to kind of get you started.  

       

      [Previous Open OnDemand Cluster Status Webpage]

      So any other questions, if not, thank you for attending and definitely let us know if we can help at any point.

       

      Terry Miller:  

      Quick question. Are you going to make available these slides?

       

      Kate Cahill:  

      Yeah. So I I’ll send everybody who registered an email with the slides and the recording. So you can have access to that. And then, like I said, the ScarletCanvas courses cover a lot of this material, too. So it's another way, you could refer back to it, or work through it, or share it with anybody that that you think would benefit.  

       

      Terry Miller:  

      Okay, thank you. I enjoyed your presentation.

       

      Kate Cahill:  

      So any other questions? So, Michael, let's talk about Python.

       

      Michael Broe:  

      So I stuck link into the chat that shows that within R studio you can now access Python code. And I teach a course for introduction to computation and biology and most people know.

       

      OSC Custom Commands

      There are some commands that OSC has created custom versions of to be more useful to OSC users.

       

      OSCfinger

      Introduction

      OSCfinger is a command developed at OSC for use on OSC's systems and is similar to the standard finger command. It allows various account information to be viewed.

      Availability

      owens PITZER
      X

      X

       

      Usage

      OSCfinger takes the following options and parameters.

      $ OSCfinger -h
      usage: OSCfinger.py [-h] [-e] [-g] USER
      
      positional arguments:
        USER
      
      optional arguments:
        -h, --help   show this help message and exit
        -e           Extend search to include gecos/full name (user) or
                     category/institution (group)
        -g, --group  Query group instead of users
      
      Query user:
          OSCfinger foobar
      
      Query by first or last name:
          OSCfinger -e Foo
          OSCfinger -e Bar
      
      Query group:
          OSCfinger -g PZS0001
      
      Query group by category or insitituion:
          OSCfinger -e -g OSC    

       

      View information by username

      The OSCfinger command can be used to view account information given a username.

      $ OSCfinger jsmith
      Login: xxx                                   Name: John Smith
      Directory: xxx                               Shell: /bin/bash
      E-mail: xxx
      Primary Group: PPP1234
      Groups: 
      

      Project Information by Project ID

      The OSCfinger command can also reveal details about a project using the -g flag.

      $ OSCfinger -g PPP1234
      Group: PPP1234                                    GID: 1234
      Status: ACTIVE                                    Type: Academic
      Principal Investigator: xxx                       Admins: NA
      Members: xxx
      Category: NA
      Institution: OHIO SUPERCOMPUTER CENTER
      Description: xxx
      ---
      

      Search for a user via first and/or last name

      If the username is not known, a lookup can be initiated using the -e flag.

      This example is shown using the lookup for a first and last name.

      $ OSCfinger -e "John Smith"
      Login: jsmith                                     Name: John Smith
      Directory: xxx                                    Shell: /bin/bash
      E-mail: NA
      Primary Group: PPP1234
      Groups: xxx
      Password Changed: Jul 04 1776 15:47 (calculated)  Password Expires: Aug 21 1778 12:05 AM
      Login Disabled: FALSE                             Password Expired: FALSE
      ---
      

       

      One can also lookup users with only the last name:

      $ OSCfinger -e smith
      Login: jsmith                                      Name: John Smith
      Directory: xxx                                    Shell: /bin/bash
      E-mail: NA
      Primary Group: PPP1234
      Groups:
      ---
      Login: asmith                                     Name: Anne Smith
      Directory: xxx                                    Shell: /bin/bash
      E-mail: xxx
      Primary Group: xxx
      Groups: 
      ---
      

       

      Only the first name can also be used, but many accounts are likely to be returned.

      $ OSCfinger -e John
      Login: jsmith                                     Name: John Smith
      Directory: xxx                                    Shell: /bin/bash
      E-mail: xxx
      Primary Group: PPP1234
      Groups:
      ---
      Login: xxx                                        Name: John XXX
      Directory: xxx                                    Shell: /bin/bash
      E-mail: xxx
      Primary Group: xxx
      Groups:
      ---
      Login: xxx                                        Name: John XXX
      Directory: xxx                                    Shell: /bin/ksh
      E-mail: xxx
      Primary Group: xxx
      Groups:
      ---
      ...(more accounts below)...
      

      Slurm usage

      While in a slurm environment, the OSCfinger command shows some additional information:

      $ OSCfinger jsmith 
      Login: xxx Name: John Smith 
      Directory: xxx Shell: /bin/bash 
      E-mail: xxx 
      Primary Group: PPP1234 
      Groups:
      SLURM Enabled: TRUE
      SLURM Clusters: pitzer
      SLURM Accounts: PPP1234, PPP4321
      SLURM Default Account: PPPP1234
      

      It's important to note that the default account in slurm will be used if an account is not specified at job submission.

      Supercomputer: 
      Service: 

      OSCgetent

      Introduction

      OSCgetent is a command developed at OSC for use on OSC's systems and is similar to the standard getent command. It lets one view group information.

      Availability

      owens PITZER
      X

      X

       

      Usage

      OSCgetent takes the following options and parameters.

      $ OSCgetent -h
      usage: OSCgetent.py [-h] {group} [name [name ...]]
      
      positional arguments:
        {group}
        name
      
      optional arguments:
        -h, --help  show this help message and exit
      
      Query group:
          OSCgetent.py group PZS0708
      
      Query multiple groups:
          OSCgetent.py group PZS0708 PZS0709
          

      View group information

      The OSCgetent command can be used to view group(s) members:

      $ OSCgetent group PZS0712
      PZS0712:*:5513:amarcum,amarcumtest,amarcumtest2,guilfoos,hhamblin,kcahill,xwang 
      

      View information on multiple groups

      $ OSCgetent group PZS0712 PZS0708
      PZS0708:*:5509:djohnson,ewahl,kearley,kyriacou,linli,soottikkal,tdockendorf,troy
      PZS0712:*:5513:amarcum,amarcumtest,amarcumtest2,guilfoos,hhamblin,kcahill,xwang

       

      Supercomputer: 
      Service: 

      OSCprojects

      Introduction

      OSCprojects is a command developed at OSC for use on OSC's systems and is used to view your logged in accounts project information.

      Availability

      owens PITZER
      X

      X

       

      Usage

      OSCprojects does not take any arguments or options:

      $ OSCprojects
      OSC projects for user amarcumtest2:
      
      Project         Status          Members
      -------         ------          -------
      PZS0712         ACTIVE          amarcumtest2,amarcumtest,guilfoos,amarcum,xwang
      PZS0726         ACTIVE          amarcumtest2,xwangtest,amarcum
      

      This command returns the current users projects, whether those projects are active/restricted and the current members of the projects.

      Supercomputer: 
      Service: 

      OSCusage

      Introduction

      OSCusage is command developed at OSC for use on OSC's systems.  It allows for a user to see information on their project's usage, including different users and their jobs.

      Availability

      owens PITZER
      X X

       

      Usage

      OSCusage takes the following options and parameters.

      $ OSCusage --help
      usage: OSCusage.py [-h] [-u USER]
                         [-s {opt,pitzer,glenn,bale,oak,oakley,owens,ruby}] [-A]
                         [-P PROJECT] [-q] [-H] [-r] [-n] [-v]
                         [start_date] [end_date]
      
      positional arguments:
        start_date            start date (default: 2021-03-16)
        end_date              end date (default: 2021-03-17)
      
      optional arguments:
        -h, --help            show this help message and exit
        -u USER, --user USER  username to run as. Be sure to include -P or -A.
                              (default: amarcum)
        -s {opt,pitzer,glenn,bale,oak,oakley,owens,ruby}, --system {opt,pitzer,glenn,bale,oak,oakley,owens,ruby}
        -A                    Show all
        -P PROJECT, --project PROJECT
                              project to query (default: PZS0712)
        -q                    show user data
        -H                    show hours
        -r                    show raw
        -n                    show job ID
        -v                    do not summarize
        -J, --json Print data as JSON
        -C, --current-unbilled   show current unbilled usage 
        -p {month,quarter,annual}, --period {month,quarter,annual}   Period used when showing unbilled usage (default:   month)
        -N JOB_NAME, --job-name JOB_NAME
                              Filter jobs by job name, supports substring match and
                              regex (does not apply to JSON output)
      
      
      Usage Examples:
      
          Specify start time:
              OSCusage 2018-01-24
      
          Specify start and end time:
              OSCusage 2018-01-24 2018-01-25
      
          View current unbilled usage:
              OSCusage -C -p month
      
      
      

      Today's Usage

      Running OSCusage with no options or parameters specified will provide the usage information in Dollars for the current day.

      $ OSCusage
      ----------------  ------------------------------------
                        Usage Statistics for project PZS0712
      Time              2021-03-16 to 2021-03-17
      PI                guilfoos@osc.edu
      Remaining Budget  -1.15
      ----------------  ------------------------------------
      
      User          Jobs    Dollars    Status
      ------------  ------  ---------  --------
      amarcum       0       0.0        ACTIVE
      amarcumtest   0       0.0        ACTIVE
      amarcumtest2  0       0.0        ACTIVE
      guilfoos      0       0.0        ACTIVE
      hhamblin      0       0.0        ACTIVE
      kcahill       0       0.0        ACTIVE
      wouma         0       0.0        ACTIVE
      xwang         12      0.0        ACTIVE
      --            --      --
      TOTAL         12      0.0

      Usage in Timeframe

      If you specify a timeframe you can get utilization information specifically for jobs that completed within that period.

      $ OSCusage 2020-01-01 2020-07-01 -H
      ----------------  ------------------------------------
                        Usage Statistics for project PZS0712
      Time              2020-01-01 to 2020-07-01
      PI                Brian Guilfoos <guilfoos@osc.edu>
      Remaining Budget  -1.15
      ----------------  ------------------------------------
      
      User          Jobs    core-hours    Status
      ------------  ------  ------------  ----------
      amarcum       86      260.3887      ACTIVE
      amarcumtest   0       0.0           ACTIVE
      amarcumtest2  0       0.0           RESTRICTED
      guilfoos      9       29.187        ACTIVE
      hhamblin      1       1.01          ACTIVE
      kcahill       7       40.5812       ACTIVE
      wouma         63      841.2503      ACTIVE
      xwang         253     8148.2638     ACTIVE
      --            --      --
      TOTAL         419     9320.681
      

      Show only a single user's usage

      Specify -q to show only the current user's usage. This stacks with -u to specify which user you want to see.

      $ OSCusage -u xwang -q 2020-01-01 2020-07-01 -H
      ----  -------------------------------
            Usage Statistics for user xwang
      Time  2020-01-01 to 2020-07-01
      ----  -------------------------------
      
      User    Jobs    core-hours    Status
      ------  ------  ------------  --------
      xwang   253     8148.2638     -
      --      --      --
      TOTAL   253     8148.2638

      Show a particular project

      By default, the tool shows your default (first) project. You can use -P to specify which charge code to report on.

      $ OSCusage -P PZS0200 -H
      ----------------  ------------------------------------
                        Usage Statistics for project PZS0200
      Time              2020-09-13 to 2020-09-14
      PI                David Hudak <dhudak@osc.edu>
      Remaining Budget  0
      ----------------  ------------------------------------
      
      User        Jobs    core-hours    Status
      ----------  ------  ------------  ----------
      adraghi     0       0.0           ARCHIVED
      airani      0       0.0           ARCHIVED
      alingg      0       0.0           ARCHIVED

       

      You can show all of your charge codes/projects at once, by using -A .

      Select a particular cluster

      By default, all charges are shown in the output. However, you can filter to show a particular system with -s .

      $ OSCusage -s pitzer -H
      ----------------  ------------------------------------
                        Usage Statistics for project PZS0712
      Time              2021-03-16 to 2021-03-17
      PI                guilfoos@osc.edu
      Remaining Budget  -1.15
      ----------------  ------------------------------------
      
      User          Jobs    core-hours    Status
      ------------  ------  ------------  --------
      amarcum       0       0.0           ACTIVE
      amarcumtest   0       0.0           ACTIVE
      amarcumtest2  0       0.0           ACTIVE
      guilfoos      0       0.0           ACTIVE
      hhamblin      0       0.0           ACTIVE
      kcahill       0       0.0           ACTIVE
      wouma         0       0.0           ACTIVE
      xwang         0       0.0           ACTIVE
      --            --      --
      TOTAL         0       0.0

      Changing the units reported

      The report can show usage dollars. You can elect to get usage in core-hours using -H or raw seconds using -r

      $ OSCusage 2020-01-01 2020-07-01 -r
      ----------------  ------------------------------------
                        Usage Statistics for project PZS0712
      Time              2020-01-01 to 2020-07-01
      PI                Brian Guilfoos <guilfoos@osc.edu>
      Remaining Budget  -1.15
      ----------------  ------------------------------------
      
      User          Jobs    raw_used    Status
      ------------  ------  ----------  ----------
      amarcum       86      937397.0    ACTIVE
      amarcumtest   0       0.0         ACTIVE
      amarcumtest2  0       0.0         RESTRICTED
      guilfoos      9       105073.0    ACTIVE
      hhamblin      1       3636.0      ACTIVE
      kcahill       7       146092.0    ACTIVE
      wouma         63      3028500.0   ACTIVE
      xwang         253     29333749.0  ACTIVE
      --            --      --
      TOTAL         419     33554447.0
      
      
      Detailed Charges Breakdown

      Specify -v to get detailed information jobs.

      You can add the -n option to the -v option to add the job ID to the report output. OSCHelp will need the job ID to answer any questions about a particular job record.

      Please contact OSC Help with questions. 

      Supercomputer: 
      Service: 

      OSC User Code of Ethics

      The Ohio Supercomputer Center (OSC) exists to provide state-of-the-art computing services to universities and colleges; to provide supercomputer services to Ohio scientists and engineers; to stimulate unique uses of supercomputers in Ohio; to attract students, faculty, resources and industry; to catalyze inter-institutional supercomputer research and development projects; to serve as the model for other state-sponsored technology initiatives.

      OSC serves a large number and variety of users including students, faculty, staff members, and commercial clients throughout the state of Ohio.  Ethical and legal standards, in particular, that apply to the use of computing facilities are not unique to the computing field. Rather, they derive directly from standards of common sense and common decency that apply to the use of any public resource.  Indeed, OSC depends upon the spirit of mutual respect and cooperative attitudes.

      This statement on conditions of use is published in that spirit. The purpose of this statement is to promote the responsible, ethical, and secure use of OSC resources for the protection of all users.

      Authorized Use

      As a condition of use of OSC facilities, the user agrees:

      1. To respect the privacy of other users; for example, users shall not intentionally seek information on, obtain copies of, or modify files, tapes, or passwords belonging to other users unless explicitly authorized to do so by those users.
      2. To respect the legal protection provided by copyrights and licenses to programs and data; for example, users shall not make copies of a licensed computer program to avoid paying additional license fees.
      3. To respect the intended usage for which access to computing resources was granted; for example, users shall use accounts authorized for their use by the principal investigator responsible for these accounts only for the purposes specified by the principal investigator and shall not use any other user's account.
      4. To respect the integrity of computing systems; for example, users shall not intentionally develop or use programs that harass other users or infiltrate a computer or computing systems or damage or alter the software components of a computing system.
      5. To respect the financial structure of computing systems; for example, users shall not intentionally develop or use any unauthorized mechanisms to alter or avoid charges levied by OSC for computing services.
      6. To not enable other institutions or users to avoid licensing restrictions or fees by simply allowing them to use their account.
      7. To abide by software specific licensing terms and restrictions, as outlined in the specific software page or agreement.

      In addition, users are expected to report to OSC information that they may obtain concerning instances in which the above conditions have been or are being violated.

      Violations of the following conditions are certainly unethical and are possibly a criminal offense: unauthorized use of another user's account; tampering with other users' files, tapes, or passwords, harassment of other users; unauthorized alteration of computer charges; and unauthorized copying or distribution of copyrighted or licensed software or data. Therefore, when OSC becomes aware of possible violations of these conditions, it will initiate an investigation. At the same time, in order to prevent further possible unauthorized activity, OSC may suspend the authorization of computing services to the individual or account in question. In accordance with established practices, confirmation of the unauthorized use of the facilities by an individual may result in disciplinary review, expulsion from his/her university, termination of employment, and/or legal action.

      Users of computing resources should be aware that although OSC provides and preserves the security of files, account numbers, and passwords, security can be breached through actions or causes beyond reasonable control. Users are urged, therefore, to safeguard their data, to take full advantage of file security mechanisms built into the computing systems, and to change account passwords frequently.

      Appropriate Use

      Computing resources shall be used in a manner consistent with the instructional and/or research objectives of the community, in general, and consistent with the objectives of the specified project for which such use was authorized. All uses inconsistent with these objectives are considered to be inappropriate use and may jeopardize further authorization.

      Beyond the allocation of computing resources, OSC normally cannot and does not judge the value or appropriateness of any user's computing. However, the use of computing resources for playing games for purely recreational purposes, the production of output that is unrelated to the objectives of the account, and, in general, the use of computers simply to use computing resources are examples of questionable use of these resources.

      When possible inappropriate use of computing resources is encountered, OSC shall notify the principal investigator responsible. The principal investigator is expected either to take action or to indicate that such use should be considered appropriate.

      Should possible inappropriate use continue after notification of the principal investigator, or should unresolvable differences of opinion persist, these shall be brought to the attention of OSC staff for recommendations on further action.  Upon the recommendation of OSC staff, the Director may impose limitations on continued use of computing resources.

      Responsible Use

      Users are expected to use computing resources in a responsible and efficient manner consistent with the goals of the account for which the resources were approved. OSC will provide guidance to users in their efforts to achieve efficient and productive use of these resources. Novice users may not be aware of efficient and effective techniques; such users may not know how to optimize program execution; nor may such optimization necessarily lead to improved cost benefits for these users. Those who use large amounts of computing resources in production runs should attempt to optimize their programs to avoid the case where large inefficient programs deny resources to other users.

      Programming, especially in an interactive environment, involves people, computers, and systems. Efficient use of certain resources, such as computers, may lead to inefficient use of other resources, such as people. Indeed, the benefits attributed to good personal or interactive computing systems are that they speed total program development and thus lower attendant development costs even though they may require more total computer resources. Even with this understanding, however, users are expected to refrain from engaging in deliberately wasteful practices, for example, performing endless unnecessary computations.

      OSC Responsibilities

      OSC has a responsibility to provide service in the most efficient manner that best meets the needs of the total user community. At certain times the process of carrying out these responsibilities may require special actions or intervention by the staff. At all other times, OSC staff members have no special rights above and beyond those of other users. OSC shall make every effort to ensure that persons in positions of trust do not misuse computing resources or take advantage of their positions to access information not required in the performance of their duties.

      OSC prefers not to act as a disciplinary agency or to engage in policing activities. However, in cases of unauthorized, inappropriate, or irresponsible behavior the Center does reserve the right to take action, commencing with an investigation of the possible abuse. In this connection, OSC, with all due regard for the rights of privacy and other rights of users', shall have the authority to examine files, passwords, accounting information, printouts, tapes, or other material that may aid the investigation. Examination of users files must be authorized by the Director of OSC or his designee. Users, when requested, are expected to cooperate in such investigations. Failure to do so may be grounds for cancellation of access privileges.


      OSC User Code of Ethics © 2018

      Supercomputing FAQ

      General Questions

      Account Questions

      Disk Storage Questions

      Email Questions

      Linux Questions

      SSH Questions

      Batch Processing Questions

      Compiling System Questions

      Parallel Processing Questions

      Libraries/Software Questions

      Performance Analysis Questions

      Other Common Problems

      General Questions

      Who can get an account?

      Anyone can have an account with OSC, but you need access to a project to utilize our resources. If an eligible principal investigator has a current project, he/she can add the user through client protal MyOSC. Authorized users do not have to be located in Ohio or at the same institution. 

      See our webpage for more information: https://www.osc.edu/supercomputing/support/account

      Where should a new OSC user begin?

      Once you are able to connect to our HPC systems, you should start familiarizing yourself with the software and services available from the OSC, including:

      Do I have to pay for supercomputer use?

      It depends on the type of client and your rate of consumption. Please click here for more information.

      How many supercomputers does OSC have?  Which one should I use?

      OSC currently has three HPC clusters: Pitzer Cluster, a 29,664 core Dell cluster with Intel Xeon proccessors, Owens Cluster, a 23,500+ core Dell cluster with Intel Xeon processors, and Ascend Cluster with 2,304 core Dell cluster devoted to intensive GPU processing. New users have access to Pitzer and Owens clusters. To learn more,click here.

      How do I cite OSC in my publications?

      Any publication of any material, whether copyrighted or not, based on or developed with OSC services, should cite the use of OSC, and the use of the specific services (where applicable). For more information about citing OSC, please visit www.osc.edu/citation.

      How do I submit my publications and funding information to OSC?

      You can add these to your profile in MyOSC. You can then associate them with OSC project(s). 

      See our website for more information: https://www.osc.edu/supercomputing/portals/client_portal/manage_profile_information 

      Can I rceive a letter of support from OSC when I apply for outside funding?

      OSC has a standard letter of support that you can include (electronically or in hard copy) with a proposal for outside funding. This letter does not replace the budget process. To receive the letter of support, please send your request to oschelp@osc.edu. You should provide the following information: name and address of the person/organization to whom the letter should be addressed; name(s) of the principal investigator(s) and the institution(s); title of the proposal; number of years of proposed project; budget requested per year. Please allow at least two working days to process your request.

      Hardware information about the systems is available at http://www.osc.edu/supercomputing/hardware

      How do I register for a workshop?

      For a complete schedule of current training offerings, please visit the OSC Training Schedule.  To register or for more information, please email oschelp@osc.edu.  

      Where can I find documentation?

      For documentation specific to software applications, see Software.  For other available hardware, see Supercomputers.

      My question isn't answered here. Whom can I ask for help?

      Contact the OSC Help Desk. Our regular business hours are Monday - Friday, 9am - 5pm. More information on the OSC supercomputing help desk can be found on our Support Services page.

      Something seems to be wrong with the OSC systems.  Should I contact the help desk?

      Information will be coming soon for guidelines on reporting possible system problems.

      Where can I find logos for my presentations, posters, etc.?

      Please see our citation webpage.

      Account Questions

      What are projects and accounts?

      An eligible principal investigator heads a project. Under a project, authorized users have accounts with credentials that permit users to gain access to the HPC systems. A principal investigator can have more than one project. 

      How do I get/renew an account?

      For information concerning accounts (i.e., how to apply, who can apply, etc.), see Accounts.

      I'm a faculty member.  How do I get accounts for my students?

      If an eligible principal investigator is new to OSC, he/she can create a new project. If an eligible principal investigator has a current project, he/she can add the user through client protal MyOSC. Authorized users do not have to be located in Ohio or at the same institution.

      I'm continuing the research of a student who graduated.  Can I use his/her account?

      Please have your PI send an email to oschelp@osc.edu for further discussions. 

      I'm working closely with another student.  Can we share an account?

      No. Each person using the OSC systems must have his/her own account. Sharing files is possible, even with separate accounts. 

      How do I change my password?

      You can change your password through the MyOSC portal. Log in at MyOSC, and click your name in the upper right hand corner to secure a dropdown menu. Select the "change password" item. Please note that your password has certain requirements; these are specified on the "change password" portal. You may need to wait up to 20 minutes to be able to login with the new password. For security purposes, please note that our password change policy requires a password change every 180 days.

      If your password has expired, you can update by following the "Forgot your password?" link at MyOSC login page.

      I want to use csh instead of bash.  How do I change the default shell?

      You can change your default shell through the MyOSC portal. Log in at MyOSC, and use the "Unix Shell" drop-down menu in the HPC User Profile box to change your shell. You will need to log off the HPC system and log back on before the change goes into effect. Please note, that it will take about a few minutes for the changes to be applied.

      How do I find my project budget balance?

      To see usage and balance information from any system, refer to the OSCusage page.

      NOTE: Accounting is updated once a day, so the account balance is for the previous day.

      How do I get more resources?

      To request additional use of our resources, the principal investigator will need to change the budget for their project. Please see the creating budgets and projects page.

      How much will my project be charged for supercomputer usage?

      If the project is associated with an Ohio academic institution, see the academic fee structure page for pricing.

      If the project is NOT associated with an Ohio academic institution, contact OSC Sales for information on pricing.

      See Job and storage charging for how OSC calculates charges.

      Disk Storage Questions

      What is my disk quota?

      Each user has a quota of 500 gigabytes (GB) of storage and 1,000,000 files. You may also have access to a project directory with a separate quota.  See Available File Systems for more information.

      How can I determine the total disk space used by my account?

      Your quota and disk usage are displayed every time you log in. You have limits on both the amount of space you use and the number of files you have. There are separate quotas for your home directory and any project directories you have access to.

      Note: The quota information displayed at login is updated twice a day, so the information may not reflect the curent usage.

      You may display your home directory quota information with quota -s .

      How do I get more disk space?

      Your home directory quota cannot be increased. You should consider deleting, transferring, and/or compressing your files to reduce your usage. 

      A PI may request project space to be shared by all users on a project. Estimate the amount of disk space that you will need and the duration that you will need it. Send requests to oschelp@osc.edu.

      How can I find my largest directories?

      To reveal the directories in your account that are taking up the most disk space you can use the du , sort and tail commands. For example, to display the ten largest directories, change to your home directory and then run the command:

      du . | sort -n | tail -n 10
      

      Why do I receive "no space left" error when writing data to my home directory?

      If you receive the error "No space left on device" when you try to write data to your home directory, it indicates the disk is full. First, check your home directory quota. Each user has 500 GB quota of storage and the quota information is shown when you login to our systems. If your disk quota is full, consider reducing your disk space usage. If your disk quota isn't full (usage less than 500GB), it is very likely that your disk is filled up with 'snapshot' files, which are invisible to users and used to track fine-grained changes to your files for recovering lost/deleted files. In this case, please contact OSC Help for further assistance. To avoid this situation in future, consider running jobs that do a lot of disk I/O in the temporary filesystem ($TMPDIR or $PFSDIR) and copy the final output back at the end of the run. See Available File Systemsfor more information.

      How can I use tar and gzip to aggregate and compress my files?

      The commands tar and gzip can be used together to produce compressed file archives representing entire directory structures. These allow convenient packaging of entire directory contents. For example, to package a directory structure rooted at src/ use

      tar -czvf src.tar.gz src/
      

      This archive can then be unpackaged using

      tar -xzvf src.tar.gz
      

      where the resulting directory/file structure is identical to what it was initially.

      The programs zip , bzip2 and compress can also be used to create compressed file archives. See the man pages on these programs for more details.

      Tar is taking too long.  Is there a way to compress quicker?

      If using tar with the options zcvf is taking too long you can instead use pigz  in conjunction with tar.   pigz does gzip compression while taking advantage of multiple cores.

      tar cvf - paths-to-archive | pigz > archive.tgz
      

      pigz defaults to using eight cores, but you can have it use more or less with the -p argument.

      tar cvf - paths-to-archive | pigz -n 4 > archive.tgz
      
      Due to the parallel nature of pigz, if you are using it on a login node you should limit it to using 2 cores.  If you would like to use more cores you need to submit either an interactive or batch job to the queue and do the compression from within the job.

      Note: pigz does not significantly improve decompression time.  

      Email Questions

      How do I change the email address OSC uses to contact me?

      Please update your email on MyOSC, or send your new contact information to oschelp@osc.edu

      I got an automated email from OSC.  Where can I get more information about it?

      See the Knowledge Base.

      Linux Questions

      What is Linux?

      Linux is an open-source operating system that is similar to UNIX. It is widely used in High Performance Computing.

      How can I get started using Linux?

      See the Unix Basics tutorial for more information.  There are also many tutorials available on the web.

      SSH Questions

      What is SSH?

      Secure Shell (SSH) is a program to log into another computer over a network, to execute commands in a remote machine, and to move files from one machine to another. It provides strong authentication and secure communications over insecure channels. SSH provides secure X connections and secure forwarding of arbitrary TCP connections.

      How does SSH work?

      SSH works by the exchange and verification of information, using public and private keys, to identify hosts and users. The  ssh-keygen command creates a directory ~/.ssh and files that contain your authentication information. The public key is stored in ~/.ssh/id_rsa.pub and the private key is stored in  ~/.ssh/id_rsa. Share only your public key. Never share your private key. To further protect your private key you should enter a passphrase to encrypt the key when it is stored in the file system. This will prevent people from using it even if they gain access to your files. 

      One other important file is ~/.ssh/authorized_keys. Append your public keys to the authorized_keys file and keep the same copy of it on each system where you will make ssh connections. 

      In addition, on Owens the default SSH client config enables hashing of a user’s known_hosts file.  So if SSH is used on Owens the remote system’s SSH key is added to ~/.ssh/known_hosts in a hashed format which can’t be unhashed.  If the remote server’s SSH key changes, special steps must be taken to remove the SSH key entry:

      ssh-keygen -R <hostname>
      

      Can I connect without using an SSH client?

      The OSC OnDemand portal allows you to connect to our systems using your web browser, without having to install any software. You get a login shell and also the ability to transfer files.  

      How can I upload or download files?

      Most file transfers are done using sftp (SSH File Transfer Protocol) or scp (Secure CoPy). These utilities are usually provided on Linux/UNIX and Mac platforms. Windows users should read the next section, "Where can I find SSH and SFTP clients".

      Where can I find SSH and SFTP clients?

      There are many SSH and SFTP clients available, both commercial and free.  See Getting Connected for some suggestions.  

      How do I run a graphical application in an SSH session?

      Graphics are handled using the X11 protocol. You’ll need to run an X display server on your local system and also set your SSH client to forward (or "tunnel") X11 connections. On most UNIX and Linux systems, the X server will probably be running already. On a Mac or Windows system, there are several choices available, both commercial and free. See our guide to Getting Connected for some suggestions.

      Why do I get "connection refused" when trying to connect to a cluster?

      OSC temporarily blacklists some IP addresses when multiple failed logins occur. If you are connecting from behind a NAT gateway, as is commonly used for public or campus wireless networks, and get a "connection refused" message it is likely that someone recently tried to connect multiple times and failed when connected to the same network you are on. Please contact OSC Help with your public IP address and the cluster you attempted to connect to and we will remove your IP from the blacklist. You can learn your public IP by searching for "what is my IP address" in Google.

      Batch Processing Questions

      What is a batch request?

      On all OSC systems, batch processing is managed by the Simple Linux Utility for Resource Management system (Slurm). Slurm batch requests (jobs) are shell scripts that contain the same set of commands that you enter interactively. These requests may also include options for the batch system that provide timing, memory, and processor information. For more information, see our guide to Batch Processing at OSC.  

      How do I submit, check the status, and/or delete a batch job?

      Slurm uses sbatch  to submit, squeue to check the status, and scancel  to delete a batch request. For more information, see our Batch-Related Command Summary

      Can I be notified by email when my batch job starts or ends?

      Yes.  See the --mail-type  option in our Slurm docoumentation. If you are submitting a large number of jobs, this may not be a good idea.

      Why won't my job run?

      There are numerous reasons why a job might not run even though there appear to be processors and/or memory available. These include:

      • Your account may be at or near the job count or processor count limit for an individual user.
      • Your group/project may be at or near the job count or processor count limit for a group.
      • The scheduler may be trying to free enough processors to run a large parallel job.
      •  Your job may need to run longer than the time left until the start of a scheduled downtime.
      • You may have requested a scarce resource or node type, either inadvertently or by design.

      See our Scheduling Policies and Limits for more information. 

      How can I retrieve files from unexpectedly terminated jobs?

      A batch job that terminates before the script is completed can still copy files from $TMPDIR to the user's home directory via the use of signals handling. In the batch script, there should be an additional sbatch option added for --signals. See Signal handling in job scripts for details.

      If a command in a batch script is killed for excessive memory usage (see Out-of-Memory (OOM) or Excessive Memory Usage for details) then the handler may not be able to fully execute it's commands. However, normal shell scripting can handle this situation:  the exit status of a command that may possibly cause an OOM can be checked and appropriate action taken.  Here is a Bourne shell example:

      bla_bla_big_memory_using_command_that_may_cause_an_OOM
      if [ $? -ne 0 ]; then
      cd $SLURM_SUBMIT_DIR;mkdir $SLURM_JOB_ID;cp -R $TMPDIR/* $SLURM_JOB_ID
      exit
      fi
      

      Finally, if a node your job is running on crashes then the commands in the signal handler may not be executed. It may be possible to recover your files from batch-managed directories in this case. Contact OSC Help for assistance.

      How can I delete all of my jobs on a cluster?

      To delete all your jobs on one of the clusters, including those currently running, queued, and in hold, login to the cluster and run the command:

      scancel -u <username>
      

      How can I determine the number of cores in use by me or my group?

      # current jobs queued/running and cpus requested
      squeue --cluster=all --account=<proj-code> --Format=jobid,partition,name,timeLeft,timeLimit,numCPUS
      # or for a user
      squeue --cluster=all -u <username> --Format=jobid,partition,name,timeLeft,timeLimit,numCPUS
      

      How to request GPU nodes for visualization?

      By default, we don't start an X server on gpu nodes because it impacts computational performance. Add vis  in your GPU request such that the batch system uses the GPUs for visualization. For example, on Owens, it should be

      --nodes=1 --ntasks-per-node=28 --gpus-per-node=1 --gres=vis
      

      Compiling System Questions

      What languages are available?

      Fortran, C, and C++ are available on all OSC systems. The commands used to invoke the compilers and/or loaders vary from system to system. For more information, see our Compilation Guide.

      What compiler (vendor) do you recommend?

      We have Intel, PGI, and gnu compilers available on all systems. Each compiler vendor supports some options that the other doesn’t, so the choice depends on your individual needs.For more information, see our Compilation Guide.

      Will software built for one system run on another system?

      Most serial code built on one system will run on another system, although it may run more efficiently if it is built and run on the same system. Parallel (MPI) code typically must be built on the system where it will run.

      What is the difference between installing software on one's local computer and on an OSC cluster?

      One major difference is that OSC users cannot install software system wide using package managers. In general, users installing software in their home directories will follow the configure/build/test paradigm that is common on Unix-like operating systems.For more information, see our HOWTO: Locally Installing Software on an OSC cluster.

      What is this build error: "... relocation truncated to fit ..."?

      OSC users installing software on a cluster occasionally report this error. It is related to memory addressing and is usually fixed by cleaning the current build and rebuilding with the compiler option "-mcmodel=medium". For more details, see the man page for the compiler.

      Parallel Processing Questions

      What is parallel processing?

      Parallel processing is the simultaneous use of more than one computer (or processor) to solve a problem. There are many different kinds of parallel computers. They are distinguished by the kind of interconnection between processors or nodes (groups of processors) and between processors and memory.

      What parallel processing environments are available?

      On most systems, both shared-memory and distributed-memory parallel programming models can be used. Versions of OpenMP (for multithreading or shared-memory usage) and MPI (for message-passing or distributed-memory usage) are available.  A summary of parallel environments will be coming soon.

      What is a core?

      A core is a processor. When a single chip contains multiple processors, they are called cores.

      I'm not seeing the performance I expected.  How can I be sure my code is running in parallel?

      We are currently working on a guide for this. Please contact OSC Help for assistance.

      Libraries/Software Questions

      What software applications are available?

      See the Software section for more information.

      Do you have a newer version of (name your favorite software)?

      Check the Software section to see what versions are installed. You can also check the installed modules using the module spider  or module avail  command.

      How do I get authorized to use a particular software application?

      Please contact OSC Help for assistance.

      What math routines are available?  Do you have ATLAS and LAPACK?

      See the Software section for information on third-party math libraries (e.g., MKL, ACML, fftw, scalapack, etc). MKL and ACML are highly optimized libraries that include the BLAS and LAPACK plus some other math routines. 

      Do you have NumPy/SciPy?

      The NumPy and SciPy modules are installed with the python software. See the Python software page.

      OSC does not have a particular software package I would like to use. How can I request it?

      Download the Request for Software Form. Once it is complete, attach the form to an e-mail to oschelp@osc.edu

      You may install open source software yourself in your home directory. If you have your own license for commercial software, contact the OSC Help desk.

      I have a software package that must be installed as root.  What should I do?

      Most packages have a (poorly documented) option to install under a normal user account. Contact the OSC Help desk if you need assistance. We generally do not install user software as root.

      What are modules?

      Modules are used to manage the environment variable settings associated with software packages in a shell-independent way. On OSC's systems, you will by default have modules in your environment for PBS, MPI, compilers, and a few other pieces of software. For information on using the module system, see our guide to Batch Processing at OSC.

      Performance Analysis Questions

      What are MFLOPS/GFLOPS/TFLOPS/PFLOPS?

      MegaFLOPS/GigaFLOPS/TeraFLOPS/PetaFLOPS are millions/billions/trillions/quadrillions of FLoating-point Operations (calculations) Per Second.

      How do I find out about my code's performance?

      A number of performance analysis tools are available on OSC systems. Some are general to all systems and others are specific to a particular system. See our performance analysis guide for more info.

      How can I optimize my code?

      There are several ways to optimize code. Key areas to consider are CPU optimization, I/O optimization, memory optimization, and parallel optimization. See our optimization strategy guide for more info.

      Other Common Problems

      What does "CPU time limit exceeded" mean?

      Programs run on the login nodes are subject to strict CPU time limits. To run an application that takes more time, you need to create a batch request. Your batch request should include an appropriate estimate for the amount of time that your application will need. See our guide to Batch Processing at OSC for more information.

      My program or file transfer died for no reason after 20 minutes.  What happened?

      Programs run on the login nodes are subject to strict CPU time limits. Because file transfers use encryption, you may hit this limit when transferring a large file. To run longer programs, use the batch system. To transfer larger files, connect to sftp.osc.edu instead of to a login node.

      Why did my program die with a segmentation fault, address error, or signal 11?

      This is most commonly caused by trying to access an array beyond its bounds -- for example, trying to access element 15 of an array with only 10 elements. Unallocated arrays and invalid pointers are other causes. You may wish to debug your program using one of the available tools such as the TotalView Debugger.

      I created a batch script in a text editor on a Windows or Mac system, but when I submit it on an OSC system, almost every line in the script gives an error. Why is that?

      Windows and Mac have different end-of-line conventions for text files than UNIX and Linux systems do, and most UNIX shells (including the ones interpreting your batch script) don't like seeing the extra character that Windows appends to each line or the alternate character used by Mac. You can use the following commands on the Linux system to convert a text file from Windows or Mac format to UNIX format:

      dos2unix myfile.txt 
      
      mac2unix myfile.txt  
      

      I copied my output file to a Windows system, but it doesn't display correctly.  How can I fix it?

      A text file created on Linux/UNIX will usually display correctly in Wordpad but not in Notepad. You can use the following command on the Linux system to convert a text file from UNIX format to Windows format:

      unix2dos myfile.txt  
      

      What IP ranges do I need to allow in my firewall to use OSC services?

      See our knowledge base article on the topic.

      Supercomputer: 

      Supercomputing Terms

      (alphabetical listing)

      authorized users

      Authorized users include the principal investigator and secondary investigators who are part of the research team on a project. For classroom accounts, authorized users are the registered students and teaching assistants.

      authorized users, adding new ones to existing project

      To add a new authorized user to a project, the principal investigator can invite new users or add existing users through OSC client portal

      balance (budget)

      To determine your project balance (budget), please utilize MyOSC or log on to any machine and use the following command: OSCusage
      To maintain a positive balance (budget), make sure to submit new budgets using Creating projects and budgets.

      charge account

      A grouping of projects for billing purposes: a grouping for the billing at the institution level, referencing billing information, allocation of credits and discounts, and application of custom rates. 

      classroom project

      A project that allows students to learn high-performance computing or to apply high-performance computing in a particular course through applications. The budget awarded is $500 and can be renewed if needed; credits cover all costs. Please see our classroom guide for more information. 

      principal investigator

      • A full-time, permanent researcher or faculty member of an Ohio college or university.
        • Responsibilities of a principal investigator
          • Central contact and administrator of the project
          • Responsible for monitoring project balance (budget) and submitting new budget applications in a timely manner
          • Ensure the ethical use of OSC's resources by the research team

      project

      A project contains one or more research activities, which may or may not be related. Each project has a number consisting of a three- or four-letter prefix and four numbers. Principal investigators may have more than one project, but they should be aware that $1,000 annual credit can only apply to one charge account which can be applied to multiple projects.

      secondary investigators

      These are authorized users other than the principal investigator. The PI is responsible for keeping OSC updated on changes in authorized users.

      Statewide Users Group

      The Statewide Users Group comprises representatives from Ohio's colleges and universities. The members serve as an advisory body to OSC.

      support from other sources

      If your research is supported by monetary accounts from funding agencies, the Center appreciates learning of this. Such data helps the Center determine its role in Ohio's research activities.

      type of project

      The Center mainly categorizes projects as a classroom (fully subsidized) or Ohio academic ($1,000 annual grant per PI). There are other types of projects the Center may deem fit, such as commercial. 

      username

      Unique login name of a user.  Make changes to password, shell, email, project access on OSC's client portal, MyOSC (my.osc.edu). 

      Available Software

      Available Software icon

      OSC has a variety of software applications to support all aspects of scientific research. You can view the complete software list, which is being updated continually.

      Recent changes can be found by looking at the Changelog.

      OSC also offers licenses for some software packages to Ohio researchers via our statewide software program.

      Some packages are access-controlled due to license restrictions. You can find the forms necessary to request access.

      Available software by OSC System and Application

      Complete list of current software filterable by OSC system and use or field of study.

      Access Forms

      Some OSC software requires completion of a form before access can be granted.

      Statewide Software

      Statewide licensed software tools that will facilitate research.

      Software Refresh

      Information on software updates on OSC system.

      License Server Status

      Interruption details and status of the license servers.

      Browse Software

      License Server Status

      Interruption information and status of license servers are posted below. If you have any questions, please contact OSC Help .

      Current Issues

      • No active interruptions 

      Previous Issues

      • qchem academic license(license6) : unstable from 1:55pm EST July 26, 2022 Due to license software update: Stable from 2:10pm EST July 26, 2022. License software updated
      • hyperworks academic state-wide license(license6) : unstable from 1:40pm EST July 7, 2022 Due to license update: Stable from 2:15pm EST July 7, 2022. License updated
      • gurobi academic license(license6) : unstable from 9:30am EST June 30, 2022 Due to license update: Stable from 10:00am EST June 30, 2022. License updated
      • qchem academic license(license6) : unstable from 11:10am EST May 18, 2022 Due to license update: Stable from 11:30am EST May 18, 2022. License updated
      • Matlab academic license (license5) : unstable from 10:15am EST Mar 23, 2022 Due to license server update: Stable from 11:00am EST Mar 23, 2022. License server updated
      • Starccm academic license (license6) : unstable from 5:00pm EST Mar 4, 2022 Due to license server update: stable from 5:20pm EST Mar 4, 2022. License server updated
      • Starccm academic license (license6) : unstable from 10:40am EST Feb 10, 2022 Due to license update: stable from 10:50am EST Feb 10, 2022. License updated
      • Gurobi academic license (license6) : unstable from 4:40pm EST Dec 3, 2021 Due to license update: stable from 5:00pm EST Dec 3, 2021. License updated
      • Gurobi academic license (license6) : unstable from 1:35pm EST Nov 15, 2021 Due to license update: stable from 1:50pm EST Nov 15, 2021. License updated
      • Gurobi academic license (license6) : unstable from 3:30am EST Nov 3, 2021 Due to license update: stable from 3:45pm EST Nov 3, 2021. License updated
      • Hyperworks academic license (license6) : unstable from 10:15am EST Dec 31, 2020 Due to license updat: stable from 10:20am EST Dec 31, 2020. License updated
      • Abaqus academic license (license6) : unstable from 2:30pm EST Oct 26, 2020 Due to license update: stable from 2:40pm EST Oct 26, 2020. License updated
      • Hyperworks academic license (license6, state-wide) : unstable from 3:35pm EST Sep 9, 2020 Due to license update: stable from 4:00pm EST Sep 9, 2020. License updated
      • Abaqus academic license (license6) : unstable from 7:10pm EST May 16, 2020: stable from 7:50pm EST May 16, 2020. License restored
      • Comsol academic license (license6) : unstable from 1:25am EST May 16, 2020 Due to license maintenance: stable from 1:50am EST May 16, 2020. License updated
      • Intel compiler license (license5) : unstable from 12:00pm EST Mar 19, 2020 due to license update; stable from 12:20pm EST Mar 19, 2020. License updated
      • Ansys academic license (license5) : unstable from 9:50am EST Feb 28, 2020 Due to license server update: stable from 10:20am EST Feb 28, 2020. License server updated
      • ls-dyna academic license (license8) : unavailable from 1:30pm EST Oct 15, 2019 Due to the system maintenance. stable from 1:50pm EST Oct 16, 2019. system update is done. 
      • Ansys academic license (license5) : unstable from 3:55pm EST Oct 11, 2019 Due to license update: stable from 4:30pm EST Oct 11, 2019. License updated
      • matlab academic license (license5) : unstable from 4:15pm EST Sep 26, 2019 Due to license update: stable from 4:40pm EST Sep 26, 2019. License updated
      • Intel compiler license (license5) : unstable from 8:50am EST Sep 24, 2019 Due to license server update: stable from 9:10am EST Sep 24, 2019. License server updated
      • ls-dyna academic license (license8) : unavailable from 1:00pm EST Sep 12, 2019 Due to the system maintenance: stable from 2:20pm EST Sep 12, 2019. System updated
      • ArcGIS academic license (license5) : unstable from 11:10am EST Apr 3, 2019 Due to license update: stable from 11:30am EST Apr 3, 2019. License updated
      • Ansys academic license (license5) : unstable from 9:20am EST Mar 29, 2019 Due to license update: stable from 9:30am EST Mar 29, 2019. License updated
      • Intel compiler license (license5) : unstable from 10:40am EST Mar 13, 2019 Due to license update: stable from 11:10am EST Mar 13, 2019. License updated
      • Altair Hyperworks academic license (license6) : unstable from 10:15am EST Dec 27, 2018 Due to license renewal: stable from 11:15am EST Dec 17, 2018. License renewed
      • ls-dyna academic license (license5) : unavailable from 8:00am EST Oct 23, 2018 Due to the system maintenance: available from 12pm EST Oct 24, 2018. Maintenance finished
      • ArcGIS academic license (license5) : unavailable from 8:00am EST Oct 23, 2018 Due to the system maintenance: available from 4pm EST Oct 24, 2018. Maintenance finished
      • ls-dyna academic license (license5) : unavailable from 4:00pm EST Oct 18, 2018: available from 8:40pm EST Oct 18, 2018. The issue fixed.
      • Comsol academic license (license6) : unstable from 10:37am EST Oct 11, 2018 Due to license maintenance: stable from 11:30am EST Oct 11, 2018. license updated
      • Ansys academic license (license5) : unstable from 2:26pm EST Jul 18, 2018 Due to license maintenance: stable from 2:47pm EST Jul 18, 2018. license updated
      • license6 server has been rebooted between 9am to 9:10am on May 29 (Tuesday) 2018 due to the maintenance requirement. The affected software was academic abaqus, pgi, starccm, schrodinger, comsol, hyperworks, totalview and xfdtd. All the licenses are back online at 9:10am May 29, 2018.
      • StarCCM academic license (license6) : outage from 12:00am EST Nov 27, 2017 Due to license renewal: license recovered 11:30am EST Nov 30, 2017. License updated
      • Ansys academic license (license5) : unstable from 12:20pm EST Nov 8, 2017 Due to license maintenance: stable from 1:30pm EST Nov 8, 2017. license updated
      • intel academic license (license5) : unstable from 4:00pm EST Oct 13, 2017 Due to license update: stable from 4:30pm EST Oct 13, 2017. license updated
      • Starccm academic license (license6) : expecting outage from Sep 23, 2017 Due to license renewal: license recovered 08:00PM EST Sep 25, 2017
      • matlab academic license (license5) : unstable from 11:40am EST Jul 19, 2017 Due to license update: stable from 12:07pm EST Jul 19, 2017. license updated
      • intel academic license (license5) : unstable from 9:40am EST Jul 6, 2017 Due to license debug: stable from 11:00am EST Jul 6, 2017. Bug fixed
      • totalview and hyperworks academic license (license2) : unstable from 2:47pm EST Jun 26, 2017 Due to license migration: stable from Jun 28, 2017. Migration done
      • comsol academic license (license2) : unstable from 4:25pm EST May 16, 2017 Due to license maintenance: stable from 4:45pm EST May 16, 2017. New version installed
      • lstc academic license (license5) : unstable from 10:00am EST Jan 12, 2017 Due to license bug fixing: stable from 12:40pm EST Jan 12, 2017. Bug fixed
      • Ansys academic license (license2) : unstable from 10:15am EST Jan 11, 2017 Due to license maintenance: stable from 10:45am EST Jan 11, 2017. other maintenance expected
      • Altair Hyperworks academic license (license2) : stopped from 3:15am EST Dec 12, 2016 Due to license update: restarted by 3:25pm EST DEc 12, 2016: license updated
      • Intel compiler academic license (license5) : stopped from 11:20am EST Oct 27, 2016 Due to software update: restared by 11:40am EST Oct 27, 2016: software updated
      • abaqus academic license (license2) : stopped from 2:20pm EST Oct 26, 2016 Due to license renewal: restarted by 2:30pm EST Oct 26, 2016: license renewed
      • Matlab academic license (license5) : stopped from 4:10pm EST Sep 29, 2016 Due to license renewal: restored by 4:30pm EST Sep 29, 2016: license renewed.
      • starccm academic license (license2) : stopped from 2:00pm EST Sep 23, 2016 Due to license update: restored by 2:10pm EST Sep 23, 2016: license updated.
      • arcgis academic license (license3) : unstable from 3:45pm EST Aug 22, 2016 Due to troubleshooting: restored by 5:00pm EST Aug 22, 2016: Problem fixed, but test needed
      • Ansys academic license (license2) : unstable from 3:00am EST Aug 15, 2016 Due to troubleshooting: restored by 3:50pm EST Aug 15, 2016: Found another problem. Another attempt expected
      • Ansys academic license (license2) : stopped from 9:50am EST Aug 12, 2016 Due to software update: restarted on 11:10am EST Aug 12, 2016: Update failed. Another attempt expected
      • Comsol academic license (license2) : unstable from 3:20pm EST Aug 5, 2016 Due to troubleshooting: stable from 4:00pm EST Aug 5, 2016: Problem fixed
      • Comsol academic license (license2) : stopped from 11:10am EST Aug 5, 2016 Due to software update: restarted on 11:30am EST Aug 5, 2016. Update finished
      • arcGIS license: stopped from 11:20am EST Jul 21, 2016 Due to software update: restarted on 2:00pm EST Jul 21, 2016. Update finished
      • PGI statewide license: stopped from 11:20am EST Jul 20, 2016. Due to software update: restarted on 11:55am EST Jul 20, 2016. Update finished

       

       

       

      Scientific Database List

      This page provides a list of the scientific database available at OSC. 

      Supercomputer: 
      Service: 
      Fields of Science: 

      BLAST Database

       

      OSC periodically updates The NCBI BLAST database. 

      Versions

      BLAST database is available on the Owens and Pitzer clusters. The versions currently available at OSC are:

      Version Owens Pitzer
      2017-03 X  
      2017-10 X*  
      2018-08 X X*
      2019-09 X X
      2020-04 X X
      2021-5 X X
      * Current default version

      The version indicates the date of download. You can usemodule spider blast-database​ to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      BLAST database is available to all OSC users. If you have any questions, please contact OSC Help.

      Usage

      BLAST database can be accessed with the following module:

      module load blast-database/version
      

      To list all the BLAST database available

      module spider blast-database
      
      

      BLAST database can be accessed by the environmental variable BLASTDB. For blast-database/2018-08, it is as follows

      BLASTDB=/fs/project/pub_data/blast-database/2018-08

      Further Reading

      BLAST package: https://www.osc.edu/resources/available_software/software_list/blast

      Supercomputer: 
      Service: 

      Microbial Genomes Database

      Microbial Genomes is a database of prokaryotic genome sequencing project data. 

      Availability and Restrictions

      Versions

      Microbial Genomes is available on the Owens cluster. The versions currently available at OSC are:

      Version Owens
      2017-11 X*
      * Current default version

      The version indicates the date of the installation. You can use module spider microbial-database to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      Microbial Genomes is available to all OSC users. If you have any questions, please contact OSC Help.

      Usage

      Usage on Owens

      Set-up

      To configure your enviorment for use of TrimGalore, use command module load microbial-database. This will load the default version.

      The database can be accessed by the environment variable MICROBIALDB, for example

       >> ls $MICROBIALDB
      Archaea_Genome  Bacteria_Genome  Fungi_Genome  Protozoa_Genome  Virus_Genome

      Further Reading

      Supercomputer: 
      Fields of Science: 

      Software List

      Ohio Supercomputer Center (OSC) has a variety of software applications to support all aspects of scientific research. We are actively updating this documentation to ensure it matches the state of the supercomputers. This page is currently missing some content; use module spider on each system for a comprehensive list of available software.

      Supercomputer: 
      Service: 

      Abaqus

      ABAQUS is a finite element analysis program owned and supported by SIMULIA, the Dassault Systèmes brand for Realistic Simulation.

      Availability and Restrictions

      Versions

      The available programs are ABAQUS/CAE, ABAQUS/Standard and ABAQUS/Explicit. The versions currently available at OSC are:

      Version Owens Notes
      6.14 X  
      2016 X Versioning scheme was changed
      2017 X  
      2018 X  
      2020 X*  
      2021 X  
      2022 X  
      *: Default Version

      You can use  module spider abaqus to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access for Academic Users

      OSC's ABAQUS license can only be used for educational, institutional, instructional, and/or research purposes. Only users who are faculty, research staff, or students at the following institutions are permitted to utilized OSC's license:

      • The Ohio State University
      • University of Toledo
      • University of Cincinnati
      • University of Dayton
      • University of Akron
      • Miami University

      Users from additional degree granting academic institutions may request to be added to this list per a cost by contacting OSC Help.

      The use of ABAQUS for academic purposes requires validation. In order to obtain validation, please contact OSC Help for further instruction. 

      (link sends e-mail)

      Access for Commercial Users

      Contact OSC Help for getting access to ABAQUS if you are a commercial user.

      Publisher/Vendor/Repository and License Type

      Dassault Systemes, Commercial

      Usage

      Token Usage

      ABAQUS software usage is monitored though a token-based license manager. This means every time you run an ABAQUS job, tokens are checked out from our pool for your usage. To ensure your job is only started when its required ABAQUS tokens are available it is important to include a software flag within your job script's SBATCH directives.  A minimum of 5 tokens are required per job, so a 1 node, 1 processor ABAQUS job would need the following SBATCH software flag:  #SBATCH -L abaqus@osc:5 . Jobs requiring more cores will need to request more tokens as calculated with the formula:  M = int(5 x N^0.422) , where N is the total number of cores.  For common requests, you can refer to the following table:

               Cores            (nodes x cores each):

      1 2 3 4 6 8 12 16 28 32 56
      Tokens needed: 5 6 7 8 10 12 14 16 20 21 27

      Usage on Owens

      Set-up on Owens

      To load the default version of ABAQUS, use  module load abaqus . To select a particular software version, use     module load abaqus/version . For example, use  module load abaqus/2022  to load ABAQUS version 2022 on Owens. 

      Using ABAQUS

      Example input data files are available with the ABAQUS release. The  abaqus fetch  utility is used to extract these input files for use. For example, to fetch input files for one of the sample problems including 4 input files, type:

      abaqus fetch job=knee_bolster 

      abaqus fetch job=knee_bolster_ef1 

      abaqus fetch job=knee_bolster_ef2 

      abaqus fetch job=knee_bolster_ef3 

      Also, use the  abaqus help  utility to list all the abaqus execution procedures.

      Batch Usage on Owens

      When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your ABAQUS analysis to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

      Interactive Batch Session
      For an interactive batch session on Owens, one can run the following command:
      sinteractive -A <project-account> -N 1 -n 28 -t 1:00:00 -L abaqus@osc:20
      
      which gives you 28 cores ( -N 1 -n 28 ) for 1 hour ( -t 1:00:00 ). You may adjust the numbers per your need.
      Non-interactive Batch Job (Serial Run)

      batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice.

      Below is the example batch script ( job.txt ) for a serial run:

      #!/bin/bash
      #SBATCH --time=1:00:00
      #SBATCH --nodes=1 --ntasks-per-node=1
      #SBATCH -L abaqus@osc:5
      #SBATCH --account=<project-account>
      #
      # The following lines set up the ABAQUS environment
      #
      module load abaqus
      #
      cp *.inp $TMPDIR
      cd $TMPDIR
      #
      # Run ABAQUS
      #
      abaqus job=knee_bolster interactive
      #
      # Now, copy data (or move) back once the simulation has completed
      #
      cp * $SLURM_SUBMIT_DIR
      

      In order to run it via the batch system, submit the  job.txt  file with the command:  qsub job.txt 

      NOTE:

      • Make sure to copy all the files needed (input files, restart files, user subroutines, python scripts etc.) from your work directory ( $SLURM_SUBMIT_DIR ) to  $TMPDIR , and copy your results back at the end of your script. Running your job on  $TMPDIR  ensures maximum efficiency.
      • The keyword  interactive  is required in the execution line  abaqus job=knee_bolster interactive  for the following reason: If left off, ABAQUS will background the simulation process. Backgrounding a process in the OSC environment will place it outside of the batch job and it will receive the default 1 hour of CPU time and corresponding default memory limits. The keyword  interactive  in this case simply tells ABAQUS not to return until the simulation has completed.
      • The name of the input file is sometimes omitted in the execution line, which may work fine if you've copied only the input files for one specific model. However, it is better practice to designate the main input file explicitly by adding  input=<my_input_file_name>.inp  to the execution line:  abaqus job=knee_bolster input=<my_input_file_name>.inp interactive .
      • Define  nodes=1  (1<=cores<=28 for Owens) for a serial run.
      • If cores > 1, add  cpus=<n>  to the execution line, where n=cores:  abaqus job=test input=<my_input_file_name1>.inp cpus=<n> interactive .
      Non-interactive Batch Job (Parallel Run)
      Note: abaqus will not run correctly in parallel with input files in $TMPDIR!  Use the scratch file system.

      Below is an example batch script ( job.txt ) for a parallel run:

      #!/bin/bash 
      #SBATCH --time=1:00:00 
      #SBATCH --nodes=2 --ntasks-per-node=28 --gres=pfsdir
      #SBATCH -L abaqus@osc:27
      #SBATCH --account=<project-account>
      #
      # The following lines set up the ABAQUS environment
      #
      module load abaqus
      #
      # Cope input files to /fs/scratch and run Abaqus there
      #
      cp *.inp $PFSDIR
      cd $PFSDIR
      #
      # Run ABAQUS, note that in this case we have provided the names of the input files explicitly
      #
      abaqus job=test input=<my_input_file_name1>.inp cpus=$SLURM_NTASKS interactive
      #
      # Now, move data back once the simulation has completed
      #
      mv * $SLURM_SUBMIT_DIR
      

      NOTE:

      • If you request a partial node for a serial job (cores<28), you need to add 'mp_mode=threads' option in order to get the full performance.  
      • Specify  cpus=<n>  in the execution line, where n=nodes*cores.
      • Everything else is similar to the serial script above.
      • Usage of a user-defined material (UMAT) script in Fortran is limited on Owens as follows:
        1. abaqus 2017:  correctly running on single and multi-nodes
        2. abaqus 6.14 and 2016:  correctly running on a single node.

      Further Reading

       

      Supercomputer: 
      Service: 
      Fields of Science: 

      AFNI

      AFNI (Analysis of Functional Neuro Images) is a leading software suite of C, Python, and R programs and shell scripst primarily developed for the analysis and display of multiple MRI modalities: anatomical, functional MRI (FMRI) and diffusion wieghted (DW) data. It is freely available (both as open source code and as precompiled binaries) for research purposes.

      Availability and Restrictions

      Versions

      The following versions are available on OSC clusters:

      VERSION

      Pitzer
      2021.6.10 X*
      * Current default version

      You can use module spider afni to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      AFNI is available to all OSC users. If you have any questions, please contact OSC Help.

      Publisher/Vendor/Repository and License Type

      AFNI is distributed freely under the Gnu General Public License. Major portions of this software were written at the Medical College of Wisconsin, which owns the copyright to that code. For fuller details, see the file http://afni.nimh.nih.gov/pub/dist/src/README.copyright.

      Usage

      Usage on Pitzer

      Set-up

      To configure your environment for use of AFNI, run the following command: module load afni. The default version will be loaded. To select a particular AFNI version, use module load afni/version. For example, use module load afni/2021.6.10 to load AFNI 2021.6.10.

      AFNI is installed in a singularity container.  AFNI_IMG environment variable contains the container image file path. So, an example usage would be

      module load afni
      singularity exec $AFNI_IMG suma
      

      This command will open the SUMA GUI environment, and we recommend Ondemand VDI or Desktop for GUI. 

      For more information about singularity usages, please read OSC singularity page

      Further Reading

      Supercomputer: 
      Service: 
      Fields of Science: 

      AMBER

      The Assisted Model Building with Energy Refinement (AMBER) package, which includes AmberTools, contains many molecular simulation programs targeted at biomolecular systems. A wide variety of modelling techniques are available. It generally scales well on modest numbers of processors, and the GPU enabled CUDA programs are very efficient.

      Availability and Restrictions

      Versions

      AMBER is available on the Owens, Pitzer, and Ascend clusters. The following versions are currently available at OSC (S means serial executables, P means parallel, and C means CUDA, i.e., GPU enabled):

      Version Owens Pitzer Ascend Notes
      18 SPC SPC    
      19 SPC* SPC*    
      20 SPC SPC SPC  
      22 SPC SPC SPC  
      * Current default version
      *  IMPORTANT NOTE: You need to load correct compiler and MPI modules before you use Amber. In order to find out what modules you need, use module spider amber/{version} .

      You can use module spider amber to view available modules and use module spider amber/{version} to view installation details including applied Amber updates. Feel free to contact OSC Help if you need other versions or executables for your work.

      Access for Academic Users

      OSC's Amber is available to not-for-profit OSC users; simply contact OSC Help to request the appropriate form for access.

      Access for Commercial Users

      For-profit OSC users must obtain their own Amber license. 

      Publisher/Vendor/Repository and License Type

      University of California, San Francisco, Commercial

      Usage

      Usage on Owens

      Set-up

      To load the default version of AMBER module, use  module load amber . To select a particular software version, use  module load amber/version . For example, use  module load amber/16  to load AMBER version 16. 

      Using AMBER

      A serial Amber program in a short duration run can be executed interactively on the command line, e.g.:

      tleap
      

      Parallel Amber programs must be run in a batch environment with  srun, e.g.:

      srun pmemd.MPI
      

       

      Batch Usage

      When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your AMBER simulation to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

      Interactive Batch Session
      For an interactive batch session, one can run the following command:
      sinteractive -A <project-account> -N 1 -n 28 -t 1:00:00
      
      which gives you one node with 28 cores ( -N 1 -n 28 ), with 1 hour ( -t 1:00:00 ). You may adjust the numbers per your need.
      Non-interactive Batch Job (Serial Run)

      batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Sample batch scripts and Amber input files are available here:

      ~srb/workshops/compchem/amber/
      

      Below is the example batch script ( job.txt ) for a serial run:

      # AMBER Example Batch Script for the Basic Tutorial in the Amber manual
      #!/bin/bash
      #SBATCH --job-name 6pti
      #SBATCH --nodes=1 --ntasks-per-node=28
      #SBATCH --time=0:20:00
      #SBATCH --account=<project-account>
      
      module load amber
      # Use TMPDIR for best performance.
      cd $TMPDIR
      # SLURM_SUBMIT_DIR refers to the directory from which the job was submitted.
      cp -p $SLURM_SUBMIT_DIR/6pti.prmtop .
      cp -p $SLURM_SUBMIT_DIR/6pti.prmcrd .
      # Running minimization for BPTI
      cat << eof > min.in
      # 200 steps of minimization, generalized Born solvent model
      &cntrl
      maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
      /
      eof
      sander -i min.in -o 6pti.min1.out -p 6pti.prmtop -c 6pti.prmcrd -r 6pti.min1.xyz
      cp -p min.in 6pti.min1.out 6pti.min1.xyz $SLURM_SUBMIT_DIR
      

      In order to run it via the batch system, submit the  job.txt  file with the command:  sbatch job.txt

      Usage on Pitzer

      Set-up

      To load the default version of AMBER module, use  module load amber

      Using AMBER

      A serial Amber program in a short duration run can be executed interactively on the command line, e.g.:

      tleap
      

      Parallel Amber programs must be run in a batch environment with mpiexec, e.g.:

      srun pmemd.MPI
      

       

      Batch Usage

      When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your AMBER simulation to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

      Interactive Batch Session
      For an interactive batch session, one can run the following command:
      sinteractive -A <project-account> -N 1 -n 48 -t 1:00:00
      
      which gives you one node with 48 cores ( -N 1 -n 48) with 1 hour ( -t 1:00:00). You may adjust the numbers per your need.
      Non-interactive Batch Job (Serial Run)

      batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Sample batch scripts and Amber input files are available here:

      ~srb/workshops/compchem/amber/
      

      Below is the example batch script ( job.txt ) for a serial run:

      # AMBER Example Batch Script for the Basic Tutorial in the Amber manual 
      #!/bin/bash
      #SBATCH --job-name 6pti #
      SBATCH --nodes=1 --ntasks-per-node=48 
      SBATCH --time=0:20:00
      #SBATCH --account=<project-account>
      
      module load amber
      # Use TMPDIR for best performance.
      cd $TMPDIR
      # SLURM_SUBMIT_DIR refers to the directory from which the job was submitted.
      cp -p $SLURM_SUBMIT_DIR/6pti.prmtop .
      cp -p $SLURM_SUBMIT_DIR/6pti.prmcrd .
      # Running minimization for BPTI
      cat << eof > min.in
      # 200 steps of minimization, generalized Born solvent model
      &cntrl
      maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
      /
      eof
      sander -i min.in -o 6pti.min1.out -p 6pti.prmtop -c 6pti.prmcrd -r 6pti.min1.xyz
      cp -p min.in 6pti.min1.out 6pti.min1.xyz $SLURM_SUBMIT_DIR
      

      In order to run it via the batch system, submit the  job.txt  file with the command:  sbatch job.txt .

      Troubleshooting

      In general, the scientific method should be applied to usage problems.  Users should check all inputs and examine all outputs for the first signs of trouble.  When one cannot find issues with ones inputs, it is often helpful to ask fellow humans, especially labmates, to review the inputs and outputs.  Reproducibility of molecular dynamics simulations is subject to many caveats.  See page 24 of the Amber18 manual for a discussion.

      Further Reading

      Supercomputer: 
      Service: 

      ANSYS

      ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires. Supports are provided by ANSYS, Inc

      Availability and Restrictions

      Versions

      Version Owens
      17.2 X
      18.1

      X

      19.1 X
      19.2 X
      2019R1 X
      2019R2 X
      2020R1 X*
      2020R2 X
      2021R1 X
      2021R2 X
      2022R1 X
      2022R2 X
      2023R2 X
      * Current default version

      OSC has Academic Multiphysics Campus Solution license from Ansys. The license includes most of all the features that Ansys provides. See "Academic Multiphysics Campus Solution Products" in this table for all available products at OSC.

      ANSYS only works with versions 2021R1 or newer due to the license upgrade. We are working with the vendor to fix the issue now. 

      Access for Academic Users

      OSC has an "Academic Research " license for ANSYS. This allows for academic use of the software by Ohio faculty and students, with some restrictions. To view current ANSYS node restrictions, please see ANSYS's Terms of Use.

      Use of ANSYS products at OSC for academic purposes requires validation. Please contact OSC Help for further instruction.

      Access for Commercial Users

      Contact OSC Help for getting access to ANSYS if you are a commercial user.

      Publisher/Vendor/Repository and License Type

      Ansys, Inc., Commercial

      Usage

      For more information on how to use each ANSYS product at OSC systems, refer to its documentation page provided at the end of this page.

      Known Issues

      Simultaneously loading multiple of Fluent and ANSYS module cryptic error

      Due to the way our Fluent and ANSYS modules are configured, simultaneously loading multiple of either module will cause a cryptic error. The most common case of this happening is when multiple of a user's jobs are started at the same time and all load the module at once. In order for this error to manifest, the modules have to be loaded at precisely the same time; a rare occurrence, but a probable occurrence over the long term.

      If you encounter this error you are not at fault. Please resubmit the failed job(s).

      If you frequently submit large amounts of Fluent or ANSYS jobs, we recommend you stagger your job submit times to lower the chances of two jobs starting at the same time, and hence loading the module at the same time. Another solution is to establish job dependencies between jobs, so jobs will only start one after another. To do this, you would add the SLURM directive:

      #SBATCH --dependency=after:jobid
      

      To jobs you want to only start after another job has started. You would replace jobid with the job ID of the job to wait for. If you have additional questions, please contact OSC Help.

      Ansys DesignModeler with hardware acceleration

      Updated: April 2022
      Versions Affected:  < 19.1
      Ansys DesignModeler with hardware acceleration is not working. With Ansys version greater than 19.1, DesignModeler is working with software rendering mode, but it is very slow.

       

      Further Reading

      See Also

      Supercomputer: 
      Service: 

      ANSYS Mechanical

      ANSYS Mechanical is a finite element analysis (FEA) tool that enables you to analyze complex product architectures and solve difficult mechanical problems. You can use ANSYS Mechanical to simulate real world behavior of components and sub-systems, and customize it to test design variations quickly and accurately.

      Availability and Restrictions

      ANSYS Mechanical is available on the Owens Cluster. You can see the currently available versions in the table on the main Ansys page here.

      You can use module spider ansys to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access for Academic Users

      Use of ANSYS for academic purposes requires validation. In order to obtain validation, please contact OSC Help for further instruction.

      Access for Commercial Users

      Contact OSC Help for getting access to ANSYS if you are a commercial user.

      Usage

      Usage on Owens

      Set-up on Owens

      To load the default version of ANSYS module, use  module load ansys . To select a particular software version, use   module load ansys/version . For example, use  module load ansys/17.2   to load ANSYS version 17.2 on Owens. 

      Using ANSYS Mechanical

      Following a successful loading of the ANSYS module, you can access the ANSYS Mechanical commands and utility programs located in your execution path:

      ansys <switch options> <file>
      

      The ANSYS Mechanical command takes a number of Unix-style switches and parameters.

      The -j Switch

      The command accepts a -j switch. It specifies the "job id," which determines the naming of output files. The default is the name of the input file.

      The -d Switch

      The command accepts a -d switch. It specifies the device type. The value can be X11, x11, X11C, x11c, or 3D.

      The -m Switch

      The command accepts a -m switch. It specifies the amount of working storage obtained from the system. The units are megawords.

      The memory requirement for the entire execution will be approximately 5300000 words more than the -m specification. This is calculated for you if you use ansnqs to construct an NQS request.

      The -b [nolist] Switch

      The command accepts a -b switch. It specifies that no user input is expected (batch execution).

      The -s [noread] Switch

      The command accepts a -s switch. By default, the start-up file is read during an interactive session and not read during batch execution. These defaults may be changed with the -s command line argument. The noread option of the -s argument specifies that the start-up file is not to be read, even during an interactive session. Conversely, the -s argument with the -b batch argument forces the reading of the start-up file during batch execution.

      The -g [off] Switch

      The command accepts a -g switch. It specifies that the ANSYS graphical user interface started automatically.

      ANSYS Mechanical parameters

      ANSYS Mechanical parameters may be assigned values on the command. The parameter must be at least two characters long and must be a legal parameter name. The ANSYS Mechanical parameter that is to be assigned a value should be given on the command line with a preceding dash (-), a space immediately after, and the value immediately after the space:

      module load ansys
      ansys -pval1 -10.2 -EEE .1e6
      sets pval1 to -10.2 and EEE to 100000
      

      Batch Usage on Owens

      When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your ANSYS Mechanical analysis to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.  Batch jobs run on the compute nodes of the system and not on the login node. It is desirable for big problems since more resources can be used.

      Interactive Batch Session

      Interactive mode is similar to running ANSYS Mechanical on a desktop machine in that the graphical user interface will be sent from OSC and displayed on the local machine. Interactive jobs are run on compute nodes of the cluster, by turning on X11 forwarding. The intention is that users can run ANSYS Mechanical interactively for the purpose of building their model and preparing their input file. Once developed this input file can then be run in no-interactive batch mode.

      To run interactive ANSYS Mechanical, a batch job need to be submitted from the login node, to request necessary compute resources, with X11 forwarding. For example, the following command requests one whole node with 28 cores ( -N 1 -n 28  ), for a walltime of 1 hour (  -t 1:00:00 ), with one ANSYS license:

      sinteractive -N 1 -n 28 -t 1:00:00 -L ansys@osc:1,ansyspar@osc:24 -A <account>
      

      You may adjust the numbers per your need. This job will queue until resources becomes available. Once the job is started, you're automatically logged in on the compute node; and you can launch ANSYS Mechanical and start the graphic interface with the following commands:

      module load ansys
      ansys -g
      
      Non-interactive Batch Job (Serial Run)

      A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. For a given model, prepare the input file with ANSYS Mechanical commands (named  ansys.in  for example) for the batch run. Below is the example batch script (   job.txt ) for a serial run:

      #!/bin/bash
      #SBATCH --job-name=ansys_test
      #SBATCH --time=1:00:00
      #SBATCH --nodes=1 --ntasks-per-node=1
      #SBATCH -L ansys@osc:1
      #SBATCH --account=<account>
      
      cd $TMPDIR  
      cp $SLURM_SUBMIT_DIR/ansys.in .    
      module load ansys  
      ansys < ansys.in   
      cp <output files> $SLURM_SUBMIT_DIR
      

      In order to run it via the batch system, submit the  job.txt  file with the command:  qsub job.txt .

      Non-interactive Batch Job (Parallel Run)

      To take advantage of the powerful compute resources at OSC, you may choose to run distributed ANSYS Mechanical for large problems. Multiple nodes and cores can be requested to accelerate the solution time. Note that you'll need to change your batch script slightly for distributed runs.

      Starting from September 15, 2015, a job using HPC tokens (with "ansyspar" flag) should be submitted to Owens clusters due to scheduler issue.

      For distributed ANSYS Mechanical jobs, the number of processors needs to be specified in the command line with options '-dis -np':

      #!/bin/bash
      #SBATCH --job-name=ansys_test
      #SBATCH --time=1:00:00
      #SBATCH --nodes=1 --ntasks-per-node=28
      #SBATCH --account=<account>
      #SBATCH -L ansys@osc:1,ansyspar@osc:24
      
      ...
      ansys -b -dis -mpi ibmmpi -np ${SLURM_NTASKS} -i ansys.in
       
      ...
      

      Notice that in the script above, the ansys parallel license is requested as well as ansys license in the format of

      #SBATCH -L ansys@osc:1,ansyspar@osc:n
      

      where n=m-4, with m being the total cpus called for this job. This part is necessary when the total cpus called is greater than 4 (m>4), which applies for the parallel example below as well.

      The following shows changes in the batch script if 2 nodes on Owens are requested for a parallel ANSYS Mechanical job:

      #!/bin/bash
      #SBATCH --job-name=ansys_test
      #SBATCH --time=3:00:00
      #SBATCH --nodes=2 --ntasks-per-node=28
      #SBATCH -L ansys@osc:1,ansyspar@osc:52
      
      ...
      ansys -b -dis -mpi ibmmpi -np ${SLURM_NTASKS} -i ansys.in 
      ...
      pbsdcp -g '<output files>' $SLURM_SUBMIT_DIR
      

      The 'pbsdcp -g' command in the last line in the script above makes sure that all result files generated by different compute nodes are copied back to the work directory.

      Further Reading

      See Also

      Supercomputer: 
      Service: 

      CFX

      ANSYS CFX (called CFX hereafter) is a computational fluid dynamics (CFD) program for modeling fluid flow and heat transfer in a variety of applications.

      Availability and Restrictions

      CFX is available on the Owens Cluster. You can see the currently available versions in the table on the main Ansys page here.

      You can use module spider ansys  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access for Academic Users

      Use of ANSYS products for academic purposes requires validation. In order to obtain validation, please contact OSC Help for further instruction.

      Currently, there are in total 50 ANSYS base license tokens and 900 HPC tokens for academic users. These base tokens and HPC tokens are shared with all ANSYS products we have at OSC. A base license token will allow CFX to use up to 4 cores without any additional tokens. If you want to use more than 4 cores, you will need an additional "HPC" token per core. For instance, a serial CFX job with 1 core will need 1 base license token while a parallel CFX job with 28 cores will need 1 base license token and 24 HPC tokens.

      Access for Commercial Users

      Contact OSC Help for getting access to CFX if you are a commercial user.

      Usage

      Usage on Owens

      Set-up on Owens

      To load the default version, use  module load ansys  . To select a particular software version, use   module load ansys/version . For example, use  module load ansys/17.2   to load CFX version 17.2 on Owens. 

      Batch Usage on owens

      When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your analysis to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.  Batch jobs run on the compute nodes of the system and not on the login node. It is desirable for big problems since more resources can be used.

      Interactive Batch Session

      Interactive mode is similar to running CFX on a desktop machine in that the graphical user interface will be sent from OSC and displayed on the local machine. Interactive jobs are run on compute nodes of the cluster, by turning on X11 forwarding. The intention is that users can run CFX interactively for the purpose of building their model and preparing their input file. Once developed this input file can then be run in no-interactive batch mode.

      To run interactive CFX GUI, a batch job need to be submitted from the login node, to request necessary compute resources, with X11 forwarding. Please follwoing the steps below to use CFX GUI interactivly:

      1. Ensure that your SSH client software has X11 forwarding enabled
      2. Connect to Owens system
      3. Request an interactive job. The command below will request one whole node with 28 cores (  -N 1 -n 28  ), for a walltime of one hour ( -t 1:00:00 ), with one ANSYS CFD license (modify as per your own needs):
        sinteractive -N 1 -n 28 -t 1:00:00 -L ansys@osc:1,ansyspar@osc:24
      4. Once the interactive job has started, run the following commands to setup and start the CFX GUI:

        module load ansys
        cfx5 
        
      Non-interactive Batch Job (Serial Run Using 1 Base Token)

      A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice.

      Below is the example batch script (  job.txt ) for a serial run with an input file test.def ) :

      #!/bin/bash
      #SBATCH --job-name=serialjob_cfx
      #SBATCH --time=1:00:00
      #SBATCH --nodes=1 --ntasks-per-node=1
      #SBATCH -L ansys@osc:1
      
      #Set up CFX environment.
      module load ansys
      #Copy CFX files like .def to $TMPDIR and move there to execute the program
      cp test.def $TMPDIR/
      cd $TMPDIR
      #Run CFX in serial with test.def as input file
      cfx5solve -batch -def test.def 
      #Finally, copy files back to your home directory
      cp  * $SLURM_SUBMIT_DIR
      

      In order to run it via the batch system, submit the job.txt  file with the command: sbatch job.txt  

      Non-interactive Batch Job (Parallel Execution using HPC token)

      CFX can be run in parallel, but it is very important that you read the documentation in the CFX Manual on the details of how this works.

      In addition to requesting the base license token ( -L ansys@osc:1 ), you need to request copies of the ansyspar license, i.e., HPC tokens ( -L ansys@osc:1,ansyspar@osc:[n] ), where [n] is equal to the number of cores you requested minus 4.

      Parallel jobs have to be submitted on Owens via the batch system. An example of the batch script follows:

      #!/bin/bash
      #SBATCH --job-name=paralleljob_cfx
      #SBATCH --time=10:00:00
      #SBATCH --nodes=2 --ntasks-per-node=28
      #SBATCH -L ansys@osc:1,ansyspar@osc:52
      
      #Set up CFX environment.
      module load ansys
      #Copy CFX files like .def to $TMPDIR and move there to execute the program
      cp test.def $TMPDIR/
      cd $TMPDIR
      #Convert the node information into format for CFX host list
      nodes=$(srun hostname | sort | \
      uniq -c | \
      awk '{print $2 "*" $1}' | \
      paste -sd, -)
      #Run CFX in parallel with new.def as input file
      #if multiple nodes
      cfx5solve -batch -def test.def  -par-dist $nodes -start-method "Platform MPI Distributed Parallel"
      #if one node
      #cfx5solve -batch -def test.def -par-dist $nodes -start-method "Platform MPI Local Parallel"
      #Finally, copy files back to your home directory
      cp  * $SLURM_SUBMIT_DIR
      

      Further Reading

      Supercomputer: 
      Service: 

      FLUENT

      ANSYS FLUENT (called FLUENT hereafter) is a state-of-the-art computer program for modeling fluid flow and heat transfer in complex geometries.

      Availability and Restrictions

      FLUENT is available on the Owens Cluster. You can see the currently available versions in the table on the main Ansys page here.

      You can use module spider ansys  for Owens to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access for Academic Users

      Use of ANSYS products for academic purposes requires validation. In order to obtain validation, please contact OSC Help for further instruction.

      Currently, there are in total 50 ANSYS base license tokens and 900 HPC tokens for academic users. These base tokens and HPC tokens are shared with all ANSYS products we have at OSC.  A base license token will allow FLUENT to use up to 4 cores without any additional tokens. If you want to use more than 4 cores, you will need an additional "HPC" token per core. For instance, a serial FLUENT job with 1 core will need 1 base license token while a parallel FLUENT job with 28 cores will need 1 base license token and 24 HPC tokens.

      Access for Commercial Users

      Contact OSC Help for getting access to FLUENT if you are a commercial user.

      Usage

      Usage on Owens

      Set-up on Owens

      To load the default version of FLUENT module, use  module load ansys  . To select a particular software version, use   module load ansys/version . For example, use  module load ansys/17.2   to load FLUENT version 17.2 on Owens. 

      Batch Usage on Owens

      When you log into owens.osc.edu you are actually logged into a Linux box referred to as the login node. To gain access to the multiple processors in the computing environment, you must submit your FLUENT analysis to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.  Batch jobs run on the compute nodes of the system and not on the login node. It is desirable for big problems since more resources can be used.

      Interactive Batch Session

      Interactive mode is similar to running FLUENT on a desktop machine in that the graphical user interface will be sent from OSC and displayed on the local machine. Interactive jobs are run on compute nodes of the cluster, by turning on X11 forwarding. The intention is that users can run FLUENT interactively for the purpose of building their model and preparing their input file. Once developed this input file can then be run in non-interactive batch mode.

      To run interactive FLUENT GUI, a batch job need to be submitted from the login node, to request necessary compute resources, with X11 forwarding. Please following the steps below to use FLUENT GUI interactively:

      1. Ensure that your SSH client software has X11 forwarding enabled
      2. Connect to Owens system
      3. Request an interactive job. The command below will request one whole node with 28 cores (  -N 1 -n 28  ), for a walltime of one hour ( -t 1:00:00 ), with one FLUENT license (modify as per your own needs):
        sinteractive -N 1 -n 28 -t 1:00:00 -L ansys@osc:1,ansyspar@osc:24
      4. Once the interactive job has started, run the following commands to setup and start the FLUENT GUI:

        module load ansys
        fluent 
        
      Non-interactive Batch Job (Serial Run Using 1 Base Token)

      A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice.

      Below is the example batch script (  job.txt ) for a serial run with an input file run.input ) on Owens:

      #!/bin/bash
      #SBATCH --job-name=serial_fluent
      #SBATCH --time=1:00:00
      #SBATCH --nodes=1 --ntasks-per-node=1
      #SBATCH -L ansys@osc:1
      #
      # The following lines set up the FLUENT environment
      #
      module load ansys
      #
      # Copy files to $TMPDIR and move there to execute the program
      #
      cp test_input_file.cas test_input_file.dat run.input $TMPDIR
      cd $TMPDIR
      #
      # Run fluent
      fluent 3d -g < run.input  
      #
      # Where the file 'run.input' contains the commands you would normally
      # type in at the Fluent command prompt.
      # Finally, copy files back to your home directory
      cp *   $SLURM_SUBMIT_DIR 
      

      As an example, your run.input file might contain:

      file/read-case-data test_input_file.cas 
      solve/iterate 100
      file/write-case-data test_result.cas
      file/confirm-overwrite yes    
      exit  
      yes  
      

      In order to run it via the batch system, submit the job.txt  file with the command: sbatch job.txt  

      Non-interactive Batch Job (Parallel Execution using HPC token)

      FLUENT can be run in parallel, but it is very important that you read the documentation in the FLUENT Manual on the details of how this works.

      In addition to requesting the FLUENT base license token ( -L ansys@osc:1 ), you need to request copies of the ansyspar license, i.e., HPC tokens ( -L ansys@osc:1,ansyspar@osc:[n] ), where [n] is equal to the number of cores you requested minus 4.

      Parallel jobs have to be submitted to Owens via the batch system. An example of the batch script follows:

      #!/bin/bash
      #SBATCH --job-name=parallel_fluent
      #SBATCH --time=3:00:00
      #SBATCH --nodes=2 --ntasks-per-node=28
      #SBATCH -L ansys@osc:1,ansyspar@osc:52
      set echo on   
      hostname   
      #   
      # The following lines set up the FLUENT environment   
      #   
      module load ansys
      #      
      # Create the config file for socket communication library   
      #   
      # Create list of nodes to launch job on   
      rm -f pnodes   
      cat  $PBS_NODEFILE | sort > pnodes   
      export ncpus=`cat pnodes | wc -l`   
      #   
      #   Run fluent   
      fluent 3d -t$ncpus -pinfiniband.ofed -cnf=pnodes -g < run.input 
      

      Further Reading

      See Also

      Supercomputer: 
      Service: 

      Workbench Platform

      ANSYS Workbench platform is the backbone for delivering a comprehensive and integrated simulation system to users. See ANSYS Workbench platform for more information. 

      Availability and Restrictions

      ANSYS Workbench is available on Owens Cluster. You can see the currently available versions in the table on the main Ansys page here.

      You can use module spider ansys  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access for Academic Users

      Use of ANSYS products for academic purposes requires validation. In order to obtain validation, please contact OSC Help for further instruction.

      Access for Commercial Users

      Contact OSC Help for getting access to ANSYS if you are a commercial user.

      Usage

      Usage on Owens

      Set-up for Structural-Fluid dynamics related applications

      To load the default version , use  module load ansys . To select a particular software version, use   module load ansys/version . For example, use  module load ansys/17.2   to load version 17.2 on Owens. After the module is loaded, use the following command to open Workbench GUI:

      runwb2
      

      Set-up for CFD related applications

      To load the default version , use  module load ansys  . To select a particular software version, use   module load ansys/version   . For example, use  module load ansys/17.2   to load version 17.2 on Owens. After the module is loaded, use the following command to open Workbench GUI:

      runwb2
      

      Further Reading

      See Also

      Supercomputer: 
      Service: 

      ARM HPC tools

      ARM HPC tools analyze how HPC software runs. It consists of three applications, ARM DDT, ARM Performance Reports and ARM MAP: 

      • ARM DDT: graphical debugger for HPC applications.
      • ARM MAP: HPC application profiler with easy-to-use GUI environment.
      • ARM Performance Reports: simple tool to generate a single-page HTML or plain text report that presents overall performance characteristics of HPC applications.

       

      NOTE: Because ARM has aquired Allinea, all Allinea module files have been renamed accordingly. Allinea modules are still available and have same functionality as new ARM modules.
      NOTE [June 29, 2022]: As ARM reported security vulnerabilities on the old ARM Forge versions prior to 22.0.x, we have removed the old versions and installed 22.0.2 version.

      Availability & Restrictions

      Versions

      The following versions of ARM HPC tools are available on OSC clusters:

      Version Owens Pitzer
      22.0.2 X* X*
      * Current default version

      You can use module spider arm to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      ARM DDT, MAP and Performance Reports are available to all OSC users.

      Publisher/Vendor/Repository and License Type

      ARM, Commercial

      Usage

      ARM DDT

      ARM DDT is a debugger for HPC software that automatically alerts users of memory bugs and divergent behavior. For more features and benefits, visit ARM HPC tools and libraries - DDT.

      For usage instructions and more iformation, read ARM DDT.

      ARM MAP

      ARM MAP produces a detailed profile of HPC software. Unlike ARM Performance Reports, you must have the source code to run ARM MAP because its analysis details the software line-by-line. For more features and benefits, visit ARM HPC tools and libraries - MAP

      For usage instructions and more information, read ARM MAP.

      ARM Performance Reports

      ARM Performance Reports analyzes and documents information on CPU, MPI, I/O, and Memory performance characteristics of HPC software, even third party code, to aid understanding about the overall performance. Although it should not be used all the time, ARM Performance Reports is recommended to OSC users as a viable option to analyze how an HPC application runs. View an example report to navigate the format of a typical report. For more example reports, features and benefits, visit ARM HPC tools and libraries - Performance Reports.

      For usage instructions and more information, read ARM Performance Reports.

      Troubleshooting

      Using ARM software with MVAPICH2

      This note from ARM's Getting Started Guide applies to both perf-report and MAP:

      Some MPIs, most notably MVAPICH, are not yet supported by ARM's Express Launch mode
      (in which you can just put “perf-report” in front of an existing mpirun/mpiexec line). These can
      still be measured using the Compatibility Launch mode.

      Instead of this Express Launch command:

      perf-report mpiexec <mpi args> <program> <program args> # BAD
      

      Use the compatibility launch version instead:

      perf-report -n <num procs> --mpiargs="<mpi args>" <program> <program args>
      

      Further Reading

      See Also

      Documentation Attachment: 
      Supercomputer: 
      Service: 
      Fields of Science: 

      ARM Performance Reports

      ARM Performance Reports is a simple tool used to generate a single-page HTML or plain text report that presents the overall performance characteristics of HPC applications. It supports pthreads, OpenMP, or MPI code on CPU, GPU, and MIC based architectures.

      Availability and Restrictions

      Versions

      The versions currently available at OSC are:

      Version Owens Pitzer
      22.0.2 X* X*
      * Current default version

      You can use module spider arm-pr to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      ARM Performance Reports is available to all OSC users. We have 64 seats with 64 HPC tokens. Users can monitor the license status here.

      Publisher/Vendor and License Type

      ARM, Commercial

      Usage

      Set-up

      To load the module for the ARM Performance Reports default version, use module load arm-pr. To select a particular software version, use module load arm-pr/version. For example, use module load arm-pr/6.0 to load ARM Performance Reports version 6.0, provided the version is available on the OSC cluster in use.

      Using ARM Performance Reports

      You can use your regular executables to generate performance reports. The program can be used to analyze third-party code as well as code you develop yourself. Performance reports are normally generated in a batch job.

      To generate a performance report for an MPI program:

      module load arm-pr
      perf-report -np <num procs> --mpiargs="<mpi args>" <program> <program args>
      

      where <num procs> is the number of MPI processes to use, <mpi args> represents arguments to be passed to mpiexec (other than -n or -np), <program> is the executable to be run and <program args> represents arguments passed to your program.

      For example, if you normally run your program with mpiexec -n 12 wave_c, you would use

      perf-report -np 12 wave_c
      

      To generate a performance report for a non-MPI program:

      module load arm-pr
      perf-report --no-mpi <program> <program args>
      

      The performance report is created in both html and plain text formats. The file names are based on the executable name, number of processes, date and time, for example,  wave_c_12p_2016-02-05_12-46.html. To open the report in html format use

      firefox wave_c_12p_2016-02-05_12-46.html
      

      For more details, download the ARM Performance Reports User Guide.

      Performance Reports with GPU

      ARM Performance Reports can be used for CUDA codes. If you have an executable compiled with the CUDA library, you can launch ARM Performance Reports with

      perf-report {executable}
      

      For more information, please read the section 6.10 of the ARM Performance Reports User Guide.

      Further Reading

      See Also

      Documentation Attachment: 
      Supercomputer: 
      Service: 

      ARM MAP

      ARM MAP is a full scale profiler for HPC programs. We recommend using ARM MAP after reviewing reports from ARM Performance Reports. MAP supports pthreads, OpenMP, and MPI software on CPU, GPU, and MIC based architectures.

      Availability & Restrictions

      Versions

      The ARM MAP versions currently available at OSC are:

      Version Owens Pitzer
      22.0.2 X* X*
      * Current default version

      You can use module spider arm-map to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      ARM MAP is available to all OSC users. We have 64 seats with 80 HPC tokens. Users can monitor the ARM License Server Status.

      Publisher/Vendor and License Type

      ARM, Commercial

      Usage

      Set-up

      To load the default version of the ARM MAP module, use module load arm-map. To select a particular software version, use module load arm-map/version. For example, use module load arm-map/6.0 to load ARM MAP version 6.0, provided the version is available on the cluster in use. 

      Note: Before you run MAP from the command line for the first time, open MAP as a GUI from OnDemand to configure with appropriate settings for your environment.

      Using ARM MAP

      Profiling HPC software with ARM MAP typically involves three steps: 

      1. Prepare the executable for profiling.

      Regular executables can be profiled with ARM MAP, but source code line detail will not be available. You need executables with debugging information to view source code line detail: re-compile your code with a -g  option added among the other appropriate compiler options. For example:

      mpicc wave.c -o wave -g -O3
      

      This executable built with the debug flag can be used for ARM Performance Reports as well.

      Note: The -g flag turns off all optimizations by default. For profiling your code you should use the same optimizations as your regular executable, so explicitly include the -On flag, where n is your normal level of optimization, typically -O2 or -O3, as well as any other compiler optimization options.

      2. Run your code to produce the profile data file (.map file).

      Profiles are normally generated in a batch job.  To generate a MAP profile for an MPI program:

      module load arm-map
      map --profile -np <num proc> --mpiargs="<mpi args>" <program> <program args>

      where <num procs> is the number of MPI processes to use, <mpi args> represents arguments to be passed to srun (other than -n), <program> is the executable to be run and <program args> represents arguments passed to your program.

      For example, if you normally run your program with mpiexec -n 12 wave_c, you would use

      map --profile -np 12 wave_c

      To profile a non-MPI program:

      module load arm-map
      map --profile --no-mpi <program> <program args>

      The profile data is saved in a .map file in your current directory.

      As a result of this step, a .map file that is the profile data file is created in your current directory. The file name is based on the executable name, number of processes, date and time, for example, wave_c_12p_2016-02-05_12-46.map.

      For more details on using ARM MAP, refer to the ARM Forge User Guide.

      3. Analyze the profile data file using either the ARM local client or the MAP GUI.

      You can open the profile data file using a client running on your local desktop computer. For client installation and usage instructions, please refer to the section: Client Download and Setup. This option typically offers the best performance.

      Alternatively, you can run MAP in interactive mode, which launches the graphical user interface (GUI).  For example:

      map wave_c_12p_2016-02-05_12-46.map

      For the GUI application, one should use an OnDemand VDI (Virtual Desktop Interface) or have X11 forwarding enabled (see Setting up X Windows). Note that X11 forwarding can be distractingly slow for interactive applications.

      MAP with GPU

      ARM MAP can be used for CUDA codes. If you have an executable compiled with the CUDA library, you can launch ARM MAP with

      map {executable}
      

      For more information, please read the Chapter 15 of the ARM Forge User Guide.

      Client Download and Setup

      1. Download the client.

      To download the client, go to the ARM website and choose the appropriate ARM Forge remote client download for Windows, Mac, or Linux. For Windows and Mac, just double click on the downloaded file and allow the installer to run. For Linux, extract the tar file using the command tar -xf file_name and run the installer in the extracted file directory with ./installer. Please contact OSC Help, if you have any issues on downloading the client.

      2. Configure the client.

      After installation, you can configure the client as follows:

      • Open the client program. For Windows or Mac, just click the desktop icon or navigate to the application through its file path. For Linux use the command {arm-forge-path}/bin/map.

      • Once the program is launched, select ARM MAP in the left column.
      • In the Remote Launch drop down menu, select "Configure...".
      • Click Add to create a new profile for your login.
      • In the Host Name section, type your ssh connection. For example: "username@ruby.osc.edu".
      • For Remote Installation Directory, type /usr/local/arm/forge-{version}, specifying the ARM Forge version number that created the data profile file you are attempting to view. For example, /usr/local/arm/forge-7.0 for ARM Forge version 7.0.
      • You can test your login information by clicking Test Remote Launch. It will ask your password. Use the same password for the cluster login.
      • Close the Configure window. You will see a new option under the Remote Launch drop down menu for the host name you entered. Select your profile and login with your password. 
      • If the login was successful, then you should see License Serial:XXX in the bottom left corner of the window.

      This login configuration is needed only for the first time of use. In subsequent times, you can just select your profile.

      3. Open the profile data file.

      After login, click on LOAD PROFILE DATA FILE. This opens a file browser of your home directory on the OSC cluster you logged onto. Go to the directory that contains the .map file and select it. This will open the file and allow you to navigate the source code line-by-line and investigate the performance characteristics. 

      A license is not required to simply open the client, so it is possible to skip 2. Configure the client, if you download the profile data file to your desktop. You can then open it by just selecting LOAD PROFILE DATA FILE and navigating through a file browser on your local system.

      Note that the client is ARM Forge, a client that contains ARM MAP and ARM DDT. ARM DDT is a debugger, and OSC has license only for ARM MAP. If you need a debugger, you can use Totalview instead.

      Further Reading

      See Also

      Documentation Attachment: 
      Supercomputer: 
      Service: 
      Fields of Science: 

      ARM DDT

      Arm DDT is a graphical debugger for HPC applications. It supports pthreads, OpenMP, or MPI code on CPU, GPU, and MIC based architectures.

      Availability & Restrictions

      Versions

      The Arm DDT versions currently available at OSC are:

      Version Owens Pitzer
      22.0.2 X* X*
      * Current default version

      You can use module spider arm-ddt to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      Arm DDT is available to all OSC users. We have 64 seats with 80 HPC tokens. Users can monitor the Arm License Server Status.

      Publisher/Vendor and License Type

      ARM, Commercial

      Usage

      Set-up

      To load the module for the Arm DDT default version, use module load arm-ddt. To select a particular software version, use module load arm-ddt/version. For example, use module load arm-ddt/7.0 to load Arm DDT version 7.0, provided the version is available on the OSC cluster in use.

      Note: Before you run DDT from the command line for the first time, open DDT as a GUI from OnDemand to configure with appropriate settings for your environment.

      Using Arm DDT

      DDT debugs executables to generate DDT reports. The program can be used to debug third-party code as well as code you develop yourself. DDT reports are normally generated in a batch job.

      To generate a DDT report for an MPI program:

      module load arm-ddt
      ddt --offline -np <num procs> --mpiargs="<mpi args>" <program> <program args>
      

      where <num procs> is the number of MPI processes to use, <mpi args> represents arguments to be passed to mpiexec (other than -n or -np), <program> is the executable to be run and <program args> represents arguments passed to your program.

      For example, if you normally run your program with mpiexec -n 12 wave_c, you would use

      ddt --offline -np 12 wave_c
      

      To debug a non-MPI program:

      module load arm-ddt
      ddt --offline --no-mpi <program> <program args>
      

      The DDT report is created in html format. The file names are based on the executable name, number of processes, date and time, for example, wave_c_12p_2016-02-05_12-46.html. To open the report use

      firefox wave_c_12p_2016-02-05_12-46.html
      

      Using the Arm DDT GUI

      To debug with the DDT GUI remove the --offline option. For example, to debug the MPI program above, use

      ddt -np 12 wave_c

      For a non-MPI program:

      ddt --no-mpi <program> <program args>

      This will open the DDT GUI, enabling interactive debugging options.

      For the GUI application, one should use an OnDemand VDI (Virtual Desktop Interface) or have X11 forwarding enabled (see Setting up X Windows). Note that X11 forwarding can be distractingly slow for interactive applications.

      For more details, see the Arm DDT developer page.

      DDT with GPU

      DDT can be used for CUDA codes. If you have an executable compiled with the CUDA library, you can launch Arm Performance Reports with

      ddt {executable}
      

      For more information, please read the chapter 14 of the Arm Forge User Guide.

      Supercomputer: 

      AlphaFold

      AlphaFold is a software package that provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and pusblished in Nature.

      Availability and Restrictions

      Versions

      Version Pitzer Ascend Model Parameters
      2.0.0 X   2021-07-14
      2.1.0 X   2021-10-27
      2.1.2 X*   2022-01-19
      2.2.2 X X* 2022-03-02; Multimer model weights: v2
      2.3.1 X X 2022-12-06; Multimer model weights: v3
      2.3.2 X X 2022-12-06; Multimer model weights: v3
      * Current default version

      You can use module spider alphafold to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      AlphaFold is available for all OSC users

      Publisher/Vendor/Repository and License Type

      Copyright 2021 DeepMind Technologies Limited

      Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at https://www.apache.org/licenses/LICENSE-2.0. Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See hte License for the specific language governing permissions and limitations under the License. See the License for specific langauge governing permissions and limitations under the License.

      The AlphaFold parameters are made available for non-commercial use only, under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) license. You can find details at: https://creativecommons.org/licenses/by-nc/4.0/legalcode.

      Usage

      Usage on Pitzer

      Set-up

      To load the default version of AlphaFold module, use module load alphafold.

      Batch Usage

      Below is the example batch script (job.txt) for an alphafold job:

      #!/bin/bash
      #SBATCH --ntasks=8
      #SBATCH --gpus-per-node=1
      #SBATCH --gpu_cmode=shared
      
      
      module reset
      module load alphafold/2.1.2
      
      run_alphafold.sh --use_gpu_relax=True --db_preset=reduced_dbs --fasta_paths=rcs_pdb_6VR4.fasta --max_template_date=2020-05-14 --output_dir=$(pwd -P)/output
      

      The control options and presets for model and database:

      Option Preset Note
      --model_preset monomer
      monomer_casp14
      monomer_ptm
      multimer
      Control which AlphaFold model to run
      --db_preset full_dbs
      reduced_dbs

      Control MSA speed/quality tradeoff

      To get full-options list

      run_alphafold.sh --helpshort

      For very large simulations use multiple GPUs and to make sure a job can access all the GPU memory, set this before run_alphafold.sh with alphafold/2.2.2:

      export TF_FORCE_UNIFIED_MEMORY=1
      run_alphafold.sh ...

      Note also that not all models are parallelized over multiple GPUs; see https://github.com/deepmind/alphafold/issues/30

      Use custom AlphaFold

      From 2.1.2 to 2.2.2, you can use own copy of AlphaFold code with our pre-installed packages and database. For example, you download a copy of AlphaFold 2.2.2 in $HOME/alphafold and make some changes. Modify the ALPHAFOLD_HOME variable before calling run_alphafold.sh, e.g.

      module reset
      module load alphafold/2.2.2
      
      export ALPHAFOLD_HOME=$HOME/alphafold
      run_alphafold.sh --db_preset=reduced_dbs --fasta_paths=rcs_pdb_6VR4.fasta --max_template_date=2020-05-14 --output_dir=$(pwd -P)/output
      

      Batch Usage (2.0.0)

      Below is the example batch script (job.txt) for an alphafold job:

      #!/bin/bash
      #SBATCH --ntasks=8
      #SBATCH --gpus-per-node=2
      
      module reset
      module load alphafold/2.0.0
      
      run_alphafold.sh --preset=reduced_dbs --fasta_paths=rcs_pdb_6VR4.fasta --max_template_date=2020-05-14 --output_dir=$(pwd -P)/output
      

      Other available job options are:

      --preset=recued_dbs, --preset=full_dbs, or --preset=casp14
      

       

      Further Reading

      Online documentation is available on the AlphaFold homepage.

      Notes on AlphaFold output.

      Notes on citing AlphaFold.

      Tag: 
      Supercomputer: 
      Service: 
      Fields of Science: 

      Altair HyperWorks

      HyperWorks is a high-performance, comprehensive toolbox of CAE software for engineering design and simulation.

      Availability & Restrictions

      Versions

      The following version of Altair Hyperworks can be found for the following environments:

      Version Owens
      13 X
      2017.1 X
      2019.2 X*
      2020.0 X
      * Current Default Version

      You can use module spider hyperworks to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      HyperWorks is available to all academic clients. Please contact OSC Help to request the appropriate form for access.

      Publisher/Vendor/Repository and License Type

      Altair Engineering, Commercial (state-wide)

      Usage

      Using HyperWorks through OSC installation

      To use HyperWorks on the OSC clusters, first ensure that X11 forwarding is enabled as the HyperWorks workbench is a graphical application. Then, load the hyperworks module:

      module load hyperworks
      

      The HyperWorks GUI can be launched then with the following command:

      hw
      

      The Hypermesh GUI can be launched then with the following command:

      hm

      State-wide access for HyperWorks

      For information on downloading and installing a local copy through the state-wide license, follow the steps below. The versions of HyperWorks available statewide differ from the versions available at OSC on the Owens cluster. To check for the available statewide versions, complete steps 1 through 5 below.

      NOTE: To run Altair HyperWorks, your computer must have access to the internet. The software contacts the license server at OSC to check out a license when it starts and periodically during execution. The amount of data transferred is small, so network connections over modems are acceptable.

       

      Usage of HyperWorks on a local machine using the statewide license will vary from installation to installation.

      1. Go to https://altairone.com/home

      2. If you have already registered with the Altair website, click on "Sign In" in the upper right hand corner of the page, enter the e-mail address that you registered with and your password and skip to step #4. Otherwise click the "Sign Up" button instead and continue with step #3.

      3. You will be prompted for some contact information and an e-mail address which will be your unique identifier.

        • IMPORTANT: The e-mail address you give must be from your academic institution. Under the statewide license agreement, registration from Ohio universities is allowed on the Altair web site. Trying to log in with a yahoo or hotmail e-mail account will not work. If you enter your university e-mail and the system will not register you, please contact OSChelp at oschelp@osc.edu.

      4. Once you have logged in, go back to the home page and click on the button labeled "Altair Marketplace", where you can then press the button "Browse the Marketplace" which takes you to the Marketplace page.

      5. From here, you can search for the app you would like to use, in this case you're looking for the one listed as "HyperWorks" which you can search for in the search bar at the upper left corner of the Marketplace page.

      6. To download, you just need to press the "Download" button that appears in the side window that pops up after selecting the HyperWorks application from the marketplace page. From there you need to select the version you'd like and the target operating system for which it will run on. Then press the button that looks like an arrow point down at a "U" (aka Download symbol). In addition to downloading the software, download the "Installation Guide and Release Notes" for instructions on how to install the software.

        • NOTE: If you are a student and you click on the HyperWorks application in the marketplace, after creating an account and logging in, but see a "Try Now" button instead of a "Download" button then you may have not been added to the university account correctly (A known issue). To remedy this, please email support@altair.com with your name plus email, and ask the support team to update the account permissions so you can download the software.

        • IMPORTANT: If you have any questions or problems, please contact OSChelp at oschelp@osc.edu, rather than HyperWorks support. The software agreements outlines that problems should first be sent to OSC. If the OSC support line cannot answer or resolve the question, they have the ability to raise the problem to Altair support. If you have any general questions, or are looking for answers to frequently asked questions, you can check the Community Forums page for possible answers or help. But if you have problems, make sure to extend them to OSC first as stated above.

      7. Please contact OSC Help for further instruction and license server information. In order to be added to the allowed list for the state-wide software access, we will need your IP address/range of machine that will be running this software. 

      8. You need to set an environment variable (ALTAIR_LICENSE_PATH) on your local machine to point at our license server (7790@license6.osc.edu). See this link for instructions if necessary.

      Further Reading

      For more information about HyperWorks, see the following:

      See Also

      Supercomputer: 
      Service: 
      Fields of Science: 

      Apptainer/Singularity

      Apptainer/Singularity is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.

      From the Docker website: "A container image is a lightweight, stand-alone, executable package of a piece of software that includes everything needed to run it: code, runtime, system tools, system libraries, settings."

      On June 21th, 2022, Singularity is replaced with Apptainer, which is just a renamed open-source project to avoid conflicts with SingularityCE so it can be accepted into the Linux Foundation. Apptainer 1.0 has the same code as Singularity after versions 3.8.x, and still provides the command singularity (apptainer is the official command). Thus, user should continue running containers on OSC systems without any issue: 

      1. Containers built with Apptainer will continue to work with installations of Singularity.
      2. User will see warnings about SINGULARITY_ and SINGULARITYENV_ environment variables.
          A future version of Apptainer may stop supporting environment variable compatibility so we recommned
          users to add respective APPTAINER_ and APPTAINERENV_ counterparts in their job environments.

      For more detail, pleae visit the Singularity Compatibility page.

      If you experience issues using Singularity after downtime, please contact OSC help.

      Availability and Restrictions

      Versions

      Apptainer/Singularity is available on all OSC clusters. Only one version is available at any given time. To find out the current version:

      singularity version
      

      Check the release page for the changelog: https://github.com/apptainer/apptainer/releases

      Access

      Apptainer/Singularity is available to all OSC users.

      Publisher/Vendor/Repository and License Type

      Apptainer project, established as Apptainer a Series of LF Projects LLC; 3-clause BSD License

      Usage

      Set-up

      No setup is required. You can use Apptainer/Singularity directly on all clusters.

      Using Singularity

      See HOWTO: Use Docker and Singularity Containers at OSC for information about using Apptainer/Singularity on all OSC clusters, including some site-specific caveats.  

      Example:  Run a container from the Singularity hub

      [owens-login01]$ singularity run shub://singularityhub/hello-world
      INFO:    Downloading library image
      Tacotacotaco
      
      If unsure about the amount of memory that a singularity process will require, then be sure to request an entire node for the job. It is common for singularity jobs to be killed by the OOM killer because of using too much RAM.


      Known Issues

      Reached your pull rate limit

      Update: 06/16/2021 
      Version: all

      You might encounter an error while pulling a large Docker image:

      ERROR: toomanyrequests: Too Many Requests.
      

      or

      You have reached your pull rate limit. You may increase the limit by authenticating and upgrading: https://www.docker.com/increase-rate-limits.

      On November 20, 2020, Docker Hub puts rate limits on anonymous and free authenticated pull requests. The rate limits for anonymous and authenticated pulls are 100 per 6 hours and 200 per 6 hours, respectively. Anonymous users have limits enforced via IP. Since all computing nodes at OSC share the same IP, anonymous pull rate limit is shared by all OSC users if you are not authenticated. 

      If you encounter this error and want to get rid of it, please consider setting up authenticated access to  Docker Hub: https://apptainer.org/docs/user/main/endpoint.html?highlight=endpoint#ma....

       

      Failed to pull a large Docker image

      Update: 05/21/2019 
      Version: all

      You might encounter an error while pulling a large Docker image:

      [owens-login01]$ singularity pull docker://qimme2/core
      FATAL: Unable to pull docker://qiime2/core While running mksquashfs: signal: killed

      The process could be killed because the image is cached in the home directory which is a slower file system or the image size might exceed a single file size limit.

      The solution is to use other file systems like /fs/ess/scratch and $TMPDIR for caches and temp files to build the squashfs filesystem:

      [owens-login01]$ sinteractive -n 1 -A PAS1234 
      bash-4.2$ export APPTAINER_CACHEDIR=$TMPDIR
      bash-4.2$ export APPTAINER_TMPDIR=$TMPDIR 
      bash-4.2$ singularity pull docker://qiime2/core:2019.1
      INFO:    Converting OCI blobs to SIF format
      INFO:    Starting build...
      ...
      INFO:    Creating SIF file...
      bash-4.2$ exit
      

      Failed to run a container directly or pull an image from Singularity or Docker hub

      Update: 03/08/2019 
      Version: all

      You might encounter an error while run a container directly from a hub:

      [owens-login01]$ singularity run shub://vsoch/hello-world
      Progress |===================================| 100.0%
      FATAL: container creation failed: mount error: can't mount image /proc/self/fd/13: failed to find loop device: could not attach image file too loop device: No loop devices available

      One solution is to remove the Singularity cached images from local cache directory $HOME/.apptainer/cache.

      singulariy cache clean

      Alternatively, you can change the Singularity cache directory to different location by setting the variable APPTAINER_CACHEDIR. For example, in a batch job:

      #/bin/bash
      #SBATCH --job-name="singularity_test"
      #SBSTCH --ntasks=1
      
      export APPTAINER_CACHEDIR=$TMPDIR
      singularity run shub://vsoch/hello-world

      Workshop

      Further Reading

      Supercomputer: 

      BLAS

      The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations.

      Availability and Restrictions

      Access

      A highly optimized implementation of the BLAS is available on all OSC clusters as part of the Intel Math Kernel Library (MKL). We recommend that you use MKL rather than building the BLAS for yourself. MKL is available to all OSC users.

      Usage

      See OSC's MKL software page for usage information. Note that there is no library named libblas.a or libblas.so. The flag "-lblas" on your link line will not work. You should modify your makefile or build script to link to the MKL libraries instead.

      Further Reading

      Service: 
      Technologies: 
      Fields of Science: 

      BLAST

      The BLAST programs are widely used tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence. While often referred to as just "BLAST", this can really be thought of as a set of programs: blastp, blastn, blastx, tblastn, and tblastx.

      Availability & Restrictions

      Versions

      The following versions of BLAST are available on OSC systems: 

      Version Owens Pitzer
      2.4.0+ X  
      2.8.0+   X
      2.8.1+ X  
      2.10.0+ X* X*
      2.11.0+ X X
      2.13.0+ X X
      * Current Default Version

      You can use module spider blast to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      If you need to use blastx, you will need to load one of the C++ implimenations modules of blast (any version with a "+").

      Access

      BLAST is available to all OSC users. If you have any questions, please contact OSC Help.

      Publisher/Vendor/Repository and License Type

      National Institutes of Health, Open source

      Usage

      Set-up

      To load BLAST, type the following into the command line:

      module load blast

      Then create a resource file .ncbirc, and put it under your home directory.

      Using BLAST

      The five flavors of BLAST mentioned above perform the following tasks:

      • blastp: compares an amino acid query sequence against a protein sequence database

      • blastn: compares a nucleotide query sequence against a nucleotide sequence database

      • blastx: compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database

      • tblastn: compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).

      • tblastx: compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. (Due to the nature of tblastx, gapped alignments are not available with this option)

      NCBI BLAST Database

      Information on the NCBI BLAST database can be found here. https://www.osc.edu/resources/available_software/scientific_database_list/blast_database 

      We provide local access to nt and refseq_protein databases. You can access the database by loading desired blast-database modules. If you need other databases, please send a request email to OSC Help .

      Batch Usage

      A sample batch script on Owens and Pitzer is below:

      #!/bin/bash
      ## --ntasks-per-node can be increased upto 48 on Pitzer
      #SBATCH --nodes=1 --ntasks-per-node=28 
      #SBATCH --time=00:10:00
      #SBATCH --job-name Blast
      #SBATCH --account=<project-account>
      
      module load blast
      module load blast-database/2018-08
      
      cp 100.fasta $TMPDIR
      cd $TMPDIR
      
      tblastn -db nt -query 100.fasta -num_threads 16 -out 100_tblastn.out
      
      cp 100_tblastn.out $SLURM_SUBMIT_DIR
      

      Further Reading

      Supercomputer: 
      Service: 
      Fields of Science: 

      BWA

      BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.

      Availability and Restrictions

      Versions

      The following versions of BWA are available on OSC clusters:

      Version Owens Pitzer
      0.7.17-r1198 X* X*
      * Current default version

      You can use module spider bwa to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      BWA is available to all OSC users. If you have any questions, please contact OSC Help.

      Publisher/Vendor/Repository and License Type

      Li H. and Durbin R., Open source

      Usage

      Usage on Owens

      Set-up

      To configure your environment for use of BWA, run the following command: module load bwa. The default version will be loaded. To select a particular BWA version, use module load bwa/version. For example, use module load bwa/0.7.13 to load BWA 0.7.13.

      Usage on Pitzer

      Set-up

      To configure your environment for use of BWA, run the following command: module load bwa. The default version will be loaded.

      Further Reading

      Supercomputer: 
      Service: 
      Fields of Science: 

      BamTools

      BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

      Availability and Restrictions

      Versions

      The following versions of BamTools are available on OSC clusters:

      Version Owens Pitzer
      2.2.2  X*  
      2.3.0   X*
      * Current default version

      You can use module spider bamtools to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      BamTools is available to all OSC users. If you have any questions, please contact OSC Help.

      Publisher/Vendor/Repository and License Type

      Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg/ Open Source

      Usage

      Usage on Owens

      Set-up

      To configure your environment for use of BamTools, run the following command: module load bamtools. The default version will be loaded. To select a particular BamTools version, use module load bamtools/version. For example, use module load bamtools/2.2.2 to load BamTools 2.2.2.

      Usage on Pitzer

      Set-up

      To configure your environment for use of BamTools, run the following command: module load bamtools. The default version will be loaded.

      Further Reading

      Supercomputer: 
      Service: 
      Fields of Science: 

      Bismark

      Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.

      Availability and Restrictions

      Versions

      The following versions of bedtools are available on OSC clusters:

      Version Owens Pitzer
      0.22.1 X* X*
      0.22.3 X X
      * Current default version

      You can use module spider bismark to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      Bismark is available to all OSC users. If you have any questions, please contact OSC Help.

      Publisher/Vendor/Repository and License Type

      Babraham Bioinformatics, GNU GPL v3

      Usage

      Usage on Owens

      Set-up

      To configure your environment for use of metilene, run the following command: module load bismark. The default version will be loaded. To select a particular Bismark version, use module load bismark/version. For example, use module load bismark/0.22.1 to load Bismark 0.22.1.

      Usage on Pitzer

      Set-up

      To configure your environment for use of metilene, run the following command: module load bismark. The default version will be loaded. To select a particular Bismark version, use module load bismark/version. For example, use module load bismark/0.22.1 to load Bismark 0.22.1.

      Further Reading

      Supercomputer: 
      Service: 
      Fields of Science: 

      Blender

      Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.

      Availability and Restrictions

      Versions

      The following versions of Blender are available on OSC systems: 

      Version Owens Pitzer
      2.79 X*  
      2.91 X X*
      3.6.3 X X
      * Current default version

      You can use module spider blender to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      Blender is available to all OSC users. If you have any questions, please contact OSC Help.

      Publisher/Vendor/Repository and License Type

      Blender Foundation, Open source

      Usage

      Set-up for Blender 3.6.3

      module load blender/3.6.3

      Using Blender 3.6.3

      To run software-accelerated Blender, run either of the following equivalent commands:

      apptainer exec $BLENDER_IMG blender
      apptainer exec $BLENDER_IMG blender-softwaregl

      Set-up for Blender 2.X

      On Pitzer or Owens-Desktop 'vis' or 'any' node type, run the following command:

      module load blender
      

      Using Blender 2.X

      To run hardware-rendering version of blender, connect to OSC OnDemand and luanch a virtual desktop, either a Lightweight Desktop or an Interactive HPC 'vis' type Desktop, and in desktop open a terminal and run blender with VirtualGL

      module load virtualgl
      vglrun blender
      

      You can also run software-rendering version of blender on any type Desktop: 

      blender-softwaregl

      Further Reading

       

      Tag: 
      Supercomputer: 
      Service: 
      Fields of Science: 

      Boost

      Boost is a set of C++ libraries that provide helpful data structures and numerous support functions in a wide range of aspects of programming, such as, image processing, gpu programming, concurrent programming, along with many algorithms.  Boost is portable and performs well on a wide variety of platforms.

      Availability & Restrictions

      Versions

      The following version of Boost are available on OSC systems:

      Version Owens Pitzer Ascend Notes
      1.53.0 System Install     No Module Needed
      1.56.0        
      1.63.0 X(GI)      
      1.64.0 X(GI)      
      1.67.0 X(GI) X(GI)    
      1.72.0 X(GI)* X(GI)*    
      1.75.0 X(I) X(I)    
      1.78.0     X(G)*  
      * Current default version; G = available with gnu; I = available with intel

      You can use module spider boost to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      Boost is available to all OSC users. If you have any questions, please contact OSC Help.

      Publisher/Vendor/Repository and License Type

      Beman Dawes, David Abrahams, Rene Rivera/ Open source

      Usage

      Usage on Owens

      Set-up

      Initalizing the system for use of the Boost library is independent of the compiler you are using.  To load the boost module run the following command:

      module load boost

      Building With Boost

      The following environment variables are setup when the Boost library is loaded:

      VARIABLE USE
      $BOOST_CFLAGS Use during your compilation step for C++ programs.
      $BOOST_LIBS Use during your link step.

       

      Below is a set of example commands used to build and run a file called  example2.cpp. First copy the example2.cpp and jayne.txt from Oakley into your home directory with the following commands:

      cp /usr/local/src/boost/boost-1_56_0/test.osc/example2.cpp ~
      cp /usr/local/src/boost/boost-1_56_0/test.osc/jayne.txt ~
      
      Then compile and test the program with the folllowing commands:
      g++ example2.cpp -o boostTest -lboost_regex
      ./boostTest < jayne.txt
      

      Usage on Pitzer

      Set-up

      Initalizing the system for use of the Boost library is independent of the compiler you are using.  To load the boost module run the following command:

      module load boost

      Building With Boost

      The following environment variables are setup when the Boost library is loaded:

      VARIABLE USE
      $BOOST_CFLAGS Use during your compilation step for C++ programs.
      $BOOST_LIBS Use during your link step.

       

      Below is a set of example commands used to build and run a file called  example2.cpp. First copy the example2.cpp and jayne.txt from Oakley into your home directory with the following commands:

      cp /usr/local/src/boost/boost-1_56_0/test.osc/example2.cpp ~
      cp /usr/local/src/boost/boost-1_56_0/test.osc/jayne.txt ~
      
      Then compile and test the program with the folllowing commands:
      g++ example2.cpp -o boostTest -lboost_regex
      ./boostTest < jayne.txt

      Usage on Ascend

      Set-up

      Initalizing the system for use of the Boost library is independent of the compiler you are using.  To load the boost module run the following command:

      module load boost

      Building With Boost

      The following environment variables are setup when the Boost library is loaded:

      VARIABLE USE
      $BOOST_CFLAGS Use during your compilation step for C++ programs.
      $BOOST_LIBS Use during your link step.

       

      Below is a set of example commands used to build and run a file called  example2.cpp. First copy the example2.cpp and jayne.txt from Oakley into your home directory with the following commands:

      cp /usr/local/src/boost/boost-1_56_0/test.osc/example2.cpp ~
      cp /usr/local/src/boost/boost-1_56_0/test.osc/jayne.txt ~
      
      Then compile and test the program with the folllowing commands:
      g++ example2.cpp -o boostTest -lboost_regex
      ./boostTest < jayne.txt

      Further Reading

       

      Supercomputer: 
      Service: 
      Fields of Science: 

      Bowtie1

      Bowtie1 is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

      Availability and Restrictions

      Versions

      The following versions of Bowtie1 are available on OSC clusters:

      Version Owens Pitzer
      1.1.2 X*  
      1.2.2   X*
      * Current default version

      You can use module spider bowtie1 to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      Bowtie1 is available to all OSC users. If you have any questions, please contact OSC Help.

      Publisher/Vendor/Repository and License Type

      Ben Langmead et al., Open source (Artistic 2.0)

      Usage

      Usage on Owens

      Set-up

      To configure your environment for use of Bowtie1, run the following command:  module load bowtie1. The default version will be loaded. To select a particular Bowtie1 version, use  module load bowtie/version. For example, use  module load bowtie1/1.1.2 to load Bowtie1 1.1.2.

      Usage on Pitzer

      Set-up

      To configure your environment for use of Bowtie1, run the following command:  module load bowtie1. The default version will be loaded. 

      Further Reading

      Supercomputer: 
      Service: 
      Fields of Science: 

      Bowtie2

      Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

      Please note that bowtie (and tophat) CANNOT run in parallel, that is, on multiple nodes.  Submitting multi-node jobs will only waste resources.  In addition you must explicitly include the '-p' option to use multiple threads on a single node.

      Availability and Restrictions

      Versions

      The following versions of Bowtie2 are available on OSC clusters:

      Version Owens Pitzer Note
      2.2.9 X    
      2.3.4.3   X  
      2.4.1 X* X* Python 3 rqeuired for all python scripts
      * Current default version

      You can use module spider bowtie2 to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      Bowtie2 is available to all OSC users. If you have any questions, please contact OSC Help.

      Publisher/Vendor/Repository and License Type

      Ben Langmead et al., Open source

      Usage

      Usage on Owens

      Set-up

      To configure your environment for use of Bowtie2, run the following command: module load bowtie2. The default version will be loaded. To select a particular Bowtie2 version, use module load bowtie2/version. For example, use  module load bowtie2/2.2.9 to load Bowtie2 2.2.9.

      Usage on Pitzer

      Set-up

      To configure your environment for use of Bowtie2, run the following command: module load bowtie2. The default version will be loaded.

      Further Reading

      Supercomputer: 
      Service: 
      Fields of Science: 

      CIAO

      CIAO (also known as Chandra Interactive Analysis of Observations) is a X-Ray telescope analysis software package for astronomical observation. CIAO focuses on the Chandra X-ray observatory. It contains a toolset used to analyze fits files and is commonly used in conjuction with DS9 and Sherpa, and focuses on data flexibility. 

      Availability and Restrictions

      Versions

      CIAO is available on Pitzer and Owens Clusters. The versions currently available at OSC are:

      Version Owens Pitzer Notes
      4.14 X* X*  
      * Current default version

      You can use module spider ciao to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Publisher/Vendor/Repository and License Type

      Harvard & Smithsonian (Public)

      Usage

      Usage on Owens

      Set-up

      To load the default version of CIAO module, use  module load ciao. For a list of all available CIAO versions and the format expected, type:  module spider ciao. To select a particular software version, use   module load ciao/version. For example, use  module load ciao/4.14 to load CIAO version 4.14. 

      Running CIAO

      The following command will start an interactive, command line version of CIAO:

      ciaorun 
      

       type ciaorun help for a complete list of command line options.

      The commands listed above will run CIAO on the login node you are connected to. As the login node is a shared resource, running scripts that require significant computational resources will impact the usability of the cluster for others. As such, you should not use interactive CIAO sessions on the login node for any significant computation. If your CIAO script requires significant time, CPU power, or memory, you should run your code via the batch system.

      Batch Usage

      When you log into owens.osc.edu you are actually logged into a Linux box referred to as the login node. To gain access to the multiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

       

      Usage on Pitzer

      Set-up

      To load the default version of CIAO module, use  module load ciao. For a list of all available CIAO versions and the format expected, type:  module spider ciao. To select a particular software version, use   module load ciao/version. For example, use  module load ciao/4.14 to load CIAO version 4.14. 

      Running CIAO

      The following command will start an interactive, command line version of CIAO:

      ciaorun 
      

       type ciaorun help  for a complete list of command line options.

      The commands listed above will run CIAO on the login node you are connected to. As the login node is a shared resource, running scripts that require significant computational resources will impact the usability of the cluster for others. As such, you should not use interactive CIAO sessions on the login node for any significant computation. If your CIAO script requires significant time, CPU power, or memory, you should run your code via the batch system.

      Batch Usage

      When you log into owens.osc.edu you are actually logged into a Linux box referred to as the login node. To gain access to the multiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

      Further Reading

      Official documentation can be obtained from the CIAO's Website

      References

      1. DS9
      Supercomputer: 
      Service: 
      Fields of Science: 

      CMake

      CMake is a family of compilation tools that can be used to build, test and package software.

      Availability and Restrictions

      Versions

      The current versions of CMake available at OSC are:

      Version Owens Pitzer Ascend
      2.8.12.2 X# X#  
      3.1.1      
      3.6.1 X    
      3.7.2 X    
      3.11.4 X X  
      3.16.5 X X  
      3.17.2 X* X*  
      3.18.2     X#
      3.20.5   X  
      3.25.2 X X X*
      * Current default version; # System version

      You can use  module spider cmake  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access

      CMake is available to all OSC users.

      Publisher/Vendor/Repository and License Type

      Aaron C. Meadows et al., Open source

      Usage

      Usage on Owens

      Set-up

      To configure your environment for use of CMake, run the following command:  module load cmake . The default version will be loaded. To select a particular CMake version, use  module load cmake/version . For example, use   module load cmake/3.6.1  to load CMake 3.6.1. For the system version of CMake, you can use it without module load

      Usage on Pitzer

      Set-up

      To configure your environment for use of CMake, run the following command:  module load cmake . The default version will be loaded.

      Further Reading

      For more information, visit the CMake homepage.

      Supercomputer: 

      COMSOL

      COMSOL Multiphysics (formerly FEMLAB) is a finite element analysis and solver software package for various physics and engineering applications, especially coupled phenomena, or multiphysics. owned and supported by COMSOL, Inc.

      Availability and Restrictions

      Versions

      COMSOL is available on the Owens clusters. The versions currently available at OSC are:

      Version Owens
      52a X
      53a X
      5.4 X
      5.5 X*
      6.0 X
      6.2 X
      * Current default version

      You can use module spider comsol  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

      Access for Academic Users

      COMSOL is for academic use, available only to the Ohio State University users. OSC does not provide COMSOL licenses for academic use to students and faculty outside of the Ohio State University due to licensing restrictions. If you or your institution have a network COMSOL license server, you may be able to use it on OSC. For connections to your license server from OSC, please read this document. If you need further help, please contact OSC Help.

      To use COMSOL you will have to be added to the license server.  Please contact OSC Help to be added.

      Access for Commercial Users

      Contact OSC Help for getting access to COMSOL if you are a commercial user. 

      Publisher/Vendor/Repository and License Type

      Comsol Inc., Commercial

      Usage

      Usage on Owens

      Set-up

      To load the default version of COMSOL module, use  module load comsol . To select a particular software version, use   module load comsol/version . For example, use  module load comsol/52a  to load COMSOL version 5.2a. 

      Batch Usage

      When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your analysis to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

      Interactive Batch Session
      For an interactive batch session, one can run the following command:
      sinteractive -A <project-account> -N 1 -n 28 -t 1:00:00 -L comsolscript@osc:1
      
      which gives you 28 cores ( -N 1 -n 28 ) with 1 hour ( -t 1:00:00 ). You may adjust the numbers per your need.
      Non-interactive Batch Job (Serial Run)

      Assume that you have had a comsol script file  mycomsol.m  in your working direcory ( $SLURM_SUBMIT_DIR ). Below is the example batch script ( job.txt ) for a serial run: 

      #!/bin/bash
      #SBATCH --time=1:00:00
      #SBATCH --nodes=1 --ntasks-per-node=1
      #SBATCH -L comsolscript@osc:1
      #SBATCH --account=<project-account>
      #
      # The following lines set up the COMSOL environment
      #
      module load comsol
      #
      # Use TMPDIR for best performance
      cp -p mycomsol.m $TMPDIR
      cd $TMPDIR
      #
      # Run COMSOL
      #
      comsol batch mycomsol
      #
      # Now, copy data (or move) back once the simulation has completed
      #
      cp -p * $SLURM_SUBMIT_DIR
      
      Non-interactive Batch Job (Parallel Run for COMSOL 6.0 and Later)

      Below is the example batch script for a parallel job using COMSOL 6.0 or later versions:

      #!/bin/bash
      #SBATCH --time=1:00:00
      #SBATCH --nodes=2 --ntasks-per-node=4 --cpus-per-task=7
      #SBATCH -L comsolscript@osc:1
      #SBATCH --account=<project-account>
      
      module load comsol
      echo "--- Copy Input Files to TMPDIR and Change Disk to TMPDIR"
      cp input_cluster.mph $TMPDIR
      cd $TMPDIR
      
      echo "--- COMSOL run"
      comsol batch -mpibootstrap slurm -inputfile input_cluster.mph -outputfile output_cluster.mph
      echo "--- Copy files back"
      cp output_cluster.mph output_cluster.mph.status ${SLURM_SUBMIT_DIR}
      echo "---Job finished at: 'date'"
      echo "---------------------------------------------"
      

      Note:

      • Use the "-mpibootstrap slurm" option to take the resource specification from the SBATCH directives, thus eliminating the -nnhost, -nn, and -np options.  For more details see https://www.comsol.com/support/knowledgebase/1001
      • Copy files from your directory to $TMPDIR.
      • Provide the name of the input file and output file.
      OLD Non-interactive Batch Job (Parallel Run for COMSOL 4.3 and Later)

      As of version 4.3, it is not necessary to start up MPD before launching a COMSOL job. Below is the example batch script ( job.txt ) for a parallel run using COMSOL 4.3 or later versions:

      #!/bin/bash
      #SBATCH --time=1:00:00
      #SBATCH --nodes=2 --ntasks-per-node=28
      #SBATCH -L comsolscript@osc:1
      #SBATCH --account=<project-account>
      
      module load comsol
      echo "--- Copy Input Files to TMPDIR and Change Disk to TMPDIR"
      cp input_cluster.mph $TMPDIR
      cd $TMPDIR
      
      echo "--- COMSOL run"
      comsol -nn 2 batch -mpirsh ssh -inputfile input_cluster.mph -outputfile output_cluster.mph
      echo "--- Copy files back"
      cp output_cluster.mph output_cluster.mph.status ${SLURM_SUBMIT_DIR}
      echo "---Job finished at: 'date'"
      echo "---------------------------------------------"
      

      Note:

      • Set nodes to 2 and ppn to 28 ( --nodes=2 --ntasks-per-node=28). You can change the values per your need.
      • Use "-mpirsh ssh" option for multi-node jobs
      • Copy files from your directory to $TMPDIR.
      • Provide the name of the input file and output file.

      Avaliable COMSOL modules with OSC's academic license

      Note: Last updated 02/05/24

      AC/DC Module
      Battery Design Module
      CAD Import Module
      CFD Module
      Chemical Reaction Engineering Module
      Heat Transfer Module
      LiveLink for MATLAB
      MEMS Module
      Microfluidics Module
      Particle Tracing Module
      RF Module
      Semiconductor Module
      Structural Mechanics Module
      Subsurface Flow Module
      

        Further Reading

        Supercomputer: 
        Service: 

        Interactive Parallel COMSOL Job

        This documentation is to discuss how to set up an interactive parallel COMSOL job at OSC. The following example demonstrates the process of using COMSOL version 5.1 on Oakley. Depending on the version of COMSOL and cluster you work on, there mighe be some differences from the example. Feel free to contact OSC Help if you have any questions. 

        • Launch COMSOL GUI application following the instructions on this page. Get the information on the node(s) allocated to your job and save it in the file named hostfile using the following command:

         

        cat $PBS_NODEFILE | uniq > hostfile
        

        Make sure the hostfile is located in the same directory where you COMSOL input file is put

        • Open COMSOL GUI application. To enable the cluster compuitng feature, click the show button and select Advanced Study Options, as shown in the picture below:

        Advanced study

        • In the Model Builder, right-click a Study node and select Cluster Computing, as shown in the picture below:

        cluster computing

        • In the Cluster Computing node's setting window, select General from the Cluster type list. Provide the name of Host file as hostfile. Browse to the directory where your COMSOL input file is located, as shown in the picture below:

        setting

        • Save all the settings. Then you should be able to run an interactive parallel COMSOL job at OSC
        Supercomputer: 

        CP2K

        CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods and classical force fields. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.

        Availability and Restrictions

        Versions

        CP2K is available on the OSC clusters. These are the versions currently available:

        VERSION Owens Pitzer Notes
        6.1* X X   (owens) gnu/7.3.0 intelmpi/2018.3
          (pitzer) gnu/4.8.5 openmpi/3.1.6-hpcx
          (pitzer) gnu/7.3.0 intelmpi/2018.3
          (pitzer) gnu/7.3.0 openmpi/3.1.4-hpcx
        7.1 X X   gnu/8.4.0 intelmpi/2019.7
        2022.2   X   gnu/11.2.0 openmpi/4.1.4-hpcx

        You can use module spider cp2k to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        CP2K is available to all OSC users.

        Publisher/Vendor/Repository and License Type

        CP2K, GNU General Public License

        Usage

        IMPORTANT NOTE: You need to load the prerequisite compiler and MPI modules before you can load CP2K. To determine those modules, use module spider cp2k/{version}.
        We have found some types of CP2K jobs would fail or crash nodes using cp2k.popt and cp2k.psmp from MVAPICH2 and OpenMPI builds due to unstable numerical issues. It is recommended to use Intel MPI, which is more stable unless you experience any other issue.

        Usage

        Set-up

        CP2K usage is controlled via modules. Load one of the CP2K modulefiles at the command line, in your shell initialization script, or in your batch scripts. You need to load the prerequisite compiler and MPI modules before you can load CP2K. To determine those modules, use module spider cp2k/7.1

        Batch Usage

        When you log into pitzer.osc.edu you are actually logged into the login node. To gain access to the vast resources in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.  Batch jobs run on the compute nodes of the system and not on the login node. It is desirable for big problems since more resources can be used.

        Interactive Batch Session

        For an interactive batch session one can run the following command:

        sinteractive -A <project-account> -n 1 -t 00:20:00
        

        which requests one core (-n 1), for a walltime of 20 minutes (-t 00:20:00). You may adjust the numbers per your need.

        Non-interactive Batch Job

        batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Below is the example batch script for a parallel run:

        #!/bin/bash 
        #SBATCH --nodes=2
        #SBATCH --time=1:00:0
        #SBATCH --account=<project-account>
        #SBATCH --gres=pfsdir
        
        module load  gnu/8.4.0 intelmpi/2019.7
        module load cp2k/7.1
        module list
        
        
        cp job.inp $PFSDIR/job.inp
        cd $PFSDIR
        srun cp2k.popt -i job.inp -o job.out.$SLURM_JOB_ID 
        cp job.out.$SLURM_JOB_ID $SLURM_SUBMIT_DIR/job.out.$SLURM_JOB_ID
        

        This script uses the Scratch storage system, which is designed to synchronize storage across nodes temporarily, more information is available under the storage documentation in the "Further reading" section.

        Known Issues

        Update: 06/10/2021 
        Version: 6.1

        CP2K 6.1 Floating-point exception on Pitzer Cascade Lakes (48-core) node:

        Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
        
        Backtrace for this error:

        Thid could be a bug in libxsmm 1.9.0 which is released on Mar 15, 2018 (Cascade Lake is launched in 2019). The bug has been fixed in cp2k/7.1.

        Further Reading

        General documentation is available from the CP2K website.
        Scratch Storage documentation is available from the Storage Guide

         
        Supercomputer: 
        Service: 

        CUDA

        CUDA™ (Compute Unified Device Architecture) is a parallel computing platform and programming model developed by Nvidia that enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).

        Availability and Restrictions

        Versions

        CUDA is available on the clusters supporting GPUs. The versions currently available at OSC are:

        Version Owens Pitzer Ascend cuDNN library
        8.0.44 X     5.1.5
        8.0.61 X     6.0.21
        9.0.176 X X   7.3.0
        9.1.85 X X   6.0.21 and 7.0.5
        9.2.88 X X   7.1.4
        10.0.130 X X   7.2.4
        10.1.168 X X   7.6.5
        10.2.89 X* X*   7.6.5
        11.0.3 X X X 8.0.5
        11.1.1 X X   8.0.5
        11.2.2 X X   8.1.1
        11.5.2 X X   8.3.2
        11.6.1 X X X 8.3.2
        11.6.2     X  
        11.7.1     X*  
        11.8.0 X X X 8.8.1
        * Current default version
        From CUDA 11 onwards, applications compiled with a CUDA major release can have minor version compatibility, meaning you may run a CUDA 11 application with any CUDA 11.x toolkit. See https://docs.nvidia.com/deploy/cuda-compatibility/#minor-version-compati... for more detail.

        You can use module spider cuda to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        CUDA is available for use by all OSC users.

        Publisher/Vendor/Repository and License Type

        Nvidia, Freeware 

        Usage

        Usage on Owens

        Set-up on Owens

        To load the default version of CUDA module, use module load cuda. To select a particular software version, use   module load cuda/version

        GPU Computing SDK

        The NVIDIA GPU Computing SDK provides hundreds of code samples and covers a wide range of applications/techniques to help you get started on the path of writing software with CUDA C/C++ or DirectCompute. 

        Programming in CUDA

        Please visit the following link to learn programming in CUDA, http://developer.nvidia.com/cuda-education-training. The link also contains tutorials on optimizing CUDA codes to obtain greater speedups.

        Compiling CUDA Code

        Many of the tools loaded with the CUDA module can be used regardless of the compiler modules loaded. However, CUDA codes are compiled with nvcc, which depends on the GNU compilers. In particular, if you are trying to compile CUDA codes and encounter a compiler error such as

        #error -- unsupported GNU version! gcc versions later than X are not supported!
        

        then you need to load an older GNU compiler with the module load gnu/version command (if compiling standard C code with GNU compilers) or the module load gcc-compatibility/version command (if compiling standard C code with Intel or PGI compilers).

        One can type module show cuda-version-number to view the list of environment variables.
        To compile a cuda code contained in a file, let say mycudaApp.cu, the following could be done after loading the appropriate CUDA module: nvcc -o mycudaApp mycudaApp.cu. This will create an executable by name mycudaApp.

        The environment variable OSC_CUDA_ARCH defined in the module can be used to specify the CUDA_ARCH, to compile with nvcc -o mycudaApp -arch=$OSC_CUDA_ARCH mycudaApp.cu.

        Important: The devices are configured in exclusive mode. This means that 'cudaSetDevice' should NOT be used if requesting one GPU resource. Once the first call to CUDA is executed, the system will figure out which device it is using. If both cards per node is in use by a single application, please use 'cudaSetDevice'.

        Debugging CUDA code

        cuda-gdb can be used to debug CUDA codes. module load cuda will make it available to you. For more information on how to use the CUDA-GDB please visit http://developer.nvidia.com/cuda-gdb.

        Detecting memory access errors

        CUDA-MEMCHECK could be used for detecting the source and cause of memory access errors in your program. For more information on how to use CUDA-MEMCHECK please visit http://developer.nvidia.com/cuda-memcheck.

        Setting the GPU compute mode on Owens

        The GPUs on Owens can be set to different compute modes as listed here.

        The default compute mode is the default setting on our GPU nodes (--gpu_cmode=shared), so you don't need to specify if you require this mode. With this mode, mulitple CUDA processes across GPU nodes are allowed, e.g CUDA processes via MPI. So, if you need to run a MPI-CUDA job, just keep the default compute mode. Should you need to use another compute mode, use --gpu_cmode to specify the mode setting. For example:

        --nodes=1 --ntasks-per-node=28 --gpus-per-node=1 --gpu_cmode=exclusive
        

        Batch Usage on Owens

        When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

        Interactive Batch Session

        For an interactive batch session one can run the following command:

        sinteractive -A <project-account> -N 1 -n 28 -g 1 -t 00:20:00 
        

        which requests one whole node with 28 cores (-N 1 -n 1), for a walltime of 20 minutes (-t 00:20:00), with one gpu (-g 1). You may adjust the numbers per your need.

        Non-interactive Batch Job (Serial Run)

        batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Below is the example batch script (job.txt) for a serial run:

        #!/bin/bash
        #SBATCH -- time=01:00:00
        #SBATCH --nodes=1 --ntasks-per-node=1:gpus=1
        #SBATCH --job-name compute
        #SBATCH --account=<project-account>
        
        module load cuda
        cd $HOME/cuda
        cp mycudaApp $TMPDIR
        cd $TMPDIR
        ./mycudaApp

        Usage on Pitzer

        Set-up on Pitzer

        To load the default version of CUDA module, use module load cuda.

        GPU Computing SDK

        The NVIDIA GPU Computing SDK provides hundreds of code samples and covers a wide range of applications/techniques to help you get started on the path of writing software with CUDA C/C++ or DirectCompute. 

        Programming in CUDA

        Please visit the following link to learn programming in CUDA, http://developer.nvidia.com/cuda-education-training. The link also contains tutorials on optimizing CUDA codes to obtain greater speedups.

        Compiling CUDA Code

        Many of the tools loaded with the CUDA module can be used regardless of the compiler modules loaded. However, CUDA codes are compiled with nvcc, which depends on the GNU compilers. In particular, if you are trying to compile CUDA codes and encounter a compiler error such as

        #error -- unsupported GNU version! gcc versions later than X are not supported!
        

        then you need to load an older GNU compiler with the module load gnu/version command (if compiling standard C code with GNU compilers) or the module load gcc-compatibility/version command (if compiling standard C code with Intel or PGI compilers).

        One can type module show cuda-version-number to view the list of environment variables.
        To compile a cuda code contained in a file, let say mycudaApp.cu, the following could be done after loading the appropriate CUDA module: nvcc -o mycudaApp mycudaApp.cu. This will create an executable by name mycudaApp.

        The environment variable OSC_CUDA_ARCH defined in the module can be used to specify the CUDA_ARCH, to compile with nvcc -o mycudaApp -arch=$OSC_CUDA_ARCH mycudaApp.cu.

        Important: The devices are configured in exclusive mode. This means that 'cudaSetDevice' should NOT be used if requesting one GPU resource. Once the first call to CUDA is executed, the system will figure out which device it is using. If both cards per node is in use by a single application, please use 'cudaSetDevice'.

        Debugging CUDA code

        cuda-gdb can be used to debug CUDA codes. module load cuda will make it available to you. For more information on how to use the CUDA-GDB please visit http://developer.nvidia.com/cuda-gdb.

        Detecting memory access errors

        CUDA-MEMCHECK could be used for detecting the source and cause of memory access errors in your program. For more information on how to use CUDA-MEMCHECK please visit http://developer.nvidia.com/cuda-memcheck.

        Setting the GPU compute mode on Pitzer

        The GPUs on Pitzer can be set to different compute modes as listed here.

        The default compute mode is the default setting on our GPU nodes (--gpu_cmode=shared), so you don't need to specify if you require this mode. With this mode, mulitple CUDA processes across GPU nodes are allowed, e.g CUDA processes via MPI. So, if you need to run a MPI-CUDA job, just keep the default compute mode. Should you need to use another compute mode, use --gpu_cmode to specify the mode setting. For example:

        --nodes=1 --ntasks-per-node=40 --gpus-per-node=1 --gpu_cmode=exclusive
        

        Batch Usage on Pitzer

        When you log into pitzer.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

        Interactive Batch Session

        For an interactive batch session one can run the following command:

        sinteractive -A <project-account> -N 1 -n 40 -g 2 -t 00:20:00
        

        which requests one whole node (-N 1), 40 cores (-n 40), 2 gpus (-g 2), and a walltime of 20 minutes (-t 00:20:00). You may adjust the numbers per your need.

        Non-interactive Batch Job (Serial Run)

        batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Below is the example batch script (job.txt) for a serial run:

        #!/bin/bash
        #SBATCH --time=01:00:00
        #SBATCH --nodes=1 --ntasks-per-node=1 --gpus-per-node=1
        #SBATCH --job-name Compute
        #SBATCH --account=<project-account>
        
        module load cuda
        cd $HOME/cuda
        cp mycudaApp $TMPDIR
        cd $TMPDIR
        ./mycudaApp
        

        GNU Compiler Support for NVCC 

        CUDA Version Max supported GCC version
        9.2.88 - 10.0.130 7
        10.1.168 - 10.2.89 8
        11.0 9
        11.1 - 11.4.0 10
        11.4.1 - 11.8 11
        12.0 12.1

        Further Reading

        Online documentation is available on the CUDA homepage.

        Compiler support for the latest version of CUDA is available here.

        CUDA optimization techniques.

         

        Supercomputer: 
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        Technologies: 
        Fields of Science: 

        Caffe

        Caffe is "a fast open framework for deep learning."

        From their README:

        Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. Yangqing Jia created  the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license.
        

        Caffe also includes interfaces for both Python and Matlab, which have been built but have not been tested.

        Availability and Restrictions

        Versions

        The following versions of Caffe are available on OSC clusters:

        Version Owens
        1.0.0-rc3 X*
        * Current Default Version

        You can use module spider caffe to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        The current version of Caffe on Owens requires cuda/8.0.44 for GPU calculations.

        Access 

        Caffe is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Berkeley AI Research, Open source

        Usage

        Usage on Owens

        Setup on Owens

        To configure the Owens cluster for the use of Caffe, use the following commands:

        module load caffe
        

        Batch Usage on Owens

        Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations for Owens, and Scheduling Policies and Limits for more info.  In particular, Caffe should be run on a GPU-enabled compute node.

        An Example of Using Caffe with MNIST Training Data on Owens

        Below is an example batch script (job.txt) for using Caffe, see this resource for a detailed explanation http://caffe.berkeleyvision.org/gathered/examples/mnist.html

        #!/bin/bash
        #SBATCH --job-name=Caffe
        #SBATCH --nodes=1 --ntask-per-node=28:gpu
        #SBATCH --time=30:00
        #SBATCH --account <project-account>
        
        . /etc/profile.d/lmod.sh
        # Load the modules for Caffe
        ml caffe
        # Migrate to job temp directory and copy folders over
        cd $TMPDIR
        cp -r $CAFFE_HOME/{examples,data} .
        # Download, create, train
        ./data/mnist/get_mnist.sh
        ./examples/mnist/create_mnist.sh
        ./examples/mnist/train_lenet.sh
        # Serialize log files
        echo; echo 'LOG 1'
        cat convert_mnist_data.bin.$(hostname)*
        echo; echo 'LOG 2'
        cat caffe.INFO
        echo; echo 'LOG 3'
        cat convert_mnist_data.bin.INFO
        echo; echo 'LOG 4'
        cat caffe.$(hostname).*
        cp examples/mnist/lenet_iter_10000.* $SLURM_SUBMIT_DIR
        

        In order to run it via the batch system, submit the job.txt file with the following command:

        sbatch job.txt
        

        Further Reading

        Supercomputer: 
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        Technologies: 
        Fields of Science: 

        Cell Ranger

        Cell Ranger is a cell analysis library for generate feature-barcode matrices, perform Analysis for RNA samples. Cell Ranger works in pipelines for it's RNA  sequencing analysis which allows it to: process raw sequencing output, read alignment, generate gene-cell matrices, and can perform downstream analyses such as clustering and gene expression analysis.

        Availability and Restrictions

        Versions

        Cell Ranger is available on the Pitzer Cluster. The versions currently available at OSC are:

        Version Pitzer Notes
        7.0.0 X*  
        * Current Default Version

        You can use module spider cellranger to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        Cell Ranger is available to only academic OSC users. Please review the license agreement and 10x Privacy Policy before use. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        The 10x Genomics group, Closed source (academic)

        Usage

        Usage on Pitzer

        Set-up

        To configure your environment for use of Cell Ranger, run the following command: module load cellranger. The default version will be loaded. To select a particular Cell Ranger version, use module load cellranger/version. For example, use module load cellranger/7.0.0 to load Cell Ranger 7.0.0.

        Further Reading

        Supercomputer: 
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        Fields of Science: 

        Clara Parabricks

        Clara Parabricks is a powerful toolkit designed for genomic analysis. It is primarily designed for GPU computation.

        Availability and Restrictions

        Versions

        Clara Parabricks is available on Pitzer and Owens Clusters. The versions currently available at OSC are the following:

        Version Owens Pitzer Notes
        4.0.0-1 X* X*  
        * Current default version

        You can use module spider clara-parabricks  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        Clara-Parabricks is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Open source

        Usage 

        Usage on Owens

        Set-up

        To load the module for the default version of Parabricks, which initializes your environment for the Clara-Parabricks application, use module load clara-parabricks. To select a particular software version, use module load clara-parabricks/version. For example, use module load clara-parabricks/4.0.0-1 to load Parabricks version 4.0.0-1; and use module help clara-parabricks/4.0.0-1 to view details, such as compiler prerequisites, additional modules required for specific executables, the suffixes of executables, etc.; some versions require specific prerequisite modules, and such details may be obtained with the command   module spider clara-parabricks/version.

        Batch Usage

        When you log into Owens you are actually connected to a login node. To access the compute nodes, you must submit a job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

        Interactive Batch Session
        For an interactive batch session, one can run the following command:
        sinteractive -A <project-account> -N 1 -n 28 -t 1:00:00
        
        which gives you one node with 28 cores (-N 1 -n 28), with 1 hour (-t 1:00:00). You may adjust the numbers per your need.

        Usage on Pitzer

        Set-up

        To load the module for the default version of Parabricks, which initializes your environment for the Clara-Parabricks application, use module load clara-parabricks. To select a particular software version, use module load clara-parabricks/version. For example, use module load clara-parabricks/4.0.0-1 to load Parabricks version 4.0.0-1; and use module help clara-parabricks/4.0.0-1 to view details, such as, compiler prerequisites, additional modules required for specific executables, the suffixes of executables, etc.; some versions require specific prerequisite modules, and such details may be obtained with the command   module spider clara-parabricks/version.

        Batch Usage

        When you log into Owens you are actually connected to a login node. To access the compute nodes, you must submit a job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

        Interactive Batch Session
        For an interactive batch session, one can run the following command:
        sinteractive -A <project-account> -N 1 -n 28 -t 1:00:00
        
        which gives you one node with 28 cores (-N 1 -n 28), with 1 hour (-t 1:00:00). You may adjust the numbers per your need.

        Further Reading

        Supercomputer: 
        Service: 
        Technologies: 
        Fields of Science: 

        Clustal W

        Clustal W is a multiple sequence alignment program written in C++.

        Availability and Restrictions

        Versions

        The following versions of bedtools are available on OSC clusters:

        Version Owens Pitzer
        2.1 X* X*
        * Current default version

        You can use module spider clustalw to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        Clustal W is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        GNU Lesser GPL.

        Usage

        Usage on Owens

        Set-up

        To configure your environment for use of metilene, run the following command: module load clustalw. The default version will be loaded. To select a particular MUSCLE version, use module load clustalw/version. For example, use module load clustalw/2.1 to load Clustal W 2.1.

        Usage on Pitzer

        Set-up

        To configure your environment for use of metilene, run the following command: module load clustalw. The default version will be loaded. To select a particular MUSCLE version, use module load clustalw/version. For example, use module load clustalw/2.1 to load Clustal W 2.1.

        Further Reading

        Supercomputer: 
        Service: 
        Fields of Science: 

        Connectome

        Connectome is an open-source visualization and discovery tool used to explore data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.

        Availability and Restrictions

        Versions

        The following versions are available on OSC clusters:

        Version Pitzer
        1.5.0 X*
        * Current default version

        You can use module spider connectome to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        Connectome is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Connectome Workbench is made available via the GNU General Public License, version 2. The full license is available from here.

        Usage

        Usage on Pitzer

        Set-up

        To configure your environment for use of connectome, run the following command: module load connectome. The default version will be loaded. To select a particular connectome version, use module load connectome/version. For example, use module load connectome/1.5.0 to load Connectome 1.5.0.

        If you want the hardware-accelerated 3D graphics, use these on a compute node with a GPU:

        module load virutalgl/2.6.5
        module load connectome
        viglrun wb_view

        The command will open the GUI environment, thus we recommend Ondemand VDI or Desktop.

        Further Reading

        Supercomputer: 
        Service: 
        Fields of Science: 

        Connectome Workbench

        Connectome Workbench is an open source, freely available visualization and analysis tool for neuroimaging data, especially data generated by the Human Connectome Project.

        Availability and Restrictions

        Versions

        Connectome Workbench is available on Owens and Pitzer clusters. These are the versions currently available:

        Version Owens Pitzer Notes
        1.3.2  X* X*  
        1.5.0 X X  
        * Current default version

        You can use module spider connectome-workbench to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        Connectome Workbench is available to all OSC users.

        Publisher/Vendor/Repository and License Type

        Washington University School of Medicine, GPL

        Usage

        Set-up

        To configure your environment for use of the workbench, run the following command:  module load connectome-workbench virtualgl. The default version will be loaded; the virtualgl module is required as well on some platforms. To select a particular version, use  module load connectome-workbench/version. For example, use  module load connectome-workbench/1.3.2 to load Connectome Workbench 1.3.2.

        Further Reading

        General documentation is available from the Connectome Workbench hompage.

         
        Supercomputer: 
        Service: 
        Fields of Science: 

        Cufflinks

        Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.

        Availability and Restrictions

        Versions

        Cufflinks is available on the Owens Cluster. The versions currently available at OSC are:

        Version Owens
        2.2.1 X*
        * Current Default Version

        You can use module spider cufflinks to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        Cufflinks is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Cole Trapnell et al., Open source

        Usage

        Usage on Owens

        Set-up

        To configure your enviorment for use of Cufflinks, use command module load cufflinks. This will load the default version.

        Further Reading

        Supercomputer: 
        Fields of Science: 

        DS9

        SAOImageDS9 is a astronomical imaging and data visualization application. DS9 provides support for FITS images, binary tables, multiple frame buffers, region manipulation, and colormaps display options

        Availability and Restrictions

        The following versions of DS9 are available on OSC clusters:

        Version Owens Pitzer
        7.8.3 X* X*
        * Current default version

        You can use  module spider ds9to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        DS9 is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Jessica Mink, Smithsonian Astrophysical Observatory/ Open source

        Usage

        Usage on Owens

        Set-up

        To configure your environment for use of DS9, run the following command: module load ds9. The default version will be loaded. To select a particular DS9 version, use module load ds9/version . For example, use module load ds9/7.8.3to load DS9 7.8.3.

        Usage on Pitzer

        Set-up

        To configure your environment for use of DS9, run the following command: module load ds9. The default version will be loaded. To select a particular DS9 version, use module load ds9/version . For example, use module load ds9/7.8.3to load DS9 7.8.3.

        Further Reading

        Supercomputer: 
        Service: 
        Fields of Science: 

        DSI Studio

        DSI Studio is a tractography software tool that maps brain connections and correlates findings with neuropsychological disorders. It is a collective implementation of several diffusion MRI methods, including diffusion tensor imaging (DTI), generalized q-sampling imaging (GQI), q-space diffeomorphic reconstruction (QSDR), diffusion MRI connectometry, and generalized deterministic fiber tracking.

        Availability and Restrictions

        The following versions of DSI Studio are available on OSC clusters:

        Version Pitzer
        2.0 X
        * Current default version

        You can use  module spider dsi-studio to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        DSI Studio is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        DSI Studio is free and licensing information for both academic and non-academic licenses is available at the DSI Studio homepage.

        Please refer to the citation page about how to acknowledge DSI Studio.

        Usage

        Usage on Pitzer

        Set-up

        To configure your environment for use of DSI Studio, run the following command: module load dsi-studio. The default version will be loaded. To select a particular version, use module load dsi-studio/version. For example, use module load dsi-studio/2021.May to load DSI Studio 2.0. It is also recommended you use in conjunction with module load singularity.
         

        DSI Studio is installed in a singularity container.  DSI_IMG environment variable contains the container image file path. So, an example usage would be

        module load dsi-studio
        singularity exec $DSI_IMG dsi_studio
        

        This command will open the DSI Studio GUI environment, and we recommend Ondemand VDI or Desktop for GUI. 

        For more information about singularity usages, please read OSC singularity page

         

        Further Reading

         
        Supercomputer: 
        Service: 
        Fields of Science: 

        Darshan

        Darshan is a lightweight "scalable HPC I/O characterization tool".  It is intended to profile I/O by emitting log files to a consistent log location for systems administrators, and also provides scripts to create summary PDFs to characterize I/O in MPI-based programs.

        Availability and Restrictions

        Versions

        The following versions of Darshan are available on OSC clusters:

        Version Owens Pitzer
        3.1.2 X  
        3.1.4 X  
        3.1.5-pre1 X  
        3.1.5 X  
        3.1.6 X X
        3.1.8 X* X*
        3.2.1 X X
        * Current default version

        You can use module spider darshan to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access 

        Darshan is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        MCSD, Argonne National Laboratory, Open source

        Usage

        Usage on Owens & Pitzer

        Setup

        To configure the Owens/Pitzer cluster for Darshan run module spider darshan/VERSION to find supported compiler and MPI implementations, e.g.

        $ module spider darshan/3.2.1
        
        ------------------------------------------------------------------------------------------------
          darshan: darshan/3.2.1
        ------------------------------------------------------------------------------------------------
        
            You will need to load all module(s) on any one of the lines below before the "darshan/3.2.1" module is available to load.
        
              intel/19.0.3  intelmpi/2019.7
              intel/19.0.3  mvapich2/2.3.1
              intel/19.0.3  mvapich2/2.3.2
              intel/19.0.3  mvapich2/2.3.3
              intel/19.0.3  mvapich2/2.3.4
              intel/19.0.3  mvapich2/2.3.5
              intel/19.0.5  intelmpi/2019.3
              intel/19.0.5  intelmpi/2019.7
              intel/19.0.5  mvapich2/2.3.1
              intel/19.0.5  mvapich2/2.3.2
              intel/19.0.5  mvapich2/2.3.3
              intel/19.0.5  mvapich2/2.3.4
              intel/19.0.5  mvapich2/2.3.5
        

        then switch to the favorite programming environment and load the Darshan module:

        $ module load intel/19.0.5 mvapich2/2.3.5
        $ module load darshan/3.2.1
        

        Batch Usage

        Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations (Owens, Pitzer) and Scheduling Policies and Limits for more info. 

        If you have an MPI-based program the syntax is as simple as

        module load darshan
        
        # basic call to darshan
        export MV2_USE_SHARED_MEM=0
        export LD_PRELOAD=$OSC_DARSHAN_DIR/lib/libdarshan.so
        srun [args] ./my_mpi_program
        
        # to show evidence that Darshan is working and to see internal timing
        export DARSHAN_INTERNAL_TIMING=yes
        srun [args] ./my_mpi_program
        
        An Example of Using Darshan with MPI-IO

        Below is an example batch script (darshan_mpi_pfsdir_test.sh) for testing MPI-IO and POSIX-IO.  Because the files generated here are large scratch files there is no need to retain them.

        #!/bin/bash
        #SBATCH --job-name="darshan_mpi_pfsdir_test"
        #SBATCH --ntasks=4
        #SBATCH --ntasks-per-node=2
        #SBATCH --output=rfm_darshan_mpi_pfsdir_test.out
        #SBATCH --time=0:10:0
        #SBATCH -p parallel
        #SBATCH --gres=pfsdir:ess
        
        # Setup Darshan
        module load intel
        module load mvapich2
        module load darshan
        export DARSHAN_LOGFILE=${LMOD_SYSTEM_NAME}_${SLURM_JOB_ID/.*/}_${SLURM_JOB_NAME}.log
        export DARSHAN_INTERNAL_TIMING=yes
        export MV2_USE_SHARED_MEM=0
        export LD_PRELOAD=$OSC_DARSHAN_DIR/lib/libdarshan.so
        
        # Prepare the scratch files and run the cases
        cp ~support/share/reframe/source/darshan/io-sample.c .
        mpicc -o io-sample io-sample.c -lm
        for x in 0 1 2 3; do  dd if=/dev/zero of=$PFSDIR/read_only.$x bs=2097152000 count=1; done
        shopt -s expand_aliases
        srun ./io-sample -p $PFSDIR -b 524288000 -v
        
        # Generat report
        darshan-job-summary.pl --summary $DARSHAN_LOGFILE
        

        In order to run it via the batch system, submit the darshan_mpi_pfsdir_test.sh file with the following command:

        sbatch darshan_mpi_pfsdir_test.sh
        

        Further Reading

        Supercomputer: 
        Service: 
        Technologies: 
        Fields of Science: 

        Desmond

        Desmond is a software package that perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters, general-purpose supercomputers, and GPUs. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer. Desmond includes code optimized for machines with an NVIDIA GPU.

        Availability and Restrictions

        Versions

        The Desmond package is available on Owens. The versions currently available at OSC are:

        Version Owens Note
        2018.2 X  
        2019.1 X*  
        2020.1 X GPU support only
        2022.4 X GPU support only
        * Current default version

        You can use  module spider desmond to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access for Academic Users 

        Desmond is available to academic OSC users. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        D. E. Shaw Research, Non-Commercial

        Usage

        Usage on Owens

        Set-up

        To set up your environment for desmond load one of its module files:

        ​​module load desmond/2018.2
        

        If you already have input and configuration files ready, here is an example batch script that uses Desmond non-interactively via the batch system:

        #!/bin/bash
        #SBATCH --job-name multisim-batch
        #SBATCH --time=0:20:00
        #SBATCH --nodes=1
        #SBATCH --ntasks-per-node=24
        #SBATCH --account=<account>
        
        # Example Desmond single-node batch script. 
        
        sstat -j $SLURM_JOB_ID
        export
        module load desmond/2018.2
        module list
        
        sbcast -p desmondbutane.msj $TMPDIR/desmondbutane.msj
        sbcast -p desmondbutane.cfg $TMPDIR/desmondbutane.cfg
        sbcast -p desmondbutane.cms $TMPDIR/desmondbutane.cms
        
        cd $TMPDIR
        $SCHRODINGER/utilities/multisim -HOST localhost -maxjob 1 -cpu 24 -m desmondbutane.msj -c desmondbutane.cfg desmondbutane.cms -mode umbrella -ATTACHED -WAIT
        ls -l
        cd $SLURM_SUBMIT_DIR
        sgather -r $TMPDIR $SLURM_SUBMIT_DIR

        The WAIT option forces the multisim command to wait until all tasks of the command are completed. This is necessary for batch jobs to run effectively. The HOST option specifies how tasks are distributed over processors.

        Set-up via Maestro

        Desmond comes with Schrodinger interactive builder, Maestro. To run maestro, connect to OSC OnDemand and luanch a virtual desktop, either a Virtual Desktop Interface (VDI) or an Interactive HPC Desktop. Click "Setup process" below for instructions.

        Setup process


        Log in to OSC OnDemand and request a Desktop/VDI session 

        Picture1.png

        In a Desktop/VDI environment, open a terminal and run

        module load desmond
        maestro
        

        In the main window of Maestro, you can open File and import structures or create new project

        Screenshot 2022-06-29 120854.png

        Screenshot 2022-06-29 121005.png

        Once the structure is ready, navigate to the top right Tasks icon and find Desmond application

            Tasks >> Browse... > Applications tab >> Desmond

        Screenshot 2022-06-29 121057 (2).png

        In this example a Minimazation job will be done.

        Screenshot 2022-06-29 121120.png

        Make sure Mode system is ready

          Model system >> Load from workspace >> Load

        You can change Job name and write out the script and configuration files by clicking Write as shown below

        Screenshot 2022-06-29 121205.png

        The green text will indicate job location with the prefix "Job written to...". The location is a new folder located on the working directory indicated earlier.

        Screenshot 2022-06-29 121315.png

        Navigate using the terminal to that location. You can modify the script to either run simulation with GPU or CPU.

        Run simulation with GPU

        Navigate using the terminal to that location and add required SLURM and module commands at the top of the script desmond_min_job_1.sh:

        #!/bin/bash
        #SBATCH --time=0:20:00
        #SBATCH --nodes=1
        #SBATCH --ntasks-per-node=8
        #SBATCH --gpus-per-node=1
        #SBATCH --account=<account>
        
        module reset
        module load desmond/2019.1
        
        # Desmond job script starts here

        The setup is complete.


        Run simulation with CPU only
        Navigate using the terminal to that location and edit the script desmond_min_job_1.sh:

        "${SCHRODINGER}/utilities/multisim" -JOBNAME desmond_min_job_1 -HOST localhost -maxjob 1 -cpu 1 -m desmond_min_job_1.msj -c desmond_min_job_1.cfg -description Minimization desmond_min_job_1.cms -mode umbrella -set stage[1].set_family.md.jlaunch_opt=["-gpu"] -o desmond_min_job_1-out.cms -ATTACHED
        

        Delete the -set stage[1].set_family.md.jlaunch_opt=["-gpu"] arguement and change the -cpu arguement from 1 to the number of CPUs you need, e.g. 8. Resulting in

        "${SCHRODINGER}/utilities/multisim" -JOBNAME desmond_min_job_1 -HOST localhost -maxjob 1 -cpu 8 -m desmond_min_job_1.msj -c desmond_min_job_1.cfg -description Minimization desmond_min_job_1.cms -mode umbrella  -o desmond_min_job_1-out.cms -ATTACHED
        

        Add required SLURM and module commands at the top of the script

        #!/bin/bash
        #SBATCH --time=0:20:00
        #SBATCH --nodes=1
        #SBATCH --ntasks-per-node=24
        #SBATCH --account=<account>
        
        module reset
        module load desmond/2019.1
        
        # Desmond job script starts here

        The setup is complete.

         

        Further Reading

        Tag: 
        Supercomputer: 
        Service: 

        FASTX-Toolkit

        The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

        Availability and Restrictions

        Verisons

        The following versions of FASTX-Toolkit are available on OSC clusters:

        Version Owens
        0.0.14 X*
        *:Current default version

        You can use  module spider fastx to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        FASTX-Toolkit is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Assaf Gordon, Open source

        Usage

        Usage on Owens

        Set-up

        To configure your environment for use of FASTX-Toolkit, run the following command: module load fastx. The default version will be loaded. To select a particular FASTX-Toolkit version, use module load fastx/version. For example, use module load fastx/0.0.14 to load FASTX-Toolkit 0.0.14.

        Further Reading

        Supercomputer: 
        Service: 
        Fields of Science: 

        FFTW

        FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. It is portable and performs well on a wide variety of platforms.

        Availability and Restrictions

        Versions

        FFTW is available on Ruby, and Owens Clusters. The versions currently available at OSC are:

        Version Owens Pitzer Ascend
        3.3.4 X    
        3.3.5 X    
        3.3.8  X* X*  
        3.3.10 X X X*
        NOTE: FFTW2 and FFTW3 are tracked separately in the module system

        You can use module spider fftw2  or module spider fftw3  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        FFTW is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        www.fftw.org, Open source

        Usage

        Usage on Owens

        Set-up

        Initalizing the system for use of the FFTW library is dependent on the system you are using and the compiler you are using. A successful build of your program will depend on an understanding of what module fits your circumstances. To load a particular version, use  module load name . For example, use  module load fftw3/3.3.4  to load FFTW3 version 3.3.4. You can use module spider fftw  to view available modules.

        Building with FFTW

        The following environment variables are setup when the FFTW library is loaded:

        Variable Use
        $FFTW3_CFLAGS Use during your compilation step for C programs.
        $FFTW3_FFLAGS Use during your compilation step for Fortran programs.
        $FFTW3_LIBS Use during your link step for the sequential version of the library.
        $FFTW3_LIBS_OMP Use during your link step for the OpenMP version of the library.
        $FFTW3_LIBS_MPI Use during your link step for the MPI version of the library.
        $FFTW3_LIBS_THREADS Use during your link step for the "threads" version of the library.

        below is a set of example commands used to build a file called my-fftw.c .

        module load fftw3
        icc $FFTW3_CFLAGS my-fftw.c -o my-fftw $FFTW3_LIBS 
        ifort $FFTW3_FFLAGS more-fftw.f -o more-fftw $FFTW3_LIBS
        

        Usage on Pitzer

        Set-up

        Initalizing the system for use of the FFTW library is dependent on the system you are using and the compiler you are using. A successful build of your program will depend on an understanding of what module fits your circumstances. To load a particular version, use  module load fftw3/.

        Building with FFTW

        The following environment variables are setup when the FFTW library is loaded:

        VARIABLE USE
        $FFTW3_CFLAGS Use during your compilation step for C programs.
        $FFTW3_FFLAGS Use during your compilation step for Fortran programs.
        $FFTW3_LIBS Use during your link step for the sequential version of the library.
        $FFTW3_LIBS_OMP Use during your link step for the OpenMP version of the library.
        $FFTW3_LIBS_MPI Use during your link step for the MPI version of the library.

        below is a set of example commands used to build a file called my-fftw.c .

        module load fftw3
        icc $FFTW3_CFLAGS my-fftw.c -o my-fftw $FFTW3_LIBS 
        ifort $FFTW3_FFLAGS more-fftw.f -o more-fftw $FFTW3_LIBS

        Usage on Ascend

        Set-up

        Initalizing the system for use of the FFTW library is dependent on the system you are using and the compiler you are using. A successful build of your program will depend on an understanding of what module fits your circumstances. To load a particular version, use  module spider fftw3 to check what other modules need to be loaded first. Use  module load [module name and version] to load the necessary modules. Then use  module load fftw3 to load the default FFTW module version.

        Building with FFTW

        The following environment variables are setup when the FFTW library is loaded:

        VARIABLE USE
        $FFTW3_CFLAGS Use during your compilation step for C programs.
        $FFTW3_FFLAGS Use during your compilation step for Fortran programs.
        $FFTW3_LIBS Use during your link step for the sequential version of the library.
        $FFTW3_LIBS_OMP Use during your link step for the OpenMP version of the library.
        $FFTW3_LIBS_MPI Use during your link step for the MPI version of the library.

        below is a set of example commands used to build a file called my-fftw.c .

        module load fftw3
        icc $FFTW3_CFLAGS my-fftw.c -o my-fftw $FFTW3_LIBS 
        ifort $FFTW3_FFLAGS more-fftw.f -o more-fftw $FFTW3_LIBS

        Further Reading

        See Also

        Supercomputer: 
        Service: 

        FSL

        FSL is a library of tools for analyzing FMRI, MRI and DTI brain imaging data.

        Availability and Restrictions

        Versions

        The following versions of FSL are available on OSC clusters:

        Version Owens Pitzer
        5.0.10

        X*

         
        6.0.4 X X
        * Curent default version

        You can use module spider fsl to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        FSL is available to academic OSC users. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Analysis Group, University of Oxford/ freeware

        Usage

        Usage on Owens and Pitzer

        Set-up

        Configure your environment for use of FSL with module load fsl. This will load the default version.

        Using FSL GUI

        Access the FSL GUI with command for bash

        source $FSLDIR/etc/fslconf/fsl.sh
        fsl

        For csh, one can use

        source $FSLDIR/etc/fslconf/fsl.csh
        fsl 

        This will bring up a menu of all FSL tools. For information on individual FSL tools see FSL Overview page.

        Using BASIL GUI

        module load fsl/6.0.4
        source $FSLDIR/etc/fslconf/fsl.sh
        asl_gui --matplotlib

        For more information, please visit https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BASIL.

        Further Reading 

        Supercomputer: 
        Fields of Science: 

        FastQC

        FastQC provides quality control checks of high throughput sequence data that identify areas of the data that may cause problems during further analysis.

        Availability and Restrictions

        Versions

        FastQC is available on the Owens cluster. The versions currently available at OSC are:

        Version Owens Pitzer
        0.11.5 X*  
        0.11.7 X  
        0.11.8   X*
        * Current Default Version

        You can use module spider fastqc to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        FastQC is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Babraham Bioinformatics, Open source

        Usage

        Usage on Owens

        Set-up

        To configure your enviorment for use of FastQC, use command module load fastqc. This will load the default version.

        Usage on Pitzer

        Set-up

        To configure your enviorment for use of FastQC, use command module load fastqc. This will load the default version.

        Further Reading

        Supercomputer: 
        Fields of Science: 

        FreeSurfer

        FreeSurfer is a software package used to anaylze nueroimaging data.

        Availability & Restrictions

        Versions

        The following versions of FreeSurfer are available on OSC clusters:

        Version Owens Pitzer Note
        5.3.0 X    
        6.0.0

         X*

        X  
        7.1.1 X X*  
        7.2.0 X X  
        7.3.0 X X  
        * Curent default version

        You can use module spider freesurfer to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        FreeSurfer is available to academic OSC users. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Athinoula A. Martinos Center, Open source

        Usage

        Usage on Owens and Pitzer

        Set-up

        Load the FreeSurfer module with  module load freesurfer. This will load the default version. Then, to continue configuring your environment, you must source the setup script for Freesurfer. Do this with the following command that corresponds to the Linux shell you are using. If using bash, use:

        source $FREESURFER_HOME/SetUpFreeSurfer.sh
        

        If using tcsh, use:

        source $FREESURFER_HOME/SetUpFreeSurfer.csh
        

        To finish configuring FreeSurfer, set the the FreeSurfer environment variable SUBJECTS_DIR to the directory of your subject data. The SUBJECTS_DIR variable defaults to the FREESURFER_HOME/subjects directory, so if this is your intended directory to use the enviornment set-up is complete.

        To alter the SUBJECTS_DIR variable, however, again use the following command that corresponds to the Linux shell you are using. For bash:

        export SUBJECTS_DIR=<path to subject data>
        

        For tcsh:

        setenv SUBJECTS_DIR=<path to subject data>
        

        Note that you can set the SUBJECT_DIR variable before or after sourcing the setup script.

        The cuda applications from FreeSurfer requires CUDA 5 library (which is not avaiable through module system). To set up cuda environment, run the following command after load the FreeSurfer module. If  you are using bash, run:

        source $FREESURFER_HOME/bin/cuda5_setup.sh
        

        If using tcsh, use:

        source $FREESURFER_HOME/bin/cuda5_setup.csh
        

        Further Reading 

        Supercomputer: 
        Service: 
        Fields of Science: 

        GAMESS

        The General Atomic and Molecular Electronic Structure System (GAMESS) is a flexible ab initio electronic structure program. Its latest version can perform general valence bond, multiconfiguration self-consistent field, Möller-Plesset, coupled-cluster, and configuration interaction calculations. Geometry optimizations, vibrational frequencies, thermodynamic properties, and solution modeling are available. It performs well on open shell and excited state systems and can model relativistic effects. The GAMESS Home Page has additional information.

        Availability and Restrictions

        Versions

        The current versions of GAMESS available on the Oakley and Owens Clusters are:

        VERSION

        owens Pitzer
        18 AUG 2016 (R1) X  
        30 Sep 2019 (R2) X* X*
        * Current default version

        You can use module spider gamess to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        GAMESS is available to all OSC users. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Gordon research group, Iowa State Univ./ Proprietary freeware

        Usage

        Set-up

        GAMESS usage is controlled via modules. Load one of the GAMESS modulefiles at the command line, in your shell initialization script, or in your batch scripts, for example:

        module load gamess  

        Examples

        Further Reading

        General documentation is available from the GAMESS Home page and in the local machine directories.

        Supercomputer: 
        Service: 

        GATK

        GATK is a software package for analysis of high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

        Availability and Restrictions

        Versions

        The following versions of GATK are available on OSC clusters:

        Version Owens Pitzer Notes
        3.5 X    
        4.0.11.0   X  
        4.1.2.0 X* X*  
        4.4.0.0 X X  
        * Current default version

        You can use module spider gatk to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access for Academic Users

        GATK4 is available to all OSC users under BSD 3-clause License.

        GATK3 is available to academic OSC users. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Broad Institute, Inc., BSD 3-clause License (GATK4 only)

        Usage

        Usage on Owens

        Set-up

        To configure your environment for use of GATK, run the following command: module load gatk. The default version will be loaded. To select a particular GATK version, use module load gatk/version. For example, use module load gatk/4.1.2.0 to load GATK 4.1.2.0.

        Usage

        This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable. From module load gatk, a new environment variable, GATK, will be set. Thus, users can use the software by running the following command: gatk {other options},e.g  run gatk -h to see all options.

        Usage on Pitzer

        Set-up

        To configure your environment for use of GATK, run the following command: module load gatk. The default version will be loaded.

        Usage

        This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable. From module load gatk, a new environment variable, GATK, will be set. Thus, users can use the software by running the following command: gatk {other options},e.g  run gatk -h to see all options.

        Known Issues

        CBLAS undefined symbol error

        Update: 05/22/2019 
        Version: all

        If you use GATK tools that need CBLAS (e.g. CreateReadCountPanelOfNormals), you might encounter an error as

        INFO: successfully loaded /tmp/jniloader1239007313705592313netlib-native_system-linux-x86_64.so
        java: symbol lookup error: /tmp/jniloader1239007313705592313netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dspr
        java: symbol lookup error: /tmp/jniloader1239007313705592313netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dspr

        The error raises because the system-default LAPACK does not support CBLAS.  The remedy is to run GATK in conjunction with lapack/3.8.0:

        $ module load lapack/3.8.0
        $ module load gatk/4.1.2.0
        $ LD_LIBRARY_PATH=$OSC_LAPACK_DIR/lib64 gatk AnyTool toolArgs
        

        Alternatively, we recommend using the GATK container. First, download the GATK container to your home or project directory

        $ qsub -I -l nodes=1:ppn=1
        $ cd $TMPDIR
        $ export SINGULARITY_CACHEDIR=$TMPDIR
        $ SINGULARITY_TMPDIR=$TMPDIR 
        $ singularity pull docker://broadinstitute/gatk:4.1.2.0
        $ cp gatk_4.1.2.0.sif ~/

        Then run any GATK tool via

        $ singularity exec ~/gatk_4.1.2.0.sif gatk AnyTool ToolArgs
        

        You can read more about container in general from here. If you have any further questions, please contact OSC Help.

        Further Reading

        Supercomputer: 
        Service: 
        Fields of Science: 

        GLPK

        GLPK (GNU Linear Programming Kit) is a set of open source LP (linear programming) and MIP (mixed integer problem) routines written in ANSI C, which can be called from within C programs. 

        Availability and Restrictions

        Versions

        The following versions are available on OSC systems:

        Version Owens
        4.60 X*
        * Current default version

        You can use module spider glpk to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        GLPK is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        GNU, Open source

        Usage

        Set-up

        To set up your environment for using GLPK on Oakley, run the following command:

        module load glpk

        Compiling and Linking

        To compile your C code using GLPK API routines, use the environment variable $GLPK_CFLAGS provided by the module:

        gcc $GLPK_CFLAGS -c my_prog.c

        To link your code, use the variable $GLPK_LIBS:

        gcc my_prog.o $GLPK_LIBS -o my_prog

        glpsol

        Additionally, the GLPK module contains a stand-alone LP/MIP solver, which can be used to process files written in the GNU MathProg modeling language.  The solver can be invoked using the following command syntax:

        glpsol [options] [filename]

        For a complete list of options, use the following command:

        glpsol --help

        Further Reading

        Supercomputer: 
        Service: 

        GMAP

        GMAP is a genomic mapping and alignment program for mRNA and EST sequences.

        Availability and Restrictions

        Versions

        The following versions of GMAP are available on OSC clusters:

        Version Owens
        2016-06-09 X*
        * Current default version

        You can use module spider gmap to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        GMAP is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        Genentech, Inc., Open source

        Usage

        Usage on Owens

        Set-up

        To configure your environment for use of GMAP, run the following command: module load gmap. The default version will be loaded. To select a particular GMAP version, use module load gmap/version. For example, use module load gmap/2016-06-09 to load GMAP 2016-06-09.

        Further Reading

        Supercomputer: 
        Service: 
        Fields of Science: 

        GNU Compilers

        Fortran, C and C++ compilers produced by the GNU Project. 

        Availability and Restrictions

        Versions

        GNU compilers are available on all our clusters. These are the versions currently available:

        Version Owens Pitzer Ascend Notes
        4.8.5 X# X#   **See note below.
        4.9.1        
        5.2.0        
        6.1.0 X      
        6.3.0 X      
        7.3.0 X X    
        8.1.0   X    
        8.4.0 X X   The variant supporting OpenMP and OpenACC offload is available.
        See the GPU offloading section below
        9.1.0 X* X* X  
        10.3.0 X X X  
        11.2.0 X X X*  
        * Current Default Version; # System version
        ** There is always some version of the GNU compilers in the environment. If you want a specific version you should load the appropriate module. If you don't have a gnu module loaded you will get either the system version or some other version, depending on what modules you do have loaded.

        You can use module spider gnu to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        To find out what version of gcc you are using, type gcc --version.

        Access

        The GNU compilers are available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        https://www.gnu.org/software/gcc/, Open source

        Usage

        Usage on Owens

        Set-up

        To configure your environment for use of the GNU compilers, run the following command (you may have to unload your selected compiler - if an error message appears, it will provide instructions): module load gnu.  The default version will be loaded. To select a particular GNU version, use module load gnu/version. For example, use module load gnu/4.8.5 to load GNU 4.8.5.

        How to Compile

        Once the module is loaded, follow the guides below for compile commands:

        Language non-mpi mpi
        Fortran 90 or 95 gfortran mpif90
        Fortran 77 gfortran mpif77
        c gcc mpicc
        c++ g++ mpicxx

        Building Options

        The GNU compilers recognize the following command line options :

        Compiler Option Purpose
        -fopenmp Enables compiler recognition of OpenMP directives (except mpif77)
        -o FILENAME

        Specifies the name of the object file

        -O0 or no -O  option Disable optimization
        -O1 or -O Ligh optimization
        -O2 Heavy optimization
        -O3 Most expensive optimization (Recommended)

        There are numerous flags that can be used. For more information run man <compiler binary name>.

        Batch Usage

        When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

        Interactive Batch Session
        For an interactive batch session, one can run the following command:
        sinteractive -A <project-account> -N 1 -n 28 -l -t 1:00:00
        
        which gives you 1 node and 28 cores (-N 1 -n 28),  with 1 hour (-t 1:00:00).  You may adjust the numbers per your need.
        Non-interactive Batch Job (Serial Run)
        batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. The following example batch script file will use the input file named hello.c and the output file named hello_results
        Below is the example batch script (job.txt) for a serial run:
        #!/bin/bash
        #SBATCH --time=1:00:00
        #SBATCH --nodes=1 --ntasks-per-node=28
        #SBATCH --job-name jobname
        #SBATCH --account=<project-account>
        
        module load gnu
        cp hello.c $TMPDIR
        cd $TMPDIR
        gcc -O3 hello.c -o hello
        ./hello > hello_results
        cp hello_results $SLURM_SUBMIT_DIR
        

        In order to run it via the batch system, submit the job.txt file with the following command:

        sbatch job.txt
        
        Non-interactive Batch Job (Parallel Run)
        Below is the example batch script (job.txt) for a parallel run:
        #!/bin/bash
        #SBATCH --time=1:00:00
        #SBATCH --nodes=2 --ntasks-per-node=28 
        #SBATCH --job-name jobname
        #SBATCH --account=<project-account>
        
        module load gnu
        mpicc -O3 hello.c -o hello
        cp hello $TMPDIR
        cd $TMPDIR
        mpiexec ./hello > hello_results
        cp hello_results $SLURM_SUBMIT_DIR
        

        Usage on Pitzer

        Set-up

        To configure your environment for use of the GNU compilers, run the following command (you may have to unload your selected compiler - if an error message appears, it will provide instructions): module load gnu.  The default version will be loaded. To select a particular GNU version, use module load gnu/version. For example, use module load gnu/8.1.0 to load GNU 8.1.0.

        How to Compile

        Once the module is loaded, follow the guides below for compile commands:

        LANGUAGE NON-MPI MPI
        Fortran 90 or 95 gfortran mpif90
        Fortran 77 gfortran mpif77
        c gcc mpicc
        c++ g++ mpicxx

        Building Options

        The GNU compilers recognize the following command line options :

        COMPILER OPTION PURPOSE
        -fopenmp Enables compiler recognition of OpenMP directives (except mpif77)
        -o FILENAME

        Specifies the name of the object file

        -O0 or no -O  option Disable optimization
        -O1 or -O Ligh optimization
        -O2 Heavy optimization
        -O3 Most expensive optimization (Recommended)

         

         

         

         

         

         

        There are numerous flags that can be used. For more information run man <compiler binary name>.

         

        Known Issues

        Type mismatch error

        GNU compiler versions 10+ may have Fortran compiler errors like

        Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(4)/REAL(8))
        

        that result in a error response during configuration

        configure: error: The Fortran compiler gfortran will not compile files that call
        the same routine with arguments of different types.

        This can be caused when codes are using types that don't match the subroutine arguement types. The mismatches are now reject with an error to warn about future errors that may occur. It is bypassable by appending the -fallow-argument-mismatch arguement while calling gfortran.

        Multiple definition error

        GNU compiler versions 10+ may have C compiler errors like

        /.libs/libmca_mtl_psm.a(mtl_psm_component.o): multiple definition of `mca_mtl_psm_component'
        

        This is a common mistake in C is omitting extern when declaring a global variable in a header file. In previous GCC versions this error is ignored. GCC 10 defaults to -fno-common, which means a linker error will now be reported.  It is bypassable by appending the -fcommon to compilation flags.

        Further Reading

        See Also

        Supercomputer: 
        Service: 
        Technologies: 
        Fields of Science: 

        GROMACS

        GROMACS is a versatile package of molecular dynamics simulation programs. It is primarily designed for biochemical molecules, but it has also been used on non-biological systems.  GROMACS generally scales well on OSC platforms. Starting with version 4.6 GROMACS includes GPU acceleration.

        Availability and Restrictions

        Versions

        GROMACS is available on Pitzer and Owens Clusters. Both single and double precision executables are installed. The versions currently available at OSC are the following:

        Version Owens Pitzer Ascend Notes
        5.1.2 SPC     Default version on Owens prior to 09/04/2018
        2016.4 SPC      
        2018.2 SPC SPC    
        2020.2 SPC* SPC*    
        2020.5 SPC SPC    
        2022.1 SPC SPC SPC*  
        2023.2 SPC SPC SPC  
        * Current default version; S = serial single node executables; P = parallel multinode; C = CUDA (GPU)

        You can use module spider gromacs  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        GROMACS is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        http://www.gromacs.org/ Open source

        Usage 

        Usage on Owens

        Set-up

        To load the module for the default version of GROMACS, which initializes your environment for the GROMACS application, use module load gromacs. To select a particular software version, use module load gromacs/version. For example, use module load gromacs/5.1.2 to load GROMACS version 5.1.2; and use module help gromacs/5.1.2 to view details, such as, compiler prerequisites, additional modules required for specific executables, the suffixes of executables, etc.; some versions require specific prerequisite modules, and such details may be obtained with the command   module spider gromacs/version.

        Using GROMACS

        To execute a serial GROMACS versions 5 program interactively, simply run it on the command line, e.g.:

        gmx pdb2gmx
        

        Parallel multinode GROMACS versions 5 programs should be run in a batch environment with srun, e.g.:

        srun gmx_mpi_d mdrun
        

        Note that '_mpi' indicates a parallel executable and '_d' indicates a program built with double precision ('_gpu' denotes a GPU executable built with CUDA).  See the module help output for specific versions for more details on executable naming conventions.

        Batch Usage

        When you log into Owens you are actually connected to a login node. To  access the compute nodes, you must submit a job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

        Interactive Batch Session
        For an interactive batch session on Owens, one can run the following command:
        sinteractive -A <project-account> -N 1 -n 28 -t 1:00:00
        
        which gives you one node with 28 cores (-N 1 -n 28), with 1 hour (-t 1:00:00). You may adjust the numbers per your need.
        Non-interactive Batch Job (Parallel Run)

        batch script can be created and submitted for a serial, cuda (GPU), or parallel run. You can create the batch script using any text editor in a working directory on the system of your choice. Sample batch scripts and input files for all types of hardware resources are available here:

        ~srb/workshops/compchem/gromacs/
        

        This simple batch script demonstrates some important points:

        #!/bin/bash
        # GROMACS Tutorial for Solvation Study of Spider Toxin Peptide
        # see fwspider_tutor.pdf
        #SBATCH --job-name fwsinvacuo.owens
        #SBATCH --nodes=2 --ntasks-per-node=28
        #SBATCH --account=PZS0711
        # turn off verbosity for noisy module commands
        set +vx
        module purge
        module load intel/18.0.3
        module load mvapich2/2.3
        module load gromacs/2018.2
        module list
        set -vx
        
        cd $SLURM_SUBMIT_DIR
        echo $SLURM_SUBMIT_DIR
        sbcast -p 1OMB.pdb $TMPDIR/1OMB.pdb
        sbcast -p em.mdp $TMPDIR/em.mdp
        
        cd $TMPDIR
        mpiexec -ppn 1 gmx pdb2gmx -ignh -ff gromos43a1 -f 1OMB.pdb -o fws.gro -p fws.top -water none
        mpiexec -ppn 1 gmx editconf -f fws.gro -d 0.7
        
        mpiexec -ppn 1 gmx editconf -f out.gro -o fws_ctr.gro -center 2.0715 1.6745 1.914
        mpiexec -ppn 1 gmx grompp -f em.mdp -c fws_ctr.gro -p fws.top -o fws_em.tpr -maxwarn 1
        mpiexec -ppn 1 ls -l 
        mpiexec gmx_mpi mdrun -s fws_em.tpr -o fws_em.trr -c fws_ctr.gro -g em.log -e em.edr
        
        cp -p * $SLURM_SUBMIT_DIR/
        

        * Note that sbcast does not recursively look through folders a loop in the jobscript is needed, please visit our Job Preparations page to learn more.

        Usage on Pitzer

        Set-up

        To load the module for the default version of GROMACS, which initializes your environment for the GROMACS application, use module load gromacs.

        Using GROMACS

        To execute a serial GROMACS versions 5 program interactively, simply run it on the command line, e.g.:

        gmx pdb2gmx
        

        Parallel multinode GROMACS versions 5 programs should be run in a batch environment with srun, e.g.:

        srun gmx_mpi_d mdrun
        

        Note that '_mpi' indicates a parallel executable and '_d' indicates a program built with double precision ('_gpu' denotes a GPU executable built with CUDA).  See the module help output for specific versions for more details on executable naming conventions.

        Batch Usage

        When you log into Pitzer you are actually connected to a login node. To  access the compute nodes, you must submit a job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

        Interactive Batch Session
        For an interactive batch session on Pitzer, one can run the following command:
        sinteractive -A <project-account> -N 1 -n 40 -t 1:00:00
        
        which gives you one node and 40 cores (-N 1 -n 40) with 1 hour (-t 1:00:00). You may adjust the numbers per your need.
        Non-interactive Batch Job (Parallel Run)

        batch script can be created and submitted for a serial, cuda (GPU), or parallel run. You can create the batch script using any text editor in a working directory on the system of your choice. Sample batch scripts and input files for all types of hardware resources are available here:

        ~srb/workshops/compchem/gromacs/
        

        This simple batch script demonstrates some important points:

        #!/bin/bash
        # GROMACS Tutorial for Solvation Study of Spider Toxin Peptide
        # see fwspider_tutor.pdf
        #SBATCH --job-name fwsinvacuo.owens
        #SBATCH --nodes=2 --ntasks-per-node=28
        #SBATCH --account=PZS0711
        # turn off verbosity for noisy module commands
        set +vx
        module purge
        module load intel/18.0.3
        module load mvapich2/2.3
        module load gromacs/2018.2
        module list
        set -vx
        
        cd $SLURM_SUBMIT_DIR
        echo $SLURM_SUBMIT_DIR
        sbcast -p 1OMB.pdb $TMPDIR/1OMB.pdb
        sbcast -p em.mdp $TMPDIR/em.mdp
        
        cd $TMPDIR
        mpiexec -ppn 1 gmx pdb2gmx -ignh -ff gromos43a1 -f 1OMB.pdb -o fws.gro -p fws.top -water none
        mpiexec -ppn 1 gmx editconf -f fws.gro -d 0.7
        
        mpiexec -ppn 1 gmx editconf -f out.gro -o fws_ctr.gro -center 2.0715 1.6745 1.914
        mpiexec -ppn 1 gmx grompp -f em.mdp -c fws_ctr.gro -p fws.top -o fws_em.tpr -maxwarn 1
        mpiexec -ppn 1 ls -l 
        mpiexec gmx_mpi mdrun -s fws_em.tpr -o fws_em.trr -c fws_ctr.gro -g em.log -e em.edr
        
        cp -p * $SLURM_SUBMIT_DIR/
        

        * Note that sbcast does not recursively look through folders a loop in the jobscript is needed, please visit our Job Preparations page to learn more 

         

        Further Reading

        Supercomputer: 
        Service: 

        GSL

        GSL is a library of mathematical methods for C and C++ languages.

        Availability and Restrictions

        Versions

        GSL is available on all clusters. The versions currently available at OSC are:

        Version Owens Pitzer Ascend
        2.6 X* X*

         

        2.7.1    

        X*

        * Current default version

        You can use module spider gslto view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access

        GSL is available to all OSC users. If you have any questions, please contact OSC Help.

        Publisher/Vendor/Repository and License Type

        GNU opensource

        Usage

        Usage on Owens

        Set-up

        To configure your environment for use of GSL, use the command module load gsl. This will load the default version.

        Usage on Pitzer

        Set-up

        To configure your environment for use of GSL, use the command module load gsl. This will load the default version.

        Usage on Ascend

        Set-up

        To configure your environment for use of GSL, use the command module load gsl. This will load the default version.

        Further Reading

        Supercomputer: 

        Gaussian

        Gaussian is a very popular general purpose electronic structure program. Recent versions can perform density functional theory, Hartree-Fock, Möller-Plesset, coupled-cluster, and configuration interaction calculations among others. Geometry optimizations, vibrational frequencies, magnetic properties, and solution modeling are available. It performs well as black-box software on closed-shell ground state systems. 

        Availability and Restrictions

        Versions

        Gaussian is available on the Pitzer and Owens Clusters. These versions are currently available at OSC (S means single node serial/parallel and C means CUDA, i.e., GPU enabled):

        Version Owens Pitzer Ascend
        g09e01 S    

        g16a03

        S

        S  
        g16b01 SC S  
        g16c01 SC* SC*  
        g16c02     SC*
        * Current default version

        You can use module spider gaussian to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

        Access for Academic Users

        Use of Gaussian for academic purposes requires validation. In order to obtain validation, please contact OSC Help for further instruction.

        Publisher/Vendor/Repository and License Type

        Gaussian, commercial

        Usage

        Usage on Owens

        Set-up on Owens

        To