Getting Started

Getting Started icon

Welcome to OSC! If you are new to supercomputing, new to OSC, or simply interested in getting an account (if you don't already have one), we have some resources to help you.

New User Resource Guide

Welcome to OSC! This document provides some useful links to get you started.

If you are new to supercomputing, or to OSC, please visit for information about how our supercomputers are configured, and some guidance about appropriate usage of the various resources.

Logging in to OSC resources is primarily accomplished via SSH (or “secure shell”). This is a method of getting a command line interface on the HPC, which is running a version of the Linux operating system. For more details on how to connect to our systems, please visit


If that sounds too intimidating, and you would like to try a zero-client web-browser approach to using OSC, you can log in to OnDemand:


SFTP (Secure File Transfer Protocol) is the primary method of moving files to and from OSC storage systems. SCP (Secure CoPy) is another common method. Small files can be moved to and from OSC systems inside of OnDemand. Moving large files to or from OSC via the login nodes can experience difficulty, since there are compute restrictions on those nodes, so the recommendation is to connect to, or If you have a large amount of data to move, you can schedule transfers via Globus Online.

Batch scripts – instructions to be executed by the node(s) assigned to you when your request for resources can be met by the scheduler – can get very complicated, so it’s best to refer to the documentation for the software you want to use to get started.


We also have a more detailed guide on the batch system that we recommend new users read. It provides information about scheduling, and how to write scripts to accomplish various tasks.


Account Maintenance and Usage: Please use MyOSC to update your password, shell, and check usage on the project. The command OSCusage will also provide usage details. 

Need Help? Support can be found by contacting OSC Help weekdays, 9AM to 5PM (1-800-686-6472 or 614-292-1800). 
Fill out a request online. 

We regulary maintain our webpages to show relevant events at the center (including training) and system notices on our main page ( We also provide important information in the “message of the day” (visible when you log in). Furthermore, you can receive notices by following @HPCNotices on Twitter. 

Useful Links:


Main Supercomputing pages:

Documentation Attachment: 

HPC Basics


Using the HPC or “supercomputer” 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

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.


You can access OnDemand by pointing a web browser to 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.
  •, 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:

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

Note: The 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 Oakley cluster with X11 forwarding:

$ ssh -X

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.

Allocations and Accounts

The Ohio Supercomputer Center provides cycles to both academic and industrial clients. The methods for gaining access to the systems are different for each user community.

Primarily, our users are Ohio-based and academic, and the vast majority of our cycles will continue to be consumed by Ohio-based academic users. Those cycles are allocated to academic PIs via an allocations process overseen by the Statewide Users Group, which evaluates applications via a peer review process. There are two basic classes of academic allocations:

  1.  an allocation of a number of resource units (RUs) that never expire
  2.  an annual allocation process that awards an RU allocation for the upcoming calendar year. The annual allocation process is designed for "discovery level" users, who consistently consume large amounts of resources, and allow the Allocations Committee to better allocate the limited Center resources.

Other users (non-Ohio academic or industrial/commercial) interested in using Center resources may purchase cycles at a rate set by the expected total consumption. Expert consulting support is also available.

You may find more information about "RU" calculation and charging here.

  Ohio Academic Other
  Rolling Annual Rolling
Duration Unlimited 1 year Unlimited
Allocation Approval SUG SUG OSC Director
Call for Proposals At any time November At any time
  Apply [By invitation] Apply

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.

Once a project has been created, the PI can create accounts for users by contacting OSC Help to add existing users to that project

I need to add authorized users to my project

Please contact OSC Help. We require PI approval. 

I need additional resources for my existing project

If you already have a project, but are running low on allocated resources, you can click on the links above for your project type to request additional resources.

See our Project Application page for more information. 

I wish to use OSC to support teaching a class

We provide special classroom allocations for this purpose. You may apply here. See our Project Application page for more information. 

I don't think I fit in the above categories

Please contact us.

Managing Your Account

Once your account is set-up, you will receive a welcome letter from us containing your username and instructions for setting up your account.

MyOSC, one of our web portals, provides services to OSC users, including:

  • Password changes and resets for your HPC accounts
  • Changing your UNIX shell
  • Updating your email address
  • Tracking your project(s) balance​

Note: HPC password changes and resets take 3-5 minutes to process. If you attempt to login with your new password, you will receive an error. Too many failed login attempts results in your account being automatically locked for 5 minutes.


Are the answers you're looking for not here? Contact OSC Help


Managing Your 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 OSC Help with the information. PIs are also responsible for monitoring their project's Resource Unit balance and for submitting a proposal to the Allocations Committee of the Statewide Users Group before the balance goes negative. Projects with negative balances are subject to restrictions, causing submitted jobs to have lower priority in the queue. We have a resource page for your convenience. 

Allocation managment for Ohio-based academic projects

Eligible Principal Investigators must be tenure-track faculty members or permanent research scientists at Ohio colleges or universities. All other researchers, such as postdoctoral researchers, graduate students, and undergraduate students, may be authorized users under a project led by an eligible PI.

Principal Investigators who plan to submit a proposal for additional resource units should have the following information ready when they fill out the application form:

  • names, departments, affiliations, and email addresses of new authorized users
  • names and email address of two or three suggested peer reviewers
  • document with performance reports and justification for request
  • electronic version of resume/CV
  • list of publications and presentations that cite OSC
  • proposal text
  • document with other pertinent information (optional)

Send a query to or to if you require more detailed information concerning the application process.

Once a proposal has been approved for peer review, any restrictions that have been accrued due to a negative balance will be lifted. The Allocations Committee meets every other month (even-numbered months), and awards are made after the meeting.

Account Maintenance and Usage: Please use MyOSC to update your password, shell, and check usage on the project. The command OSCusage will also provide usage details. 

Allocation managment for purchased cycles

Please disregard any RU messages or instructions to apply for additional resources. If you have any billing questions, please consult your contact at OSC or inquire with OSC Help.



Project Applications

Applying for Academic Projects

Statewide academic allocation of computing resources and services is a peer-reviewed account process governed by the Allocations Committee of the Statewide Users Group and subject to the Ohio Supercomputer Center (OSC) Code of Ethics for Academic Users.

The procedures described enable services to be available to approved projects conducted by eligible principal investigators (PIs) at Ohio academic institutions. 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 unviersity). 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 contact OSC Help to add new authorized user(s) to a project at any time.

All first-time PIs must submit a signature page (electronically or hard copy). Please send a copy of the signature page to the attention of the Allocations Committee, OSC, 1224 Kinnear Road, Columbus, Ohio, 43212.

OSC's online project application 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 Project Application Help page. From this help page, please note the required materials for each request. Have all information and materials (suggested reviewer names and addresses, proposal text file names, etc.) at hand before you begin the application form. You can save a partially completed project application form for later use. As a reminder, you cannot re-submit application materials if they have already been used. 

Online Project and Account Application Form (NEW OSC PI)
Online Project Application Form (EXISTING PI)
Classroom Project Application Form (use our resources and software in the classroom)

If you need assistance, please contact OSC Help.

Applying for Commercial Access

Researchers from commercial organizations who wish to use the OSC's resources should complete the Ohio business request form or request access through the form for someone other than an Ohio business or academic researcher.

Add a new user

Please submit your request to OSC Help or use our online submission form. For reference, we will need the following:

Full Name:
If not U.S. Citizen, country of citizenship:
Email address:
Special Requests?

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 account application process; it merely states that OSC is willing to support such application.] 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
  • number of RUs 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, 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. We also occasionally offer training classes on this topic.


Classroom Project Resource Guide

Welcome to OSC! 

This document includes some useful information to help your classroom use of our resources be effective.

Application: Please submit an application for a classroom project. We will require your resume/CV as the instructor and PI of the project, a class roster with email addresses, and a class syllabus. 

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; included are basics on getting connected, HPC system structure, file transfers, and batch systems.

Resources: We currently have three production clusters, Oakley, Ruby, and Owens, with Nvidia GPUs available. All systems have "debug" queues, during typical business hours, that allow small jobs of less than 1 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.

Account Maintenance: Please use MyOSC to update your password, shell, and check usage on the project.

SupportHelp can be found by contacting OSC Help weekdays, 9AM to 5PM (1-800-686-6472 or 614-292-1800).
Fill out a request online. 


We regulary maintain our webpages to show relevant events at the center (including training) and system notices on our main page ( We also provide important information in the “message of the day” (visible when you log in). Furthermore, you can receive notices by following @HPCNotices on Twitter. 

Useful Links:


Main Supercomputing pages:


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.


HOWTO: Add python packages using the conda package manager

While our python installations come with many popular packages installed, you may come upon a case where you need an addiditonal package that is not installed.  If the specific package you are looking for is available from (formerlly you can easily install it and required dependencies by using the Conda package manager.

To be able to install a package using the conda package manager:

  • You must use a Anaconda distribution of python:
    • On Oakley the following modules:
      • python/2.7.latest*, python/2.7.8, python/3.4.2
    • On Ruby:
      • python/2.7.latest*, python/2.7.8, python/3.4.2
    • On Owens:
      • python/2.7, python/3.5
  • * = latest suffix refers to a distribution that will be electively updated
  • Package should be available through and/or using pip (see next section).

If you would like to freeze a distribution so that you can control how often you update Anaconda, please send us a help request at

But I use virtualenv and/or pip!

See the comparison to these package management tools here:

Pip installations are supported:

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

If binaries exist in a pip installation they are usually installed in:


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 Python 2 and Python 3, then be aware of the potential trouble in using the same installation location for all Python versions.

Virtualenv may also work, but is not under active testing at OSC.


We will install the yt package to a local directory in this example.

Load proper python module

module load python/2.7.8

Clone python installation to local directory

conda create -n local --clone="$PYTHON_HOME"

This will clone the entire python installation to ~/envs/local directory. The process will take serveral minutes.

conda create -n local

This will create a local python installation without any packages. If you need a small number of packages, you may choose this option.

conda create -n local python={version} anaconda

If you like to install a specific version of python, you can specify it with "python" option. For example, you can use "python=2.4" for version 2.4.

Activate clone environment

source activate local

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 package

conda install yt
  • Replace yt with the name of the package you want to install, as listed by
If there are errors on this step you will need to resolve them before continuing.

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.

python -c "import yt;print yt.__file__"


  • Replace both instances of yt  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 newlly installed package.  Packages are only installed to one version of python.

Install your own python modules

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

Further Reading:

Conda Test Drive: 

HOWTO: Install your own python modules

While we provide a number of Python 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 Python modules, and make them available inside of Python. 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.

Please consider using conda python package manager before you try to build python using the method explained here. We have an instruction on conda here.

Gather your materials

First, you need to collect up what you need in order to do the installation. To keep things tidy, we will do all of our work in $HOME/local/src . You should make this directory now.

mkdir -p $HOME/local/src

Now, we will need to download the source code for the module we want to install. In our example, we will use "NumExpr", a module we already provide in the system version of Python. 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

Now, 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-2.0.1.tar.gz

You can delete the downloaded archive now, if you wish, or leave it around should you want to start the installation from scratch.

Build it!


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

export INSTALL_DIR=${HOME}/local/numexpr/2.0.1

I am following, roughly, 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 (2.0.1). Now, to be consistent with python installations, we're going to create a second temporary environment variable, which will contain the actual installation location.

export TREE=${INSTALL_DIR}/lib/python2.7/site-packages

Now, make the directory tree.

mkdir -p $TREE


To compile the module, 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 module, if it hasn't already been loaded.

module swap intel gnu
module load python

Now, build it. This step may vary a bit, depending on the module you are compiling. You can execute python --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.

python install --prefix=$INSTALL_DIR

Make it usable

At this point, the module is compiled and installed in ~/local/numexpr/2.0.1/lib/python2.7/site-packages . Occasionally, some files will be installed in ~/local/numexpr/2.0.1/bin as well. To ensure Python can locate these files, we need to modify our environment.


The most immediate way - but the one that must be repeated every time you wish to use the module - 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/2.0.1/bin

And, for the python libraries:

export PYTHONPATH=$PYTHONPATH:~/local/numexpr/2.0.1/lib/python2.7/site-packages

Hardcode it

We don't really 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 - 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/modulefiles/numexpr/2.0.1.lua :

-- This is a Lua modulefile, this file 2.0.1.lua can be located anywhere
-- But if you are following a local modulefile location convention, we place them in
-- $HOME/local/share/modulefiles/
-- For numexpr we place it in $HOME/local/share/modulefiles/numexpr/2.0.1.lua
-- This finds your home directory
local homedir = os.getenv("HOME")
pathJoin(homedir, "/local/numexpr/2.0.1/lib/python2.7/site-packages"))
prepend_path(homedir, "local/numexpr/2.0.1/bin"))


Once your module is created (again, see the guide), you can use your python module simply by loaded the software module you created.

module use $HOME/local/share/modulefiles/
module load numexpr/2.0.1

HOWTO: Configure the MATLAB Parallel Computing Toolbox


The MATLAB Parallel Computing Toolbox and Distributed Computing Server are designed to allow users to create and launch parallel MATLAB jobs on a cluster of compute nodes. It also allows users to remotely connect to OSC resources, whether to run parallel jobs in MATLAB or to use toolboxes for which users own their own licenses. This guide will explain the basics of how to configure your Parallel Computing Toolbox for OSC systems.


The following versions of the MATLAB Parallel Computing Toolbox are supported at OSC:

R2013a X
R2013b X
R2014a X
R2014b X
R2015a X
R2015b X

Usage Overview

When you use the MATLAB Parallel Computing Toolbox, you have a MATLAB client session and one or more MATLAB workers. The client session may run on your laptop/desktop computer ("remote client") or it may run on an OSC login, OnDemand, or compute node. The MATLAB workers always run on the OSC cluster as part of a batch job. In the client session you will run MATLAB commands to set up and run a batch job, and MATLAB submits the job for you.

This document describes how to perform a computation on a single worker (one processor) or on multiple workers using a script with a "parfor" loop.

Licensing issues

You must have a license for MATLAB and the MATLAB PCT to allow you to run the MATLAB client session on your laptop/desktop computer. OSC has licenses for the MATLAB Distributed Computing Server, which covers the MATLAB workers running on the cluster.

OSC is included in the OSU site license for MATLAB, so OSC users have the option of running the client session on an OSC machine. You can manage and view your MATLAB licenses using the Mathworks License Center.

In any case, in order to use MDCS license on OSC, you need to be added to the license server. So, please contact OSC Help

Remote client

If you run your MATLAB client session on your local computer, it is considered a remote client. You will be able to use any toolboxes that you have a license for by submitting batch jobs from your MATLAB client. The batch jobs you submit from your MATLAB client through the PCT will be able to utilize functions such as "parfor" and "spmd" to run your code in parallel, in addition to being able to run normal MATLAB code.

Client running on Oakley

Through the MATLAB installations on Oakley, you will be able to take advantage of the interactive capabilities in the MATLAB PCT, as well as submitting batch jobs through the MATLAB client sessions. OnDemand or VNC is needed to use this (the MATLAB PCT is GUI only at this time), but it will allow you to debug your parallel jobs using various tools in real time. Jobs submitted through the client sessions on Oakley behave the same as jobs submitted by qsub, but can utilize the PCT functions such as "parfor" and "spmd".

Performance limitations

Parallel MATLAB on a cluster has a lot of overhead. It may not give you the speedup you expect, especially if you're solving small problems. Another consideration is that the MATLAB workers are single-threaded. They don't take advantage of the multithreading built into many MATLAB functions.

Download and Install the Configuration Files

The first step is to download the necessary configuration files to the computer where you will be running the MATLAB client session.

    Click the link below to download the files.


    OSCMatlabPCT Configuration Resources -- Directory Structure

    The OSC MATLAB PCT Configuration package contains the following files and directories:

    OSCMatlabPCT (top-level directory)

    • config - A directory containing the cluster profiles and configuration functions for using the MATLAB PCT at  OSC.  Note: the only function that users should edit is the "addSubmitArgs" function, as this allows setting some additional batch options, such as walltime, email, and custom job name.  All the other functions have been specially prepared by OSC staff to allow MATLAB to work in harmony with the HPC system on Oakley.
    • launch - A directory containing two scripts, "client_session_script.m" for launching jobs and "reconnect_client_session.m" for reconnecting to a job.  These scripts illustrate key concepts of using the PCT when accessing our system remotely via the MATLAB client on your personal computer.  They also apply to submitting batch jobs from a MATLAB client running in OnDemand.  Both scripts are heavily commented and give usage details beyond what this document can provide.  Note that these scripts contain commands to be run in your client session; do not submit them using the batch command.
    • PCTtestfiles -  A directory containing parfor use-cases. The first, "eigtest", is an example of how to program an extremely simple entry function using parfor.  It simply computes the eigenvalues of multiple large, random matrices.  The second case, is an example of how to run a parallel Simulink simulation using parfor.  The entry function is "paralleltestv2", which calls the function "parsim" inside a parfor loop.  The "parsim" script contains commands that initialize Simulink and run the simulation on each of the parfor workers.

    Import and Configure the Cluster Profile

    These configuration steps need to be done once before you use PCT.  (If you upgrade to a new version of MATLAB you'll have to reconfigure.)  There are also command line options for performing these tasks.

    1. After launching MATLAB, click the "Parallel" dropdown menu from the "Environment" menu and select "Manage Cluster Profiles".  At this time, a new window should open displaying the Cluster Profile Manager.  

    Image of MATLAB Parallel Menu

    2. In the Cluster Profile Manager window, click the "Import" button and locate the "clusterProfiles" directory contained within the OSCMatlabPCT/config/clusterProfiles directory.  

    Cluster profiles are named according to filesystem configuration and version.  Select the file which corresponds to your current version of MATLAB and your filesystem configuration.  If you're running remotely on your laptop/desktop computer select a "NonShared" version.  If you're running on Oakley, select a "Shared" version.  Click "Open" to proceed.  

    Screen shot 2014-06-06 at 11.14.32 AM.png

    3. If you are using a shared filesystem configuration: No further modifications will need to be made to the cluster profile, and you can close the Cluster Profile Manager and continue with configuring your job. 

    If you are using a non-shared filesystem configuration: You will need to make some changes to your cluster profile before exiting the Cluster Profile Manager.  Click the "Edit" button to enable editing.

    Screen shot 2014-06-06 at 11.36.41 AM.png

    4. In the editing window under "Submit Functions", you should see two entries -- IndependentSubmitFcn and CommunicatingSubmitFcnIntel.  These fields contain cell arrays with three values: a handle to the submit function, the hostname of the cluster, and the remote job storage location where results files and logs will be stored.  You only need to change the remote job storage location.  Use an absolute path to a location in your OSC home directory where you'd like the output of your job (or jobs) to be retained.  

    Image of MATLAB Cluster Profile Properties

    Here is an example of the full syntax:

    {@independentSubmitFcn, '', '/my/home/dir/MATLAB'}

    {@communicatingSubmitFcnIntel, '', '/my/home/dir/MATLAB'}

    Note:  If you try to validate your configuration, the last test will always fail for remote clients, even if the configuration is correct.

    5. Include the configuration files in your MATLAB path.  Click on "Set Path", then "Add Folder".  Locate and select the OSCMatlabPCT\config directory.  Click "Select Folder" and "Save".  (Alternatively you can use the "addpath" command in the MATLAB command window.)

    Configure and Run a Batch Job

    The primary way to utilize the MATLAB PCT at OSC is to submit batch jobs from the MATLAB client, either on your local PC or on Oakley via OnDemand.  These instructions assume that you have already configured your MATLAB client as described above.

    IMPORTANT: MATLAB treats the output directory specified with the submit functions as SCRATCH file space, and will cleanup this directory after you have successfully retrieved your data.  However, in practice it has been observed that MATLAB sometimes cleans up this directory even if the commands are unsuccessful (such as in the case of a large file transfer).  To avoid data loss, please make sure your entry function/script copies any important output files to an alternate location for redundancy.  Or simply save your data to a directory of your choice.
    1. Write your script to be run on the cluster.  This can be just a serial script or it may contain parallel commands such as "parfor".  Some example scripts are provided in the directory OSCMatlabPCT/PCTtestfiles.  The example below uses "eigtest.m" as the script to be run.
    2. In your client session:  Using "client_session_script.m" as a guide, run the commands to connect to the cluster and launch a batch job.  We don't recommend that you run the script as written, at least at first.  Until you're familiar with using the PCT, simply copy commands out of the script and paste them into your MATLAB command window as needed.  There are two important functions involved in launching a job.  The command "parcluster" creates a cluster object in the MATLAB workspace, which is used to store information sent between the remote cluster and your MATLAB client.  The command "batch" begins an automated process that can connect to the Oakley cluster, submit a job to PBS, and initialize the MATLAB Distributed Computing Server (MDCS).  For more on the batch command, see the "client_session_script.m" file, and the MATLAB help.
    3. When your job has been successfully configured, you will be prompted for your username and password at OSC.  After entering this, your job will be submitted to the system, and assigned an OSC job ID.  Please note: as explained in the "client_session_script" example, MATLAB remembers your jobs on the cluster by the job index number, not the OSC job ID.  Also, if you are unable to qstat your job immediately after it is submitted, don't worry!  There seems to be some latency between the MATLAB MDCS and the batch system when it comes to exchanging job status info, but this should not affect your ability to track your job.  In fact, as shown in the example, there are several ways to get information about your jobs directly from your MATLAB client. After submission you can check your job's progress or retrieve results at any time (even after closing the MATLAB client), and you can continue using the MATLAB client for other work if you wish.
    4. Wait for your job to complete.  You may use the "wait" command in your client session or simply monitor your job's status with "qstat" on an Oakley login node to know when your job has completed.
    5. Reconnect after closing your MATLAB client session.  The script "reconnect_client_session.m" illustrates how to find your job information again if you restart your MATLAB client session.
    6. Retrieve your results.  The "load" or "fetchOutputs" command retrieves the results of your computations from your MATLAB working directory on Oakley after the job has finished.  They also report errors if your run failed.  "Load" is used for exporting the workspace from an entry script, and "fetchOutputs" is used for retrieving the specified output arguments of an entry function.  For large data, there is an important caveat: MATLAB does not utilize sftp when fetching your files, so large files might take a long time to retrieve.  Additionally, if your output arguments/workspace is over a certain size (around 2GB), using the "load" or "fetchOutputs" commands will give an "index out of range" error caused by the MDCS failing to save the output to file.  This is due to an internal limitation in the default version of MATLAB's ".mat" files.  However, you may work around this limitation by manually saving your workspace or arguments in your entry script, using the '-v7.3' switch in the "save" command.

    Specifying Additional PBS Options for Your Batch Job

    The submit functions are MATLAB functions which serve two primary purposes: to create the appropriate connections to the cluster where your job will run, and to procedurally generate and submit a shell script to the queue on Oakley.  Your nodes and cores (ppn) are determined by the number of MATLAB workers you request in your submit script, however to change or add additional arguments or resource requests you must add the PBS commands to the string in the function "addSubmitArgs" (located in config).  The default arguments in the string are for a walltime of 1:00:00, a job name "default", and emails sent on abort, begin, and end of the job.  This function is called in the submit functions, so advanced users may choose to do what they wish with how this file is called in the submit functions to streamline their workflow if multiple configurations are needed.

    Configure and Run an Interactive Job

    There are a couple useful ways for OSU users to use the interactive features of the MATLAB PCT.  Because of our license terms, this option is available only to OSU faculty, staff, and students.

    Using OnDemand with a Shared Cluster Profile

    OSU users may take advantage of the MATLAB licenses on Oakley to submit interactive "parpool" (R2013b or later) or "matlabpool" (R2013a) jobs the batch system.  These MATLAB PCT functions allow you to run parallel functions such as "parfor" or "spmd" directly from command line or a script, and allow users to debug or interact with parallel jobs in real time.  OSC offers this functionality in MATLAB clients running through the OnDemand portal.  In this method, simply start on Oakley desktop session in OnDemand, open a terminal window, load the correct module, and start MATLAB.  Be sure the OSCMatlabPCT/config directory is in your path.  You will then import the correct shared cluster profile for your version of MATLAB, and use the "parpool" (R2013b or later) or "matlabpool" (R2013a) command to initialize an automatic parallel pool. This might take a while to set up, as the pool request must go throught the batch system like everything else, so be patient!  After a couple minutes or more (depending on the resource request), your pool will connect to the MATLAB workers, and you may begin running parallel commands. This will allow simulation of how jobs will behave when submitted to the MDCS as a batch job.

    Using VNC with the "local" Cluster Profile

    Another way to run an interactive parallel job using the MATLAB PCT is to submit an Interactive Batch job from using qsub, and run MATLAB on a compute node using VNC to utilize the GUI.  You can then import the "local" cluster profile, which runs the workers directly on the node.  Only one node can be used, but workers will run on multiple processors on the node.  This can be used in situations when using OnDemand is not ideal, but users should carefully follow the directions provided so as to not leave VNC processes behind on the node.  Directions for using VNC in a batch job are located here:">

    Additional Documentation">">Mathworks has written extensive documentation covering all of the public functions within the Parallel Computing Toolbox. The PCT homepage is located at">">The Mathworks Parallel Computing Toolbox Homepage.

    For more information about how to construct and run an independent job, see the Mathworks documentation page "">">Program Independent Jobs".  

    For more information about how to construct and run a communicating job, see the Mathworks documentation page "">">Program Communicating Jobs".


    If you have any errors related to the OSC MATLAB PCT configuration files, or have any other questions about utilizing the MATLAB PCT at OSC please contact OSC Help with: your user id, any relevant error messages, a job ID(s) if applicable, and the version of MATLAB you are using.

    HOWTO: Connect to OSC services using OSC Connect

    To connect to OSC services, a secure tunnel to a session is required. This can be done relatively simply in OSX and Linux by using the SSH functionality built into the system, but Windows users have had to configure and use third party applications like PuTTY or Java to access secure resources at OSC. OSC Connect is a native windows application written in C# and compiled for .NET 2.0, providing preconfigured management of secure tunnel connections for Windows users, as well as providing a launcher for secure file transfer, VNC, terminal, and web based services. 

    OSC Connect is supported on Windows versions from Windows XP through Windows 10.

    Getting Started

    1. Download the latest release of OSC Connect from here: Latest Build
      • Click OSCConnect.exe  and download. Use "Save link as" to download this file to a folder of your choice. 
      • See here for all the previous releases. 
    2. Double-Click the OSCConnect.exe icon to run the application. In the current state, OSC Connect is entirely deployed by a single executable file; no further installation is required.   ​
    3. When you run OSC Connect, a temporary folder named "ConnectFiles" with four additional files will be created. These are required for proper functionality of the application. Please ensure that these files are permitted by your IT administrator:
      • plink.exe is the command-line version of PuTTY used by the application to create the secure connection to OSC resources.
      • putty.exe  is the GUI application of PuTTY used to provide terminal emulation remote console connections to OSC resources.
      • vncviewer.exe is the VNC viewer client used to view a remote desktop session.
      • WinSCP.exe  is the SFTP client used for file transfer.
    4. Once your connections to OSC services as well as the OSC Connect app is closed, the temporary folder named "ConnectFiles" will be removed automatically. 

    OSC Connect Graphical User Interface

    After you double-click the  OSCConnect.exe  icon oscconnect_icon , the application graphical user interface is shown as below:


    • Network Status: it indicates which OSC cluster you will be connected to. The option can be changed in "Settings". 

    • Settings: it provides several configuration options to modify the behavior of the application. 

      • Connection Settings: use this dropdown to select the default host/cluster. Selecting a server here will change the endpoint for tunneling, sftp connections, console connections, and connectivity checking.

      • System Settings

        • Detect Clipboard Activity: when this option is enabled, the application will detect valid data on the Windows clipboard and populate the application. ( Default: Off )

        • Check for New Versions: when this option is enabled, the application will check for version updates. (Default: on)

      • Automation Settings:

        • Save User Credentials: when this option is enabled, it allows the application to remember the user when the application is reopened. This saves the user credentials to the user settings using DPAPI Encryption. Passwords are decrypted only by current the Windows user account. ( Default: Off )

        • Launch Tunnel On Import: when this option is enabled, the tunnel will automatically connect when the application detects a valid clipboard string and the user credentials have been entered. ( Default: On )

      • VNC Settings

    • ​About: it provides additional information about OSC Connect.

    After you provide your OSC Credentials, i.e. your OSC HPC username and password, more functionalities are available as shown below:


    • SFTP: it uses WinSCP as the SFTP client to securely connect to the OSC file system over SFTP.
    • Console: it uses PuTTY to provides you shell access to OSC cluster.

    In addition, Session Type is provided such that advanced users can connect to a running session mannually.

    For most users, you can ingore Session Type and are able to connect to a running session through OSC OnDemand using the configuration generated after your session starts. See "Connecting to a Session" for more details. 

    Connecting to a Session

    The OSC Connect application can be used to connect to a running session launched through OSC OnDemand.

    OSC Connect does not have the ability to launch a new session
    1. Navigate to OSC Demand to create a new session under either "Desktops" or "Desktop Apps". 
      • More information on how to use OSC OnDemand can be found here
    2. Once your session is running, you have two options to connect to the session: "noVNC Instructions" and "Native Client Instructions". Click "Native Client Instructions" to use OSC Connect. 
    3. Follow the steps below to connect to the running session:
      • Step 1: Download the latest OSC Connect if you don't already have it. See "Getting Started" for more details. 
      • Step 2: Launch OSC Connect. 
      • Step 3: Click - osc://xxxxx. osc://xxxxx is a custom URI scheme that is registered when you launch the application. Simply click the link to populate the configuration information and connect to your running session. If OSCConnect.exe is not running when you click the URI, the OSC Connect application will be popped up. Enter your OSC HPC username and password and you will be able to connect to the session by clicking the "Connect" button.
      • For advanced users, you can skip step 3 and connect to a running session mannually. Depending on the type of application, you can choose either "iHPC VNC Desktop" to create a VNC tunnel or "Web Browser Session" to create a browser tunnel. 
    Be sure to launch OSCConnect.exe at least once before you use it to connect to a running session. The initial launch will add a key to your user registry that initializes the URI scheme.  


    I've clicked the osc:// link and nothing happened.

    Be sure to run OSCConnect.exe at least once. The initial launch will add a key to your user registry that initializes the URI scheme. If you move or rename the OSCConnect.exe file, you will need to run the application again manually to update the path in the handler.

    I've received the error "Unable to open helper application. The protocol specified in this address is not valid."

    This issue appears in some earlier versions of Internet Explorer when attempting to launch the application from a Temporary location. Download and run the OSCConnect.exe application, being sure to save the file to a non-temporary location.




    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 you know the project account (projectID), the following command will list all users on the project:

    getent 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  getent group PZS0530  lists all users on the project account PZS0530 as below:

    bash-4.1$ getent group PZS0530

    If you don't know the project acccount, but know the user account

    If you don't know the project account, but know the user account, userID, use the  groups  command to list all of the groups the userID belongs to:

    groups userID

    The returned information is in the format of:

    userID : list of groups

    where the first item after " userID : " is the primary group, i.e. the project account (projectID) which userID is on. Once you know the project account, use the command  getent group projectID  as discussed in the previous session to list all users on this project.

    For example, with the userID as xwang, the command groups xwang  returns the information as below:

    bash-4.1$ groups xwang
    xwang : oscgen lstc gaussian ...

    It lists all groups xwang belongs to, and oscgen is the project account which xwang is on. The command  getent group oscgen  lists all user accounts on the project account oscgen:

    bash-4.1$ getent group oscgen

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

    If you don't know either the project account or user account, you can use ldapsearch  command to get the user account based on the user's registration information such as name, email address, etc. 

    Use the following command to list all of the user accounts accociated with the name First Last:

    ldapsearch -x -LLL "(gecos=First Last)" | grep cn | awk '{print $2}'

    Use the following command to list all of the user accounts accociated with the email address email@address:

    ldapsearch -x -LLL "(mail=email@address)" | grep cn | awk '{print $2}'

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

    ldapsearch -x -LLL "(gecos=Summer Wang)" | grep cn | awk '{print $2}' returns the information as below:

    bash-4.1$ ldapsearch -x -LLL "(gecos=Summer Wang)" | grep cn | awk '{print $2}'

    With user's email address as, the command ldapsearch -x -LLL "(" | grep cn | awk '{print $2}' returns the information as below:

    bash-4.1$ ldapsearch -x -LLL "(" | grep cn | awk '{print $2}'

    Once you know the user account userID, follow the discussions in previous session 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  finger  command to check the status of  a user account userID as below:

    finger userID

    For example, if the userID is xwang, the command  finger xwang  will return:

    bash-4.1$ finger xwang
    Login: xwang                            Name: Summer Wang
    Directory: /nfs/17/xwang                Shell: /bin/bash
    On since Tue Apr 19 09:58 (EDT) on pts/190 from localhost:43.0
    Mail forwarded to
    No mail.
    No Plan.
    • The home directory of xwang is on /nfs/17 ( Directory: /nfs/17/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 resticted. Please contact OSC Help if you'd like to reactivate this user account.
    • is the associated email with the user account xwang; that is, all OSC emails related to the account xwang will be sent to ( Mail forwarded to ). Please contact OSC Help if the email address asscoiated with this user account has been changed to ensure important notifications/messages/remindars from OSC may be received in a timely manner.

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

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

    As of 2016 Apr 20 04:02 userid userID on /nfs/nn used XGB of quota 500GB and Y files of quota 1000000 files

    The information is from the file /usr/local/quotas/quota_report.txt, which is updated daily. Some users may see multiple lines asscoiated with userid, as well as information on project space usage and quota, if there is one. The usage and quota of the home diretory of userID 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 ingored. 

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

    grep <userID OR projectID > /usr/local/quotas/quota_report.txt

    HOWTO: Install Local R Packages

    This document shows you the steps to install R packages locally without root access on OSC's Oakley cluster. 

    R comes with a single library  $R_HOME/library which contains the standard and recommended packages. This is usually in a system location. On Oakley cluster, it is   /usr/local/R/3.0.1/lib64/R/library . R also has a default value for a directory where users can install their own R packages. On Oakley cluster, it is ~/R/x86_64-unknown-linux-gnu-library/3.0 if the default R-3.0.1 module is loaded. This directory doesn't exist by default. The first time a user installs an R package, R will ask the user if s/he wants to use the default location and if yes, will create the directory.

    A Simple Example

    First you need to load the module for R:

    module load R

    On Oakley, the default R module is version 3.0.1 .

    Then fire up an R session:


    To install package lattice, use this command inside R:

    > install.packages("lattice", repos="")

    It gives a warning: 

    Warning in install.packages("lattice") :
    'lib = "/usr/local/R/3.0.1/lib64/R/library"' is not writable
    Would you like to create a personal library
    to install packages into?  (y/n) 

    Answer y , and it will create the directory and install the package there.

    Setting the Local R Library Path

    If you want to use another location rather than the default location, for example, ~/local/R_libs/ ,  you need to create the directory first:

    mkdir ~/local/R_libs

    Then type the following command inside R:

    > install.packages("lattice", repos="", lib="~/local/R_libs/")

    It is a bit of burden having to type the long string of library path every time. To avoid doing that, you can create a file .Renviron in your home directory, and add the following line to the file:

    export R_LIBS=~/local/R_libs/ 

    Whenever R is started, the directory ~/local/R_libs/ is added to the list of places to look for R packages and so:

    > install.packages("lattice", repos="")

    will have the same effect as the previous install.packages() command. 

    To see the directories where R searches for libraries, use the command:


    Setting The Repository

    When you install an R package, you are asked which repository R should use. To set the repository and avoid having to specify this at every package install, create a file .Rprofile in your home directory. This is the start up code for R. Add the following line to the file:

    cat(".Rprofile: Setting R repository:")
    repo = getOption("repos") 
    # set up the server from which you will download the package.
    repo["CRAN"] = "" 
    options(repos = repo)

    Now you only need to do 

    > install.packages("lattice")

    That will download the package lattice from and install it in ~/local/R_libs  .

    Updating Packages

    > update.packages() inside an R session is the simplest way to ensure that all the packages in your local R library are up to date. It downloads the list of available packages and their current versions, compares it with those installed and offers to fetch and install any that have later versions on the repositories.

    Removing packages

    > remove.packages("lattice") inside an R session to remove package lattice . An even easier way is just to go into the directory ~/local/R_libs and remove the directory lattice from there.



    Add-on packages in R installation guide (


    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, we must first load it, if it hasn't already been loaded.

    module load cpanminus

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

    perl -I /usr/local/cpanminus/perl5/lib/perl5 -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



    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.

    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:

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

    This structure is 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.

    NOTE: Ensure $HOME is the full path of your home directory. You can identify this from the command line with the command echo $HOME.

    After navigating to where you want to create the directory structure, run:

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

    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

    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.

    We will be useing 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("MANPATH", pathJoin(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

    Oakley, Ruby, and Owens 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 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" needs 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 created 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 give the output "~/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 shuold give the output "git version 2.9.0".

    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


    HOWTO: Reduce Disk Space Usage

    This "how to" 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, 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 bytess 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 {} \;

    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 conformation 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

    rm 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 a archive file system.  Requests for data to be moved to the archive file system should be larger than 1TB. 


    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.


    HOWTO: Submit multiple jobs using parameters

    Often users want to submit a large amount 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:

    #PBS -l nodes=1:ppn=12
    #PBS -l walltime=80:00:00
    #PBS -n week42_data8
    # Copy input data to the nodes fast local disk 
    cp ~/week42/data/source1/data8.out $TMPDIR
    cd $TMPDIR
    # Run the analysis 
    full_analysis data8.out
    # Copy results to proper folder
    cp  data8.out ~/week42/results

    Lets 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 thus 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:

    #PBS -l nodes=1:ppn=12
    #PBS -l walltime=80:00:00
    #PBS -n ${WEEK}_${DATA}
    # Copy input data to the nodes fast local disk 
    cp ~/${WEEK}/data/${SOURCE}/${DATA}.out $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 qsub's -v option to pass parameters to our template script.  The format for passing parameters is:

    qsub -v par_name=par_value[,par_name=par_value...]

    Submitting a 100 jobs using qsub -v 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 scritping language feel free to interpret/translate this python code for your own use.

    Here is the script that submits the jobs using the parameters:

    #!/usr/bin/env python
    import csv, subprocess
    parameter_file_full_path = "/nfs/12/user0123/week42/job_params.csv"
    with open(parameter_file_full_path, "rb") as csvfile:
        reader = csv.reader(csvfile)
        for job in reader:
            qsub_command = """qsub -v WEEK={0},SOURCE={1},DATA={2} template_1.pbs""".format(*job)
            #print qsub_command # Uncomment this line when testing to view the qsub command
            # Comment the following 3 lines when testing to prevent jobs from being submitted
            exit_status =, shell=True)
            if exit_status is 1:  # Check to make sure the job submitted
                print "Job {0} failed to submit".format(qsub_command)
    print "Done submitting jobs!"

    This script will open the CSV file specified by the variable parameter_file_full_path and step through the file line by line, submitting a job for each line using the lines values.  If the qsub 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:


    Where WEEK_VALUE ,SOURCE_VALUE, and DATA_VALUE are the first, second, and third comma separated values in the CSV file's current row, and template_1.pbs is the name of our template script.

    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:


    The submit script would read in the first row of this CSV file and form and  submit the following qsub command:

    qsub -v WEEK=week42,SOURCE=source1,DATA=data1 template_1.pbs

    Submitting Jobs

    Once all the above is done all you need to do to submit your jobs is make sure the CSV file is populated with the proper parameters and run the automatic submission script.  

    Before submitting a large amount of jobs for the first time using this method it is recommended you test our your implimentation with a small amount of jobs.

    HOWTO: Transfer files using Globus Connect

    Globus Connect Logo

    Globus Connect is a reliable, high-performance file transfer platform allowing users to transfer large amounts of data seamlessly between systems.  It aims to make transfers a "click-and-forget" process by setting up configuration details in the background and automating fault recovery.  

    Globus can be used for both file transfers between OSC and:

    • A computing institution with Globus installed (check with your site provider for availability) or
    • A personal computer (known as a personal endpoint)

    Users transferring between OSC and another computing institution with​ Globus installed do not need to install Globus Connect Personal, and can skip to Usage.

    More on how Globus works can be found on the Globus "How It Works" page.

    If you are looking to transfer smaller sized files you can utilize OnDemand's file transfer capabilities, or use a SFTP client to connect to . Our general recommendation is that for small files - measured in MB to several hundred MB - to use OnDemand or SFTP. You can continue to use SFTP and get reasonable performance up to file sizes of several GB. For transfers of several GB or larger, you should consider using Globus Online.

    Install Globus Connect Personal

    To use Globus to transfer from a personal computer, you will need to install the Globus Connect Personal client on your computer following the steps below. Those transferring between OSC and another computing institution can skip to Usage.

    1. Sign up for a free Globus account
    2. Download the Globus Connect Personal Client 
      • Click "Manage Endpoints" under the "Manage Transfers/Data" menu
      • Click "add Globus Connect" on the top-right of the page
      • Choose a unique name for your endpoint and generate the setup key
      • Download the Globus Connect client for your operating system
    3. Install Globus Connect Personal Client
      • Windows
        1. Run the Installer
        2. Copy-Paste the setup key to complete the installation
      • Mac​​
        1. Mount your drives
        2. Copy the Globus Client to your application Folder
        3. Start The Globus Client, and enter the provided setup key
      • Linux
        1. Un-tar the .tgz file with the command tar -zxvf
        2. Run globusconnect , found within the unzipped directory
        3. Copy-Paste the setup key when prompted
    4. (Optional) Changing directories accessible to Globus

    By default Globus will only add certain default folders to the list of files and directories accessible by Globus. To change/add/remove files and directories from this list:


    1. Start Globus Connect Personal
    2. Go to "Options"
    • Add directories/files using the  "+" button
    • Remove directories/files using the "-" button
    • Revert to the default accessible directories/files using the "Reset to Defaults" button
    • Any changes you make are not made permanent until you press the "Save" button


    1. Start Globus Connect Personal
    2. Go to Preferences -> Access
    • Add directories/files using the  "+" button
    • Remove directories/files using the "-" button
    • Revert to the default accessible directories/files using the "Reset to Defaults" button
    • Any changes you make are not made permanent until you press the "Save" button


    1. Configure the   ~/.globusonline/lta/config-paths  file. This file is a plain text file, with each line corresponding to the configuration of a particular directory path you wish to make accessible. Each line consists of 3 comma separated fields as below
      <path1>,<sharing flag>,<R/W flag>
      <path2>,<sharing flag>,<R/W flag>
      <path3>,<sharing flag>,<R/W flag>

      Path: an absolute directory/path to be permitted. A leading tilde "~" can be used to represent the home directory of the user that runs globusconnectpersonal.

      Sharing Flag: it controls sharing, with a value of "1" allowing sharing for the path and a value of "0" disallowing sharing for the path.

      R/W Flag: it determines whether the path will be accessible read-only or read/write, with a "1" permitting read/write access and a "0" marking the path as read-only. 

    2. After making a change to the ~/.globusonline/lta/config-paths file, you must stop and restart Globus Connect Personal before the changes will take effect as below
    $ ./globusconnectpersonal -stop
    $ ./globusconnectpersonal -start &


    1. Login to Globus and navigate to the "Transfer Files" under the "Manage Data" menu
    2. Enter your end point in one of the boxes
      • If transferring to a computer with Globus Connect Personal installed, this will be the unique name chosen during installation. It is also listed under "Administered by Me"
    3. Enter osc#gcs (OSC Globus Connect Server) as the other endpoint
      • Enter your OSC username and password for the authetication
    4. You can now transfer files and directories both ways by selecting them and pressing the arrow indicating which way you'd like to transfer
    If you are doing a large transfer you should transfer to/from the parallel file system or project space for best performance.
    Once a transfer has begun, you do not need to keep the Globus webpage up, but you will need to make sure the Globus Connect Personal Client is running on your computer until it has completed.  If the transfer is interrupted for any reason, Globus will attempt to re-initiate the transfer automatically.

    Further Reading

    HOWTO: Add InCommon Authentication to Globus

    (OPTIONAL) Adding InCommon Authentication 

    Adding InCommon authentication to your Globus account allows you to login to Globus Online using your university credentials.  Using this process you can store your Globus username password for safe keeping, and instead use your university username and password to login.  If your already logged in to your university authentication system, logging in to Globus can be as simple as two clicks away.

    To use this feature, your university needs to be a InCommon participant.  Some Ohio universities active in InCommon include: Ohio State University, Case Western University, Columbus State Community College, Miami University, Ohio Northern University, Ohio University, University of Findlay, University of Dayton, and many more.  

    For a complete list, visit .

    To add InCommon Authentication:
    1. Login to Globus Online
    2. Go to "Manage Identities" under your username
    3. Click "Add External Identity"
      • Choose a name for the Identity Settings. 
      • Choose InCommon / CILogon from the drop down menu
    4. On the next page, choose your University / Identity Provider
    • Click "Remember this selection"
    • Click "Log on"
    • You may be prompted to login to your university authentication system if you are not already

    When you go to login next, click "alternative login" and then "InCommon / CILogon".  Select your university on the next page, and login using your university credentials.  Globus will remember this preference, and automatically prompt you to login using your university authentication next time.

    HOWTO: Use Docker and Singularity Containers at OSC

    It is now possible to run Docker and Singularity containers on the Owens cluster 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."

    This document will describe how to run Docker and Singularity containers on Owens. You can use containers from Docker Hub, Singularity Hub, or any other source. As examples we will use vsoch/singularity-hello-world and ubuntu from Docker Hub.

    If you want to create your own container or modify a container, you will have to do it on a system where you have root access. You cannot build or update a container on Owens or any other OSC system.

    Getting help

    The most up-to-date help on Singularity comes from the command itself.

    singularity help
    singularity help exec

    The Singularity web site has documentation including a User Guide and examples.

    Setting up your environment for Singularity usage

    To load the Singularity environment on Owens, run the following command:

    module load singularity

    Accessing a container

    A Singularity container is a single file with a .img or .simg extension.

    You can either download (“pull”) a container from a hub or run it directly from the hub. Or just copy the container from anywhere.

    Examples of “pulling” a container:

    Example:  Pull from the 7.2.0 branch of the gcc repository on Docker Hub. The 7.2.0 is called a tag.

    singularity pull docker://gcc:7.2.0

    Filename:  gcc-7.2.0.img

    Example:  Pull the vsoch/singularity-hello-world container from the Singularity hub. Since no tag is specified it pulls from the master branch of the repository.

    singularity pull shub://vsoch/hello-world

    Filename:  vsoch-hello-world-master.img

    Example:  Pull an Ubuntu container from Docker Hub.

    singularity pull docker://ubuntu

    Filename:  ubuntu.img

    Running a container

    There are four ways to run a container under Singularity.

    You can do all 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.)

    We note that the operating system on Owens is Red Hat:

    [owens-login01]$ cat /etc/os-release
    NAME="Red Hat Enterprise Linux Server"
    VERSION="7.3 (Maipo)"
    PRETTY_NAME="Red Hat Enterprise Linux"
    REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 7"
    REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"

    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 an Ubuntu shell. (See also the “shell” sub-command below.)

    [owens-login01]$ ./ubuntu.img
    [owens-login01]$ cat /etc/os-release
    VERSION="16.04.3 LTS (Xenial Xerus)"
    PRETTY_NAME="Ubuntu 16.04.3 LTS"
    [owens-login01]$ exit

    Example:  Run vsoch/hello-world

    Note that this container returns you to your native OS after you run it.

    [owens-login01]$ ./vsoch-hello-world-master.img

    Use the “run” sub-command

    The Singularity “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]$ singularity run vsoch-hello-world-master.img

    Example:  Run a container from a hub without explicitly downloading it

    [owens-login01]$ singularity run shub://vsoch/hello-world
    Progress |===================================| 100.0%

    Use the “exec” sub-command

    The Singularity “exec” sub-command lets you execute an arbitrary command within your container instead of just the runscript.

    Example:  Find out what operating system the vsoch/hello-world container uses

    [owens-login01]$ singularity exec vsoch-hello-world-master.img cat /etc/os-release
    VERSION="14.04.5 LTS, Trusty Tahr"
    PRETTY_NAME="Ubuntu 14.04.5 LTS"

    Use the “shell” sub-command

    The Singularity “shell” sub-command invokes an interactive shell within a container.

    Example:  Examine the contents of the vsoch/hello-world container

    Note:  A container’s runscript is the file /singularity within the container.

    [owens-login01]$ singularity shell vsoch-hello-world-master.img
    Singularity: Invoking an interactive shell within container...
    Singularity vsoch-hello-world-master.img:~/singularity> ls /
    bin   dev  home  lib64       media  opt  run   singularity  sys  users  var
    boot  etc  lib   lost+found  mnt    proc  root     sbin  srv          tmp  usr
    Singularity vsoch-hello-world-master.img:~/singularity> cat /singularity
    exec /bin/bash /
    Singularity vsoch-hello-world-master.img:~/singularity> cat /
    echo "RaawwWWWWWRRRR!!"
    Singularity vsoch-hello-world-master.img:~/singularity> exit

    Example:  Run an Ubuntu shell. Note the “Singularity” prompt within the shell.

    [owens-login01]$ singularity shell ubuntu.img
    Singularity: Invoking an interactive shell within container...
    Singularity ubuntu.img:~/singularity> cat /singularity
    exec /bin/bash "$@"Singularity ubuntu.img:~/singularity> 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 (Owens) are

    • your home directory
    • working directory (directory you were in when you ran the container)
    • /fs/project
    • /fs/scratch
    • /tmp

    If you run the container within a job you will have the usual access to the $PFSDIR environment variable. In order to access $TMPDIR you must specify it on the command line as in this example:

    SINGULARITYENV_TMPDIR=$TMPDIR singularity shell ubuntu.img
    Note: Most environment variables are passed into the container by default, but for obscure reasons $TMPDIR is not. The above syntax passes it in explicitly.

    GPU usage within a container

    If you have a GPU-enabled container you can easily run it on Owens just by adding the --nv flag to the singularity exec or run command.  The example below comes from the exec command section of Singularity User Guide.  It runs a TensorFlow example using a GPU on Owens.  (Output has been omitted from the example for brevity.)

    [owens-login01]$ qsub -I -l nodes=1:ppn=28:gpus=1
    [o0756]$ cd $PBS_O_WORKDIR
    [o0756]$ module use /usr/local/share/lmodfiles/project/osc
    [o0756]$ module load singularity
     git clone
     singularity exec --nv docker://tensorflow/tensorflow:latest-gpu \
    python ./models/tutorials/image/mnist/



    HOWTO: Use NFSv4 ACL

    This document shows you how to use the NFSv4 ACL permissions system. An ACL 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.

    Understanding NFSv4 ACL

    This is an example of an NFSv4 ACL

    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 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

    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 '' 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


    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.



    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



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


    View ACLs

    To view ACLs, use the following command:

    nfs4_getfacl file

    Where file is your file or directory



    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 Oakley. 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 entire node, and then once your job starts, you can start the VNC server.

    qsub -I -l nodes=1:ppn=12:gpus=2:vis

    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/2.0

    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.)


    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

    Option 2: Batch

    This option is less optimal, because it is slightly more difficult to get the hostname and screen. However, by submitting a non-interactive batch job, you can go away and have the system email you when your desktop is ready to be connected to, and more importantly if your SSH connection to OSC is somewhat unstable and intermittent, you do not run the risk of being disconnected during your interactive session and having your VNC server terminated. In general, it is recommended you only use this option if running via an interactive session is not feasible.

    In order to start an VNC session non-interactively, you can submit the following script to the scheduler using qsub (adjusting your walltime to what you need):

    #PBS -l nodes=1:ppn=12:gpus=2:vis
    #PBS -l walltime=00:15:00
    #PBS -m b
    #PBS -N VNCjob
    #PBS -j oe
    module load virtualgl
    module load turbovnc/2.0
    sleep 100
    vncpid=`pgrep -s 0 Xvnc`
    while [ -e /proc/$vncpid ]; do sleep 0.1; done

    This script will send you an email when your job has started, which includes the hostname.

    PBS Job Id:
    Job Name:   VNCjob
    Exec host:  n0311/0-11
    Begun execution

    The screen is virtually always "1", unless someone else started a VNC server on that node outside of the batch system. You can verify the output of the vncserver command by using qpeek on a login node:

    qpeek jobid

    Where "jobid" is the batch system job number, for example, "9200155".


    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.


    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 Oakley.

    ssh -L

    Open your VNC client, and connect to "localhost:1" - this will tunnel to the correct node on Oakley.

    Option 2: Use your VNC software to tunnel 

    This example uses Chicken of the VNC, a MacOS VNC client.

    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.



    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.

    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!


    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

    Diagram showing network setup of license server that is directly externally reachable


    License Server is Behind Port Forwarding Firewall

    Diagram showing network setup of license server that is behind a port forwarding firewall



    If you are unsure about which category your situation falls under contact your local IT administrator.

    Configure Remote Firewall

    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), or two backup servers.

    The license server should be configured to allow connections from the following IP addresses to the SERVER:PORT where the license server is running:

    • (

    A typical FlexNet-based license server uses two ports: one is server port and the other is demon port, and the firewall should be configured for the both ports. A typical license file looks, for example,

    SERVER 0050XXXXX5C 28000
    VENDOR {license name} port=28001

    In this example, "28000" is the server port, and "28001" is the demon port. The demon 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 demon 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

    setenv LSTC_LICENSE network
    setenv LSTC_LICENSE_SERVER 2345@

    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 the environment variables instead of the IP address.
    2. Contact OSC Help 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.  


    Uses the following environment variables:



    HOWTO: Use ulimit command to set soft limits

    This document shows you how to set soft limits using 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.


    ulimit [-H] [-S] [-a] [-c] [-d] [-f] [-m] [-n] [-s] [-t] [Limit]
    flags description


    Lists all of the current resource limits


    Specifies the size of core dumps, in number of 512-byte blocks


    Specifies the size of the data area, in number of K bytes


    Sets the file size limit in blocks when the Limit parameter is used, or reports the file size limit if no parameter is specified. The -f flag is the default


    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


    Specifies the size of physical memory, in number of K bytes


    Specifies the limit on the number of file descriptors a process may have


    Specifies the stack size, in number of K bytes


    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


    Specifies the number of seconds to be used by each process

    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

    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 mpiexec 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 5-hour 2-node on Oakley cluster):
    #PBS -l nodes=2:ppn=12
    #PBS -l walltime=5:00:00
    #PBS ...
    mpiexec ./test1
    1. Prepare the wrapper script named "test1" as below:
    ulimit –c unlimited
    .....(your own program)
    1. qsub myjob

    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 connect to OSC system, professor runs submit_prepare as

    $ /fs/scratch/xwang/bin/submit_prepare

    Follow the instructions. It will create 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.


    The PI can also enforce 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, student will get an error message when he/she tries to submit assignment to this directory.

    Usage for Students

    Student should create one directory which includes all the files he/she wants to submit before running this script to sumit his/her assignment. Also, the previous submission of the same assignment from the student will be replaced by the new submission. 

    To submit the assignemt, student runs submit after connecting to OSC system as

    $ /path/to/directory/from/professor/submit

    Follow the instructions. It will allow students to submit assignment to designated directory speficifed by professor and send a confirmation email, or return error message.



    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.


    OSC services can be cited by visiting the documentation for the service in question and finding the "Citation" page (located in the menu on the left of the screen).

    HPC systems currently in production use can be found here:

    Decommissioned HPC systems can be found here:


    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.


    ark = {ark:/19495/f5s1ph73},
    howpublished = {\url{}},
    year  = {1987},
    author = {Ohio Supercomputer Center},
    title = {Ohio Supercomputer Center}


    %0 Generic
    %T Ohio Supercomputer Center
    %A Ohio Supercomputer Center
    %R ark:/19495/f5s1ph73
    %D 1987

    Here is an .ris file to better suit your needs. Please change the import option to .ris

    Documentation Attachment: 



    OSCusage is command developed at OSC for use on OSC's systems.  It allows for a user to see information on their project's current RU balance, including which users and jobs incurred what charges.


    Oakley ruby owens
    X X X



    OSCusage takes the following options and parameters.

    usage: OSCusage [-qvn] -[r|h] [MM/DD/YYYY] [MM/DD/YYYY]
             or [-i]
    Note: the year requires all 4 digits.
    OSCusage can only provide information on a user's primary project, visible with the command id -gn.  If you are a part of other projects, visible under id -Gn, you will be unable to pull information on those projects.  Contact OSC Help for assistance in getting such information.

    Today's Usage

    Running OSCusage with no options or parameters specified will provide RU usage information per a user for the current day.

    $ OSCusage
                         Usage Statistics for project PAS0435
                                for 5/3/2016 to 5/3/2016
                       PI: Dr. Judith Gardiner
                                 RU Balance: -17.88635
            Username  Dates                            RUs  Status
              osu525    5/3/2016 to   5/3/2016     0.00000  ACTIVE
             *osu391    5/3/2016 to   5/3/2016     0.00000  ACTIVE
             osu6396    5/3/2016 to   5/3/2016     0.00000  ACTIVE
             osu6445    5/3/2016 to   5/3/2016     0.00000  PASSWORD
             osu8968    5/3/2016 to   5/3/2016     0.00000  ACTIVE
     ===============   PAS0435 TOTAL    0.00000

    Users on Project

    Specifying -i provides information on the accounts under the project.

    $ OSCusage -i
                            Information for project PAS0435
                       PI: Dr. Judith Gardiner
                                 RU Balance: -17.88635
                Username    Status  Full Name
                 *osu391    ACTIVE  Dr. Judith Gardiner
                 osu6396    ACTIVE  Dr. Judith Gardiner
                 osu8968    ACTIVE  Koh Schooley

    RU Usage in Timeframe

    If you specify a timeframe you can get RU utilization information specifically for jobs that completed within that period.

    $ OSCusage 01/01/2016 05/01/2016
                         Usage Statistics for project PAS0435
                              for 01/01/2016 to 05/01/2016
                       PI: Dr. Judith Gardiner
                                 RU Balance: -17.88635
            Username  Dates                            RUs  Status
              osu525  01/01/2016 to 05/01/2016     0.00000  ACTIVE
             *osu391  01/01/2016 to 05/01/2016     0.00000  ACTIVE
             osu6396  01/01/2016 to 05/01/2016     0.00000  ACTIVE
             osu6445  01/01/2016 to 05/01/2016     0.00000  PASSWORD
             osu8968  01/01/2016 to 05/01/2016     0.15752  ACTIVE
     ===============   PAS0435 TOTAL    0.15752

    Show only my usage

    Specify -q to show only the current user's usage.

    $ OSCusage -q 01/01/2016 05/01/2016
                         Usage Statistics for project PAS0435
                              for 01/01/2016 to 05/01/2016
                       PI: Dr. Judith Gardiner
                                 RU Balance: -17.88635
            Username  Dates                            RUs  Status
             osu8968  01/01/2016 to 05/01/2016     0.15752  ACTIVE
     ===============   PAS0435 TOTAL    0.15752

    Detailed Charges Breakdown

    Specify -v to get detailed information on what job's incurred what charges.

    $ OSCusage -v 01/01/2016 05/01/2016
                         Usage Statistics for project PAS0435
                              for 01/01/2016 to 05/01/2016
                       PI: Dr. Judith Gardiner
                                 RU Balance: -17.88635
                            Start                 RUs     Charge           Status
            Username  Date  Date & Time          Used       Type     Queue           Job
     -------------            osu525 TOTAL    0.00000
     -------------           *osu391 TOTAL    0.00000
     -------------           osu6396 TOTAL    0.00000
     -------------           osu6445 TOTAL    0.00000
             osu8968 03/30  03/29 15:14:31    0.00277   CPU-Ruby    serial  E      STDIN
             osu8968 03/22  03/21 11:38:14    0.00005 CPU-Oakley    serial  E   login_en
             osu8968 03/22  03/21 11:48:25    0.00005 CPU-Oakley    serial  E   test_env
             osu8968 03/10  03/09 12:30:36    0.00066 CPU-Oakley    serial  E   test_pat
             osu8968 02/20  02/19 17:14:23    0.01266 CPU-Oakley  parallel  E   initial_
             osu8968 02/20  02/19 17:16:24    0.14133 CPU-Oakley  parallel  E   initial_
     -------------           osu8968 TOTAL    0.15752
     ===============   PAS0435 TOTAL    0.15752

    View Usage in Hours

    Specify -h to view the usage information in core hours, as opposed to RUs.

    $ OSCusage -h 01/01/2016 05/01/2016
                         Usage Statistics for project PAS0435
                              for 01/01/2016 to 05/01/2016
                       PI: Dr. Judith Gardiner
                                 RU Balance: -17.88635
                     Note: Listing is in HOURS, as opposed to RUs.
            Username  Dates                            HRS  Status
              osu525  01/01/2016 to 05/01/2016     0.00000  ACTIVE
             *osu391  01/01/2016 to 05/01/2016     0.00000  ACTIVE
             osu6396  01/01/2016 to 05/01/2016     0.00000  ACTIVE
             osu6445  01/01/2016 to 05/01/2016     0.00000  PASSWORD
             osu8968  01/01/2016 to 05/01/2016     1.57520  ACTIVE
     ===============   PAS0435 TOTAL    1.57520

    Usage on Secondary Group Projects

    Oct 3, 2017: This function is broken now. We are working to fix it soon. 

    Specifying -A provides usage information for all of the secondary group projects authorized under your account, including the primary project. This is mainly for Annual Allocations PIs. 

    $ OSCusage -A
    $ OSCusage -A 01/01/2016 05/01/2016

    No examples can be shown for this command. Please contact OSC Help with questions. 


    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?

    Any faculty member or research scientist at an academic institution in Ohio is eligible for an academic account at OSC. These researchers/educators may request accounts for their students and collaborators. Commercial accounts are also available.  More information about applying for both academic and commercial accounts at OSC can be found at

    Where should a new OSC user begin?

    The first thing you should do as a new OSC user is to check the email account that was given to OSC when you were registered.  If you are a PI, this will be the email address you entered in the primary contact information on your Project Request application. When your account is created, you will receive an email giving you information on how to start using the services at OSC.  Attached will be a letter you can keep for reference that contains your username and temporary password, as well as some other important information about using the systems at OSC.  After carefully reading the email, please first go to to change your temporary password.

    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?

    OSC receives funding from the state of Ohio. There is no charge for Ohio academic use. 

    How many supercomputers does OSC have?  Which one should I use?

    OSC currently has three HPC clusters: Owens Cluster, a 23,500+ core Dell cluster with Intel Xeon processors, Ruby Cluster, a 4800 core Intel Xeon machine from HP, and Oakley Cluster, a 8,300+ core HP Intel Xeon machine. New users have access to Owens and Oakley clusters. Ruby is currently unavailable for general access. 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

    How do I submit my publications and funding information to OSC?

    Please submit a list of publications, noting which cite OSC, as well as a list of current funding with your application materials for additional resources. Alternatively, please email the lists to OSC Help

    Can I receive 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 application process for time on OSC's systems. To receive the letter of support, please send your request to 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; number of RUs requested per year. Please allow at least two working days to process your request.

    Hardware information about the systems is available at

    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  

    Where can I find documentation?

    For documentation specific to software applications, see Software.  For other available documentation, see Manuals.

    My question isn't answered here. Whom can I ask for help?

    Contact the OSC Help Desk. Support is available 24x7x365, but more complicated questions will need to wait for regular business hours (Monday - Friday, 9am - 5pm) to be addressed. 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, and authorized users can have more than one account. 

    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 apply for a start-up request and include the contact information for authorized users. Please refer to for the on-line form. If an eligible principal investigator has a current project, he/she can email OSC Help to add the user. Authorized users do not have to be located in Ohio.

    I'm continuing the research of a student who graduated.  Can I use his/her account?

    Yes, but you must have the account transferred into your name. Have your PI send an email to

    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. Ask your PI to request an account for you by emailing OSC Help.

    How do I change my password?

    You can change your password through the My OSC portal. Log in at, and click the "change password" button at the bottom left corner of the HPC User Profile box. Please note that your password has certain requirements; these are specified on the "change password" portal. Please wait an hour before attempting to log in with the new password. For security purposes, please note that our password change policy requires a password change every 90 days.

    I want to use csh instead of bash.  How do I change the default shell?

    You can change your default shell through the My OSC portal. Log in at, 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 an hour for the changes to be applied.

    What is an RU?

    An RU is a resource unit. A resource unit is an aggregate measure of the use of CPU, memory, and file storage. For details on charging algorithms, see Charging.

    How do I find my account 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 more resources, the principal investigator must prepare a proposal that will be sent for peer review. After the review process is complete, the Allocations Committee of the Statewide Users Group meets to determine the number of resource units to be awarded. The committee meets on the second Thursday of even-numbered months. PIs should submit their proposals at least three weeks before the meeting date to ensure inclusion on the agenda.

    The application form is located at A complete application comprises the following items:

    • Contact information of new authorized users
    • Contact information of at least three recommended reviewers
    • Electronic version of PI’s resume
    • Publications list (publications, presentations, and articles that cite OSC)
    • Justification and performance (quantitative estimation of the number of RUs per run times; the number of runs for the estimated duration of the request; performance reports of the code to be used or explanations about performance; report of any optimization performed on the code
    • Proposal text

    How much will my account be charged for supercomputer usage?

    For details on charging algorithms, see Charging.

    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

    See the Allocations and Accounts section for more information. 

    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 assitance. 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 Systems for 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, or send your new contact information to

    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/ 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.

    Batch Processing Questions

    What is a batch request?

    On all OSC systems, batch processing is managed by the Portable Batch System (PBS). PBS 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?

    PBS uses qsub to submit, qstat to check the status, and qdel 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 -m option in our PBS Directives Summary. 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. 

    Why is my job being rejected with the error "Group: is not valid"?

    If you are a part of a annual allocations project, usually designated by the prefix PAA-, in addition to another project you must explicitly specify which project you want to charge a jobs usage to.  This can be done with the -A PBS directive.  For example if a user was a part of both projects PAA0999 and PAQ0343 and wanted to charge a job to PAA0999 they would need to add the following line to their script:

    #PBS -A PAA0999

    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 trap command ( trap commands do not work in csh and tcsh shell batch scripts). In the batch script, the trap command needs to precede the command causing the TERMination. It could be placed immediately after the PBS header lines. Here is a generic form:

    trap "cd $PBS_O_WORKDIR;mkdir $PBS_JOBID;cp -R $TMPDIR/* $PBS_JOBID;exit" TERM

    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 trap command may not be executed.  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:

    if [ $? -ne 0 ]; then
        cd $PBS_O_WORKDIR;mkdir $PBS_JOBID;cp -R $TMPDIR/* $PBS_JOBID

    Finally, if a node your job is running on crashes then the trap command 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:

    qselect -u <username> | xargs qdel

    How can I determine the number of cores in use by me or my group?

    To determine the number of cores (processors) in use by you account on a particular system run:

    showq -u $USER | grep "local jobs"

    To determine the number of cores (processors) in use by your primary project on a particular system run:

    showq -w acct=$GROUP | grep "local jobs"

    Genrerally, to see the number of cores in use by a particular project on a particular system run:

    showq -w acct=<project> | grep "local jobs"

    replacing <project> with the project ID.

    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


    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.

    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?

    Please refer to the Software Forms page. You will see a link to Request for Software Form. Download the form, complete the information, and attach the form to an e-mail to The Statewide Users Group will consider the request.

    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


    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 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.