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. 

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 grant@osc.edu or to oschelp@osc.edu 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.

Application if you are based at an Ohio Academic Institution

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.  Ohio Academic Clients are eligible for highly subsidized access to OSC resources, with fees generally only being charged above certain resource thresholds.  These clients must submit a proposal that is potentially peer-reviewed and/or approved by their host insitution.  More information is available here.

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.

Application if you are NOT based at an Ohio Academic Institution

Researchers from business, non-Ohio academic, nonprofit or other organizations who wish to use the OSC's resources should complete the Other Client request form available here. All clients not affiliated with an Ohio academic institution must sign a service agreement, provide a $500 deposit, and pay for resource usage per a standard price list.

Add a new user

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

Project:
Full Name:
If not U.S. Citizen, country of citizenship:
Institution:
Department:
Affiliation:
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 oschelp@osc.edu, and your inquiry will be directed to the appropriate staff member.:

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

Description

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

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

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

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

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

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

More Advanced:

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

Prerequisites

None.

Introduction

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

Common Tasks on OSC Clusters

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

The Kernel and the Shell

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

The Command Prompt

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

-bash-3.2$

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

$ exit <Enter>

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

First Simple Commands

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

$ date

$ cal

$ finger

$ who

$ whoami

$ finger -l

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

man

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

$ man

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

$ man finger

then at the colon of the man page type

: q

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

$ man finger

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

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

SYNOPSIS

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

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

$ whoami

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

$ finger osu0000

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

$ finger -l osu0000

$ finger -lp osu0000

$ finger -s osu0000 osu0001

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

Note that a unix command consists of three parts:

• command
• option(s)
• argument(s)

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

$ man man

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

$ man man finger

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

Combining Commands

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

$ man more

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

$ man less

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

$ less foo.txt

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

$ finger | less

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

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

$ finger | grep osu0000

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

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

$ whoami | finger

You see that it does not give the same output as

$ finger osu0000

(assuming "whoami" returns osu0000.)

In this case what you can do is the following:

$ finger `whoami`

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

apropos

Enter the following command:

$ man apropos

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

$ apropos

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

So try

$ apropos calendar

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

Description

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

Prerequisites

• Familiarity with a text editor (emacs, nano, vim)
• Basic understanding of the unix command line
• Linux Command Line Fundamentals tutorial

Goals

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

Step 1 - Organize your directories

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

$ pwd
/users/PRJ0001/osu0001

$ touch foo1
$ touch foo2
$ ls
$ ls -l
$ ls -lt
$ ls -ltr

$ mkdir BatchTutorial
$ ls -ltr

$ pwd
/users/PRJ0001/osu0001

$ cd BatchTutorial
$ pwd

$ cd ..
$ pwd

Step 2 -- Get familiar with some more unix commands

Try the following:

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

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

Some more commands to try:

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

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

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

$ cp foo3 foo4
$ ls -ltr

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

$ mv foo4 foo5
$ ls -ltr

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

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

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

Now try the following:

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

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

$ cp foo3 FooDir

Now what happens when you do the following:

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

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

Step 3 -- Environment Variables

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

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

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

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

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

Step 4 -- Create and run a script

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

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

$ nano tutorial.sh

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

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

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

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

cd $SH_WORKDIR

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

To run it:

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

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

Step 5 -- Create and run a batch job

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

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

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

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

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

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

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

$ qsub tutorial.pbs

$ qstat -u osu0001

                                                                             Req'd  Req'd   Elap
Job ID             Username    Queue    Jobname          SessID NDS   TSK    Memory Time  S Time
------------------ ----------- -------- ---------------- ------ ----- ------ ------ ----- - -----
458842.oak-batch   osu0001     serial   foobar              --      1      1    --  00:02 Q   --

If you see something like this:
                                                                             Req'd  Req'd   Elap
Job ID             Username    Queue    Jobname          SessID NDS   TSK    Memory Time  S Time
------------------ ----------- -------- ---------------- ------ ----- ------ ------ ----- - -----
458842.oak-batch   osu0001     serial   foobar            26276     1      1    --  00:02 R   --

$ ls -ltr
$ cat foobar.oNNNNNN

1. The name you give the job in the script file with the header line #PBS -N foobar
2. The job id number assigned to the job.

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

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

$ echo $PBS_O_WORKDIR

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

#PBS -l nodes=1:ppn=1

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

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

$ ls /tmp/pbstmp.NNNNNN

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

Prerequisites

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

Start off with the following:

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

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

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

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

Now do this:

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

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

Now do this:

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

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

x: extract the contents of the tar file

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

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

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

$ du .

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

$ du -h .
$ ls -ltrh

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

Step 3 -- create your own "tarball"

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

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

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

c: create a tar file

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

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

$ gzip mywrf.tar
$ ls -ltrh

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

Step 4 -- Clean up!

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

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

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

$ rmdir WRFDA

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

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

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

$ rm -Rf WRFDA

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

R: recursively remove all files and directories

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

I encourage you to do

$ man rm

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

Description

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

Prerequisites

Linux command line fundamentals.

Goals

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

Step 1 -- The Arrow Keys

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

$ cd
$ mkdir Shortcuts
$ cd Shortcuts

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

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

Try the following:

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

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

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

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

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

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

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

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

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

Step 2 -- Using the TAB key

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

Go back to the Shortcuts directory:

$ cd
$ cd Shortcuts

Now enter the following:

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

Now type the following, without hitting the Return key:

$ cat oth <Tab>

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

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

$ cat d <Tab>

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

What if you enter

$ cat fi <Tab>

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

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

With the comman line showing this:

$ cat file

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

Try

$ cat f <Tab>

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

$ cat f

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

Now enter the following:

$ cat directory1/directory2/directory3/directory4/file3

That's kind of a painful to type.

Now type the following without entering Return:

$ ls dir <Tab>

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

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

Now type this:

$ ls dir <Tab>

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

$ ls directory1/directory2/

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

Now try this:

$ ls dir <Tab>

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

$ ls directory1/directory2/directory3/

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

Step 3 -- The Exclamation Point

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

Go back to the Shortcuts directory

$ cd ~/Shortcuts

and enter the following:

$ hostname
$ cal
$ date
$ whoami

Now enter this:

$ !c

and hit return.

What happened? Now try

$ !h

and hit return.

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

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

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

$ cat file1
$ cal
$ !cat

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

Step 4 -- Ctrl-r

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

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

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

You should see the following on your command line:

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

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

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

Step 5 -- history

Now type

$ history

and hit return.

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

$ history | grep cal

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

$ !874

re-executes the command number 874 in your history.

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

Step 6 -- Ctrl-t

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

$ cat file1

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

Step 7 -- The alias command

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

$ alias cf5='cat folio5'

Now type

$ cf5

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

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

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

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 anaconda.org (formerlly binstar.org) 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 an 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 anaconda.org 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 oschelp@osc.edu.

But I use virtualenv and/or pip!

See the comparison to these package management tools here:

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

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:

$HOME/.local/bin

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.

Procedure

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

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

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.

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

conda info -e

For additional conda command documentation see https://conda.io/docs/commands.html

Activate clone environment

For the bash shell:

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 anaconda.org.

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__"

Output:

$HOME/.conda/envs/local/lib/python2.7/site-packages/yt/__init__.py

• Replace both instances of yt  with the name of the package you installed.

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: https://conda.io/docs/test-drive.html 

NOTE:  OSC Ondemand now provides in-browser connectivity via VNC.  OSC Connect is no longer required nor recommended.  We recommend contacting OSC Help if you need assistance using the in-browser capabilities or if there is other functionality that is forcing you to still use OSC Connect.  This page is still available primarily for reference.

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.

We've created a brief video:

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  , 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.

Connecting to a Session

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

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. 

FAQ

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.

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
PZS0530:*:2959:yli,osc0539,elton,ananth,osc0413,dhudak,osc0695,ksaantha,changlee,buss,osc0414,osc0478,nsharma,kmanalo,nwadih,bsmith,...

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
oscgen:*:200:jordan,jpu,mlewis,rmonroe,rmarshal,spears,sengupta,jtm,adraghi,lepage,ian,karin,remote,njustice,bedford,hjiang,tom,mudronja,elainep,gisadmin,airani,guilfoos,osc0498,osc0722,ngagnet,mfaerman,justinw,arya,mattm,echong,rahmed,jwright,...

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}'
xwang
xwangnd
... 

With user's email address as xwang@osc.edu, the command ldapsearch -x -LLL "(mail=xwang@osc.edu)" | grep cn | awk '{print $2}' returns the information as below:

bash-4.1$ ldapsearch -x -LLL "(mail=xwang@osc.edu)" | grep cn | awk '{print $2}'
xwang
xwangnd
...

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: /users/oscgen/xwang          Shell: /bin/bash
On since Thu Jan 25 15:32 (EST) on pts/49 from localhost:25.0
   6 seconds idle
Mail forwarded to xwang@osc.edu
No mail.
No Plan.

• The home directory of xwang is  Directory: /users/oscgen/xwang 
• The shell of xwang is bash ( Shell: /bin/bash ). If the information is Shell:/access/denied , it means this user account has been either archived or resticted. Please contact OSC Help if you'd like to reactivate this user account.
• xwang@osc.edu is the associated email with the user account xwang; that is, all OSC emails related to the account xwang will be sent to xwang@osc.edu ( Mail forwarded to xwang@osc.edu ). Please contact OSC Help if the email address 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 2018-01-25T04:02:23.749853 userid userID on /users/projectID used XGB of quota 500GB and Y files of quota 1000000 files

The information is from the file /users/reporting/storage/quota/*_quota.txt , which is updated twice a day. Some users may see multiple lines 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 -h <userID OR projectID > /users/reporting/storage/quota/*_quota.txt 

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

R comes with a single library  $R_HOME/library which contains the standard and recommended packages. This is usually in a system location. On Owens, it is   /usr/local/R/3.3.2/lib64/R/library . R also has a default value for a directory where users can install their own R packages. On the Owens cluster, it is ~/R/x86_64-unknown-linux-gnu-library/3.3 if the default R-3.3.2 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 Owens, the default R module is version 3.3.2 .

Then fire up an R session:

R

To install package lattice, use this command inside R:

> install.packages("lattice", repos="http://cran.r-project.org")

It gives a warning: 

Warning in install.packages("lattice") :
'lib = "/usr/local/R/3.3.2/lib64/R/library"' is not writable
Would you like to create a personal library
~/R/x86_64-unknown-linux-gnu-library/3.3
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="http://cran.r-project.org", 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="http://cran.r-project.org")

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

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

>.libPaths();

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"] = "http://cran.case.edu" 
options(repos = repo)
rm(repo)

Now you only need to do 

> install.packages("lattice")

That will download the package lattice from  http://cran.case.edu 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.

Note that attempting to update centrally installed packages will fail. You will have to use install.packages() to install a newer copy in your home directory instead. For example, if you are installing Bioconductor, the installation routine will try to update a bunch of centrally installed packages. To clone those into your personal library, tell biocLite() not to update any of the packages, and copy the list from the output into your own install.packages() command. See the example below (the c function creates an array of strings).

> install.packages(c('Rmpi', 'assertthat', 'backports'))

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.

Installing Packages from GitHub

Users can install R packages directly from Github using devtools package as follows

module load R/3.4.2
R

>library(devtools)
>install_github("author/package")

References

Add-on packages in R installation guide (http://cran.r-project.org/doc/manuals/R-admin.pdf)

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

Gather your materials

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

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

Now you can extract the downloaded file.

Adding the path

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

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

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

Running the toolbox

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

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. Note that this is not necessary if you loaded a version of Perl with the module load command.

module load cpanminus

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

perl -I $CPANMINUS_INC -Mlocal::lib

Using CPAN Minus

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

cpanm [Module::Name]

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

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

Testing Perl Modules

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

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

The modules are installed correctly if no output is printed.

What Local Modules are Installed in my Account?

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

perldoc perllocal

Reseting Module Collection

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

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

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.

Getting Started

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

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

This structure is 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
    wget https://github.com/git/git/archive/v2.9.0.tar.gz

Now extract the tar file:

    tar zxvf v2.9.0.tar.gz

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

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

Then, we can build Git using the following commands:

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

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

Creating a Module

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

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

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. 

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 oschelp@osc.edu.

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

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

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

Preventing Excessive Data Usage Before It Starts

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

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

Identifying Old and Large Data

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

Find 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

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

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

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

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

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

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

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

Archiving Data

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

Compressing

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

Moving Data to a Local File System

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

Globus is recommended for large transfers.

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

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.in 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...] script.sh

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 = subprocess.call(qsub_command, 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:

qsub -v WEEK=WEEK_VALUE,SOURCE=SOURCE_VALUE,DATA=DATA_VALUE template_1.pbs

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:

week42,source1,data1
week42,source1,data2
week42,source1,data3
...
week42,source2,data98
week42,source2,data99
week42,source2,data100

The submit script would read in the first row of this CSV file and form and  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.  

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.

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:

Windows

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

​​Mac

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

​Linux​

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 &

Usage

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

Further Reading

• https://www.globus.org/
• www.youtube.com/GlobusOnline

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. Or, you can use Singularity Hub to create a container from a recipe. But, 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 simply download ("pull") a container from a hub. Popular hubs are Docker Hub and Singularity Hub. You can go there and search if they have a container that meets your needs. Docker Hub has more containers and may be more up to date but supports a much wider community than just HPC. Singularity Hub is for HPC, but the number of available containers are fewer. Additionally there are domain and vendor repositories such as biocontainers and NVIDIA HPC containers that may have relevant containers.

Examples of “pulling” a container from the both hubs:

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

singularity pull docker://gcc:7.2.0

Filename:  gcc-7.2.0.img

When you pull from docker, there will be a message:

WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.

As we mentioned, containers from Singularity Hub are more likely to be compatible with our container environment. But, since Docker Hub has more updated versions, it is more likely to have a container that you are looking for.

Singularity Hub:  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

Downloading containers from the hubs is not the only way to get one. You can, for example get a copy from your colleague's computer or directory. If you would like to create your own container you can start from the user guide below. If you have any questions, please contact OSC Help.

Running a container

There are four ways to run a container under Singularity.

You can do this either in a batch job or on a login node. (Don’t run on a login node if the container will be performing heavy computation, of course.)

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)"
ID="rhel"
ID_LIKE="fedora"
VERSION_ID="7.3"
PRETTY_NAME="Red Hat Enterprise Linux"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:redhat:enterprise_linux:7.3:GA:server"
HOME_URL="https://www.redhat.com/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 7"
REDHAT_BUGZILLA_PRODUCT_VERSION=7.3
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.3"

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
NAME="Ubuntu"
VERSION="16.04.3 LTS (Xenial Xerus)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 16.04.3 LTS"
VERSION_ID="16.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
VERSION_CODENAME=xenial
UBUNTU_CODENAME=xenial
[owens-login01]$ exit
exit
[owens-login01]$

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
RaawwWWWWWRRRR!!
[owens-login01]$

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
RaawwWWWWWRRRR!!
[owens-login01]$

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

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

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
NAME="Ubuntu"
VERSION="14.04.5 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.5 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
[owens-login01]$ 

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   rawr.sh  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
#!/bin/sh
exec /bin/bash /rawr.sh
Singularity vsoch-hello-world-master.img:~/singularity> cat /rawr.sh
#!/bin/bash
echo "RaawwWWWWWRRRR!!"
Singularity vsoch-hello-world-master.img:~/singularity> exit
exit
[owens-login01]$

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
#!/bin/sh
exec /bin/bash "$@"Singularity ubuntu.img:~/singularity> exit
exit
[owens-login01]$

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

You can review our Available File Systems page for more details about our file system access policy.

If you run the container within a job you will have the usual access to the $PFSDIR environment variable with adding node attribute "pfsdir" in the job request (nodes=XX:ppn=XX:pfsdir). You can access most of our file systems from a container without any special treatment, however, if you need TMPDIR you must specify it on the command line as in this example:

SINGULARITYENV_TMPDIR=$TMPDIR singularity shell ubuntu.img

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
[o0756]$

 git clone https://github.com/tensorflow/models.git

[o0756]$

 singularity exec --nv docker://tensorflow/tensorflow:latest-gpu \
python ./models/tutorials/image/mnist/convolutional.py

References

• http://singularity.lbl.gov/user-guide
• https://hpc.nih.gov/apps/singularity.html
• https://www.docker.com/

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

A::user@nfsdomain.org:rxtncy

A::alice@nfsdomain.org:rxtncy

A::alice@nfsdomain.org:rxtncy

A::alice@nfsdomain.org:rxtncy

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

ACE Type

The 'A' in the example is known as the ace 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.

ACE Flags

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

A:d:user@osc.edu:rxtncy

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

ACE Principal

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

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

  • A:g:group@osc.edu:rxtncy
    

ACE Permissions

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

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.

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

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

Commands

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

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.

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.)

vncserver

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 n0302.ten.osc.edu:1

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
vncserver
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: 9200155.oak-batch.osc.edu
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.

Linux/MacOS

Option 1: Manually create an SSH tunnel 

I will be providing the basic command line syntax, which works on Linux and MacOS. You would issue this in a new terminal window on your local machine, creating a new connection to Oakley.

ssh -L 5901:n0302.ten.osc.edu:5901 guilfoos@oakley.osc.edu

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.

Windows

This example shows how to create a SSH tunnel through your ssh client.  We will be using Putty in this example, but these steps are applicable to most SSH clients.

First, make sure you have x11 forwarding enabled in your SSH client.

Next, open up the port forwarding/tunnels settings and enter the hostname and port you got earlier in the destination field.  You will need to add 5900 to the port number when specifiying it here.  Some clients may have separate boxes for the desination hostname and port.  

For source port, pick a number between 11-99 and add 5900 to it.  This number between 11-99 will be the port you connect to in your VNC client.

Make sure to add the forwaded port, and save the changes you've made before exiting the configutations window.

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.

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.

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.

Introduction

Broadly speaking, there are two different ways in which the external license server's network may be configured.  These differ by whether the license server is directly externally reachable or if it sits behind a private internal network with a port forwarding firewall.  

If your license server sits behind a private internal network with a port forwarding firewall you will need to take additional steps to allow the connection from our systems to the license server to be properly routed. 

License Server is Directly Externally Reachable

License Server is Behind Port Forwarding Firewall

Unsure?

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:

• nat.osc.edu (192.157.5.13)
• 192.148.248.35
• 192.148.248.186

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 licXXX.osc.edu 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 1.2.3.4:

setenv LSTC_LICENSE network
setenv LSTC_LICENSE_SERVER 2345@1.2.3.4

License Server is Behind Port Forwarding Firewall

If the license server is behind a port forwarding firewall, and has a different IP address from the IP address of the firewall, additional steps must be taken to allow connections to be properly routed within the license server's internal network.  

1. Use the license server's fully qualified domain name in 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.  

ANSYSLI_SERVERS=<port>@<IP>
ANSYSLMD_LICENSE=<port>@<IP>

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.

Syntax

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

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 ...

#!/bin/bash

cd $PBS_O_WORKDIR
...
mpiexec ./test1
...

2. Prepare the wrapper script named "test1" as below:

#!/bin/bash
ulimit –c unlimited
.....(your own program)

3. qsub myjob

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

Usage for Professor

After connecting to OSC system, professor runs submit_prepare as

$ /fs/scratch/xwang/bin/submit_prepare

Follow the instructions. It will create a designated directory where students submit their assignments, as well as generate submit for students used to submit homework to OSC, both of which are located in the directory specified by the professor.

Note:

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, the student will get an error message when he/she tries to submit an assignment to this directory.

Usage for Students

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

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

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

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

This page lists all proposed OSC policies for public comments. Your comments help inform our policies and are encouraged. We will provide response to comments on this webpage after the public comment period closes. Please submit your comments via our online form by the deadline. 

Currently Open for Public Comment:

Scratch Storage Policy

OSC provides a scratch file system as high-performance, high-capacity, shared space. It is temporary without backup. No customer should rely upon the retention of data placed on scratch storage. The purpose of this policy is to (1) keep sufficient scratch space available at all times, (2) maintain good performance of the scratch file system, (3) protect users from misuse of scratch which will result in data loss and (4) reduce manual management of scratch data by OSC staff. 

View this PDF for the proposed policy. 

We need to receive your comments via online form by Friday, April 28, 2017.