HOWTO

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

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HOWTO: Configure the MATLAB Parallel Computing Toolbox

Introduction

In some cases, it may be necessary for you to use the MATLAB Parallel Computing Toolbox to remotely connect to OSC resources, whether to run parallel jobs in MATLAB or to use toolboxes for which you own your own licenses.  This guide will explain the basics for how to configure your MATLAB installation in order to connect remotely to Oakley using MATLAB 2013a.

Download the configuration files

The first step is to download the necessary configuration files.  Click the link below to download the files.  Be sure to save the files in a convenient location that you can easily remember.

Parallel Computing Toolbox Configuration Files  

Note:  These configuration files are only for use with MATLAB 2013a to connect to Oakley at this time.  Other versions of MATLAB and connections to other clusters are currently not supported.

Importing the Cluster Profile

Image of MATLAB Parallel Menu

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

Image of MATLAB Cluster Profile Manager

In the Cluster Profile Manager window, click the "Import" button and locate the directory containing your configuration files using the file browser.  

Select the file: "genericNonSharedOakleyIntel.settings" and click "Open".  

Then, in the Cluster Profile Manager window, you will need to modify some of the properties of the Cluster Profile that you just imported.  Select "generic NonSharedOakleyIntel" from the list of cluster profiles, and click the "Edit" button in the lower right-hand corner of this window to enable editing. 

Image of MATLAB Cluster Profile Properties

In the editing window under "Submit Functions", you should see two entries -- IndependentSubmitFcn and CommunicatingSubmitFcn.  In these entries, you will need to change the directory path provided to a directory of your choice within your home directory on OSC systems.  This will be the destination for log files and intermediate data created as a result of submitting a job using the Parallel Computing Toolbox.  These locations are not intended to be the destination for your results.  Once these have been changed, click "Done" and close the Cluster Profile Manager window.

Running your first batch job

In the directory of configuration files, the file called "testremote.m" is the entry point for job submission using the Parallel Computing Toolbox.  In this file, you will need to modify the "batch" command in order to run your particular MATLAB program.  How this command is modified depends largely on whether you want to run a serial or parallel job.  At the very least, you will need to provide a function or script name to be executed.  For more information about the "batch" command and its various forms and arguments, see the Mathworks documentation for "batch"

Obtaining your results

Your results will not automatically be offloaded from the cluster when your job completes.  In order to obtain the results of your calculations, you will need to save the relevant variables from your workspace in a .mat file using the "save" command in MATLAB.  For more information about the "save" command and its various forms and arguments, see the Mathworks documentation for "save".

Further Reading

The Mathworks Parallel Computing Toolbox Homepage

HOWTO: Install Local R Packages

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

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

A Simple Example

First you need to load the module for R:

module load R

On Oakley, the default R module is version 3.0.1.

Then fire up an R session:

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/3.0.1/lib64/R/library"' is not writable
Would you like to create a personal library
~/R/x86_64-unknown-linux-gnu-library/3.0
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.

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.

 

References

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

HOWTO: Install your own python modules

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

Gather your materials

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

mkdir -p ~/local/src

Now, we will need to download the source code for the module we want to install. In our example, we will use "NumExpr", a module we already provide in the system version of Python. You can either download the file to your desktop, and then upload it to OSC, or directly download it using the wget utility (if you know the URL for the file).

cd ~/local/src
wget http://numexpr.googlecode.com/files/numexpr-2.0.1.tar.gz

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

tar xvfz numexpr-2.0.1.tar.gz

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

Build it!

Environment

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

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

I am following, roughly, the convention we use at the system level. This allows us to easily install new versions of software without risking breaking anything that uses older versions. As you can see, I have specified a folder for the program (numexpr), and for the version (2.0.1). Now, to be consistent with python installations, we're going to create a second temporary environment variable, which will contain the actual installation location.

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

Now, make the directory tree.

mkdir -p $TREE

Compile

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

module swap intel gnu
module load python.

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

python setup.py install --prefix=$INSTALL_DIR

Make it usable

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

Manual

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

export PATH=$PATH:~/local/numexpr/2.0.1/bin

And, for the python libraries:

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

Hardcode it

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

Make a module (recommended!)

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

prepend-path    PYTHONPATH      /nfs/10/guilfoos/local/oakley/numexpr/2.0.1/lib/python2.7/site-packages
prepend-path    PATH    /nfs/10/guilfoos/local/oakley/numexpr/2.0.1/bin

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

module load numexpr/2.0.1

 

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HOWTO: Locally Installing Software

Sometimes the best way to get access to a piece of software on the HPC systems is to install it yourself as a "local install". This document will walk you through the OSC-recommended procedure for maintaining local installs in your home directory or project space.

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

Getting Started

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

    local
    |-- src
    |   `-- tars
    `-- share
        `-- modulefiles

This structure is quite common in the UNIX world, and is also 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.
  • local/src/tars - Stores the compressed archives ("tarballs") of your installers. Useful if you want to reinstall later using different build options.
  • local/share/modulefiles - 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. After navigating to where you want to create the directory structure, run:

    mkdir -p local/src/tars local/share/modulefiles

Finally, you need to add your local modulefiles directory to the module system's search path. To do this, append the following line to your .bashrc, .cshrc, .tcshrc, or other shell startup script:

    module use /nfs/01/username/local/share/modulefiles

Replace "/nfs/01/username" with the full path of your home directory. (You can identify this from the command line with the command "echo $HOME".) If you already have a .modulerc file, just add the "module use" line to the end of it.

Installing Software

Now that you have your directory structure in space, you can install your software. For demonstration purposes, we will install a local copy of the Git version control system.

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 ~/local/src/tars:

    cd ~/local/src/tars
    wget http://git-core.googlecode.com/files/git-1.7.9.3.tar.gz

Now extract into the src directory above. If you're working with a tar file, you can use the -C command to specify the directory to extract to:

    tar zxvf git-1.7.9.3.tar.gz -C ../

Next, we'll go into the source directory and build the program. Consult your application's documentation to determine how to specify to install into ~/local/app/version. Replace app with the application'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.

With these things in mind, we can build Git using the following commands:

    cd ../git-1.7.9.3
    ./configure --prefix=$HOME/local/git/1.7.9.3 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. They are written in the Tcl language, though you do not need to be familiar with it to create a simple module.

All modules begin with the string "#%Module". After that, they contain several commands to tell the module system how to modify your environment. Some of the commonly used ones are:

  • prepend-path VARIABLE path - Adds path to the beginning of VARIABLE, where VARIABLE is a colon-separated list of paths. Generally use to modify PATH, LD_LIBRARY_PATH, and MANPATH.
  • setenv VARIABLE value - Sets the environment variable VARIABLE to value.
  • set VARIABLE value - Used to set local variables to be used within the module.

You can read about all of the available commands by reading the manpage for "modulefile":

    man modulefile
This manpage is only available on Glenn. Oakley has a slightly different module system. Modules written for Glenn will work, but there are additional features available in Oakley's module system. That documentation can be found at http://www.tacc.utexas.edu/tacc-projects/mclay/lmod or by executing module help.

A simple module for our Git installation would be:

    #%Module

    ## Local variables
    set name git
    set version 1.7.9.3
    set root /nfs/01/username/local/$name/$version

    ## Environment modifications

    # Set basic paths
    prepend-path PATH       $root/bin
    prepend-path MANPATH    $root/share/man

    # Git includes some Python and Perl modules that may be useful
    prepend-path PERL5LIB   $root/lib
    prepend-path PERL5LIB   $root/lib64
    prepend-path PYTHONPATH $root/lib

Installation

Any modulefile you create you should be saved into your local modulefiles directory. For maximum future-proofing, create a subdirectory within modulefiles named after your app and add one modulefile to that directory for each version of the app installed.

In the case of our Git example, you would create the directory $HOME/local/share/modulefiles/git and create a modulefile within that directory named "1.7.9.3". To make this module usable, you need to tell the modules utility where to look for it. You can do this by issuing the command module use $HOME/local/share/modulefiles, in our example. This will allow you to load your app using either module load git or module load git/1.7.9.3. If you installed version 1.8 later on and created a modulefile for it called "1.8", the module system would automatically load the newer version whenever you loaded git. If you needed to go back to the older version for some reason, you can do so by specifying the version you wanted: module load git/1.7.9.3.

module use [/path/to/modulefiles] is not persistent between sessions.

For a starting point, copy our sample modulefile from ~support/doc/modules/sample_module. This modulefile follows the recommended design patterns laid out above, and includes samples of many common module operations.

Further Reading

For more information about modules, be sure to read the module(1) and modulefile(4) manpages. If you have any questions about modules or local installations, feel free to contact the OSC Help Desk and oschelp@osc.edu.

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HOWTO: Transfer files using Globus Connect

Globus Connect Logo

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

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

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

Users transfering between OSC and another computing insitution with Globus installed do not need to install Globus Connect Personal or add OSC certificate authority files, and can skip to Step 3.

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

If you are looking to transfer smaller sized files you can utilize OnDemand's file transfer capabilities, or use a SFTP client to connect to sftp.osc.edu.

Setup

To use Globus to transfer from a personal computer, you will need to:

  1. Install the Globus Connect Personal client on your computer
  2. Add the certificate authority files to your installation
  3. Create a MyProxy certificate through Glenn

Those transfering between OSC and another computing insitution can skip to Step 3.

1. Installing and Setting Up Globus Connect Personal

  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
    • 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

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 Tools -> 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

2. Adding OSC Certificate Authority Files

This process will add Certificate Authority files to your computer to ensure you are a trusted endpoint.  If you installed Globus on a Windows computer, and also installed it to the default directory, we have provided this as a automated process.  Linux and Mac installations, as well as Windows installations to non-default locations, will need to follow the manual instructions below.

  • Automated Process -- Windows Default Installations ONLY

  1. Download the Certificate Authentication zip archive
  2. Unzip the archive 
  3. Run the copy_auth Windows batch file from the unzipped archive
  • You will be prompted whether to allow Windows Command Prompt to make changes to your computer.  Press Yes to continue.
  • If the process was a success, the command prompt should read:

Copy was successful!

  • If an error occurred, the command prompt will read:

Copy was unsuccessful!

       You will need to follow the manual instructions below.

  • Manual Process -- Linux, Mac +  Windows installations to non-default locations

  1. Download the Certificate Authentication zip archive
  2. Unzip the archive
  3. Find your Globus Connect Personal installation directory
    • Mac - located within /Applications/Globus Connect Personal.app/Contents/MacOS/
    • To open the contents of the Globus Connect Personal.app folder, right click the folder in Finder and select "Show Package Contents"
    • Windows - Typically found within /Program Files
    • Linux - Where you unzipped the tarball 
  4. Open the ca directory within the etc directory found in the installation directory
  5. Copy all the files in the unzipped archive, except copy_auth, to the ca directory located previously

3. Creating a MyProxy Certificate 

These steps will create a short lived certificate on OSC's systems to ensure you are a valid OSC user.  This certificate will be good for 0.5 days (11 hours), after which you will need to repeat this process to transfer to/from OSC again.  Repeating this process will overwrite your old certificate, meaning you will need to change the Credentials for osc#Glenn on the Globus website imediately after.

  1. Login to Glenn using your OSC username and password (ssh to Glenn.osc.edu)
  2. Run the command gcp2osc
  • At the first prompt reading "Enter MyProxy pass phrase:" enter your OSC password
  • A second prompt reading "Enter MyProxy pass phrase:" should appear.  You need to enter a new password/passphrase to use to connect to OSC from Globus.  This should be different from your OSC password

Usage

  1. Login to Globus and navigate to the "start transfer" page under the "Manage Transfers" menu
  2. Enter your endpoint in one of the boxes
    • If transferring to a computer with Globus Connect Personal installed, this will be the unique name chosen during installation
  3. Enter osc#glenn as the other endpoint
    • If this is your first time connecting to Glenn through Globus, or if your credentials have expired, you will be prompted to Activate the Endpoint
    • Enter your OSC username
    • Enter the passphrase created during the "Creating a MyProxy Certifcate"
  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
Once a transfer has begun, you do not need to keep the Globus webpage up, but you will need to make sure the Globus Connect Personal Client is running on your computer until it has completed.  If the transfer is interrupted for any reason, Globus will attempt to re-initiate the transfer automatically.
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HOWTO: Add InCommon Authentication to Globus

(OPTIONAL) Adding InCommon Authentication 

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

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

For a complete list, visit https://incommon.org/participants/ .

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

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

HOWTO: Use VNC in a batch job

SSHing directly to a compute node at OSC - even if that node has been assigned to you in a current batch job - and starting VNC is an "unsafe" thing to do. When your batch job ends (and the node is assigned to other users), stray processes will be left behind and negatively impact other users. However, it is possible to use VNC on compute nodes safely.

If your work is too big for the regular login nodes, but still not a very large, very intensive computation (for example, you do not expect to saturate all of the cores on a machine for a significant portion of the time you have the application you require open - e.g., you are using the GUI to set up a problem for a longer non-interactive compute job), OnDemand is a much easier way to access desktops.

The examples below are for Oakley.

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

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

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: 935621.oak-batch.osc.edu
Job Name:   VNCjob
Exec host:  n0282/11+n0282/10+n0282/9+n0282/8+n0282/7+n0282/6+n0282/5+n0282/4+n0282/3+n0282/2+n0282/1+n0282/0
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, "935621".

Connecting to your VNC server

Because the compute nodes of our clusters are not directly accessible, you must log in to one of the login nodes and allow your VNC client to "tunnel" through SSH to the compute node. The specific method of doing so may vary depending on your client software.

Option 1: Manually create an SSH tunnel

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

ssh -L 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.

Supercomputer: 
Service: