Getting Started with Shamu

Shamu is the Research Support Groups premier cluster consisting of many compute cores and GPU cores.

Connecting from Windows environment

We cover two different options to work from a Windows environment.

We recommend following the MobaXTerm option as that will provide a complete environment for connecting to the clusters, to copy/retrieve files from them and to launch graphical apps requiring an X server:

• Setup MobaXTerm (Prefered)

If you are an experienced user of the Linux command line, you might find it interesting to try the recent feature called Windows Subsystem for Linux, note that only Windows 10 after October 2017 build support this:

• Setup Windows Subsystem for Linux (Advanced)

Connecting from a Unix-like environment (Linux, Mac OS X)

Open the Terminal app for your system and type:

ssh abc123@login.shamu.utsa.edu -p1209

If you have successfully logged in, you should see something like:

Welcome to the Research Computing cluster Shamu.

Rules for using Shamu:

* Do *NOT* execute directly on the Shamu head node. Grab a compute node with
qlogin or script your jobs with qsub.

* Do *NOT* ssh directly to a compute node to run your code. Offending users will
be locked out temporarily.

We are now gathering statistics to help promote Shamu in the UTSA Research
Community.

We are looking for the following information:
  * Number of presentations and papers published
  * Number of grants, awards or funding
  * Number of patents, copyrights, etc...

If you have used the computational resources of Shamu for any of the above, please
email your information to rcisg@utsa.edu. Thanks!

Navigating the filesystem

Shamu has a high speed Infiniband based file system consisting of two (2) mounts, /work and /home-new.

/home-new is where your home directories are located

/work is where you should place all of your input or output files from your jobs. If you currently do not have a /work/abc123 directory, please contact the Research Support Group and request a directory to be created.

X Forwarding

X Forwarding is used to forward any X enabled (GUI) program you with to run on Shamu. There are two (2) SSH terminals for Windows that automatically provides the necessary X libraries to accomplish this. They are SmarTTY and MobaXTerm.

Linux

If you are using a Linux desktop, you will need to connect to the login node with a special argument to enable X Forwarding:

ssh -Y abc123@login.shamu.coe.utsa.edu -p1209

Windows

For Windows, we recommend MobaXTerm because it includes an X server and sets everything up automatically for you once you log in.

Mac

For Mac users, please follow the directions below:

1. Install XQuartz on your Mac, which is the official X server software for Mac
2. Run Applications > Utilities > XQuartz.app

3. Right click on the XQuartz icon in the dock and select Applications > Terminal. This should bring up a new xterm terminal windows.

4. In this xterm windows, ssh into the linux system of your choice using the -X (or -Y) argument (secure X11 forwarding). For example, to log into login.shamu.utsa.edu you would run something like:
   

    ssh -Y username@login.shamu.utsa.edu

5. Once you are logged into the linux system, you can just run the GUI program of your choice (ie. matlab, mathematics, etc) and it will display on your Mac.

-- AdminUser - 17 May 2016