Linux HPC Grid Instructions

1. SSH into the Grid headnode with some SSH client (Built in on Mac OS/Linux, for Windows you need something like Putty/OpenSSH/Cygwin).

Enter the following command into the terminal:

    ssh -Y [bowdoin username]@moosehead.bowdoin.edu

2. Navigate to research space using the command line.

Enter the following command into the terminal:

    cd /mnt/research/enyhus/dphipps

There should be 2 directories, code and Sessions.  The former contains Matlab scripts, the latter contains data.  The script we are running is currently KAHN2linux.m

3. Submit the job to the queue.

Enter the following commands into the terminal:

    cd code

    matsub [matlab script] [output file]

This adds the job to the queue, and you can see the progress the grid is making by checking for updates to the output file, which you can do via the command:

    tail -f [output file]

What this command does it shows you last 10 lines of the file initially, but shows new data as anything new happens to it.

For further instructions, here's Bowdoin's help page:  https://hpc.bowdoin.edu/hpcwiki/index.php?title=Main_Page

Also:  Running Matlab with a GUI (Do this on dover.bowdoin.edu NOT moosehead)

Same instructions, just type matlab in the terminal.  The only caveat is you need to have X11 setup.  So download Xming for Windows and whatever it is for Mac and set ssh flags appropriately (ssh -X).

For Windows (at least with Putty) you have to find where X11 is an option and check that it is enabled.  Matlab will now run on your computer over ssh.  Not as quick as on your machine, but better than VNC.