Case for Interactive HPC Session on Mac

You already have an HPC account and you are a Mac user. You have developed your MATLAB code on your workstation, but it is not sufficient to run your entire data set. You have an account on the KSU HPC and you have tested your code on the HPC in an interactive session against some sample data. Now, it is time to run against a larger data set.

  • In top menu bar access (globe icon).

    Be sure vpn-groups selected when you connect.

  • $ scp /Users/your_netid/new_data_file

    your_netid@hpc.kennesaw.edu:/data/home/your_netid/data_folder/

  • SSH your_netid@hpc.kennesaw.edu

  • $ cp ~/data_folder /path to your scratch directory/

    Note: Assume the matlab_script.m below will access the new data file (read-only).
    fileID = fopen(’new_data_file’, r);

  • #!/bin/bash
    #PBS -l nodes=1:ppn=1
    #PBS -l walltime=10:00:00
    #PBS -m abe
    #PBS -M your_email@kennesaw.edu

    JOBID=`echo $PBS_JOBID | cut -f1 -d.`

    module load MATLAB

    # Create a temp workdir under scratch
    mkdir -p ${HOME}/scratch/matlab
    export PBS_MATLAB_WORKDIR=$( mktemp -d -p ${HOME}/scratch/matlab workdir_XXXXXXXXXX )

    matlab -nodisplay -nosplash -logfile ${FILE}.log -r "run ${FILE}"

    # Delete temp workdir
    rm -rf ${PBS_MATLAB_WORKDIR}

  • qsub run_matlab.pbs -vFILE=${PWD}/matlab_script.m

  • $ cat file_with_results   

    or   

    $ cat o.job_id 

  • $ exit