THPC Quick Start

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Last updated: Jun 06, 2023 by RIS-SVC-conf-publish
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Compute Resources

Docker Usage

Video

Interactive Command-Line

Starting a Session

  • Connect to compute client.

ssh wustlkey@compute1-client-1.ris.wustl.edu

  • Start up a session.

compute1-terminal /bin/bash

  • If you are a member of more than one compute group, you will be prompted to specify an LSF User Group with -G group_name or by setting the LSB_SUB_USER_GROUP variable.

Using the Command-Line

  • View available modules.

# view all available modules
module avail

# filter module search (case specific)
module avail <search_criteria>

  • Load a specific module for use.

module load <software_module>

  • Unload module when finished.

module unload <software_module>

Interactive GUI

Starting a Session

  • Connect to compute client.

ssh wustlkey@compute1-client-1.ris.wustl.edu

  • Start up a session.

compute1-gui-desktop

A password for the GUI will automatically generate on the initial run and be output in the terminal. To choose your own password, prepend the job command with VNC_PW=password, replacing “password” with that of your choosing.

If you are a member of more than one compute group, you will be prompted to specify an LSF User Group with -G group_name or by setting the LSB_SUB_USER_GROUP variable.

  • Open a browser and insert the URL received in the terminal as output.

Given the large size of the THPC environment, it may take up to a minute for the session to be fully loaded and viewable in the browser.

  • The below page should now be displayed. Select ‘Connect’ and submit your password. Select the ‘Terminal Emulator’ icon at the bottom of the browser page or from the ‘Applications’ dropdown to open a terminal.

Using the GUI

  • View available software modules.

# view all available modules
module avail

# filter module search (case specific)
module avail <search_criteria>

  • Load a specific module for use (the generic listed first will always run the latest version available).

module load <software_module>

  • Unload module when finished.

module unload <software_module>

Extra Features

  • Settings, clipboard and extra features are available by clicking to extend the minimized tab on the left.

Non-Interactive Batch Job

Job Submission

  • Connect to compute client.

ssh wustlkey@compute1-client-1.ris.wustl.edu

  • Submit a non-interactive batch job, replacing script.sh with your submission script.

compute1-batch /bin/zsh script.sh

Example Gaussian Batch Job

Replace ${COMPUTE_ALLOCATION} with the name of the compute allocation you are a member of when running the code blocks below.

  • Create a folder in your scratch folder named gaussian.

mkdir -p /scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian

  • Create a submission script named gaussian_job.sh in your home folder.

cat <<EOF > $HOME/gaussian_job.sh
    #!/bin/bash

    cd /scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian
    module load gaussian09
    export GAUSS_SCRDIR=/scratch1/fs1/${COMPUTE_ALLOCATION}
    g09 < test.inp >& test.out
EOF

  • Create sample Gaussian input data (the empty line at the end is important).

cat <<EOF > /scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian/test.inp
    $ RunGauss

    #n test rohf/sto-3g pop=full GFINPUT

    O sto-3g triplet

    0 3
    O

EOF

  • Submit the non-interactive Gaussian batch job

LSF_DOCKER_VOLUMES="/scratch1/fs1/${COMPUTE_ALLOCATION}:/scratch1/fs1/${COMPUTE_ALLOCATION}" compute1-batch /bin/zsh $HOME/gaussian_job.sh

  • Once the job is complete, you can access the output file at /scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian/test.out.

cat /scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian/test.out