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HEC Cheat Sheet

All commands when used are cluster specific. There are two clusters the main CPU cluster and the GPU cluster. When you login to the HEC you are always on the CPU cluster. To switch between clusters use switch-cpu and switch-gpu to switch to the CPU and GPU cluster respectively.

Table of contents

  1. Job Submission commands
  2. Resource Allocation commands
  3. General Monitoring commands
    1. GPU Monitoring commands
  4. Module commands

Job Submission commands

Command Options Example Description
qsub qsub submission_script Submit the submission_script to be processed by the HEC
qdel qdel job_id Cancel the job which is associated with the given job_id.

If your using an array job and want to stop specific tasks see the HEC documentation.

Resource Allocation commands

Command Options Example Description
qslots qslots Reports the number of available job slots
-v qslots -v Verbose/detailed version of qslots
gpfsquota gpfsquota View your home, storage, and scratch space usage
qquota qquota Amount of resources your using on the HEC in relation to the amount of resources your allowed to use. Outputs nothing if your not running any jobs.

General Monitoring commands

To get an email notification on when a job completes see the HEC documentation.:

Command Options Example Description
qstat qstat Output a list of all your jobs currently waiting qw, transferring t, running r, or error state Eqw.
qtop -u qtop -u username Outputs/displays the top command for all your running jobs, it can be difficult to interpret if you are running multiple jobs, in this case read the HEC documentation to get a better understanding.
qacct -j qacct -j job_id Reports various resource usage statistics for a completed job_id e.g. memory and time taken. For details on the statistics see accounting man page
-t qacct -j job_id -t task_id Same as -j option but only reports for the task id. Only used when an array job has been submitted. Requires -j option.

GPU Monitoring commands

Command Options Example Description
qgputop -u qgputop -u username Displays the nvidia-smi output for all GPUs your using.

Module commands

For more details on these commands see the HEC documentation.

Command Options Example Description
module avail module avail View all available modules
module avail package_name View all available modules for that particular package_name
module whatis module whatis matlab A description of a software package, in this case matlab
module show module show matlab A detailed description of a software package, in this case matlab
module add module add matlab To use/access a module, in this case to use the matlab module.
module list module list List all modules currently added to your environment.
module rm module rm matlab To remove a module from your environment, in this case the matlab module.
module switch module switch pgi/6.2-32-bit To switch versions of a module, in this case we switch from a version of pgi to pgi/6.2-32-bit.