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Pittsburgh Super Computer

To log in to the supercomputer ssh userid@bridges2.psc.edu

To test what resources you have access to (via what projects), type projects

Quick test for interactive queue: salloc. See slurm for more

Jobs are submitted on the PSC via sbatch. See sbatch options here https://www.psc.edu/resources/bridges-2/user-guide/#system-configuration. A description of some options is below:

  • -p RM-shared : the partition you are requesting resources from. The most common one is RM-shared, but there is also RM, RM-512, and EM (extreme memory)
  • –time hh:mm:ss : maximum run time for your job. On RM-shared, the max run time appears to be 48:00:00
  • –nodes : The number of nodes to use. Typically 1 is sufficient (and appears to be the max you can request on RM-shared)
  • –ntasks-per-node : The number of cores to use per node. Importantly, increasing the number of cores requested increases your job's memory (RAM) allocation. On RM-shared, each core comes with 1.95G memory. So four nodes e.g. will get you 7.81 GB.
  • -n : number of cores requested in total
  • -J “$subid-$script” : The name of your job. By default, jobs are named by their job id, however you can customize the job name via variables like $subid
  • -o : output log file name
  • -e : error log file name

If you need to run a script that requires command line arguments, you can export them, for example: export bids_dir freesurfer_dir freesurfer_sif license acq_label in your script and then –export=“ALL,SUBJECT_ID=$subject_id,ACQ=$acq_label,BIDS_DIR=$bids_dir,FS_DIR=$freesurfer_dir,FS_SIF=$freesurfer_sif,LIC=$license” in your sbatch call

  • allocation hour calculator: TODO

Resources