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tools:psc [2023/12/14 22:58] – vsydnor | tools:psc [2024/04/26 10:31] (current) – [Getting an account] will | ||
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====== Pittsburgh Super Computer ====== | ====== Pittsburgh Super Computer ====== | ||
+ | |||
+ | **General information** | ||
For planned outages see: https:// | For planned outages see: https:// | ||
- | To log in to the supercomputer '' | + | To log in to the supercomputer '' |
+ | , [[: | ||
- | To test what resources you have access to type '' | ||
+ | To test what resources you have access to type '' | ||
Quick test for interactive queue: '' | Quick test for interactive queue: '' | ||
- | Jobs are submitted on the PSC via sbatch. | + | ===== Getting an account ===== |
+ | - https:// | ||
+ | - you [[https:// | ||
+ | - send user account to PI (Finn or Bea) for approval in the project/ | ||
+ | - request matlab access from https:// | ||
+ | |||
+ | ===== Getting data to and from the PSC ===== | ||
+ | |||
+ | |||
+ | You can copy files to/from rhea-PSC via rsync, for example '' | ||
+ | |||
+ | Alternatively, | ||
+ | |||
+ | ===== Submitting jobs on the PSC ===== | ||
+ | |||
+ | |||
+ | Jobs are submitted on the PSC via '' | ||
+ | |||
+ | **If you need to run a script that requires command line arguments**, | ||
+ | |||
+ | < | ||
+ | # in your script to be run by the job queue | ||
+ | export bids_dir freesurfer_dir freesurfer_sif license acq_label | ||
+ | do_thing $bids_dir | ||
+ | |||
+ | #in your sbatch call | ||
+ | --export=" | ||
+ | </ | ||
+ | |||
+ | Not sure what resources to request? You can run 1 job with more resources than you think you will need. When the job completes successfully, | ||
+ | |||
+ | ===== Checking the status and resource usage of your submitted jobs ===== | ||
- | * -p RM-shared : the partition | + | When you have launched some jobs, you can check on whether they are running via '' |
- | * --time hh:mm:ss : maximum run time for your job. On RM-shared, the max run time appears to be 48:00:00 | + | |
- | * --nodes : The number of nodes to use. Typically 1 is sufficient (and appears to be the max you can request | + | |
- | * --ntasks-per-node : The number of cores to use per node. Importantly, | + | |
- | * -n : number of cores requested in total | + | |
- | * -J "$subid-$script" | + | |
- | * -o : output log file name | + | |
- | * -e : error log file name | + | |
+ | To find the jobid of jobs that you previously ran (that are either running, completed successfully, | ||
- | If you need to run a script that requires command line arguments, you can export them, for example: | ||
- | '' | ||
* allocation hour calculator: TODO | * allocation hour calculator: TODO |