Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
tools:psc [2024/04/24 11:48] – [Submitting jobs on the PSC] will | tools:psc [2024/04/26 10:31] (current) – [Getting an account] will | ||
---|---|---|---|
Line 15: | Line 15: | ||
- https:// | - https:// | ||
- you [[https:// | - you [[https:// | ||
- | - ?? | ||
- send user account to PI (Finn or Bea) for approval in the project/ | - 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 ===== | ===== Getting data to and from the PSC ===== | ||
Line 28: | Line 28: | ||
- | Jobs are submitted on the PSC via '' | + | Jobs are submitted on the PSC via '' |
- | | + | **If you need to run a script that requires command line arguments**, you can export |
- | | + | |
- | | + | |
- | | + | |
- | * -n : number of cores requested in total (useful if you are requesting >1 node and dividing requested cores over nodes) | + | |
- | * -J " | + | |
- | * -o : output log file name | + | |
- | * -e : error log file name | + | |
- | * --export: | + | |
- | *//If you need to run a script that requires command line arguments, you can export them, for example: | + | < |
- | '' | + | # in your script |
+ | export bids_dir freesurfer_dir freesurfer_sif license acq_label | ||
+ | do_thing $bids_dir | ||
+ | |||
+ | #in your sbatch call | ||
+ | --export=" | ||
+ | </code> | ||
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, | 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** | + | ===== Checking the status and resource usage of your submitted jobs ===== |
When you have launched some jobs, you can check on whether they are running via '' | When you have launched some jobs, you can check on whether they are running via '' |