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tools:psc [2024/04/24 10:38] – [Getting an account] will | tools:psc [2024/04/26 10:31] (current) – [Getting an account] will | ||
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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 '' | ||
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===== Getting an account ===== | ===== Getting an account ===== | ||
- https:// | - https:// | ||
- | - ?? | + | - you [[https:// |
- | - get approval from PI (Finn or Bea) | + | - 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 ===== | ||
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You can copy files to/from rhea-PSC via rsync, for example '' | You can copy files to/from rhea-PSC via rsync, for example '' | ||
+ | |||
+ | Alternatively, | ||
===== Submitting jobs on the PSC ===== | ===== Submitting jobs on the PSC ===== | ||
- | Jobs are submitted on the PSC via sbatch. | + | Jobs are submitted on the PSC via '' |
+ | |||
+ | **If you need to run a script that requires command line arguments**, | ||
- | * -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 | + | # in your script |
- | * --nodes : The number of nodes to use. Typically 1 is sufficient (and appears to be the max you can request on RM-shared) | + | export bids_dir freesurfer_dir freesurfer_sif license acq_label |
- | * --ntasks-per-node : The number of cores to use per node. Importantly, | + | do_thing |
- | * -n : number of cores requested in total (useful if you are requesting >1 node and dividing requested cores over nodes) | + | |
- | * -J "$subid-$script" | + | |
- | * -o : output log file name | + | |
- | * -e : error log file name | + | |
- | * --export: //see below// | + | |
- | *//If you need to run a script that requires command line arguments, you can export them, for example: | + | #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 '' |