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tools:psc [2023/12/14 23:02] – vsydnortools:psc [2026/06/01 15:33] (current) – [Checking hour allocations] will
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 ====== Pittsburgh Super Computer ====== ====== Pittsburgh Super Computer ======
  
-For planned outages see: https://www.psc.edu/calendar/+**General information**
  
-To log in to the supercomputer ''ssh userid@bridges2.psc.edu''+  * To log in to the supercomputer ''ssh userid@bridges2.psc.edu''.  
 +    * For graphical apps (eg. AFNI), see [[:tools:ssh display forwarding]] 
 +    * This is world accessible and total independent for either the pitt or UPMC network. **no myapps, [[:tools:globalconnect]], or other [[:admin:remoteaccess]] needed!** 
 +  * To test what resources you have access to type ''projects'' 
 +  * Quick test for interactive queue: ''salloc''. See [[:tools:slurm]] for more 
 +  * <wrap tip> use ''%%-p RM-shared --ntasks-per-node=1%%'' for lowest hour burn rate</wrap> 
 +    * ''RM-shared'' memory limited to ''2GB*$ntasks_per_node'' (will see out-of-memory "oom" errors when exceeding). See [[:tools:slurm]]. 
 +  * User Guide: https://www.psc.edu/resources/bridges-2/user-guide/ 
 +  * For planned outages see: https://www.psc.edu/calendar/ 
 +  * see [[:tools:usage_profiling]] for determining runtime and memory usage 
 +  
 +Command line notes: 
 +<code=base> 
 +ssh -Y $USER@bridges2.psc.edu # -Y for X11 display forwarding 
 +projects                      # see account information  
 +</code> 
 +===== Getting an account ===== 
 +  - https://operations.access-ci.org/identity/new-user 
 +  - you [[https://www.psc.edu/resources/bridges-2/user-guide/|may need (20240424)]] to set a bridges/PSC specific password via reset at https://apr.psc.edu/ 
 +  - send user account to PI (Finn or Bea) for approval in the project/grant settings 
 +  - request matlab access from https://www.psc.edu/resources/software/matlab/permission-form/ 
 + 
 +===== Getting data to and from the PSC =====
  
-To test what resources you have access to type ''projects'' 
  
 You can copy files to/from rhea-PSC via rsync, for example ''rsync --size-only -avhi --exclude CuBIDS --exclude miniconda3 $software_dir $psc:${psc_destdir}''. Check which files will be rsynced before officially running it by adding ''--dry-run'' to the rsync call. You can copy files to/from rhea-PSC via rsync, for example ''rsync --size-only -avhi --exclude CuBIDS --exclude miniconda3 $software_dir $psc:${psc_destdir}''. Check which files will be rsynced before officially running it by adding ''--dry-run'' to the rsync call.
  
-Quick test for interactive queue: ''salloc''. See [[:tools:slurm]] for more+Alternatively, setting up [[:tools:globus]] endpoints, while more work, can transfer large amounts of data very fast and in the background (for rsync, see [[:tools:tmux]]). 
 + 
 +===== Submitting jobs on the PSC ===== 
 + 
 + 
 +Jobs are submitted on the PSC via ''sbatch''. sbatch is part of [[:tools:slurm]]. Usage and links are described on the [[:tools:slurm|slurm wiki page]], including links to [[https://www.psc.edu/resources/bridges-2/user-guide/#system-configuration|PSC's user guide]], especially the ''[[https://www.psc.edu/resources/bridges-2/user-guide/#:~:text=Bridges-2%20RM-,nodes,-RM|RM]]'' and ''[[https://www.psc.edu/resources/bridges-2/user-guide/#:~:text=of%20the%20EM-,partition,-EM%20partition|EM]]'' nodes RAM and cores summary table 
 + 
 +<WRAP alert>Jobs run on ''RM'' partition [[https://www.psc.edu/resources/bridges-2/user-guide/#:~:text=jobs%20in%20the%20rm%20partition%20are%20charged%20for%20all%20128%20cores%20on%20every%20node%20they%20use.%20|request the whole node (128 cores), and always bill 128 hours for every hour spent in the node]]. Use ''%%-p RM-shared --ntasks-per-node=N%%'' to restrict to N cores.  
 + 
 +If your job uses a lot of memory, you will see OOM (out-of-memory) errors with any ''RM'' partition. Request and use ''-p EM'' for high memory jobs. </WRAP> 
 + 
 +**If you need to run a script that requires command line arguments**, you can export them, for example: 
 + 
 +<code> 
 +# in your script to be run by the job queue 
 +export bids_dir freesurfer_dir freesurfer_sif license acq_label 
 +do_thing $bids_dir 
 + 
 +#in your sbatch call 
 +--export="ALL,SUBJECT_ID=$subject_id,ACQ=$acq_label,BIDS_DIR=$bids_dir,FS_DIR=$freesurfer_dir,FS_SIF=$freesurfer_sif,LIC=$license"  
 +</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, check the resources it used via ''seff $jobid''; this will tell you the CPU utilized, the job wall-clock run time, the amount of memory utilized, etc. Hence, when initially testing an sbatch submission, it is recommended to launch just one test participant (or one test run) in order to figure out if the job will complete successfully. If you are launching jobs for a list of participants or range of runs, this can be accomplished by adding ''break'' to a bash loop that launches the jobs in succession.  
 + 
 +===== 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 ''squeue -u $userid''
  
-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:+To find the jobid of jobs that you previously ran (that are either running, completed successfully, or exited with an error),  use ''sacct --starttime yyyy-mm-dd''. This will list the JobID, JobName, Partition, Account, AllocCPUs, State, and ExitCode of the job.
  
-  * -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) +===== Checking hour allocations =====
-  * --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 +
-*//When initially testing an sbatch submission, it is recommended to launch on just one test participant (or one test run). If you are launching jobs for a list of participants or range of runs, this can be accomplished by adding ''break'' to your bash script that launches the jobs//+
  
 +To check the hours of specific job (also see [[:tools:usage_profiling]]) <code> sacct -j <job name>.batch --format=JobID,MaxRSS,AveRSS,TotalCPU </code>
  
 +To check the hours in general: <code> projects </code>
  
-If you need to run a script that requires command line arguments, you can export them, for example: +To check the hours per person: <code> projects --usage-by-user soc230004p </code>
-''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    * allocation hour calculator: TODO