Petprep on Biowulf
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Documentation
Notes
Interactive job
Batch job
Swarm of jobs

Petprep: Pre-processing tools for PET imaging datasets.

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load petprep

[user@cn3144 ~]$ petprep -h

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. petprep.sh). For example (using test data below):

#!/bin/bash
#SBATCH --job-name=petprep
#SBATCH --gres=lscratch:20
#SBATCH --exclusive
#SBATCH --mem=32g
#SBATCH --time=8:00:00

module load petprep/0.0.8

petprep /lscratch/${SLURM_JOB_ID}/PET_BIDS_TEST_DATA \
        /lscratch/${SLURM_JOB_ID}/petprep.out.PET_BIDS_TEST_DATA \
        participant \
        --participant-label sub-01 \
        -w /lscratch/${SLURM_JOB_ID} \
        --output-spaces MNI152NLin2009cAsym T1w

Submit this job using the Slurm sbatch command.

sbatch petprep.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. petprep.swarm). For example:

petprep /lscratch/${SLURM_JOB_ID}/PET_BIDS_TEST_DATA1 \
        /lscratch/${SLURM_JOB_ID}/petprep.out.PET_BIDS_TEST_DATA1 \
        participant \
        --participant-label sub-01 \
        -w /lscratch/${SLURM_JOB_ID} \
        --output-spaces MNI152NLin2009cAsym T1w
petprep /lscratch/${SLURM_JOB_ID}/PET_BIDS_TEST_DATA2 \
        /lscratch/${SLURM_JOB_ID}/petprep.out.PET_BIDS_TEST_DATA2 \
        participant \
        --participant-label sub-01 \
        -w /lscratch/${SLURM_JOB_ID} \
        --output-spaces MNI152NLin2009cAsym T1w
petprep /lscratch/${SLURM_JOB_ID}/PET_BIDS_TEST_DATA3 \
        /lscratch/${SLURM_JOB_ID}/petprep.out.PET_BIDS_TEST_DATA3 \
        participant \
        --participant-label sub-01 \
        -w /lscratch/${SLURM_JOB_ID} \
        --output-spaces MNI152NLin2009cAsym T1w

Submit this job using the swarm command.

swarm -f petprep.swarm [--gres=lscratch:#] [-g #] -t auto --module petprep
where
-gres=lscratch:# Number of Gigabytes of local disk space allocated per process (1 line in the swarm command file)
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file). We set this to auto to allocate all CPUs in each node.
--module petprep Loads the petprep module for each subjob in the swarm