Smriprep on Biowulf

Smriprep is a computational pipeline for preprocessing of structural MRI datasets. The output of smriprep can be used as an input to dmriprep and fmriprep.

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 smriprep

[user@cn3144 ~]$ smriprep -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. For example (using test data below):

#SBATCH --job-name=smriprep
#SBATCH --gres=lscratch:20
#SBATCH --exclusive
#SBATCH --mem=32g
#SBATCH --time=72:00:00

module load smriprep

smriprep /lscratch/${SLURM_JOB_ID}/input001 /lscratch/${SLURM_JOB_ID}/smriprep.out.ds001 \
         participant --participant_label sub-01 -w /lscratch/${SLURM_JOB_ID}

Submit this job using the Slurm sbatch command.

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. smriprep.swarm). For example:

smriprep /data/${USER}/BIDS-dataset/input001/ /data/$USER/BIDS-dataset/smriprep.out.ds001 \
         participant --participant_label sub-01 -w /lscratch/${SLURM_JOB_ID} \
smriprep /data/${USER}/BIDS-dataset/input002/ /data/$USER/BIDS-dataset/smriprep.out.ds002 \
         participant --participant_label sub-02 -w /lscratch/${SLURM_JOB_ID} \
smriprep /data/${USER}/BIDS-dataset/input003/ /data/$USER/BIDS-dataset/smriprep.out.ds003 \
         participant --participant_label sub-03 -w /lscratch/${SLURM_JOB_ID} \

Submit this job using the swarm command.

swarm -f smriprep.swarm [--gres=lscratch:#] [-g #] -t auto --module smriprep
-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 smriprep Loads the smriprep module for each subjob in the swarm