Biowulf High Performance Computing at the NIH
Nibabies on Biowulf

Nibabies is an MRI preprocessing pipeline for the infant and neonate brain.

References:

Web site


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, run the program and download some imaging datasets to test. 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 nibabies

[user@cn3144 ~]$ nibabies --help

[user@cn3144 ~]$ cd /data/$USER

[user@cn3144 ~]$ mkdir NIBABIES_TEST

[user@cn3144 ~]$ cd NIBABIES_TEST

[user@cn3144 ~]$ module load aws

[user@cn3144 ~]$ aws s3 sync --no-sign-request s3://openneuro.org/ds003778 ds003778

[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. nibabies.sh). For example:

#!/bin/bash
#SBATCH --job-name=nibabies
#SBATCH --gres=lscratch:20
#SBATCH --exclusive
#SBATCH --mem=32g
#SBATCH --time=72:00:00

module load nibabies

nibabies /data/$USER/NIBABIES_TEST/ds003778 /data/$USER/NIBABIES_TEST/nibabies.out.ds003778 \
         participant --participant-label sub-01 -w /lscratch/${SLURM_JOB_ID} \
         --age-months 12 --notrack

Submit this job using the Slurm sbatch command.

sbatch nibabies.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. nibabies.swarm). For example:

nibabies /data/$USER/NIBABIES_TEST/ds003778 /data/$USER/NIBABIES_TEST/nibabies.out.ds003778-01 \
         participant --participant-label sub-01 -w /lscratch/${SLURM_JOB_ID} \
         --age-months 12 --notrack
nibabies /data/$USER/NIBABIES_TEST/ds003778 /data/$USER/NIBABIES_TEST/nibabies.out.ds003778-02 \
         participant --participant-label sub-02 -w /lscratch/${SLURM_JOB_ID} \
         --age-months 12 --notrack
nibabies /data/$USER/NIBABIES_TEST/ds003778 /data/$USER/NIBABIES_TEST/nibabies.out.ds003778-03 \
         participant --participant-label sub-03 -w /lscratch/${SLURM_JOB_ID} \
         --age-months 12 --notrack

Submit this job using the swarm command.

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