Biowulf High Performance Computing at the NIH
Broccoli on Biowulf

Broccoli is a BIDS-compliant pipeline for fast analysis of fMRI data.

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 and run the program.
Sample session to display usage (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 12345678
salloc.exe: job 12345678 queued and waiting for resources
salloc.exe: job 12345678 has been allocated resources
salloc.exe: Granted job allocation 12345678
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1234 are ready for job

[user@cn1234 ~]$ module load broccoli
[+] Loading singularity  on cn1234 
[+] Loading broccoli 1.0.1  ... 

[user@cn1234 ~]$ broccolipeline
usage: broccolipipeline bids_dir output_dir analysis_type [participant(s)]

[user@cn1234 ~]$ exit
salloc.exe: Relinquishing job allocation 12345678
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. broccoli.sh). For example:

#!/bin/bash
# sbatch --mem=10g --cpus-per-task=48 --time=05:00:00 broccoli.sh

set -e

function fail {
    echo "FAIL: $@" >&2
    exit 1  # signal failure
}

module load broccoli/1.0.1 
broccolipipeline /data/user/BROCCOLI_TEST/ds001 /data/user/BROCCOLI_TEST/OUTPUT participant

Submit this job using the Slurm sbatch command.

sbatch [--gres=lscratch:#] [--cpus-per-task=#] [--mem=#] broccoli.sh