Biowulf High Performance Computing at the NIH
Baracus on Biowulf

BARACUS is a BIDS-compliant application that predicts brain age, based on combining data from cortical thickness, cortical surface area, and subcortical information

Web site

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 baracus

[user@cn3144 ~]$ baracus -h
usage: [-h]
                             [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                             [--freesurfer_dir FREESURFER_DIR]
                             [--models {Liem2016__OCI_norm,Liem2016__full_2samp_training} [{Liem2016__OCI_norm,Liem2016__full_2samp_training} ...]]
                             [--skip_missing] --license_key LICENSE_KEY
                             [--n_cpus N_CPUS] [-v]
                             bids_dir out_dir {participant,group}

BARACUS: Brain-Age Regression Analysis and Computation Utility Software. BIDS
mode. You specify a BIDS-formatted freesurfer folder as input. All data is
extracted automatiacally from that folder.

positional arguments:
  bids_dir              The directory with the input dataset formatted
                        according to the BIDS standard.
  out_dir               Results are put into {out_dir}/baracus.
  {participant,group}   Level of the analysis that will be performed.
                        "participant": predicts single subject brain age,
                        "group": collects single subject predictions.

optional arguments:
  -h, --help            show this help message and exit
                        The label of the participant that should be analyzed.
                        The label corresponds to sub- from
                        the BIDS spec (so it does not include "sub-"). If this
                        parameter is not provided all subjects should be
                        analyzed. Multiple participants can be specified with
                        a space separated list.
  --freesurfer_dir FREESURFER_DIR
                        Folder with FreeSurfer subjects formatted according to
                        BIDS standard. If subject's recon-all folder cannot be
                        found, recon-all will be run. If not specified
                        freesurfer data will be saved to {out_dir}/freesurfer
  --models {Liem2016__OCI_norm,Liem2016__full_2samp_training} [{Liem2016__OCI_norm,Liem2016__full_2samp_training} ...]
  --skip_missing        Flag to skip not segmented subjects
  --license_key LICENSE_KEY
                        FreeSurfer license key - letters and numbers after "*"
                        in the email you received after registration. To
                        register (for free) visit
  --n_cpus N_CPUS       Number of CPUs/cores available to use.
  -v, --version         show program's version number and exit

[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:

# sbatch --gres=lscratch:100 --mem=3g --cpus-per-task=48 --time=10:00:00

set -e

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

module load baracus
cp /data/$USER/BARACUS_TEST/ds001.tar.gz /lscratch/$SLURM_JOB_ID/.
cd /lscratch/$SLURM_JOB_ID
tar -xzvf ds001.tar.gz
baracus --participant_label 01 \
        --license_key /usr/local/apps/freesurfer/license.txt \
        --n_cpus $SLURM_CPUS_PER_TASK \
        /lscratch/$SLURM_JOB_ID/ds001 \
        /lscratch/$SLURM_JOB_ID \
cp -R /lscratch/$SLURM_JOB_ID/baracus /data/$USER/BARACUS_TEST/.
cp -R /lscratch/$SLURM_JOB_ID/freesurfer /data/$USER/BARACUS_TEST/.

Submit this job using the Slurm sbatch command.

sbatch [--gres=lscratch:#] [--cpus-per-task=#] [--mem=#]
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. baracus.swarm). For example:

# swarm -f baracus.swarm --gres=lscratch:100 -g 4 -t 48 --time 10:00:00 --module baracus
cp /data/$USER/BARACUS_TEST/ds001.tar.gz /lscratch/$SLURM_JOB_ID/.; \
cd /lscratch/$SLURM_JOB_ID; \
tar -xzvf ds001.tar.gz; \
baracus --participant_label 01 \
        --license_key /usr/local/apps/freesurfer/license.txt \
        --n_cpus $SLURM_CPUS_PER_TASK \
        /lscratch/$SLURM_JOB_ID/ds001 \
        /lscratch/$SLURM_JOB_ID \
        participant; \
mv /lscratch/$SLURM_JOB_ID/baracus /data/$USER/BARACUS_TEST/baracus_01; \
mv /lscratch/$SLURM_JOB_ID/freesurfer /data/$USER/BARACUS_TEST/freesurfer_01
cp /data/$USER/BARACUS_TEST/ds001.tar.gz /lscratch/$SLURM_JOB_ID/.; \
cd /lscratch/$SLURM_JOB_ID; \
tar -xzvf ds001.tar.gz; \
baracus --participant_label 02 \
        --license_key /usr/local/apps/freesurfer/license.txt \
        --n_cpus $SLURM_CPUS_PER_TASK \
        /lscratch/$SLURM_JOB_ID/ds001 \
        /lscratch/$SLURM_JOB_ID \
        participant; \
mv /lscratch/$SLURM_JOB_ID/baracus /data/$USER/BARACUS_TEST/baracus_02; \
mv /lscratch/$SLURM_JOB_ID/freesurfer /data/$USER/BARACUS_TEST/freesurfer_02

Submit this job using the swarm command.

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