Biowulf High Performance Computing at the NIH
Mango on Biowulf

Mango (Multi-image Analysis GUI) is a viewer for medical research images. Mango contains analysis tools and a GUI to navigate image volumes. Mango also comes with the following command-line utilities: mango (loads image), mango-applytransform (applies transform to image), mango-convert2avw (converts to AVW format), mango-convert2des (converts to DES format), mango-convert2nii (converts to NIFTI format), mango-imageinfo (prints image metadata summary), mango-makeroi (makes ROI based on image threshold), mango-resizer (resizes image), mango-script (runs mango script), mango-vols2series (concatenates volumes into series).

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 (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 mango

[user@cn3144 ~]$ mango-imageinfo sub-01_T1w.nii.gz

[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. mango_job.sh). For example:

#!/bin/bash

export TMPDIR=/lscratch/$SLURM_JOB_ID

module load mango
mango-convert2avw sub-01_T1w.nii.gz

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] mango_job.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. mango_jobs.swarm). For example:

mango-convert2avw sub-01_T1w.nii.gz
mango-convert2avw sub-02_T1w.nii.gz
mango-convert2avw sub-03_T1w.nii.gz
mango-convert2avw sub-04_T1w.nii.gz
mango-convert2avw sub-05_T1w.nii.gz

Submit this job using the swarm command.

swarm -f mango_jobs.swarm [-g #] [-t #] --module mango
where
-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 mango Loads the mango module for each subjob in the swarm