Biowulf High Performance Computing at the NIH
mrtrix on Biowulf

MRtrix provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI

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 mrtrix
[+] Loading eigen 3.3.4  ...
[+] Loading Zlib 1.2.11  ...
[+] Loading GSL 2.4 for GCC 4.8.5 ...
[+] Loading FFTW 3.3.7 , compiled with gcc4.8.5  and openmpi2.1.2  ...
[+] Loading mrtrix 3.0_RC2  ...

[user@cn3144 ~]$ mrinfo /usr/local/apps/mrtrix/sample_data/data_slice_0000.nii.gz
mrinfo: [WARNING] transform matrix contains invalid entries - resetting to sane defaults
Image:               "/usr/local/apps/mrtrix/sample_data/data_slice_0000.nii.gz"
  Dimensions:        128 x 104 x 1 x 65
  Voxel size:        2 x 2 x 2 x 1
  Data strides:      [ 1 2 4 3 ]
  Format:            NIfTI-1.1 (GZip compressed)
  Data type:         signed 16 bit integer (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:                    1           0           0        -127
                                0           1           0        -103
                                0           0           1          -0
  comments:          FSL5.0
[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:

set -e
module load mrtrix
mrstats /usr/local/apps/mrtrix/sample_data/nodif_brain_mask.nii.gz
mrhistogram /usr/local/apps/mrtrix/sample_data/nodif.nii.gz  out.hist

Submit this job using the Slurm sbatch command.

sbatch [--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. mrtrix.swarm). For example:

mrstats file1.nii.gz
mrstats file2.nii.gz
mrstats file3.nii.gz

Submit this job using the swarm command.

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