Biowulf High Performance Computing at the NIH
C3D on Biowulf

C3D is a command-line tool for converting 3D images between common file formats. The tool also includes a growing list of commands for image manipulation, such as thresholding and resampling.

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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 c3d

[user@cn3144 ~]$ c3d -h

[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 c3d
c3d minimal.nii output.img

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. c3d_jobs.swarm). For example:

c3d minimal.nii -interpolation Cubic -resample 50x30x40vox -o output_0.img
c3d minimal.nii -interpolation Cubic -resample 25x15x20vox -o output_1.img
c3d minimal.nii -interpolation Cubic -resample 12x7x10vox -o output_2.img

Submit this job using the swarm command.

swarm -f c3d_jobs.swarm [-g #] [-t #] --module c3d
-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 c3d Loads the cmtk module for each subjob in the swarm