Biowulf High Performance Computing at the NIH
Connectome Workbench on Biowulf


Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.


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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@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 connectome-workbench

[user@cn3144 ~]$ wb_command -help

[user@cn3144 ~]$ wb_view -help

[user@cn3144 ~]$ wb_import

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Additionally, if you have X11 forwarding enabled you can use the workbench gui by entering wb_view with no arguments.

Batch jobs on Biowulf

wb_command gives access to a wide variety of commands related to data analysis iand image processing that can be used in your scripts. Use the following argument to view the documentation.

[user@helix ~]$ wb_command -all-commands-help

After selecting the command(s) you want to run in a batch script, set it up like so.

# this file is called myjob.bat

cd /data/$USER/my_workbench_data
module load connectome-workbench

wb_command ...my_command1...
wb_command ...my_command2...
wb_command ...my_command3...
wb_command ...my_commandN...

Submit the job to SLURM with:

[user@helix ~]$ sbatch  myjob.bat
Swarm of jobs on Biowulf

If you need to run a large number of batch jobs, you can run them in parallel using the swarm program. For this example, imagine we have a large number of files to convert from cifti to nifti format. We would create a swarm file (called "workbench.swarm") that looked something like this:

 wb_command -cifti-convert -to-nifti /path/to/file1.cifti /path/to/file1.nifti
 wb_command -cifti-convert -to-nifti /path/to/file2.cifti /path/to/file2.nifti
 wb_command -cifti-convert -to-nifti /path/to/file3.cifti /path/to/file3.nifti
 wb_command -cifti-convert -to-nifti /path/to/fileN.cifti /path/to/fileN.nifti

We would submit it to the queue with

[user@helix ~]$ swarm -f workbench.swarm --module connectome-workbench 

See the swarm webpage for more information, or contact the Biowulf staff at