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Connectome Workbench on Biowulf

Description

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.

Reference

Web sites

On Helix

To prepare your environment for using Connectome Workbench, enter the following:

[user@helix ~]$ module load connectome-workbench

The commands wb_command, wb_import, and wb_view will now be available to you. To learn more about wb_command or wb_view use the help arguments like so:

[user@helix ~]$ wb_command -help
[user@helix ~]$ wb_view -help

To learn more about wb_import enter the command without any arguments.

[user@helix ~]$ wb_import

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 and 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.

#!/bin/bash
# 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 staff@hpc.nih.gov

Interactive job on Biowulf

Running an interactive job on Biowulf is identical to running interactively On Helix with the caveat that one must first allocate resources for an interactive session using:

[user@helix ~]$ sinteractive

This command will allocate 2 cpus (1 hyperthreaded core) and 4GB of RAM. If your interactive session needs more resources, you can specify the requirements at job submission. Use the -h argument to see a list of available options for sinteractive.

[user@helix ~]$ sinteractive -h
Documentation