Biowulf High Performance Computing at the NIH
SAMsrcV3 on Biowulf

Synthetic Aperture Magnetometry

The SAMsrcV3 suite implements the latest advances in MEG source localization. Compared with the older CTF tools, there are many new features (some of them experimental). Filtering options, more flexible control over active, control, and noise covariance matrices, dual-state imaging, realistic head models, and several flavors of multipole source imaging are available.

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 samsrcv3

[user@cn3144 ~]$ sam_cov -r my_dataset -m settings.param

[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. samsrc.sh). For example:

#!/bin/bash
set -e
module load samsrcv3
sam_cov -r my_dataset -m settings.param

Submit this job using the Slurm sbatch command.

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

sam_cov -r dataset01 -m settings.param
sam_cov -r dataset02 -m settings.param
sam_cov -r dataset03 -m settings.param
sam_cov -r dataset04 -m settings.param

Submit this job using the swarm command.

swarm -f samsrc.swarm [-g #] [-t #] --module samsrcv3
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 samsrcv3 Loads the SAMsrcV3 module for each subjob in the swarm