BSOFT on Biowulf

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Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages.

BSoft was developed by groups at the University of Basel, NIAMS, and Caltech.
BSoft website

Running a single Bsoft job

The Bsoft programs have standard Unix command-line syntax, and so are ideally suited to running as a batch job or as a swarm of batch jobs.

Sample Bsoft batch script:

#!/bin/bash
#PBS -m be

module load bsoft

cd /data/user/myjob
bimg -verbose 7 -truncate 0,100 input.img output.img

This job would be submitted with

biowulf% qsub -l nodes=1 jobscript

Running a swarm of Bsoft jobs

Biowulf users will typically want to process large numbers of image files via Bsoft. This is most easily done using the swarm utility. The Bsoft binaries should be added to your path by loading the bsoft module:

module load bsoft

This command can be added to your .bashrc or .cshrc files if you are running swarms of bsoft jobs.

Now set up a swarm command file along the following lines:

# this file is called swarmfile

bimg -verbose 7 -truncate 0,100 input1.img output1.img
bimg -verbose 7 -truncate 0,100 input2.img output2.img
bimg -verbose 7 -truncate 0,100 input3.img output3.img
bimg -verbose 7 -truncate 0,100 input4.img output4.img
bimg -verbose 7 -truncate 0,100 input5.img output5.img
[...]

Submit this with

biowulf% swarm -f swarmfile

If each Bsoft process in the swarm command file requires more than 1 GB of memory, use

biowulf% swarm -g # -f swarmfile

where # is the number of Gigabytes required by each process.

Documentation

Bsoft website