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Bsoft on Biowulf & Helix

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

On Helix

Load the Bsoft module, and then type any Bsoft commands. Sample session:

[susanc@helix]$ module spider bsoft

  Bsoft: Bsoft/1.9.0

    This module can be loaded directly: module load Bsoft/1.9.0

[susanc@helix]$ module load Bsoft

[susanc@helix]$ bimg -verbose 7 -truncate 0,100 input.img output.img

Batch job on Biowulf

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:


module load Bsoft

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

This job would be submitted with

sbatch  jobscript

This job would be submitted to a single core (2 hyperthreaded CPUs) and 4 GB of memory. If more than the default 4 GB of memory is required, you would submit with:

sbatch --mem=#g  jobscript
where '#' is the number of GigaBytes of memory required.

Swarm of jobs

Biowulf users will typically want to process large numbers of image files via Bsoft. This is most easily done using the swarm utility.

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 --module Bsoft/1.9.0

If each Bsoft process in the swarm command file requires more than 4 GB of memory, use

biowulf% swarm -g # -f swarmfile --module Bsoft/1.9.0
where # is the number of Gigabytes required by each process.

Interactive job

To run Bsoft interactively on Biowulf, allocate an interactive session and run the process there.

Sample session:

biowulf% sinteractive

cn0203% module load bsoft

cn0203% ...bsoft commands ...

cn0203% exit

Bsoft website