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BSOFT on Biowulf

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:

#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.

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/1.8.6

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

biowulf% swarm -g # -f swarmfile --module bsoft/1.8.6
where # is the number of Gigabytes required by each process.


Bsoft website