GPU-Blast

GPU-BLAST is an accelerated version of the popular NCBI-BLAST (www.ncbi.nlm.nih.gov) that uses general-purpose graphics processing unit (GPU). In comparison to the sequential NCBI-BLAST, GPU-BLAST is nearly four times faster, while producing identical results.

Availability & Restrictions

GPU-BLAST is available without restriction to all OSC users.

The following versions of GPU-BLAST are available on OSC systems:

VERSION NCBI-Blast Version GLENN OAKLEY
1.0 2.2.24+   X
1.1 2.2.25+   X
1.1 2.2.26+   X

Usage

Set-up

To set up the environment for gpu-blast on Oakley cluster, do the following:

module load cuda/4.1.28
module load gpu-blast

Batch Usage

A sample batch script is below:

#PBS -l nodes=1:ppn=1:gpus=1
#PBS -l walltime=10:00
#PBS -N GPU-Blast
#PBS -S /bin/bash
#PBS -j oe

module load blast
module load cuda/4.1.28
set -x

cd $PBS_O_WORKDIR
mkdir $PBS_JOBID

cp 100.fasta $TMPDIR
cd $TMPDIR
/usr/bin/time blastn -db nt -query 100.fasta  -out test.out

cp * $PBS_O_WORKDIR/$PBS_JOBID

Further Reading

See Also