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 to all OSC users. If you have any questions, please contact OSC Help.
The following versions of GPU-BLAST are available on OSC systems:
VERSION | NCBI-Blast Version | OAKLEY | ruby |
---|---|---|---|
1.0 | 2.2.24+ | X | |
1.1 | 2.2.25+ | X | |
1.1 | 2.2.26+ | X* | |
1.1 | 2.2.28+ | X* |
* Current default version
Usage
Usage on Oakley
Set-up
To set up the environment for gpu-blast on Ruby cluster, do the following:
module load cuda/4.1.28 module load gpu-blast
Batch Usage
Provided is a sample batch script:
#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 gpu-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
Usage on Ruby
Set-up
To set up the environment for gpu-blast on Ruby cluster, do the following:
module load cuda/7.5.18 module load gpu-blast
Batch Usage
Provided is a sample batch script:
#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 gpu-blast module load cuda/7.5.18 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