On September 22nd OSC will be switching to Slurm for job scheduling and resource management on the Pitzer Cluster, along with the deployment of the new Pitzer hardware. We are in the process of updating the example job scripts for each software. If a Slurm example is not yet available, please consult our general Slurm information page or contact OSC help.

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 and Restrictions

Versions

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

VERSION NCBI-BLAST VERSION RUBY
1.1 2.2.28+ X*
* Current default version

You can use module spider gpu-blast to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Note that GPU-BLAST is not available on the Owens system. GPU-BLAST requires the CUDA nvcc compiler, but the GPU-BLAST software is only compatible with CUDA versions up to 7.5. CUDA 8, installed on the Owens cluster, is incompatible with GPU-BLAST.

Access

GPU-BLAST is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Panagiotis D. Vouzis and Nikolaos V. Sahinidis/ freeware

Usage

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

Further Reading

See Also

Supercomputer: 
Service: 
Fields of Science: