Scalable Informatics (http://www.scalableinformatics.com), provider of high performance computing and storage solutions, in cooperation with researchers at the University at Buffalo, announced the introduction of GPU-HMMER, an NVIDIA CUDA implementation and extension of MPI-HMMER. GPU-HMMER and MPI-HMMER are open-source implementations of the HMMER protein sequence analysis suite that profoundly reduce computation times.

The MPI-HMMER implementation capitalizes on the computational power of multiple processors on large clusters, whereas GPU-HMMER is designed to leverage NVIDIA GPUs (graphics processing units) to accelerate processing on computing systems. Performance of up to 100x faster than a single core of AMD Shanghai 2.3 GHz has been measured for 3 GPU units.

AVAILABILITY

HMMer, GPU-HMMer, and mpiHMMer are all GPL v2 licensed. This work is based upon the 2.3.2 version of HMMer. Version 3.0 of HMMer is in alpha at http://hmmer.janelia.org.

FOR MORE INFORMATION

See http://insidehpc.com/2009/02/04/gpu-hmmer-announced/ for some details, and the mpiHMMer site http://mpihmmer.org for downloads, documentation, support, etc.