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GPU-HMMER on Tesla GPUs

GPU-HMMER is a bioinformatics software that does protein sequence alignment using profile HMMs by taking advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs. GPU-HMMER is 60-100x faster than HMMER (2.0).

Download and Installation

• Download GPU-HMMER
• GPU-HMMER Installation Guide
• GPU-HMMER User Guide

Benchmark Data

GPU-HMMER accelerates the hmmsearch tool using GPUs and gets speed-ups ranging from 60-100x. GPU-HMMER can take advantage of multiple Tesla GPUs in a workstation to reduce the search from hours on a CPU to minutes using a GPU.

Technical Papers

• "Evaluating the use of GPUs in Liver Image Segmentation and HMMER Database Searches, J. P. Walters, V. Balu, S. Kompalli, and V. Chaudhary: International Parallel and Distributed Processing Symposium (IPDPS), 2009
• More publications on accelerating bio-informatics applications using GPUs

Discussion Forums

• GPU computing communities on GPUcomputing.net

The Tesla Bio Workbench applications can be deployed on GPU-based desktop personal supercomputers or in data center solutions. Built on the revolutionary massively parallel CUDA architecture, these solutions are designed to accelerate the pace of computational science.

RECOMMENDED HARDWARE CONFIGURATION

Desktop Workstation Configuration	Data Center Configuration
GPUs 4 Tesla C1060 Computing GPUs CPU and Main Memory 2.33 GHz x86 CPU >16 GB (4 GB main memory per Tesla C1060 GPU)	Not applicable (GPU-HMMER is not yet MPI enabled)

WORKSTATION SOLUTIONS TESLA PERSONAL SUPERCOMPUTER For personal supercomputing at your desk Learn more >		DATA CENTER SOLUTIONS TESLA GPU COMPUTING CLUSTERS For computing with large-scale installations Learn more >