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MUMmerGPU on Tesla GPUs

MUMmerGPU is a bio-informatics software for high-throughput sequence alignment using GPUs. It accelerates the alignment of multiple query sequences against a single reference sequence by taking advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs.

Download and Installation

• Download MUMmerGPU
• Installation instructions are also in the software download

Benchmark Data

MUMmerGPU (version 2.0) provides 3x-4x speedup compared to running MUMmer on CPUs. The data shown in the chart below is based on MUMmerGPU version 1.0 and will soon be updated.

Data Courtesy of University of Maryland

Technical Papers And Presentations

• "High-throughput sequence alignment using Graphics Processing Units", M. Schatz et al.: BMC Bioinformatics 2007
• "Optimizing data intensive GPGPU computations for DNA sequence alignment", C. Trapnell, M. Schatz: Parallel Computing Aug 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 1 Tesla C1060 Computing GPU (MUMmerGPU supports a single GPU so far) CPU and Main Memory 2.33 GHz x86 CPU >8 GB (4 GB main memory per Tesla C1060 GPU)	Not applicable (MUMmerGPU 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 >