New Bioinformatics Cluster features NAMD, InfiniBand

January 2009 - The latest cluster to come out of Nor-Tech's lab is a Rocks/Linux-based system designed for use in medical research relating to diseases such as Alzheimer's, Parkinson's and diabetes II. The cluster features the NAMD simulation package as well as InfiniBand. The cluster also includes CHARMM, a versatile molecular simulation program.

NAMD (Nanoscale Molecular Dynamics) is an open source parallel molecular dynamics simulation package based on Charm++. Designed to conduct high-performance simulation of large biomolecular systems, NAMD scales to a multitude of processors on each cluster.

In addition to GigE, Nor-Tech's Bioinformatic cluster uses InfiniBand to flow data between its processors. InfiniBand offers significa ntly higher throughput low latency as compared to GigE.

Rocks in an open-source Linux cluster distribution for HPC clusters developed by NPACI and SDSC. Rocks includes integral applications that tie together the components of a cluster.

A case study detailing this project is avalable here..

The Bioinformatics Cluster uses a Qlogic Inifiband switch and Mellanox InfiniBand HCA's

Further reading: Nor-Tech HPC Clusters | Nor-Tech Case Studies | More about Nor-Tech

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