Exxact GPU Cluster Accelerates Cancer Research at Notre Dame

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Exxact Corporation, a leading provider of HPC solutions and sole provider of AMBER certified molecular dynamics systems, announced its joint effort with AMBER GPU Development Lead, Dr. Ross Walker, for providing the University of Notre Dame with a GPU solution to help assist cancer research efforts. Notre Dame scientists closely collaborated with Exxact, the Center for Research Computing, and Dr. Ross Walker to develop a solution fully optimized for AMBER software, featuring 40 NVIDIA Maxwell-based GPU accelerators installed in 10 Intel-based servers.

Exxact Corporation, a leading provider of HPC solutions and sole provider of AMBER certified molecular dynamics systems, announced its joint effort with AMBER GPU Development Lead, Dr. Ross Walker, for providing the University of Notre Dame with a GPU solution to help assist cancer research efforts. Notre Dame scientists closely collaborated with Exxact, the Center for Research Computing, and Dr. Ross Walker to develop a solution fully optimized for AMBER software, featuring 40 NVIDIA Maxwell-based GPU accelerators installed in 10 Intel-based servers.

The research effort is led by Professor Brian Baker, Associate Dean for Research and Graduate Studies in the College of Science and Professor of Chemistry and Biochemistry at the University of Notre Dame. Baker and a vastly talented team of biophysicists, biochemists, and immunologists are relying on GPU computing power to develop new immunotherapeutics. Cory Ayres, a biochemistry graduate student, leads the computational production while being co-advised by Professor Baker and Professor Steven Corcelli from the Department of Chemistry and Biochemistry.

Ayres uses the AMBER software to examine the interactions of T-Cell receptors and major histocompatibility complex proteins bound to peptide antigens. By researching these interactions, the Notre Dame scientists will have a better understanding for creating personalized cancer vaccine therapies. Simulating the interactions with AMBER requires an extensive amount of computing power to provide optimal results. The University of Notre Dame was previously using central processing units, which could only simulate a nanosecond a day. Due to these limited results, Notre Dame turned to GPU-based computational modeling to accelerate their simulations.

“AMBER users can benefit greatly from GPUs and their ability to process massive amounts of complex data quickly and efficiently,” said Jason Chen, Vice President of Exxact Corporation. “Working closely with Ross Walker, we were able to fine tune a solution for Notre Dame, and we are excited by the potential impact that their research can have on advancing cancer research.”

With Exxact’s assistance, Notre Dame was able to implement an AMBER optimized GPU Cluster and produce rapid results. The AMBER optimized solution has the ability to leverage the NVIDIA GPU accelerators to simulate up to 1.2 microseconds a day, which is a factor of 1,000 times greater than when the scientists originally started their research efforts. This accelerated output increases Notre Dame’s research results in hopes of creating advances for personalized cancer vaccines.

Read the full case study on Notre Dame’s cancer research and the Exxact Amber Optimized GPU Solution here: http://exxactcorp.com/index.php/company/prod_list/12

About Exxact Corporation
Exxact develops and manufactures innovative computing platforms and solutions that include workstation, server, cluster, and storage products developed for Life Sciences, HPC, Big Data, Cloud, Visualization, Video Wall, and AV applications. With a full range of engineering and logistics services, including consultancy, initial solution validation, manufacturing, implementation, and support, Exxact enables their customers to solve complex computing challenges, meet product development deadlines, improve resource utilization, reduce energy consumption, and maintain a competitive edge.

About the Center for Research Computing
The Center for Research Computing at University of Notre Dame is an innovative and multidisciplinary research environment that supports collaboration to facilitate discoveries in science and engineering, the arts, humanities and social sciences, through advanced computation, data analysis and other digital research tools. The Center enhances the University’s cyberinfrastructure, provides support for interdisciplinary research and education, and conducts computational research.

About AMBER Molecular Dynamics Software
AMBER is a key application in molecular dynamics used to simulate biocatalysis and the interaction between drug candidates and protein receptors. An exemplary feature of AMBER is the ability to use NVIDIA GPUs to massively accelerate complex molecular simulations. This massively enhances sampling efficiency, improves research accuracy, enables more advanced science, and speeds up the research process.

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Michael Hwang
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