Visit additional Tabor Communication Publications
May 05, 2010
PITTSBURGH, May 5 -- The National Institute of General Medical Sciences (NIGMS), part of the National Institutes of Health (NIH), has awarded a two-year, $2.7 million grant to the National Resource for Biomedical Supercomputing (NRBSC) at the Pittsburgh Supercomputing Center (PSC) to host a specialized supercomputer for biomolecular simulation designed by D. E. Shaw Research (DESRES). The machine, called Anton, will be made available without cost by DESRES for non-commercial research use by universities and other not-for-profit institutions.
Anton was designed to dramatically increase the speed of molecular dynamics (MD) simulations compared with the previous state of the art, allowing biomedical researchers to understand the motions and interactions of proteins and other biologically important molecules over much longer time periods than have previously been accessible to computational study. The machine and the novel algorithms it employs were designed by a team of researchers led by David E. Shaw, chief scientist of DESRES.
NRBSC will soon be inviting US biomedical researchers to submit proposals for allocations of time on the Anton machine. A peer review committee to be convened by the National Research Council will review proposals. Although the NIH has supported MD-related research by individual scientists for many years, it has never before provided funds to make a supercomputing system for MD simulations available as a national resource. For more information about proposal submission,
"This is an incredibly exciting project in many ways," said Joel Stiles, the director of NRBSC. "With this very generous gift from D. E. Shaw Research and the funding provided by NIH, we are deploying a tool of unprecedented power for the benefit of biomedical researchers nationally. We hope and expect that this project will help to significantly advance our understanding of biomolecular structure and function, and to spur ongoing scientific and technological development in MD research and in other areas of computational biology."
As part of the NIGMS award, NRBSC also will install a new data storage and analysis subsystem, including nearly half a petabyte of online disk capacity (one petabyte is one million gigabytes), to host and make widely available the tremendous amount of data that will be produced by MD simulations on Anton. In addition, Stiles, a faculty member in Biological Sciences and the Lane Center for Computational Biology at Carnegie Mellon University, is collaborating with Christopher Langmead in the Carnegie Mellon School of Computer Science to develop specialized software for the analysis of data as it streams off the machine.
The award is one of 14 made by NIGMS using funding from the American Recovery and Reinvestment Act of 2009 for projects the NIH views as "Grand Opportunities" for major scientific progress. "The Grand Opportunities grants fund projects that promise to have a significant impact on a field of biomedical science," said NIGMS Director Jeremy M. Berg. "By closing specific knowledge gaps, creating new technologies, or building community-wide resources, these awards will dramatically propel progress in key scientific fields."
While experimental methods such as X-ray crystallography can determine rigid molecular structures at near atomic resolution, MD simulations track atomic positions over the course of time. Changes in the shape of a biomolecule are often intimately related to its function, suggesting that atomic-level molecular dynamics simulations may ultimately play an important role in the design of therapeutic drugs. Because atomic-level MD simulations of proteins require an enormous number of calculations to simulate even a very short period of biological time, many of the most important biological phenomena have historically fallen outside the reach of even the most powerful general-purpose scientific supercomputers. Anton has now run simulations extending for more than a millisecond of biological time -- about 100 times longer than the longest previously published all-atom MD simulation.
D. E. Shaw Research is an independent research laboratory that conducts basic scientific research in the field of computational biology. At present, the lab is involved primarily in the design of novel algorithms and machine architectures for high-speed molecular dynamics simulations of proteins and other biological macromolecules, and in the application of such simulations to basic research in structural biology and biochemistry and to the process of computer-aided drug design.
Established in 1987 as part of PSC, with support from NIH's National Center for Research Resources, NRBSC was the first external biomedical supercomputing program funded by NIH. NRBSC scientists conduct basic research in areas spanning molecular and cellular modeling, massive 3D reconstruction of biological tissues, and bioinformatics. In addition, NRBSC fosters exchange among experts in computational science and biomedicine, provides computational resources and training to biomedical researchers, and provides state-of-the-art educational outreach to students at all levels across the nation.
More about NRBSC: www.nrbsc.org
More about DESRES: www.DEShawResearch.com
More about PSC: www.psc.edu
About the Pittsburgh Supercomputing Center
The Pittsburgh Supercomputing Center is a joint effort of Carnegie Mellon University and the University of Pittsburgh together with Westinghouse Electric Company. Established in 1986, PSC is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry, and is a partner in the National Science Foundation TeraGrid program.
Source: Pittsburgh Supercomputing Center
The Xeon Phi coprocessor might be the new kid on the high performance block, but out of all first-rate kickers of the Intel tires, the Texas Advanced Computing Center (TACC) got the first real jab with its new top ten Stampede system.We talk with the center's Karl Schultz about the challenges of programming for Phi--but more specifically, the optimization...
Although Horst Simon was named Deputy Director of Lawrence Berkeley National Laboratory, he maintains his strong ties to the scientific computing community as an editor of the TOP500 list and as an invited speaker at conferences.
Supercomputing veteran, Bo Ewald, has been neck-deep in bleeding edge system development since his twelve-year stint at Cray Research back in the mid-1980s, which was followed by his tenure at large organizations like SGI and startups, including Scale Eight Corporation and Linux Networx. He has put his weight behind quantum company....
May 16, 2013 |
When it comes to cloud, long distances mean unacceptably high latencies. Researchers from the University of Bonn in Germany examined those latency issues of doing CFD modeling in the cloud by utilizing a common CFD and its utilization in HPC instance types including both CPU and GPU cores of Amazon EC2.
May 15, 2013 |
Supercomputers at the Department of Energy’s National Energy Research Scientific Computing Center (NERSC) have worked on important computational problems such as collapse of the atomic state, the optimization of chemical catalysts, and now modeling popping bubbles.
May 10, 2013 |
Program provides cash awards up to $10,000 for the best open-source end-user applications deployed on 100G network.
May 09, 2013 |
The Japanese government has revealed its plans to best its previous K Computer efforts with what they hope will be the first exascale system...
May 08, 2013 |
For engineers looking to leverage high-performance computing, the accessibility of a cloud-based approach is a powerful draw, but there are costs that may not be readily apparent.
05/10/2013 | Cleversafe, Cray, DDN, NetApp, & Panasas | From Wall Street to Hollywood, drug discovery to homeland security, companies and organizations of all sizes and stripes are coming face to face with the challenges – and opportunities – afforded by Big Data. Before anyone can utilize these extraordinary data repositories, however, they must first harness and manage their data stores, and do so utilizing technologies that underscore affordability, security, and scalability.
04/15/2013 | Bull | “50% of HPC users say their largest jobs scale to 120 cores or less.” How about yours? Are your codes ready to take advantage of today’s and tomorrow’s ultra-parallel HPC systems? Download this White Paper by Analysts Intersect360 Research to see what Bull and Intel’s Center for Excellence in Parallel Programming can do for your codes.
In this demonstration of SGI DMF ZeroWatt disk solution, Dr. Eng Lim Goh, SGI CTO, discusses a function of SGI DMF software to reduce costs and power consumption in an exascale (Big Data) storage datacenter.
The Cray CS300-AC cluster supercomputer offers energy efficient, air-cooled design based on modular, industry-standard platforms featuring the latest processor and network technologies and a wide range of datacenter cooling requirements.