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© 2011 Pittsburgh Supercomputing Center The Anton Project at the National Resource for Biomedical Supercomputing HPC User Forum Houston, TX April 6, 2011.

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Presentation on theme: "© 2011 Pittsburgh Supercomputing Center The Anton Project at the National Resource for Biomedical Supercomputing HPC User Forum Houston, TX April 6, 2011."— Presentation transcript:

1 © 2011 Pittsburgh Supercomputing Center The Anton Project at the National Resource for Biomedical Supercomputing HPC User Forum Houston, TX April 6, 2011

2 © 2011 Pittsburgh Supercomputing Center Contributors Joel Stiles, Ph.D, M.D. Director, NRBSC Markus Dittrich, Senior Scientific Specialist NRBSC Ralph Roskies, Scientific Director, PSC Jim Kasdorf, Director of Special Projects, PSC

3 © 2011 Pittsburgh Supercomputing Center Disclaimer Nothing in this presentation represents an official view or position of the U.S. National Institutes of Health, nor of D.E. Shaw Research, nor of the Pittsburgh Supercomputing Center nor of Carnegie Mellon University. All material is from public sources. All errors are my own (JK).

4 © 2011 Pittsburgh Supercomputing Center The PSC Biomedical Initiative Founded in 1987 Funded by U.S. National Institutes of Health –First extramural NIH supercomputing program Renewed every five years With 2006 grant, renamed: National Resource for Biomedical SuperComputing

5 © 2011 Pittsburgh Supercomputing Center National Resource for Biomedical Supercomputing Performs leading-edge research in high performance computing and the life sciences Fosters exchange between PSC expertise in computational science and biomedical researchers nationwide

6 © 2011 Pittsburgh Supercomputing Center National Resource for Biomedical Supercomputing Computational biomedical research Outreach to the national biomedical research community –User training –Software distribution –Publications –Online courses and workshop webcasts.

7 © 2011 Pittsburgh Supercomputing Center NRBSC Research Areas Microphysiology Volumetric visualization and analysis Computational structural biology

8 © 2011 Pittsburgh Supercomputing Center Anton Anton van Leeuwenhoek (October 24, 1632 – August 26, 1723) Perfected the microscope “Father of microbiology”

9 © 2011 Pittsburgh Supercomputing Center Anton Massively parallel supercomputer Designed and built by D.E. Shaw Research (DESRES) Special-purpose system for Molecular Dynamics (MD) simulations of proteins and other biological macromolecules

10 © 2011 Pittsburgh Supercomputing Center David E. Shaw B.S. / M.S. UCSD Ph.D. Stanford, 1980 Columbia CS Department until 1986 Formed D.E. Shaw Group in 1988 –“King Quant” (Fortune, Feb. 5,1996) –Assets Under Management ~$20B Net worth: $2.2B (March 2011)

11 © 2011 Pittsburgh Supercomputing Center David E. Shaw Founded DESRES, 2002 Senior Research Fellow, Columbia University, 2005 PCAST appointments, 1994 and 2009 Council of Competitiveness Executive Committee Fellow of AAAS –American Academy of Arts and Sciences –American Association for the Advancement of Science

12 © 2011 Pittsburgh Supercomputing Center D.E. Shaw Research (www.deshawresearch.com) Independent research laboratory Conducts basic scientific research in computational biochemistry Involved primarily in: The design of novel algorithms and machine architectures for high-speed molecular dynamics (MD) simulations of proteins and other biological macromolecules The application of these simulations to basic scientific research in structural biology and biochemistry, and to the process of computer-aided drug design

13 © 2011 Pittsburgh Supercomputing Center The MD Challenge Molecular dynamics (MD) simulation allows scientists to study the microscopic dynamics of biomolecular systems and thus gain crucial insight into processes such as: Protein folding How drug molecules interact with proteins and nucleic acids The mode of operation of many important cellular proteins such as ion channels or other transport proteins Importantly, most relevant biological events take place on a timescale of milliseconds (10 -3 s) or longer

14 © 2011 Pittsburgh Supercomputing Center Anton Anton is a special-purpose supercomputer designed to specifically address the need of MD simulations to access the biologically-relevant realm of millisecond timescales. Anton was designed to dramatically increase the speed of MD simulations. Anton runs MD simulations fully in hardware (as opposed to running MD software on general purpose hardware).

15 © 2011 Pittsburgh Supercomputing Center Anton Compared to the previous state-of-the-art Anton provides a speedup of ~100x, rendering millisecond timescales attainable Anton uses custom-designed ASICs and novel simulation algorithms

16 © 2011 Pittsburgh Supercomputing Center Anton Processing Node

17 © 2011 Pittsburgh Supercomputing Center Anton ASIC

18 © 2011 Pittsburgh Supercomputing Center A 512-Node Anton Machine

19 © 2011 Pittsburgh Supercomputing Center Anton Benchmarks Computational platformSpeed (ns/day) single CPU codes~1 Parallel supercomputers~100 Anton (512 node machine)17,400 DHFR benchmark, simulated biological time)

20 © 2011 Pittsburgh Supercomputing Center MD Simulations on Anton Standard, unbiased MD runs in NVE, NVT, and NPT ensembles are possible. Simulate proteins, lipids, water, RNA, DNA. On a 512-processor Anton, simulation systems with up to 120,000 atoms can be simulated effectively. Supports standard MD forcefields (CHARMM, AMBER, OPLSAA,...). Input is in Maestro format (similar to what is used in the DESRES Desmond code).

21 © 2011 Pittsburgh Supercomputing Center Anton Benchmarks Chemical system (PDB ID) System Size (# atoms) Speed (μs/machine day) DHFR (5dfr) 23, aSFP (1sfp)48, FtsZ (1fsz) 98, T7Lig (1a01) 116, All simulations used 2.5-femtosecond time steps with long-range interactions evaluated at every other time step and a Berendsen thermostat applied every 100 time steps

22 © 2011 Pittsburgh Supercomputing Center The availability of Anton at the National Resource for Biomedical Supercomputing (NRBSC) at PSC was made possible by a partnership with DESRES. DESRES made available an Anton machine without cost for non-commercial research use by not-for-profit institutions. The Anton at NRBSC is the only one available outside DESRES.

23 © 2011 Pittsburgh Supercomputing Center Operations are funded by a two-year $2.7 million grant from the National Institute of General Medical Sciences (NIGMS), part of NIH. This is the first time NIH has provided funds to make available a supercomputing system for national use. Grand Opportunities (GO) grant mechanism from ARRA funds One of only 14 GO awards from NIGMS

24 © 2011 Pittsburgh Supercomputing Center

25 Anton 512-node Anton production machine –Four cabinets, each with 128 special-purpose ASICs –Operational since October node Anton test machine –One cabinet with 64 special-purpose ASICs –Operational since May 2010 Access to both Anton back-ends is via a Linux front- end running a standard PBS queuing system.

26 © 2011 Pittsburgh Supercomputing Center Anton AntonFS storage cluster –Dedicated to Anton MD trajectory storage –Lustre-based file system with ~450 TB of storage Kollman analysis cluster –Dedicated to analysis of MD trajectories generated on Anton –Four nodes each with 12 cores (2 * 3.33GHz Intel Xeon Westmere EP X core), 96 GB of RAM and one NVIDIA Tesla C2050 card, QDR IB

27 © 2011 Pittsburgh Supercomputing Center Anton Allocations In spring of 2010 NRBSC solicited proposals from the scientific community; 67 proposals were received. Proposal review and assignment of allocations was conducted by a committee convened by the National Research Council at the National Academies of Science. 15 proposals were awarded 100,000 node-hours each during the first phase of the project (October 2010 through March 2011).

28 © 2011 Pittsburgh Supercomputing Center Anton Allocations 32 proposals were awarded ~50,000 node hours each during the second phase of the project (April 2011 through September 2011).

29 © 2011 Pittsburgh Supercomputing Center Science Projects on Anton The range of science topics proposed for simulation on Anton is quite diverse: Studies of membrane channels and transporters Protein folding Design and evaluation of novel enzyme catalysts DNA sequencing Protein dynamics Signal transduction Force field development ….

30 © 2011 Pittsburgh Supercomputing Center Science Projects on Anton Currently (as of March 2011), the investigators of phase 1 are wrapping up their simulations and are conducting preliminary analyses of their generated data.

31 © 2011 Pittsburgh Supercomputing Center References “New Architectures for a New Biology”, Martin Deneroff, February 22, E07/SIAM_2-07-desres.pdf“New Architectures for a New Biology”, Martin Deneroff, February 22, E07/SIAM_2-07-desres.pdf “Anton, a special-purpose machine for molecular dynamics simulation”, D.E. Shaw, et al., Communications of the ACM, Volume 51, Issue 7, July 2008“Anton, a special-purpose machine for molecular dynamics simulation”, D.E. Shaw, et al., Communications of the ACM, Volume 51, Issue 7, July 2008 “Herculean Device for Molecular Mysteries”, John Markoff, The New York Times, July 8, 2008“Herculean Device for Molecular Mysteries”, John Markoff, The New York Times, July 8, 2008

32 © 2011 Pittsburgh Supercomputing Center References “Millisecond-scale molecular dynamics simulations on Anton”, D.E. Shaw, et al., SC’09 Proceedings “Exploiting 162-Nanosecond End-to-End Communication Latency on Anton”, Ron O. Dror, et al., SC10 Proceedings

33 © 2011 Pittsburgh Supercomputing Center References “Atomic-Level Characterization of the Structural Dynamics of Proteins”, D.E. Shaw, et al. Science 15 October 2010: Vol. 330 no pp “Custom-Built Supercomputer Brings Protein Folding Into View”, Robert F. Service, Science 15 October 2010:

34 © 2011 Pittsburgh Supercomputing Center References “Anton Supercomputer Proves Its Mettle”, Chemical & Engineering News, October 14, “Supercomputer sets protein-folding record”, Nature, October 14, 2010,

35 © 2011 Pittsburgh Supercomputing Center Jim Kasdorf


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