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High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation

Richard H. Larson, John K. Salmon, Ron O. Dror, Martin M. Deneroff, Cliff Young, J.P. Grossman, Yibing Shan, John L. Klepeis, David E. Shaw
2008 High-Performance Computer Architecture  
In Anton, such range-limited interactions are handled by a high-throughput interaction subsystem (HTIS).  ...  Anton is a massively parallel special-purpose supercomputer designed to accelerate molecular dynamics (MD) simulations by several orders of magnitude, making possible for the first time the atomic-level  ...  Acknowledgments The authors wish to extend their thanks to Joe Bank, Greg Lund and John Schomburg for valuable contributions to the work reported in this paper.  ... 
doi:10.1109/hpca.2008.4658650 dblp:conf/hpca/LarsonSDDYGSKS08 fatcat:vzkzlzv5freqhndfnypbynwv7m

Anton, a special-purpose machine for molecular dynamics simulation

David E. Shaw, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Douglas J. Lerardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Martin M. Deneroff (+15 others)
2008 Communications of the ACM  
The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication network  ...  Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation.  ...  CONCLUSION We have designed, and are currently in the process of implementing, a specialized, massively parallel machine, called Anton, for the high-speed execution of molecular dynamics simulations.  ... 
doi:10.1145/1364782.1364802 fatcat:fhohu3mfmzddjcqq4hwt3i76cy

Anton, a special-purpose machine for molecular dynamics simulation

David E. Shaw, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Martin M. Deneroff (+15 others)
2007 Proceedings of the 34th annual international symposium on Computer architecture - ISCA '07  
The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication network  ...  Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation.  ...  CONCLUSION We have designed, and are currently in the process of implementing, a specialized, massively parallel machine, called Anton, for the high-speed execution of molecular dynamics simulations.  ... 
doi:10.1145/1250662.1250664 dblp:conf/isca/ShawDDKLSYBBCEGGHIKKLMMMPSSTTW07 fatcat:lfa6hizfi5cwhj3rznaf32vlmm

Anton, a special-purpose machine for molecular dynamics simulation

David E. Shaw, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Martin M. Deneroff (+15 others)
2007 SIGARCH Computer Architecture News  
The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication network  ...  Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation.  ...  CONCLUSION We have designed, and are currently in the process of implementing, a specialized, massively parallel machine, called Anton, for the high-speed execution of molecular dynamics simulations.  ... 
doi:10.1145/1273440.1250664 fatcat:lygdje54hnca5an6lwjfppn22u

Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer

David E. Shaw, J.P. Grossman, Joseph A. Bank, Brannon Batson, J. Adam Butts, Jack C. Chao, Martin M. Deneroff, Ron O. Dror, Amos Even, Christopher H. Fenton, Anthony Forte, Joseph Gagliardo (+33 others)
2014 SC14: International Conference for High Performance Computing, Networking, Storage and Analysis  
Anton 2 is a second-generation special-purpose supercomputer for molecular dynamics simulations that achieves significant gains in performance, programmability, and capacity compared to its predecessor  ...  A 512-node Anton 2 machine, currently in operation, is up to ten times faster than Anton 1 with the same number of nodes, greatly expanding the reach of all-atom biomolecular simulations.  ...  ACKNOWLEDGMENTS We thank Cristi Predescu for developing the u-series decomposition; Robert Dirks for assistance with the DPPC simulation; Stefano Piana  ... 
doi:10.1109/sc.2014.9 dblp:conf/sc/ShawGBBBCDDEFFGGGHIIKLLLLLKMMMMNPQRSSSSSSTTTTVWY14 fatcat:5djwsecvenfkziflnxi6yecxma

Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation

Jeffrey S. Kuskin, Cliff Young, J.P. Grossman, Brannon Batson, Martin M. Deneroff, Ron O. Dror, David E. Shaw
2008 High-Performance Computer Architecture  
Anton executes its most computationally demanding calculations on a highly specialized, enormously parallel, but largely non-programmable high-throughput interaction subsystem (HTIS).  ...  Achieving this balance was a significant challenge in the design of Anton, a parallel machine that will accelerate MD simulations by several orders of magnitude.  ...  Acknowledgments The authors wish to extend their thanks to Ken Mackenzie for valuable contributions to the work reported in this paper, and to Matthew Farrens and the anonymous reviewers for their insightful  ... 
doi:10.1109/hpca.2008.4658651 dblp:conf/hpca/KuskinYGBDDS08 fatcat:4nsazah77rd2heexl47hdoueue

Hierarchical simulation-based verification of Anton, a special-purpose parallel machine

J.P. Grossman, John K. Salmon, C. Richard Ho, Douglas J. Ierardi, Brian Towles, Brannon Batson, Jochen Spengler, Stanley C. Wang, Rolf Mueller, Michael Theobald, Cliff Young, Joseph Gagliardo (+3 others)
2008 2008 IEEE International Conference on Computer Design  
One of the major design verification challenges in the development of Anton, a massively parallel special-purpose machine for molecular dynamics, was to provide evidence that computations spanning more  ...  These explicit couplings between adjacent levels of the simulation hierarchy created a continuous verification chain from molecular dynamics to individual logic gates.  ...  ACKNOWLEDGEMENTS We would like to thank Joe Bank, Ken Mackenzie and Bill Vick for their valuable contributions to this work, and the anonymous reviewers for their helpful suggestions.  ... 
doi:10.1109/iccd.2008.4751883 dblp:conf/iccd/GrossmanSHITBSWMTYGDDS08 fatcat:irtuvjhh35ea3ipduqwt4v2oqy

Millisecond-scale molecular dynamics simulations on Anton

David E. Shaw, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Douglas J. Ierardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Ron O. Dror (+10 others)
2009 Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis - SC '09  
ABSTRACT Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems.  ...  Figure 1 : Two renderings of a protein (BPTI) taken from a molecular dynamics simulation on Anton.  ...  software and test infrastructure; Tiankai Tu for helpful comments on the paper; and Rebecca Kastleman and Jennifer McGrady for editorial assistance.  ... 
doi:10.1145/1654059.1654126 dblp:conf/sc/ShawDSGMBYDBBCEIKKLLMMPST09a fatcat:zn37hseoxveyxdmorr5joc5fj4

Simulative Analysis of a Multidimensional Torus-Based Reconfigurable Cluster for Molecular Dynamics

Abhijeet Lawande, Hanchao Yang, Alan D. George, Herman Lam
2014 2014 43rd International Conference on Parallel Processing Workshops  
Molecular dynamics (MD) is a large-scale, communication-intensive problem that has been the subject of high-performance computing research and acceleration for years.  ...  In this paper, we present a performance model for the 3D FFT kernel that forms the core of MD simulation on Anton.  ...  ACKNOWLEDGMENT This work was supported in part by the I/UCRC Program of the National Science Foundation under Grant Nos. EEC-0642422 and IIP-1161022.  ... 
doi:10.1109/icppw.2014.58 dblp:conf/icppw/LawandeYGL14 fatcat:zabjkzffczdwfbjw3nkp564dhm

Simulation and embedded software development for Anton, a parallel machine with heterogeneous multicore ASICs

J. P. Grossman, Cliff Young, Joseph A. Bank, Kenneth Mackenzie, Douglas J. Ierardi, John K. Salmon, Ron O. Dror, David E. Shaw
2008 Proceedings of the 6th IEEE/ACM/IFIP international conference on Hardware/Software codesign and system synthesis - CODES/ISSS '08  
Anton, a special-purpose parallel machine currently under construction, is the result of a significant hardware-software codesign effort that relied heavily on an architectural simulator.  ...  Third, a portion of the embedded software is dynamically generated at simulation time. This paper discusses the various ways in which the Anton simulator addresses these challenges.  ...  Each ASIC contains two computational subsystems: a high-throughput interaction subsystem (HTIS) [8] , in which specialized datapaths compute pairwise interactions between particles, and a flexible subsystem  ... 
doi:10.1145/1450135.1450165 dblp:conf/codes/GrossmanYBMISDS08 fatcat:f6atfkrb6zabjbyhlbkuanzihq

Extending the Generality of Molecular Dynamics Simulations on a Special-Purpose Machine

Daniele P. Scarpazza, Douglas J. Ierardi, Adam K. Lerer, Kenneth M. Mackenzie, Albert C. Pan, Joseph A. Bank, Edmond Chow, Ron O. Dror, J.P. Grossman, Daniel Killebrew, Mark A. Moraes, Cristian Predescu (+2 others)
2013 2013 IEEE 27th International Symposium on Parallel and Distributed Processing  
We have previously described a massively parallel special-purpose supercomputer, called Anton, and have shown that it executes traditional molecular dynamics simulations orders of magnitude faster than  ...  Here, we describe how we extended Anton's software to support a more diverse set of methods, allowing scientists to simulate a broader class of biological phenomena at extremely high speeds.  ...  While Anton is specialized for molecular dynamics, a similar combination of hardware and software design strategies may be useful in accommodating a diverse set of methods on machines designed for other  ... 
doi:10.1109/ipdps.2013.93 dblp:conf/ipps/ScarpazzaILMPBCDGKMPSS13 fatcat:wg7jtjrhtfg3xf2tpxnuxk57j4

On the Feasibility of FPGA Acceleration of Molecular Dynamics Simulations [article]

Michael Schaffner, Luca Benini
2018 arXiv   pre-print
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail.  ...  However, we also note that scaled multi-node systems could potentially benefit from a hybrid composition, where GPUs are used for compute intensive parts and FPGAs for latency and communication sensitive  ...  processors and specialized pairwise point interaction modules (PPIMs).  ... 
arXiv:1808.04201v1 fatcat:yzos5gym5ndojoooesfsmw2iwq

Biophysical experiments and biomolecular simulations: A perfect match?

Sandro Bottaro, Kresten Lindorff-Larsen
2018 Science  
A fundamental challenge in biological research is achieving an atomic-level description and mechanistic understanding of the function of biomolecules.  ...  Techniques for biomolecular simulations have undergone substantial developments, and their accuracy and scope have expanded considerably.  ...  integrated circuits for calculating the costly parts of the force-field interactions, a specialized communication network tailored to match the periodic boundary conditions used in simulation, and special  ... 
doi:10.1126/science.aat4010 pmid:30049874 fatcat:qhvu4i33ujapzomdonac5dd2m4

Biomolecular Modeling in the Era of Petascale Computing [chapter]

Abhinav Bhatele, Klaus Schulten, Laxmikant Kalé, James Phillips
2007 Chapman & Hall/CRC Computational Science  
protein BAR domains, for the proposed machine: A molecular dynamics (MD) simulation of curvature-inducing protein BAR domains binding to a charged phospholipid vesicle over 10 ns simulation time under  ...  calculation of pairwise forces for atoms within a cutoff radius r c .  ... 
doi:10.1201/9781584889106.ch9 fatcat:q4hyrd22p5dbrelo5n3ees55jm

Computational 'microscopy' of cellular membranes

Helgi I. Ingólfsson, Clément Arnarez, Xavier Periole, Siewert J. Marrink
2016 Journal of Cell Science  
Computational 'microscopy' refers to the use of computational resources to simulate the dynamics of a molecular system.  ...  We illustrate the power of computational modelling approaches by providing a few in-depth examples of largescale simulations that move up from molecular descriptions into the subcellular arena.  ...  Acknowledgements Alex H. de Vries is acknowledged for stimulating discussions. Competing interests The authors declare no competing or financial interests.  ... 
doi:10.1242/jcs.176040 pmid:26743083 fatcat:hsmpccwi2zd3ppuv5gdt3n6jjm
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