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- research-articleNovember 2021
Anton 3: twenty microseconds of molecular dynamics simulation before lunch
- David E. Shaw,
- Peter J. Adams,
- Asaph Azaria,
- Joseph A. Bank,
- Brannon Batson,
- Alistair Bell,
- Michael Bergdorf,
- Jhanvi Bhatt,
- J. Adam Butts,
- Timothy Correia,
- Robert M. Dirks,
- Ron O. Dror,
- Michael P. Eastwood,
- Bruce Edwards,
- Amos Even,
- Peter Feldmann,
- Michael Fenn,
- Christopher H. Fenton,
- Anthony Forte,
- Joseph Gagliardo,
- Gennette Gill,
- Maria Gorlatova,
- Brian Greskamp,
- J.P. Grossman,
- Justin Gullingsrud,
- Anissa Harper,
- William Hasenplaugh,
- Mark Heily,
- Benjamin Colin Heshmat,
- Jeremy Hunt,
- Douglas J. Ierardi,
- Lev Iserovich,
- Bryan L. Jackson,
- Nick P. Johnson,
- Mollie M. Kirk,
- John L. Klepeis,
- Jeffrey S. Kuskin,
- Kenneth M. Mackenzie,
- Roy J. Mader,
- Richard McGowen,
- Adam McLaughlin,
- Mark A. Moraes,
- Mohamed H. Nasr,
- Lawrence J. Nociolo,
- Lief O'Donnell,
- Andrew Parker,
- Jon L. Peticolas,
- Goran Pocina,
- Cristian Predescu,
- Terry Quan,
- John K. Salmon,
- Carl Schwink,
- Keun Sup Shim,
- Naseer Siddique,
- Jochen Spengler,
- Tamas Szalay,
- Raymond Tabladillo,
- Reinhard Tartler,
- Andrew G. Taube,
- Michael Theobald,
- Brian Towles,
- William Vick,
- Stanley C. Wang,
- Michael Wazlowski,
- Madeleine J. Weingarten,
- John M. Williams,
- Kevin A. Yuh
SC '21: Proceedings of the International Conference for High Performance Computing, Networking, Storage and AnalysisArticle No.: 1, Pages 1–11https://doi.org/10.1145/3458817.3487397Anton 3 is the newest member in a family of supercomputers specially designed for atomic-level simulation of molecules relevant to biology (e.g., DNA, proteins, and drug molecules). Anton 3 achieves order-of-magnitude improvements in time-to-solution ...
- research-articleNovember 2014
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,
- Gennette Gill,
- Brian Greskamp,
- C. Richard Ho,
- Douglas J. Ierardi,
- Lev Iserovich,
- Jeffrey S. Kuskin,
- Richard H. Larson,
- Timothy Layman,
- Li-Siang Lee,
- Adam K. Lerer,
- Chester Li,
- Daniel Killebrew,
- Kenneth M. Mackenzie,
- Shark Yeuk-Hai Mok,
- Mark A. Moraes,
- Rolf Mueller,
- Lawrence J. Nociolo,
- Jon L. Peticolas,
- Terry Quan,
- Daniel Ramot,
- John K. Salmon,
- Daniele P. Scarpazza,
- U. Ben Schafer,
- Naseer Siddique,
- Christopher W. Snyder,
- Jochen Spengler,
- Ping Tak Peter Tang,
- Michael Theobald,
- Horia Toma,
- Brian Towles,
- Benjamin Vitale,
- Stanley C. Wang,
- Cliff Young
SC '14: Proceedings of the International Conference for High Performance Computing, Networking, Storage and AnalysisPages 41–53https://doi.org/10.1109/SC.2014.9Anton 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, Anton 1. The architecture of Anton 2 is tailored ...
- research-articleMarch 2013
Hardware support for fine-grained event-driven computation in Anton 2
- J. P. Grossman,
- Jeffrey S. Kuskin,
- Joseph A. Bank,
- Michael Theobald,
- Ron O. Dror,
- Douglas J. Ierardi,
- Richard H. Larson,
- U. Ben Schafer,
- Brian Towles,
- Cliff Young,
- David E. Shaw
ASPLOS '13: Proceedings of the eighteenth international conference on Architectural support for programming languages and operating systemsPages 549–560https://doi.org/10.1145/2451116.2451175Exploiting parallelism to accelerate a computation typically involves dividing it into many small tasks that can be assigned to different processing elements. An efficient execution schedule for these tasks can be difficult or impossible to determine in ...
Also Published in:
ACM SIGARCH Computer Architecture News: Volume 41 Issue 1ACM SIGPLAN Notices: Volume 48 Issue 4 - research-articleJuly 2008
Anton, a special-purpose machine for molecular dynamics simulation
- David E. Shaw,
- Martin M. Deneroff,
- Ron O. Dror,
- Jeffrey S. Kuskin,
- Richard H. Larson,
- John K. Salmon,
- Cliff Young,
- Brannon Batson,
- Kevin J. Bowers,
- 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,
- Mark A. Moraes,
- Rolf Mueller,
- Edward C. Priest,
- Yibing Shan,
- Jochen Spengler,
- Michael Theobald,
- Brian Towles,
- Stanley C. Wang
Communications of the ACM (CACM), Volume 51, Issue 7Pages 91–97https://doi.org/10.1145/1364782.1364802The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, ...
- research-articleJune 2008
Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic
DAC '08: Proceedings of the 45th annual Design Automation ConferencePages 268–271https://doi.org/10.1145/1391469.1391537Design verification of complex digital circuits typically starts only after the register-transfer level (RTL) description is complete. This frequently makes verification more difficult than necessary because logic that is intrinsically hard to verify, ...
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- ArticleJune 2007
Anton, a special-purpose machine for molecular dynamics simulation
- David E. Shaw,
- Martin M. Deneroff,
- Ron O. Dror,
- Jeffrey S. Kuskin,
- Richard H. Larson,
- John K. Salmon,
- Cliff Young,
- Brannon Batson,
- Kevin J. Bowers,
- 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,
- Mark A. Moraes,
- Rolf Mueller,
- Edward C. Priest,
- Yibing Shan,
- Jochen Spengler,
- Michael Theobald,
- Brian Towles,
- Stanley C. Wang
ISCA '07: Proceedings of the 34th annual international symposium on Computer architecturePages 1–12https://doi.org/10.1145/1250662.1250664The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, ...
Also Published in:
ACM SIGARCH Computer Architecture News: Volume 35 Issue 2 - articleMarch 2006
Special issue on formal methods for globally asynchronous and locally synchronous (GALS) systems
Formal Methods in System Design (FMSD), Volume 28, Issue 2Pages 91–92https://doi.org/10.1007/s10703-006-7840-zThis special issue is based on innovative ideas presented and discussed during the first International Workshop on Formal Methods for Globally Asynchronous and Locally Synchronous Systems (FMGALS) held in conjunction with the Formal Methods in Europe (...
- ArticleJanuary 2005
Proof-guided underapproximation-widening for multi-process systems
POPL '05: Proceedings of the 32nd ACM SIGPLAN-SIGACT symposium on Principles of programming languagesPages 122–131https://doi.org/10.1145/1040305.1040316This paper presents a procedure for the verification of multi-process systems based on considering a series of underapproximated models. The procedure checks models with an increasing set of allowed interleavings of the given set of processes, starting ...
Also Published in:
ACM SIGPLAN Notices: Volume 40 Issue 1 - ArticleFebruary 2004
Generalized Latency-Insensitive Systems for Single-Clock and Multi-Clock Architectures
DATE '04: Proceedings of the conference on Design, automation and test in Europe - Volume 2Page 21008Latency-insensitive systems were recently proposed by Carloni et al. as a correct-by-construction methodology for single-clock system-on-a-chip (SoC) design using predesigned IP blocks. Their approach overcomes the problem of long latencies of global ...
- ArticleOctober 2003
SAT-Based Algorithms for Logic Minimization
This paper introduces a new method for two-level logic minimization. Unlike previous approaches, the new method uses a SAT solver as an underlying engine. While the overall minimization strategy of the new method is based on the operators as defined in ...
- ArticleApril 2003
Verification of hybrid systems based on counterexample-guided abstraction refinement
Hybrid dynamic systems include both continuous and discrete state variables. Properties of hybrid systems, which have an infinite state space, can often be verified using ordinary model checking together with a finite-state abstraction. Model checking ...
- doctoral_thesisJanuary 2002
Efficient algorithms for the design of asynchronous control circuits
Asynchronous (or “clock-less”) digital circuit design has received much attention over the past few years, including its introduction into consumer products. One major bottleneck to the further advancement of clock-less design is the lack of optimizing ...
- ArticleJune 2001
Transformations for the synthesis and optimization of asynchronous distributed control
DAC '01: Proceedings of the 38th annual Design Automation ConferencePages 263–268https://doi.org/10.1145/378239.378480Asynchronous design has been the focus of renewed interest. However, a key bottleneck is the lack of high-quality CAD tools for the synthesis of large-scale systems which also allow design-space exploration. This paper proposes a new synthesis method ...
- research-articleJuly 2000
Self-Timed Carry-Lookahead Adders
IEEE Transactions on Computers (ITCO), Volume 49, Issue 7Pages 659–672https://doi.org/10.1109/12.863035Integer addition is one of the most important operations in digital computer systems because the performance of processors is significantly influenced by the speed of their adders. This paper proposes a self-timed carry-lookahead adder in which the ...
- ArticleMarch 1998
An Implicit Method for Hazard-Free Two-Level Logic Minimization
None of the available minimizers for exact 2-level hazard-free logic minimization can synthesize very large circuits. This limitation has forced researchers to resort to heuristic minimization, or to manual and automated circuit partitioning techniques. ...
- articleJuly 1997
On the Expressive Power of OKFDDs
Formal Methods in System Design (FMSD), Volume 11, Issue 1Pages 5–21https://doi.org/10.1023/A:1008635324476Ordered Decision Diagrams (ODDs) as a means for the representation of Boolean functions are used in many applications in CAD. Depending on the decomposition type, various classes of ODDs have been defined, among them being the Ordered Binary Decision ...
- ArticleJanuary 1997
Delay-Insensitive Carry-Lookahead Adders
Integer addition is one of the mast important operations in digital computer systems because the performance of processors is significantly influenced by the speed of their adders. This paper proposes a delay insensitive, carry-lookahead adder in which ...
- research-articleNovember 1996
Fast OFDD-Based Minimization of Fixed Polarity Reed-Muller Expressions
IEEE Transactions on Computers (ITCO), Volume 45, Issue 11Pages 1294–1299https://doi.org/10.1109/12.544485We present methods to minimize fixed polarity Reed-Muller expressions (FPRMs), i.e., two-level fixed polarity AND/EXOR canonical representations of Boolean functions, using ordered functional decision diagrams (OFDDs). We investigate the close relation ...