Joseph Gagliardo

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6ranked-venue papers

0as first author

2since 2021 · last 2021

—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Systems, architecture and hardware · 6 · 2 since 2021Software engineering, systems software and programming languages · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Computer architecture, parallel and distributed computing, and storage systems 4 papers		High-performance computing · 63% Hardware accelerators and domain-specific architectures · 29% Electronic design automation · 8%
Interdisciplinary, comprehensive, and emerging computing 3 papers		Computational science and engineering · 52% Bioinformatics and computational biology · 48%

Topics — the 9 heaviest of 10, each with the papers that count most for it

Topic	Weight	Papers	Last	Evidence papers
High-performance computing › scientific computing systems molecular dynamics simulation	0.8	3	2021	Anton 3: twenty microseconds of molecular dynamics simulation before lunch · SC 2021 Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer · SC 2014 Anton, a special-purpose machine for molecular dynamics simulation · ISCA 2007
High-performance computing scientific computing systems	0.8	3	2021	Anton 3: twenty microseconds of molecular dynamics simulation before lunch · SC 2021 Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer · SC 2014 Anton, a special-purpose machine for molecular dynamics simulation · ISCA 2007
Hardware accelerators and domain-specific architectures › scientific computing accelerator molecular dynamics accelerator	0.7	2	2021	Anton 3: twenty microseconds of molecular dynamics simulation before lunch · SC 2021 Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer · SC 2014
Bioinformatics and computational biology › molecular informatics › molecular modeling biomolecular simulation	0.2	2	2021	Anton 3: twenty microseconds of molecular dynamics simulation before lunch · SC 2021 Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer · SC 2014
Computational science and engineering › computational chemistry molecular simulation	0.2	2	2021	Anton 3: twenty microseconds of molecular dynamics simulation before lunch · SC 2021 Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer · SC 2014
Electronic design automation › hardware verification and test formal verification	0.1	1	2008	Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic · DAC 2008
Electronic design automation hardware verification and test	0.1	1	2008	Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic · DAC 2008
Electronic design automation › hardware verification and test coverage analysis	0.0	1	2008	Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic · DAC 2008
Computational science and engineering › computational chemistry › molecular simulation molecular dynamics	0.0	1	2007	Anton, a special-purpose machine for molecular dynamics simulation · ISCA 2007

Methods — techniques the papers use, named apart from their topics

application-specific hardware · 1.4custom chip design · 1.0event-driven architecture · 0.4conditional coverage points · 0.1

Year	Publication	Venue	Position
2021	The ΛNTON 3 ASIC: a Fire-Breathing Monster for Molecular Dynamics Simulations abstract • Understand biomolecular systems through their motions •Numerical integration of Newton's laws of motion — Model atoms as point masses — Compute forces on every atom based on current positions — Update atom velocities and positions in discrete time steps of a few femtoseconds • Force computation described by a model: the force field Peter J. Adams, Brannon Batson, Alistair Bell, Jhanvi Bhatt, J. Adam Butts, Timothy Correia, Bruce Edwards, Peter Feldmann, Christopher H. Fenton, Anthony Forte, Joseph Gagliardo, Gennette Gill, Maria Gorlatova, Brian Greskamp, J. P. Grossman, Jeremy Hunt, Bryan L. Jackson, Mollie M. Kirk, Jeffrey Kuskin, Roy J. Mader, Richard McGowen, Adam McLaughlin, Mark A. Moraes, Mohamed Nasr, Lawrence J. Nociolo, Lief O'Donnell, Jon L. Peticolas, Terry Quan, T. Carl Schwink, Keun Sup Shim, Naseer Siddique, Jochen Spengler, Michael Theobald, Brian Towles, William Vick, Stanley C. Wang, Michael E. Wazlowski, Madeleine J. Weingarten, John M. Williams, David E. Shaw	HCS	11
2021	Anton 3: twenty microseconds of molecular dynamics simulation before lunch abstract Anton 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 over its predecessor, Anton 2 (the current state of the art), and is over 100-fold faster than any other currently available supercomputer, thereby enabling broad new avenues of research on critical questions in biology and drug discovery. This speedup means that a 512-node Anton 3 simulates a million atoms at over 100 microseconds per day. Furthermore, Anton 3 attains this performance while consuming an order of magnitude less energy per simulated microsecond than any other machine. Like its predecessors, Anton 3 was designed from the ground up around a new custom chip to best exploit the capabilities offered by new technologies. We present here the main architectural and algorithmic developments that were necessary to achieve such significant advances. 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, Doug Ierardi, Lev Iserovich, Bryan L. Jackson, Nick P. Johnson, Mollie M. Kirk, John L. Klepeis, Jeffrey Kuskin, Kenneth M. Mackenzie, Roy J. Mader, Richard McGowen, Adam McLaughlin, Mark A. Moraes, Mohamed H. Nasr, Lawrence J. Nociolo, Lief O'Donnell, 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	20
2014	Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer abstract 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, Anton 1. The architecture of Anton 2 is tailored for fine-grained event-driven operation, which improves performance by increasing the overlap of computation with communication, and also allows a wider range of algorithms to run efficiently, enabling many new software-based optimizations. 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 bio molecular simulations. Anton 2 is the first platform to achieve simulation rates of multiple microseconds of physical time per day for systems with millions of atoms. Demonstrating strong scaling, the machine simulates a standard 23,558-atom benchmark system at a rate of 85 μs/day -- 180 times faster than any commodity hardware platform or general-purpose 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, Richard Ho 0001, Doug Ierardi, Lev Iserovich, Jeffrey 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, Lawrence J. Nociolo, Jon L. Peticolas, Terry Quan, Daniel Ramot, John K. Salmon, Daniele Paolo 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	12
2008	Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic abstract Design 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, such as memories, counters and deep first-in, first-out (FIFO) structures, becomes immutable in the design. This paper proposes a new approach that exploits formal verification of conditional coverage points with the goal of early identification of hard-to-verify logic. We use the difficulty of formal verification problems as an early estimator of the verification complexity of a design. While traditional verification methods consider conditional coverage only in the design verification phase, we describe an approach that uses conditional coverage at a much earlier stage---the design phase, during which changes to the RTL code are still possible. The method is illustrated using real examples from the verification of an ASIC designed for a specialized supercomputer. Richard Ho 0001, Michael Theobald, Martin M. Deneroff, Ron O. Dror, Joseph Gagliardo, David E. Shaw	DAC	5
2008	Hierarchical simulation-based verification of Anton, a special-purpose parallel machine abstract 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 than a quadrillion clock cycles will produce valid scientific results. Our verification methodology addressed this problem by using a hierarchy of RTL, architectural, and numerical simulations. Block- and chip-level RTL models were verified by means of extensive co-simulation with a detailed C++ architectural simulator, ensuring that the RTL models could perform the same molecular dynamics computations as the architectural simulator. The output of the architectural simulator was compared to a parallelized numerical simulator that produces bitwise identical results to Anton, and is fast enough to verify the long-term numerical stability of computations on Anton. These explicit couplings between adjacent levels of the simulation hierarchy created a continuous verification chain from molecular dynamics to individual logic gates. J. P. Grossman, John K. Salmon, Richard Ho 0001, Doug Ierardi, Brian Towles, Brannon Batson, Jochen Spengler, Stanley C. Wang, Michael Theobald, Cliff Young, Joseph Gagliardo, Martin M. Deneroff, Ron O. Dror, David E. Shaw	ICCD	12
2007	Anton, a special-purpose machine for molecular dynamics simulation abstract The 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, chemistry and medicine. A wide range of biologically interesting phenomena, however, occur over time scales on the order of a millisecond--about three orders of magnitude beyond the duration of the longest current MD simulations. David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey 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, Richard Ho 0001, Doug Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Mark A. Moraes, Edward C. Priest, Yibing Shan, Jochen Spengler, Michael Theobald, Brian Towles, Stanley C. Wang	ISCA	12