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.

Strong scaling of scientific applications on parallel architectures is increasingly limited by communication latency. This paper describes the techniques used to mitigate latency in Anton, a massively parallel special-purpose machine that accelerates molecular dynamics (MD) simulations by orders of magnitude compared with the previous state of the art. Achieving this speedup required a combination of hardware mechanisms and software constructs to reduce network latency, sender and receiver overhead, and synchronization costs. Key elements of Anton's approach, in addition to tightly integrated communication hardware, include formulating data transfer in terms of counted remote writes, leveraging fine-grained communication, and establishing fixed, optimized communication patterns. Anton delivers software-to-software inter-node latency significantly lower than any other large-scale parallel machine, and the total critical-path communication time for an Anton MD simulation is less than 4% that of the next fastest MD platform.

Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware dramatically increases the speed of MD calculations, making possible for the first time the simulation of biological molecules at an atomic level of detail for periods on the order of a millisecond---about two orders of magnitude beyond the previous state of the art. Anton is now running simulations on a timescale at which many critically important, but poorly understood phenomena are known to occur, allowing the observation of aspects of protein dynamics that were previously inaccessible to both computational and experimental study. Here, we report Anton's performance when executing actual MD simulations whose accuracy has been validated against both existing MD software and experimental observations. We also discuss the manner in which novel algorithms have been coordinated with Anton's co-designed, application-specific hardware to achieve these results.

Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware dramatically increases the speed of MD calculations, making possible for the first time the simulation of biological molecules at an atomic level of detail for periods on the order of a millisecond---about two orders of magnitude beyond the previous state of the art. Anton is now running simulations on a timescale at which many critically important, but poorly understood phenomena are known to occur, allowing the observation of aspects of protein dynamics that were previously inaccessible to both computational and experimental study. Here, we report Anton's performance when executing actual MD simulations whose accuracy has been validated against both existing MD software and experimental observations. We also discuss the manner in which novel algorithms have been coordinated with Anton's co-designed, application-specific hardware to achieve these results.

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.

An effective special-purpose supercomputer for molecular dynamics (MD) requires much more than high-performance acceleration of computational kernels: such accelerators must be balanced with general-purpose computation and communication resources. 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. Anton executes its most computationally demanding calculations on a highly specialized, enormously parallel, but largely non-programmable high-throughput interaction subsystem (HTIS). Other elements of the simulation have a less uniform algorithmic structure, and may also change in response to future advances in physical models and simulation techniques. Such calculations are executed on Antonpsilas flexible subsystem, which combines programmability with the computational power required to avoid ldquoAmdahlpsilas Lawrdquo bottlenecks arising from the extremely high throughput of the HTIS. Antonpsilas flexible subsystem is a heterogeneous multiprocessor with 12 cores, each organized around a 128-bit data path. This subsystem includes hardware support for synchronization, data transfer and certain types of particle interactions, along with specialized instructions for geometric operations. All aspects of the flexible subsystem were designed specifically to accelerate MD simulations, and although it relies primarily on what may be regarded as ldquogeneral-purposerdquo processors, even this subsystem contains more application-specific features than many recently proposed ldquospecializedrdquo architectures.

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 simulation of many biologically important phenomena that take place over microsecond to millisecond time scales. The majority of the computation required for MD simulations involves the calculation of pairwise interactions between particles and/or gridpoints separated by no more than some specified cutoff radius. In Anton, such range-limited interactions are handled by a high-throughput interaction subsystem (HTIS). The HTIS on each of Antonpsilas 512 ASICs includes 32 computational pipelines running at 800 MHz, each producing a result on every cycle that would require approximately 50 arithmetic operations to compute on a general-purpose processor. In order to feed these pipelines and collect their results at a speed sufficient to take advantage of this computational power, Anton uses two novel techniques to limit inter- and intra-chip communication. The first is a recently developed parallelization algorithm for the range-limited N-body problem that offers major advantages in both asymptotic and absolute terms by comparison with traditional methods. The second is an architectural feature that processes pairs of points chosen from two point sets in time proportional to the product of the sizes of those sets, but with input and output volume proportional only to their sum. Together, these features allow Anton to perform pairwise interactions with very high throughput and unusually low latency, enabling MD simulations on time scales inaccessible to other general- and special-purpose parallel systems.

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.

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.