• 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

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.

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.

We describe a high-performance digit-recurrence algorithm for computing exactly rounded reciprocals, square roots, and reciprocal square roots in hardware at a rate of three result bits - one radix-8 digit - per recurrence iteration. To achieve a single-cycle recurrence at a short cycle time, we adapted the digit-by-rounding algorithm, which is normally applied at much higher radices, for efficient operation at radix 8. Using this approach avoids in the recurrence step the lookup table required by SRT - the usual algorithm used for hardware digit recurrences. The increasing access latency of this table, the size of which grows super linearly in the radix, limits high-frequency SRT implementations to radix 4 or lower. We also developed a series of novel optimizations focused on further reducing the critical path through the recurrence. We propose, for example, decreasing data path widths to a point where erroneous results sometimes occur and then correcting these errors off the critical path. We present a specific implementation that computes any of these functions to 31 bits of precision in 13 cycles. Our implementation achieves a cycle time only 11% longer than the best reported SRT design for the same functions, yet delivers results in five fewer cycles. Finally, we show that even at lower radices, a digit-by-rounding design is likely to have a shorter critical path than one using SRT at the same radix.

Digit-by-rounding algorithms enable efficient hardware implementations of algebraic functions such as the reciprocal, square root, or reciprocal square root, but certifying the correctness of such algorithms is a nontrivial endeavor. Traditionally, sufficient conditions for correctness are derived as closed-form formulae relating key design parameters. These sufficient conditions, however, often prove stricter than necessary, excluding correct and efficient designs. In this paper, we present a rigorous, computer-aided method for correctness certification that better approximates the necessary conditions, lowering the risk of rejecting correct designs. We also present two specific applications of this method. First, when applied to a conventional digit-by-rounding reciprocal square root design, our method enabled a fourfold reduction in lookup table size relative to the minimum dictated by a standard sufficient condition. Second, our method certified the correctness of a novel reciprocal square root design that we developed to parallelize two computational steps whose sequential execution lies on the critical path of conventional designs. The difficulty in deriving closed-form sufficient conditions to ascertain this design's correctness provided the original motivation for development of the new certification method.

Wide, deep pipelines need many physical registers to hold the results of in-flight instructions. Simultaneously, high clock frequencies prohibit using large register files and bypass networks without a significant performance penalty. Previously proposed techniques using register caching to reduce this penalty suffer from several problems including poor insertion and replacement decisions and the need for a fully-associative cache for good performance. We present novel mechanisms for managing and indexing register caches that address these problems using knowledge of the number of consumers of each register value. The insertion policy reduces pollution by not caching a register value when all of its predicted consumers are satisfied by the bypass network. The replacement policy selects register cache entries with the fewest remaining uses (often zero), lowering the miss rate. We also introduce a new, general method of mapping physical registers to register cache sets that improves the performance of set-associative cache organizations by reducing conflicts. Our results indicate that a 64-entry, two-way set associative cache using these techniques outperforms multi-cycle monolithic register files and previously proposed hierarchical register files.

We observe a non-negligible fraction--3 to 16% in our benchmarks--of dynamically dead instructions, dynamic instruction instances that generate unused results. The majority of these instructions arise from static instructions that also produce useful results. We find that compiler optimization (specifically instruction scheduling) creates a significant portion of these partially dead static instructions. We show that most of the dynamically instructions arise from a small set of static instructions that produce dead values most of the time.We leverage this locality by proposing a dead instruction predictor and presenting a scheme to avoid the execution of predicted-dead instructions. Our predictor achieves an accuracy of 93% while identifying over 91% of the dead instructions using less than 5 KB of state. We achieve such high accuracies by leveraging future control flow information (i.e., branch predictions) to distinguish between useless and useful instances of the same static instruction.We then present a mechanism to avoid the register allocation, instruction scheduling, and execution of predicted dead instructions. We measure reductions in resource utilization averaging over 5% and sometimes exceeding 10%, covering physical register management (allocation and freeing), register file read and write traffic, and data cache accesses. Performance improves by an average of 3.6% on an architecture exhibiting resource contention. Additionally, our scheme frees future compilers from the need to consider the costs of dead instructions, enabling more aggressive code motion and optimization. Simultaneously, it mitigates the need for good path profiling information in making inter-block code motion decisions.

A value's degree of use - the number of dynamic uses of that value $provides the most essential information needed to optimize its communication. We present simulation results demonstrating the properties of degree of use of values, including their predictability: most static instructions generate values with few degrees of use and these exhibit temporal locality. We use these results to guide the design of a degree of use predictor. The development and detailed characterization of this predictor is the focus of this paper. Our predictor leverages future control flow information (e.g., branch predictions) to select among different possible degrees of use. We study the effects of several optimizations and variations in the predictor's algorithms to tune the predictor for maximum performance. The resulting predictor generates correct degree of use predictions for over 92% of all dynamic values and has a misprediction rate below 2.5%. Such a predictor has a wide range of potential applications in optimizing value communication.

Static power dissipation due to transistor leakage constitutes an increasing fraction of the total power in modern semiconductor technologies. Current technology trends indicate that the contribution will increase rapidly, reaching one half of total power dissipation within three process generations. Developing power efficient products will require consideration of static power in the earliest phases of design, including architecture and microarchitecture definition. We propose a simple equation for estimating static power consumption at the architectural level: P/sub static/=V/sub CC//spl middot/N/spl middot/k/sub design//spl middot/I/spl circ//sub leak/, where V/sub CC/ is the supply voltage, N is the number of transistors, k/sub design/ is a design dependent parameter, and I/spl circ//sub leak/ is a technology dependent parameter. This model enables high-level reasoning about the likely static power demands of alternative microarchitectures. Reasonably accurate values for the factors within the equation may be obtained directly from the high-level designs or by straightforward scaling arguments. The factors within the equation also suggest opportunities for static power optimization, including reducing the total number of devices, partitioning the design to allow for lower supply voltages or slower, less leaky transistors, turning off unused devices, favoring certain design styles, and favoring high bandwidth over low latency. Speculation is also examined as a means to employ slower transistors without a significant performance penalty.