Molecular dynamics (MD) simulation, a computationally intensive method that provides invaluable insights into the behavior of biomolecules, typically requires large-scale parallelization. Implementation of fast parallel MD simulation demands both high bandwidth and low latency for inter-node communication, but in current semiconductor technology, neither of these properties is scaling as quickly as intra-node computational capacity. This disparity in scaling necessitates architectural innovations to maximize the utilization of computational units. For Anton 3, the latest in a family of highly successful special-purpose supercomputers designed for MD simulations, we thus designed and built a completely new specialized network as part of our ASIC. Tightly integrating this network with specialized computation pipelines enables Anton 3 to perform simulations orders of magnitude faster than any general-purpose supercomputer, and to outperform its predecessor, Anton 2 (the state of the art prior to Anton 3), by an order of magnitude. In this paper, we present the three key features of the network that contribute to the high performance of Anton 3. First, through architectural optimizations, the network achieves very low end-to-end inter-node communication latency for fine-grained messages, allowing for better overlap of computation and communication. Second, novel application-specific compression techniques reduce the size of most messages sent between nodes, thereby increasing effective inter-node bandwidth. Lastly, a new hardware synchronization primitive, called a network fence, supports fast fine-grained synchronization tailored to the data flow within a parallel MD application. These application-driven specializations to the network are critical for Anton 3’s MD simulation performance advantage over all other machines.

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.

• 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

Parallel implementations of molecular dynamics (MD) simulation require significant inter-node communication, but off-chip communication bandwidth is not scaling as quickly as on-chip logic density. We present three network features targeting this problem that have been implemented in Anton 2, a massively parallel special-purpose supercomputer for MD simulations. The first is a mechanism to dynamically identify packets that do not need to be delivered to all endpoints within a multicast tree, these packets are filtered to conserve network bandwidth. The second is hardware for in-network reductions that supports over a thousand concurrent neighbourhood reductions per node and fast all-to-all global reductions. The third is a log-weight synchronization mechanism for multicast-reduce communication patterns that can be used to efficiently detect the completion of reduction operations when the number of summands is difficult to predict. We use the combination of packet filtering, in-network reductions and log-weight synchronization to decrease the communication requirements of MD simulations by as much as 51% on Anton 2, yielding application-level performance improvements of up to 14%.

The design of network architectures has become increasingly complex as the chips connected by inter-node networkshave emerged as distributed systems in their own right, complete with their own on-chip networks. In Anton 2, a massively parallel special-purpose supercomputer for molecular dynamics simulations, we managed this complexity by reusing the on-chip network as a switch for inter-node traffic. This unified network approach introduces several design challenges. Maintaining fairness within the inter-node network is difficult, as each hop becomes a sequence of many on-chip routing decisions. We addressed this problem with an inverse-weighted arbiter that ensures fairness with low implementation costs. Balancing the load of inter-node traffic across the on-chip network is also critical, and we adopted an optimization approach to design an appropriate routing algorithm. Finally, the on-chip routers carry inter-node traffic, so they must implement inter-node virtual channels to avoid deadlock. In order to keep the routers small and fast, we developed a deadlock-free routing algorithm that reduces the number of virtual channels by one-third relative to previous approaches. The resulting Anton 2 network implementation efficiently utilizes its inter-node channels and provides low messaging latency, while occupying a modest amount of silicon area

This article consists of a collection of slides from the author's conference presentation on the special features, supercomputing capabilities; system design and architectures, processing capabilities, and targeted markets for D.E. Shaw Research's ANTON2 chip, a massively parallel supercomputer.

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.