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The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but with much of the work shared by the host CPU; or prototype demonstrations, e.g., using OpenCL, that neither implement a whole system nor have competitive performance. In this paper, we present what we believe to be the first full-scale FPGA-based simulation engine, and show that its performance is competitive with a GPU (running Amber in an industrial production environment). The system features on-chip particle data storage and management, short-and long-range force evaluation, as well as bonded forces, motion update, and particle migration. Other contributions of this work include exploring numerous architectural trade-offs and analysis on various mappings schemes among particles/cells and the various on-chip compute units. The potential impact is that this system promises to be the basis for long timescale Molecular Dynamics with a commodity cluster.

Deep Neural Networks (DNNs) have revolutionized numerous applications, but the demand for ever more performance remains unabated. Scaling DNN computations to larger clusters is generally done by distributing tasks in batch mode using methods such as distributed synchronous SGD. Among the issues with this approach is that to make the distributed cluster work with high utilization, the workload distributed to each node must be large, which implies nontrivial growth in the SGD mini-batch size. In this paper, we propose a framework called FPDeep, which uses a hybrid of model and layer parallelism to configure distributed reconfigurable clusters to train DNNs. This approach has numerous benefits. First, the design does not suffer from batch size growth. Second, novel workload and weight partitioning leads to balanced loads of both among nodes. And third, the entire system is a fine-grained pipeline. This leads to high parallelism and utilization and also minimizes the time features need to be cached while waiting for back-propagation. As a result, storage demand is reduced to the point where only on-chip memory is used for the convolution layers. We evaluate FPDeep with the Alexnet, VGG-16, and VGG-19 benchmarks. Experimental results show that FPDeep has good scalability to a large number of FPGAs, with the limiting factor being the FPGA-to-FPGA bandwidth. With 6 transceivers per FPGA, FPDeep shows linearity up to 83 FPGAs. Energy efficiency is evaluated with respect to GOPs/J. FPDeep provides, on average, 6.36x higher energy efficiency than comparable GPU servers.Deep convolutional neural networks (CNNs) have revolutionized applications such as image classification and object recognition [1,2,3,4]. As there remains an open-ended demand for more complex networks and larger datasets, new computing solutions are critical.Distributed synchronous stochastic gradient descent (SGD) has enabled large-scale CNN training by partitioning SGD mini-batches into smaller data batches that can then be processed in parallel and so accelerate CNN training [5]. A drawback of this method is scalability: to enable continued high utilization as the number of nodes increases, each node must be allocated an ever larger workload. But larger mini-batches slow training convergence. Thus, while larger clusters provide increased computation capacity, the training time is not proportionally reduced [5].