FPGA-based range-limited molecular dynamics acceleration

Molecular Dynamics (MD) is a computer simulation technique that executes iteratively over discrete, infinitesimal time intervals. It has been a widely utilized application in the fields of material sciences and computer-aided drug design for many years, serving as a crucial benchmark in high-performance computing (HPC). Numerous MD packages have been developed and effectively accelerated using GPUs. However, as the limits of Moore's Law are reached, the performance of an individual computing node has reached its bottleneck, while the performance of multiple nodes is primarily hindered by scalability issues, particularly when dealing with small datasets. In this thesis, the acceleration with respect to small datasets is the main focus. With the recent COVID-19 pandemic, drug discovery has gained significant attention, and Molecular Dynamics (MD) has emerged as a crucial tool in this process. Particularly, in the critical domain of drug discovery, small simulations involving approximately ~50K particles are frequently employed. However, it is important to note that small simulations do not necessarily translate to faster results, as long-term simulations comprising billions of MD iterations and more are essential in this context. In addition to dataset size, the problem of interest is further constrained. Referred to as the most computationally demanding aspect of MD, the evaluation of range-limited (RL) forces not only accounts for 90% of the MD computation workload but also involves irregular mapping patterns of 3-D data onto 2-D processor networks. To emphasize, this thesis centers around the acceleration of RL MD specifically for small datasets. In order to address the single-node bottleneck and multi-node scaling challenges, the thesis is organized into two progressive stages of investigation. The first stage delves extensively into enhancing single-node efficiency by examining various factors such as workload mapping from 3-D to 2-D, data routing, and data locality. The second stage focuses on studying multi-node scalability, with a particular emphasis on strong scaling, bandwidth demands, and the synchronization mechanisms between nodes. Through our study, the results show our design on a Xilinx U280 FPGA achieves 51.72x and 4.17x speedups with respect to an Intel Xeon Gold 6226R CPU, and a Quadro RTX 8000 GPU. Our research towards strong scaling also demonstrates that 8 Xilinx U280 FPGAs connected to a switch achieves 4.67x speedup compared to an Nvidia V100 GP

Configurable data center switch architectures

In this thesis, we explore alternative architectures for implementing con_gurable Data Center Switches along with the advantages that can be provided by such switches. Our first contribution centers around determining switch architectures that can be implemented on Field Programmable Gate Array (FPGA) to provide configurable switching protocols. In the process, we identify a gap in the availability of frameworks to realistically evaluate the performance of switch architectures in data centers and contribute a simulation framework that relies on realistic data center traffic patterns. Our framework is then used to evaluate the performance of currently existing as well as newly proposed FPGA-amenable switch designs. Through collaborative work with Meng and Papaphilippou, we establish that only small-medium range switches can be implemented on today's FPGAs. Our second contribution is a novel switch architecture that integrates a custom in-network hardware accelerator with a generic switch to accelerate Deep Neural Network training applications in data centers. Our proposed accelerator architecture is prototyped on an FPGA, and a scalability study is conducted to demonstrate the trade-offs of an FPGA implementation when compared to an ASIC implementation. In addition to the hardware prototype, we contribute a light weight load-balancing and congestion control protocol that leverages the unique communication patterns of ML data-parallel jobs to enable fair sharing of network resources across different jobs. Our large-scale simulations demonstrate the ability of our novel switch architecture and light weight congestion control protocol to both accelerate the training time of machine learning jobs by up to 1.34x and benefit other latency-sensitive applications by reducing their 99%-tile completion time by up to 4.5x. As for our final contribution, we identify the main requirements of in-network applications and propose a Network-on-Chip (NoC)-based architecture for supporting a heterogeneous set of applications. Observing the lack of tools to support such research, we provide a tool that can be used to evaluate NoC-based switch architectures.Open Acces

Tiled microprocessors

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.Includes bibliographical references (p. 251-258).Current-day microprocessors have reached the point of diminishing returns due to inherent scalability limitations. This thesis examines the tiled microprocessor, a class of microprocessor which is physically scalable but inherits many of the desirable properties of conventional microprocessors. Tiled microprocessors are composed of an array of replicated tiles connected by a special class of network, the Scalar Operand Network (SON), which is optimized for low-latency, low-occupancy communication between remote ALUs on different tiles. Tiled microprocessors can be constructed to scale to 100's or 1000's of functional units. This thesis identifies seven key criteria for achieving physical scalability in tiled microprocessors. It employs an archetypal tiled microprocessor to examine the challenges in achieving these criteria and to explore the properties of Scalar Operand Networks. The thesis develops the field of SONs in three major ways: it introduces the 5-tuple performance metric, it describes a complete, high-frequency SON implementation, and it proposes a taxonomy, called AsTrO, for categorizing them.(cont.) To develop these ideas, the thesis details the design, implementation and analysis of a tiled microprocessor prototype, the Raw Microprocessor, which was implemented at MIT in 180 nm technology. Overall, compared to Raw, recent commercial processors with half the transistors required 30x as many lines of code, occupied 100x as many designers, contained 50x as many pre-tapeout bugs, and resulted in 33x as many post-tapeout bugs. At the same time, the Raw microprocessor proves to be more versatile in exploiting ILP, stream, and server-farm workloads with modest to large amounts of parallelism.by Michael Bedford Taylor.Ph.D

3rd Many-core Applications Research Community (MARC) Symposium. (KIT Scientific Reports ; 7598)

This manuscript includes recent scientific work regarding the Intel Single Chip Cloud computer and describes approaches for novel approaches for programming and run-time organization

Programming models for many-core architectures: a co-design approach

Common many-core processors contain tens of cores and distributed memory. Compared to a multicore system, which only has a few tightly coupled cores sharing a single bus and memory, several complex problems arise. Notably, many cores require many parallel tasks to fully utilize the cores, and communication happens in a distributed and decentralized way. Therefore, programming such a processor requires the application to exhibit concurrency. In contrast to a single-core application, a concurrent application has to deal with memory state changes with an observable (non-deterministic) intermediate state. The complexity introduced by these problems makes programming a many-core system with a single-core-based programming approach notoriously hard.\ud \ud The central concept of this thesis is that abstractions, which are related to (many-core) programming, are structured in a single platform model. A platform is a layered view of the hardware, a memory model, a concurrency model, a model of computation, and compile-time and run-time tooling. Then, a programming model is a specific view on this platform, which is used by a programmer. In this view, some details can be hidden from the programmer's perspective, some details cannot. For example, an operating system presents an infinite number of parallel virtual execution units to the application whilst it hides details regarding scheduling. On the other hand, a programmer usually has balance workload among threads by hand.\ud \ud This thesis presents modifications to different abstraction layers of a many-core architecture, in order to make the system as a whole more efficient, and to reduce the programming complexity. These modifications influence other abstractions in the platform, and especially the programming model. Therefore, this thesis applies co-design on all models. Notably, co-design of the memory model, concurrency model, and model of computation is required for a scalable implementation of lambda-calculus. Moreover, only the combination of requirements of the many-core hardware from one side and the concurrency model from the other leads to a memory model abstraction. Hence, this thesis shows that to cope with the current trends in many-core architectures from a programming perspective, it is essential and feasible to inspect and adapt all abstractions collectively

Performance measurement and analysis of PC based cluster server using SET of Architecture and modeling a scalable High performance cluster

Not availabl

Multipass communication systems for tiled processor architectures

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.Includes bibliographical references (p. 191-202).Multipass communication systems utilize multiple sets of parallel baseband receiver functions to balance communication data rates and available computation capabilities. This is achieved by spatially pipelining baseband functions across parallel resources to perform multiple processing passes on the same set of received values, thus allowing the system to simultaneously convey multiple sequences of data using a single wireless link. The use of multiple passes mitigates the effects of data rate on receiver processing bottlenecks, making the use of general-purpose processing elements for high data rate communication functions viable. The flexibility of general-purpose processing, in turn, allows the receiver composition to trade-off resource usage and required processing rate. For instance, a communication system could be distributed across 2 passes using 2x the overall area, but reducing the data rate for each pass and the resultant overall required processing rate, and hence clock speed, by 1/2. Lowering the clock speed can also be leveraged to reduce power through voltage scaling and/or the use of higher Vt devices. The characteristics of general-purpose parallel processors for communications processing are explored, as well as the applicability of specific parallel designs to communications processing.(Cont.) In particular, an in depth look is taken of the Raw processor's tiled architecture as a general-purpose parallel processor particularly well suited to portable communications processing. An example of a multipass system, based on the 802.11a baseband, implemented on the Raw processor along with the accompanying hardware implementation is presented as both a proof-of-concept, as well as a means to explore some of the advantages and trade-offs of such a system. A bit-error rate study is presented which shows this multipass system to be within a small fraction of dB of the performance of an equivalent data rate single pass system, thus demonstrating the viability of the multipass algorithm. In addition, the capability of tiled processors to maximize processing capabilities at the system block level, as well as the system architectural level, is shown. Parallel implementations of two processing intensive functions: the FFT and the Viterbi decoder are shown. A parallelized assembly language FFT utilizing 16 tiles is shown to have a 1,000x improvement , and a parallelized 48-tile assembly language Viterbi decoder is shown to have a 10, 000x improvement over corresponding serial C implementations.by Nathan Robert Shnidman.Ph.D