Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

This paper presents and characterizes the Princeton Application Repository for Shared-Memory Computers (PARSEC), a benchmark suite for studies of Chip-Multiprocessors (CMPs). Previous available benchmarks for multiprocessors have focused on high-performance computing applications and used a limited number of synchronization methods. PARSEC includes emerging applications in recognition, mining and synthesis (RMS) as well as systems applications which mimic large-scale multithreaded commercial programs. Our characterization shows that the benchmark suite covers a wide spectrum of working sets, locality, data sharing, synchronization and off-chip traffic. The benchmark suite has been made available to the public.

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The PARSEC benchmark suite: characterization and architectural implications

Benchmarking has become one of the most important methods for quantitative performance evaluation of processor and computer system designs. Benchmarking of modern multiprocessors such as chip multiprocessors is challenging because of their application domain, scalability and parallelism requirements. In my thesis, I have developed a methodology to design effective benchmark suites and demonstrated its effectiveness by developing and deploying a benchmark suite for evaluating multiprocessors. 
More specifically, this thesis includes several contributions. First, the thesis shows that a new benchmark suite for multiprocessors is needed because the behavior of modern parallel programs is significantly different from those represented by SPLASH-2, the most popular parallel benchmark suite developed over ten years ago. Second, the thesis quantitatively describes the requirements and characteristics of a set of multithreaded programs and their underlying technology trends. Third, the thesis presents a systematic approach to scale and select benchmark inputs with the goal of optimizing benchmarking accuracy subject to constrained execution or simulation time. Finally, the thesis describes a parallel benchmark suite called PARSEC for evaluating modern shared-memory multiprocessors. Since its initial release, PARSEC has been adopted by many architecture groups in both research and industry.

Benchmarking modern multiprocessors

The computing world today is in the middle of a revolution: mobile clients and cloud computing have emerged as the dominant paradigms driving programming and hardware innovation today. The Fifth Edition of Computer Architecture focuses on this dramatic shift, exploring the ways in which software and technology in the "cloud" are accessed by cell phones, tablets, laptops, and other mobile computing devices. Each chapter includes two real-world examples, one mobile and one datacenter, to illustrate this revolutionary change. Updated to cover the mobile computing revolutionEmphasizes the two most important topics in architecture today: memory hierarchy and parallelism in all its forms.Develops common themes throughout each chapter: power, performance, cost, dependability, protection, programming models, and emerging trends ("What's Next")Includes three review appendices in the printed text. Additional reference appendices are available online.Includes updated Case Studies and completely new exercises.

Computer Architecture, Fifth Edition: A Quantitative Approach

Transactional Memory (TM) is emerging as a promising technology to simplify parallel programming. While several TM systems have been proposed in the research literature, we are still missing the tools and workloads necessary to analyze and compare the proposals. Most TM systems have been evaluated using microbenchmarks, which may not be representative of any real-world behavior, or individual applications, which do not stress a wide range of execution scenarios. We introduce the Stanford Transactional Application for Multi-Processing (STAMP), a comprehensive benchmark suite for evaluating TM systems. STAMP includes eight applications and thirty variants of input parameters and data sets in order to represent several application domains and cover a wide range of transactional execution cases (frequent or rare use of transactions, large or small transactions, high or low contention, etc.). Moreover, STAMP is portable across many types of TM systems, including hardware, software, and hybrid systems. In this paper, we provide descriptions and a detailed characterization of the applications in STAMP. We also use the suite to evaluate six different TM systems, identify their shortcomings, and motivate further research on their performance characteristics.

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STAMP: Stanford Transactional Applications for Multi-Processing

This paper explores Speculative Precomputation, a technique that uses idle thread context in a multithreaded architecture to improve performance of single-threaded applications. It attacks program stalls from data cache misses by pre-computing future memory accesses in available thread contexts, and prefetching these data. This technique is evaluated by simulating the performance of a research processor based on the Itanium™ ISA supporting Simultaneous Multithreading. Two primary forms of Speculative Precomputation are evaluated. If only the non-speculative thread spawns speculative threads, performance gains of up to 30% are achieved when assuming ideal hardware. However, this speedup drops considerably with more realistic hardware assumptions. Permitting speculative threads to directly spawn additional speculative threads reduces the overhead associated with spawning threads and enables significantly more aggressive speculation, overcoming this limitation. Even with realistic costs for spawning threads, speedups as high as 169% are achieved, with an average speedup of 76%.

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Speculative precomputation: long-range prefetching of delinquent loads

Intel has recently introduced Intel® Transactional Synchronization Extensions (Intel® TSX) in the Intel 4th Generation Core™ Processors. With Intel TSX, a processor can dynamically determine whether threads need to serialize through lock-protected critical sections. In this paper, we evaluate the first hardware implementation of Intel TSX using a set of high-performance computing (HPC) workloads, and demonstrate that applying Intel TSX to these workloads can provide significant performance improvements. On a set of real-world HPC workloads, applying Intel TSX provides an average speedup of 1.41x. When applied to a parallel user-level TCP/IP stack, Intel TSX provides 1.31x average bandwidth improvement on network intensive applications. We also demonstrate the ease with which we were able to apply Intel TSX to the various workloads.

Performance evaluation of Intel® transactional synchronization extensions for high-performance computing

High performance parallel programs are currently difficult to write and debug. One major source of difficulty is protecting concurrent accesses to shared data with an appropriate synchronization mechanism. Locks are the most common mechanism but they have a number of disadvantages, including possibly unnecessary serialization, and possible deadlock. Transactional memory is an alternative mechanism that makes parallel programming easier. With transactional memory, a transaction provides atomic and serializable operations on an arbitrary set of memory locations. When a transaction commits, all operations within the transaction become visible to other threads. When it aborts, all operations in the transaction are rolled back.Transactional memory can be implemented in either hardware or software. A straightforward hardware approach can have high performance, but imposes strict limits on the amount of data updated in each transaction. A software approach removes these limits, but incurs high overhead. We propose a novel hybrid hardware-software transactional memory scheme that approaches the performance of a hardware scheme when resources are not exhausted and gracefully falls back to a software scheme otherwise.

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Hybrid transactional memory

Chip multiprocessors (CMPs) are now commonplace, and the number of cores on a CMP is likely to grow steadily. However, in order to harness the additional compute resources of a CMP, applications must expose their thread-level parallelism to the hardware. One common approach to doing this is to decompose a program into parallel "tasks" and allow an underlying software layer to schedule these tasks to different threads. Software task scheduling can provide good parallel performance as long as tasks are large compared to the software overheads.We examine a set of applications from an important emerging domain: Recognition, Mining, and Synthesis (RMS). Many RMS applications are compute-intensive and have abundant thread-level parallelism, and are therefore good targets for running on a CMP. However, a significant number have small tasks for which software task schedulers achieve only limited parallel speedups.We propose Carbon, a hardware technique to accelerate dynamic task scheduling on scalable CMPs. Carbon has relatively simple hardware, most of which can be placed far from the cores. We compare Carbon to some highly tuned software task schedulers for a set of RMS benchmarks with small tasks. Carbon delivers significant performance improvements over the best software scheduler: on average for 64 cores, 68% faster on a set of loop-parallel benchmarks, and 109% faster on aset of task-parallel benchmarks.

Carbon: architectural support for fine-grained parallelism on chip multiprocessors

The early 1990s saw several announcements of commercial shared-memory systems using processors that aggressively exploited instruction-level parallelism (ILP), including the MIPS R10000, Hewlett-Packard PA8000, and Intel Pentium Pro. These processors could potentially reduce memory read stalls by overlapping read latency with other operations, possibly changing the nature of performance bottlenecks in the system. The authors' experience with Rsim demonstrates that modeling ILP features is important even in shared-memory multiprocessor systems. In particular, current simple processor-based approximations cannot model significant performance effects for applications exhibiting parallel read misses. Further, recent shared-memory designs such as aggressive implementations of sequential consistency use the aggressive ILP-enhancing features of modern processors that simple processor-based simulators do not model. As microprocessor systems become more complex, the availability of shared infrastructure source code is likely to become increasingly crucial. The authors plan to release a new Rsim version shortly that will include instruction caches, TLBs, multimedia extensions, simultaneous multithreading, Rabbit fast simulation mode, and ports to Linux platforms.

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Christopher J. Hughes

Papers

Speculative precomputation: long-range prefetching of delinquent loads

Performance evaluation of Intel® transactional synchronization extensions for high-performance computing

Hybrid transactional memory

Carbon: architectural support for fine-grained parallelism on chip multiprocessors

Rsim: simulating shared-memory multiprocessors with ILP processors