Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems

Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatial-decomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.Comment: 33 pages, 19 figures, add references and figures are revise

Investigation of a simultaneous multithreaded architecture

Many enhancements have been made to the traditional general purpose load-store computer architectures. Among the enhancements are memory hierarchy improvements, branch prediction, and multiple issue processors. A major problem that exists with current microprocessor design is the disparity in the much larger increase in speed of the CPU versus the moderate increase in speed accessing main memory. The simultaneous multithreaded architecture is an extension of the single-threaded architecture that helps hide the performance penalty created by long-latency instructions, branch mispredictions, and memory accesses. Simultaneous multithreaded architectures use a more flexible parallelism, which takes advantage of both instruction-level, and thread-level parallelism. The goal of this project was to design, simulate, and analyze a model of a simultaneous multithreaded architecture in order to evaluate design alternatives. The simulator was created by modifying a version of the Simple Scalar toolset, developed at the University of Wisconsin. The simulations provide documentation for an overall system performance improvement of a simulta neous multithreaded architecture. In early simulation results, performed with the same number of functional units, an improvement in the number of instructions per cycle (IPC) of between 43% and 58% was found using four threads versus a single thread. The horizontal waste rate, which measures the number of unused issue slots, was reduced between 35% and 46%. The vertical waste rate, which measures the percentage- of unused issue cycles (no issue slots used in a cycle), was reduced between 46% and 61%. These results are derived from a set of four sample programs. It was also found that increasing the number of certain functional units did not improve performance, whereas increasing the number of other types of functional units did have a significant positive impact on performance

Optimizing SIMD execution in HW/SW co-designed processors

SIMD accelerators are ubiquitous in microprocessors from different computing domains. Their high compute power and hardware simplicity improve overall performance in an energy efficient manner. Moreover, their replicated functional units and simple control mechanism make them amenable to scaling to higher vector lengths. However, code generation for these accelerators has been a challenge from the days of their inception. Compilers generate vector code conservatively to ensure correctness. As a result they lose significant vectorization opportunities and fail to extract maximum benefits out of SIMD accelerators. This thesis proposes to vectorize the program binary at runtime in a speculative manner, in addition to the compile time static vectorization. There are different environments that support runtime profiling and optimization support required for dynamic vectorization, one of most prominent ones being: 1) Dynamic Binary Translators and Optimizers (DBTO) and 2) Hardware/Software (HW/SW) Co-designed Processors. HW/SW co-designed environment provides several advantages over DBTOs like transparent incorporations of new hardware features, binary compatibility, etc. Therefore, we use HW/SW co-designed environment to assess the potential of speculative dynamic vectorization. Furthermore, we analyze vector code generation for wider vector units and find out that even though SIMD accelerators are amenable to scaling from the hardware point of view, vector code generation at higher vector length is even more challenging. The two major factors impeding vectorization for wider SIMD units are: 1) Reduced dynamic instruction stream coverage for vectorization and 2) Large number of permutation instructions. To solve the first problem we propose Variable Length Vectorization that iteratively vectorizes for multiple vector lengths to improve dynamic instruction stream coverage. Secondly, to reduce the number of permutation instructions we propose Selective Writing that selectively writes to different parts of a vector register and avoids permutations. Finally, we tackle the problem of leakage energy in SIMD accelerators. Since SIMD accelerators consume significant amount of real estate on the chip, they become the principle source of leakage if not utilized judiciously. Power gating is one of the most widely used techniques to reduce leakage energy of functional units. However, power gating has its own energy and performance overhead associated with it. We propose to selectively devectorize the vector code when higher SIMD lanes are used intermittently. This selective devectorization keeps the higher SIMD lanes idle and power gated for maximum duration. Therefore, resulting in overall leakage energy reduction.Postprint (published version

A general framework to realize an abstract machine as an ILP processor with application to java

Ph.DDOCTOR OF PHILOSOPH

Time-predictable Chip-Multiprocessor Design

Abstract—Real-time systems need time-predictable platforms to enable static worst-case execution time (WCET) analysis. Improving the processor performance with superscalar techniques makes static WCET analysis practically impossible. However, most real-time systems are multi-threaded applications and performance can be improved by using several processor cores on a single chip. In this paper we present a time-predictable chipmultiprocessor system that aims to improve system performance while still enabling WCET analysis. The proposed chip-multiprocessor (CMP) uses a shared memory with a time-division multiple access (TDMA) based memory access scheduling. The static TDMA schedule can be integrated into the WCET analysis. Experiments with a JOP based CMP showed that the memory access starts to dominate the execution time when using more than 4 processor cores. To provide a better scalability, more local memories have to be used. We add a processor local scratchpad memory and split data caches, which are still time-predictable, to the processor cores. I

The Potential for a GPU-Like Overlay Architecture for FPGAs

We propose a soft processor programming model and architecture inspired by graphics processing units (GPUs) that are well-matched to the strengths of FPGAs, namely, highly parallel and pipelinable computation. In particular, our soft processor architecture exploits multithreading, vector operations, and predication to supply a floating-point pipeline of 64 stages via hardware support for up to 256 concurrent thread contexts. The key new contributions of our architecture are mechanisms for managing threads and register files that maximize data-level and instruction-level parallelism while overcoming the challenges of port limitations of FPGA block memories as well as memory and pipeline latency. Through simulation of a system that (i) is programmable via NVIDIA's high-level Cg language, (ii) supports AMD's CTM r5xx GPU ISA, and (iii) is realizable on an XtremeData XD1000 FPGA-based accelerator system, we demonstrate the potential for such a system to achieve 100% utilization of a deeply pipelined floating-point datapath

Multi-core architectures with coarse-grained dynamically reconfigurable processors for broadband wireless access technologies

Broadband Wireless Access technologies have significant market potential, especially the WiMAX protocol which can deliver data rates of tens of Mbps. Strong demand for high performance WiMAX solutions is forcing designers to seek help from multi-core processors that offer competitive advantages in terms of all performance metrics, such as speed, power and area. Through the provision of a degree of flexibility similar to that of a DSP and performance and power consumption advantages approaching that of an ASIC, coarse-grained dynamically reconfigurable processors are proving to be strong candidates for processing cores used in future high performance multi-core processor systems. This thesis investigates multi-core architectures with a newly emerging dynamically reconfigurable processor – RICA, targeting WiMAX physical layer applications. A novel master-slave multi-core architecture is proposed, using RICA processing cores. A SystemC based simulator, called MRPSIM, is devised to model this multi-core architecture. This simulator provides fast simulation speed and timing accuracy, offers flexible architectural options to configure the multi-core architecture, and enables the analysis and investigation of multi-core architectures. Meanwhile a profiling-driven mapping methodology is developed to partition the WiMAX application into multiple tasks as well as schedule and map these tasks onto the multi-core architecture, aiming to reduce the overall system execution time. Both the MRPSIM simulator and the mapping methodology are seamlessly integrated with the existing RICA tool flow. Based on the proposed master-slave multi-core architecture, a series of diverse homogeneous and heterogeneous multi-core solutions are designed for different fixed WiMAX physical layer profiles. Implemented in ANSI C and executed on the MRPSIM simulator, these multi-core solutions contain different numbers of cores, combine various memory architectures and task partitioning schemes, and deliver high throughputs at relatively low area costs. Meanwhile a design space exploration methodology is developed to search the design space for multi-core systems to find suitable solutions under certain system constraints. Finally, laying a foundation for future multithreading exploration on the proposed multi-core architecture, this thesis investigates the porting of a real-time operating system – Micro C/OS-II to a single RICA processor. A multitasking version of WiMAX is implemented on a single RICA processor with the operating system support