On the efficiency of reductions in µ-SIMD media extensions

Many important multimedia applications contain a significant fraction of reduction operations. Although, in general, multimedia applications are characterized for having high amounts of Data Level Parallelism, reductions and accumulations are difficult to parallelize and show a poor tolerance to increases in the latency of the instructions. This is specially significant for µ-SIMD extensions such as MMX or AltiVec. To overcome the problem of reductions in µ-SIMD ISAs, designers tend to include more and more complex instructions able to deal with the most common forms of reductions in multimedia. As long as the number of processor pipeline stages grows, the number of cycles needed to execute these multimedia instructions increases with every processor generation, severely compromising performance. The paper presents an in-depth discussion of how reductions/accumulations are performed in current µ-SIMD architectures and evaluates the performance trade-offs for near-future highly aggressive superscalar processors with three different styles of µ-SIMD extensions. We compare a MMX-like alternative to a MDMX-like extension that has packed accumulators to attack the reduction problem, and we also compare it to MOM, a matrix register ISA. We show that while packed accumulators present several advantages, they introduce artificial recurrences that severely degrade performance for processors with high number of registers and long latency operations. On the other hand, the paper demonstrates that longer SIMD media extensions such as MOM can take great advantage of accumulators by exploiting the associative parallelism implicit in reductions.Peer ReviewedPostprint (published version

Optimizing the MapReduce Framework on Intel Xeon Phi Coprocessor

With the ease-of-programming, flexibility and yet efficiency, MapReduce has become one of the most popular frameworks for building big-data applications. MapReduce was originally designed for distributed-computing, and has been extended to various architectures, e,g, multi-core CPUs, GPUs and FPGAs. In this work, we focus on optimizing the MapReduce framework on Xeon Phi, which is the latest product released by Intel based on the Many Integrated Core Architecture. To the best of our knowledge, this is the first work to optimize the MapReduce framework on the Xeon Phi. In our work, we utilize advanced features of the Xeon Phi to achieve high performance. In order to take advantage of the SIMD vector processing units, we propose a vectorization friendly technique for the map phase to assist the auto-vectorization as well as develop SIMD hash computation algorithms. Furthermore, we utilize MIMD hyper-threading to pipeline the map and reduce to improve the resource utilization. We also eliminate multiple local arrays but use low cost atomic operations on the global array for some applications, which can improve the thread scalability and data locality due to the coherent L2 caches. Finally, for a given application, our framework can either automatically detect suitable techniques to apply or provide guideline for users at compilation time. We conduct comprehensive experiments to benchmark the Xeon Phi and compare our optimized MapReduce framework with a state-of-the-art multi-core based MapReduce framework (Phoenix++). By evaluating six real-world applications, the experimental results show that our optimized framework is 1.2X to 38X faster than Phoenix++ for various applications on the Xeon Phi

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

A Comparative Study of Scheduling Techniques for Multimedia Applications on SIMD Pipelines

Parallel architectures are essential in order to take advantage of the parallelism inherent in streaming applications. One particular branch of these employ hardware SIMD pipelines. In this paper, we analyse several scheduling techniques, namely ad hoc overlapped execution, modulo scheduling and modulo scheduling with unrolling, all of which aim to efficiently utilize the special architecture design. Our investigation focuses on improving throughput while analysing other metrics that are important for streaming applications, such as register pressure, buffer sizes and code size. Through experiments conducted on several media benchmarks, we present and discuss trade-offs involved when selecting any one of these scheduling techniques.Comment: Presented at DATE Friday Workshop on Heterogeneous Architectures and Design Methods for Embedded Image Systems (HIS 2015) (arXiv:1502.07241

Three-dimensional memory vectorization for high bandwidth media memory systems

Vector processors have good performance, cost and adaptability when targeting multimedia applications. However, for a significant number of media programs, conventional memory configurations fail to deliver enough memory references per cycle to feed the SIMD functional units. This paper addresses the problem of the memory bandwidth. We propose a novel mechanism suitable for 2-dimensional vector architectures and targeted at providing high effective bandwidth for SIMD memory instructions. The basis of this mechanism is the extension of the scope of vectorization at the memory level, so that 3-dimensional memory patterns can be fetched into a second-level register file. By fetching long blocks of data and by reusing 2-dimensional memory streams at this second-level register file, we obtain a significant increase in the effective memory bandwidth. As side benefits, the new 3-dimensional load instructions provide a high robustness to memory latency and a significant reduction of the cache activity, thus reducing power and energy requirements. At the investment of a 50% more area than a regular SIMD register file, we have measured and average speed-up of 13% and the potential for power savings in the L2 cache of a 30%.Peer ReviewedPostprint (published version

Developing performance-portable molecular dynamics kernels in Open CL

This paper investigates the development of a molecular dynamics code that is highly portable between architectures. Using OpenCL, we develop an implementation of Sandia’s miniMD benchmark that achieves good levels of performance across a wide range of hardware: CPUs, discrete GPUs and integrated GPUs. We demonstrate that the performance bottlenecks of miniMD’s short-range force calculation kernel are the same across these architectures, and detail a number of platform- agnostic optimisations that improve its performance by at least 2x on all hardware considered. Our complete code is shown to be 1.7x faster than the original miniMD, and at most 2x slower than implementations individually hand-tuned for a specific architecture

On Designing Multicore-aware Simulators for Biological Systems

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.Comment: 19 pages + cover pag