Intel announces a high-performance SPMD compiler for the CPU

June 26th, 2011

Intel has announced ispc, The Intel SPMD Program Compiler, now available in source and binary form from http://ispc.github.com.

ispc is a new compiler for “single program, multiple data” (SPMD) programs; the same model that is used for (GP)GPU programming, but here targeted to CPUs. ispc compiles a C-based SPMD programming language to run on the SIMD units of CPUs; it frequently provides a a 3x or more speedup on CPUs with 4-wide SSE units, without any of the difficulty of writing intrinsics code. There were a few principles and goals behind the design of ispc:

  • To build a small C-like language that would deliver excellent performance to performance-oriented programmers who want to run SPMD programs on the CPU.
  • To provide a thin abstraction layer between the programmer and the hardware—in particular, to have an execution and data model where the programmer can cleanly reason about the mapping of their source program to compiled assembly language and the underlying hardware.
  • To make it possible to harness the computational power of the SIMD vector units without the extremely low-programmer-productivity activity of directly writing intrinsics.
  • To explore opportunities from close coupling between C/C++ application code and SPMD ispc code running on the same processor—to have lightweight function calls between the two languages, to share data directly via pointers without copying or reformatting, and so forth.

ispc is an open source compiler with a BSD license. It uses the LLVM Compiler Infrastructure for back-end code generation and optimization and is hosted on github. It supports Windows, Mac, and Linux, with both x86 and x86-64 targets. It currently supports the SSE2 and SSE4 instruction sets, though support for AVX should be available soon.

CUDA 4.0 Library Performance Overview

June 26th, 2011

The performance of many math functions has improved with the release of the CUDA 4.0 Toolkit. This presentation includes the performance results of many of the key functions. Results include performance measurements for:

  • cuFFT – Fast Fourier Transforms Library
  • cuBLAS – Complete BLAS Library
  • cuSPARSE – Sparse Matrix Library
  • cuRAND – Random Number Generation (RNG) Library
  • NPP – Performance Primitives for Image & Video Processing
  • Thrust – Templated Parallel Algorithms & Data Structures
  • math.h – C99 floating-point Library

 

Parallel Solution of Sparse Triangular Linear Systems

June 26th, 2011

Abstract:

A novel algorithm for solving in parallel a sparse triangular linear system on a graphical processing unit is proposed. It implements the solution of the triangular system in two phases. First, the analysis phase builds a dependency graph based on the matrix sparsity pattern and groups the independent rows into levels. Second, the solve phase obtains the full solution by iterating sequentially across the constructed levels. The solution elements corresponding to each single level are obtained at once in parallel. The numerical experiments are also presented and it is shown that the incomplete-LU and Cholesky preconditioned iterative methods, using the parallel sparse triangular solve algorithm, can achieve on average more than 2x speedup on graphical processing units (GPUs) over their CPU implementation.

(Maxim Naumov: “Parallel Solution of Sparse Triangular Linear Systems in the Preconditioned Iterative Methods on the GPU”, NVIDIA Technical Report, June 2011. [WWW])

GPU Computing and C++: An Evening with Microsoft and NVIDIA

June 26th, 2011

In Silicon Valley? Interested in C++? Join in an evening with Microsoft & NVIDIA to discuss new C++ technology for parallel computing. Register here: http://vnextmsvc.eventbrite.com/

  • 5:45 PM Welcome & Registration
  • 6:00 PM Heterogeneous Parallelism in General, C++ in AMP in Particular, presented by Herb Sutter, Principal Architect for Windows C++, Microsoft
  • 7:15 PM ALM tools for C++ in Visual Studio V.NEXT, presented by Rong Lu, Program Manager C++, Microsoft
  • 8:00 PM The Power of Parallel, presented by the NVIDIA Team;
    • Parallel Nsight: Programming GPUs in Visual Studio, Stephen Jones, NVIDIA;
    • CUDA 4.0: Parallel Programming Made Easy, Justin Luitjens, NVIDIA;
    • Thrust: C++ Template Library for GPGPUs, Jared Hoberock, NVIDIA

Refreshments provided.

Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems

June 26th, 2011

Abstract:

This paper describes the approach and the speedup obtained in performing Smith-Waterman database searches on heterogeneous platforms comprising of multi core CPU and multi GPU systems. Most of the advanced and optimized Smith-Waterman algorithm versions have demonstrated remarkable speedup over NCBI BLAST versions, viz., SWPS3 based on x86 SSE2 instructions and CUDASW++ v2.0 CUDA implementation on GPU. This work proposes a hybrid Smith-Waterman algorithm that integrates the state-of-the art CPU and GPU solutions for accelerating Smith-Waterman algorithm in which GPU acts as a co-processor and shares the workload with the CPU enabling us to realize remarkable performance of over 70 GCUPS resulting from simultaneous CPU-GPU execution. In this work, both CPU and GPU are graded equally in performance for Smith-Waterman rather than previous approaches of porting the computationally intensive portions onto the GPUs or a naive multi-core CPU approach.

(J. Singh and I. Aruni: “Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems”, Proceedings of Bioinformatics and Biomedical Engineering (iCBBE), May 2011. [DOI])

Scalable instruction set simulator for thousand-core architectures running on GPGPUs.

June 26th, 2011

Abstract:

Simulators are still the primary tools for development and performance evaluation of applications running on massively parallel architectures. However, current virtual platforms are not able to tackle the complexity issues introduced by 1000-core future scenarios. We present a fast and accurate simulation framework targeting extremely large parallel systems by specifically taking advantage of the inherent potential processing parallelism available in modern GPGPUs.

(S. Raghav, M. Ruggiero, D. Atienza, C. Pinto, A. Marongiu and L. Benini: “Scalable instruction set simulator for thousand-core architectures running on GPGPUs”, Proceedings of High Performance Computing and Simulation (HPCS), pp.459-466, June/July 2010. [DOI] [WWW])

CUDA and OpenCL supported in Indigo Renderer 3.0 and Indigo RT

June 26th, 2011

From a recent announcement:

Glare Technologies is proud to announce the release of Indigo Renderer 3.0 and Indigo RT. We use a hybrid GPU acceleration approach, which typically results in a 2-3x speedup when paired with a sufficiently powerful CPU. Realtime scene changes are possible, also in conjunction with network rendering to further accelerate rendering performance. A page outlining the other features and improvements of Indigo 3.0 and Indigo RT can be found at http://www.indigorenderer.com/indigo3 and http://www.indigorenderer.com/indigo_rt.

 

GPIUTMD 0.9.6 released

June 26th, 2011

GPIUTMD stands for Graphic Processors at Isfahan University of Technology for Many-particle Dynamics. It performs general-purpose many-particle dynamic simulations on a single workstation, taking advantage of NVIDIA GPUs to attain a level of performance equivalent to thousands of cores on a fast cluster. Flexible and configurable, GPIUTMD is currently being used for all atom and coarse-grained molecular dynamics simulations of nano-materials, glasses, and surfactants; dissipative particle dynamics simulations (DPD) of polymers; and crystallization of metals using EAM potentials. GPIUTMD 0.9.6 adds many new features. Highlights include:

  • Morse bond potential
  • Adding constant acceleration to a group of particles. (useful for modeling gravity effects)
  • Computes the full virial stress tensor (useful in mechanical characterization of materials)
  • Long-ranged electrostatics via PPPM
  • Support for CUDA 3.2
  • Theory manual
  • Up to twenty percent boost in simulations
  • and more

A demo version of GPIUTMD 0.9.6 will be available soon for download under an open source license. Check out the quick start tutorial to get started, or check out the full documentation to see everything it can do.

 

CheCL: Transparent Checkpointing and Process Migration of OpenCL Applications

June 26th, 2011

Abstract:

We propose a new transparent checkpoint/restart (CPR) tool, named CheCL, for high performance and dependable GPU computing. CheCL can perform CPR on an OpenCL application program without any modification and recompilation of its code. A conventional checkpointing system fails to checkpoint a process if the process uses OpenCL. Therefore, in CheCL, every API call is forwarded to another process called an API proxy, and the API proxy invokes the API function; two processes, an application process and an API proxy, are launched for an OpenCL application. In this case, as the application process is not an OpenCL process but a standard process, it can be safely checkpointed. While CheCL intercepts all API calls, it records the information necessary for restoring OpenCL objects. The application process does not hold any OpenCL handles, but CheCL handles to keep such information. Those handles are automatically converted to OpenCL handles and then passed to API functions. Upon restart, OpenCL objects are automatically restored based on the recorded information. This paper demonstrates the feasibility of transparent checkpointing of OpenCL programs including MPI applications, and quantitatively evaluates the runtime overheads. It is also discussed that CheCL can enable process migration of OpenCL applications among distinct nodes, and among different kinds of compute devices such as a CPU and a GPU.

(Hiroyuki Takizawa, Kentaro Koyama, Katuto Sato, Kazuhiko Komatsu, and Hiroaki Kobayashi: “CheCL: Transparent Checkpointing and Process Migration of OpenCL Applications”, Proceedings of International Parallel and Distributed Processing Symposium (IPDPS11), 2011. [PDF])

 

Fast analysis of molecular dynamics trajectories with graphics processing units—Radial distribution function histogramming

June 14th, 2011

Abstract:

The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU’s memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.

(Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer: “Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units — Radial Distribution Function Histogramming”, Journal of Computational Physics, 230(9):3556-3569, 2011. [DOI: 10.1016/j.jcp.2011.01.048])

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