Scientific Programming - Volume 18, issue 3-4

Authors: Jost, Gabriele | Koniges, Alice

Article Type: Other

DOI: 10.3233/SPR-2011-0312

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 125-126, 2010

Authors: Jost, Gabriele | Robins, Bob

Article Type: Research Article

Abstract: Today most systems in high-performance computing (HPC) feature a hierarchical hardware design: shared-memory nodes with several multi-core CPUs are connected via a network infrastructure. When parallelizing an application for these architectures it seems natural to employ a hierarchical programming model such as combining MPI and OpenMP. Nevertheless, there is the general lore that pure MPI outperforms the hybrid MPI/OpenMP approach. In this paper, we describe the hybrid MPI/OpenMP parallelization of IR3D (Incompressible Realistic 3-D) code, a full-scale real-world application, which simulates the environmental effects on the evolution of vortices trailing behind control surfaces of underwater vehicles. We discuss performance, scalability …and limitations of the pure MPI version of the code on a variety of hardware platforms and show how the hybrid approach can help to overcome certain limitations. Show more

Keywords: Hybrid MPI/OpenMP, CFD solver, scalability, performance

DOI: 10.3233/SPR-2010-0308

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 127-138, 2010

Authors: Preissl, Robert | Koniges, Alice | Ethier, Stephan | Wang, Weixing | Wichmann, Nathan

Article Type: Research Article

Abstract: Application codes in a variety of areas are being updated for performance on the latest architectures. In this paper we examine an application, which comes from magnetic fusion for performance acceleration with a particular emphasis on methods that are applicable for many/multicore and future architectural designs. We take an important magnetic fusion particle code that already includes several levels of parallelism including hybrid MPI combined with OpenMP. We study how to include new advanced hybrid models, which extend the applicability of OpenMP tasks and exploit multi-threaded MPI support to overlap communication and computation. Experiments carried out on Cray XT4 and …XT5 machines resulting in a speed-up of up to 35% of the investigated GTS particle shifter kernel show the benefits and applicability of this approach. Show more

Keywords: GTS, OpenMP task, communication overlap, hybrid MPI and OpenMP computing

DOI: 10.3233/SPR-2010-0311

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 139-151, 2010

Authors: Shan, Hongzhang | Blagojević, Filip | Min, Seung-Jai | Hargrove, Paul | Jin, Haoqiang | Fuerlinger, Karl | Koniges, Alice | Wright, Nicholas J.

Article Type: Research Article

Abstract: Harnessing the power of multicore platforms is challenging due to the additional levels of parallelism present. In this paper we use the NAS Parallel Benchmarks to study three programming models, MPI, OpenMP and PGAS to understand their performance and memory usage characteristics on current multicore architectures. To understand these characteristics we use the Integrated Performance Monitoring tool and other ways to measure communication versus computation time, as well as the fraction of the run time spent in OpenMP. The benchmarks are run on two different Cray XT5 systems and an Infiniband cluster. Our results show that in general the three …programming models exhibit very similar performance characteristics. In a few cases, OpenMP is significantly faster because it explicitly avoids communication. For these particular cases, we were able to re-write the UPC versions and achieve equal performance to OpenMP. Using OpenMP was also the most advantageous in terms of memory usage. Also we compare performance differences between the two Cray systems, which have quad-core and hex-core processors. We show that at scale the performance is almost always slower on the hex-core system because of increased contention for network resources. Show more

Keywords: Programming model, performance study, UPC, OpenMP, MPI, memory usage

DOI: 10.3233/SPR-2010-0306

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 153-167, 2010

Authors: Huang, Lei | Jin, Haoqiang | Yi, Liqi | Chapman, Barbara

Article Type: Research Article

Abstract: Locality of computation is key to obtaining high performance on a broad variety of parallel architectures and applications. It is moreover an essential component of strategies for energy-efficient computing. OpenMP is a widely available industry standard for shared memory programming. With the pervasive deployment of multi-core computers and the steady growth in core count, a productive programming model such as OpenMP is increasingly expected to play an important role in adapting applications to this new hardware. However, OpenMP does not provide the programmer with explicit means to program for locality. Rather it presents the user with a “flat” memory model. …In this paper, we discuss the need for explicit programmer control of locality within the context of OpenMP and present some ideas on how this might be accomplished. We describe potential extensions to OpenMP that would enable the user to manage a program's data layout and to align tasks and data in order to minimize the cost of data accesses. We give examples showing the intended use of the proposed features, describe our current implementation and present some experimental results. Our hope is that this work will lead to efforts that would help OpenMP to be a major player on emerging, multi- and many-core architectures. Show more

Keywords: Locality of computation, memory programming, OpenMP, programming models

DOI: 10.3233/SPR-2010-0307

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 169-181, 2010

Authors: Zheng, Yili

Article Type: Research Article

Abstract: The Partitioned Global Address Space (PGAS) model of Unified Parallel C (UPC) can help users express and manage application data locality on non-uniform memory access (NUMA) multi-core shared-memory systems to get good performance. First, we describe several UPC program optimization techniques that are important to achieving good performance on NUMA multi-core computers with examples and quantitative performance results. Second, we use two numerical computing kernels, parallel matrix–matrix multiplication and parallel 3-D FFT, to demonstrate the end-to-end development and optimization for UPC applications. Our results show that the optimized UPC programs achieve very good and scalable performance on current multi-core systems …and can even outperform vendor-optimized libraries in some cases. Show more

Keywords: UPC, PGAS

DOI: 10.3233/SPR-2010-0310

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 183-191, 2010

Authors: Jespersen, Dennis C.

Article Type: Research Article

Abstract: The Computational Fluid Dynamics code OVERFLOW includes as one of its solver options an algorithm which is a fairly small piece of code but which accounts for a significant portion of the total computational time. This paper studies some of the issues in accelerating this piece of code by using a Graphics Processing Unit (GPU). The algorithm needs to be modified to be suitable for a GPU and attention needs to be given to 64-bit and 32-bit arithmetic. Interestingly, the work done for the GPU produced ideas for accelerating the CPU code and led to significant speedup on the CPU.

Keywords: GPU, CUDA, acceleration, OVERFLOW code

DOI: 10.3233/SPR-2010-0309

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 193-201, 2010

Authors: Budimlić, Zoran | Burke, Michael | Cavé, Vincent | Knobe, Kathleen | Lowney, Geoff | Newton, Ryan | Palsberg, Jens | Peixotto, David | Sarkar, Vivek | Schlimbach, Frank | Taşırlar, Sağnak

Article Type: Research Article

Abstract: We introduce the Concurrent Collections (CnC) programming model. CnC supports flexible combinations of task and data parallelism while retaining determinism. CnC is implicitly parallel, with the user providing high-level operations along with semantic ordering constraints that together form a CnC graph. We formally describe the execution semantics of CnC and prove that the model guarantees deterministic computation. We evaluate the performance of CnC implementations on several applications and show that CnC offers performance and scalability equivalent to or better than that offered by lower-level parallel programming models.

Keywords: Concurrent Collections (CnC), programming model, parallel programming

DOI: 10.3233/SPR-2011-0305

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 203-217, 2010

Authors: Gundy-Burlet, Karen

Article Type: Book Review

DOI: 10.3233/SPR-2010-0302

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 219-220, 2010

Authors: Lesk, Michael

Article Type: Book Review

DOI: 10.3233/SPR-2010-0304

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 221-223, 2010

Article Type: Other

Citation: Scientific Programming, vol. 18, no. 3-4, pp. 225-226, 2010