While multicore architectures are used in the whole product range from server systems to handheld computers, the deployed software still undergoes the slow transition from sequential to parallel. This transition, however, is gaining more and more momentum due to the increased availability of more sophisticated parallel programming environments. Combined with the ever increasing complexity of multicore architectures, this results in a scheduling problem that is different from what it has been, because concurrently executing parallel programs and features such as non-uniform memory access, shared caches, or simultaneous multithreading have to be considered. In this paper, we compare different ways of scheduling multiple parallel applications on multicore architectures. Due to emerging parallel programming environments, we primarily consider applications where the parallelism degree can be changed on the fly. We propose TACO, a topology-aware scheduling scheme that combines equipartitioning and coscheduling, which does not suffer from the drawbacks of the individual concepts. Additionally, TACO is conceptually compatible with contention-aware scheduling strategies. We find that topology-awareness increases performance for all evaluated workloads. The combination with coscheduling is more sensitive towards the executed workloads and NUMA effects. However, the gained versatility allows new use cases to be explored, which were not possible before.

Jan H. Sch&#xf6;nherr

Ben Juurlink

Jan Richling

TACO: A Scheduling Scheme for Parallel Applications on Multicore Architectures

Three object-oriented implementations of a prototype solver of the advection equation are introduced. The presented programs are based on Blitz++ (C++), NumPy (Python) and Fortran's built-in array containers. The solvers constitute implementations of the Multidimensional Positive-Definite Advective Transport Algorithm (MPDATA). The introduced codes serve as examples for how the application of object-oriented programming (OOP) techniques and new language constructs from C++11 and Fortran 2008 allow to reproduce the mathematical notation used in the literature within the program code. A discussion on the tradeoffs of the programming language choice is presented. The main angles of comparison are code brevity and syntax clarity (and hence maintainability and auditability) as well as performance. All performance tests are carried out using free and open-source compilers. In the case of Python, a significant performance gain is observed when switching from the standard interpreter (CPython) to the PyPy implementation of Python. Entire source code of all three implementations is embedded in the text and is licensed under the terms of the GNU GPL license.

Sylwester Arabas

Dorota Jarecka

Anna Jaruga

Maciej Fija&#x142;kowski

Formula Translation in Blitz++, NumPy and Modern Fortran: A Case Study of the Language Choice Tradeoffs

Although there are a lot of robust and effective scientific libraries in Java, the utilization of these libraries in pure Java is difficult and cumbersome, especially for the average scientist that does not expertise in software development. We illustrate that ScalaLab presents an easier and productive MATLAB like front end. Also, the main strengths and weaknesses of the core Java libraries of ScalaLab are elaborated. Since performance is of paramount importance for scientific computation, the article discusses extensively performance aspects of the ScalaLab environment. Also, Java bytecode performance is compared to native code.

Stergios Papadimitriou

Seferina Mavroudi

Kostas Theofilatos

Spiridon Likothanasis

MATLAB-Like Scripting of Java Scientific Libraries in ScalaLab

The ever-increasing scale of scientific data has become a significant challenge for researchers that rely on networks to interact with remote computing systems and transfer results to collaborators worldwide. Despite the availability of high-capacity connections, scientists struggle with inadequate cyberinfrastructure that cripples data transfer performance, and impedes scientific progress. The Science DMZ paradigm comprises a proven set of network design patterns that collectively address these problems for scientists. We explain the Science DMZ model, including network architecture, system configuration, cybersecurity, and performance tools, that creates an optimized network environment for science. We describe use cases from universities, supercomputing centers and research laboratories, highlighting the effectiveness of the Science DMZ model in diverse operational settings. In all, the Science DMZ model is a solid platform that supports any science workflow, and flexibly accommodates emerging network technologies. As a result, the Science DMZ vastly improves collaboration, accelerating scientific discovery.

Eli Dart

Lauren Rotman

Brian Tierney

Mary Hester

Jason Zurawski

The Science DMZ: A Network Design Pattern for Data-Intensive Science

Domain decomposition methods are, alongside multigrid methods, one of the dominant paradigms in contemporary large-scale partial differential equation simulation. In this paper, a lightweight implementation of a theoretically and numerically scalable preconditioner is presented in the context of overlapping methods. The performance of this work is assessed by numerical simulations executed on thousands of cores, for solving various highly heterogeneous elliptic problems in both 2D and 3D with billions of degrees of freedom. Such problems arise in computational science and engineering, in solid and fluid mechanics. While focusing on overlapping domain decomposition methods might seem too restrictive, it will be shown how this work can be applied to a variety of other methods, such as non-overlapping methods and abstract deflation based preconditioners. It is also presented how multilevel preconditioners can be used to avoid communication during an iterative process such as a Krylov method.

Pierre Jolivet

Fr&#xe9;d&#xe9;ric Hecht

Fr&#xe9;d&#xe9;ric Nataf

Christophe Prud'homme

Scalable Domain Decomposition Preconditioners for Heterogeneous Elliptic Problems

This paper examines whether lossy compression can be used effectively in physics simulations as a possible strategy to combat the expected data-movement bottleneck in future high performance computing architectures. We show that, for the codes and simulations we tested, compression levels of 3&#x2013;5X can be applied without causing significant changes to important physical quantities. Rather than applying signal processing error metrics, we utilize physics-based metrics appropriate for each code to assess the impact of compression. We evaluate three different simulation codes: a Lagrangian shock-hydrodynamics code, an Eulerian higher-order hydrodynamics turbulence modeling code, and an Eulerian coupled laser-plasma interaction code. We compress relevant quantities after each time-step to approximate the effects of tightly coupled compression and study the compression rates to estimate memory and disk-bandwidth reduction. We find that the error characteristics of compression algorithms must be carefully considered in the context of the underlying physics being modeled.

Daniel Laney

Steven Langer

Christopher Weber

Peter Lindstrom

Al Wegener

Assessing the Effects of Data Compression in Simulations Using Physically Motivated Metrics

Drawing parallels to the rise of general purpose graphical processing units (GPGPUs) as accelerators for specific high-performance computing (HPC) workloads, there is a rise in the use of non-volatile memory (NVM) as accelerators for I/O-intensive scientific applications. However, existing works have explored use of NVM within dedicated I/O nodes, which are distant from the compute nodes that actually need such acceleration. As NVM bandwidth begins to out-pace point-to-point network capacity, we argue for the need to break from the archetype of completely separated storage. Therefore, in this work we investigate co-location of NVM and compute by varying I/O interfaces, file systems, types of NVM, and both current and future SSD architectures, uncovering numerous bottlenecks implicit in these various levels in the I/O stack. We present novel hardware and software solutions, including the new Unified File System (UFS), to enable fuller utilization of the new compute-local NVM storage. Our experimental evaluation, which employs a real-world Out-of-Core (OoC) HPC application, demonstrates throughput increases in excess of an order of magnitude over current approaches.

Myoungsoo Jung

Ellis H. Wilson

Wonil Choi

John Shalf

Hasan Metin Aktulga

Chao Yang

Erik Saule

Umit V. Catalyurek

Mahmut Kandemir

Exploring the Future of Out-of-Core Computing with Compute-Local Non-Volatile Memory

We apply object-oriented software design patterns to develop code for scientific software involving sparse matrices. Design patterns arise when multiple independent developments produce similar designs which converge onto a generic solution. We demonstrate how to use design patterns to implement an interface for sparse matrix computations on NVIDIA GPUs starting from PSBLAS, an existing sparse matrix library, and from existing sets of GPU kernels for sparse matrices. We also compare the throughput of the PSBLAS sparse matrix&#x2013;vector multiplication on two platforms exploiting the GPU with that obtained by a CPU-only PSBLAS implementation. Our experiments exhibit encouraging results regarding the comparison between CPU and GPU executions in double precision, obtaining a speedup of up to 35.35 on NVIDIA GTX 285 with respect to AMD Athlon 7750, and up to 10.15 on NVIDIA Tesla C2050 with respect to Intel Xeon X5650.

Valeria Cardellini

Salvatore Filippone

Damian W.I. Rouson

Design Patterns for Sparse-Matrix Computations on Hybrid CPU/GPU Platforms

About this journal

Scientific Programming provides a forum for research results in, and practical experience with, software engineering environments, tools, languages, and models of computation aimed specifically at supporting scientific and engineering computing.

Journal profile

Meet the editorial board

Chief Editor&nbsp;Professor Tramontana&nbsp;is based at the University of Catania and his research primarily concerns the areas of software engineering and distributed systems.

Editor spotlight

Submit your proposal

Do you think there is an emerging area of research that really needs to be highlighted? Or an existing research area that has been overlooked or would benefit from deeper investigation? Raise the profile of a research area by leading a Special Issue.

Special Issues

Author guidelines

Editorial board

Databases and indexing

Scientific Programming - Table of contents 2014

title

Scientific Programming provides a forum for research results in, and practical experience with, software engineering environments, tools, languages, and models of computation aimed specifically at supporting scientific and engineering computing.

Scientific Programming