2,897 research outputs found
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
Teaching Parallel Programming Using Java
This paper presents an overview of the "Applied Parallel Computing" course
taught to final year Software Engineering undergraduate students in Spring 2014
at NUST, Pakistan. The main objective of the course was to introduce practical
parallel programming tools and techniques for shared and distributed memory
concurrent systems. A unique aspect of the course was that Java was used as the
principle programming language. The course was divided into three sections. The
first section covered parallel programming techniques for shared memory systems
that include multicore and Symmetric Multi-Processor (SMP) systems. In this
section, Java threads was taught as a viable programming API for such systems.
The second section was dedicated to parallel programming tools meant for
distributed memory systems including clusters and network of computers. We used
MPJ Express-a Java MPI library-for conducting programming assignments and lab
work for this section. The third and the final section covered advanced topics
including the MapReduce programming model using Hadoop and the General Purpose
Computing on Graphics Processing Units (GPGPU).Comment: 8 Pages, 6 figures, MPJ Express, MPI Java, Teaching Parallel
Programmin
A review of parallel computing for large-scale remote sensing image mosaicking
Interest in image mosaicking has been spurred by a wide variety of research and management needs. However, for large-scale applications, remote sensing image mosaicking usually requires significant computational capabilities. Several studies have attempted to apply parallel computing to improve image mosaicking algorithms and to speed up calculation process. The state of the art of this field has not yet been summarized, which is, however, essential for a better understanding and for further research of image mosaicking parallelism on a large scale. This paper provides a perspective on the current state of image mosaicking parallelization for large scale applications. We firstly introduce the motivation of image mosaicking parallel for large scale application, and analyze the difficulty and problem of parallel image mosaicking at large scale such as scheduling with huge number of dependent tasks, programming with multiple-step procedure, dealing with frequent I/O operation. Then we summarize the existing studies of parallel computing in image mosaicking for large scale applications with respect to problem decomposition and parallel strategy, parallel architecture, task schedule strategy and implementation of image mosaicking parallelization. Finally, the key problems and future potential research directions for image mosaicking are addressed
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