275 research outputs found
Towards a Mini-App for Smoothed Particle Hydrodynamics at Exascale
The smoothed particle hydrodynamics (SPH) technique is a purely Lagrangian
method, used in numerical simulations of fluids in astrophysics and
computational fluid dynamics, among many other fields. SPH simulations with
detailed physics represent computationally-demanding calculations. The
parallelization of SPH codes is not trivial due to the absence of a structured
grid. Additionally, the performance of the SPH codes can be, in general,
adversely impacted by several factors, such as multiple time-stepping,
long-range interactions, and/or boundary conditions. This work presents
insights into the current performance and functionalities of three SPH codes:
SPHYNX, ChaNGa, and SPH-flow. These codes are the starting point of an
interdisciplinary co-design project, SPH-EXA, for the development of an
Exascale-ready SPH mini-app. To gain such insights, a rotating square patch
test was implemented as a common test simulation for the three SPH codes and
analyzed on two modern HPC systems. Furthermore, to stress the differences with
the codes stemming from the astrophysics community (SPHYNX and ChaNGa), an
additional test case, the Evrard collapse, has also been carried out. This work
extrapolates the common basic SPH features in the three codes for the purpose
of consolidating them into a pure-SPH, Exascale-ready, optimized, mini-app.
Moreover, the outcome of this serves as direct feedback to the parent codes, to
improve their performance and overall scalability.Comment: 18 pages, 4 figures, 5 tables, 2018 IEEE International Conference on
Cluster Computing proceedings for WRAp1
A Comparative study and evaluation of parallel programming models for shared-memory parallel architectures
Nowadays, shared-memory parallel architectures have evolved and new programming frameworks have appeared that exploit these architectures: OpenMP, TBB, Cilk Plus, ArBB and OpenCL. This article focuses on the most extended of these frameworks in commercial and scientific areas. This paper shows a comparative study of these frameworks and an evaluation. The study covers several capacities, such as task deployment, scheduling techniques, or programming language abstractions. The evaluation measures three dimensions: code development complexity, performance and efficiency, measure as speedup per watt. For this evaluation, several parallel benchmarks have been implemented with each framework. These benchmarks are created to cover certain scenarios, like regular memory access or irregular computation. The conclusions show some highlights, like the fact that some frameworks (OpenMP, Cilk Plus) are better for transforming quickly a sequential code, others (TBB) have a small footprint which is ideal for small problems, and others (OpenCL) are suited for heterogeneous architectures but they require a very complex development process. The conclusions also show that the vectorization support is more critical than multitasking to achieve efficiency for those problems where this approach fits.This work has been partially funded by the project “Input/Output Scalable Techniques for distributed and high-performance computing environments” of MINISTERIO DE CIENCIA E INNOVACIĂ“N, TIN2010-16497. The work of J. Daniel GarcĂa has been funded by "FUNDACIĂ“N CAJAMADRID" through a grant for Mobility of Madrid Public Universities Professors
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
SPH-EXA: Enhancing the Scalability of SPH codes Via an Exascale-Ready SPH Mini-App
Numerical simulations of fluids in astrophysics and computational fluid
dynamics (CFD) are among the most computationally-demanding calculations, in
terms of sustained floating-point operations per second, or FLOP/s. It is
expected that these numerical simulations will significantly benefit from the
future Exascale computing infrastructures, that will perform 10^18 FLOP/s. The
performance of the SPH codes is, in general, adversely impacted by several
factors, such as multiple time-stepping, long-range interactions, and/or
boundary conditions. In this work an extensive study of three SPH
implementations SPHYNX, ChaNGa, and XXX is performed, to gain insights and to
expose any limitations and characteristics of the codes. These codes are the
starting point of an interdisciplinary co-design project, SPH-EXA, for the
development of an Exascale-ready SPH mini-app. We implemented a rotating square
patch as a joint test simulation for the three SPH codes and analyzed their
performance on a modern HPC system, Piz Daint. The performance profiling and
scalability analysis conducted on the three parent codes allowed to expose
their performance issues, such as load imbalance, both in MPI and OpenMP.
Two-level load balancing has been successfully applied to SPHYNX to overcome
its load imbalance. The performance analysis shapes and drives the design of
the SPH-EXA mini-app towards the use of efficient parallelization methods,
fault-tolerance mechanisms, and load balancing approaches.Comment: arXiv admin note: substantial text overlap with arXiv:1809.0801
vSMC: Parallel Sequential Monte Carlo in C++
Sequential Monte Carlo is a family of algorithms for sampling from a sequence of distributions. Some of these algorithms, such as particle filters, are widely used in physics and signal processing research. More recent developments have established their application in more general inference problems such as Bayesian modeling.
These algorithms have attracted considerable attention in recent years not only be- cause that they have desired statistical properties, but also because they admit natural and scalable parallelization. However, they are perceived to be difficult to implement. In addition, parallel programming is often unfamiliar to many researchers though conceptually appealing.
A C++ template library is presented for the purpose of implementing generic sequential Monte Carlo algorithms on parallel hardware. Two examples are presented: a simple particle filter and a classic Bayesian modeling problem
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