The Message Passing Interface (MPI) standard continues to dominate the landscape of parallel computing as the de facto API for writing large-scale scientific applications. But the critics argue that it is a low-level API and harder to practice than shared memory approaches. This paper addresses the issue of programming productivity by proposing a high-level, easy-to-use, and efficient programmi...

Clustering is one of the most popular methods for exploratory data analysis, which is prevalent in many disciplines such as image segmentation, bioinformatics, pattern recognition and statistics etc. The most famous clustering algorithm is K-means because of its easy implementation, simplicity, efficiency and empirical success. However, the real-world applications produce huge volumes of data, ...

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks.We present a hybrid algorithmusingMPI (Message Passing Interface) with OpenMP threads for parallelizing a generalizedMD computation scheme for systemswith short range interatomic interactions. The algorithm is discussed in the context of nano-indentati...

We describe the parallel full-f gyrokinetic particle-in-cell plasma simulation code ELMFIRE and the issue of solving a electrostatic potential from particle data distributed across several MPI (Message Passing Interface) processes. The potential is solved through a linear system with a strongly sparse matrix and ELMFIRE stores data of the estimated nonzero diagonals of the whole matrix in every...

LogGP is a simple parallel machine model that reflects the important parameters required to measure the real performance of parallel computers (Alexandrov et al., 1995). The message passing interface (MPI) standard provides new opportunities for developing high performance parallel and distributed applications. We use LogGP as a conceptual framework for evaluating the performance of MPI communi...

This project examines the performance and methodology of diierent communication paradigms, shared memory communication and BSD socket communication. Goals for this work include installation of Message Passing Interface, enabling shared memory via MPI devices, and benchmarking the performance of a system with shared memory and without shared memory. We will show the compilation method required b...

FermiQCD is a collection of classes, functions and parallel algorithms for lattice QCD [1], written in C++. It is based on Matrix Distributed Processing (MDP) [2]. The latter is a library that includes C++ methods for matrix manipulation, advanced statistical analysis (such as Jackknife and Boostrap) and optimized algorithms for interprocess communications of distributed lattices and fields. Th...

MatlabMPI is a Matlab implementation of the Message Passing Interface (MPI) standard and allows any Matlab program to exploit multiple processors. MatlabMPI currently implements the basic six functions that are the core of the MPI point-to-point communications standard. The key technical innovation of MatlabMPI is that it implements the widely used MPI " look and feel " on top of standard Matla...

The realization of support for workstation clusters with the integrated tool environment Annai is discussed in this paper. Annai prototypes developed at CSCS supportparallel program developmentwith standard paradigms: implicitlyparallel High Performance Fortran (HPF) and explicit communication with the Message Passing Interface (MPI). The port to this new platform required only minor changes to...

We introduce an MPI Python module, MYMPI, for parallel programming in Python using the Message Passing Interface (MPI). This is a true Python module which runs with a standard Python interpreter. In this paper we discuss the motivation for creating the MYMPI module, along with differences between MYMPI and pyMPI, another MPI Python interpreter. Additionally, we discuss three projects that have ...