Message Passing Interface

Abstract: This book offers a thoroughly updated guide to the MPI (Message-Passing Interface) standard library for writing programs for parallel computers Since the publication of the previous edition of Using MPI, parallel computing has become mainstream Today, applications run on computers with millions of processors; multiple processors sharing memory and multicore processors with multiple hardware threads per core are common The MPI-3 Forum recently brought the MPI standard up to date with respect to developments in hardware capabilities, core language evolution, the needs of applications, and experience gained over the years by vendors, implementers, and users This third edition of Using MPI reflects these changes in both text and example code The book takes an informal, tutorial approach, introducing each concept through easy-to-understand examples, including actual code in C and Fortran Topics include using MPI in simple programs, virtual topologies, MPI datatypes, parallel libraries, and a comparison of MPI with sockets For the third edition, example code has been brought up to date; applications have been updated; and references reflect the recent attention MPI has received in the literature A companion volume, Using Advanced MPI, covers more advanced topics, including hybrid programming and coping with large data

Abstract: From the Publisher: MPI, the Message Passing Interface, is a standard and portable library of communications subroutines for parallel programming designed to function on a wide variety of parallel computers. It is useful on both parallel computers, such as IBM's SP2, the Cray ResearchT3D, and the Connection Machine, as well as networks of workstations. Written by five of the principal creators of the latest MPI standard MPI: The Complete Reference is an annotated manual for the latest 1.1 version of the standard that illuminates the more advanced and subtle features of MPI. It can be read in conjunction with the companion tutorial volume, Using MPI: Portable Parallel Programming with the Message-Passing Interface, by William Gropp, Ewing Lusk, and Anthony Skjellum. MPI: The Complete Reference is the only source that covers such advanced issues in parallel computing and programming as true portability, deadlock, high-performance message passing, and libraries for distributed and parallel computing. The annotations provide numerous illustrative programming examples and delve into even the most esoteric features or consequences of the standard. They explain why certain design choices were made, how users should use the interface, and how implementors should construct their own version of MPI. Scientific and Engineering Computation series

Abstract: SUMMARY TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers. AVAILABILITY http://www.tree-puzzle.de. The program is written in ANSI C. TREE-PUZZLE can be run on UNIX, Windows and Mac systems, including Mac OS X. To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/).

Abstract: MPI (Message Passing Interface) is a specification for a standard library for message passing that was defined by the MPI Forum, a broadly based group of parallel computer vendors, library writers, and applications specialists. Multiple implementations of MPI have been developed. In this paper, we describe MPICH, unique among existing implementations in its design goal of combining portability with high performance. We document its portability and performance and describe the architecture by which these features are simultaneously achieved. We also discuss the set of tools that accompany the free distribution of MPICH, which constitute the beginnings of a portable parallel programming environment. A project of this scope inevitably imparts lessons about parallel computing, the specification being followed, the current hardware and software environment for parallel computing, and project management; we describe those we have learned. Finally, we discuss future developments for MPICH, including those necessary to accommodate extensions to the MPI Standard now being contemplated by the MPI Forum.