The parallelization of SPIDER on distributed-memory computers using MPI

被引：7

作者：

Yang, Chao ^{[1
]}

Penczek, Pawel A.

Leith, ArDean

Asturias, Francisco J.

Ng, Esmond G.

Glaeser, Robert M.

Frank, Joachim

机构：

[1] Univ Calif Berkeley, Lawrence Berkeley Lab, Computat Res Div, Berkeley, CA 94720 USA

[2] Baylor Univ, Houton Med Ctr, Dept Biochem & Mol Biol, Houston, TX 77030 USA

[3] New York State Dept Hlth, Wadsworth Ctr Labs & Res, Albany, NY 12201 USA

[4] Scripps Res Inst, Dept Cell Biol, La Jolla, CA 92037 USA

[5] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA

[6] Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA

[7] New York State Dept Hlth, Wadsworth Ctr Labs & Res, Howard Hughes Med Inst, Albany, NY 12201 USA

来源：

JOURNAL OF STRUCTURAL BIOLOGY | 2007年 / 157卷 / 01期

基金：

美国国家卫生研究院;

关键词：

3-D structure determination; electron microscopy; parallel computing; message passing interface;

D O I：

10.1016/j.jsb.2006.05.011

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We describe the strategies and implementation details we employed to parallelize the SPIDER software package on distributed-memory parallel computers using the message passing interface (MPI). The MPI-enabled SPIDER preserves the interactive command line and batch interface used in the sequential version of SPIDER, thus does not require users to modify their existing batch programs. We show the excellent performance of the MPI-enabled SPIDER when it is used to perform multi-reference alignment and 3-D reconstruction operations on a number of different computing platforms. We point out some performance issues when the MPI-enabled SPIDER is used for a complete 3-D projection matching refinement run, and propose several ways to further improve the parallel performance of SPIDER on distributed-memory machines. (c) 2006 Elsevier Inc. All rights reserved.

引用

页码：240 / 249

页数：10

共 24 条

[1] Three-dimensional structure of the human TFIID-IIA-IIB complex [J].

Andel, F ;

Ladurner, AG ;

Inouye, C ;

Tjian, R ;

Nogales, E .

SCIENCE, 1999, 286 (5447) :2153-2156

[2] RNA polymerase II at initiation [J].

Asturias, FJ ;

Craighead, JL .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (12) :6893-6895

[3]

Bernaschi M, 1998, CONCURRENCY-PRACT EX, V10, P359, DOI 10.1002/(SICI)1096-9128(19980425)10:5<359::AID-CPE323>3.0.CO

[4]

2-7

[5]

BURNS G, 1994, P SUP S, P379

[6]

Chandra R., 2000, Parallel Programming in OpenMP

[7] SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields [J].

Frank, J ;

Radermacher, M ;

Penczek, P ;

Zhu, J ;

Li, YH ;

Ladjadj, M ;

Leith, A .

JOURNAL OF STRUCTURAL BIOLOGY, 1996, 116 (01) :190-199

[8]

Frank J, 2000, METHOD ENZYMOL, V317, P276

[9]

Frank J., 2006, Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State

[10]

Gilat A., 2004, MATLAB: An introduction with Applications

← 1 2 3 →