使用MPI在分布式内存计算机上实现SPIDER的并行化。

The parallelization of SPIDER on distributed-memory computers using MPI.

作者信息

Yang Chao, Penczek Pawel A, Leith ArDean, Asturias Francisco J, Ng Esmond G, Glaeser Robert M, Frank Joachim

机构信息

Lawrence Berkeley National Laboratory, Computational Research Division, Berkeley, CA 94720, USA.

出版信息

J Struct Biol. 2007 Jan;157(1):240-9. doi: 10.1016/j.jsb.2006.05.011. Epub 2006 Jun 8.

DOI:10.1016/j.jsb.2006.05.011

PMID:16859923

Abstract

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.

摘要

我们描述了为使用消息传递接口（MPI）在分布式内存并行计算机上并行化SPIDER软件包所采用的策略和实现细节。启用MPI的SPIDER保留了SPIDER顺序版本中使用的交互式命令行和批处理接口，因此无需用户修改其现有的批处理程序。我们展示了启用MPI的SPIDER在多个不同计算平台上执行多参考对齐和三维重建操作时的出色性能。我们指出了启用MPI的SPIDER用于完整的三维投影匹配细化运行时的一些性能问题，并提出了几种进一步提高SPIDER在分布式内存机器上并行性能的方法。