title: The parallelization of SPIDER on distributed-memory computers using MPI.
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.
authors.affiliation: Lawrence Berkeley National Laboratory, Computational Research Division, Berkeley, CA 94720, USA. CYang@lbl.gov
authors.forename: Chao
authors.initials: C
authors.lastname: Yang
authors.forename: Pawel A
authors.initials: PA
authors.lastname: Penczek
authors.forename: ArDean
authors.initials: A
authors.lastname: Leith
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Asturias
authors.forename: Esmond G
authors.initials: EG
authors.lastname: Ng
authors.forename: Robert M
authors.initials: RM
authors.lastname: Glaeser
authors.forename: Joachim
authors.initials: J
authors.lastname: Frank
mesh_terms: D000465:Algorithms; D003199:Computer Systems; D007089:Image Enhancement / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods*; D012984:Software; D012985:Software Design