Using SPIDER with MPI

Supported operations

Operations in SPIDER which currently contain MPI parallelizing directives:

• AP REF
• AP SH
• BP 3F
• BP 32F
• BP CG
• BP RP

The SPIDER distribution contains an executable: spider_linux_mpi_opt64 which was compiled/linked dynamically using Makefile_linux_mpi_opt64 You may need to have the MPI libraries from this OpenMPI release to use this executable. The operation: ldd spider_linux_mpi_opt64 will tell you what libraries are available for running this executable on your system.

Sample Usage

mpirun -v -host node1,node2,node3 -n 3 spider_linux_mpi_opt64 tst @testapsh --

Hints

Avoiding conflict with mpirun.

When starting SPIDER under MPI with 'mpirun', a '--' at end of SPIDER's command line arguments allows SPIDER to ignore any arguments appended by 'mpirun'.