[gmx-developers] message passing in GROMACS

Nathan Moore nmoore at physics.umn.edu
Thu Jun 16 22:35:01 CEST 2005


I've ported Gromacs to an IBM Blue Gene machine and would like to try a
different message passing scheme to see if scaling can be extended to a
larger number of processors.  I've spent some time reading through the
source, notably, <sim_util.c>, <network.c>, and <mvxvf.c>, and I think I
understand roughly how the message passing works.  I'd like to compare to
this routine with an alternate version which sharings the F, and X arrays
with an mpi All to All command.  Are the force (f) and position (x) arrays
stored flatly or do they enclosed in a data structure.  It looks like
they're passed presently in small chunks - is the form of these variables
documented in the source?


Nathan Moore

More information about the gromacs.org_gmx-developers mailing list