[gmx-users] suggestion that mdrun should ensure npme < the numberof processes

Carsten Kutzner ckutzne at gwdg.de
Wed Aug 17 10:47:10 CEST 2011


On Aug 17, 2011, at 1:24 AM, <chris.neale at utoronto.ca> <chris.neale at utoronto.ca> wrote:

> Currently, gromacs4.5.4 gives a segfault if one runs mpirun -np 8 mdrun_mpi -npme 120 with no warning of the source of the problem.
> Obviously npme>nnodes is a bad setup, but a check would be nice.
cr->npmenodes is set in mdrun.c right after the command line args are
passed, and in the code there is also a comment that npme>nnodes should not
cause a problem at that point.

However, if npme>nnodes, in init_domain_decomposition / dd_choose_grid / optimize_ncells
the number of pp nodes = nnodes-npme turns out to be negative such that in factorize
the memory allocation does not work. 

I would have filed a bug report, however the web page seems to be down at the 


> Thank you,
> Chris.
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