[gmx-users] about parallel work

[Carsten Kutzner]

Hi,

On Apr 21, 2009, at 5:53 PM, sheerychen wrote:

> yes, both versions are compiled as mpi version. However the start  
> mpi messages are different. For MPICH, it would show that 1D domain  
> decomposition like 3*1*1, and only 1 file would be produced. However  
> for MPICH2, no such information appears and it would produce many  
> files as (8 nodes):
> complex_em.edr      complex_em.log      #complex_em.trr.7#   
> #complex_pr.log.5#
> #complex_em.edr.1#  #complex_em.log.1#  complex_pr.cpt       
> #complex_pr.log.6#
> #complex_em.edr.2#  #complex_em.log.2#  #complex_pr.cpt.1#   
> #complex_pr.log.7#
> #complex_em.edr.3#  #complex_em.log.3#  complex_pr.edr       
> complex_pr_prev.cpt
> #complex_em.edr.4#  #complex_em.log.4#  #complex_pr.edr.1#   
> complex_pr.tpr
> #complex_em.edr.5#  #complex_em.log.5#  #complex_pr.edr.2#   
> complex_pr.trr
> #complex_em.edr.6#  #complex_em.log.6#  #complex_pr.edr.3#   
> #complex_pr.trr.1#
> #complex_em.edr.7#  #complex_em.log.7#  #complex_pr.edr.4#
That means that in this case 8 serial instances run instead of one  
parallel.
Either gromacs was not compiled properly with appropriate MPI  
libraries or something
during startup did not work. You should check if the mpich2 ring of  
daemons is running
with mpdtrace. If not, look up mpdboot.

Carsten