[gmx-users] MPI gromacs usage

Alan Dodd anoddlad at yahoo.com
Tue Jul 18 16:53:56 CEST 2006

The information must be out there, somewhere, because
I found it... But in summary:
You'll need to compile gromacs with MPI support.  See
the installation instructions for details about that. 
Once you've got MPI-enabled gromacs, you need to run
grompp with the option -np (number of nodes to run
over).  So no, you can't use the same tpr.  mdrun then
needs to be run, also with the option -np (might be -N
- it seems to change sometimes) as an command within
an mpi command, depending on which flavour of MPI you
are using.  So for LAM, the command looks something
like :
mpirun -c (number of processors) mdrun -N (number of
processors) -s topol.tpr etc.
But it varies according to which MPI you use, your
hardware etc.

Have a closer look at the options available in grompp
and mdrun, and the manual for whatever MPI you use.
--- Diane Fournier <diane.fournier at crchul.ulaval.ca>

> Hi gromacs users
> I've already used gromacs single-processor version
> and I want to use the parallel version of gromacs on
> a SGI Altix 2700 with 32 processors. I'm wondering
> how to proceed, because this does not seem to be
> explained properly anywhere. Do I have to give
> special instructions in grompp to split the
> simulation on several processors, or can I use the
> same .tpr file I'm using with the single-processor
> version of mdrun ?
> Thank you
> > _______________________________________________
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