[gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)

Alan alanwilter at gmail.com
Fri Aug 1 08:58:40 CEST 2008

Steffen, if don't intend to use GMX double precision, why not use
Gromacs from FINK? It's all there. Use ommpi also, instead of lammpi
(seems broken in Fink too).

Then you can do something like:

#  with openmpi, for a dual core
grompp -f em.mdp -c Complex_b4em.pdb -p Complex.top -o em.tpr -np 2
om-mpirun -n 2 mdrun_mpi -v -deffnm em

grompp -f md.mdp -c em.gro -p Complex.top -o md.tpr -np 2 -sort -shuffle
om-mpirun -n 2 mdrun_mpi -v -deffnm md


On Thu, Jul 31, 2008 at 4:40 PM, <swolf at bph.rub.de> wrote:

> Hi all,
> I'm having trouble with the compilation of GROMACS on a Mac Pro (OS X).
> It's a  machine with two Quad-Core Intel Xeon, so 8 nodes in all. As
> compiler I used the programs delivered with the Xcode tools 3.0 and for
> parallelisation the LAM/MPI package delivered with the Xcode tools. The
> problem now is: If I try to start a job on the 8 nodes, the program is
> started 8 times (one time each node) instead of one time and distributed
> on 8 nodes. The result is the same for GROMACS 3.3.1, 3.3.3 and the recent
> CVS. Does anybody have a suggestion? Is the problem more related to LAM
> then to GROMACS?
> Greetings
> Steffen

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

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