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

Steffen Wolf swolf at bph.rub.de
Fri Aug 8 16:04:33 CEST 2008

Hi Alan,
thanks for the hint!!! Seems like it really was a problem with lammpi. 
The download from FINK worked beautifully, and GROMACS/open mpi works 
> 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
> Cheers,
> Alan
> 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

Dipl.-Chem. Steffen Wolf
Fellow of the Ruhr-University Research School
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
Web: http://www.bph.rub.de 

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