[gmx-users] Running MPI-enabled GROMACS

[Choon Peng Chng]

Hi everyone,

  First of all, thanks to Jithesh for advising me to run mdrun as an
executable to mpirun, instead of running it
as it is. Initially it still does not work and I got:
Missing: program name
Program mdrun either does not exist, is not
executable, or is an erroneous argument to mpirun.

But then I decide to specify the whole path to mdrun instead:
mpirun -np 2 /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun -s topol.tpr
-o traj.trr -c confout.gro -e ener.edr -g md.log -np 2

and it worked!!
Finally after so many trials, it worked...

So, in summary after configuring gromacs with --enable-mpi, we run
MPI-aware mdrun using the native mpirun, in
MPICH or LAM.


Have a wonderful New Year!
cheers,
choon peng

--
Choon-Peng Chng
Scientific Programmer
BioInformatics Institute (BII)
30 Medical Drive, Level 1 IMCB Building, Singapore 117609
Tel: (65)8746173
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