[gmx-users] time of simulation

Jussi Lehtola jussi.lehtola at helsinki.fi
Sun Jul 26 00:34:30 CEST 2009

On Sat, 2009-07-25 at 15:16 -0700, mahmoud wrote:
> Hello Dear GMX Users,
> I have installed Gromacs 4 on a QUAD computer by Fedora 11.
> When I do not use the "mpirun -np 4 g_mdrun ... " command, just one
> CPU is used.
> When I use the "mpirun -np 4 g_mdrun ... " command, all of the 4
> CPUs are used.
> But the problem is that the time of simulation, although 4 CPUs are
> used, does not change by using the mpirun command!
> Can you help me please how I can fasten the time of simulation!

If you are using the Fedora RPMs, you need to run
$ mpirun -np 4 g_mdrun_mpi
instead of
$ mpirun -np 4 g_mdrun
as the latter will just get you four independent processes that all
perform the same calculation.
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50632
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi

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