[gmx-users] LAM OpenMPI conflict?

Jussi Lehtola jussi.lehtola at helsinki.fi
Thu Oct 15 21:42:29 CEST 2009

On Thu, 2009-10-15 at 21:04 +0200, Francesco Pietra wrote:

> $ lamboot
> $ mpirun.lam -np 4 mdrun_mpi.lam -s mod21.tpr -o minim_mod21_traj.trr
> -c minim_mod21.gro -e minim_mod21_ener.edr


> Program mdrun_mpi.lam, VERSION 3.3.3
> Source code file: ../../../../src/mdlib/init.c, line: 69
> Fatal error:
> run input file mod21.tpr was made for 1 nodes,
>              while mdrun_mpi.lam expected it to be for 4 nodes.

So now it works, you're just using the obsolete version 3.3.3 of
Gromacs, which needs the -np argument in grompp, too.

> When installing debian-offered gromacs I avoided the OpenMPI version
> because of my Intel-installation of OpenMPI. On the other hand, I need
> the latter for running amber, so that if I want to use OpenMPI I
> should probably compile gromacs by myself. Don't know if the Intel
> installation of OpenMPI will be accepted.

That is a possibility, even more so if you want to run a modern
installation of Gromacs since the Debian packages are _old_.

You should be able to install and use the Debian version Open MPI if you
didn't use system directories for your Intel version. Remember to check
that LD_LIBRARY_PATH isn't set to the Intel version, since otherwise the
system will prefer the Intel versions of the libraries instead of the
system ones.

> Somewhere in gromacs I have read that the command to start a parallel
> job is the same for lam- or openmpi-based installation. May be I don't
> remember correctly.

MPI is a standard so Gromacs works the same on every MPI runtime. Your
problem was with the Debian packages.
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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