[gmx-users] LAM OpenMPI conflict?

[Jussi Lehtola]

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

clip

> 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.
-- 
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Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50632
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Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi
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