[gmx-users] LAM OpenMPI conflict?

Jussi Lehtola jussi.lehtola at helsinki.fi
Thu Oct 15 19:55:35 CEST 2009

On Thu, 2009-10-15 at 18:23 +0200, Francesco Pietra wrote:
> Hi: I was trying to minimize in vacuum a pure CG protein on a four
> core (two dual operons), getting errors:
> $ lamboot
> $ mpirun -np 4 mdrun -s mod21.tpr -o minim_mod21_traj.trr -c
> minim_mod21.gro -e minim_mod21_ener.edr
> ...................
> ...................
> WARNING: Writing ompirun noticed that job rank 2 with PID 4385 on node
> tya64 exited on signal 11 (Segmentation fault).
> 3 processes killed (possibly by Open MPI)
> Writing out atom name (SCSP1) longer than 4 characters to .pdb file

This looks like you are trying to run the LAM binary with Open MPI's
mpirun command. Use the LAM version instead (mpirun.lam in Debian).

Furthermore, the Debian packages use suffixes, for instance the binaries
in the gromacs-lam package are /usr/bin/mdrun_mpi.lam
and /usr/bin/mdrun_mpi_d.lam, so you should switch mdrun to
mdrun_mpi.lam . So all in all:

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

What is also possible is that your installation of the Intel compiled
Open MPI is visible in your environment, which may quite well lead into

(Also, LAM has been obsoleted by Open MPI years ago, so you might just
try switching from LAM to Open MPI, then you wouldn't have to run
lamboot at the beginning.)
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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