[gmx-users] LAM OpenMPI conflict?

[Francesco Pietra]

For your information, the procedure is:

$ grompp ... (to generate minimize.tpr)

$ lamboot

$ l$ mdrun_mpi -np 4 -v -s minimize.tpr -o mod21_traj.trr -c mod21.gro
-e mod21_ener.edr

It worked nicely, exactly as the serial run "mdrun -v -s minimize.tpr ...".
No interference with installed openmpi, no need to mention lam in the
md command line. Forget about the Debian compilation, it does not
require any special command.

Have a nice day

francesco

On Thu, Oct 15, 2009 at 7:55 PM, Jussi Lehtola
<jussi.lehtola at helsinki.fi> wrote:
> 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
> problems.
>
> (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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