[gmx-users] Parallel run

Carsten Kutzner ckutzne at gwdg.de
Wed Jan 4 11:23:34 CET 2006

On Wed, 4 Jan 2006, Dhananjay wrote:

> Dear all,
> When gromacs parallel version is installed on two nodes and tried to
> fire a parallel job following error occour.
> -bash-2.05b$ mdrun -np 2 -s 1WMI_em.tpr -o 1WMI_em.trr -c 1WMI_b4pr.gro -e
> em.edr -g em.log
> -----------------------------------------------------------------------------
> It seems that there is no lamd running on this host, which indicates
> that the LAM/MPI runtime environment is not operating.  The LAM/MPI
> runtime environment is necessary for MPI programs to run (the MPI
> program tired to invoke the "MPI_Init" function).
> Please run the "lamboot" command the start the LAM/MPI runtime
> environment.  See the LAM/MPI documentation for how to invoke
> "lamboot" across multiple machines.
> -----------------------------------------------------------------------------
> I have simply installed gromacs-3.3 on two nodes as per the procedure given
> on web.
> Yet I didn't fing "lamboot" command. I have installed lam-7.0.6

The lamboot command (and the mpirun command you also need) should be in
the directory where you installed lam (to be more specific: in the 'bin'
subdirectory). Put this in your path environment variable. You definitely
need to run 'lamboot' before you can do parallel mdruns. Then use

mpirun -np 2 mdrun <your options>

Good luck,

Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
eMail ckutzne at gwdg.de

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