[gmx-users] Parallel run

[Dhananjay]

Hello all,

As per the instructions, I have done the following...

for the path of lam:

bash-2.05b$ whereis lam
lam: /etc/lam /usr/share/lam /usr/man/man7/lam.7
/usr/share/man/man7/lam.7.gz

for the path of mpirun :

-bash-2.05b$ whereis mpirun
mpirun: /usr/bin/mpirun /usr/man/man1/mpirun.1
/usr/share/man/man1/mpirun.1.gz

for the path of lamboot::

-bash-2.05b$ whereis lamboot
lamboot: /usr/bin/lamboot /usr/man/man1/lamboot.1
/usr/share/man/man1/lamboot.1.gz

when I checked the PATH I found following.

-bash-2.05b$ echo $PATH
/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/share/lam:/etc/lam

As path /usr/share/lam is there I have tried again grompp and mdrun command
but still I am getting an error as follows:

-bash-2.05b$ mdrun -np 2 -f 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.
-----------------------------------------------------------------------------

Please tell me what is wrong  here ?


On 1/4/06, Carsten Kutzner <ckutzne at gwdg.de> wrote:
>
> 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,
>    Carsten
>
>
> ---------------------------------------------------
> 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
> http://www.gwdg.de/~ckutzne
>
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