Hello all,<br>
<br>
As per the instructions, I have done the following...<br>
<br>
for the path of lam: <br>
<br>
bash-2.05b$ whereis lam<br>
lam: /etc/lam /usr/share/lam /usr/man/man7/lam.7 /usr/share/man/man7/lam.7.gz<br>
<br>
for the path of mpirun :<br>
<br>
-bash-2.05b$ whereis mpirun<br>
mpirun: /usr/bin/mpirun /usr/man/man1/mpirun.1 /usr/share/man/man1/mpirun.1.gz<br>
<br>
for the path of lamboot::<br>
<br>
-bash-2.05b$ whereis lamboot<br>
lamboot: /usr/bin/lamboot /usr/man/man1/lamboot.1 /usr/share/man/man1/lamboot.1.gz<br>
<br>
when I checked the PATH I found following.<br>
<br>
-bash-2.05b$ echo $PATH<br>
/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/share/lam:/etc/lam<br>
<br>
As path /usr/share/lam is there I have tried again grompp and mdrun command but still I am getting an error as follows: <br><br>
-bash-2.05b$ mdrun -np 2 -f 1WMI_em.tpr -o 1WMI_em.trr -c 1WMI_b4pr.gro -e em.edr -g em.log<br>
-----------------------------------------------------------------------------<br>
It seems that there is no lamd running on this host, which indicates<br>
that the LAM/MPI runtime environment is not operating. The LAM/MPI<br>
runtime environment is necessary for MPI programs to run (the MPI<br>
program tired to invoke the "MPI_Init" function).<br>
<br>
Please run the "lamboot" command the start the LAM/MPI runtime<br>
environment. See the LAM/MPI documentation for how to invoke<br>
"lamboot" across multiple machines.<br>
-----------------------------------------------------------------------------<br>
<br>
Please tell me what is wrong here ?<br>
<br>
<br><div><span class="gmail_quote">On 1/4/06, <b class="gmail_sendername">Carsten Kutzner</b> <<a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Wed, 4 Jan 2006, Dhananjay wrote:<br><br>> Dear all,<br>><br>> When gromacs parallel version is installed on two nodes and tried to<br>> fire a parallel job following error occour.<br>><br>> -bash-2.05b$
mdrun -np 2 -s 1WMI_em.tpr -o 1WMI_em.trr -c 1WMI_b4pr.gro -e<br>> em.edr -g em.log<br>><br>><br>> -----------------------------------------------------------------------------<br>> It seems that there is no lamd running on this host, which indicates
<br>> that the LAM/MPI runtime environment is not operating. The LAM/MPI<br>> runtime environment is necessary for MPI programs to run (the MPI<br>> program tired to invoke the "MPI_Init" function).<br>
><br>> Please run the "lamboot" command the start the LAM/MPI runtime<br>> environment. See the LAM/MPI documentation for how to invoke<br>> "lamboot" across multiple machines.<br>> -----------------------------------------------------------------------------
<br>><br>> I have simply installed gromacs-3.3 on two nodes as per the procedure given<br>> on web.<br>><br>> Yet I didn't fing "lamboot" command. I have installed lam-7.0.6<br><br>The lamboot command (and the mpirun command you also need) should be in
<br>the directory where you installed lam (to be more specific: in the 'bin'<br>subdirectory). Put this in your path environment variable. You definitely<br>need to run 'lamboot' before you can do parallel mdruns. Then use
<br><br>mpirun -np 2 mdrun <your options><br><br>Good luck,<br> Carsten<br><br><br>---------------------------------------------------<br>Dr. Carsten Kutzner<br>Max Planck Institute for Biophysical Chemistry<br>Theoretical and Computational Biophysics Department
<br>Am Fassberg 11<br>37077 Goettingen, Germany<br>Tel. +49-551-2012313, Fax: +49-551-2012302<br>eMail <a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a><br><a href="http://www.gwdg.de/~ckutzne">http://www.gwdg.de/~ckutzne
</a><br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br>