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Hi, I was having this same problem. I tried running like this:<br>
<br>
/opt/mpich/intel/bin/mpirun -v -np $NPROC
-machinefile \$TMPDIR/machines ~/gromacs-mpi/bin/mdrun -np $NPROC -s
$CONF -o $CONF -c After$CONF -e $CONF -g $CONF >& $CONF.job<br>
<br>
mpirun with the -v option (I'm not exactly sure what that does, but it
seemed to circumvent the problem). <br>
<br>
But then I got another problem. GMX seems to start up ok, but then
stalls. I just posted to the group about this, you should have it in
your inbox soon. <br>
<br>
If this helps, and you do get GMX running in parallel, please let me
know. <br>
<br>
thanks, <br>
<br>
Arneh <br>
<br>
Sridhar Acharya wrote:
<blockquote cite="mid44A0BC29.6010603@gmail.com" type="cite">
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<pre class="moz-signature" cols="72"><font color="#000000">Hi All,
I am facing a problem for parallel mdrun.
I tried to run in 2 nodes with the following command. The program reports that lamd is not running as follows.</font><font
color="#000000">
####################################################################################################
</font><font color="#000000">mpirun -np 2 /users/soft/GromacsSingle/bin/mdrun_mpi -s b4em_1CYP_WT.tpr -o em_1CYP_WT.trr -np 2
-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n0).
mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------
##################################################################################################
</font>
<font color="#000000">But lamd is very well running, because I could get the status of lam nodes with the "lamnodes" command.
</font><font color="#000000">########################################################################################
[msridhar@cdfd-grid-node17 WT_SINGLE_PARALLEL]$ lamnodes
n0 cdfd-grid-node2:1:
n1 cdfd-grid-node4:1:
n2 cdfd-grid-node12:1:
n3 cdfd-grid-node13:1:
n4 cdfd-grid-node14:1:
n5 cdfd-grid-node16:1:
n6 cdfd-grid-node17:1:origin,this_node
###########################################################################################
Do I have to define any paths so that it could recognise this?
Waiting for your suggessions.
sridhar
</font></pre>
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