Hi lina,<br><br>As you have given, Is it needed to set LD_LIBRARY_PATH ? I had loaded module for mpi and set LDFLAGS, CPPFLAGS ,at the time of installation.<br><br>My cluster has LSF, I use following command to submit job-<br>
<br>$ <font face="arial">bsub -q <queue_name> -n <no_of_core> mpirun -srun
/sfs3/home/bharati/gromacs/bin/mdrun -pd -v -s Ag6A12_equil.tpr
-o Ag6A12_equil.trr -c Ag6A12_equil.gro -e Ag6A12_equil.edr -g
Ag6A12_equil.log<br>
</font><br><br><br><div class="gmail_quote">On Tue, May 3, 2011 at 6:38 PM, lina <span dir="ltr"><<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br>
I don't know the specific cluster you mentioned.<br>
<br>
but when I met such problems, I used to check the .log which usually<br>
gave me very helpful information.<br>
and I used to use some script to submit job,<br>
<br>
I post one as example, please set the proper one according to your cluster.<br>
<br>
more openmpi_parallel.sh<br>
#!/bin/bash<br>
#PBS -N jobname<br>
#PBS -j oe<br>
#PBS -V<br>
<br>
#PBS -l nodes=2:ppn=8<br>
<br>
## pre-processing script<br>
cd $PBS_O_WORKDIR<br>
NCPUS=`cat $PBS_NODEFILE | wc -l`<br>
echo $NCPUS<br>
<br>
# ###########################################<br>
# PATH for Intel Compiler and OpenMPI<br>
# ############################################<br>
export PATH=/opt/intel/composerxe-2011.2.137/bin/intel64:/usr/local/mpi/intel/bi<br>
n:/usr/local/fftw/bin:/usr/local/gromacs/bin:i${PATH}<br>
<br>
export LD_LIBRARY_PATH=/usr/local/fftw/lib:/opt/intel/composerxe-2011.2.137/mkl/<br>
lib/intel64:/opt/intel/lib/intel64:/usr/local/mpi/intel/lib:${LD_LIBRARY_PATH}<br>
<br>
# ################################<br>
# commands to launch OpenMPI jobs<br>
# ################################<br>
/usr/local/mpi/intel/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE $PBS_O_WOR<br>
KDIR/$file<br>
<br>
<br>
# #############################<br>
# PATH for GNU Compiler and OpenMPI<br>
# ##############################<br>
# export PATH=/usr/local/mpi/gnu/bin:/usr/local/fftw/bin:/usr/local/gromacs/bin:<br>
${PATH}<br>
# export LD_LIBRARY_PATH=/usr/local/fftw/lib:/usr/lib64:${LD_LIBRARY_PATH}<br>
<br>
# ##############################<br>
# Using GNU Compiler and OpenMPI<br>
# ##############################<br>
# /usr/local/mpi/gnu/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE $PBS_O_WOR<br>
KDIR/$file<br>
<br>
# #########################################<br>
# Optional LD_LIBRARY_PATH if not using MKL<br>
# #########################################<br>
# export LD_LIBRARY_PATH=/usr/local/atlas/lib:${LD_LIBRARY_PATH}<br>
# export LD_LIBRARY_PATH=/usr/local/blacs/lib:${LD_LIBRARY_PATH}<br>
# export LD_LIBRARY_PATH=/usr/local/lapack/lib:${LD_LIBRARY_PATH}<br>
# export LD_LIBRARY_PATH=/usr/local/salapack/lib:${LD_LIBRARY_PATH}<br>
<br>
<br>
You are welcome,<br>
<br>
<br>
--<br>
Best Regards,<br>
<br>
lina<br>
<font color="#888888">--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharati Singh<br>System Administrator<br>Centre for Computational Materials Science(CCMS)<br>Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),<br>
Bangalore - 560 064 <br>
India.<br>mob. : 08970898515<br>Phone : +91 80 2208 2944 + Ext. 26 & 28<br>Fax : +91 80 2208 2906<br>Email : <a href="mailto:amit@jncasr.ac.in" target="_blank">bharati_singh@jncasr.ac.in</a><br><br><br><a href="http://www.jncasr.ac.in/ccms" target="_blank">http://www.jncasr.ac.in/ccms</a><br>
<a href="http://www.jncasr.ac.in/" target="_blank">http://www.jncasr.ac.in/</a><br>