Hi lina, 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.
My cluster has LSF, I use following command to submit job- $ 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 On Tue, May 3, 2011 at 6:38 PM, lina <lina.lastn...@gmail.com> wrote: > Hi, > > I don't know the specific cluster you mentioned. > > but when I met such problems, I used to check the .log which usually > gave me very helpful information. > and I used to use some script to submit job, > > I post one as example, please set the proper one according to your cluster. > > more openmpi_parallel.sh > #!/bin/bash > #PBS -N jobname > #PBS -j oe > #PBS -V > > #PBS -l nodes=2:ppn=8 > > ## pre-processing script > cd $PBS_O_WORKDIR > NCPUS=`cat $PBS_NODEFILE | wc -l` > echo $NCPUS > > # ########################################### > # PATH for Intel Compiler and OpenMPI > # ############################################ > export > PATH=/opt/intel/composerxe-2011.2.137/bin/intel64:/usr/local/mpi/intel/bi > n:/usr/local/fftw/bin:/usr/local/gromacs/bin:i${PATH} > > export > LD_LIBRARY_PATH=/usr/local/fftw/lib:/opt/intel/composerxe-2011.2.137/mkl/ > > lib/intel64:/opt/intel/lib/intel64:/usr/local/mpi/intel/lib:${LD_LIBRARY_PATH} > > # ################################ > # commands to launch OpenMPI jobs > # ################################ > /usr/local/mpi/intel/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE > $PBS_O_WOR > KDIR/$file > > > # ############################# > # PATH for GNU Compiler and OpenMPI > # ############################## > # export > PATH=/usr/local/mpi/gnu/bin:/usr/local/fftw/bin:/usr/local/gromacs/bin: > ${PATH} > # export LD_LIBRARY_PATH=/usr/local/fftw/lib:/usr/lib64:${LD_LIBRARY_PATH} > > # ############################## > # Using GNU Compiler and OpenMPI > # ############################## > # /usr/local/mpi/gnu/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE > $PBS_O_WOR > KDIR/$file > > # ######################################### > # Optional LD_LIBRARY_PATH if not using MKL > # ######################################### > # export LD_LIBRARY_PATH=/usr/local/atlas/lib:${LD_LIBRARY_PATH} > # export LD_LIBRARY_PATH=/usr/local/blacs/lib:${LD_LIBRARY_PATH} > # export LD_LIBRARY_PATH=/usr/local/lapack/lib:${LD_LIBRARY_PATH} > # export LD_LIBRARY_PATH=/usr/local/salapack/lib:${LD_LIBRARY_PATH} > > > You are welcome, > > > -- > Best Regards, > > lina > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Bharati Singh System Administrator Centre for Computational Materials Science(CCMS) Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR), Bangalore - 560 064 India. mob. : 08970898515 Phone : +91 80 2208 2944 + Ext. 26 & 28 Fax : +91 80 2208 2906 Email : bharati_si...@jncasr.ac.in <a...@jncasr.ac.in> http://www.jncasr.ac.in/ccms http://www.jncasr.ac.in/
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists