[gmx-users] running job parallel

[Bharati Singh]

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.lastname at 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
> --
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-- 
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_singh at jncasr.ac.in <amit at jncasr.ac.in>


http://www.jncasr.ac.in/ccms
http://www.jncasr.ac.in/
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