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Re: pbs file for a workstation !

Alex Granovsky
gran@classic.chem.msu.su


Dear Masoud,

I think there should be

export NCPU=$(wc -l $PBS_NODEFILE)

rather than

export NCPU='wc -l $PBS_NODEFILE'

It seems that mpirun is looking for "-l" executable and this
is most likely caused by the wrong syntax.

Hope this helps.

All the best,
Alex Granovsky


On Wed May 8 '13 2:54am, Masoud Nahali wrote
--------------------------------------------
>Hi

>I have installed openmpi-1.4.5 (32 bit) and the ff8_rc_40_linux binary file is executable on my machine but I get the following error:

>--------------------------------------------------------------------------
>mpirun was unable to launch the specified application as it could not find an executable:

>Executable: -l
>Node: p005

>while attempting to start process rank 0.
>--------------------------------------------------------------------------

>the pbs file:
>
>
>#!/bin/bash
>#!bin/sh
>#PBS -q zebra
>#PBS -l nodes=2:ppn=8
>#PBS -l mem=500mb
>#PBS -l walltime=01:00:00

>export Looki=/u/cm/mnahali
>export INPUT=C8.inp
>export OUTPUT=C8.out
>export WORKDIR=$PBS_O_WORKDIR

>source /etc/profile.d/modules.sh
>module purge
>module load intel/11.1
>module load mkl/10.2
>
>
>export MPI=/u/cm/mnahali/openmpi-1.4.5

>export PATH=$PATH:$MPI/bin
>export PATH=$PATH:$Looki/ff8_rc_40_linux
>export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MPI/lib
>
>
>export FF_PATH=$Looki/ff8_rc40_linux
>export FF_LIB=$Looki/FF_LIB/BASIS.LIB
>export FF_TMP=$Looki/FF_TMP
>export NCPU='wc -l $PBS_NODEFILE'

>cd $PBS_O_WORKDIR

>$MPI/bin/mpirun -np $NCPU $FF_PATH/FF8 -f -r -p -stdext -ex $FF_PATH -i $WORKDIR\$INPUT -o $WORKDIR\$OUTPUT -b $FF_LIB -t $FF_TMP
>
>
>everything was loaded to be on the path but still the mpirun command cannot launch the binary file (FF8).
>I would appreciate for any comment on this problem. Many Thanks
>
>
>
>                                                                            Best Wishes, m

>                                                                        
>
>
>
>----------------------------------------
>Masoud Nahali
>SUT
>masoud.nahali@gmail.com
>alum.sharif.edu/~m_nahali
>
>
>
>


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