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Re^2: pbs file for a workstation !

Masoud Nahali
masoudnahali@gmail.com


Dear Alex

Many thanks for your help and kind attentions as always. Now I am writing since it would be be useful for others that may experience such issues. I have revised the line about NCPU and it is fine right now. Also I had some typos that were revised. The "export INPUT=$JOB.inp" and the related lines were replaced by "export FINPUT=$JOB.inp" ! it may seem strange but when I used "export INPUT=$JOB.inp" Firefly was looking for a input file called "INPUT" ! but the input name is C8.inp. After renaming the INPUT=... Firefly can find my input file which called C8.inp. I hope the following script can be useful to whom they may use a workstation with Linux OS.

Happy World Migratory Bird Day (11-12 May) :)

Best Wishes
Masoud  


----------------------------------------------------------------------------------------------
#!/bin/bash

#PBS -q nehalem
#PBS -l nodes=2:ppn=8
#PBS -l mem=4000mb
#PBS -l walltime=01:00:00

cd $PBS_O_WORKDIR

export Looki=/u/cm/mnahali
export JOB=C8
export FINPUT=$JOB.inp
export FOUTPUT=$JOB.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 | awk '{print $1}')



$MPI/bin/mpirun -np $NCPU $FF_PATH/FF8 -f -r -p -stdext -ex $FF_PATH -i $WORKDIR/$FINPUT -o $WORKDIR/$FOUTPUT -b $FF_LIB -t $FF_TMP
--------------------------------------------------------------------------------------------------------


 




On Fri May 10 '13 9:06pm, Alex Granovsky wrote
----------------------------------------------
>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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