[Pw_forum] error loading shared libraries on parallel execution

[Duy Le]

Hi,I am not sure if this help. Could you please try to add
#$ -V in your submitting script. Like this:

#!/bin/bash
#
#$ -V
#$ -cwd
#$ -j y
#$ -S /bin/bash
#

Good luck.
D.

On Sat, Sep 5, 2009 at 7:20 PM, sreekar guddeti
<colonel.sreekar at gmail.com>wrote:

> i know this issuehas been addressed and documented in troubleshooting
> section of the users guide.
> but i giveup in despair trying for a whole day to figure this problem
> i run my jobs on rocks cluster by using SGE's facility of submitting batch
> jobs
>
> http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html
>
> what i 'apparently' observe(or doubtfully infer) is that i can successfully
> run a single parallel job, but on submitting a second job i get the error
> ____________________________________________
> /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared
> libraries: libgfortran.so.3: cannot open shared object file: No such
> file or directory
> ____________________________________________
>
>
> i find out the path for the library and added to the LD_LIBRARY_PATH by
> writing
> _______________________________________
> #set the library path to include gfortran libraries
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
>
>
> $ECHO
> $ECHO "$LD_LIBRARY_PATH"
> $ECHO
> _______________________________________
>
> in the file which acts as script for qsub ($qsub -pe orte 4
> dosroutine.qsub) which is
>
> dosroutine.qsub
> -----------------------------------------------------------------
>
> #!/bin/bash
> #
> #$ -cwd
> #$ -j y
> #$ -S /bin/bash
> #
>
> #extract the info about no of processors involved from command line
> arguments of 'qsub'
> PROCESSORS=$NSLOTS
>
> #heuristically assign the no of processors per pool NPR
> NPR=4
> #as a result no of pools are give by
> NPK=`expr $PROCESSORS / $NPR`
>
> #!/bin/bash
> #
> #
> #Script for performing a dos calculation on a parallel processor
> WORKINGDIR=`pwd`
> ECHO="echo"
>
> #set the library path to include gfortran libraries
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
>
>
> $ECHO
> $ECHO "$LD_LIBRARY_PATH"
> $ECHO
>
> # set the needed environment variables
>
> PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd`
> $ECHO $PREFIX
> BIN_DIR=$PREFIX/bin
> PSEUDO_DIR=$PREFIX/pseudo
> TMP_DIR=$HOME/tmp
> PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS"
> PARA_POSTFIX="-npool $NPK"
>
> # required executables and pseudopotentials
> $ECHO
> $ECHO "  executables directory: $BIN_DIR"
> $ECHO "  pseudo directory:      $PSEUDO_DIR"
> $ECHO "  temporary directory:   $TMP_DIR"
>
> #create results directory
> for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do
>     if test ! -d $DIR ; then
>         mkdir $DIR
>     fi
> done
> cd $WORKINGDIR/results
>
>
> # variables to represent programs
> PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
> DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX"
> PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"
>
>
> # DOS calculation for 0Ni0
> cat > 0ni0.dos.in << EOF
>  &control
>     calculation='nscf'
>     restart_mode='from_scratch',
>     prefix='0ni0',
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/'
>  /
>  &system
>     ibrav=2, celldm(1) =6.48, nat=1, ntyp=1,
>     nspin = 2,  starting_magnetization(1)=0.7,
>     ecutwfc = 24.0, ecutrho = 288.0, nbnd=8,
>     occupations='tetrahedra'
>  /
>  &electrons
>     conv_thr = 1.0e-10
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Ni 58.69 NiUS.RRKJ3.UPF
> ATOMIC_POSITIONS
>  Ni 0.0 0.0 0.0
> K_POINTS {automatic}        !special points generated by tetrahedra method
>  12 12 12 0 0 0
> EOF
>
> $ECHO "  running DOS calculation for 0Ni0 ...\c"
> $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out
> $ECHO
> $ECHO "   done"
>
> -------------------------------------------------------------
>
> the output i get is
>
> ************************************************
> :/usr/lib64:/usr/lib
>
> /home3/colonel/espresso-4.0.5
>
>   executables directory: /home3/colonel/espresso-4.0.5/bin
>   pseudo directory:     /home3/colonel/espresso-4.0.5/pseudo
>   temporary directory:   /home3/colonel/tmp
>   running DOS calculation for 0Ni0 ...\c
> /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared
> libraries: libgfortran.so.3: cannot open shared object file: No such
> file or directory
> /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared
> libraries: libgfortran.so.3: cannot open shared object file: No such
> file or directory
> /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared
> libraries: libgfortran.so.3: cannot open shared object file: No such
> file or directory
> /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared
> libraries: libgfortran.so.3: cannot open shared object file: No such
> file or directory
>
>    done
> *************************************************
> plz suggest solutions which donot require root permissions , as i dont have
> thanks in advance
> --
> Sreekar Guddeti
> Department of Physics
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.
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