[Pw_forum] error loading shared libraries on parallel execution

Bipul Rakshit bipulrr at gmail.com
Sun Sep 6 08:58:49 CEST 2009


hi,
Just from root user type
yum install libgfortran.so.3

then it will install this files which is not present in your machine

On Sun, Sep 6, 2009 at 12:20 AM, 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
>
>


-- 
Dr. Bipul Rakshit
Research Associate,
S N Bose Centre for Basic Sciences,
Salt Lake,
Kolkata 700 098
India
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