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