@duy lee i inserted the line #$ -V in my qsub script and the env variable $LD_LIBRARY_PATH is being set from script... thanks for that but still problem persists.
@rakshit ----------------------------- $find /usr/lib -name libgfortran* ----------------------------- and output is _______________________ /usr/lib/libgfortran.so.1.0.0 /usr/lib/libgfortran.so.1 /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so _______________________ whereas on doing ----------------------------- $find /usr/lib64 -name libgfortran* ----------------------------- ouput is _________________ /usr/lib64/libgfortran.so.3.0.0 /usr/lib64/libgfortran.so.1.0.0 /usr/lib64/libgfortran.so.1 find: /usr/lib64/audit: Permission denied */usr/lib64/libgfortran.so.3* _________________ it means my OS has the required library, i guess i installed the QE on the head node This cluster is a Rocks cluster with # of nodes: 10 (1 head node + 9 compute nodes) # of processors/node: 8 # Total # of processors: 10X8 = 80 i tested the sample program for submitting batch jobs using SGE utility and it is working fine( http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html) sincerely, sreekar guddeti Dept. Physics IIT Bombay India On Sun, Sep 6, 2009 at 12:28 PM, <pw_forum-request at pwscf.org> wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: error loading shared libraries on parallel execution (Duy Le) > 2. pw.x running but nothing happens (wangqj1) > 3. Re: error loading shared libraries on parallel execution > (Bipul Rakshit) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 5 Sep 2009 19:39:17 -0400 > From: Duy Le <ttduyle at gmail.com> > Subject: Re: [Pw_forum] error loading shared libraries on parallel > execution > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi,I am not sure if this help. Could you please try to add > #$ -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. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Sun, 6 Sep 2009 08:33:25 +0800 (CST) > From: wangqj1 <wangqj1 at 126.com> > Subject: [Pw_forum] pw.x running but nothing happens > To: pw_forum <pw_forum at pwscf.org> > Message-ID: > <25470012.218281252197205181.JavaMail.coremail at bj126app52.126.com> > Content-Type: text/plain; charset="gbk" > > > Dear pwscf users > When I run vc-relax on the computing cluster use one node which has 8 > CPUs. > The output file is as following: > > Program PWSCF v.4.0.1 starts ... > Today is 6Sep2009 at 7:49:30 > Parallel version (MPI) > Number of processors in use: 8 > R & G space division: proc/pool = 8 > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > ..................................................................... > Initial potential from superposition of free atoms > starting charge 435.99565, renormalised to 436.00000 > Starting wfc are 254 atomic + 8 random wfc > > After one day ,it still like this and no iteration has completed ,there is > also no error was turn up .There is no error in the input file because I > have test it on anthoer computer which has 4 CPUs and it runs well . > I can't find the reason about this ,any help will be appreciated . > Best Regards > Q.J.Wang > XiangTan University > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Sun, 6 Sep 2009 07:58:49 +0100 > From: Bipul Rakshit <bipulrr at gmail.com> > Subject: Re: [Pw_forum] error loading shared libraries on parallel > execution > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <3a749910909052358m6f23c3sf5bdbba1b595d8d5 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/d919f229/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 23 > **************************************** > -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... 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