[Pw_forum] Pw_forum Digest, Vol 27, Issue 23
sreekar guddeti
colonel.sreekar at gmail.com
Sun Sep 6 20:05:26 CEST 2009
@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
-----------------------------
$find /usr/lib64 -name libgfortran*
-----------------------------
ouput is
_________________
/usr/lib64/libgfortran.so.3.0.0
/usr/lib64/libgfortran.so.1.0.0
/usr/lib64/libgfortran.so.1
find: /usr/lib64/audit: Permission denied
*/usr/lib64/libgfortran.so.3*
_________________
it means my OS has the required library, i guess
i installed the QE on the head node
This cluster is a Rocks cluster with
# of nodes: 10 (1 head node + 9 compute nodes)
# of processors/node: 8
# Total # of processors: 10X8 = 80
i tested the sample program for submitting batch jobs using SGE utility and
it is working fine(
http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html)
sincerely,
sreekar guddeti
Dept. Physics
IIT Bombay
India
On Sun, Sep 6, 2009 at 12:28 PM, <pw_forum-request at pwscf.org> wrote:
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> Today's Topics:
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> 1. Re: error loading shared libraries on parallel execution (Duy Le)
> 2. pw.x running but nothing happens (wangqj1)
> 3. Re: error loading shared libraries on parallel execution
> (Bipul Rakshit)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 5 Sep 2009 19:39:17 -0400
> From: Duy Le <ttduyle at gmail.com>
> Subject: Re: [Pw_forum] error loading shared libraries on parallel
> execution
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,I am not sure if this help. Could you please try to add
> #$ -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.
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> ------------------------------
>
> 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
>
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> ------------------------------
>
> 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
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>
> End of Pw_forum Digest, Vol 27, Issue 23
> ****************************************
>
--
Sreekar Guddeti
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