[Pw_forum] Pw_forum Digest, Vol 27, Issue 24
sreekar guddeti
colonel.sreekar at gmail.com
Mon Sep 7 01:53:12 CEST 2009
i have set variable LD_FLAGS = static in make.sys file
and on $make all
i get error
----------------------------------------
libiotk.a
mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW
-D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW
-I../PH -c iotk_print_kinds.f90
make loclib_only
make[3]: Entering directory `/home3/colonel/espresso-4.0.5/iotk/src'
make[3]: Nothing to be done for `loclib_only'.
make[3]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src'
mpif90 -static -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a
/opt/openmpi/lib/libopen-pal.a(dlopen.o): In function `vm_open':
(.text+0x123): warning: Using 'dlopen' in statically linked applications
requires at runtime the shared libraries from the glibc version used for
linking
/opt/openmpi/lib/libopen-rte.a(sys_info.o): In function `orte_sys_info':
(.text+0x16f): warning: Using 'getpwuid' in statically linked applications
requires at runtime the shared libraries from the glibc version used for
linking
/opt/openmpi/lib/libopen-pal.a(if.o): In function `opal_ifaddrtoname':
(.text+0x780): warning: Using 'gethostbyname' in statically linked
applications requires at runtime the shared libraries from the glibc version
used for linking
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):
In function `__malloc_check_init':
(.text+0x1060): multiple definition of `__malloc_check_init'
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3a0): first defined
here
/usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from 144
in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 105 in
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):
In function `_int_free':
(.text+0x2230): multiple definition of `_int_free'
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1030): first defined
here
/usr/bin/ld: Warning: size of symbol `_int_free' changed from 1219 in
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 2080 in
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):
In function `_int_malloc':
(.text+0x2a50): multiple definition of `_int_malloc'
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x18c0): first defined
here
/usr/bin/ld: Warning: size of symbol `_int_malloc' changed from 3916 in
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 3754 in
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):
In function `_int_memalign':
(.text+0x3900): multiple definition of `_int_memalign'
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2d40): first defined
here
/usr/bin/ld: Warning: size of symbol `_int_memalign' changed from 577 in
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 550 in
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):
In function `_int_valloc':
(.text+0x3c30): multiple definition of `_int_valloc'
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2f90): first defined
here
/usr/bin/ld: Warning: size of symbol `_int_valloc' changed from 378 in
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 62 in
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):
In function `_int_realloc':
(.text+0x3d80): multiple definition of `_int_realloc'
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3180): first defined
here
/usr/bin/ld: Warning: size of symbol `_int_realloc' changed from 875 in
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1411 in
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):
In function `free':
(.text+0x5f20): multiple definition of `free'
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1500): first defined
here
/usr/bin/ld: Warning: size of symbol `free' changed from 256 in
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 454 in
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):
In function `malloc':
(.text+0x4690): multiple definition of `malloc'
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3830): first defined
here
/usr/bin/ld: Warning: size of symbol `malloc' changed from 363 in
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 466 in
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):
In function `realloc':
(.text+0x60f0): multiple definition of `realloc'
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3bc0): first defined
here
/usr/bin/ld: Warning: size of symbol `realloc' changed from 490 in
/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1184 in
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)
collect2: ld returned 1 exit status
make[2]: *** [iotk_print_kinds.x] Error 1
make[2]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src'
make[1]: *** [lib+util] Error 2
make[1]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk'
make: *** [libiotk] Error 2
---------------------------------------------
sincerely
On Sun, Sep 6, 2009 at 11:35 PM, <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
> 1. Re: pw.x running but nothing happens (Bipul Rakshit)
> 2. pseudo potential (Mansoureh Pashangpour)
> 3. Re: error loading shared libraries on parallel execution
> (Paolo Giannozzi)
> 4. Re: pw.x running but nothing happens (Lorenzo Paulatto)
> 5. Re: Pw_forum Digest, Vol 27, Issue 23 (sreekar guddeti)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 6 Sep 2009 08:03:29 +0100
> From: Bipul Rakshit <bipulrr at gmail.com>
> Subject: Re: [Pw_forum] pw.x running but nothing happens
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <3a749910909060003k38e7f62fn4aa040900b71b42c at mail.gmail.com>
> Content-Type: text/plain; charset="gb2312"
>
> Dear Wangqj,
> The same thing happens to me.
> since you are using large no. of wfc, although it shows the job is running
> in 8 procs, but sometimes if the installation is not proper, it is running
> in 1 procs only.
>
> So better you check the parallel installation using a small job, with
> different no. of procs and see whether its taking lesser time as no. of
> procs increases or not?
>
> cheers
>
> 2009/9/6 wangqj1 <wangqj1 at 126.com>
>
> >
> > 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
> >
> >
> >
> > ------------------------------
> > ???????????,www.yeah.net <http://www.yeah.net/?from=footer>
> > _______________________________________________
> > 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 --------------
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>
> ------------------------------
>
> Message: 2
> Date: Sun, 6 Sep 2009 11:25:06 +0330
> From: Mansoureh Pashangpour <mansourehp at gmail.com>
> Subject: [Pw_forum] pseudo potential
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <cbe1626b0909060055o66690789yc0ae02efdfa5391e at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all
> how can I plot these pseudo potentials? how can I discribe the properties
> of pseudo potentials?
>
> *Fe.pbe-nd-rrkjus.UPF*<
> http://www.pwscf.org/pseudo/1.3/UPF/Fe.pbe-nd-rrkjus.UPF>
> (
> *details*<
> http://www.pwscf.org/pseudo/upfdetails.php?upf=Fe.pbe-nd-rrkjus.UPF>)
>
>
> Perdew-Burke-Ernzerhof (PBE) exch-corr
> nonlinear core-correction
> semicore state d in valence
> Rabe Rappe Kaxiras Joannopoulos (ultrasoft)
>
> and
>
> *H.pbe-rrkjus.UPF* <http://www.pwscf.org/pseudo/1.3/UPF/H.pbe-rrkjus.UPF>
> (*details* <
> http://www.pwscf.org/pseudo/upfdetails.php?upf=H.pbe-rrkjus.UPF>)
>
>
> Perdew-Burke-Ernzerhof (PBE) exch-corr
> Rabe Rappe Kaxiras Joannopoulos (ultrasoft)
>
>
> and
>
> *O.pbe-rrkjus.UPF*
> <http://www.pwscf.org/pseudo/1.3/UPF/O.pbe-rrkjus.UPF> (*details*
> <http://www.pwscf.org/pseudo/upfdetails.php?upf=O.pbe-rrkjus.UPF>)
>
> Perdew-Burke-Ernzerhof (PBE) exch-corr
> Rabe Rappe Kaxiras Joannopoulos (ultrasoft)
>
>
> Thanks
> Mansoureh Pashangpour
> Ph.D student
> Islami Azad university
> science & reaserch branch
> Tehran, IRAN
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> ------------------------------
>
> Message: 3
> Date: Sun, 6 Sep 2009 10:24:48 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] error loading shared libraries on parallel
> execution
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <E6918F77-0C97-4F26-9F7E-BE790E9EFC6B at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>
> On Sep 6, 2009, at 1:20 , sreekar guddeti wrote:
>
> > plz suggest solutions which donot require root permissions ,
> > as i dont have
>
> somebody must have it. Report the problem and the
> solution (i.e. install gfortran on ALL processors) to
> whoever has root access. As an alternative, try static
> link (add -static to LDFLAGS in make.sys).
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 6 Sep 2009 12:20:40 +0200 (CEST)
> From: "Lorenzo Paulatto" <paulatto at sissa.it>
> Subject: Re: [Pw_forum] pw.x running but nothing happens
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <46134.78.12.159.112.1252232440.squirrel at webmail.sissa.it>
> Content-Type: text/plain;charset=iso-8859-1
>
>
> On Sun, September 6, 2009 02:33, wangqj1 wrote:
> > 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 .
>
>
> Dear QJ,
> this is strange. But we would need more information on your hardwre
> configuration in order to help you. In the mean while you can check the
> behaviour of te pw.x processes with "top". E.g. if they are all runing at
> 100% CPU, how much memory they are taking and so on.
>
> regards
>
>
> --
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www: http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
>
>
> ----------------------------------------------------------------
> SISSA Webmail https://webmail.sissa.it/
> Powered by SquirrelMail http://www.squirrelmail.org/
>
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 6 Sep 2009 23:35:26 +0530
> From: sreekar guddeti <colonel.sreekar at gmail.com>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 23
> To: pw_forum at pwscf.org
> Message-ID:
> <c864e4460909061105i43b1885dh6141b2789b8ae51 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> @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 --------------
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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
> >
> > -------------- next part --------------
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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
> > -------------- next part --------------
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> > ------------------------------
> >
> > _______________________________________________
> > 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
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> ------------------------------
>
> _______________________________________________
> 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 24
> ****************************************
>
--
Sreekar Guddeti
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