<DIV>Dear Lorenzo</DIV>
<DIV>I now use 16 CPUs(2 nodes) to run the task ,the job runs but very slower than use 4 CPUs in my personal computer ,I use top to look CPU information,it as following:</DIV>
<DIV> </DIV>
<DIV>Tasks: 176 total, 1 running, 175 sleeping, 0 stopped, 0 zombie<BR>Cpu0 : 0.4%us, 0.4%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st<BR>Cpu1 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st<BR>Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st<BR>Cpu3 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st<BR>Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st<BR>Cpu5 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st<BR>Cpu6 : 0.7%us, 0.0%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st<BR>Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st<BR>Mem: 8048812k total, 5537848k used, 2510964k free, 315448k buffers<BR>Swap: 4192956k total, 0k used, 4192956k free, 5022856k cached</DIV>
<DIV><BR>Why only display 8 CPUs information and the usage of CPU is so small ? </DIV>
<DIV> </DIV>
<DIV>Best regards</DIV>
<DIV>Q.J.Wang</DIV>
<DIV>XiangTan University<BR><BR></DIV>
<DIV></DIV><BR><PRE>在2009-09-07 02:05:35，pw_forum-request@pwscf.org 写道：
>Send Pw_forum mailing list submissions to
> pw_forum@pwscf.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
> http://www.democritos.it/mailman/listinfo/pw_forum
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>
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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@gmail.com>
>Subject: Re: [Pw_forum] pw.x running but nothing happens
>To: PWSCF Forum <pw_forum@pwscf.org>
>Message-ID:
> <3a749910909060003k38e7f62fn4aa040900b71b42c@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@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@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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>------------------------------
>
>Message: 2
>Date: Sun, 6 Sep 2009 11:25:06 +0330
>From: Mansoureh Pashangpour <mansourehp@gmail.com>
>Subject: [Pw_forum] pseudo potential
>To: PWSCF Forum <pw_forum@pwscf.org>
>Message-ID:
> <cbe1626b0909060055o66690789yc0ae02efdfa5391e@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@democritos.it>
>Subject: Re: [Pw_forum] error loading shared libraries on parallel
> execution
>To: PWSCF Forum <pw_forum@pwscf.org>
>Message-ID: <E6918F77-0C97-4F26-9F7E-BE790E9EFC6B@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@sissa.it>
>Subject: Re: [Pw_forum] pw.x running but nothing happens
>To: "PWSCF Forum" <pw_forum@pwscf.org>
>Message-ID: <46134.78.12.159.112.1252232440.squirrel@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/
>
>
>
>----------------------------------------------------------------
> 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@gmail.com>
>Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 23
>To: pw_forum@pwscf.org
>Message-ID:
> <c864e4460909061105i43b1885dh6141b2789b8ae51@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@pwscf.org> wrote:
>
>> Send Pw_forum mailing list submissions to
>> pw_forum@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@pwscf.org
>>
>> You can reach the person managing the list at
>> pw_forum-owner@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@gmail.com>
>> Subject: Re: [Pw_forum] error loading shared libraries on parallel
>> execution
>> To: PWSCF Forum <pw_forum@pwscf.org>
>> Message-ID:
>> <8974d3b20909051639u575aed19xdf474c53f9a7d877@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@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@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@126.com>
>> Subject: [Pw_forum] pw.x running but nothing happens
>> To: pw_forum <pw_forum@pwscf.org>
>> Message-ID:
>> <25470012.218281252197205181.JavaMail.coremail@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@gmail.com>
>> Subject: Re: [Pw_forum] error loading shared libraries on parallel
>> execution
>> To: PWSCF Forum <pw_forum@pwscf.org>
>> Message-ID: <3a749910909052358m6f23c3sf5bdbba1b595d8d5@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@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@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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>>
>
>
>
>--
>Sreekar Guddeti
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