Dear Lorenzo 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: Tasks: 176 total, 1 running, 175 sleeping, 0 stopped, 0 zombie 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 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 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 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 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 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 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 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 Mem: 8048812k total, 5537848k used, 2510964k free, 315448k buffers Swap: 4192956k total, 0k used, 4192956k free, 5022856k cached
Why only display 8 CPUs information and the usage of CPU is so small ? Best regards Q.J.Wang XiangTan University ?2009-09-07?02:05:35?pw_forum-request at pwscf.org???? >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:?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?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm? > >------------------------------ > >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 >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm? > >------------------------------ > >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/ > > > >---------------------------------------------------------------- >??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?-------------- >>?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... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/b1909ffa/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?24 >**************************************** -------------- next part -------------- An HTML attachment was scrubbed... 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