[Pw_forum] Pw_forum Digest, Vol 27, Issue 82
Q.J.Wang
wangqj1 at 126.com
Fri Sep 25 17:01:28 CEST 2009
Thank you very much Lorenzo Paulatto and Gabriele Sclauzero .
The problem was solved ,because I specified same prefix for the two tasks .
But another problem turn up . When I use R & G space division run the task ,it was interrupted at the 2 iteration of 18 time of vc-relax and turns up as following :
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
pw.x 40000000005D8710 Unknown Unknown
Unknown
pw.x 40000000005D8BF0 Unknown Unknown
Unknown
pw.x 40000000005F4A40 Unknown Unknown
Unknown
pw.x 400000000003C740 Unknown Unknown
I use 1 node(8 CPUs) on the cluster . I am puzzled by the phenomena ,please give me some advice about this problem ,thank you .
--
Best regards
Q.J.Wang
XiangTan University
在2009-09-25?22:26:04，pw_forum-request at pwscf.org?写道：
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>Today's?Topics:
>
>???1.?Re:?problem?in?phonon?in?prallel?(dev?sharma)
>???2.?Re:?problem?in?phonon?in?prallel?(Paolo?Giannozzi)
>???3.?Running?on?cluster?often?turn?up?(Q.J.Wang)
>???4.?Re:?Running?on?cluster?often?turn?up?(Giovanni?Cantele)
>???5.?about?OMP_NUM_THREADS?(Q.J.Wang)
>???6.?Re:?about?OMP_NUM_THREADS?(Lorenzo?Paulatto)
>???7.?Re:?about?OMP_NUM_THREADS?(Gabriele?Sclauzero)
>???8.?About?example?22?(xirainbow)
>
>
>----------------------------------------------------------------------
>
>Message:?1
>Date:?Fri,?25?Sep?2009?13:46:44?+0530
>From:?dev?sharma?<decboy9 at gmail.com>
>Subject:?Re:?[Pw_forum]?problem?in?phonon?in?prallel
>To:?PWSCF?Forum?<pw_forum at pwscf.org>
>Message-ID:
> <a591fe200909250116g7a121b6ave4460eadd70c179f at mail.gmail.com>
>Content-Type:?text/plain;?charset="iso-8859-1"
>
>Hi,
>
>?when?i?am?running?the?same?file?with?the?following?inputs?,?it?is?running
>well
>
>phonons?at?gamma
>?&inputph
>??tr2_ph=1.0e-10,
>??prefix='yvo',
>??trans=.false.,
>??epsil=.true.,
>??amass(1)=?44.995,
>??amass(2)=?50.9415,
>??amass(3)=15.9994,
>??outdir?=?'/home/devsharma/work/newscvo/temp',
>??fildyn='yvo.dyn1',
>?/
>0.0?0.0?0.0
>
>means?there?is?some?problem?in?inputs.?Any?comment?on?the?extra?parameters?i
>gave?in?previous?file?i.e.?fpol?and?elop.
>
>Thanks
>sincerly,
>Dev?Sharma,
>University??of?Delhi,
>~
>
>
>~
>On?Fri,?Sep?25,?2009?at?11:03?AM,?dev?sharma?<decboy9 at gmail.com>?wrote:
>
>>?hi?2?all,
>>??i?have?done?scf?,?phonon??and?the?running?ph.x?in?parallel?for?some
>>?optical?properties.?my?programme?stops?without?giving?any?error?in?the
>>?ph.out?file?and?without?any?CRASH.?My?input?file?is?listed?below.?Please
>>?help.
>>?Thanks?in?advance.
>>?phonons?at?gamma
>>??&inputph
>>???tr2_ph=1.0e-10,
>>???prefix='yvo',
>>????fpol=.true.,
>>????trans=.false.,
>>???epsil=.true.,
>>???elop=.true.,
>>???amass(1)=?44.995,
>>???amass(2)=?50.9415,
>>???amass(3)=15.9994,
>>???outdir?=?'/home/devsharma/work/newscvo/temp',
>>???fildyn='yvo.dyn1',
>>??/
>>?0.0?0.0?0.0
>>
>>?FREQUENCIES
>>?65
>>?7.889e+14
>>?/
>>?/
>>?4.389e+14
>>
>>?and?mssg?in?terminal?is?coming
>>
>>?[devsharma at headnode?newscvo]$?[headnode.du.ac.in:6309]?***?An?error
>>?occurred?in?MPI_Allreduce
>>?[headnode.du.ac.in:6309]?***?on?communicator?MPI?COMMUNICATOR?28?SPLIT
>>?FROM?4
>>?[headnode.du.ac.in:6309]?***?MPI_ERR_TRUNCATE:?message?truncated
>>?[headnode.du.ac.in:6309]?***?MPI_ERRORS_ARE_FATAL?(your?MPI?job?will?now
>>?abort)
>>?--------------------------------------------------------------------------
>>?mpirun?has?exited?due?to?process?rank?1?with?PID?6309?on
>>?node?headnode.du.ac.in?exiting?without?calling?"finalize".?This?may
>>?have?caused?other?processes?in?the?application?to?be
>>?terminated?by?signals?sent?by?mpirun?(as?reported?here).
>>
>>?----------------------------------------------------------
>>?and?the?output?file?runs?upto
>>
>>
>>??Representation????52??????1?modes?-?To?be?done
>>??????PHONON???????:??0m41.95s?CPU?time,?????2m31.11s?wall?time
>>
>>
>>??????Alpha?used?in?Ewald?sum?=???1.0000
>>
>>??????Frequency?Dependent?Polarizability?Calculation
>>
>>?and?after?here?it?stops.
>>
>>
>>?Please?help,
>>
>>?sincerly,
>>?Dev?Sharma,
>>?Univeristy?of?Delhi
>>
>>
>>
>--------------?next?part?--------------
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>
>------------------------------
>
>Message:?2
>Date:?Fri,?25?Sep?2009?10:18:39?+0200
>From:?Paolo?Giannozzi?<giannozz at democritos.it>
>Subject:?Re:?[Pw_forum]?problem?in?phonon?in?prallel
>To:?PWSCF?Forum?<pw_forum at pwscf.org>
>Message-ID:?<4ABC7CDF.2050209 at democritos.it>
>Content-Type:?text/plain;?charset=ISO-8859-1;?format=flowed
>
>dev?sharma?wrote:
>
>>?Any?comment?on?the?extra?
>>?parameters?i?gave?in?previous?file?i.e.?fpol?and?elop.
>
>don't?give?any?extra?parameters?unless?you?know?what?they?do,
>and?unless?you?need?them
>
>P.
>--?
>Paolo?Giannozzi,?Democritos?and?University?of?Udine,?Italy
>
>
>------------------------------
>
>Message:?3
>Date:?Fri,?25?Sep?2009?21:02:50?+0800?(CST)
>From:?"Q.J.Wang"?<wangqj1 at 126.com>
>Subject:?[Pw_forum]?Running?on?cluster?often?turn?up
>To:?pw_forum?<pw_forum at pwscf.org>
>Message-ID:
> <10083410.509721253883770555.JavaMail.coremail at bj126app104.126.com>
>Content-Type:?text/plain;?charset="gbk"
>
>Dear?all
>?????When?I?running?on?cluster?,it?often?turn?up?some?bizarre?errors?,which?not?turn?up?ong?single?computer?.I?don't?know?why?.Whether?is?it?because?the?computing?environment?settings???I?don'?know?how?to?do?.Plese?help?me?.
>
>--
>
>Best?regards
>?
>Q.J.Wang
>?
>XiangTan?University?
>--------------?next?part?--------------
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>
>------------------------------
>
>Message:?4
>Date:?Fri,?25?Sep?2009?15:08:14?+0200
>From:?Giovanni?Cantele?<Giovanni.Cantele at na.infn.it>
>Subject:?Re:?[Pw_forum]?Running?on?cluster?often?turn?up
>To:?PWSCF?Forum?<pw_forum at pwscf.org>
>Message-ID:?<4ABCC0BE.40302 at na.infn.it>
>Content-Type:?text/plain;?charset=x-gbk;?format=flowed
>
>Q.J.Wang?wrote:
>>?Dear?all
>>?When?I?running?on?cluster?,it?often?turn?up?some?bizarre?errors?,which?
>>?not?turn?up?ong?single?computer?.I?don't?know?why?.Whether?is?it?
>>?because?the?computing?environment?settings???I?don'?know?how?to?do?
>>?.Plese?help?me?.
>>
>Well,?I?think?that?it?will?be?rather?difficult?for?anybody?to?answer?
>unless?you?provide?much?more
>extensive?information?than?you?did.
>
>Which?kind?of?errors??Parallel?or?serial?runs?
>
>Some?issues?might?be?related?to?your?cluster?configuration?/?hardware?/?
>software?rather?than?to?the?Quantum-ESPRESSO.
>
>You?can?also?try?to?search?the?forum?to?find?if?some?of?these?errors?
>have?been?ever?discussed?before.
>
>Giovanni
>
>--?
>
>
>
>Dr.?Giovanni?Cantele
>Coherentia?CNR-INFM?and?Dipartimento?di?Scienze?Fisiche
>Universita'?di?Napoli?"Federico?II"
>Complesso?Universitario?di?Monte?S.?Angelo?-?Ed.?6
>Via?Cintia,?I-80126,?Napoli,?Italy
>Phone:?+39?081?676910
>Fax:???+39?081?676346
>E-mail:?giovanni.cantele at cnr.it
>????????giovanni.cantele at na.infn.it
>Web:?http://people.na.infn.it/~cantele
>Research?Group:?http://www.nanomat.unina.it
>Skype?contact:?giocan74
>
>
>
>------------------------------
>
>Message:?5
>Date:?Fri,?25?Sep?2009?21:41:03?+0800?(CST)
>From:?"Q.J.Wang"?<wangqj1 at 126.com>
>Subject:?[Pw_forum]?about?OMP_NUM_THREADS
>To:?pw_forum?<pw_forum at pwscf.org>
>Message-ID:
> <12872053.521841253886063499.JavaMail.coremail at bj126app104.126.com>
>Content-Type:?text/plain;?charset="gbk"
>
>Dear?all
>?????According?to?the?advice?of?the?forum,I?added?OMP_NUM_THREADS=1?in?my?PBS?script?.But?I?can?only?run?a?task?on?the?cluster?.When?one?was?running?,I?run?another?task?,and?one?of?them?will?turn?up?error?and?stop?.
>
>
>
>--
>
>Best?regards
>?
>Q.J.Wang
>?
>XiangTan?University?
>--------------?next?part?--------------
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>
>------------------------------
>
>Message:?6
>Date:?Fri,?25?Sep?2009?15:45:13?+0200
>From:?"Lorenzo?Paulatto"?<paulatto at sissa.it>
>Subject:?Re:?[Pw_forum]?about?OMP_NUM_THREADS
>To:?"PWSCF?Forum"?<pw_forum at pwscf.org>
>Message-ID:?<op.u0te5nn5a8x26q at paulax>
>Content-Type:?text/plain;?charset=utf-8;?format=flowed;?delsp=yes
>
>In?data?25?settembre?2009?alle?ore?15:41:03,?Q.J.Wang?<wangqj1 at 126.com>?ha??
>scritto:
>>??????According?to?the?advice?of?the?forum,I?added?OMP_NUM_THREADS=1?in??
>>?my?PBS?script?.But?I?can?only?run?a?task?on?the?cluster?.When?one?was??
>>?running?,I?run?another?task?,and?one?of?them?will?turn?up?error?and?stop
>
>Dear?Q.J.?Wang,
>as?usual,?you?MUST?provide?the?error?message?and?as?many?details?as??
>possible?on?how?you?run?the?job,?there?is?very?little?we?can?say?about?you??
>problem?with?any?information.
>
>To?begin?you?should?check?that?the?jobs?do?not?have?the?same?prefix?and??
>outdir,?if?it?is?the?case?they?will?crash?after?a?while.
>
>best?regards
>
>
>--?
>Lorenzo?Paulatto
>SISSA??&??DEMOCRITOS?(Trieste)
>phone:?+39?040?3787?511
>skype:?paulatz
>www:???http://people.sissa.it/~paulatto/
>
>?????***?save?italian?brains?***
>??http://saveitalianbrains.wordpress.com/
>
>
>------------------------------
>
>Message:?7
>Date:?Fri,?25?Sep?2009?15:45:54?+0200
>From:?Gabriele?Sclauzero?<sclauzer at sissa.it>
>Subject:?Re:?[Pw_forum]?about?OMP_NUM_THREADS
>To:?PWSCF?Forum?<pw_forum at pwscf.org>
>Message-ID:?<4ABCC992.30009 at sissa.it>
>Content-Type:?text/plain;?charset=UTF-8;?format=flowed
>
>Q.J.Wang?wrote:
>>?Dear?all
>>??????According?to?the?advice?of?the?forum,I?added?OMP_NUM_THREADS=1?in?
>>?my?PBS?script?.But?I?can?only?run?a?task?on?the?cluster?.When?one?was?
>>?running?,I?run?another?task?,and?one?of?them?will?turn?up?error?and?stop?.
>
>Have?you?specified?different?outdir?and/or?prefix?for?the?two?tasks?
>Have?you?checked?that?you?have?enough?memory?on?a?node?to?run?two?pw.x?runs?
>...?
>
>GS
>
>
>>?
>>?
>>?--
>>?Best?regards
>>??
>>?Q.J.Wang
>>??
>>?XiangTan?University
>>?
>>?
>>?------------------------------------------------------------------------
>>?"????",????60????
>>?<http://news.163.com/madeinchina/index.html?from=mailfooter>
>>?
>>?
>>?------------------------------------------------------------------------
>>?
>>?_______________________________________________
>>?Pw_forum?mailing?list
>>?Pw_forum at pwscf.org
>>?http://www.democritos.it/mailman/listinfo/pw_forum
>
>--?
>
>
>o?------------------------------------------------?o
>|?Gabriele?Sclauzero,?PhD?Student??????????????????|
>|?c/o:???SISSA?&?CNR-INFM?Democritos,??????????????|
>|????????via?Beirut?2-4,?34014?Trieste?(Italy)?????|
>|?email:?sclauzer at sissa.it?????????????????????????|
>|?phone:?+39?040?3787?511??????????????????????????|
>|?skype:?gurlonotturno?????????????????????????????|
>o?------------------------------------------------?o
>
>
>------------------------------
>
>Message:?8
>Date:?Fri,?25?Sep?2009?14:25:37?+0000
>From:?xirainbow?<nkxirainbow at gmail.com>
>Subject:?[Pw_forum]?About?example?22
>To:?pw_forum at pwscf.org
>Message-ID:
> <21fbc4790909250725r70d71cc3i3d271a58c4e382d2 at mail.gmail.com>
>Content-Type:?text/plain;?charset="iso-8859-1"
>
>Dear?developers:
>There?are?three?trivial?slip?of?example22.
>
>In?the?"README"?file?of?example22:
>ONE:?"2)?make?a?band?structure?calculation?for?Pt?(input=pt.band.in,
>output=pt.band.out)."
>should?be?"(input=pt.nscf.in,???output=pt.nscf.out)."
>TWO:"9)?make?a?self-consistent?calculation?for?Pt?in?a?tetragonal?cell?with
>4?atoms??(input=pt.tet4.in,?output=pt.tet4.out)."
>should?be?"?(input=pt4.in,?output=pt4.out)."
>
>THREE:?When?I?try?to?open?"pt.nscf_ph.in"?with?PWgui,?I?get?the?follow
>error"syntax?error?in?the?input?file:expecting?keyword?ATOMIC?SPECIES,?but
>read?PHONON?instead"
>I?use?espresso4.0.4.?But?I?notice?that?in?espresso4.1,?there?is?not?"
>pt.nscf_ph.in"?file?any?more.
>The?"pt.nscf_ph.in"?is?given?below:
>"Pt
>Pt
>?&control
>????calculation?=?'phonon'
>????restart_mode='from_scratch',
>????prefix='Pt',
>????pseudo_dir?=?'/home/raman/espresso-4.0.4/pseudo/',
>????outdir='/home/raman/tmp/'
>?/
>?&system
>????ibrav=??2,?celldm(1)?=7.42,?nat=??1,?ntyp=?1,
>????lspinorb=.true.,
>????noncolin=.true.,
>????starting_magnetization=0.0,
>????occupations='smearing',
>????degauss=0.02,
>????smearing='mp',
>????ecutwfc?=30.0,
>????ecutrho?=250.0,
>?/
>?&electrons
>????mixing_beta?=?0.7,
>????conv_thr?=??1.0d-8
>?/
>?&phonon
>?xqq(1)=1.d0,
>?xqq(2)=0.d0,
>?xqq(3)=0.d0,
>?/
>ATOMIC_SPECIES
>Pt??79.90????Ptrel.RRKJ3.UPF
>ATOMIC_POSITIONS
>Pt??0.0000000???0.00000000???0.0
>K_POINTS?AUTOMATIC
>2?2?2?1?1?1"
>
>
>--?
>____________________________________
>Hui?Wang
>School?of?physics,?Nankai?University,?Tianjin,?China
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>------------------------------
>
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>
>End?of?Pw_forum?Digest,?Vol?27,?Issue?82
>****************************************
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