?009-09-23 18:46:48?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. how to improve the calculation speed ? (wangqj1) > 2. Re: how to improve the calculation speed ? (Giovanni Cantele) > 3. Re: how to improve the calculation speed ? (Lorenzo Paulatto) > 4. write occupancy (ali kazempour) > 5. Re: write occupancy (Prasenjit Ghosh) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 23 Sep 2009 16:05:46 +0800 (CST) >From: wangqj1 <wangqj1 at 126.com> >Subject: [Pw_forum] how to improve the calculation speed ? >To: pw_forum <pw_forum at pwscf.org> >Message-ID: > <21870763.369701253693146938.JavaMail.coremail at bj126app103.126.com> >Content-Type: text/plain; charset="gbk" > > >Dear PWSCF users > When I use R and G parallelization to run job ,it as if wait for the > input . According peoples advice ,I use k-point parallelization ,it runs > well . But it runs too slow .The information I can offerred as following: >(1) : CUP usage of one node is as >Tasks: 143 total, 10 running, 133 sleeping, 0 stopped, 0 zombie >Cpu0 : 99.7%us, 0.3%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu1 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu2 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu3 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu4 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu5 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu6 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu7 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Mem: 8044120k total, 6683720k used, 1360400k free, 1632k buffers >Swap: 4192956k total, 2096476k used, 2096480k free, 1253712k cached > >(2) The input file of PBS >#!/bin/sh >#PBS -j oe >#PBS -N pw >#PBS -l nodes=1:ppn=8 >#PBS -q small >cd $PBS_O_WORKDIR >hostname >/usr/local/bin/mpirun -np 8 -machinefile $PBS_NODEFILE /home/wang/bin/pw.x >-npool 8 -in ZnO.pw.inp>ZnO.pw.out >(3) >wang at node22:~> netstat -s >Ip: > 1894215181 total packets received > 0 forwarded > 0 incoming packets discarded > 1894215181 incoming packets delivered > 979205769 requests sent out > 30 fragments received ok > 60 fragments created >Icmp: > 2 ICMP messages received > 1 input ICMP message failed. > ICMP input histogram: > destination unreachable: 2 > 2 ICMP messages sent > 0 ICMP messages failed > ICMP output histogram: > destination unreachable: 2 >IcmpMsg: > InType3: 2 > OutType3: 2 >Tcp: > 5662 active connections openings > 9037 passive connection openings > 68 failed connection attempts > 1 connection resets received > 18 connections established > 1894049565 segments received > 979043182 segments send out > 284 segments retransmited > 0 bad segments received. > 55 resets sent >Udp: > 165614 packets received > 0 packets to unknown port received. > 0 packet receive errors > 162301 packets sent > RcvbufErrors: 0 > SndbufErrors: 0 >UdpLite: > InDatagrams: 0 > NoPorts: 0 > InErrors: 0 > OutDatagrams: 0 > RcvbufErrors: 0 > SndbufErrors: 0 >TcpExt: > 10 resets received for embryonic SYN_RECV sockets > ArpFilter: 0 > 5691 TCP sockets finished time wait in fast timer > 25 time wait sockets recycled by time stamp > 17369935 delayed acks sent > 1700 delayed acks further delayed because of locked socket > 18 packets directly queued to recvmsg prequeue. > 8140 packets directly received from backlog > 1422037027 packets header predicted > 7 packets header predicted and directly queued to user > TCPPureAcks: 2794058 > TCPHPAcks: 517887764 > TCPRenoRecovery: 0 > TCPSackRecovery: 56 > TCPSACKReneging: 0 > TCPFACKReorder: 0 > TCPSACKReorder: 0 > TCPRenoReorder: 0 > TCPTSReorder: 0 > TCPFullUndo: 0 > TCPPartialUndo: 0 > TCPDSACKUndo: 0 > TCPLossUndo: 1 > TCPLoss: 357 > TCPLostRetransmit: 6 > TCPRenoFailures: 0 > TCPSackFailures: 0 > TCPLossFailures: 0 > TCPFastRetrans: 235 > TCPForwardRetrans: 46 > TCPSlowStartRetrans: 0 > TCPTimeouts: 3 > TCPRenoRecoveryFail: 0 > TCPSackRecoveryFail: 0 > TCPSchedulerFailed: 0 > TCPRcvCollapsed: 0 > TCPDSACKOldSent: 0 > TCPDSACKOfoSent: 0 > TCPDSACKRecv: 2 > TCPDSACKOfoRecv: 0 > TCPAbortOnSyn: 0 > TCPAbortOnData: 0 > TCPAbortOnClose: 0 > TCPAbortOnMemory: 0 > TCPAbortOnTimeout: 0 > TCPAbortOnLinger: 0 > TCPAbortFailed: 0 > TCPMemoryPressures: 0 > TCPSACKDiscard: 0 > TCPDSACKIgnoredOld: 1 > TCPDSACKIgnoredNoUndo: 0 > TCPSpuriousRTOs: 0 > TCPMD5NotFound: 0 > TCPMD5Unexpected: 0 >IpExt: > InNoRoutes: 0 > InTruncatedPkts: 0 > InMcastPkts: 0 > OutMcastPkts: 0 > InBcastPkts: 0 > OutBcastPkts: 0 >when I install the PWSCF ,I only use the command line : >./configure >make all . >And it install successful . > >I don't know why it run so slow ,how to solve this problem ? Any advice will >be appreciated ! > >Best regard >Q . J. Wang >XiangTan University > > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://www.democritos.it/pipermail/pw_forum/attachments/20090923/f82797a3/attachment-0001.htm > > >------------------------------ > >Message: 2 >Date: Wed, 23 Sep 2009 10:45:51 +0200 >From: Giovanni Cantele <Giovanni.Cantele at na.infn.it> >Subject: Re: [Pw_forum] how to improve the calculation speed ? >To: PWSCF Forum <pw_forum at pwscf.org> >Message-ID: <4AB9E03F.7080600 at na.infn.it> >Content-Type: text/plain; charset=x-gbk; format=flowed > >wangqj1 wrote: >> >> Dear PWSCF users >> When I use R and G parallelization to run job ,it as if wait for the >> input . > >What does it mean? Does it print the output header or the output up to >some point or nothing happens? It only print the output heander and not have iteration .
> >>?According?peoples?advice?,I?use?k-point?parallelization?,it?runs?well? >>?.?But?it?runs?too?slow?.The?information?I?can?offerred?as?following: >>?(1)?:?CUP?usage?of?one?node?is?as >>?Tasks:?143?total,?10?running,?133?sleeping,?0?stopped,?0?zombie >>?Cpu0?:?99.7%us,?0.3%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu1?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu2?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu3?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu4?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu5?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu6?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu7?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Mem:?8044120k?total,?6683720k?used,?1360400k?free,?1632k?buffers >>?Swap:?4192956k?total,?2096476k?used,?2096480k?free,?1253712k?cached >I'm?not?very?expert?about?reading?such?information,?but?it?seams?that? >your?node?is?making?swap,?maybe?because?the?job?is?requiring?too?much? >memory?with?respect?to?the?available?one.?This?usually?induces?a?huge? >performance?degradation. > >In?choosing?the?optimal?number?of?nodes,?processes?per?node,?etc.,? >several?factors?should?be?taken?into?account:?memory?requirements,? >communication?hardware,?etc.?You?might?want?have?a?look?to?this?page? >from?the?user?guide:?http://www.quantum-espresso.org/user_guide/node33.html 8 processes per node in our cluster, model name????? : Intel(R) Xeon(R) CPU??? E5410? @ 2.33GHz stepping??????? : 10 cpu MHz???????? : 2327.489 cache size????? : 6144 KB >Also,?consider?that,?at?least?for?not?very?very?recent?CPU?generation,? >using too many cores per CPU (e.g. if your cluster configuration is with >>quad-core processors), might not improve (maybe also make worse) the >code >performances (this is also reported in previous threads in this >forum, you >can make a search).> >Also this can be of interest for you: >>http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Why_is_my_parallel_job_running_in_such_a_lousy_way.3F I am not the supperuser,I don't know how to Set the environment variable OPEN_MP_THREADS to 1,I can't find where is OPEN_MP_THREADS ? > >>?I?don't?know?why?it?run?so?slow?,how?to?solve?this?problem???Any? >>?advice?will?be?appreciated?! >Apart?from?better?suggestions?coming?from?more?expert?people,?it?would? >be?important?to?see?what?kind?of?job?you?are?trying?to?run.?For?example:? >did?you?start?directly?with?a?"production?run"?(many?k-points?and/or? >large?unit?cells?and/or?large?cut-off)??Did?pw.x?ever?run?on?your? >cluster?with?simple?jobs,?like?bulk?silicon?or?any?other?(see?the? >examples?directory)? The input file I had run on my single computer(4 CPUs).It runs well . > >Another?possibility?would?be?starting?with?the?serial?executable? >(disabling?parallel?at?configure?time)?and?then?switch?to?parallel?once? >you?check?that?everything?is?working?OK. > > > >Unfortunately,?in?many?cases?the?computation?requires?lot?of?work?to? >correctly?set-up?and?optimize?compilation,?performances,?etc.?(not?to? >speak?about?results?convergence?issues!!!!). >The?only?way?is?trying?to?isolate?problems?and?solve?one?by?one.?Yet,?I? >would?say?that?in?this?respect?quantum-espresso?is?one?of?the?best? >choices,?being?the?code?made?to?properly?work?in?as?many?cases?as? >possible,?rather?then?implementing?all?the?human?knowledge?but?just?for? >those?who?wrote?it!!! >;-) > >Good?luck, > >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:?3 >Date:?Wed,?23?Sep?2009?10:50:48?+0200 >From:?"Lorenzo?Paulatto"?<paulatto at sissa.it> >Subject:?Re:?[Pw_forum]?how?to?improve?the?calculation?speed?? >To:?Giovanni.Cantele at na.infn.it,?"PWSCF?Forum"?<pw_forum at pwscf.org> >Message-ID:?<op.u0pb6yqfa8x26q at paulax> >Content-Type:?text/plain;?charset=utf-8;?format=flowed;?delsp=yes > >In?data?23?settembre?2009?alle?ore?10:45:51,?Giovanni?Cantele?? ><Giovanni.Cantele at na.infn.it>?ha?scritto: >>?I'm?not?very?expert?about?reading?such?information,?but?it?seams?that >>?your?node?is?making?swap,?maybe?because?the?job?is?requiring?too?much >>?memory?with?respect?to?the?available?one.?This?usually?induces?a?huge >>?performance?degradation. > >If?this?is?the?case,?reducing?the?number?of?pools?will?reduce?the?amount?? >of?memory?required?per?node. > >cheers > > >--? >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:?4 >Date:?Wed,?23?Sep?2009?03:13:18?-0700?(PDT) >From:?ali?kazempour?<kazempoor2000 at yahoo.com> >Subject:?[Pw_forum]?write?occupancy >To:?pw?<pw_forum at pwscf.org> >Message-ID:?<432077.46189.qm at web112513.mail.gq1.yahoo.com> >Content-Type:?text/plain;?charset="us-ascii" > >Hi >How?do?we?can?force?the?code?to?print?the?occupancy?in?simple?scf?run? >I?know?partial?dos?calculation?,?but?I?don't?know?wheather?another?way?also?exist?or?not? >thanks?a?lot > >?Ali?Kazempour >Physics?department,?Isfahan?University?of?Technology >84156?Isfahan,?Iran.????????????Tel-1:??+98?311?391?3733 >Fax:?+98?311?391?2376??????Tel-2:??+98?311?391?2375 > > > >?????? >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090923/97a9ee58/attachment-0001.htm? > >------------------------------ > >Message:?5 >Date:?Wed,?23?Sep?2009?12:46:45?+0200 >From:?Prasenjit?Ghosh?<prasenjit.jnc at gmail.com> >Subject:?Re:?[Pw_forum]?write?occupancy >To:?PWSCF?Forum?<pw_forum at pwscf.org> >Message-ID: > <627e0ffa0909230346wbdf3399i1b2a48f4edfa9c65 at mail.gmail.com> >Content-Type:?text/plain;?charset="iso-8859-1" > >use?verbosity='high' > >Prasenjit. > >2009/9/23?ali?kazempour?<kazempoor2000 at yahoo.com> > >>?Hi >>?How?do?we?can?force?the?code?to?print?the?occupancy?in?simple?scf?run? >>?I?know?partial?dos?calculation?,?but?I?don't?know?wheather?another?way?also >>?exist?or?not? >>?thanks?a?lot >> >>?Ali?Kazempour >>?Physics?department,?Isfahan?University?of?Technology >>?84156?Isfahan,?Iran.?Tel-1:?+98?311?391?3733 >>?Fax:?+98?311?391?2376?Tel-2:?+98?311?391?2375 >> >> >>?_______________________________________________ >>?Pw_forum?mailing?list >>?Pw_forum at pwscf.org >>?http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > >--? >PRASENJIT?GHOSH, >POST-DOC, >ROOM?NO:?265,?MAIN?BUILDING, >CM?SECTION,?ICTP, >STRADA?COSTERIA?11, >TRIESTE,?34104, >ITALY >PHONE:?+39?040?2240?369?(O) >?????????????+39?3807528672?(M) >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090923/bc129707/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?74 >**************************************** -------------- next part -------------- An HTML attachment was scrubbed... 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