Hi, Q.J Wang.<br>I just notice several times that you always break the thread of the mail-list.  Please donot start a new-thread for an old topic , or reply a digest.<br><br><br>Regards<br><br><div class="gmail_quote">2009/9/25 Q.J.Wang <span dir="ltr"><<a href="mailto:wangqj1@126.com">wangqj1@126.com</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Thank you very much Lorenzo Paulatto and Gabriele Sclauzero .</div>
<div>Â </div>
<div>The problem was solved ,because I specified  same  prefix for the two tasks .</div>
<div>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 :</div>
<div>Â </div>
<div>forrtl: severe (174): SIGSEGV, segmentation fault occurred<br>Image             PC               Routine           Line       Source                                                                                <br>
pw.x              40000000005D8710 Unknown              Unknown <br>Unknown<br>pw.x              40000000005D8BF0 Unknown              Unknown <br>Unknown<br>pw.x              40000000005F4A40 Unknown              Unknown <br>
Unknown<br>pw.x              400000000003C740 Unknown              Unknown <br><br>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 . <br><br>
--<br></div>
<div>
<div>Best regards</div>
<div>Â </div>
<div>Q.J.Wang</div>
<div>Â </div>
<div>XiangTan University </div></div><br><pre>在2009-09-25 22:26:04，<a href="mailto:pw_forum-request@pwscf.org" target="_blank">pw_forum-request@pwscf.org</a> 写é“：
>Send Pw_forum mailing list submissions to
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>or, via email, send a message with subject or body 'help' 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: 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:Â 1
>Date: Fri, 25 Sep 2009 13:46:44 +0530
>From: dev sharma <<a href="mailto:decboy9@gmail.com" target="_blank">decboy9@gmail.com</a>>
>Subject: Re: [Pw_forum] problem in phonon in prallel
>To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>>
>Message-ID:
> <<a href="mailto:a591fe200909250116g7a121b6ave4460eadd70c179f@mail.gmail.com" target="_blank">a591fe200909250116g7a121b6ave4460eadd70c179f@mail.gmail.com</a>>
>Content-Type:Â text/plain;Â charset="iso-8859-1"
>
>Hi,
>
> when i am running the same file with the following inputs , it is running
>well
>
>phonons at gamma
>Â &inputph
>Â Â tr2_ph=1.0e-10,
>Â Â prefix='yvo',
>Â Â trans=.false.,
>Â Â epsil=.true.,
>Â Â amass(1)=Â 44.995,
>Â Â amass(2)=Â 50.9415,
>Â Â amass(3)=15.9994,
>  outdir = '/home/devsharma/work/newscvo/temp',
>Â Â fildyn='yvo.dyn1',
>Â /
>0.0Â 0.0Â 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 <<a href="mailto:decboy9@gmail.com" target="_blank">decboy9@gmail.com</a>> 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
>>Â help.
>> Thanks in advance.
>> phonons at gamma
>>Â Â &inputph
>>Â Â Â tr2_ph=1.0e-10,
>>Â Â Â prefix='yvo',
>>Â Â Â Â fpol=.true.,
>>Â Â Â Â trans=.false.,
>>Â Â Â epsil=.true.,
>>Â Â Â elop=.true.,
>>Â Â Â amass(1)=Â 44.995,
>>Â Â Â amass(2)=Â 50.9415,
>>Â Â Â amass(3)=15.9994,
>>   outdir = '/home/devsharma/work/newscvo/temp',
>>Â Â Â fildyn='yvo.dyn1',
>>Â Â /
>>Â 0.0Â 0.0Â 0.0
>>
>>Â FREQUENCIES
>>Â 65
>>Â 7.889e+14
>>Â /
>>Â /
>>Â 4.389e+14
>>
>> and mssg in terminal is coming
>>
>> [devsharma@headnode newscvo]$ [<a href="http://headnode.du.ac.in:6309" target="_blank">headnode.du.ac.in:6309</a>] *** An error
>> occurred in MPI_Allreduce
>> [<a href="http://headnode.du.ac.in:6309" target="_blank">headnode.du.ac.in:6309</a>] *** on communicator MPI COMMUNICATOR 28 SPLIT
>>Â FROMÂ 4
>> [<a href="http://headnode.du.ac.in:6309" target="_blank">headnode.du.ac.in:6309</a>] *** MPI_ERR_TRUNCATE: message truncated
>> [<a href="http://headnode.du.ac.in:6309" target="_blank">headnode.du.ac.in:6309</a>] *** MPI_ERRORS_ARE_FATAL (your MPI job will now
>>Â abort)
>>Â --------------------------------------------------------------------------
>> mpirun has exited due to process rank 1 with PID 6309 on
>> node <a href="http://headnode.du.ac.in" target="_blank">headnode.du.ac.in</a> exiting without calling "finalize". This may
>> have caused other processes in the application to be
>> terminated by signals sent by mpirun (as reported here).
>>
>>Â ----------------------------------------------------------
>> 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,
>>
>>Â sincerly,
>> Dev Sharma,
>> Univeristy of Delhi
>>
>>
>>
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>
>------------------------------
>
>Message:Â 2
>Date: Fri, 25 Sep 2009 10:18:39 +0200
>From: Paolo Giannozzi <<a href="mailto:giannozz@democritos.it" target="_blank">giannozz@democritos.it</a>>
>Subject: Re: [Pw_forum] problem in phonon in prallel
>To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>>
>Message-ID:Â <<a href="mailto:4ABC7CDF.2050209@democritos.it" target="_blank">4ABC7CDF.2050209@democritos.it</a>>
>Content-Type:Â text/plain;Â charset=ISO-8859-1;Â format=flowed
>
>dev sharma wrote:
>
>> Any comment on the extraÂ
>> 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.
>--Â
>Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>------------------------------
>
>Message:Â 3
>Date: Fri, 25 Sep 2009 21:02:50 +0800 (CST)
>From:Â "Q.J.Wang"Â <<a href="mailto:wangqj1@126.com" target="_blank">wangqj1@126.com</a>>
>Subject: [Pw_forum] Running on cluster often turn up
>To: pw_forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>>
>Message-ID:
> <<a href="mailto:10083410.509721253883770555.JavaMail.coremail@bj126app104.126.com" target="_blank">10083410.509721253883770555.JavaMail.coremail@bj126app104.126.com</a>>
>Content-Type:Â text/plain;Â 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
>Â
>Q.J.Wang
>Â
>XiangTan UniversityÂ
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>
>------------------------------
>
>Message:Â 4
>Date: Fri, 25 Sep 2009 15:08:14 +0200
>From: Giovanni Cantele <<a href="mailto:Giovanni.Cantele@na.infn.it" target="_blank">Giovanni.Cantele@na.infn.it</a>>
>Subject: Re: [Pw_forum] Running on cluster often turn up
>To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>>
>Message-ID:Â <<a href="mailto:4ABCC0BE.40302@na.infn.it" target="_blank">4ABCC0BE.40302@na.infn.it</a>>
>Content-Type:Â text/plain;Â charset=x-gbk;Â format=flowed
>
>Q.J.Wang wrote:
>> Dear all
>> When I running on cluster ,it often turn up some bizarre errors ,whichÂ
>> not turn up ong single computer .I don't know why .Whether is itÂ
>> because the computing environment settings ? I don' know how to doÂ
>> .Plese help me .
>>
>Well, I think that it will be rather difficult for anybody to answerÂ
>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 /Â
>software rather than to the Quantum-ESPRESSO.
>
>You can also try to search the forum to find if some of these errorsÂ
>have been ever discussed before.
>
>Giovanni
>
>--Â
>
>
>
>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:Â +39Â 081Â 676910
>Fax:Â Â Â +39Â 081Â 676346
>E-mail:Â <a href="mailto:giovanni.cantele@cnr.it" target="_blank">giovanni.cantele@cnr.it</a>
>Â Â Â Â Â Â Â Â <a href="mailto:giovanni.cantele@na.infn.it" target="_blank">giovanni.cantele@na.infn.it</a>
>Web:Â <a href="http://people.na.infn.it/%7Ecantele" target="_blank">http://people.na.infn.it/~cantele</a>
>Research Group: <a href="http://www.nanomat.unina.it" target="_blank">http://www.nanomat.unina.it</a>
>Skype contact: giocan74
>
>
>
>------------------------------
>
>Message:Â 5
>Date: Fri, 25 Sep 2009 21:41:03 +0800 (CST)
>From:Â "Q.J.Wang"Â <<a href="mailto:wangqj1@126.com" target="_blank">wangqj1@126.com</a>>
>Subject: [Pw_forum] about OMP_NUM_THREADS
>To: pw_forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>>
>Message-ID:
> <<a href="mailto:12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com" target="_blank">12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com</a>>
>Content-Type:Â text/plain;Â 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
>Â
>Q.J.Wang
>Â
>XiangTan UniversityÂ
>-------------- next part --------------
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>
>------------------------------
>
>Message:Â 6
>Date: Fri, 25 Sep 2009 15:45:13 +0200
>From: "Lorenzo Paulatto" <<a href="mailto:paulatto@sissa.it" target="_blank">paulatto@sissa.it</a>>
>Subject: Re: [Pw_forum] about OMP_NUM_THREADS
>To:Â "PWSCFÂ Forum"Â <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>>
>Message-ID:Â <op.u0te5nn5a8x26q@paulax>
>Content-Type:Â text/plain;Â charset=utf-8;Â format=flowed;Â delsp=yes
>
>In data 25 settembre 2009 alle ore 15:41:03, Q.J.Wang <<a href="mailto:wangqj1@126.com" target="_blank">wangqj1@126.com</a>> ha Â
>scritto:
>>      According to the advice of the forum,I added OMP_NUM_THREADS=1 in Â
>> my PBS script .But I can only run a task on the cluster .When one was Â
>> 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 Â
>possible on how you run the job, there is very little we can say about you Â
>problem with any information.
>
>To begin you should check that the jobs do not have the same prefix and Â
>outdir, if it is the case they will crash after a while.
>
>best regards
>
>
>--Â
>Lorenzo Paulatto
>SISSAÂ Â &Â Â DEMOCRITOSÂ (Trieste)
>phone:Â +39Â 040Â 3787Â 511
>skype:Â paulatz
>www:Â Â Â <a href="http://people.sissa.it/%7Epaulatto/" target="_blank">http://people.sissa.it/~paulatto/</a>
>
>     *** save italian brains ***
>Â Â <a href="http://saveitalianbrains.wordpress.com/" target="_blank">http://saveitalianbrains.wordpress.com/</a>
>
>
>------------------------------
>
>Message:Â 7
>Date: Fri, 25 Sep 2009 15:45:54 +0200
>From: Gabriele Sclauzero <<a href="mailto:sclauzer@sissa.it" target="_blank">sclauzer@sissa.it</a>>
>Subject: Re: [Pw_forum] about OMP_NUM_THREADS
>To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>>
>Message-ID:Â <<a href="mailto:4ABCC992.30009@sissa.it" target="_blank">4ABCC992.30009@sissa.it</a>>
>Content-Type:Â text/plain;Â charset=UTF-8;Â format=flowed
>
>Q.J.Wang wrote:
>> Dear all
>>      According to the advice of the forum,I added OMP_NUM_THREADS=1 inÂ
>> my PBS script .But I can only run a task on the cluster .When one wasÂ
>> 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
>
>
>>Â
>>Â
>>Â --
>> Best regards
>>Â Â
>>Â Q.J.Wang
>>Â Â
>> XiangTan University
>>Â
>>Â
>>Â ------------------------------------------------------------------------
>>Â "????",????60???Â
>>Â <<a href="http://news.163.com/madeinchina/index.html?from=mailfooter" target="_blank">http://news.163.com/madeinchina/index.html?from=mailfooter</a>>
>>Â
>>Â
>>Â ------------------------------------------------------------------------
>>Â
>>Â _______________________________________________
>> Pw_forum mailing list
>>Â <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a>
>>Â <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a>
>
>--Â
>
>
>o ------------------------------------------------ o
>| Gabriele Sclauzero, PhD Student                  |
>| c/o:   SISSA & CNR-INFM Democritos,              |
>|        via Beirut 2-4, 34014 Trieste (Italy)     |
>|Â email:Â <a href="mailto:sclauzer@sissa.it" target="_blank">sclauzer@sissa.it</a>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â |
>|Â phone:Â +39Â 040Â 3787Â 511Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â |
>| skype: gurlonotturno                             |
>o ------------------------------------------------ o
>
>
>------------------------------
>
>Message:Â 8
>Date: Fri, 25 Sep 2009 14:25:37 +0000
>From: xirainbow <<a href="mailto:nkxirainbow@gmail.com" target="_blank">nkxirainbow@gmail.com</a>>
>Subject: [Pw_forum] About example 22
>To:Â <a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>
>Message-ID:
> <<a href="mailto:21fbc4790909250725r70d71cc3i3d271a58c4e382d2@mail.gmail.com" target="_blank">21fbc4790909250725r70d71cc3i3d271a58c4e382d2@mail.gmail.com</a>>
>Content-Type:Â text/plain;Â 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=<a href="http://pt.band.in" target="_blank">pt.band.in</a>,
>output=pt.band.out)."
>should be "(input=<a href="http://pt.nscf.in" target="_blank">pt.nscf.in</a>,   output=pt.nscf.out)."
>TWO:"9) make a self-consistent calculation for Pt in a tetragonal cell with
>4 atoms  (input=<a href="http://pt.tet4.in" target="_blank">pt.tet4.in</a>, output=pt.tet4.out)."
>should be " (input=<a href="http://pt4.in" target="_blank">pt4.in</a>, output=pt4.out)."
>
>THREE: When I try to open "<a href="http://pt.nscf_ph.in" target="_blank">pt.nscf_ph.in</a>" 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 "
><a href="http://pt.nscf_ph.in" target="_blank">pt.nscf_ph.in</a>" file any more.
>The "<a href="http://pt.nscf_ph.in" target="_blank">pt.nscf_ph.in</a>" is given below:
>"Pt
>Pt
>Â &control
>    calculation = 'phonon'
>Â Â Â Â restart_mode='from_scratch',
>Â Â Â Â prefix='Pt',
>    pseudo_dir = '/home/raman/espresso-4.0.4/pseudo/',
>Â Â Â Â outdir='/home/raman/tmp/'
>Â /
>Â &system
>    ibrav=  2, celldm(1) =7.42, nat=  1, ntyp= 1,
>Â Â Â Â lspinorb=.true.,
>Â Â Â Â noncolin=.true.,
>Â Â Â Â starting_magnetization=0.0,
>Â Â Â Â occupations='smearing',
>Â Â Â Â degauss=0.02,
>Â Â Â Â smearing='mp',
>    ecutwfc =30.0,
>    ecutrho =250.0,
>Â /
>Â &electrons
>    mixing_beta = 0.7,
>    conv_thr =  1.0d-8
>Â /
>Â &phonon
>Â xqq(1)=1.d0,
>Â xqq(2)=0.d0,
>Â xqq(3)=0.d0,
>Â /
>ATOMIC_SPECIES
>Pt  79.90    Ptrel.RRKJ3.UPF
>ATOMIC_POSITIONS
>Pt  0.0000000   0.00000000   0.0
>K_POINTSÂ AUTOMATIC
>2Â 2Â 2Â 1Â 1Â 1"
>
>
>--Â
>____________________________________
>Hui Wang
>School of physics, Nankai University, Tianjin, China
>-------------- next part --------------
>An HTML attachment was scrubbed...
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>
>------------------------------
>
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>End of Pw_forum Digest, Vol 27, Issue 82
>****************************************
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<br></blockquote></div><br><br clear="all"><br>-- <br>Hai-Ping Lan <br>Department of Electronics ,<br>Peking University , Bejing, 100871<br><a href="mailto:lanhaiping@gmail.com">lanhaiping@gmail.com</a>, <a href="mailto:hplan@pku.edu.cn">hplan@pku.edu.cn</a><br>