Hi Wang,<br><br>1. Good to hear that your problem was solved.<br><br>2. It seems to be memory problem. Please make sure that your cluster can afford the calculation and make sure the memory is in good condition :)<br><br>3. <a href="http://www.democritos.it/pipermail/pw_forum/2009-September/014269.html">http://www.democritos.it/pipermail/pw_forum/2009-September/014269.html</a><br>
<a href="http://www.democritos.it/pipermail/pw_forum/2009-September/014389.html">http://www.democritos.it/pipermail/pw_forum/2009-September/014389.html</a><br><br><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> </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> </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> </div>
<div>Q.J.Wang</div>
<div> </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 <<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: 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 <<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
>> 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@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
>> FROM 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
>> abort)
>> --------------------------------------------------------------------------
>> 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).
>>
>> ----------------------------------------------------------
>> 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
>>
>>
>>
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>
>------------------------------
>
>Message: 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: <<a href="mailto:4ABC7CDF.2050209@democritos.it" target="_blank">4ABC7CDF.2050209@democritos.it</a>>
>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" <<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: 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
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>
>------------------------------
>
>Message: 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: <<a href="mailto:4ABCC0BE.40302@na.infn.it" target="_blank">4ABCC0BE.40302@na.infn.it</a>>
>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: <a href="mailto:giovanni.cantele@cnr.it" target="_blank">giovanni.cantele@cnr.it</a>
> <a href="mailto:giovanni.cantele@na.infn.it" target="_blank">giovanni.cantele@na.infn.it</a>
>Web: <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: 5
>Date: Fri, 25 Sep 2009 21:41:03 +0800 (CST)
>From: "Q.J.Wang" <<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: 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
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>
>------------------------------
>
>Message: 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: "PWSCF Forum" <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>>
>Message-ID: <op.u0te5nn5a8x26q@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 <<a href="mailto:wangqj1@126.com" target="_blank">wangqj1@126.com</a>> 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: <a href="http://people.sissa.it/%7Epaulatto/" target="_blank">http://people.sissa.it/~paulatto/</a>
>
> *** save italian brains ***
> <a href="http://saveitalianbrains.wordpress.com/" target="_blank">http://saveitalianbrains.wordpress.com/</a>
>
>
>------------------------------
>
>Message: 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: <<a href="mailto:4ABCC992.30009@sissa.it" target="_blank">4ABCC992.30009@sissa.it</a>>
>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???
>> <<a href="http://news.163.com/madeinchina/index.html?from=mailfooter" target="_blank">http://news.163.com/madeinchina/index.html?from=mailfooter</a>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Pw_forum mailing list
>> <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a>
>> <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a>
>
>--
>
>
>o ------------------------------------------------ o
>| Gabriele Sclauzero, PhD Student |
>| c/o: SISSA & CNR-INFM Democritos, |
>| via Beirut 2-4, 34014 Trieste (Italy) |
>| email: <a href="mailto:sclauzer@sissa.it" target="_blank">sclauzer@sissa.it</a> |
>| phone: +39 040 3787 511 |
>| skype: gurlonotturno |
>o ------------------------------------------------ o
>
>
>------------------------------
>
>Message: 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: <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: 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=<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
> &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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>End of Pw_forum Digest, Vol 27, Issue 82
>****************************************
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<br></blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------<br>Duy Le<br>PhD Student<br>Department of Physics<br>University of Central Florida.<br>