[Pw_forum] Pw_forum Digest, Vol 27, Issue 82

lan haiping lanhaiping at gmail.com
Fri Sep 25 22:03:56 CEST 2009


Hi, Q.J Wang.
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.


Regards

2009/9/25 Q.J.Wang <wangqj1 at 126.com>

> 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:
> >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: 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 --------------
> >An HTML attachment was scrubbed...
> >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/270ab22b/attachment-0001.htm
> >
> >------------------------------
> >
> >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 --------------
> >An HTML attachment was scrubbed...
> >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/9b5d0c9e/attachment-0001.htm
> >
> >------------------------------
> >
> >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 <http://people.na.infn.it/%7Ecantele>
> >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 --------------
> >An HTML attachment was scrubbed...
> >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/1089ca3e/attachment-0001.htm
> >
> >------------------------------
> >
> >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/ <http://people.sissa.it/%7Epaulatto/>
> >
> >     *** 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
> >-------------- next part --------------
> >An HTML attachment was scrubbed...
> >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/642bd62b/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 82
> >****************************************
>
>
>
> ------------------------------
> 网易邮箱用户购物独享现金返还 <http://fanxian.163.com/fanxian/?keyfrom=163mail.footer>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20090926/f8aa4836/attachment.html>


More information about the users mailing list