[Pw_forum] Pw_forum Digest, Vol 27, Issue 82
Duy Le
ttduyle at gmail.com
Fri Sep 25 17:51:37 CEST 2009
Hi Wang,
1. Good to hear that your problem was solved.
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 :)
3. http://www.democritos.it/pipermail/pw_forum/2009-September/014269.html
http://www.democritos.it/pipermail/pw_forum/2009-September/014389.html
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：
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> >than "Re: Contents of Pw_forum digest..."
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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 <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 --------------
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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/ <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
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> >------------------------------
> >
> >_______________________________________________
> >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
> >****************************************
>
>
>
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--
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.
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