[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
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> >
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> >
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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: 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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--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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