[Pw_forum] Pw_forum Digest, Vol 29, Issue 68

Johnson, D. Ray johnsondr at ornl.gov
Tue Nov 24 16:31:40 CET 2009


Lisa,
I will likely be at USCAR on Dec 9.

Regards,

Ray




On 11/24/09 10:19 AM, "pw_forum-request at pwscf.org" <pw_forum-request at pwscf.org> wrote:

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Today's Topics:

   1. Re: about pbs (Gabriele Sclauzero) (Gabriele Sclauzero)
   2. Re: about pbs (Q.J.Wang)
   3. Re: about pbs (Paolo Giannozzi)
   4. Re: about pbs (lan haiping)
   5. Thanks (Shyam Khambholja)
   6. about relax in electric field (Q.J.Wang)


----------------------------------------------------------------------

Message: 1
Date: Tue, 24 Nov 2009 09:12:20 +0100
From: Gabriele Sclauzero <sclauzer at sissa.it>
Subject: Re: [Pw_forum] about pbs (Gabriele Sclauzero)
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <4B0B9564.1050209 at sissa.it>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Q.J.Wang wrote:
> Dear Gabriele
>      Thank you very much for your advice ,I have found the problem in
> forum archives ,but no problem as mine .
>      You said that it is the problem of input file ,but when I use
> "mpirun -np 8 pw.x<input >out 'instead of pbs to submit the job ,it runs
> well .This puzzled me .
>

Sorry, I don't understand well what you are doing. When you speak of PBS I suppose that
you run your job with mpirun as well, but using a batch scheduler which does not need
human interaction (i.e. you submit a script to the queuing system of your cluster).
So, if your job runs with mpirun in interactive mode and not in batch mode, it could be a
problem in your batch environment setup: you have to check environment variables,
libraries, disk access and space, etc. etc. and maybe contact your system administrators...


GS

--


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: 2
Date: Tue, 24 Nov 2009 17:42:03 +0800 (CST)
From: "Q.J.Wang" <wangqj1 at 126.com>
Subject: Re: [Pw_forum] about pbs
To: pw_forum <pw_forum at pwscf.org>
Message-ID:
        <23429577.1103331259055723256.JavaMail.coremail at bj126app29.126.com>
Content-Type: text/plain; charset="gbk"

Dear Paolo
     Thank you very much ,but I still have some puzzled problem as following.

>From: Paolo Giannozzi <giannozz at democritos.it>
>Subject: Re: [Pw_forum] about pbs (Gabriele Sclauzero)
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID: <9CF0CCC9-7FE9-42C3-8CC7-1982851EABAD at democritos.it>
>Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>
>On Nov 24, 2009, at 2:04 , Q.J.Wang wrote:
>
>>  when I use "mpirun -np 8 pw.x<input >out 'instead
>> of pbs to submit the job ,it runs well
>
>batch queue environment differs from the environment
>for interactive execution. You are reading data from a
>different data file in the two cases.
Yes,the former read from pbs date ,the latter read from the input file .
But why the error will turm up use pbs ? How can I solve this problem ? Can you give me specific illustration about this ,I am not understand about this .Thank you very much !
Best regards
?
Q.J.Wang
?
XiangTan University
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Message: 3
Date: Tue, 24 Nov 2009 10:47:44 +0100
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] about pbs
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <4B0BABC0.4080509 at democritos.it>
Content-Type: text/plain; charset=x-gbk; format=flowed

Q.J.Wang wrote:

> How can I solve this problem ?

exactly in the same way as all problems are solved: observe,
experiment, think, make an hypothesis, verify...computer
problems  are infinitely simpler than physics problems

--
Paolo Giannozzi, Democritos and University of Udine, Italy


------------------------------

Message: 4
Date: Tue, 24 Nov 2009 17:48:27 +0800
From: lan haiping <lanhaiping at gmail.com>
Subject: Re: [Pw_forum] about pbs
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
        <c92002fa0911240148g707df3efw457c1529afee678c at mail.gmail.com>
Content-Type: text/plain; charset="gb2312"

Why not to get a userguide for a PBS  ?
Different environmental settings will give rise to different behaviors of
your scripts.

Best

2009/11/24 Q.J.Wang <wangqj1 at 126.com>

> Dear Paolo
>      Thank you very much ,but I still have some puzzled problem as
> following.
>
> >From: Paolo Giannozzi <giannozz at democritos.it>
> >Subject: Re: [Pw_forum] about pbs (Gabriele Sclauzero)
> >To: PWSCF Forum <pw_forum at pwscf.org>
> >Message-ID: <9CF0CCC9-7FE9-42C3-8CC7-1982851EABAD at democritos.it>
> >Content-Type: text/plain; charset=US-ASCII; format=flowed
> >
> >
> >On Nov 24, 2009, at 2:04 , Q.J.Wang wrote:
> >
> >>  when I use "mpirun -np 8 pw.x<input >out 'instead
> >> of pbs to submit the job ,it runs well
> >
> >batch queue environment differs from the environment
> >for interactive execution. You are reading data from a
> >different data file in the two cases.
> Yes,the former read from pbs date ,the latter read from the input file .
> But why the error will turm up use pbs ? How can I solve this problem ? Can
> you give me specific illustration about this ,I am not understand about this
> .Thank you very much !
>
> Best regards
>
> Q.J.Wang
>
> XiangTan University
>
>
>
> ------------------------------
> 09???3D??????????????????<http://allyes.nie.163.com/main/adfclick?db=afanie&bid=1254,611,23&cid=145,4,1&sid=1351&show=ignore&url=http://tx2.163.com/fab.html>
> _______________________________________________
> 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
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Message: 5
Date: Tue, 24 Nov 2009 16:40:50 +0530
From: Shyam Khambholja <physik.shyam at gmail.com>
Subject: [Pw_forum] Thanks
To: pw_forum at pwscf.org
Message-ID:
        <9b382fa70911240310s65a1ed37j261cae8085899248 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear friends,
                  Thank you all fro your help and suggestions.

--
Shyam G Khambholja
Reseach student,
Depratment of Physics,
Sardar Patel University
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Message: 6
Date: Tue, 24 Nov 2009 22:47:35 +0800 (CST)
From: "Q.J.Wang" <wangqj1 at 126.com>
Subject: [Pw_forum] about relax in electric field
To: pw_forum <pw_forum at pwscf.org>
Message-ID:
        <26724746.1247551259074055444.JavaMail.coremail at bj126app104.126.com>
Content-Type: text/plain; charset="gbk"

Dear all
   When I add external electric field to optimize the structure .It runs very very slower than not add the electric field , after 2 days ,the output file is still as following :

 iteration #  1     ecut=    30.00 Ry     beta=0.20
     Davidson diagonalization with overlap
     ethr =  1.00E-02,  avg # of iterations =  4.4
 PAY ATTENTION: EL FIELD AND OCCUPATIONS
     Expectation value of exp(iGx):
 (2.751012649613009E-016,-3.679346535033460E-017)  0.866025403784439
     Electronic Dipole per cell (a.u.) -0.482785724081663
     Ionic Dipole per cell (a.u.)   3794.73195575151
 PAY ATTENTION: EL FIELD AND OCCUPATIONS
My input file adhere here:
&CONTROL
                 calculation = 'relax' ,
                restart_mode = 'from_scratch' ,
                  pseudo_dir = './' ,
                      prefix = 'ZnO' ,
                       nstep = 250 ,
                     tprnfor = .true. ,
                    lelfield = .true. ,
                   nberrycyc = 1 ,
                        gdir = 3 ,
 /
 &SYSTEM
                       ibrav = 14,
                   celldm(1) = 18.6286,
                   celldm(2) = 0.6666667,
                   celldm(3) = 1.0733333,
                   celldm(4) = 0,
                   celldm(5) = 0,
                   celldm(6) = -0.5,
                         nat = 48,
                        ntyp = 3,
                     ecutwfc = 30 ,
                     ecutrho = 300 ,
                       nosym = .true. ,
                 occupations = 'smearing' ,
                     degauss = 0.008 ,
                    smearing = 'gaussian' ,
                       nspin = 2 ,
   starting_magnetization(1) = 0.5,
   starting_magnetization(2) = 0.5,
   starting_magnetization(3) = 0.5,
                 lda_plus_u = .false. ,
 /
 &ELECTRONS
                    conv_thr = 1.D-7 ,
                 mixing_mode = 'plain' ,
                 mixing_beta = 0.2 ,
                 startingwfc = 'random' ,
                      efield = 0 ,
 /
 &IONS
                ion_dynamics = 'bfgs' ,
                 phase_space = 'full' ,
 /
ATOMIC_SPECIES
    O   15.00000  O.pbe-rrkjus.UPF
   Zn   65.00000  Zn.pbe-van.UPF
   Mn   54.94000  Mn.pbe-sp-van.UPF
ATOMIC_POSITIONS angstrom
   Zn      0.000000000    1.875966909    0.000000000    1  1  1
    O      0.000000000    1.875966909    1.991601344    1  1  1
....................................................
K_POINTS automatic
  3 3 3   1 1 1
I don't know why after I add the electric field ,the speed of relax is so slow ?
Any advice will be appreciated !

--

Best regards

Q.J.Wang

XiangTan University
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