[Pw_forum] Ph.x code help
Vincenzo Verdolino
vincenzo.verdolino at gmail.com
Wed Aug 27 18:31:00 CEST 2014
I don't know for sure but and i encourage someone else to give a better explenation if any. However, i suggest two things:
1) in the scf you can use as many nodes and processors you need. You might want to use
wf_collect=.true.
It works in writing and not in the reading process and it avoids conflicts between pw.x and ph.x
2) i personally do not use the wavefunction collector because once i find the best number of nodes and processors in terms of scalability (but this is architecture dependent) i freez it forever for that system. So you might want to try and error apprach i.e. 1 proc- 10 proc-20proc but it debends on the architecture of your nodes. Still i suggest to use 1 node and n processors which you are going to define by testing.
3) you found that problem because of the very small number of k-points. Just to give e try use
K_POINTS automatic
4 4 4 0 0 0
In the scf run and try to use more processors in your ph.x
Sent from my iPhone
> On 27/ago/2014, at 15:44, "Samin, Adib J." <samin.2 at buckeyemail.osu.edu> wrote:
>
> Actually, I was running it with two processors on one node but after trying it with one processor it worked. So thanks again for all your help.
>
> In any case, I was just doing this example to get familiar with the procedure and I am planning to use it for my own research. In that case the simulation will be more complicated involving many atoms. How would I know how many processors to use?
>
> Is there a general rule of thumb that I can use to help guide me for the future?
>
>
>
> Thanks,
>
> Adib Samin
>
>
>
>
>
>
>
>
> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Vincenzo Verdolino <vincenzo.verdolino at gmail.com>
> Sent: Wednesday, August 27, 2014 3:53 AM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] Ph.x code help
>
> did you try to run both the scf and the ph.x job with 1 node and 1 proc?
>
>
>> On Tue, Aug 26, 2014 at 6:32 PM, Samin, Adib J. <samin.2 at buckeyemail.osu.edu> wrote:
>> Yes it is.
>>
>> Thanks,
>>
>> Adib Samin
>>
>>
>>
>>
>>
>>
>> ________________________________________
>> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Vincenzo Verdolino <vincenzo.verdolino at gmail.com>
>> Sent: Tuesday, August 26, 2014 12:12 PM
>> To: PWSCF Forum
>> Subject: Re: [Pw_forum] Ph.x code help
>>
>> Quick question
>>
>> Is the Pseudo Potential the one suggested in the test input file? I see you are usin a pz one...i don't know but could you double check that??
>>
>> Sent from my iPhone
>>
>> > On 26/ago/2014, at 17:53, "Samin, Adib J." <samin.2 at buckeyemail.osu.edu> wrote:
>> >
>> > Dear Quantum Espresso Users,
>> >
>> > Thanks again for all your help. I was finally able to run the ph.x code but I am still not generating the dynamical matrix but rather a blank file.
>> > I have attached the output of the ph.x code for the input files below. Any help on this matter would be appraciated.
>> >
>> > Atomic displacements:
>> > There are 2 irreducible representations
>> >
>> > Representation 1 3 modes -T_2g G_25' G_5+ To be done
>> >
>> > Representation 2 3 modes -T_1u G_15 G_4- Not done in this run
>> >
>> > Compute atoms: 1, 2,
>> >
>> >
>> >
>> > Alpha used in Ewald sum = 0.7000
>> > PHONON : 0.56s CPU 0.61s WALL
>> >
>> >
>> >
>> > Representation # 1 modes # 1 2 3
>> >
>> > Self-consistent Calculation
>> >
>> > iter # 1 total cpu time : 0.9 secs av.it.: 5.0
>> > thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.189E-06
>> >
>> > iter # 2 total cpu time : 1.3 secs av.it.: 9.5
>> > thresh= 0.434E-04 alpha_mix = 0.700 |ddv_scf|^2 = 0.320E-08
>> >
>> > iter # 3 total cpu time : 1.7 secs av.it.: 9.5
>> > thresh= 0.566E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.278E-10
>> >
>> > iter # 4 total cpu time : 2.1 secs av.it.: 8.8
>> > thresh= 0.528E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.296E-13
>> >
>> > iter # 5 total cpu time : 2.5 secs av.it.: 9.4
>> > thresh= 0.172E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.287E-15
>> >
>> > End of self-consistent calculation
>> >
>> > Convergence has been achieved
>> >
>> > Stopping because representation 2 is not done
>> >
>> >
>> > Thanks,
>> >
>> > Adib Samin
>> >
>> >
>> > Adib Samin
>> > Postdoc
>> > The Department of Aerospace and Mechanical Engineering
>> > The Ohio State University
>> >
>> >
>> >
>> > ________________________________________
>> > From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Samin, Adib J. <samin.2 at buckeyemail.osu.edu>
>> > Sent: Tuesday, August 26, 2014 11:08 AM
>> > To: PWSCF Forum
>> > Subject: Re: [Pw_forum] Ph.x code help
>> >
>> > Thank you so much for all your help. I was finally able to run the code by reducing the number of processors being used.
>> > I still have one question however. The si.dynG file I am creating seems to be a blank file. Is that correct?
>> > I am currently attempting to run dynmat.x to diagonalize the matrix but I am concerned because I don't see the matrix.
>> >
>> > Thanks,
>> >
>> > Adib Samin
>> >
>> >
>> >
>> >
>> >
>> >
>> > ________________________________________
>> > From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Vincenzo Verdolino <vincenzo.verdolino at gmail.com>
>> > Sent: Tuesday, August 26, 2014 10:53 AM
>> > To: PWSCF Forum
>> > Subject: Re: [Pw_forum] Ph.x code help
>> >
>> > 12 pros is fine for the scf but try to change it for ph.x
>> >
>> > Sent from my iPhone
>> >
>> >> On 26/ago/2014, at 16:19, "Samin, Adib J." <samin.2 at buckeyemail.osu.edu> wrote:
>> >>
>> >> Thank you for your response. I am still getting errors running the code. I am indeed running it in parallel using 12 processors. How do I check for the consistencies mentioned below?
>> >> Any clarification would be greatly appreciated.
>> >>
>> >> Thanks,
>> >>
>> >> Adib Samin
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> ________________________________________
>> >> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>
>> >> Sent: Tuesday, August 26, 2014 9:59 AM
>> >> To: PWSCF Forum
>> >> Subject: Re: [Pw_forum] Ph.x code help
>> >>
>> >> Dear Adib Samin,
>> >>
>> >> How did you try to run the example, parallellising over the
>> >> representations/q vectors? If yes, how many MPI tasks did you ask for, how
>> >> many partitions for the representations/q vectors? Please check whether
>> >> these are consistent.
>> >>
>> >> Greetings from Sunny Montrouge,
>> >>
>> >> apsi
>> >>
>> >> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>> >> Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>> >> Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>> >> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935
>> >>
>> >>
>> >>> On Tue, 26 Aug 2014, Samin, Adib J. wrote:
>> >>>
>> >>>
>> >>> Thank you for your help.
>> >>>
>> >>> I have attached below the scf.in file. I hope that helps in diagnosing the
>> >>> problem.
>> >>>
>> >>> &control
>> >>> calculation='scf'
>> >>> restart_mode='from_scratch',
>> >>> pseudo_dir='./'
>> >>> outdir='/nfs/11/osu7834/'
>> >>> prefix='SIPH',
>> >>> /
>> >>> &system
>> >>> ibrav=2, celldm(1)=10.20, nat=2, ntyp=1,
>> >>> ecutwfc =16.0
>> >>> /
>> >>> &electrons
>> >>> conv_thr = 1.0d-9
>> >>> mixing_beta = 0.7
>> >>> /
>> >>> ATOMIC_SPECIES
>> >>> Si 28.0855 Si.pz-vbc.UPF
>> >>> ATOMIC_POSITIONS
>> >>> Si 0.00 0.00 0.00
>> >>> Si 0.25 0.25 0.25
>> >>> K_POINTS
>> >>> 10
>> >>> 0.1250000 0.1250000 0.1250000 1.00
>> >>> 0.1250000 0.1250000 0.3750000 3.00
>> >>> 0.1250000 0.1250000 0.6250000 3.00
>> >>> 0.1250000 0.1250000 0.8750000 3.00
>> >>> 0.1250000 0.3750000 0.3750000 3.00
>> >>> 0.1250000 0.3750000 0.6250000 6.00
>> >>> 0.1250000 0.3750000 0.8750000 6.00
>> >>> 0.1250000 0.6250000 0.6250000 3.00
>> >>> 0.3750000 0.3750000 0.3750000 1.00
>> >>> 0.3750000 0.3750000 0.6250000 3.00
>> >>>
>> >>>
>> >>> Thanks,
>> >>>
>> >>> Adib Samin
>> >>>
>> >>>
>> >>> Adib Samin
>> >>>
>> >>> Postdoc
>> >>>
>> >>> The Department of Aerospace and Mechanical Engineering
>> >>>
>> >>> The Ohio State University
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> ____________________________________________________________________________
>> >>> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of
>> >>> Vincenzo Verdolino <vincenzo.verdolino at gmail.com>
>> >>> Sent: Tuesday, August 26, 2014 5:38 AM
>> >>> To: PWSCF Forum
>> >>> Subject: Re: [Pw_forum] Ph.x code help
>> >>> Dear,
>> >>>
>> >>> just make sure you
>> >>>
>> >>> cp -r -f SIPH.save /nfs/11/osu7834/
>> >>>
>> >>> sometimes it happens that your outir in the scf calculation is not the same
>> >>> specified in your ph.x calculation
>> >>>
>> >>> could you also paste the scf.in job file?
>> >>>
>> >>> thanks
>> >>>
>> >>> vincenzo
>> >>>
>> >>>
>> >>> On Mon, Aug 25, 2014 at 10:07 PM, Samin, Adib J.
>> >>> <samin.2 at buckeyemail.osu.edu> wrote:
>> >>>
>> >>> Dear Quantum Espresso users,
>> >>>
>> >>>
>> >>> I am trying to run the ph.x executable using a simple silicon
>> >>> example which I found online. I first perform the scf
>> >>> calculation and save the results and then use the same
>> >>> outdirectory and prefix when running the ph.x code. However, I
>> >>> keep getting the same error which says:
>> >>>
>> >>> 'Error in routine image_q_irr (1):
>> >>>
>> >>> some images have no rapp'
>> >>>
>> >>> I have attached the ph input file.
>> >>>
>> >>> I would really appreciate it if someone can help explain to me
>> >>> why this is happening.
>> >>>
>> >>>
>> >>> Phonons of Si at Gamma
>> >>> &inputph
>> >>> tr2_ph=1.0d-14,
>> >>> amass(1)=28.0855,
>> >>> prefix='SIPH',
>> >>> outdir='/nfs/11/osu7834/'
>> >>> fildyn='si.dynG',
>> >>> /
>> >>> 0.0 0.0 0.0
>> >>>
>> >>>
>> >>>
>> >>> Thanks,
>> >>>
>> >>> Adib Samin
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> Adib Samin
>> >>>
>> >>> Postdoc
>> >>>
>> >>> The Department of Aerospace and Mechanical Engineering
>> >>>
>> >>> The Ohio State University
>> >>>
>> >>>
>> >>> _______________________________________________
>> >>> Pw_forum mailing list
>> >>> Pw_forum at pwscf.org
>> >>> http://pwscf.org/mailman/listinfo/pw_forum
>> >>
>> >> _______________________________________________
>> >> Pw_forum mailing list
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