[gpaw-users] Regarding 'RuntimeError: Atoms objects on different processors are not identical!'
Ask Hjorth Larsen
asklarsen at gmail.com
Tue Mar 3 20:15:57 CET 2015
I recently changed something having to do with that part. You could try
with trunk. Which version are you using?
After the change, when the code runs the check it will allow for an error
of 1e-8 (approx. square root of machine precision), then simply use the
positions from the master process if it doesn't raise the error.
Best regards
Ask
2015-03-03 14:26 GMT+01:00 Yuriy Elesin <yuel at topsoe.dk>:
> Thank you Morten and Ask!
>
> It has generated the output as a bunch of
> compare_atoms_r00**_positions.pickle files. Plus it generated one
> compare_atoms_fps_positions.pickle file. When I compare all the r00** files
> it indicates that positions on most of the cores are identical, except a
> few cores where the difference between positions generates one line with
> 4.33680869e-19 as difference:
> ....
> [ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00]
> [ 0.00000000e+00, 4.33680869e-19, 0.00000000e+00]
> [ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00]
> ....
>
> It is always the same value, when the positions are different. But again
> out of 24 cores there are only 8 (I think) cores with different then the
> rest coordinates.
>
> The compare_atoms_fps_positions.pickle file has the following content:
>
> array([-8145271529702367328, 3281356470061976748, 3281356470061976748,
> 3281356470061976748, 3281356470061976748, 3281356470061976748,
> 3281356470061976748, 3281356470061976748, 3281356470061976748,
> -8145271529702367328, 3281356470061976748, 3281356470061976748,
> 3281356470061976748, 3281356470061976748, -8145271529702367328,
> -8145271529702367328, 3281356470061976748, 3281356470061976748,
> 3281356470061976748, 3281356470061976748, -8145271529702367328,
> 3281356470061976748, 3281356470061976748, 3281356470061976748])
>
> Does it tell you anything? If it is just minor inaccuracies then how do we
> prevent the following error that seem to stop the calculation:
>
> RuntimeError: Atoms objects on different processors are not identical!
> GPAW CLEANUP (node 23): <type 'exceptions.RuntimeError'> occurred.
> Calling MPI_Abort!
>
>
> Kind regards
> Yuriy
>
>
> From: Morten Niklas Gjerding <mogje at fysik.dtu.dk> To: Yuriy Elesin <
> yuel at topsoe.dk>, Ask Hjorth Larsen <asklarsen at gmail.com>, Cc: gpaw-users
> <gpaw-users at listserv.fysik.dtu.dk> Date: 03/03/2015 11:15 AM Subject: RE:
> [gpaw-users] Regarding 'RuntimeError: Atoms objects on different processors
> are not identical!'
> ------------------------------
>
>
>
> Hi Yury.
>
> I think that:
>
> gpaw-python script.py --debug
>
> is what you want.
>
> KR. Morten.
> ------------------------------
>
> *From:* gpaw-users-bounces at listserv.fysik.dtu.dk [
> gpaw-users-bounces at listserv.fysik.dtu.dk] on behalf of Yuriy Elesin [
> yuel at topsoe.dk]
> * Sent:* Tuesday, March 03, 2015 9:56 AM
> * To:* Ask Hjorth Larsen
> * Cc:* gpaw-users
> * Subject:* Re: [gpaw-users] Regarding 'RuntimeError: Atoms objects on
> different processors are not identical!'
>
> Hi Ask
>
> How do we enable the debug mode in GPAW? I tried gpaw-python with -d
> option but it says it is only for the parser, so no files with faulty
> positions were generated.
>
> Kind regards
> Yuiry
>
> From: Ask Hjorth Larsen <asklarsen at gmail.com> To: Hanne Falsig <
> hafa at topsoe.dk>, Cc: gpaw-users <gpaw-users at listserv.fysik.dtu.dk>,
> yuel at topsoe.dk Date: 03/02/2015 04:03 PM Subject: Re: [gpaw-users]
> Regarding 'RuntimeError: Atoms objects on different processors are not
> identical!'
>
> ------------------------------
>
>
>
> Hi Hanne
>
> In trunk (and possibly in the old version; this I don't remember) the
> faulty positions will be dumped to files if you use debug mode. Then you
> can check whether they completely disagree (something is wrong with the
> parallelization, probably of the XC functional) or whether there's just
> some numerical noise (some calculation is duplicated in a way that allows
> numerical inaccuracies across different cores).
>
> Best regards
> Ask
>
> 2015-03-02 11:30 GMT+01:00 Hanne Falsig <*hafa at topsoe.dk* <hafa at topsoe.dk>>:
>
> Dear all,
>
> I get the following error message:
> RuntimeError: Atoms objects on different processors are not identical!
>
> I can see there have been a number of questions about this. Did someone
> find a solution to this problem?
>
> My input is:
> calc =
> GPAW(xc='BEEF-vdW',kpts=[1,1,1],h=0.20,mixer=MixerSum(),spinpol=True,
> maxiter=300,occupations=FermiDirac(width=0.1),txt='gpaw.txt')
>
> We use gpaw version 0.10.0.11364
>
> Best regards,
> Hanne
> ------------------------------
> *Hanne Falsig *
> Research Scientist | Physical Analytical, R&D
>
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