[gpaw-users] Error when relaxing atoms

[Torsten Hahn]

Probably we could do this but my feeling is, that this would only cure the symptoms not the real origin of this annoying bug.


In fact there is code in 

mpi/__init__.py

that says:

# Construct fingerprint:
# ASE may return slightly different atomic positions (e.g. due
# to MKL) so compare only first 8 decimals of positions


The code says that only 8 decimal positions are used for the generation of atomic „fingerprints“. These code relies on numpy and therefore lapack/blas functions. However i have no idea what that md5_array etc. stuff really does. But there is some debug-code which should at least tell you which Atom(s) causes the problems.  

However, that error is *very* strange because mpi.broadcast(...) should result in *exactly* the same objects on all cores. No idea why there should be any difference at all and what was the intention behind the fancy fingerprint-generation stuff in the compare_atoms(atoms, comm=world) method.

Best,
Torsten.

> Am 04.02.2015 um 10:00 schrieb jingzhe <jingzhe.chen at gmail.com>:
> 
> Hi Torsten,
> 
>              Thanks for quick reply, but I use gcc and lapack/blas, I mean if the positions
> of the atoms are slightly different for different ranks because of compiler/lib stuff,
> can we just set a tolerance in the check_atoms and jump off the error?
> 
>              Best.
> 
>              Jingzhe
> 
> 
> 
> 
> 
> 于 2015年02月04日 14:32, Torsten Hahn 写道:
>> Dear Jingzhe,
>> 
>> we often recognized this error if we use GPAW together with Intel MKL <= 11.x on Intel CPU’s. I never tracked down the error because it was gone after compiler/library upgrade.
>> 
>> Best,
>> Torsten.
>> 
>> 
>> --
>> Dr. Torsten Hahn
>> torstenhahn at fastmail.fm
>> 
>>> Am 04.02.2015 um 07:27 schrieb jingzhe Chen <jingzhe.chen at gmail.com>:
>>> 
>>> Dear GPAW guys,
>>> 
>>>         I used the latest gpaw to run a relaxation job, and find the below
>>> error message.
>>> 
>>>      RuntimeError: Atoms objects on different processors are not identical!
>>> 
>>>         I find a line in the force calculator  'wfs.world.broadcast(self.F_av, 0)'
>>> so that all the forces on different ranks should be the same, which makes
>>> me confused, I can not think out any other reason can lead to this error.
>>> 
>>>        Could anyone take a look at it?
>>> 
>>>        I attached the structure file and running script here, I used 24 cores.
>>> 
>>>        Thanks in advance.
>>> 
>>>          Jingzhe
>>> 
>>> <main.py><model.traj>_______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>> 
>