[gmx-developers] distance restraints and domain decomposition

[Berk Hess]

Hi,

But OpenMP runs could be incorrect when the restraint distance can pick 
up the wrong PBC image.

Cheers,

Berk

On 2018-06-07 14:06, Bert de Groot wrote:
> Hi,
>
> OK, thanks, that sounds reasonable. It is admittedly a somewhat 
> unusual setup, but as the openMP jobs ran without issues, the problems 
> with the MPI jobs surprised us.
> The system is small enough that we can use openMP nodes as workaround 
> for now.
>
> The anticipated issues with analysis tools/trjconv have indeed showed 
> up as well (inconsistent shift warnings), but there they can be 
> resolved by feeding a tpr without the distance restraints.
>
> cheers
>
> Bert
>
> On 06/07/18 13:29, Berk Hess wrote:
>> Hi,
>>
>> I "resolved" this by adding a fatal error. The error message says 
>> that the only solution is increasing the box size.
>> For special cases one could do better by introducing special 
>> interations that would only link monomers together. But here you 
>> actually have interactions that a longer than half the box size. 
>> Theoretically one could also support this, but that gets complicated 
>> and bug-prone.
>>
>> Cheers,
>>
>> Berk
>>
>> On 2018-06-07 10:22, Berk Hess wrote:
>>> Hi,
>>>
>>> I filed a redmine issue: https://redmine.gromacs.org/issues/2549
>>>
>>> Cheers,
>>>
>>> Berk
>>>
>>> On 2018-06-07 09:51, Berk Hess wrote:
>>>> Hi,
>>>>
>>>> This is a complicated case. You have multiple monomers that are 
>>>> only linked by distance restraints. Some of these restraints work 
>>>> over more than half the box length. These interactions cause parts 
>>>> of monomers to be shifted by a box vector in the shift code. This 
>>>> is obviously incorrect. This can affect more things than the DD 
>>>> distance calculation that you report, e.g. analysis tools.
>>>> This is not easy to fix, one could image that all distance 
>>>> restraints are at distances of more than half the box length. The 
>>>> least we should do is detect such inconsistencies and generate a 
>>>> fatal error.
>>>> I was about to say that you could use multiple molecule types and 
>>>> intermolecular interactions, but could cause incorrect distances to 
>>>> be used for the restraints.
>>>> The only proper solution is to add some kind of proximity 
>>>> interaction the user can specify to tell what part of the monomers 
>>>> are close, such that GROMACS can set up the correct PBC.
>>>>
>>>> Cheers,
>>>>
>>>> Berk
>>>>
>>>>
>>>> On 06/07/2018 08:42 AM, Berk Hess wrote:
>>>>> Hi,
>>>>>
>>>>> The code takes PBC into account, both for intra- and 
>>>>> intermolecular interactions.
>>>>>
>>>>> Could you provide me with the input to grompp?
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Berk
>>>>>
>>>>> On 06/07/2018 08:37 AM, Kutzner, Carsten wrote:
>>>>>>
>>>>>>> On 7. Jun 2018, at 07:02, David van der Spoel 
>>>>>>> <spoel at xray.bmc.uu.se> wrote:
>>>>>>>
>>>>>>> Den 2018-06-06 kl. 15:07, skrev Kutzner, Carsten:
>>>>>>>> Dear developers,
>>>>>>>> we have a ~ 40,000 atom MD system with distance restraints 
>>>>>>>> (bond type 6)
>>>>>>>> that does not want to run in parallel, although I assume it 
>>>>>>>> should.
>>>>>>>> It runs fine without DD, e.g. -ntmpi 1 -ntomp 20, however with 
>>>>>>>> DD the
>>>>>>>> following happens:
>>>>>>>> mdrun -ntmpi 2
>>>>>>>> Fatal error:
>>>>>>>> There is no domain decomposition for 2 ranks that is compatible 
>>>>>>>> with the given
>>>>>>>> box and a minimum cell size of 11.4939 nm
>>>>>>>> The maximum distance restraint distance is however at 4.0 nm, 
>>>>>>>> so 11.49 nm as
>>>>>>>> reported cannot be true, unless the PBC distance is not taken 
>>>>>>>> properly
>>>>>>>> into account. Is this the expected behaviour or worth 
>>>>>>>> generating a redmine
>>>>>>>> issue?
>>>>>>>> Thanks,
>>>>>>>>   Carsten
>>>>>>> Which version?
>>>>>> 2018
>>>>>>
>>>>>>> It should work with OpenMP anyway.
>>>>>> Yes, that works, however we might want to use multiple nodes 
>>>>>> and/or multiple
>>>>>> GPUs for similar setups in the future.
>>>>>>
>>>>>> Carsten
>>>>>>
>>>>>>> -- 
>>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>>>>> http://www.icm.uu.se
>>>>>>> -- 
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>>>>>> -- 
>>>>>> Dr. Carsten Kutzner
>>>>>> Max Planck Institute for Biophysical Chemistry
>>>>>> Theoretical and Computational Biophysics
>>>>>> Am Fassberg 11, 37077 Goettingen, Germany
>>>>>> Tel. +49-551-2012313, Fax: +49-551-2012302
>>>>>> http://www.mpibpc.mpg.de/grubmueller/kutzner
>>>>>> http://www.mpibpc.mpg.de/grubmueller/sppexa
>>>>>>
>>>>>
>>>>
>>>
>>
>
>