[gmx-developers] distance restraints and domain decomposition

Thu Jun 7 15:51:20 CEST 2018

Not if the wrong image is used consistently, which is not unlikely, 
since a large complex rotates rather slowly.

Berk

On 06/07/2018 03:49 PM, Bert de Groot wrote:
> Hi,
>
> right, but this would be expected to lead to jumps in the restraint 
> energies, right? So far there are no signs of these.
>
> cheers
>
> Bert
>
> On 06/07/18 14:08, Berk Hess wrote:
>> 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
>>>>>>>>> -- 
>>>>>>>>> Gromacs Developers mailing list
>>>>>>>>>
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>>>>>>>>> or send a mail to gmx-developers-request at gromacs.org.
>>>>>>>> -- 
>>>>>>>> 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
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
>