[gmx-developers] Hacking domain decomposition for long range bonded terms.

[Berk Hess]

Hi,

Ah, I overlooked that the option is on by default, that explains a lot.
But with DD 2x2x2 I think everything should work. Your distance can't be 
larger than half the box size, right?

Cheers,

Berk

On 11/19/2013 09:08 AM, XAvier Periole wrote:
>
> Hi Berk,
>
> Thank you for your comments.
>
> I looked at the -ddbondcomm (in gmx4.6.1). It is a hidden option and 
> turned on by default.
>
> - Adding this option explicitly to my command line did not affect the 
> complain concerning the minimum box size needing to be ~15 nm.
> - adding explicitly -dd 2 2 2 (as you email seemed to suggest) did 
> remove the complain but then we get to the same point as when hacking 
> the code which was a complain for missing the long range bonded 
> interactions.
> - adding -rdd 17.0 did not help, then of course the box size force by 
> -dd 2 2 2 is smaller than the minimum allowed (17.0 nm).
>
> I am not sure if I am missing something here?
>
> Thanks again,
> XAvier.
>
> On Nov 19, 2013, at 7:50 AM, Berk Hess <hess at kth.se 
> <mailto:hess at kth.se>> wrote:
>
>> Hi,
>>
>> I think the hidden mdrun option -ddbondcomm should solve your issues. 
>> Then the communication should always work up to 2x2x2.
>> I don't know why I made this option hidden. We should probably make 
>> this a normal option. We could also hint at the option in the error 
>> message you quote.
>>
>> What will also help with your issue is the Verlet scheme. I uploaded 
>> change https://gerrit.gromacs.org/#/c/2775/ which adds support for LJ 
>> shift (through vdw-modifier=Force-switch) to the Verlet scheme. This 
>> will make Martini run twice as fast and allows you to use OpenMP only 
>> parallelization on a single node (which is like PD, bu faster). On 
>> multiple nodes you can run MPI+OpenMP parallelization, which will 
>> allow you to run less domains and avoid the issue in many cases. Note 
>> that I have not (and will not) implement shift functions for Coulomb, 
>> but I heard from Groningen that reaction-field should work OK with 
>> Martini.
>>
>> Cheers,
>>
>> Berk
>>
>> On 11/18/2013 09:59 PM, XAvier Periole wrote:
>>>
>>> Dears,
>>>
>>> Following on the issue of long range bonded terms preventing the use 
>>> of DD and before fixed using PD.
>>>
>>> We have looked into the groupcoord.c solution but are currently 
>>> stuck. Our idea was to supplement at each step the local atom list 
>>> of each node with the atoms involved in those long range bonded 
>>> terms (total of six atoms). We have bypassed the check on the 
>>> minimum DD box size (15 nm) by forcing the code to take the 
>>> decomposition we choose. Here 2x2x2.
>>>
>>> Of course now mdrun crashes when getting to calculate those long 
>>> range bonded interactions and complains that they are missing. The 
>>> error message is given bellow. We have trouble finding where exactly 
>>> the code determines which coordinates to communicate to each domain.
>>>
>>> Any suggestion or hint would be greatly appreciated.
>>>
>>> XAvier and Manel.
>>>
>>> ...
>>> A list of missing interactions:
>>> Bond of  60636 missing      1
>>> Improper Dih. of     12 missing      2
>>>
>>> Molecule type 'rhodimmer'
>>> the first 10 missing interactions, except for exclusions:
>>> Improper Dih. atoms  117  423  279 1066 global 117   423   279  1066
>>> Bond atoms  279 1066           global   279  1066
>>> Improper Dih. atoms  279 1066 1210  904 global 279  1066  1210   904
>>>
>>> -------------------------------------------------------
>>> Program mdrun, VERSION 4.6.3
>>> Source code file: /src/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393
>>>
>>> Fatal error:
>>> 3 of the 103492 bonded interactions could not be calculated because 
>>> some atoms involved moved further apart than the multi-body cut-off 
>>> distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see 
>>> option -rdd, for pairs and tabulated bonds also see option -ddcheck
>>> For more information and tips for troubleshooting, please check the 
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>>
>>>
>>
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