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

[XAvier Periole]

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> 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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