[gmx-developers] available contribution: loop over pull code

[chris.neale at utoronto.ca]

Thanks Berk, this makes a lot of sense.

Quoting hess at sbc.su.se:

> I was already thinking about being able to specify multiple pull pairs.
> You had asked about that before and it would indeed be a useful option
> and not too complicated too implement.
> Now you ask asking for several more things.
> I don't know if different pull types would be of general use and that
> would complicate the code and make it more bug-prone, especially for
> checking what options do and don't work together. We've already had
> several bugs in 4.0 in combinations of pull options.
>
> Communication cost will be an issue at high parallelization.
> For you this might (usually) not be an issue, but in Gromacs we would like
> to keep everything compatible and fast, also at high parallelization.
>
> Ideally users should be able to write plugins for things like complex
> pulling. We will start working on modularization and making the code more
> object oriented now.
>
> Berk
>
>> Alright. We do not have such code, so I guess that answers it in the
>> negative. Thank you for providing clarity on this issue. Your
>> preferred method makes it difficult to apply different pull-types or
>> dimensions to different reference groups, but I understand that you
>> would like to keep the code simple. As for speed, I tested that and
>> the loss is negligible.
>>
>> Quoting hess at sbc.su.se:
>>
>>> Hi,
>>>
>>> I would not like a loop over the pull code.
>>> That complicates things a lot and increases the communication cost.
>>> I would simply want to add something like a reference group number
>>> to each pull group.
>>>
>>> Berk
>>>
>>>> Dear Gromacs Developers:
>>>>
>>>> A colleague of mine, Pawel Pomorski working at Sharcnet Canada, has
>>>> modified gromacs version 4.0.5 to put a loop around the pull code.
>>>> This has made it possible to have multiple reference groups (each
>>>> reference group will multiple pulled groups). I have found this very
>>>> useful for my work and have thoroughly tested the code modifications.
>>>>
>>>> We would like to get this code added to the main gromacs code for the
>>>> next release. I assume that Pawel would need to update the code
>>>> modifications to fit into the git master.
>>>>
>>>> Before Pawel does this work, we would like to get some assurance that
>>>> the modification will be accepted (or not accepted) into the main
>>>> gromacs code. I already have a number of test cases that I used to
>>>> validate the modified 4.0.5 code and can run these on the new code as
>>>> well.
>>>>
>>>> The purpose of this email is to ensure that Pawel doesn't end up doing
>>>> any work for naught. I can always continue to use the 4.0.5 version
>>>> that I have, but I think that this pull code modification will be
>>>> useful for many users.
>>>>
>>>> In gromacs version <3.3.3, a loop over the pull code was easily
>>>> implemented in an hour or so. The situation was quite a bit more
>>>> complex in version 4.
>>>>
>>>> Finally, Pawel has many responsibilities and may not be able to port
>>>> his modifications immediately. If he does, is it important that he
>>>> download the git master one night and submit his new code the next
>>>> day? the next week? the next month?
>>>>
>>>> Thank you,
>>>> Chris.
>>>>
>>>>
>>>>
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