[gmx-developers] [gmx-users] Gromacs with Plumed

[Szilárd Páll]

Hi Giovanni,

Let me take this discussion to the gmx-developers list, I think that
is the right audience for it.

Firstly, regarding the version info: all you need to do is to set e.g.
GMX_VERSION_SUFFIX='-PLUMED-2.0' in cmake/gmxVersionInfo.cmake to get
a version string that looks like this: "2016.2-PLUMED-2.0.


To your second question: I did mean upstream contribution! I think
such efforts would greatly benefit the simulation community and likely
make your work easier too. I think it would be not only feasible, but
a desired direction by many of the GROMACS developers too. So to
answer directly: yes, I do think it is feasible, but it will require
some short- and long-term work and commitment from the PLUMED devs.

The exact details of how to contribute the code will require a few
iterations, but here are a few relevant points:

- Developer guide:
http://manual.gromacs.org/documentation/2016/dev-manual/index.html;
- I recommend taking technical discussion to our issue management
server: https://redmine.gromacs.org; filing a "Feature" issue is the
appropriate starting point;

-  There are ongoing concerted efforts (see
https://redmine.gromacs.org/issues/2045) to design an (internal and
external) GROMACS API. The outcome of that project will certainly be
beneficial to PLUMED. Your feedback could also be useful in order that
current and future needs of PLUMED can be taken into considerations in
the API design.
However, given the simplicity of the current PLUMED <-> GROMACS
interaction (at least from what I've seen last time I checked), it
seems to me that it should be possible to introduce with moderate
effort a _much_ simpler API that could on the short-term be used by
PLUMED. This should allow that no patching and perhaps not even
recompilation is needed in order to use GROMACS with PLUMED!


To be honest, the question why is there such a barrier and limited
communication between projects that build on top of our code and the
GROMACS dev community has come up and puzzled me before, so I'm glad
there might be an opportunity here to move things in a good direction!

Cheers,
--
Szilárd


On Fri, Mar 3, 2017 at 9:36 AM, Giovanni Bussi <bussi at sissa.it> wrote:
> Hi,
>
> thanks Szilárd for the comment.
>
> About changing the version string, which would be the right place to do it
> in the code?
>
> About the last point, do you mean that we should try to put our code into
> gromacs main trunk? This would be very nice for us (plumed developers), and
> we discussed several times about this. Do you think it would be feasible?
> Are there clear guidelines about what should be included, how, and where in
> the code (e.g. a developer manual)?
>
> Honestly, the current patch is very dirty (we use some global variables
> here and there to avoid modifying function declarations), but with some
> help we could perhaps make it clean and try to contribute it.
>
> Thanks!
>
> Giovanni
>
>
>
> On Thu, Mar 2, 2017 at 3:43 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
>
>> Hi,
>>
>> I'd recommend keeping a vanilla/untainted GROMACS installation
>> available to users at all times. No matter how much awareness there is
>> about issues or unwanted code interaction, as long as a user is not
>> running an official GROMACS release, they can and should not claim
>> (e.g. in a publication) that they used "GROMACS vX.Y". This is not
>> just nitpicking, but a matter of scientific reproducibility.
>>
>> I hope that PLUMED patching also changes the version string not just
>> the code so installations from "patched" source do not claim to be
>> vanilla, official GROMACS. Can you or someone else aware confirm that?
>>
>>
>> On a side-note, the uncomfortable side-effect of the patch-based
>> software distribution model would of course be easy to solve if thin
>> API abstractions were designed and submitted upstream in the main
>> GROMACS source.
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>> On Thu, Mar 2, 2017 at 9:09 AM, Åke Sandgren <ake.sandgren at hpc2n.umu.se>
>> wrote:
>> > Hi!
>> >
>> > Are there any known drawbacks to building Gromacs with Plumed?
>> >
>> > I'm mainly talking about Gromacs 2016 and later, using PLumed 2.3.0,
>> > both if there are problems with any version combination i'd like to know
>> > that too.
>> >
>> > I.e., will it cause problems for non-plumed runs, will gromacs behave
>> > identical to a non-plumed build when not using plumed in the
>> > plumed-build, etc.?
>> >
>> > Having just a single build makes my life easier :-)
>> >
>> > --
>> > Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
>> > Internet: ake at hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
>> > Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> Giovanni Bussi
> Scuola Internazionale Superiore di Studi Avanzati - SISSA
> via Bonomea 265, 34136 Trieste, Italy
> email: bussi at sissa.it
> web:   http://people.sissa.it/~bussi
>           http://srnas.sissa.it
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.