[gmx-users] Gromacs with Plumed

[Szilárd Páll]

PS: Unfortunately
cmake -D GMX_VERSION_SUFFIX="FOO"
won't work so the gmxVersionInfo.cmake file needs to be manually edited/
--
Szilárd


On Fri, Mar 10, 2017 at 5:59 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
> Hi,
>
> The discussion will continue on gmx-developers, those interested in
> following it should head there (subscribe or read it here
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2017-March/009540.html)
>
>
> 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?
>
> This however concerns users too, so let me repeat what I wrote on the
> other list:
>
> 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.
>
> Until this is done by the PLUMED installer/patch, I would strongly
> recommend users and especially admins doing shared installations that,
> for the sake of reproducibility add a version suffix in the above
> suggested manner so that
> gmx -version
> mdrun_mpi -version
> reflects the code that the respective tool was compiled from!
>
> Cheers,
> --
> Szilárd
>
>
>> 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
>>> > --
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>>> >
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>>
>>
>>
>> --
>> 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
>> --
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>>
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