[gmx-developers] plans for GROMACS 2017 release cycle

Mark Abraham mark.j.abraham at gmail.com
Thu Mar 9 17:03:38 CET 2017


On Thu, Mar 9, 2017 at 3:49 PM Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>

> Hi!
> I'd like to add python api for gromacs as a suggestion (however we need
> to fix it first to work with current changes for trajectoryanalysis)

I suspect we've not done anywhere near enough groundwork (yet) for this.
Offhand, we should have a clear understanding of the scope ("expose the
trajectoryanalysis C++ API" seems to be that of the current RFC patch in
gerrit), how that adds value to users, and whether the approach will be
able to offer a suitably stable UI. We also need to consider which versions
of Python make sense to support

How does a script using it look? (Your link to https://biod.pnpi.spb.ru from
the Redmine no longer seems to work?) Does that compare reasonably to
offerings like http://www.mdanalysis.org/pages/basic_example/ or
http://mdtraj.org/1.8.0/examples/introduction.html. What lessons have we
learned from them, and what aspects of other related python toolsets should
we plan to incorporate, so that users will find themselves able to get the
benefit of rapid compiler-free prototyping?

There's widespread interest in something like this, and active work over
the medium term from some of our US colleagues, but if SIP is the vehicle
for exposing a C++ API to python, then we probably need first to do some
design work to make a C++ layer suitable for that, or a python layer on top
of the SIP. Particularly because "exposure to Python" was never part of
Teemu's initial design.


Mark Abraham писал 09-03-2017 17:42:
> > Hi,
> >
> > It's time to start preparing for this year's release. Consistent with
> > previous practice, we will have a soft deadline for work proposed for
> > inclusion to have appeared in Gerrit in approximately final form, then
> > we'll make a release candidate from the first patch on a new
> > release-2017 branch. That branch will thereafter be open, in the usual
> > way, for all manner of fixes, docs and tests, with patches expected to
> > focus on stability, correctness and minimal disruption. Thereafter,
> > from that branch, we might make a future release candidate, and at
> > some point a final release.
> >
> > For target dates I propose:
> > * April 1 - proposals available in gerrit in approximately final form
> > * May 1 - ship release candidate
> > * May 15 - ship second release candidate if that seems useful
> > * June 1 - ship 2017 final if there are no known serious problems
> >
> > There's a fair bit of work currently in gerrit that is refactoring to
> > suit long term needs. There's no strong reason to push to get such
> > things in the release, but review and submission are welcome in the
> > usual way. I do suggest that we avoid any further cleanup patches that
> > touch lots of lines or lots of files until after the 2017 release, to
> > make life easier on those preparing work for that release and merging
> > fixes forward.
> >
> > After we ship 2017, and have incorporated any bug fixes we want to
> > back port, I will make a final 5.1 patch release and declare that
> > branch closed to future work. Similarly, I'll make another 2016 patch
> > release, and thereafter that branch will have the policy of being open
> > only to fixes for things that might affect scientific results.
> >
> > My focus will be on the integration of Aleksei's PME-on-GPU
> > implementation, as well as several non-code GROMACS activities.
> >
> > Erik hopes to rush out some new templated kernel infrastructure, but
> > he has a grant application on April 6, so perhaps we will relax the
> > April 1 cutoff for that - but based on history, there will be no
> > promises either way ;-)
> >
> > David's energy analysis framework is pretty close to good shape, so
> > some final effort there would be a nice achievement.
> >
> > Berk hopes to get in some more of his conserved quantities for
> > integrators, and perhaps with Viveca some of the AWH implementation
> > (that needs a lot of refactoring, however...)
> >
> > Are there any other things people would like to flag for attention?
> > Are there good reasons to suggest alternative dates?
> >
> > Mark
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov, PhD
> Department of Molecular and Radiation Biophysics
> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
> Leningrad region, Gatchina, Russia
> mailto:alexxyum at gmail.com
> mailto:alexxy at omrb.pnpi.spb.ru
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