[gmx-developers] Re: 4.6.1 soon!

[Mark Abraham]

On Mon, Feb 18, 2013 at 8:39 PM, Christoph Junghans <junghans at votca.org>wrote:

> 2013/2/18 Berk Hess <hess at kth.se>:
> > Hi,
> >
> > I fully agree.
> > Since OpenMM is not fully supported 6.1.12 should be removed from the
> > manual.
> Apropos OpenMM, currently there are some directory offsets wrong in
> the build system, which make it practically impossible to enable the
> OpenMM support:
> <https://gerrit.gromacs.org/#/c/2087/>
> A fix should go into 4.6.1. The above change set is not complete yet
> as some CMAKE_CXX variables are missing.
>

I looked at that patch last week, and it seemed to me like there was not
much consensus about what solution was appropriate. I thought we'd probably
not reach an acceptable solution in time for 4.6.1. Thus it's not in the
list of commits I plan for 4.6.1. The choice of commits and timing for a
release is normally pretty arbitrary, but there has to be one or we never
deliver anything!

If fixing OpenMM to build and/or work from src/contrib is important to
someone, then they're welcome to spend some time on it. Frankly, there's
not much of value in 4.6 that will also benefit someone who needs an
OpenMM-capable mdrun. If I needed the latter, I'd be installing a 4.5.x
version of GROMACS for OpenMM and hoping for the best!

I'd be perfectly happy removing it entirely from the repo. One of the joys
of version control is that it is easy to revert the deletion patch.

Mark


> Cheers,
>
> Christoph
>
>
> > Are there any other issues with the manual you know of?
> >
> > Cheers,
> >
> > Berk
> >
> >
> > On 02/18/2013 02:18 PM, Justin Lemkul wrote:
> >>
> >>
> >> Hi All,
> >>
> >> I'm assuming fixes to the manual are being considered separately then?
>  To
> >> me, we really shouldn't release 4.6.1 unless we have a corresponding
> manual
> >> out at least within 24 hr of the code being made public.  In my mind,
> >> released code necessitates a definitive manual, and there have been
> >> questions on the user list related to the manual.  There are still some
> >> glaring inaccuracies and outdated information, mostly in section 6.12
> >> related to GPU usage (basically it needs to be scrapped, since OpenMM
> isn't
> >> even fully supported any more) and Appendix A. My patch related to
> >> environment variables (https://gerrit.gromacs.org/#/c/2055/) is
> basically
> >> done since Szilard finished off the last few items, but hasn't even been
> >> reviewed.
> >>
> >> -Justin
> >>
> >> On 2/18/13 8:07 AM, Mark Abraham wrote:
> >>>
> >>> Hi GROMACS developers,
> >>>
> >>> There's a release branch constructed, containing a number of minor
> fixes,
> >>> documentation updates and a few remaining fixes of critical issues.
> Below
> >>> is a
> >>> list of commits that are ancestors of the 4.6.1 release patch - please
> >>> review
> >>> things that you know about!
> >>>
> >>> https://gerrit.gromacs.org/#q,I60998e3b,n,z New patch release 4.6.1
> >>> https://gerrit.gromacs.org/#q,I9a551260,n,z Update outdated admin
> things
> >>> https://gerrit.gromacs.org/#q,Iba5b4c66,n,z Fixes for install guide
> page.
> >>> https://gerrit.gromacs.org/#q,Ia0a571d2,n,z Updated install guide
> >>> https://gerrit.gromacs.org/#q,I33495d57,n,z Uncrustified code changes
> >>> since 4.6
> >>> https://gerrit.gromacs.org/#q,If96fd044,n,z Bump shared object
> version to
> >>> 8
> >>> https://gerrit.gromacs.org/#q,I79a06b20,n,z fixed issues with FEP
> >>> soft-core and
> >>> cut-off's
> >>> https://gerrit.gromacs.org/#q,Ib90ac4e5,n,z Merge release-4-5-patches
> >>> into
> >>> release-4-6
> >>> https://gerrit.gromacs.org/#q,I146592c3,n,z fixed GPU particle
> gridding
> >>> performance issue
> >>> https://gerrit.gromacs.org/#q,I268bbf65,n,z Made g_tune_pme work with
> 4.6
> >>> if
> >>> user sets "-p" command line option
> >>> https://gerrit.gromacs.org/#q,I79fd46e1,n,z Fix CMake namespace
> pollution
> >>> https://gerrit.gromacs.org/#q,I3c37844c,n,z Issue errors/warnings for
> ICC
> >>> before
> >>> 12.0.0
> >>> https://gerrit.gromacs.org/#q,Ia6157db8,n,z bugfix for md-vv +
> >>> nose-hoover +
> >>> (nstcalcenergy > nsttcouple)
> >>> https://gerrit.gromacs.org/#q,Ia071c6a1,n,z Use explicit kernel
> pointer
> >>> typecasts
> >>>
> >>> Mark
> >>>
> >>> On Tue, Feb 12, 2013 at 9:15 PM, Mark Abraham <
> mark.j.abraham at gmail.com
> >>> <mailto:mark.j.abraham at gmail.com>> wrote:
> >>>
> >>>     Hi GROMACS developers,
> >>>
> >>>     We've made a number of bug fixes to 4.6, and it's time we got those
> >>> out to
> >>>     the world in 4.6.1. There's a few bits and pieces still sitting in
> >>> gerrit,
> >>>     so please see what you can get done. I'll plan to construct a
> release
> >>> branch
> >>>     on Friday and release Monday Feb 17.
> >>>
> >>>     Cheers,
> >>>
> >>>     Mark
> >>>
> >>>
> >>>
> >>>
> >>
> >
> > --
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
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