[gmx-developers] Re: 4.6.1 soon!

Tue Feb 19 04:02:11 CET 2013

2013/2/18 Mark Abraham <mark.j.abraham at gmail.com>:
>
>
> 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 guess, we just need to enable CXX, before the compiler checks to fix
the above issue, but then we would have an openmm conditional in main
cmakelists.txt file, which is also not nice.
>
>
> 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!
I like to have deadlines, but that also means we have to find a
consensus in time and not just ignore things.
As far as I can see only Szilard had an opinion on that issue.

>
> 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.
I haven't heard any complains on the user's list, so I guess removing
it would be the easiest, quickest and cleanest solution, but Szilard
had the opposite opinion. In the current state nobody will realize
when md_openmm.c and normal md.c get out of sync as it is hard to
build in the first place,  it is just a matter of time until openmm
support gets completely broken.

Christoph

>
> 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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--
Christoph Junghans
Web: http://www.compphys.de