[FFE] Freeze Exception for gromacs 2016.3

Asked by Szilárd Páll

I was going to file an FFE, but decided to ask here first whether at this stage it makes sense at all or whether I should just file a bug report against 2016.2 and have the fix in question cherry-picked from 2016.3 for a new "2016.2-2" Ubuntu version to make it by the 17.04 release. Below is what I was going to post as an FFE.

Zesty currently has GROMACS 2016.2 which has been reported to have a quite important usability bug.

Under certain (not uncommon) circumstances the mdrun simulation tool of GROMACS can deadlock and hang before exit, for more details see the release notes (and the bug report linked there):

The bugfix (along with a few other minor fixes) has been released in the GROMACS 2016.3 patch release. This is a fairly small release with only ~20 commits (see the full release notes below or at http://manual.gromacs.org/documentation/2016.3/ReleaseNotes/release-notes.html).

To avoid including a known to be buggy GROMACS version in Ubuntu 17.04, I'd like to have a freeze exception made and the gromacs* packages bumped to 2016.3. If not done, the usability of the gromacs package will be limited (given the bug causing deadlock).

Ubnutu release: Ubuntu 17.04
current package: gromacs 2016.2-1


GROMACS 2016.3 release notes:

Fixes where mdrun could behave incorrectly:
* Fixed mdrun with separate PME ranks hanging upon exit
* Fixed handling of previous virials with md-vv integrator
* Fixed an incorrect check that nstlog != 0 for expanded ensembles

Fixes for gmx tools
* Fixed gmx tune_pme detection of GPU support
* Fixed spacing in gmx tune_pme call to thread-MPI mdrun
*Fixed minor issues in gmx traj -av -af
*Removed rogue printing to xvg file in gmx mindist
*Fixed bug in gmx solvate -shell if it yielded 0 SOL.
* Corrected output of gmx do_dssp -sc

Improved documentation
* Made several minor improvements to documentation and messages to users
* Documented that we now support AMD GCN on Mesa/LLVM
* Documented running Clang static analyzer manually

Portability enhancements
* Enabled avx512 in the GROMACS FFTW build only if the compiler supports it
* Worked around false positives in SIMD test from bug in xlc 13.1.5
* Fixed compile with icc of GMX_SIMD=None

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Szilárd Páll
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Manfred Hampl (m-hampl) said :

I suggest that you file this as a bug report.

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Szilárd Páll (sin-pecado) said :

Thanks for getting back, I will file the report.