[gmx-developers] plans for Gromacs 5.1 release

Szilárd Páll pall.szilard at gmail.com
Wed Nov 26 19:27:39 CET 2014

I'm hoping to be able to get in:
- non-bonded CUDA module split into multiple compilation units (WIP/in gerrit)
- non-bonded task-splitting (for now w/o DD across multiple GPUs and
perhaps CPU & GPU(s)).
- multiple heterogeneous load balancing improvements (WIP, but some of
it will probably miss the deadline as it greatly depends on the GPU
bonded kernels which will most likely still take quite some time to

I assume that
i) Verlet kernel generation and
ii) extending the testing framework
are not considered anymore for 5.1, right?

The former would be important to know because we've held back adding
new sets of kernels to the Verlet scheme as the preprocessor generated
kernels have been considered an undesired direction (for fair
reasons). But now there is a need for feature completion of the Verlet
scheme, so adding new kernels is unavoidable.

I know I'm partly responsible for letting the discussion on latter
issue die out (sorry Teemu), but given the rather low level of
interest in discussing the matter, I don't think that resurrecting the
discussion before 5.1 makes much sense.


On Wed, Nov 26, 2014 at 6:18 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi,
> It's time we got organized for the next minor release. Generally policy is
> unchanged - we do a feature-change release at least once a year, and bugfix
> releases periodically on the last minor/major release. An "extra" release
> for some special purpose is negotiable.
> I propose
> * now:
>     + get code you want to be considered for 5.1 into gerrit (tag the first
> line of the commit message [RFC] or [WIP] if you know that the current state
> of the code is not a serious candidate for merging)
>     + get your karma up by participating in review of others' code
>     + reply to this email (or comment on your patches in gerrit) to guide
> other people about what might be important for them to review
> * mid-January:
>     + release 5.0.x
>     + release 5.1-beta from whatever is the tip of master branch at the time
>     + fork release-5-1 branch then (still open for functionality changes
> until the 5.1-rc1 releases; gerrit's feature for cherry picking between
> branches will make this fork manageable)
> * early-to-mid February:
>     + release 5.1-rc1
>     + close release-5-1 to new functionality, it remains open for bug fixes,
> test cases, and documentation only
>     + test widely on any plausible machine and compiler for portability and
> correctness
>     + release 5.1-rc[234] if that seems like a good idea
> * mid-March:
>     + release 5.0.x for hopefully the last time, pretty much close
> release-5-0 branch
>     + release 5.1
>     + remove the group cutoff scheme
>     + ...
>     + Profit!
> Do speak up if you have a suggestion for a change / request for special
> consideration / whatever. I've deliberately left the Christmas period open
> for people who might want to do a last code push at that time, but a huge
> patch landing without warning on January 10... will probably get ignored by
> me.
> Please note that things like ongoing contribution with testing and code
> review are the primary things that might earn an authorship on Gromacs
> papers (5.0 is still on my TODO list, sorry) - adding some feature is
> awesome, but what reward structure we can offer needs to focus on the large
> amount of inglorious work that has to happen.
> Things team Stockholm are actively working on that we'd like to have ready
> for 5.1 (and the names of the primary people involved)
> * new DD communication support (Berk)
> * enhancements to pull code (Berk)
> * Verlet scheme support for tables, vacuum, Generalized Born (Berk, Alfredo)
> * GPU support for tabulated interactions (Alfredo)
> * GPU acceleration of (at least) dihedral interactions (Iman)
> * combined FFTs for LJ-PME (Christian)
> * offload of bonded interactions for enhancing load balance (Mark)
> * support for latest CUDA offerings (Szilard)
> * OpenCL non-bonded support (mostly Anca from http://www.streamcomputing.eu,
> Mark)
> * support for CPU-based SIMD on everything on the horizon (Erik)
> Like everything else, none of that's going to block releases, but since 5.1
> will be the last minor release with the group cutoff scheme, feature
> completion of the Verlet scheme will be an internal priority for
> development, review, and testing. Full feature completion is unlikely to
> happen, so support for twin-range multiple-time stepping, QM/MM, and AdReS
> may disappear unless people want to put the work in.
> There's a lot of code already in Gerrit awaiting review, particularly from
> Teemu on the analysis tools. I need to help out more there, but do check if
> he's fixing stuff that you might care about!
> If you're working on code that you might want to get into 5.1, speak up!
> Happy reviewing!
> Mark
> --
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