[gmx-developers] plans for Gromacs 5.1 release

Mark Abraham mark.j.abraham at gmail.com
Thu Nov 27 14:13:25 CET 2014

On Wed, Nov 26, 2014 at 6:42 PM, Shirts, Michael R. (mrs5pt) <
mrs5pt at eservices.virginia.edu> wrote:

>  Hi, all-
> My goals for 5.1:
>    - High priority:
>       - Resolve any lingering issues with proper framework to do free
>       energy changes, so that everything is better documented and consistent, and
>       addressing lingering questions.
>          - Topics include verifying Hamiltonian replica exchange, making
>          sure integrated with pull code, deciding on best practices, clearing out
>          redmine with free energy related issues, partially unifying analysis
>          approaches.  Adding a MBAR option into GROMACS would be nice, but may need
>          to wait.
Great. These are things also very important here. It's not healthy for the
code to have Shirts-style and old-style implementations not properly
integrated, tested and documented.

>    -
>       -
>     - Finally remove the iteration code  (literally in the middle of
>       rebasing the removed-iteration code to the current master when receiving
>       this email)
Great. I recently considered throwing a birthday party for this patch :-)
The mechanics of the rebase would be very easy for me to do (main issue is
the ongoing header file reorganization in master) - but we need more eyes
than mine on the result!

>    -
>       -
>     - At least partially reorganize the integrator framework bookkeeping
>       to be cleaner and in the Trotter decomposition style.  This would be a code
>       reorganization, but should not be a feature change at this point. So the
>       scope would be whatever is manageable.
Good; it will also be easier to see the wood once the iteration trees are


>    -
>    - Going to try very hard
>       - Add an MC Barostat (especially important if removing iterative
>       MTTK in above).
>     - Better document existing expanded ensemble framework and adding
>       features from with Viveca's expanded ensemble framework to reduce code
>       duplication and harmonize approaches.
>    - Priorities for 5.2
>       - Fully trotterizing the code to support multiple time steps
>       - A more complete MC framework
>       - Free energy calculations using linear basis scheme (requires
>       GPU-accelerated tabulated functions); this should accelerate free energy
>       calculations by removing it form the inner , as well as removing the need
>       to ever write free energy inner loops for SIMD or GPU.
>       - Multiple end states (instead of just A and B)
>       - Enveloping distribution sampling
>  Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434) 243-1821
>   From: Mark Abraham <mark.j.abraham at gmail.com>
> Reply-To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Date: Wednesday, November 26, 2014 at 12:18 PM
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>,
> Christian Wennberg <chriwen at kth.se>, Iman Pouya <iman.pouya at gmail.com>,
> Alfredo Metere <alfredo.metere at scilifelab.se>, Anca Hamuraru <
> anca at streamcomputing.eu>, Vincent Hindriksen <vincent at streamcomputing.eu>
> Subject: [gmx-developers] plans for Gromacs 5.1 release
>   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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