[gmx-developers] plans for Gromacs 5.1 release
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
> 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
> 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
> + 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 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
> 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,
> * 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!
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