[gmx-developers] plans for Gromacs 5.1 release

Justin Lemkul jalemkul at vt.edu
Wed Nov 26 19:16:19 CET 2014

Hi All,

My code for polarizable simulations with extended Lagrangian for our Drude force 
field is basically done.  I have a few issues related to pdb2gmx left to 
address, but I plan to do that probably in the coming week.  The changes are 
basically an extension of the md-vv integrator and are largely confined to:

1. A few new thermostat functions
2. A few new .mdp settings
3. Small changes within the Trotter decomposition/update functions to call our 
special Drude routines
4. Compatibility with DD

I need to merge in master at some point soon, and the code is all in the "drude" 
branch in git, but it should hopefully be reasonably easy to merge in.  Most of 
the code is simply new, rather than large-scale modifications of existing stuff.


On 11/26/14 12:42 PM, Shirts, Michael R. (mrs5pt) wrote:
> Hi, all-
> My goals for 5.1:
>   * High priority:
>       o 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.
>       o Finally remove the iteration code  (literally in the middle of rebasing
>         the removed-iteration code to the current master when receiving this email)
>       o 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.
>   * Going to try very hard
>       o Add an MC Barostat (especially important if removing iterative MTTK in
>         above).
>       o 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
>       o Fully trotterizing the code to support multiple time steps
>       o A more complete MC framework
>       o 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.
>       o Multiple end states (instead of just A and B)
>       o 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 <mailto:mark.j.abraham at gmail.com>>
> Reply-To: "gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>"
> <gmx-developers at gromacs.org <mailto: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
> <mailto:gmx-developers at gromacs.org>>, Christian Wennberg <chriwen at kth.se
> <mailto:chriwen at kth.se>>, Iman Pouya <iman.pouya at gmail.com
> <mailto:iman.pouya at gmail.com>>, Alfredo Metere <alfredo.metere at scilifelab.se
> <mailto:alfredo.metere at scilifelab.se>>, Anca Hamuraru <anca at streamcomputing.eu
> <mailto:anca at streamcomputing.eu>>, Vincent Hindriksen
> <vincent at streamcomputing.eu <mailto: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


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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