[gmx-developers] Verlet-Tables integration

Berk Hess hess at kth.se
Wed Nov 14 09:11:55 CET 2018


I don't really think we need a usecase, but more people motivated to 
work on it.

We have delayed the work also because we are waiting for a new 
non-bonded kernel structure. But we just as well start without that, 
since it will not take much work to port the additional tabulated 
kernels to a new framework.

What is a dependency is a selecting the table index based on atom type 
(pairs). We want to get rid of the (mis)use of energy groups for this 
purpose in the group scheme.



On 13/11/2018 23.53, Mark Abraham wrote:
> Hi,
> Not much has happened. I did some basic cleanup, and Erik has worked 
> on some table classes in src/gromacs/tables. Alfredo has some old GPU 
> kernels buried somewhere on Gerrit.
> It would be good to identify a use case that someone has interest in 
> to e.g. contribute coding time, test cases, design idea sounding 
> board. AFAIK none of the GROMACS core developers uses this feature, so 
> their priorities tend to align elsewhere. However, we know it's useful 
> to people, so we'd like to find a group that can work together to make 
> it happen!
> Some of those dot points are a bit out of date, but the general list 
> of things to do is about right.
> Mark
> On Tue, Nov 13, 2018 at 3:48 PM Adriaan Riet <adriaan.riet at case.edu 
> <mailto:adriaan.riet at case.edu>> wrote:
>     Hello everyone,
>     I know that Feature #1347 talks about the necessary steps to get
>     tables into Verlet (pasted below). I'm curious to know where this
>     sits. I'm happy to contribute where (if) I can, but don't see
>     clearly where to jump in. Have the points of the list been
>     integrated into redmine feature requests? Have any of these been
>     implemented yet?
>     Thanks,
>     Adriaan Riet
>     Things to do (roughly in order):
>       * support regressiontests being able to read tables from grompp
>         or mdrun, so that new functionality in the code doesn't need
>         matching changes to the other repo for valid testing in the
>         few cases where they use tables (|*CSTab*| in group-scheme
>         kernels)
>       * add integration tests, e.g. a Martini-style(?) non-bonded, and
>         several kinds of bonded interactions
>       * extract code from mdlib (particularly init_forcerec) so that
>         it is callable at grompp time, make sure grompp can issue all
>         notes and warnings, permit mdrun to repeat any of those that
>         it might need to. Keep code for making hardware-specific
>         layout decisions in mdrun, because we won't know whether the
>         kernels need tables for CPUs or GPUs until then. If we can do
>         it without significant loss of accuracy, grompp should handle
>         any regularization of the user input (e.g. by constructing and
>         testing CPU and GPU tables, if necessary).
>       * move e.g. dihedral-interaction table reading to grompp, bump
>         .tpr version, write to .tpr, read in mdrun, add infrastructure
>         to support gmx check and gmx dump on new .tpr contents
>       * move angle- and bond-interaction table reading to grompp,
>         probably another .tpr version bump
>       * move short-range interaction tables to grompp for group scheme
>       * extend |[pairs]| to permit atom-type pairs to use an
>         interaction shape read from a table, e.g. from a file named on
>         that line of the topology. Should we have a per-pair-type
>         scaling parameter? Requirements for simulations that use only
>         user tables, and those that mix user tables with normal
>         short-ranged interaction types probably differ.
>       * add Verlet-scheme table-support infrastructure
>       * add CPU kernels (hopefully in new scheme)
>       * add GPU kernels (recycle from Alfredo's patch in gerrit)
>       * after some time passes and master branch rebases enough,
>         remove workaround from regressiontests (which is anyway only
>         needed for group-scheme kernel testing)
>     -- 
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