[gmx-developers] API planning

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Wed Dec 21 18:09:04 CET 2016


There already is somehow working python interface capable for writing 
analysis tools. It wraps C++ API. Also one of its version support 
pipelines with many modules analysing same trajectory at same time (e.g. 
you need to read it only once)


Also there is standalone version for GROMACS 2016


Eric Irrgang писал 21-12-2016 19:10:
> Hello Developers,
> I am interested in starting, rekindling and/or joining conversations
> about planning, implementing, and using various sorts of abstraction
> in the Gromacs public and internal interfaces. I am hoping to identify
> other developers working in the same areas, find out where efforts are
> being coordinated, or to volunteer to help coordinate efforts through
> new Redmine issues or reviving old ones.
> Generally, I'm looking at encapsulation or abstraction of
> * Terminal I/O
> * File I/O
>   - trajectory output
>   - input and configuration files
>   - log files
> * Prompted user interaction
> * CLI and runtime options
> * Simulation configuration, input state
> * Gathered parallel data, running state
> * task modules (gmx tools)
> * Compute kernels used within do_md() (for plug-ins as well as
> external access)
> * Domain--rank binding / Interprocess communication / MPI communicator
> It might be possible to break down the areas of focus as follows:
> * data I/O
> * user/controller interface
> * core compute tasks
> In the coming months, I will be working on new ways to use libgromacs
> for workflows implemented at higher levels, such as through Python
> interfaces, expanded ensemble workflow tools, and data flow based
> tools. In some cases, it looks like the C++ API I want already exists
> but may not be widely used within the code, in other cases I know that
> the features I want are under active development, in others I see old
> discussions but no recent comments, and in others I can't tell if any
> conversations have happened. I am trying to determine the best way to
> coordinate with plans or development already under way or with other
> interested developers.
> To some degree, I may just not have found the right search terms to
> find an appropriate Redmine issue or wasn't sure if an existing issue
> was the right place, so I would be grateful if you could point me at
> relevant discussions or suggest that I start new issues. If it is most
> appropriate that I just have a conversation with certain people
> already on certain tasks, I would appreciate some help connecting.
> I am also happy to volunteer to compile what information I can and
> help coordinate documentation, if lack of time is the major obstacle.
> I could start by sharing all of the cross-references I have already
> compiled, but I refrained from that in the current email to keep it to
> a manageable size and relevant to the mailing list.
> Cheers,
> M. Eric Irrgang

Best Regards,
Alexey 'Alexxy' Shvetsov, PhD
Department of Molecular and Radiation Biophysics
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
mailto:alexxyum at gmail.com
mailto:alexxy at omrb.pnpi.spb.ru

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