[gmx-developers] looking for co-mentor for GSoC 2020: TNG format

Magnus Lundborg magnus.lundborg at scilifelab.se
Thu Mar 19 09:14:03 CET 2020


As the main developer of the TNG API I'm happy to hear about this 
initiative as we needed more hands already from the beginning, and 
no-one has taken the development over since I moved on to other things.

On 2020-03-18 21:17, David van der Spoel wrote:
> Den 2020-03-18 kl. 19:20, skrev Oliver Beckstein:
>> Hello Gromacs Developers,
>> As part of Google Summer of Code 2020 with MDAnalysis 
>> <https://www.mdanalysis.org/2020/02/22/gsoc2020/#google-summer-of-code-2020> 
>> we proposed a project to work on the TNG format. Originally the plan 
>> was to just make sure that MDAnalysis can work with TNG but after a 
>> chat with Erik at BPS (and in the spirit of the last MolSSI 
>> interoperability workshop) we thought that it would be more useful to 
>> take a step back and possibly work towards finalizing the TNG format 
>> <https://github.com/MDAnalysis/mdanalysis/wiki/Project-Ideas-2020#project-6-implement-tng-support> with 
>> the goal to make it usable in any MD analysis code (including 
>> MDAnalysis). The preliminary objectives would be:
> Great initiative!
>>  1. Fully define the API and capabilities of TNG.
> The existing functionality or would you add stuff that has been 
> disccussed for a long time like energies and other data blocks?
As far as I know the API should be complete as it is, but perhaps not as 
polished as would be nice. Adding energies and other data blocks are 
more a matter of adding it in the software packages using the library. 
The only exception is that data block IDs are kept as a central 
repository in the library. But this is just to keep track of them and to 
avoid ID conflicts. As far as I remember, there is in principle nothing 
that prevents anyone from writing anything in TNG.
>>  2. Write documentation.
>>  3. Write a reference library implementation (C or C++).
> How would that be different from the existing implementation?
Yes, what is the difference between the existing API and library (in C)? 
There are plans to make it more C++ compliant. That could be a good 
project. A full rewrite to proper C++ would be even better. One problem 
since early on was that the API and ABI was promised to be fully 
backwards compatible. That makes a redesign harder and explains some of 
the "late add-ons".
>>  4. Write tests.
There are some functionality tests in the TNG library, but more 
extensive unit tests would of course be good.
>>  5. Bonus: Write Python bindings (see start in our pytng
>>     <https://github.com/MDAnalysis/pytng> library) and integrate with
>>     MDAnalysis
>> This project outline is not set in stone and we would be more than 
>> happy to adapt it according to your expert input.
>> We have at least one promising candidate student who is interested in 
>> working on this project during 10 weeks this summer.
>> We would need at least one knowledgable co-mentor from the GROMACS 
>> developer community who could commit to mentoring. See 
>> https://google.github.io/gsocguides/mentor/ what is expected of 
>> mentors. In short, you would be involved in selecting students, 
>> communicating with the student (primarily using mailing lists and 
>> issue trackers) on a near-daily basis, help with keeping the project 
>> on track, and evaluating the student for GSoC (midterm and final 
>> evaluation at pass/fail level). About 5h/week is a realistic minimum.
I could hopefully clarify some things in the beginning of the project 
and possible during as well, but I'm afraid I cannot promise any regular 
>> We completely understand that in the current global crisis, you might 
>> have more urgent things to do. But if you think that you could be a 
>> co-mentor for this project, please let us know soon because students 
>> have to write their applications; their deadline is March 31 but they 
>> can submit applications now and unless we have a GROMACS co-mentor we 
>> will not be offering the TNG project so students.
>> Thank you!
>> Oliver (for the MDAnalysis GSoC 2020 Mentors)
>> -- 
>> Oliver Beckstein, DPhil * oliver.beckstein at asu.edu 
>> <mailto:oliver.beckstein at asu.edu>
>> https://becksteinlab.physics.asu.edu/
>> Associate Professor of Physics
>> Arizona State University
>> Center for Biological Physics and Department of Physics
>> Tempe, AZ 85287-1504
>> USA
>> Office: PSF 348
>> Phone: +1 (480) 727-9765
>> FAX: +1 (480) 965-4669
>> Department of Physics: https://physics.asu.edu/content/oliver-beckstein
>> Center for Biological 
>> Physics: https://cbp.asu.edu/content/oliver-beckstein

More information about the gromacs.org_gmx-developers mailing list