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

Paul bauer paul.bauer.q at gmail.com
Thu Mar 19 09:16:49 CET 2020


I concur with Magnus that moving the TNG codebase to C++ would be a 
major win and make integration in e.g. GROMACS even better.
I can also see that I help with mentoring from the GROMACS side, to help 
with providing a smooth integration process.



On 19/03/2020 09:13, Magnus Lundborg wrote:
> Hi,
> 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 co-mentoring.
>>> 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

Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab

More information about the gromacs.org_gmx-developers mailing list