[gmx-developers] looking for co-mentor for GSoC 2020: TNG format
Oliver Beckstein
obeckste at asu.edu
Mon Mar 23 21:40:28 CET 2020
Hello Paul,
> On Mar 23, 2020, at 4:17 AM, Paul bauer <paul.bauer.q at gmail.com> wrote:
>
> Hello Oliver,
>
> I can see what I can do for mentoring, but would need to make sure I understand the guidelines from GSoC better.
https://google.github.io/gsocguides/mentor/ <https://google.github.io/gsocguides/mentor/>
“Mentor: Mentors are people from the community who volunteer to work with a student. Mentors provide guidance such as pointers to useful documentation, code reviews, etc. In addition to providing students with feedback and pointers, a mentor acts as an ambassador to help student contributors integrate into their project’s community. Some organizations choose to assign more than one mentor to each of their students. Many members of the community provide guidance to their project’s GSoC students without mentoring in an “official” capacity, much as they would answer anyone’s questions on the project’s mailing list or IRC channel.”
https://google.github.io/gsocguides/mentor/what-makes-a-good-mentor <https://google.github.io/gsocguides/mentor/what-makes-a-good-mentor>
There’s also a 3-4 weeks “community bonding” period in which the selected student starts interacting directly with mentors and projects. https://google.github.io/gsocguides/mentor/mind-the-gap <https://google.github.io/gsocguides/mentor/mind-the-gap> For the TNG project we would need the time to define the milestones clearly (see https://google.github.io/gsocguides/mentor/setting-expectations <https://google.github.io/gsocguides/mentor/setting-expectations> and https://google.github.io/gsocguides/mentor/managing-the-plan <https://google.github.io/gsocguides/mentor/managing-the-plan> ) and get the student started with the code base, especially as any of the students who are applying have only worked on MDAnalysis before.
>
> I think having a polished version on TNG would be quite helpful not just for core GROMACS but also for our interoperability with other packages, so this should definitely be worth my time.
That’s good, otherwise I would say “no”.
> One thing that concerns me is that we usually have quite a long lag time for code contributions coming from external people or new team members, so porting the whole code to C++ might not be done in the given time span, but it should be possible to get patches at least to the point of being reviewed here.
I admit to having limited experience in large C/C++ projects so your expertise is crucial. My 2 cents would be that in this case I would start with a good test suite that passes under the current version and attack the project with test-driven development. Would be feasible to start from a separate fork of the current TNG repository as a complete rewrite to speed up development? If the library is not immediately integrated into Gromacs itself then maybe separate development strands for the C and new C++ version might be ok? But I do defer to how you would want to handle it – let me know.
It is a concern if the student has to wait for code reviews for days because the student is supposed to work on this specific project for the duration of GSoC. Furthermore, we must evaluate the student three times (https://google.github.io/gsocguides/mentor/evaluations <https://google.github.io/gsocguides/mentor/evaluations>). If we fail the student, they are kicked out (and don’t get paid). If they cannot submit work then we cannot evaluate them fairly.
> Let's see if this gets chosen in the end!
Please have a quick look through my comments above. If you think that this remains a feasible project for a student then I’ll put you down as a co-mentor (do you have a GitHub username and/or let me know another way to reference you, e.g., on the new GitLab installation; please also let me know the official TNG repo – is it really https://github.com/gromacs/tng <https://github.com/gromacs/tng> ?)
It’s also ok to say “no thank you” , it might simply not be a perfect fit, and then I’d rather have students focus on other projects. We can then see if there are other ways to move TNG forward.
Best,
Oliver
>
> Cheers
>
> Paul
>
> On 22/03/2020 23:14, Oliver Beckstein wrote:
>> Hello TNG people,
>>
>> Apologies for the delayed reply.
>>
>> My take-away from your comments on the TNG library are:
>>
>> 1. TNG has all major features defined (although a more polished API might be desirable).
>> 2. You consider the current C code in https://github.com/gromacs/tng <https://github.com/gromacs/tng> as the reference implementation
>> 3. More tests would be welcome.
>> 4. At the moment there is no-one who is really looking after the code. (At least at a cursory glance, documentation is hard to find; presumably https://github.com/gromacs/tng/blob/master/Trajectoryformatspecification.mk <https://github.com/gromacs/tng/blob/master/Trajectoryformatspecification.mk> is important as well as the JCC 2014 paper (and the 2011 one). )
>> 5. You consider porting the existing C code to C++ would be the next important step so that at least Gromacs itself can move towards TNG adoption.
>>
>> We can advertise the project as
>>
>> 1. Port existing TNG C code to C++
>> 2. Write the API documentation (doxygen strings + minimal example for how to use the library)
>> 3. Stretch goal: Create a Python wrapper (based on https://github.com/MDAnalysis/pytng <https://github.com/MDAnalysis/pytng> or other approaches).
>>
>> Questions:
>>
>> Is this a realistic plan for a student with no previous experience with the specifics but knowledge of C/C++ & python, for May 18 – Aug 10 (~3 months)?
>>
>> @Paul: would you be able to co-mentor a student (primarily 1 and 2)?
>>
>> @Magnus: would you be available for consultations – basically, replying to emails on whatever mailing list/issue tracker the conversation will happen?
>>
>> Would you think that this would be worth everyone’s time? Mentors will be involved in choosing students so you won’t get someone that you don’t feel is suitable.
>>
>> There’s no guarantee that this project will be chosen but we would see by March 31 (application deadline).
>>
>>
>> Oliver
>>
>>
>>
>>
>>
>>> On Mar 19, 2020, at 1:16 AM, Paul bauer <paul.bauer.q at gmail.com <mailto:paul.bauer.q at gmail.com>> wrote:
>>>
>>> Hello,
>>>
>>> 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.
>>>
>>> Cheers
>>>
>>> Paul
>>>
>>> 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 <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 <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 <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/ <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> <mailto:oliver.beckstein at asu.edu <mailto:oliver.beckstein at asu.edu>>
>>>>>> https://becksteinlab.physics.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 <https://physics.asu.edu/content/oliver-beckstein>
>>>>>> Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein <https://cbp.asu.edu/content/oliver-beckstein>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>> --
>>> Paul Bauer, PhD
>>> GROMACS Development Manager
>>> KTH Stockholm, SciLifeLab
>>> 0046737308594
>>>
>>> --
>>> Gromacs Developers mailing list
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>>
>>
>> --
>> Oliver Beckstein, DPhil * oliver.beckstein at asu.edu <mailto:oliver.beckstein at asu.edu>
>> https://becksteinlab.physics.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
>>
>> Department of Physics: https://physics.asu.edu/content/oliver-beckstein <https://physics.asu.edu/content/oliver-beckstein>
>> Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein <https://cbp.asu.edu/content/oliver-beckstein>
>>
>
> --
> Paul Bauer, PhD
> GROMACS Development Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
> --
> Gromacs Developers mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before posting!
>
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--
Oliver Beckstein, DPhil * 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
Department of Physics: https://physics.asu.edu/content/oliver-beckstein
Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein
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