GSoC 2017 mentors and projects

[Max Linke]

Hi All

GSoC 2017 is getting closer and we should start to think about new
projects
and add descriptions for them. I've added a new projects

[wiki-page](https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-2017-Project-Ideas)
with some projects from last year that would still be great to have
this time.

I can be the official org admin again but I won't be a primary mentor
next
year as I anticipate to be busy finishing up several projects. Others
who want
to be a primary mentor, like Richard and Jonathon this year, should
either
pick a project on the ideas page and enter them self as mentors or
add new
projects. I recommend that you feel passionate about the project. I
noticed
myself as a mentor that I had more fun doing it when I worked on a
project
that I cared about.

New projects that would fit GSoC:
- Add universal random access to all readers #314
- Unify Analysis classes API where applicable.

There have also been some other possible fits in the issue tracker
recently
but I can't find them right now.

If David is OK with it we could also offer datreant based projects with
MDAnalysis.

best Max

[Richard Gowers]

I think I'll be free to mentor someone this year, I'll double check the dates.

With the parallelisation project, I think this is a good project, but we should probably do some groundwork to have an analysis case ready.  To avoid having to download a huge trajectory, we could write a script that creates a trajectory that follows an analytical function (eg move atoms according to a sine function).  We could then have the analysis do distance between two atoms, which should follow the same analytical function.

I'm pretty keen to get cellgrid done, I think this would be a very nice library feature.

Richard

[Jonathan Barnoud]

I would be happy to mentor as well. But I did not think yet about what project to offer. Is there a deadline?

Best,
Jonathan

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[Richard Gowers]

https://developers.google.com/open-source/gsoc/timeline

Looks like Feb 9th.  Iirc last year we got feedback that our project ideas weren't well presented, so perhaps this year we should do something like strictly 1 project per mentor to try and make them all good quality.

[Max Linke]

> I would be happy to mentor as well. But I did not think yet about
> what project to offer. Is there a deadline?

Nice to hear. Then we just need one more person and we have two full
mentor teams. About a deadline I just emailed early so you have time to
think about a project. GSoC usually works best when the mentors are
themselves invested in the project.

> https://developers.google.com/open-source/gsoc/timeline
>
> Looks like Feb 9th.

That is the hard deadline. But we should already have some project ideas
before and iterate on them.

> Iirc last year we got feedback that our project
> ideas weren't well presented, so perhaps this year we should do
> something like strictly 1 project per mentor to try and make them all
> good quality.

Maybe not 1 project per main-mentor that we offer. 2-3 should still be
fine to offer. But I would also go for quality instead of quantity. If
we have a better overview of the problem our self it will also help the
student later. I would argue though that the discussions about the
project ideas should happen in issues to which we link in the ideas
pages. The ideas page itself should contain a short description of the
problem.

For the parallelization program we should have do a bit of research on
serializing atomgroups beforehand.

best Max

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[Jan Domanski]

I wanna give it a shot actually

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[Oliver Beckstein]

> On 25 Nov, 2016, at 10:08, Max Linke <max.l...@gmail.com> wrote:
>
> For the parallelization program we should have do a bit of research on serializing atomgroups beforehand.

Serialization is important to discuss. Random access for all readers is essential.

Mahzad (at ASU) has also been benchmarking a range of file formats (DCD, XTC, NCDF) with a dask-based parallelizaton for a map-reduce approach on local and XSEDE HPC resources. She's in the process of putting it together as a technical report that can be more easily discussed. The efficiency and scalability depends highly on the file format (!) and the hardware (SSD, Lustre, NFS, …) as well presumably on how expensive the computation is. It's not entirely straightforward to decide what the best approach is. It should be an interesting discussion. I'd like to find out which approach(es) to paralellization are the most promising and if there is anything that we can do in MDAnalysis to facilitate these approaches.

Oliver

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[Richard Gowers]

For what it's worth, I've got a PR up that gives random access to all readers.

I'd be very interested in reading that technical report.

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[Max Linke]

Random Access is now available in develop. We can start to formalize it
in the next release with regard to offset handling.

For the serialization discussion. In which issue/wikipage/mail thread
did we make the most progress. I know we did discuss this in several
places. It would be nice to gather that information in one place.

About the parralel backend. I would like to have support for joblib
(that means multiprocessing library) since it's by far the easiest
library I have come across to parallelize a for loop.

It would be realy nice it Mahzad could make the report public for all of us.

Max

[Manuel Nuno Melo]

Parallelization is definitely a hot topic to pursue, in all those aspects. I'd be very happy to mentor someone in that project. (My feeling is that dask/joblib may be a bit too high level to get max performance out of it, though)

As I stated earlier I'd rather focus on a single potential project, and this would be it for me. If no-one chooses it, too bad, I'll mentor some other time.

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[Oliver Beckstein]

> On 1 Dec, 2016, at 02:31, Manuel Nuno Melo <manuel.n...@gmail.com> wrote:
>
> Parallelization is definitely a hot topic to pursue, in all those aspects. I'd be very happy to mentor someone in that project. (My feeling is that dask/joblib may be a bit too high level to get max performance out of it, though)

I think for parallelization we simply have to do a lot of prototyping to figure out what works, if there are common patterns, and if and how it makes sense to support it inside MDAnalysis.

>
> On Dec 1, 2016 9:01 AM, "Max Linke" <max.l...@gmail.com> wrote:
>
>
>> On 11/26/2016 12:23 AM, Oliver Beckstein wrote:

[…]

>>>
>>> Mahzad (at ASU) has also been benchmarking a range of file formats (DCD, XTC, NCDF) with a dask-based parallelizaton for a map-reduce approach on local and XSEDE HPC resources. She's in the process of putting it together as a technical report that can be more easily discussed. The efficiency and scalability depends highly on the file format (!) and the hardware (SSD, Lustre, NFS, …) as well presumably on how expensive the computation is. It's not entirely straightforward to decide what the best approach is. It should be an interesting discussion. I'd like to find out which approach(es) to paralellization are the most promising and if there is anything that we can do in MDAnalysis to facilitate these approaches.
>>>
>>

[…]

>>
>> It would be realy nice it Mahzad could make the report public for all of us.

She just has to finish writing it…

[Max Linke]

As a reminder it would be nice if mentors could assign themselves to
ideas on the [ideas-page]. You can also add projects that extend last
year's projects, i.e. the auxillary framework and dependent analysis.

Volunteering this year are: Manuel, Richard, Jonathan and Jan

Merry Christmas everyone
Max

[ideas-page]
https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-2017-Project-Ideas

[Max Linke]

News for the GSoC application. I'm the administrator for NumFOCUS this
year and asked that we can take part under their umbrella. It shouldn't
be a problem that we aren't a NumFOCUS affiliated project right now.

https://github.com/numfocus/gsoc/issues/153

best Max

[Richard Gowers]

Ok I've put myself down for the CellGrid integration and new formats projects.

With the parallelisation project, maybe we should make the scope of this clearer?  (To the best of my understanding...) Realistically what this will need is for Universe to get serialised, and then used with something like dask.  Then once this is complete we can look at making it work automagically with AnalysisBase (but not before!).

Currently the Py3 port doesn't have an assigned mentor, which should mean it doesn't get offered unless someone steps up.  I wasn't sure if there was really enough coherent content there for a GSOC project?  I think it's mostly the DCD port that Tyler and Max have started, then odds and ends until the tests pass?

[Jonathan Barnoud]

I can step up for python 3. The extend of the work is still unknown until the DCD reader is finished, though. It may be too small for GSoC.

I also thought about proposing time aware slicing (<https://github.com/MDAnalysis/mdanalysis/issues/800>). I'll try to write that down latter today.

I can help with the TNG format.

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[Richard Gowers]

Yeah time aware slicing would be a fun project.

We can double up on the formats project afaik, so feel free to put yourself down for that one too.  We could also implement your edr reader as an aux in the same project? (mda.Universe(topol.tpr, traj.trr, aux=ener.edr) anyone?)  Maybe edr as aux is big enough for a project on its own?

I also worry with Python3 there's not really a clear theme to the project.. it will be jumping around fixing various small things in the code base.

[Max Linke]

On 01/17/2017 01:01 PM, Richard Gowers wrote:
> Yeah time aware slicing would be a fun project.
>
> We can double up on the formats project afaik, so feel free to put
> yourself down for that one too. We could also implement your edr reader
> as an aux in the same project? (mda.Universe(topol.tpr, traj.trr,
> aux=ener.edr) anyone?) Maybe edr as aux is big enough for a project on
> its own?
>
> I also worry with Python3 there's not really a clear theme to the
> project.. it will be jumping around fixing various small things in the
> code base.

I would leave python3 out to be honest. After the DCDReader is finished
we can pick at everything that comes up ourselves.

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[Jonathan Barnoud]

I would wait to see the auxiliary data taking some momentum before investing a student on the feature. Also, once we can feed a numpy array as an auxiliary there is not much more to do to plug the EDR parser.

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[Richard Gowers]

Ok I removed it from the list.

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[Oliver Beckstein]

Sorry to jump into the GSOC thread. One other thing that would be useful in the long run would be to move forward with making trajectory readers MDAnalysis-independent. Max has already done this for the Gromacs XDR reader. What I mean by this is that someone else could, in principle, use lib.formats and then use it independently from MDA itself.

Why?

Because between MDAnalysis, mdtraj, pytraj, VMD … we are duplicating code and that's a waste of time and bad software engineering. It would be much better if (eventually) we (the community) have bare-bones readers and then everyone else can use them as part of their library. Generally, people liked that idea, judging from my interactions with others at meetings. Certainly, something like this is not happening overnight but we could take a leadership role and start by moving some of our readers/writers into lib.format. We would then be ready to move forward if we wanted to.

A GSOC project related to trajectory formats could be to

1. formally define the api (basically, numpy arrays or array_like)… follow the Gromacs XDR code
2. move some/all readers/writers to lib.format

[Max Linke]

I like that idea. The DCD reader will also be independent in the future.

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[Hai Nguyen]

On Tue, Jan 17, 2017 at 12:07 PM, Oliver Beckstein <orbe...@gmail.com> wrote:

Sorry to jump into the GSOC thread. One other thing that would be useful in the long run would be to move forward with making trajectory readers MDAnalysis-independent. Max has already done this for the Gromacs XDR reader. What I mean by this is that someone else could, in principle, use lib.formats and then use it independently from MDA itself.

Why?

 

Because between MDAnalysis, mdtraj, pytraj, VMD … we are duplicating code and that's a waste of time and bad software engineering. It would be much better if (eventually) we (the community) have bare-bones readers and then everyone else can use them as part of their library. Generally, people liked that idea, judging from my interactions with others at meetings. Certainly, something like this is not happening overnight but we could take a leadership role and start by moving some of our readers/writers into lib.format. We would then be ready to move forward if we wanted to.

I agree with this. Readers are just readers, just for reading data to memory and nothing else. It would be great if different packages can share the reader and focus more

on data analysis (which is the main aim).

Hai

 

A GSOC project related to trajectory formats could be to

1. formally define the api (basically, numpy arrays or array_like)… follow the Gromacs XDR code
2. move some/all readers/writers to lib.format

Oliver

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[Max Linke]

While we are talking about new projects.

We could also have a GSoC project to convert the tests from nose to
pytest. Scipy is thinking about such a GSoC project. It would be a very
good fit for someone starting to learn python.

best Max

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[Jonathan Barnoud]

It would be a good idea indeed. Does anybody looked at what level of
heacache we are looking at?

[Max Linke]

Not sure. So first it would be to get all tests running again. Then we
have to get rid of the `yield` stuff to parametrize tests and replace it
with `pytest.mark.parametrize` and see if we can rewrite the tests
with pytest idoms.

[Jonathan Barnoud]

We might also want to port some of the plugins.

Alse, just for a matter of scale (because I was curious), there are 140
`yield` statements in the tests, spanning 26 files.

[Max Linke]

Oh this would also mean to replace the tempdir code with the `tmpdir`
parameter available in pytest. This is a lot of work but a GSoC student
could get a reasonable chunk of it done. There are also clear goals that
can be defined.

[Richard Gowers]

Yeah I'd be interested in seeing how a pytest refactor would look like.

https://github.com/MDAnalysis/mdanalysis/blob/develop/testsuite/MDAnalysisTests/core/test_groups.py#L15

So something like that with fixtures instead of the test generator.

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[Manuel Nuno Melo]

+1 for the pytest overhaul initiative.

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[Jan Domanski]

Re pytest overhaul issue, would it be advantageous to have some a single set of tests (a file) converted from nose to py.test – sort of "before and after" example? 

For one thing, it would help to estimate the amount of time needed, secondly, it would be some "preliminary" code for GSoc helping asses the viability of the project. i'm happy to put something together. 

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[Max Linke]

Mosts tests should just work. Some research about porting the plugins to pytest would be good though.

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[Richard Gowers]

Hey Jan. Some of the core tests are best maybe, there's a lot of tests where we go through AtomGroup ResidueGroup and SegmentGroup and check they all slice the same. Obviously crying out for a fixture instead.

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[Max Linke]

I found an interesting blog post that explains how we can
port some if not most of our nose-plugins to pytest

https://nvbn.github.io/2017/02/02/pytest-leaking/

On 01/21/2017 09:30 PM, Richard Gowers wrote:
> Hey Jan. Some of the core tests are best maybe, there's a lot of tests
> where we go through AtomGroup ResidueGroup and SegmentGroup and check
> they all slice the same. Obviously crying out for a fixture instead.
>
>
> On Sat, 21 Jan 2017, 8:10 p.m. Max Linke, <max.l...@gmail.com
> <mailto:max.l...@gmail.com>> wrote:
>
> Mosts tests should just work. Some research about porting the
> plugins to pytest would be good though.
>
>
> On Sat, Jan 21, 2017, 20:47 Jan Domanski <jan...@gmail.com
> <mailto:jan...@gmail.com>> wrote:
>
> Re pytest overhaul issue, would it be advantageous to have some
> a single set of tests (a file) converted from nose to py.test –
> sort of "before and after" example?
>
> For one thing, it would help to estimate the amount of time
> needed, secondly, it would be some "preliminary" code for GSoc
> helping asses the viability of the project. i'm happy to put
> something together.
>
>
> On 20 January 2017 at 14:17, Manuel Nuno Melo

> <manuel.n...@gmail.com <mailto:manuel.n...@gmail.com>>

> wrote:
>
> +1 for the pytest overhaul initiative.
>
> On Fri, Jan 20, 2017 at 11:31 AM, Richard Gowers

> <richard...@gmail.com <mailto:richard...@gmail.com>>

> https://groups.google.com/d/msgid/mdnalysis-devel/995b4574-a1f2-4392-ac31-93aa580b8047%40googlegroups.com
> <https://groups.google.com/d/msgid/mdnalysis-devel/995b4574-a1f2-4392-ac31-93aa580b8047%40googlegroups.com?utm_medium=email&utm_source=footer>.

>
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[Manuel Nuno Melo]

Good find.

On the particular case they implement, it's a leak finder at a lower level than ours, and probably a good idea to add to/replace our check.

On Sat, Feb 4, 2017 at 8:43 AM, Max Linke <max.l...@gmail.com> wrote:

I found an interesting blog post that explains how we can
port some if not most of our nose-plugins to pytest

https://nvbn.github.io/2017/02/02/pytest-leaking/

On 01/21/2017 09:30 PM, Richard Gowers wrote:

Hey Jan. Some of the core tests are best maybe, there's a lot of tests
where we go through AtomGroup ResidueGroup and SegmentGroup and check
they all slice the same. Obviously crying out for a fixture instead.


On Sat, 21 Jan 2017, 8:10 p.m. Max Linke, <max.l...@gmail.com
<mailto:max.l...@gmail.com>> wrote:

    Mosts tests should just work. Some research about porting the
    plugins to pytest would be good though.


    On Sat, Jan 21, 2017, 20:47 Jan Domanski <jan...@gmail.com
    <mailto:jan...@gmail.com>> wrote:

        Re pytest overhaul issue, would it be advantageous to have some
        a single set of tests (a file) converted from nose to py.test –
        sort of "before and after" example?

        For one thing, it would help to estimate the amount of time
        needed, secondly, it would be some "preliminary" code for GSoc
        helping asses the viability of the project. i'm happy to put
        something together.


        On 20 January 2017 at 14:17, Manuel Nuno Melo

        <manuel.n...@gmail.com <mailto:manuel.nuno.melo@gmail.com>>

        wrote:

            +1 for the pytest overhaul initiative.

            On Fri, Jan 20, 2017 at 11:31 AM, Richard Gowers

            <richard...@gmail.com <mailto:richardjgowers@gmail.com>>

                    >>>>> <mailto:mdnalysis-devel%2Bunsubsc...@googlegroups.com>.

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                    >>>>>
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[Max Linke]

We should continue future discussions about the testing on the github issue

https://github.com/MDAnalysis/mdanalysis/issues/884

On 02/06/2017 04:32 PM, Manuel Nuno Melo wrote:
> Good find.
>
> On the particular case they implement, it's a leak finder at a lower
> level than ours, and probably a good idea to add to/replace our check.
>
>
> On Sat, Feb 4, 2017 at 8:43 AM, Max Linke <max.l...@gmail.com
> <mailto:max.l...@gmail.com>> wrote:
>
> I found an interesting blog post that explains how we can
> port some if not most of our nose-plugins to pytest
>
> https://nvbn.github.io/2017/02/02/pytest-leaking/
> <https://nvbn.github.io/2017/02/02/pytest-leaking/>
>
> On 01/21/2017 09:30 PM, Richard Gowers wrote:
>
> Hey Jan. Some of the core tests are best maybe, there's a lot of
> tests
> where we go through AtomGroup ResidueGroup and SegmentGroup and
> check
> they all slice the same. Obviously crying out for a fixture instead.
>
>
> On Sat, 21 Jan 2017, 8:10 p.m. Max Linke, <max.l...@gmail.com
> <mailto:max.l...@gmail.com>

> <mailto:max.l...@gmail.com <mailto:max.l...@gmail.com>>>

> wrote:
>
> Mosts tests should just work. Some research about porting the
> plugins to pytest would be good though.
>
>
> On Sat, Jan 21, 2017, 20:47 Jan Domanski <jan...@gmail.com
> <mailto:jan...@gmail.com>

> <mailto:jan...@gmail.com <mailto:jan...@gmail.com>>> wrote:
>
> Re pytest overhaul issue, would it be advantageous to
> have some
> a single set of tests (a file) converted from nose to
> py.test –
> sort of "before and after" example?
>
> For one thing, it would help to estimate the amount of time
> needed, secondly, it would be some "preliminary" code
> for GSoc
> helping asses the viability of the project. i'm happy to put
> something together.
>
>
> On 20 January 2017 at 14:17, Manuel Nuno Melo
> <manuel.n...@gmail.com

> <mailto:manuel.n...@gmail.com>
> <mailto:manuel.n...@gmail.com
> <mailto:manuel.n...@gmail.com>>>

> wrote:
>
> +1 for the pytest overhaul initiative.
>
> On Fri, Jan 20, 2017 at 11:31 AM, Richard Gowers
> <richard...@gmail.com

> <mailto:richard...@gmail.com>
> <mailto:richard...@gmail.com <mailto:richard...@gmail.com>>>

> >>>>> <mailto:orbe...@gmail.com

> <mailto:orbe...@gmx.net

> <mailto:orbe...@gmx.net>>
> >>>>> skype: orbeckst *
> orbe...@gmail.com <mailto:orbe...@gmail.com>

> <mailto:orbe...@gmail.com

> <mailto:orbe...@gmail.com>>
> >>>>>
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