Gaël Varoquaux

Tue 01 April 2008


Of travels and sprints

This month I have traveled a bit for scientific-computing related reasons.

In England

First of all, I was speaking at the OKcon, open knowledge conference in London, about Scientific tools in Python in general, and Mayavi in particular. I jumped on the occasion to visit the Airbus campus in Bristol. We have had some contacts with these guys, because they use Mayavi in some of their homegrown applications, and I was curious to put faces on friendly names on the mailing list. In addition, I was eager to find out how they were using Mayavi and Python scientific tools in an industrial environment, as I have never worked in another place than a physics lab.

Visiting the Airbus campus

The Airbus visit was enlightening: the Bristol campus is a major research facility (several thousands people) dedicated to wing design. A good part of the work is done through simulations deployed on big clusters. These calculations have historically been run in Fortran and C, but apparently the engineers are switching to a mix of compiled languages and Python. Moreover, steering of these simulations, through mesh-design, visualization of the results, analysis of the data, is done mainly through an interact program, ‘flightpad’, that is developed fully in Python, using the Envisage framework to couple together a bunch of scientific components, including Mayavi. I got to spend a fair amount of time with the guys doing this, and it was great to see how they did it. They have a good approach to scientific software design (loosely coupled components, reuse of all the existing libraries), eventhough their goal (automatic generation of Python scripts from user interaction) is way more ambitious than anything I have in mind. I was pleased to see that they where using Mayavi in a way completely consistent with its design, and did not have to hack around limitation.

It was really very encouraging to talk with the software strategist. He obviously completely got it as far as how an open-source model can be profitable to a company like Airbus. See so many people using open source tools as their main tools, as well as a manager ready to back this position, and explaining how it can be beneficial to contribute to an open-source project, really filled me with hope.

Of course visiting the Airbus campus was not only about software, it was also about planes (I got a drive around the campus, and it is quite fun to ride a mini cooper between to 747), and beers (reinventing the world to make it a better place at the pub, after work). I must say there is something special about the scientific Python community, it is the nicest community I know (with the sailing one :->). You meet people that you have never seen before, and you immediately feel at ease.

Open Knowledge conference

The Open Knowledge conference was fun. Not too much like the geek conferences I am used to, as here the focus was on the data, and not the tools , aka the software (for instance, the big deal is when you can get access to the complete public transport time-tables, and you can make maps of poorly connected areas). I met Martin Albrecht from the sage project. It was very interesting to discuss with him. I generally consider myself as doing rather fundamental research (Bose-Einstein condensation), but for him I was in the applied science section, because I use math and computers to do applied things. This distinction between applied and fundamental maths yields a distinction in the application of the code, and therefore the way an open-source scientific project can survive. It was very interesting to see the way sage’s development process therefore differed from scipy’s. I think that both Martin’s talk on sage, and mine on Python and interactive visualization had a lot of success: the room was full of scholars, and they wanted tools to do their work.

In London, I had the occasion to catch up with my brother, and Rob, a former colleague. That was nice too (and yielded more beers).


Nipy Sprint

The week after, I was attending a sprint in Paris on nipy: neuroimaging in Python. We were a bunch of enthusiastic scientific Python users crammed in a small room during the day. There was the team from Berkeley with including Jarrod and Fernando, and all their friends. I got to make new friends, and catch up with old ones. The goal of the nipy effort is to build a complete processing pipeline for neuroimaging data, especially fMRI, in Python. This is a lot of work, as many transformations are applied to the raw data to make it useful for scientific publications. As the field matures, these transformations pile up, and the processing pipeline gets more and more complex. There already exists a good pipeline under MatLab (SPM), the problem is that, due to the poor language features of MatLab, it is a codebase hard to extend and to modify. One of the goals of the nipy project is to make a pluggable architecture, for researcher to be able to replace part of the pipeline by their own code, and thus explore new methods while comparing them to the reference one. This means that there are some interesting software engineering problems in here (pluggable pipelines, framework…, the kind of stuff I like), however the current focus is to get the algorithms right, before trying to do software over-engineering.

The Berkeley group got an NSF grant to work on the project and has been able to hire two developers for two years (Chris Burns and Tom Waite). The effort is lead by Jarrod Millman, and they have put a lot of work in making the underlying libraries better (that is improving numpy and scipy).

I had difficulties contributing any useful code, as I don’t know neuroimaging, but I had the pleasure of seeing people pick up the mayavi API and use it to quickly build domain-specific tools for displaying brains and activation regions. As usual this also revealed some shortcomings in the mlab API that I plan to address ASAP.

IPython Sprint

The week end after Fernando, Laurent Dufréchou, Stefan van der Waalt and myself crashed at my parent’s place to work on ipython1 and the front ends. My mother cooked us some fabulous food and I had a great time.

Unfortunately we did get as far as I would have like. The right abstraction for talking between the ipython1 execution engine, and the front end are not really easy to get right, as the engine is nothing more than an abstract execution engine, that basically only has a namespace and knows how to execute stuff in a non-blocking mode (that’s where it gets hard: how do you know what is going on with your engine and the commands you have sent to it? How do you deal with introspections requests such as tab-completion or docstring exploration). We want as little logics in the front ends as possible: let us not duplicate tab-completion or history. This is why we are progressively building an object, that Fernando dubbed “InputStateManager” that is doing the impedance matching between the front end and the engine. I am starting to believe that the best way to connect this object (ISM) to the front end is via a callback-based mechanism: the front-end calls the ISM methods and gives them a callback to call when finished (for instance if running in a different thread, a Wx frontend would pass something based on Wx.CallAfter to display the result). That way the mechanism is very general, can adapt to event-driven front ends or readline-based one, and knows nothing about the front end. Of course not much code got written, because I am way too slow, and it took me ages to figure this out.

We had a lot of fun, and for me the highlight of the week end was when my girlfriend joined us to do some hacking on a really cool project trying to use the wiki to edit the numpy docstring.

Fernando has pictures of all these happy moments. and I hope he will publish them somewhere (Fernando, get a blog :->). Next time I hope there will be more of us.

Edit:my slides at OKcon

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