Status update week 3 GSoC

Fast callbacks from SymPy using SymEngine

My main focus the past week has been to get Lambdify in SymEngine to work with multiple output parameters. Last year Isuru Fernando lead the development to support jit-compiled callbacks using LLVM in SymEngine. I started work on leveraging this in the Python wrappers of SymEngine but my work stalled due to time constraints.

But since it is very much related to code generation in SymPy I did put it into my time-line (later in the summer) in my GSoC application. But with the upcoming SciPy conference, and the fact that it would make a nice addition to our tutorial, I have put in work to get this done earlier than first planned.

Another thing on my to-do-list from last week was to get numba working with lambdify. But for this to work we need to wait for a new upstream release of numba (which they are hoping to release before the SciPy conference).

Status of codegen-tutorial material

I have not added any new tutorial material this week, but have been working on making all notebooks work under all targeted operating systems. However, every change to the notebooks have to be checked on all operating systems using both Python 2 and Python 3. This becomes tedious very quickly so I decided to enable continuous integration on our repository. I followed conda-forges approach: Travis CI for OS X, CircleCI for Linux and AppVeyor for Windows (and a private CI server for another Linux setup). And last night I finally got green light on all 4 of our CI services.

Plans for the upcoming week

We have had a performance regression in sympy.cse which has bit me multiple times this week. I managed to craft a small test case indicating that the algorithmic complexity of the new function is considerably worse than before (effectively making it useless for many applications). In my weekly mentor-meeting (with Aaron) we discussed possibly reverting that change. I will first try to see if I can identify easy-to-fix bottlenecks by profiling the code. But the risk is that it is too much work to be done before the upcoming new release of SymPy, and then we will simply revert for now (choosing speed over extensiveness of the sub-expression elimination).

I still need to test the notebooks using not only msvc under Windows (which is currently used in the AppVeyor tests), but also mingw. I did manage to get it working locally but there is still some effort left in order to make this work on AppVeyor. It's extra tricky since there is a bug in distutils in Python 3 which causes the detection of mingw to fail. So we need to either:

  • Patch in distutils (which I believe we can do if we create a conda package for our tutorial material).
  • ...or use something else than pyximport (I'm hesitant to do this before the conference).
  • ...or provide a gcc executable (not a .bat file) that simply spawns gcc.bat (but that executable would need to be compiled during build of our conda package).

Based on my work on making the CI services work, we will need to provide test scripts for the participants to run. We need to provide the organizers with these scripts by June 27th so this needs to be decided upon during next week. I am leaning towards providing an environment.yml file together with a simple instruction of activating said environment, e.g.:

$ conda env create -f environment.yml
$ source activate codegen17
$ python -c "import scipy2017codegen as cg; cg.test()"

This could even be tested on our CI services.

I also intend to add a (perhaps final) tutorial notebook for chemical kinetics where we also consider diffusion. We will solve the PDE using the method of lines. The addition of a spatial dimension in this way is simple in principle, things do tend to become tricky when handling boundary conditions though. I will try to use the simplest possible treatment in order to avoid taking focus from what we are teaching (code-generation).

It is also my hope that this combined diffusion-reaction model is a good candidate for ufuncify from sympy.utilities.autowrap.


Comments powered by Disqus