Posts tagged 'cython'

Overview of the new QuTiP data layer

This post is partial documentation for the implementation of the data-layer that I wrote in the last week or so as part of Google Summer of Code with QuTiP. I may return to talk a bit more about how various algorithms are achieved internally, but for now, this is some indication of what I’ve been working on.

I had previously replaced the old fast_csr_matrix type with the new, custom CSR type as the data backing for Qobj, and all internal QuTiP data representations. This produced some speed-ups in some places due to improved algorithms and better cache usage in places, but its principle advantage was the massive reduction in overhead for function calls between Python and C space, which largely affected small objects.

The full aim, however, is to have QuTiP 5 support many different data representations as the backing of Qobj, and use the most suitable representation for the given data. This will not require every single QuTiP function to have an exponential number of versions for every possible combination of inputs, but only to have specialisations for the most common data combinations. This concept is the “data layer”.

All code examples in this post are prefixed with

1>>> from qutip.core import data

Contiguous memory and finding segfaults in Cython

One of the main advantages of using Cython in the algebraic core of scientific code is fast, non-bounds-checked access to contiguous memory. Of course, when you elide safety-checking, it’s not surprising when you start to get segfaults due to out-of-bounds access and use-after-free bugs in your Cython code.

This post talks a little about why we chose to use raw pointers to access our memory in the upcoming major version of QuTiP rather than other possible methods, and how I tracked down a couple of memory-safety bugs in my code which would have been caught had we been using safer alternatives.

Getting the Cython debugger running on macOS

Debuggers are complicated, especially ones that attach to compiled executables. In Python pdb runs inside the interpreter, so it does not need to control other processes, but this will not work once we have Cython-compiled components (or other C extensions) in our Python programmes. Unfortunately, Cython offers us plenty of opportunities to shoot ourselves in the foot, and it is more likely we will need to debug use-after-free, double-free or other nasty segfault situations.

Cython does come with a debugger, which is more properly a set of Python extensions to gdb, the GNU debugger. Macs come with lldb installed and functional, but sadly getting gdb running is a bit tricky. At the time of writing, I have macOS 10.14 Mojave, the current version of gdb is 9.2, and Cython is 0.29.14. Further, the Cython extensions require Python 2.7, but I need to be able to debug Python 3 programmes since it’s the only supported version of Python.

As of right now, I do not have a fully working debugger, but hopefully I will update this post after rebuilding gdb with some minor patches.