Wrapping C-Blosc2 in Python (a beginner's view)

Marta Iborra — Mon, 10 May 2021 07:32:20 GMT

An initial release of the Python wrapper for C-Blosc2 is now available in: https://github.com/Blosc/python-blosc2. In this blog I will try to explain some of the most difficult aspects that I had to learn in doing this and how I solved them.

This work is being made thanks to a grant from the Python Software Foundation.

Python views

At university, the first programming language that I learned was Python. But because programming was new for the majority of the class the subject only covered the basics: basic statements and classes. And although these were easy to understand, the views were unknown to me (until now).

To explain what the views are, let’s suppose we have the following code in Python:

>>> import sys
>>> a = []
>>> b = a
>>> sys.getrefcount(a)
3

The reference count for the object is 3: a, b and the argument passed to sys.getrefcount().

Basically, to avoid making copies of a same variable, Python uses views. Every variable has its counter and until the counter is 0, the variable is not deleted. But that means that two threads cannot access the counter at the same time. Because having a lock for every variable would be inefficient and could produce deadlocks (which means that several threads are waiting for each other), the GIL was created. So GIL was my next thing to learn.

GIL and Cython

GIL stands for Global Interpreter Lock. With a single lock on the interpreter there are no deadlocks. But the execution of any Python program must acquire the interpreter lock, which prevents some programs to take advantage of the multi-threading execution.

When writing C extensions, this lock is very useful because it can be released. Thus, the program can be more efficient (i.e. threads can actually run in parallel). To write a function with the GIL I spent many time reading about it. Unfortunately, nothing seemed to expain what I wanted to do until I found this nice blog from Nicolas Hug in which he explains the 3 rules you have to follow to make Cython release the GIL.

First of all, Cython needs to know which C functions that were imported are thread-safe. This is done by using the nogil statement in the function declaration. Then, inside the function the with nogil statement lets Cython know that this block is going to be executed with the GIL released. But to make that code block safe, there cannot be any Python interaction inside that block.

To understand it better, an example is shown below:

cdef extern from "math_operation.h":
    int add(int a, int b)nogil

cpdef sum(src, dest):
    cdef int len_src = len(src)
    cdef int len_dest = len(dest)
    cdef int result
    with nogil:
        # Code with the GIL released
        result = add(len_src, len_dest)
    # Code with the GIL, any Python interaction can be done here

The function sum returns the result of adding the length of src and dest. As you can see, the function has been defined with the cpdef statement instead of the def. The c lets Cython know that this function can be called with C. So this is necessary when writing a function with the GIL released, otherwise you will be trying to execute a Python program without the GIL (which, as explained previously cannot be done). Notice that len_src and len_dest have also been defined as C integers with the cdef int statement. If not, it would not be possible to work with them with the GIL released (the with nogil block).

On the other hand, the p lets Cython know that this function can be called through Python. This does not have to be done always, only when you want to call that function from Python.

Cython typed memoryviews

One of the main differences between the python-blosc and python-blosc2 API, is that the functions compress_ptr and decompress_ptr are no longer supported. We decided to do so, because the Pickle protocol 5 already makes an optimization of the copies. That way, we could have a similar performance for compress_ptr and decompress_ptr but with the functions pack and unpack.

However, when timing the functions I realised that in the majority of the cases, although the compress function from python-blosc2 was faster than the compress_ptr, the decompress function was slower than the decompress_ptr. Thus I checked the code to see if the speed could somehow be increased.

Originally, the code used the Python Buffer Protocol. which is part of the Python/C API. The Python Buffer Protocol lets you (among other things) obtain a pointer to the raw data of an object. But because it wasn't clear for me wether it needed to do a copy or not we decided to work with Cython typed memoryviews.

Cython typed memoryviews are very similar to Python memory views, but with the main difference that the first ones are a C-level type and therefore they do not have much Python overhead. Because it is a C-level type you have to know the dimension of the buffer from which you want to obtain the typed memoryview as well as its data type.

The shape dimension of the buffer is expressed writing as many : between brackets as dimensions it has. If the memory is allocated contiguously, you can write ::1 instead in the corresponding dimension. On the other hand, the type is expressed as you would do it in Cython. In the following code, you can see an example for a one-dimensional numpy array:

import numpy as np
arr = np.ones((10**6,), dtype=np.double)
cdef double [:] typed_view = arr

However, if you want to define a function that receives an object whose type may be unknown, you will have to create a Python memoryview and then cast it into the type you wish as in the next example:

# Get a Python memoryview from an object
mem_view = memoryview(object)
# Cast that memory view into an unsigned char memoryview
cdef unsigned char[:]typed_view = mem_view.cast('B')

The 'B' indicates to cast the memoryview type into an unsigned char.

But if I run the latter code for a binary Python string, it produces a runtime error. It took me 10 minutes to fix the error adding the const statement to the definition of the Cython typed memoryview (as shown below), but I spent two days trying to understand the error and its solution.

# Get a Python memoryview from an object
mem_view = memoryview(object)
# Cast that memory view into an unsigned char memoryview
cdef const unsigned char[:]typed_view = mem_view.cast('B')

The reason why the const statement fixed it, is that a binary Python string is a read-only buffer. By declaring the typed memoryview to const, Cython is being told that the object from the memory view is a read-only buffer so that it cannot change it.

Conclusions

So far, my experience wrapping C-Blosc2 has had some ups and downs.

One method that I use whenever I learn something new is to write down a summary of what I read. Sometimes is almost a copy (therefore some people may find it useless), but it always works really well for me. It helps me connect the ideas better or to build a global idea of what I have or want to do.

Another aspect I realized when doing this wrapper is that because I am a stubborn person, I usually tend to force myself to try to understand something and get frustrated if I do not. However, I have to recognize that sometimes it is better to forget about it until the next day. Your brain will organize your ideas at night so that you can invest better your time the next morning.

But maybe the most difficult part for me was the beginning, and therefore I have to thank Francesc Alted and Aleix Alcacer for giving me a push into the not always easy world of Python extensions.

Blosc Home Page (Posts about blosc2 python)

Wrapping C-Blosc2 in Python (a beginner's view)

Python views

GIL and Cython

Cython typed memoryviews

Conclusions