Creating NumPy universal functions¶
There are two types of universal functions:
- Those which operate on scalars, these are “universal functions” or ufuncs
- Those which operate on higher dimensional arrays and scalars, these are
“generalized universal functions” or gufuncs (
Numba’s vectorize allows Python functions taking scalar input arguments to
be used as NumPy ufuncs. Creating a traditional NumPy ufunc is
not the most straightforward process and involves writing some C code.
Numba makes this easy. Using the
vectorize() decorator, Numba
can compile a pure Python function into a ufunc that operates over NumPy
arrays as fast as traditional ufuncs written in C.
vectorize(), you write your function as operating over
input scalars, rather than arrays. Numba will generate the surrounding
loop (or kernel) allowing efficient iteration over the actual inputs.
vectorize() decorator has two modes of operation:
- Eager, or decoration-time, compilation: If you pass one or more type signatures to the decorator, you will be building a Numpy universal function (ufunc). The rest of this subsection describes building ufuncs using decoration-time compilation.
- Lazy, or call-time, compilation: When not given any signatures, the
decorator will give you a Numba dynamic universal function
DUFunc) that dynamically compiles a new kernel when called with a previously unsupported input type. A later subsection, “Dynamic universal functions”, describes this mode in more depth.
As described above, if you pass a list of signatures to the
vectorize() decorator, your function will be compiled
into a Numpy ufunc. In the basic case, only one signature will be
from numba import vectorize, float64 @vectorize([float64(float64, float64)]) def f(x, y): return x + y
If you pass several signatures, beware that you have to pass most specific signatures before least specific ones (e.g., single-precision floats before double-precision floats), otherwise type-based dispatching will not work as expected:
@vectorize([int32(int32, int32), int64(int64, int64), float32(float32, float32), float64(float64, float64)]) def f(x, y): return x + y
The function will work as expected over the specified array types:
>>> a = np.arange(6) >>> f(a, a) array([ 0, 2, 4, 6, 8, 10]) >>> a = np.linspace(0, 1, 6) >>> f(a, a) array([ 0. , 0.4, 0.8, 1.2, 1.6, 2. ])
but it will fail working on other types:
>>> a = np.linspace(0, 1+1j, 6) >>> f(a, a) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: ufunc 'ufunc' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
You might ask yourself, “why would I go through this instead of compiling a simple iteration loop using the @jit decorator?”. The answer is that NumPy ufuncs automatically get other features such as reduction, accumulation or broadcasting. Using the example above:
>>> a = np.arange(12).reshape(3, 4) >>> a array([[ 0, 1, 2, 3], [ 4, 5, 6, 7], [ 8, 9, 10, 11]]) >>> f.reduce(a, axis=0) array([12, 15, 18, 21]) >>> f.reduce(a, axis=1) array([ 6, 22, 38]) >>> f.accumulate(a) array([[ 0, 1, 2, 3], [ 4, 6, 8, 10], [12, 15, 18, 21]]) >>> f.accumulate(a, axis=1) array([[ 0, 1, 3, 6], [ 4, 9, 15, 22], [ 8, 17, 27, 38]])
Standard features of ufuncs (NumPy documentation).
Only the broadcasting features of ufuncs are supported in compiled code.
vectorize() decorator supports multiple ufunc targets:
This creates an ufunc-like object. See documentation for CUDA ufunc for detail.
A general guideline is to choose different targets for different data sizes and algorithms. The “cpu” target works well for small data sizes (approx. less than 1KB) and low compute intensity algorithms. It has the least amount of overhead. The “parallel” target works well for medium data sizes (approx. less than 1MB). Threading adds a small delay. The “cuda” target works well for big data sizes (approx. greater than 1MB) and high compute intensity algorithms. Transferring memory to and from the GPU adds significant overhead.
vectorize() allows you to write ufuncs that work on one
element at a time, the
guvectorize() decorator takes the concept
one step further and allows you to write ufuncs that will work on an
arbitrary number of elements of input arrays, and take and return arrays of
differing dimensions. The typical example is a running median or a
functions don’t return their result value: they take it as an array
argument, which must be filled in by the function. This is because the
array is actually allocated by NumPy’s dispatch mechanism, which calls into
the Numba-generated code.
Here is a very simple example:
@guvectorize([(int64[:], int64, int64[:])], '(n),()->(n)') def g(x, y, res): for i in range(x.shape): res[i] = x[i] + y
The underlying Python function simply adds a given scalar (
y) to all
elements of a 1-dimension array. What’s more interesting is the declaration.
There are two things there:
- the declaration of input and output layouts, in symbolic form:
(n),()->(n)tells NumPy that the function takes a n-element one-dimension array, a scalar (symbolically denoted by the empty tuple
()) and returns a n-element one-dimension array;
- the list of supported concrete signatures as per
@vectorize; here, as in the above example, we demonstrate
1D array type can also receive scalar arguments (those with shape
In the above example, the second argument also could be declared as
int64[:]. In that case, the value must be read by
We can now check what the compiled ufunc does, over a simple example:
>>> a = np.arange(5) >>> a array([0, 1, 2, 3, 4]) >>> g(a, 2) array([2, 3, 4, 5, 6])
The nice thing is that NumPy will automatically dispatch over more complicated inputs, depending on their shapes:
>>> a = np.arange(6).reshape(2, 3) >>> a array([[0, 1, 2], [3, 4, 5]]) >>> g(a, 10) array([[10, 11, 12], [13, 14, 15]]) >>> g(a, np.array([10, 20])) array([[10, 11, 12], [23, 24, 25]])
Overwriting input values¶
In most cases, writing to inputs may also appear to work - however, this behaviour cannot be relied on. Consider the following example function:
@guvectorize([(float64[:], float64[:])], '()->()') def init_values(invals, outvals): invals = 6.5 outvals = 4.2
Calling the init_values function with an array of float64 type results in visible changes to the input:
>>> invals = np.zeros(shape=(3, 3), dtype=np.float64) >>> outvals = init_values(invals) >>> invals array([[6.5, 6.5, 6.5], [6.5, 6.5, 6.5], [6.5, 6.5, 6.5]]) >>> outvals array([[4.2, 4.2, 4.2], [4.2, 4.2, 4.2], [4.2, 4.2, 4.2]])
This works because NumPy can pass the input data directly into the init_values function as the data dtype matches that of the declared argument. However, it may also create and pass in a temporary array, in which case changes to the input are lost. For example, this can occur when casting is required. To demonstrate, we can use an array of float32 with the init_values function:
>>> invals = np.zeros(shape=(3, 3), dtype=np.float32) >>> outvals = init_values(invals) >>> invals array([[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]], dtype=float32)
In this case, there is no change to the invals array because the temporary casted array was mutated instead.
Dynamic universal functions¶
from numba import vectorize @vectorize def f(x, y): return x * y
f() is a
DUFunc instance that
starts with no supported input types. As you make calls to
Numba generates new kernels whenever you pass a previously unsupported
input type. Given the example above, the following set of interpreter
interactions illustrate how dynamic compilation works:
>>> f <numba._DUFunc 'f'> >>> f.ufunc <ufunc 'f'> >>> f.ufunc.types 
The example above shows that
DUFunc instances are not
ufuncs. Rather than subclass ufunc’s,
instances work by keeping a
ufunc member, and
then delegating ufunc property reads and method calls to this member
(also known as type aggregation). When we look at the initial types
supported by the ufunc, we can verify there are none.
Let’s try to make a call to
>>> f(3,4) 12 >>> f.types # shorthand for f.ufunc.types ['ll->l']
If this was a normal Numpy ufunc, we would have seen an exception
complaining that the ufunc couldn’t handle the input types. When we
f() with integer arguments, not only do we receive an
answer, but we can verify that Numba created a loop supporting C
We can add additional loops by calling
f() with different inputs:
>>> f(1.,2.) 2.0 >>> f.types ['ll->l', 'dd->d']
We can now verify that Numba added a second loop for dealing with
If we mix input types to
f(), we can verify that Numpy ufunc
casting rules are still in effect:
>>> f(1,2.) 2.0 >>> f.types ['ll->l', 'dd->d']
This example demonstrates that calling
f() with mixed types
caused Numpy to select the floating-point loop, and cast the integer
argument to a floating-point value. Thus, Numba did not create a
DUFunc behavior leads us to a point similar to
the warning given above in “The @vectorize decorator” subsection,
but instead of signature declaration order in the decorator, call
order matters. If we had passed in floating-point arguments first,
any calls with integer arguments would be cast to double-precision
floating-point values. For example:
>>> @vectorize ... def g(a, b): return a / b ... >>> g(2.,3.) 0.66666666666666663 >>> g(2,3) 0.66666666666666663 >>> g.types ['dd->d']
If you require precise support for various type signatures, you should
specify them in the
vectorize() decorator, and not rely
on dynamic compilation.