Scipy numba 的特殊功能

Question

此代码失败：

import numpy as np
from numba import jit
import scipy.special as sp

@jit(nopython=True)
def f(a):
    return sp.xlogy(a, a)
  

a = np.array([1,2,0,1], dtype=float)
f(a)

出现如下错误

TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Unknown attribute 'xlogy' of type Module(<module 'scipy.special' from '/home/yair/.local/lib/python3.8/site-packages/scipy/special/__init__.py'>)

但是，我相信它应该可以工作，因为它说 here that xlogy could be overloaded. An 说这不能完成（对于某些其他功能）但也许我认为它改变了。

当然，我可以自己实现，但最好使用已知的解决方案。

编辑：根据下面 Andras Deak 的建议，我尝试使用 numba-scipy。我无法让它工作，希望有一些使用示例。这是我的尝试 - 它们都失败了，请参阅以下错误：

import numpy as np
from numba import jit
import numba_scipy
import scipy as sp
from scipy import special as spc

@jit(nopython=True)
def f1(a):
    return numba_scipy.special.xlogy(a,a)

@jit(nopython=True)
def f2(a):
    return numba_scipy.xlogy(a,a)


@jit(nopython=True)
def f3(a):
    return sp.special.xlogy(a,a)

@jit(nopython=True)
def f4(a):
    return spc.xlogy(a,a)


a = np.array([0,1,2])

try:
    f1(a)
except Exception as e:
    print('f1 fails')
    print(e)

try:
    f2(a)
except Exception as e:
    print('f2 fails')
    print(e)

try:
    f3(a)
except Exception as e:
    print('f3 fails')
    print(e)

try:
    f4(a)
except Exception as e:
    print('f4 fails')
    print(e)

完整的错误信息：

/home/yair/.local/lib/python3.8/site-packages/numba/core/dispatcher.py:238: UserWarning: Numba extension module 'numba_scipy' failed to load due to 'ValueError(No function '__pyx_fuse_0pdtr' found in __pyx_capi__ of 'scipy.special.cython_special')'.
  entrypoints.init_all()
f1 fails
Failed in nopython mode pipeline (step: nopython rewrites)
module 'numba_scipy' has no attribute 'special'
f2 fails
Failed in nopython mode pipeline (step: nopython rewrites)
module 'numba_scipy' has no attribute 'xlogy'
f3 fails
Failed in nopython mode pipeline (step: nopython frontend)
Unknown attribute 'xlogy' of type Module(<module 'scipy.special' from '/home/yair/.local/lib/python3.8/site-packages/scipy/special/__init__.py'>)

File "example.py", line 19:
    def f3(a):
        return sp.special.xlogy(a,a)
        ^

During: typing of get attribute at example.py (19)

File "example.py", line 19:
    def f3(a):
        return sp.special.xlogy(a,a)
        ^

f4 fails
Failed in nopython mode pipeline (step: nopython frontend)
Unknown attribute 'xlogy' of type Module(<module 'scipy.special' from '/home/yair/.local/lib/python3.8/site-packages/scipy/special/__init__.py'>)

File "example.py", line 23:
    def f4(a):
        return spc.xlogy(a,a)
        ^

During: typing of get attribute at example.py (23)

File "example.py", line 23:
    def f4(a):
        return spc.xlogy(a,a)
        ^

Answer 1

由于您根据评论遇到安装问题，我特别建议使用 numba-scipy instead, from the creators of numba itself (link to pypi)。使用 first-party 包扩展总是一个好主意。

very documentation you linked relates to numba_special. If you look at the main page你会看到第一个例子：

>>> import numba
>>> import scipy.special as sc
>>> import numba_special  # The import generates Numba overloads for special
>>> @numba.njit
... def gamma_plus_1(x):
...     return sc.gamma(x) + 1.0
...
>>> gamma_plus_1(5.0)
25.0

请注意您遗漏的 import numba_special 行。

您还必须先安装 numba-special。另请注意项目页面上的警告：

Installing

Numba special depends on SciPy and Numba. Until the fix for this issue is included in a Numba release, numba_special must be installed against the master branch of Numba.

Answer 2

你是从scipy.special调用xlogy函数，其实对于@jit修饰函数调用的函数也需要@jit修饰。所以这就是为什么 xlogy 与您的 f 函数和 numba 抛出错误不兼容。解决方法可能是：

import numpy as np
from numba import jit


@jit(nopython=True)
def myxlogy(x,y):
    return x*np.log(y)


@jit(nopython=True)
def f(a):
    return myxlogy(a,a)

a = np.array([1,2,0,1], dtype=float)
f(a)
>>array([0.        , 1.38629436,        nan, 0.        ])

Scipy numba 的特殊功能

Scipy special functions with numba

python

jit

scipy

python-3.x

numba