python 优化函数_使用Parakeet优化Python函数

Parakeet仍然很年轻,对NumPy的支持还不完善,您的代码涉及了一些尚无法使用的功能.

1)您正在包装一个方法,而Parakeet到目前为止只知道如何处理函数.常见的解决方法是制作一个@jit包装的辅助函数,并使用所有必需的成员数据调用您的方法.方法不起作用的原因是,将有意义的类型分配给“自身”并不容易.这不是不可能的,但是足够棘手,以至于在摘下垂悬的果实之前,方法不会进入Parakeet.说到低落的水果…

2)布尔索引.尚未实现,但将在下一版本中发布.

3)np.tile：也不起作用,可能还会在下一个版本中发布.如果您想查看哪些内置函数和NumPy库函数将起作用,请查看Parakeet的mappings模块.

我重写了您的代码,使其对Parakeet更加友好：

@jit

def parakeet_dist(x, y, z, L, periodicX, periodicY, periodicZ):

# perform all-pairs computations more explicitly

# instead of tile + broadcasting

def periodic_diff(x1, x2, periodic):

diff = x1 - x2

if periodic:

if diff > (L / 2): diff -= L

if diff < (-L/2): diff += L

return diff

dx = np.array([[periodic_diff(x1, x2, periodicX) for x1 in x] for x2 in x])

dy = np.array([[periodic_diff(y1, y2, periodicY) for y1 in y] for y2 in y])

dz = np.array([[periodic_diff(z1, z2, periodicZ) for z1 in z] for z2 in z])

d= np.sqrt(dx**2 + dy**2 + dz**2)

# since we can't yet use boolean indexing for masking out zero distances

# have to fall back on explicit loops instead

for i in xrange(len(x)):

for j in xrange(len(x)):

if d[i,j] == 0: d[i,j] = -1

return d, dx, dy, dz

在我的机器上,对于N = 2000,它的运行速度仅比NumPy快3倍(NumPy为0.39s,而Parakeet为0.14s).如果我重写数组遍历以更明确地使用循环,那么性能将比NumPy快约6倍(Parakeet的运行时间约为0.06s)：

@jit

def loopy_dist(x, y, z, L, periodicX, periodicY, periodicZ):

N = len(x)

dx = np.zeros((N,N))

dy = np.zeros( (N,N) )

dz = np.zeros( (N,N) )

d = np.zeros( (N,N) )

def periodic_diff(x1, x2, periodic):

diff = x1 - x2

if periodic:

if diff > (L / 2): diff -= L

if diff < (-L/2): diff += L

return diff

for i in xrange(N):

for j in xrange(N):

dx[i,j] = periodic_diff(x[j], x[i], periodicX)

dy[i,j] = periodic_diff(y[j], y[i], periodicY)

dz[i,j] = periodic_diff(z[j], z[i], periodicZ)

d[i,j] = dx[i,j] ** 2 + dy[i,j] ** 2 + dz[i,j] ** 2

if d[i,j] == 0: d[i,j] = -1

else: d[i,j] = np.sqrt(d[i,j])

return d, dx, dy, dz

通过一些创造性的重写,您还可以使以上代码在Numba中运行,但是仅比NumPy(0.25秒)快约1.5倍.编译时间为Parakeet w /理解：1秒,Parakeet w /循环：.5秒,Numba w /循环：0.9秒.

希望接下来的几个发行版将使NumPy库函数更加惯用,但就目前而言,理解或循环通常是要走的路.