8000 memcpy-based fast, typed shuffle. by anntzer · Pull Request #6933 · numpy/numpy · GitHub
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memcpy-based fast, typed shuffle. #6933

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Merged
merged 3 commits into from
Jan 17, 2016
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memcpy-based fast, typed shuffle. #6933

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5be93a2
MAINT: memcpy-based ~4x faster, typed shuffle.
anntzer Dec 6, 2015
b8cf7f9
Top shuffle speed for machine-sized ints/floats.
anntzer Jan 7, 2016
309fdd4
Revert to non-generative test.
anntzer Jan 13, 2016
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Top shuffle speed for machine-sized ints/floats. 
Apparently gcc only specializes one branch (the last one) so I went for
another 33% performance increase (matching #6776) in what's likely the
most common use case.
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@anntzer
anntzer committed Jan 17, 2016
commit b8cf7f904974294d4e3af43c68ef23f87385f2f6
26 changes: 18 additions & 8 deletions numpy/random/mtrand/mtrand.pyx
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Expand Up @@ -4982,8 +4982,7 @@ cdef class RandomState:

"""
cdef:
npy_intp i, j, n = len(x)
size_t stride, nbytes
npy_intp i, j, n = len(x), stride, itemsize
char* x_ptr
char* buf_ptr

Expand All @@ -4993,15 +4992,17 @@ cdef class RandomState:
# as MaskedArrays may not support this approach).
x_ptr = <char*><size_t>x.ctypes.data
stride = x.strides[0]
nbytes = x[:1].nbytes
itemsize = x.dtype.itemsize
buf = np.empty_like(x[0]) # GC'd at function exit
buf_ptr = <char*><size_t>buf.ctypes.data
with self.lock:
for i in reversed(range(1, n)):
j = rk_interval(i, self.internal_state)
string.memcpy(buf_ptr, x_ptr + j * stride, nbytes)
string.memcpy(x_ptr + j * stride, x_ptr + i * stride, nbytes)
string.memcpy(x_ptr + i * stride, buf_ptr, nbytes)
# We trick gcc into providing a specialized implementation for
# the most common case, yielding a ~33% performance improvement.
# Note that apparently, only one branch can ever be specialized.
if itemsize == sizeof(npy_intp):
self._shuffle_raw(n, sizeof(npy_intp), stride, x_ptr, buf_ptr)
else:
self._shuffle_raw(n, itemsize, stride, x_ptr, buf_ptr)
elif isinstance(x, np.ndarray) and x.ndim > 1 and x.size:
# Multidimensional ndarrays require a bounce buffer.
buf = np.empty_like(x[0])
Expand All @@ -5018,6 +5019,15 @@ cdef class RandomState:
j = rk_interval(i, self.internal_state)
x[i], x[j] = x[j], x[i]

cdef inline _shuffle_raw(self, npy_intp n, npy_intp itemsize,
npy_intp stride, char* data, char* buf):
cdef n 5583 py_intp i, j
for i in reversed(range(1, n)):
j = rk_interval(i, self.internal_state)
string.memcpy(buf, data + j * stride, itemsize)
string.memcpy(data + j * stride, data + i * stride, itemsize)
string.memcpy(data + i * stride, buf, itemsize)

def permutation(self, object x):
"""
permutation(x)
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