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ENH: Vectorize np.partition and np.argpartition using AVX-512 #24201

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Merged
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Oct 1, 2023
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dddc046
Update submodule to latest
r-devulap Jul 13, 2023
489acbb
Add benchmarks for np.partition
r-devulap Jun 29, 2023
4a9ac25
ENH: Use avx512_qselect for np.partition
r-devulap Jul 13, 2023
12ae67d
TST: Add tests for np.partition
r-devulap Jul 15, 2023
234754d
BENCH: Add benchmarks for argpartition
r-devulap Jul 24, 2023
f3ac24b
Update x86-simd-sort submodule to latest
r-devulap Jul 24, 2023
d8643a4
get_partition_func does not need an extra argument
r-devulap Jul 24, 2023
0c86047
ENH: Use avx512_argselect for np.argpartition
r-devulap Jul 24, 2023
1a3caed
TST: add tests for np.argpartition
r-devulap Jul 24, 2023
8e58998
Enable AVX-512 partition and argpartition on Windows
r-devulap Jul 25, 2023
1999828
Move PyArray_PartitionFunc and PyArray_ArgPartitionFunc out of ndarra…
r-devulap Jul 26, 2023
c0bdd18
MAINT: Prevent re-definition of quickselect dispatch on ARM 32-bit
r-devulap Aug 1, 2023
ae33785
Avoid using template specializations for quickselect and argquicksele…
r-devulap Aug 2, 2023
cd9df94
Update submodule to latest
r-devulap Aug 8, 2023
25a2efb
Update x86-simd-sort submodule to latest
r-devulap Sep 5, 2023
29a9267
Update x86-simd-sort submodule to latest
r-devulap Sep 6, 2023
f3f6111
ifdef remove avx512 instantiations for CYGWIN
r-devulap Sep 7, 2023
fc5b215
Enable quicksort on WIN32
r-devulap Sep 8, 2023
9d986f7
BUG: Fix compile error for avx512_qselect
r-devulap Sep 8, 2023
fcb6249
BUG: Fix qselect function declaration argument
r-devulap Sep 8, 2023
6c1b8c7
Disable avx512_qselect on 32-bit systems
r-devulap Sep 8, 2023
cb176c1
Add may vary to output of np.partition and np.argpartition in docs
r-devulap Sep 8, 2023
6cd06c0
Use np::Half instead of np_tag::npy_half::type
r-devulap Sep 19, 2023
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36 changes: 33 additions & 3 deletions benchmarks/benchmarks/bench_function_base.py
Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ def memoize(f):
def wrapped(*args):
if args not in _memoized:
_memoized[args] = f(*args)

return _memoized[args].copy()

return f
Expand All @@ -154,7 +154,7 @@ def random(size, dtype):
arr = np.arange(size, dtype=dtype)
np.random.shuffle(arr)
return arr

@staticmethod
@memoize
def ordered(size, dtype):
Expand Down Expand Up @@ -237,7 +237,6 @@ def random_bubble(cls, size, dtype, bubble_num, bubble_size=None):

return cls.random_unsorted_area(size, dtype, frac, bubble_size)


class Sort(Benchmark):
"""
This benchmark tests sorting performance with several
Expand Down Expand Up @@ -288,6 +287,37 @@ def time_argsort(self, kind, dtype, array_type):
np.argsort(self.arr, kind=kind)


class Partition(Benchmark):
params = [
['float64', 'int64', 'float32', 'int32', 'int16', 'float16'],
[
('random',),
('ordered',),
('reversed',),
('uniform',),
('sorted_block', 10),
('sorted_block', 100),
('sorted_block', 1000),
],
[10, 100, 1000],
]
param_names = ['dtype', 'array_type', 'k']

# The size of the benchmarked arrays.
ARRAY_SIZE = 100000

def setup(self, dtype, array_type, k):
np.random.seed(1234)
array_class = array_type[0]
self.arr = getattr(SortGenerator, array_class)(self.ARRAY_SIZE,
dtype, *array_type[1:])

def time_partition(self, dtype, array_type, k):
temp = np.partition(self.arr, k)

def time_argpartition(self, dtype, array_type, k):
temp = np.argpartition(self.arr, k)

class SortWorst(Benchmark):
def setup(self):
# quicksort median of 3 worst case
Expand Down
2 changes: 1 addition & 1 deletion numpy/core/_add_newdocs.py
Original file line number Diff line number Diff line change
Expand Up @@ -4239,7 +4239,7 @@
>>> a = np.array([3, 4, 2, 1])
>>> a.partition(3)
>>> a
array([2, 1, 3, 4])
array([2, 1, 3, 4]) # may vary

>>> a.partition((1, 3))
>>> a
Expand Down
8 changes: 4 additions & 4 deletions numpy/core/fromnumeric.py
Original file line number Diff line number Diff line change
Expand Up @@ -740,7 +740,7 @@ def partition(a, kth, axis=-1, kind='introselect', order=None):
>>> a = np.array([7, 1, 7, 7, 1, 5, 7, 2, 3, 2, 6, 2, 3, 0])
>>> p = np.partition(a, 4)
>>> p
array([0, 1, 2, 1, 2, 5, 2, 3, 3, 6, 7, 7, 7, 7])
array([0, 1, 2, 1, 2, 5, 2, 3, 3, 6, 7, 7, 7, 7]) # may vary

``p[4]`` is 2; all elements in ``p[:4]`` are less than or equal
to ``p[4]``, and all elements in ``p[5:]`` are greater than or
Expand Down Expand Up @@ -838,13 +838,13 @@ def argpartition(a, kth, axis=-1, kind='introselect', order=None):

>>> x = np.array([3, 4, 2, 1])
>>> x[np.argpartition(x, 3)]
array([2, 1, 3, 4])
array([2, 1, 3, 4]) # may vary
>>> x[np.argpartition(x, (1, 3))]
array([1, 2, 3, 4])
array([1, 2, 3, 4]) # may vary

>>> x = [3, 4, 2, 1]
>>> np.array(x)[np.argpartition(x, 3)]
array([2, 1, 3, 4])
array([2, 1, 3, 4]) # may vary

Multi-dimensional array:

Expand Down
6 changes: 0 additions & 6 deletions numpy/core/include/numpy/ndarraytypes.h
Original file line number Diff line number Diff line change
Expand Up @@ -400,12 +400,6 @@ typedef int (PyArray_FillFunc)(void *, npy_intp, void *);

typedef int (PyArray_SortFunc)(void *, npy_intp, void *);
typedef int (PyArray_ArgSortFunc)(void *, npy_intp *, npy_intp, void *);
typedef int (PyArray_PartitionFunc)(void *, npy_intp, npy_intp,
npy_intp *, npy_intp *,
void *);
typedef int (PyArray_ArgPartitionFunc)(void *, npy_intp *, npy_intp, npy_intp,
npy_intp *, npy_intp *,
void *);

typedef int (PyArray_FillWithScalarFunc)(void *, npy_intp, void *, void *);

Expand Down
7 changes: 7 additions & 0 deletions numpy/core/src/common/npy_partition.h
Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,19 @@

#define NPY_MAX_PIVOT_STACK 50

typedef int (PyArray_PartitionFunc)(void *, npy_intp, npy_intp,
npy_intp *, npy_intp *, npy_intp,
void *);
typedef int (PyArray_ArgPartitionFunc)(void *, npy_intp *, npy_intp, npy_intp,
npy_intp *, npy_intp *, npy_intp,
void *);
#ifdef __cplusplus
extern "C" {
#endif

NPY_NO_EXPORT PyArray_PartitionFunc *
get_partition_func(int type, NPY_SELECTKIND which);

NPY_NO_EXPORT PyArray_ArgPartitionFunc *
get_argpartition_func(int type, NPY_SELECTKIND which);

Expand Down
6 changes: 3 additions & 3 deletions numpy/core/src/multiarray/item_selection.c
Original file line number Diff line number Diff line change
Expand Up @@ -832,7 +832,7 @@ npy_fastrepeat(

return npy_fastrepeat_impl(
n_outer, n, nel, chunk, broadcast, counts, new_data, old_data, elsize,
cast_info, needs_refcounting);
cast_info, needs_refcounting);
}


Expand Down Expand Up @@ -1255,7 +1255,7 @@ _new_sortlike(PyArrayObject *op, int axis, PyArray_SortFunc *sort,
npy_intp npiv = 0;
npy_intp i;
for (i = 0; i < nkth; ++i) {
ret = part(bufptr, N, kth[i], pivots, &npiv, op);
ret = part(bufptr, N, kth[i], pivots, &npiv, nkth, op);
if (needs_api && PyErr_Occurred()) {
ret = -1;
}
Expand Down Expand Up @@ -1439,7 +1439,7 @@ _new_argsortlike(PyArrayObject *op, int axis, PyArray_ArgSortFunc *argsort,
npy_intp npiv = 0;

for (i = 0; i < nkth; ++i) {
ret = argpart(valptr, idxptr, N, kth[i], pivots, &npiv, op);
ret = argpart(valptr, idxptr, N, kth[i], pivots, &npiv, nkth, op);
/* Object comparisons may raise an exception in Python 3 */
if (needs_api && PyErr_Occurred()) {
ret = -1;
Expand Down
21 changes: 7 additions & 14 deletions numpy/core/src/npysort/quicksort.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -69,23 +69,12 @@
#define SMALL_MERGESORT 20
#define SMALL_STRING 16

// Temporarily disable AVX512 sorting on WIN32 and CYGWIN until we can figure
// Disable AVX512 sorting on CYGWIN until we can figure
// out why it has test failures
#if defined(_MSC_VER) || defined(__CYGWIN__)
template<typename T>
inline bool quicksort_dispatch(T*, npy_intp)
{
return false;
}
template<typename T>
inline bool aquicksort_dispatch(T*, npy_intp*, npy_intp)
{
return false;
}
#else
template<typename T>
inline bool quicksort_dispatch(T *start, npy_intp num)
{
#if !defined(__CYGWIN__)
using TF = typename np::meta::FixedWidth<T>::Type;
void (*dispfunc)(TF*, intptr_t) = nullptr;
if (sizeof(T) == sizeof(uint16_t)) {
Expand All @@ -104,12 +93,15 @@ inline bool quicksort_dispatch(T *start, npy_intp num)
(*dispfunc)(reinterpret_cast<TF*>(start), static_cast<intptr_t>(num));
return true;
}
#endif // __CYGWIN__
(void)start; (void)num; // to avoid unused arg warn
return false;
}

template<typename T>
inline bool aquicksort_dispatch(T *start, npy_intp* arg, npy_intp num)
{
#if !defined(__CYGWIN__)
using TF = typename np::meta::FixedWidth<T>::Type;
void (*dispfunc)(TF*, npy_intp*, npy_intp) = nullptr;
#ifndef NPY_DISABLE_OPTIMIZATION
Expand All @@ -124,9 +116,10 @@ inline bool aquicksort_dispatch(T *start, npy_intp* arg, npy_intp num)
(*dispfunc)(reinterpret_cast<TF*>(start), arg, num);
return true;
}
#endif // __CYGWIN__
(void)start; (void)arg; (void)num; // to avoid unused arg warn
return false;
}
#endif // _MSC_VER || CYGWIN

/*
*****************************************************************************
Expand Down
86 changes: 82 additions & 4 deletions numpy/core/src/npysort/selection.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -25,13 +25,83 @@
#include <array>
#include <cstdlib>
#include <utility>
#include "simd_qsort.hpp"

#define NOT_USED NPY_UNUSED(unused)

template<typename T>
inline bool quickselect_dispatch(T* v, npy_intp num, npy_intp kth)
{
#ifndef __CYGWIN__
/*
* Only defined for int16_t, uint16_t, float16, int32_t, uint32_t, float32,
* int64_t, uint64_t, double
* TODO: Enable quickselect for 32-bit. np.argpartition is only vectorized
* for 64-bit when npy_intp is 8 bytes, which means np.partition and
* np.argpartition will produces different results on 32-bit systems.
* Several tests in test_multiarray.py rely on these results being
* identical. We should get rid of this constraint and re-write
* these tests once we enable this for 32-bit.
*/
if constexpr (
(std::is_integral_v<T> || std::is_floating_point_v<T> || std::is_same_v<T, np::Half>) &&
(sizeof(T) == sizeof(uint16_t) || sizeof(T) == sizeof(uint32_t) || sizeof(T) == sizeof(uint64_t)) &&
sizeof(npy_intp) == sizeof(int64_t)) {
using TF = typename np::meta::FixedWidth<T>::Type;
void (*dispfunc)(TF*, npy_intp, npy_intp) = nullptr;
if constexpr (sizeof(T) == sizeof(uint16_t)) {
#ifndef NPY_DISABLE_OPTIMIZATION
#include "simd_qsort_16bit.dispatch.h"
#endif
NPY_CPU_DISPATCH_CALL_XB(dispfunc = np::qsort_simd::template QSelect, <TF>);
}
else if constexpr (sizeof(T) == sizeof(uint32_t) || sizeof(T) == sizeof(uint64_t)) {
#ifndef NPY_DISABLE_OPTIMIZATION
#include "simd_qsort.dispatch.h"
#endif
NPY_CPU_DISPATCH_CALL_XB(dispfunc = np::qsort_simd::template QSelect, <TF>);
}
if (dispfunc) {
(*dispfunc)(reinterpret_cast<TF*>(v), num, kth);
return true;
}
}
#endif
(void)v; (void)num; (void)kth; // to avoid unused arg warn
return false;
}
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Windows will never get the faster version?

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The quicksort patch ran into some problem with WIN32 builds and I never quite figured it out. Let me try running the partition patch through the CI, may be this one has better luck on windows.

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Looks like this one had no trouble. Windows will get the faster version too :) Might be worth checking if quicksort can be enabled, but will do it in a separate PR.

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It seems to work. Should we circle back to enabling AVX512 quicksort for windows?

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Yup, separate PR?

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Yes, sorry, separate PR would be good.

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@r-devulap r-devulap Sep 8, 2023

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AVX512 quicksort, argsort, partition and argpartition are all enabled on windows (64-bit only though).


template<typename T>
inline bool argquickselect_dispatch(T* v, npy_intp* arg, npy_intp num, npy_intp kth)
{
#ifndef __CYGWIN__
/*
* Only defined for int32_t, uint32_t, float32, int64_t, uint64_t, double
*/
if constexpr (
(std::is_integral_v<T> || std::is_floating_point_v<T>) &&
(sizeof(T) == sizeof(uint32_t) || sizeof(T) == sizeof(uint64_t)) &&
// x86-simd-sort uses 8-byte int to store arg values, npy_intp is 4 bytes in 32-bit
sizeof(npy_intp) == sizeof(int64_t)) {
using TF = typename np::meta::FixedWidth<T>::Type;
#ifndef NPY_DISABLE_OPTIMIZATION
#include "simd_qsort.dispatch.h"
#endif
void (*dispfunc)(TF*, npy_intp*, npy_intp, npy_intp) = nullptr;
NPY_CPU_DISPATCH_CALL_XB(dispfunc = np::qsort_simd::template ArgQSelect, <TF>);
if (dispfunc) {
(*dispfunc)(reinterpret_cast<TF*>(v), arg, num, kth);
return true;
}
}
#endif
(void)v; (void)arg; (void)num; (void)kth; // to avoid unused arg warn
return false;
}

template <typename Tag, bool arg, typename type>
NPY_NO_EXPORT int
introselect_(type *v, npy_intp *tosort, npy_intp num, npy_intp kth,
npy_intp *pivots, npy_intp *npiv);
introselect_(type *v, npy_intp *tosort, npy_intp num, npy_intp kth, npy_intp *pivots, npy_intp *npiv);

/*
*****************************************************************************
Expand Down Expand Up @@ -397,17 +467,25 @@ introselect_(type *v, npy_intp *tosort, npy_intp num, npy_intp kth,
template <typename Tag>
static int
introselect_noarg(void *v, npy_intp num, npy_intp kth, npy_intp *pivots,
npy_intp *npiv, void *)
npy_intp *npiv, npy_intp nkth, void *)
{
using T = typename std::conditional<std::is_same_v<Tag, npy::half_tag>, np::Half, typename Tag::type>::type;
if ((nkth == 1) && (quickselect_dispatch((T *)v, num, kth))) {
return 0;
}
return introselect_<Tag, false>((typename Tag::type *)v, nullptr, num, kth,
pivots, npiv);
}

template <typename Tag>
static int
introselect_arg(void *v, npy_intp *tosort, npy_intp num, npy_intp kth,
npy_intp *pivots, npy_intp *npiv, void *)
npy_intp *pivots, npy_intp *npiv, npy_intp nkth, void *)
{
using T = typename Tag::type;
if ((nkth == 1) && (argquickselect_dispatch((T *)v, tosort, num, kth))) {
return 0;
}
return introselect_<Tag, true>((typename Tag::type *)v, tosort, num, kth,
pivots, npiv);
}
Expand Down
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