8000 ENH: turn quicksort into introsort by juliantaylor · Pull Request #7863 · numpy/numpy · GitHub
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ENH: turn quicksort into introsort #7863

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Merged
merged 2 commits into from
Jul 25, 2016
Merged

ENH: turn quicksort into introsort #7863

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f3c994a
MAINT: move integer msb into a sort util function
juliantaylor Jul 21, 2016
c3cea45
ENH: turn quicksort into introsort
juliantaylor Jul 21, 2016
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6 changes: 6 additions & 0 deletions doc/release/1.12.0-notes.rst
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Original file 8000 line number Diff line number Diff line change
Expand Up @@ -266,6 +266,12 @@ numpy.sctypes now includes bytes on Python3 too
Previously, it included str (bytes) and unicode on Python2, but only str
(unicode) on Python3.

quicksort has been changed to an introsort
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The quicksort kind of ``np.sort`` and ``np.argsort`` is now an introsort which
is regular quicksort but changing to a heapsort when not enough progress is
made. This retains the good quicksort performance while changing the worst case
runtime from ``O(N^2)`` to ``O(N*log(N))``.

Deprecations
============
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6 changes: 6 additions & 0 deletions numpy/core/fromnumeric.py
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Expand Up @@ -776,6 +776,12 @@ def sort(a, axis=-1, kind='quicksort', order=None):
placements are sorted according to the non-nan part if it exists.
Non-nan values are sorted as before.

.. versionadded:: 1.12.0

quicksort has been changed to an introsort which will switch
heapsort when it does not make enough progress. This makes its
worst case O(n*log(n)).

Examples
--------
>>> a = np.array([[1,4],[3,1]])
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36 changes: 36 additions & 0 deletions numpy/core/src/npysort/quicksort.c.src
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8000
Original file line number Diff line number Diff line change
Expand Up @@ -69,8 +69,13 @@ quicksort_@suff@(void *start, npy_intp num, void *NOT_USED)
@type@ *stack[PYA_QS_STACK];
@type@ **sptr = stack;
@type@ *pm, *pi, *pj, *pk;
npy_intp depth_limit = npy_get_msb(num) * 2;

for (;;) {
if (depth_limit-- < 0) {
heapsort_@suff@(pl, pr - pl + 1, NULL);
goto stack_pop;
}
while ((pr - pl) > SMALL_QUICKSORT) {
/* quicksort partition */
pm = pl + ((pr - pl) >> 1);
Expand Down Expand Up @@ -114,6 +119,7 @@ quicksort_@suff@(void *start, npy_intp num, void *NOT_USED)
}
*pj = vp;
}
stack_pop:
if (sptr == stack) {
break;
}
Expand All @@ -135,9 +141,14 @@ aquicksort_@suff@(void *vv, npy_intp* tosort, npy_intp num, void *NOT_USED)
npy_intp *stack[PYA_QS_STACK];
npy_intp **sptr = stack;
npy_intp *pm, *pi, *pj, *pk, vi;
npy_intp depth_limit = npy_get_msb(num) * 2;

for (;;) {
while ((pr - pl) > SMALL_QUICKSORT) {
if (depth_limit-- < 0) {
aheapsort_@suff@(vv, pl, pr - pl + 1, NULL);
goto stack_pop;
}
/* quicksort partition */
pm = pl + ((pr - pl) >> 1);
if (@TYPE@_LT(v[*pm],v[*pl])) INTP_SWAP(*pm, *pl);
Expand Down Expand Up @@ -181,6 +192,7 @@ aquicksort_@suff@(void *vv, npy_intp* tosort, npy_intp num, void *NOT_USED)
}
*pj = vi;
}
stack_pop:
if (sptr == stack) {
break;
}
Expand Down Expand Up @@ -217,12 +229,17 @@ quicksort_@suff@(void *start, npy_intp num, void *varr)
@type@ *pl = start;
@type@ *pr = pl + (num - 1)*len;
@type@ *stack[PYA_QS_STACK], **sptr = stack, *pm, *pi, *pj, *pk;
npy_intp depth_limit = npy_get_msb(num) * 2;

if (vp == NULL) {
return -NPY_ENOMEM;
}

for (;;) {
if (depth_limit-- < 0) {
heapsort_@suff@(pl, (pr - pl) / len + 1, varr);
goto stack_pop;
}
while ((size_t)(pr - pl) > SMALL_QUICKSORT*len) {
/* quicksort partition */
pm = pl + (((pr - pl)/len) >> 1)*len;
Expand Down Expand Up @@ -268,6 +285,7 @@ quicksort_@suff@(void *start, npy_intp num, void *varr)
}
@TYPE@_COPY(pj, vp, len);
}
stack_pop:
if (sptr == stack) {
break;
}
Expand All @@ -292,8 +310,13 @@ aquicksort_@suff@(void *vv, npy_intp* tosort, npy_intp num, void *varr)
npy_intp *stack[PYA_QS_STACK];
npy_intp **sptr=stack;
npy_intp *pm, *pi, *pj, *pk, vi;
npy_intp depth_limit = npy_get_msb(num) * 2;

for (;;) {
if (depth_limit-- < 0) {
aheapsort_@suff@(vv, pl, pr - pl + 1, varr);
goto stack_pop;
}
while ((pr - pl) > SMALL_QUICKSORT) {
/* quicksort partition */
pm = pl + ((pr - pl) >> 1);
Expand Down Expand Up @@ -338,6 +361,7 @@ aquicksort_@suff@(void *vv, npy_intp* tosort, npy_intp num, void *varr)
}
*pj = vi;
}
stack_pop:
if (sptr == stack) {
break;
}
Expand Down Expand Up @@ -370,12 +394,17 @@ npy_quicksort(void *start, npy_intp num, void *varr)
char *stack[PYA_QS_STACK];
char **sptr = stack;
char *pm, *pi, *pj, *pk;
npy_intp depth_limit = npy_get_msb(num) * 2;

if (vp == NULL) {
return -NPY_ENOMEM;
}

for (;;) {
if (depth_limit-- < 0) {
npy_heapsort(pl, (pr - pl) / elsize + 1, varr);
goto stack_pop;
}
while(pr - pl > SMALL_QUICKSORT*elsize) {
/* quicksort partition */
pm = pl + (((pr - pl) / elsize) >> 1) * elsize;
Expand Down Expand Up @@ -431,6 +460,7 @@ npy_quicksort(void *start, npy_intp num, void *varr)
}
GENERIC_COPY(pj, vp, elsize);
}
stack_pop:
if (sptr == stack) {
break;
}
Expand All @@ -456,8 +486,13 @@ npy_aquicksort(void *vv, npy_intp* tosort, npy_intp num, void *varr)
npy_intp *stack[PYA_QS_STACK];
npy_intp **sptr = stack;
npy_intp *pm, *pi, *pj, *pk, vi;
npy_intp depth_limit = npy_get_msb(num) * 2;

for (;;) {
if (depth_limit-- < 0) {
npy_aheapsort(vv, pl, pr - pl + 1, varr);
goto stack_pop;
}
while ((pr - pl) > SMALL_QUICKSORT) {
/* quicksort partition */
pm = pl + ((pr - pl) >> 1);
Expand Down Expand Up @@ -512,6 +547,7 @@ npy_aquicksort(void *vv, npy_intp* tosort, npy_intp num, void *varr)
}
*pj = vi;
}
stack_pop:
if (sptr == stack) {
break;
}
Expand Down
12 changes: 2 additions & 10 deletions numpy/core/src/npysort/selection.c.src
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Expand Up @@ -292,7 +292,7 @@ int
{
npy_intp low = 0;
npy_intp high = num - 1;
npy_intp depth_limit;
int depth_limit;

if (npiv == NULL)
pivots = NULL;
Expand Down Expand Up @@ -338,15 +338,7 @@ int
return 0;
}

/* dumb integer msb, float npy_log2 too slow for small parititions */
{
npy_uintp unum = num;
depth_limit = 0;
while (unum >>= 1) {
depth_limit++;
}
depth_limit *= 2;
}
depth_limit = npy_get_msb(num) * 2;

/* guarantee three elements */
for (;low + 1 < high;) {
Expand Down
8 changes: 8 additions & 0 deletions numpy/core/src/private/npy_sort.h
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Expand Up @@ -9,6 +9,14 @@
#define NPY_ENOMEM 1
#define NPY_ECOMP 2

static NPY_INLINE int npy_get_msb(npy_uintp unum)
{
int depth_limit = 0;
while (unum >>= 1) {
depth_limit++;
}
return depth_limit;
}

int quicksort_bool(void *vec, npy_intp cnt, void *null);
int heapsort_bool(void *vec, npy_intp cnt, void *null);
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15 changes: 15 additions & 0 deletions numpy/core/tests/test_multiarray.py
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Expand Up @@ -1349,6 +1349,21 @@ def test_sort(self):
msg = 'test empty array sort with axis=None'
assert_equal(np.sort(a, axis=None), a.ravel(), msg)

def test_sort_degraded(self):
# test degraded dataset would take minutes to run with normal qsort
d = np.arange(1000000)
do = d.copy()
x = d
# create a median of 3 killer where each median is the sorted second
# last element of the quicksort partition
while x.size > 3:
mid = x.size // 2
x[mid], x[-2] = x[-2], x[mid]
x = x[:-2]

assert_equal(np.sort(d), do)
assert_equal(d[np.argsort(d)], do)

def test_copy(self):
def assert_fortran(arr):
assert_(arr.flags.fortran)
Expand Down
0