Optional out parameter for np.dot() by luispedro · Pull Request #14 · numpy/numpy

luispedro · 2010-11-12T16:17:45Z

Hello,

This adds an optional out array for np.dot(). I measured it to be faster, but mostly it is easier to not always reallocate memory if you are manipulating large matrices.

I would appreciate a review as I am not an expert in this code.

Thank you,
Luis

charris · 2010-11-13T01:45:47Z

Looks close, but I think it need work.

luispedro · 2010-11-13T02:00:39Z

Thanks for your feedback. I'll improve it and resubmit.

pv · 2010-11-20T00:36:33Z

Might be better to make the out a keyword argument -- people will expect to be able to do dot(a, b, out=Foo).
You'll also need to add an out= argument to multiarraymodule.c:array_matrixproduct -- it's used as the dot() function when accelerated BLAS is not available.

pv · 2010-12-11T19:21:35Z

The signature of PyArray_MatrixProduct cannot be changed, since it is a public function in the Numpy C-API.
There was also a refcount error in the PyArray_MatrixProduct implementation.

Relevant fixes here: https://github.com/pv/numpy/commits/bug/luispedro-dot-out
It should be close to ready now -- needs maybe some more testing.

luispedro · 2010-12-14T18:38:53Z

Thank you for your work. I am just working out the last details and will issue a pull request on numpy/numpy soon.

This avoids the memory allocation. It is very strict in checking that the types are correct, but since it is intended as an optimisation, it should only be used when the user knows what they are doing.

Using the toy example in the test as a benchmark, I clocked 63ms with an `out` parameter, versus 91ms without. Here is the full benchmark (requires ipython):: import numpy as np np.random.seed(22) f = np.random.rand(1024*128, 16) v = np.random.rand(16,32) r = np.empty((1024*128, 32)) _ip.magic("timeit np.dot(f,v,r)") _ip.magic("timeit np.dot(f,v)")

(Pointed out by pv on github)

This allows `np.dot(a, b, out=r)`. Suggested by pv.

…ture in PyArray_MatrixProduct2

This indicates that the function takes 3 arguments

ENH: Add fast path for randint broadcasting

Digitize2

# This is the 1st commit message: Add Windows config to GHA # This is the commit message numpy#2: update script [wheel build] # This is the commit message numpy#3: typo [wheel build] # This is the commit message numpy#4: fix typo? [wheel build] # This is the commit message numpy#5: fix linux builds? [wheel build] # This is the commit message numpy#6: typo [wheel build] # This is the commit message numpy#7: add license and pin to windows 2016 # This is the commit message numpy#8: skip tests [wheel build] # This is the commit message numpy#9: pin to windows 2019 instead [wheel build] # This is the commit message numpy#10: try to find out the error on windows [wheel build] # This is the commit message numpy#11: maybe fix? [wheel build] # This is the commit message numpy#12: maybe fix? [wheel build] # This is the commit message numpy#13: fix? [wheel build] # This is the commit message numpy#14: cleanup [wheel build]

commit 30228578ac65ec6b90961700a5783c23d8e1b879 Author: Thomas Li <47963215+lithomas1@users.noreply.github.com> Date: Wed Nov 17 16:21:27 2021 -0800 Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Update LICENSE_win32.txt Update LICENSE_win32.txt Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Update LICENSE_win32.txt Update LICENSE_win32.txt Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Update LICENSE_win32.txt Update LICENSE_win32.txt Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Update LICENSE_win32.txt Update LICENSE_win32.txt commit 4bd12df Author: Thomas Li <47963215+lithomas1@users.noreply.github.com> Date: Mon Nov 15 17:28:47 2021 -0800 # This is a combination of 14 commits. # This is the 1st commit message: Add Windows config to GHA # This is the commit message numpy#2: update script [wheel build] # This is the commit message numpy#3: typo [wheel build] # This is the commit message numpy#4: fix typo? [wheel build] # This is the commit message numpy#5: fix linux builds? [wheel build] # This is the commit message numpy#6: typo [wheel build] # This is the commit message numpy#7: add license and pin to windows 2016 # This is the commit message numpy#8: skip tests [wheel build] # This is the commit message numpy#9: pin to windows 2019 instead [wheel build] # This is the commit message numpy#10: try to find out the error on windows [wheel build] # This is the commit message numpy#11: maybe fix? [wheel build] # This is the commit message numpy#12: maybe fix? [wheel build] # This is the commit message numpy#13: fix? [wheel build] # This is the commit message numpy#14: cleanup [wheel build] commit 444a721 Merge: 376ad69 22448b4 Author: Charles Harris <charlesr.harris@gmail.com> Date: Mon Nov 15 17:47:23 2021 -0700 Merge pull request numpy#20274 from h-vetinari/fix_15179 TST: Some fixes & refactoring around glibc-dependent skips in test_umath.py commit 376ad69 Merge: b75fe57 546c47a Author: Charles Harris <charlesr.harris@gmail.com> Date: Mon Nov 15 17:31:41 2021 -0700 Merge pull request numpy#20327 from seberg/rename-interpolation BUG,DEP: Fixup quantile/percentile and rename interpolation->method commit 546c47a Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Mon Nov 15 16:13:50 2021 -0600 DOC: Fixups for interpolation rename comments from review Co-authored-by: Charles Harris <charlesr.harris@gmail.com> commit b75fe57 Merge: 7310c09 cbc25d2 Author: Warren Weckesser <warren.weckesser@gmail.com> Date: Mon Nov 15 17:27:08 2021 -0500 Merge pull request numpy#20369 from bilderbuchi/missing_diagnostics_newlines MAINT: Fix newlines in diagnostics output of numpy.f2py. commit cbc25d2 Author: Christoph Buchner <bilderbuchi@phononoia.at> Date: Sun Nov 14 08:36:03 2021 +0100 MAINT: Fix newlines in diagnostics output of numpy.f2py. Linebreaks were not consistently added to errmess/outmess arguments, which led to very long lines and wrong concatenation with compiler messages in f2py console output. commit be15716 Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Fri Nov 12 12:10:20 2021 -0600 DOC: Add release not for quantile `interpolation` rename Also updates the old release note to include the info (and generally tweaks it a bit) commit 7d8a8e7 Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Fri Nov 12 11:57:22 2021 -0600 DOC: Update percentile/quantile docs Mainly fixes the method list slightly, tones down the warning a bit and fixes the link to the paper (I did not realize that the link failed to work due only because the reference was missing from nanquantile/nanpercentile). commit 5bd71fb Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Tue Nov 9 09:48:59 2021 -0600 DOC: Add ticks to quantile interpolation/method error Co-authored-by: abel <aoun@cerfacs.fr> commit 0d5fb81 Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Mon Nov 8 20:39:50 2021 -0600 DOC: Remove reference to paper from quantile `method` kwarg Apparently, sphinx does not resolve references to footnotes from parameter descriptions. commit 8437663 Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Mon Nov 8 18:25:37 2021 -0600 MAINT: Rename interpolation to method in percentile stubs commit 8cfb6b5 Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Mon Nov 8 16:47:27 2021 -0600 TST: Add deprecation testcase for quantile interpolation rename commit a5ac5a5 Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Mon Nov 8 16:41:24 2021 -0600 DOC: Fixup the percentile methods plot commit 85f3dda Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Mon Nov 8 16:37:41 2021 -0600 BUG: quantile discrete methods ended up using -1 as index sometimes Also, the closest-observation did not correctly support multiple quantiles calculated at the same time (broadcasting error). commit 3993408 Author: Sebastian Berg <sebastian@sipsolutions.net> Date: Mon Nov 8 15:38:30 2021 -0600 API,DEP: Rename percentile/quantile `interpolation=` to `method=` commit 22448b4 Author: H. Vetinari <h.vetinari@gmx.com> Date: Tue Nov 2 16:51:59 2021 +1100 TST: parametrize glibc-version check in test_umath.py commit 12923c2 Author: H. Vetinari <h.vetinari@gmx.com> Date: Tue Nov 2 14:21:01 2021 +1100 TST: skip coverage of large elements in sincos_float32 for ancient glibc Fixes numpy#15179 commit 56268d5 Author: H. Vetinari <h.vetinari@gmx.com> Date: Tue Nov 2 14:19:24 2021 +1100 TST: use existence of glibc-version to clean up a test commit 01443e8 Author: H. Vetinari <h.vetinari@gmx.com> Date: Tue Nov 2 14:18:52 2021 +1100 TST: turn glibc_older_than_2.17 into boolean instead of xfail this anticipates reuse of this boolean within the test module

commit 9c833bed5879d77e625556260690c349de18b433 Author: Thomas Li <47963215+lithomas1@users.noreply.github.com> Date: Wed Nov 17 16:21:27 2021 -0800 Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Update LICENSE_win32.txt Update LICENSE_win32.txt Add Windows config to GHA update script [wheel build] typo [wheel build] fix typo? [wheel build] fix linux builds? [wheel build] typo [wheel build] add license and pin to windows 2016 skip tests [wheel build] pin to windows 2019 instead [wheel build] try to find out the error on windows [wheel build] maybe fix? [wheel build] maybe fix? [wheel build] fix? [wheel build] cleanup [wheel build] Update LICENSE_win32.txt Update LICENSE_win32.txt Update cibw_test_command.sh commit 4bd12df Author: Thomas Li <47963215+lithomas1@users.noreply.github.com> Date: Mon Nov 15 17:28:47 2021 -0800 # This is a combination of 14 commits. # This is the 1st commit message: Add Windows config to GHA # This is the commit message numpy#2: update script [wheel build] # This is the commit message numpy#3: typo [wheel build] # This is the commit message numpy#4: fix typo? [wheel build] # This is the commit message numpy#5: fix linux builds? [wheel build] # This is the commit message numpy#6: typo [wheel build] # This is the commit message numpy#7: add license and pin to windows 2016 # This is the commit message numpy#8: skip tests [wheel build] # This is the commit message numpy#9: pin to windows 2019 instead [wheel build] # This is the commit message numpy#10: try to find out the error on windows [wheel build] # This is the commit message numpy#11: maybe fix? [wheel build] # This is the commit message numpy#12: maybe fix? [wheel build] # This is the commit message numpy#13: fix? [wheel build] # This is the commit message numpy#14: cleanup [wheel build]

Merge in ~STEPAN.SINDELAR_ORACLE.COM/numpy-hpy from ss/array_array2 to labs-hpy-port * commit 'bebf094010c275b747e1115881d67fa85a9f6751': Remove dtypemeta_dealloc, visit the new HPyFields in DTypeMeta_traverse_impl Fix more C API usages in HPyArray_AssignArray Last C API usage removed from HPyArray_CheckCastSafety NPY_DType_Slots.within_dtype_castingimpl is HPyField NPY_DType_Slots.castingimpls is HPyField HPyArray_CheckCastSafety (partial port)

refactor: Refactor to register-based algorithm

…ighway (numpy#14) * ENH, SIMD: Initial implementation of Highway wrapper A thin wrapper over Google's Highway SIMD library to simplify its interface. This commit provides the implementation of that wrapper, consisting of: - simd.hpp: Main header defining the SIMD namespaces and configuration - simd.inc.hpp: Template header included multiple times with different namespaces The wrapper eliminates Highway's class tags by: - Using lane types directly which can be deduced from arguments - Leveraging namespaces (np::simd and np::simd128) for different register widths A README is included to guide usage and document design decisions. * SIMD: Update wrapper with improved docs and type support - Fix hardware/platform terminology in documentation for clarity - Add support for long double in template specializations - Add kMaxLanes constant to expose maximum vector width information - Follows clang formatting style for consistency with NumPy codebase. * SIMD: Improve isolation and constexpr handling in wrapper - Add anonymous namespace around implementation to ensure each translation unit gets its own constants based on local flags - Use HWY_LANES_CONSTEXPR for Lanes function to ensure proper constexpr evaluation across platforms * Update Highway submodule to latest master * SIMD: Fix compile error by using MaxLanes instead of Lanes for array size Replace hn::Lanes(f64) with hn::MaxLanes(f64) when defining the index array size to fix error C2131: "expression did not evaluate to a constant". This error occurs because Lanes() isn't always constexpr compatible, especially with scalable vector extensions. MaxLanes() provides a compile-time constant value suitable for static array allocation and should be used with non-scalable SIMD extensions when defining fixed-size arrays. * Convert unary_complex to highway. --------- Co-authored-by: Sayed Adel <seiko@imavr.com>

Luis Pedro Coelho and others added 15 commits January 8, 2011 16:21

ENH: Allow user to pass in output array for dot()

d77dcba

This avoids the memory allocation. It is very strict in checking that the types are correct, but since it is intended as an optimisation, it should only be used when the user knows what they are doing.

ENH: Limit lines to 80 chars.

dfe809a

TST: Test matrix x vector dot() with output array

221ed68

TST: Test that error conditions raise ValueError

9cbbeff

ENH: Have non-BLAS dot also support out parameter

82e9dad

ENH: Make code C89

9ea97d9

(Pointed out by pv on github)

BUG: Fix typo. Call new MatrixMultiply with 3 args

5f064ed

ENH: Named arguments

b42f326

This allows `np.dot(a, b, out=r)`. Suggested by pv.

BUG: core: restore PyArray_MatrixProduct signature, put the new signa…

bc7478d

…ture in PyArray_MatrixProduct2

TST: core: some new tests for multiarray/blas dot()

34a7130

BUG: core: fix refcount error in multiarraymodule.c:new_array_for_sum

a774d96

TMP: fix some issues in tests

bcebd31

ENH: Use the name PyArray_MatrixProduct3

48eecd5

This indicates that the function takes 3 arguments

BUG: position 221 was taken for PyHalfArrType_Type

c6c62e7

This was referenced Oct 19, 2012

importing umath_tests and then CTRL-D crashes with core dump (Trac #1425) #2023

Closed

segfault in any() on large object array (Trac #1522) #2119

Closed

numpy-gitbot mentioned this pull request Oct 19, 2012

numpy.ndarray.clip segfaults on big-endian dtype (Trac #1588) #2184

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njsmith mentioned this pull request Dec 16, 2012

Segfault ufunc_object.c:1750 #2843

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njsmith mentioned this pull request Jul 3, 2014

Segmentation fault when using memory allocation tracker #4834

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LeeKamentsky mentioned this pull request Jul 8, 2014

Universal OS/X build segfault 11 in arch -i386 mode #4853

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njsmith mentioned this pull request May 2, 2016

Segmentation fault in PyArray_Item_INCREF #7595

Closed

roachlord mentioned this pull request Feb 18, 2019

Passing MagicMock to np.dtype causes a segmentation fault #12982

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UKeyboard mentioned this pull request Feb 26, 2019

BUG: Segmentation fault in temporary eliding (backtrace() fails, probably related to pthread locking) #13042

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bashtage referenced this pull request in bashtage/numpy Apr 16, 2019

Merge pull request #14 from bashtage/small-sync

8e9aee2

ENH: Add fast path for randint broadcasting

siddharth-singh-mindtickle mentioned this pull request Jul 24, 2019

numpy throws munmap_chunk(): invalid pointer when freeing its cache #14102

Closed

leakec mentioned this pull request Sep 29, 2020

Potential Issue with 2-D ARGOUTVIEWM Wrapping #17398

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prototype99 referenced this pull request in prototype99/numpy Jan 4, 2021

Merged in sergem/numpy/digitize2 (pull request ganesh-k13#14)

15bcd04

Digitize2

luyahan referenced this pull request in plctlab/numpy Apr 25, 2024

Merge pull request #14 from howjmay/vcgt_s8

24a1304

refactor: Refactor to register-based algorithm

vtomole mentioned this pull request May 28, 2025

BUG: Importing numpy 2.2.6 for Python 3.12.10, GCC 11.4.0 on linux throws a segmentation fault #29075

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Optional out parameter for np.dot()#14

Optional out parameter for np.dot()#14
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luispedro commented Nov 12, 2010

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