numpy 1.23.x #26

dimpase · 2022-09-13T14:53:16Z

Issue created by migration from Trac.

Original creator: @mkoeppe

Original creation time: 2022-07-03 19:41:33

CC: tmonteil

(split out from #34081)

https://numpy.org/doc/stable/release/1.23.0-notes.html# (released)

The upgrade looks harmless.

1.23.x requires GCC >= 6.5. (This has been documented in numpy/numpy#22155 - to be included in 1.23.3.)

We set #34266 as a dependency, which increases our requirement from GCC >= 6.3 to GCC >= 8)

Previous update:

#32423 Update numpy to 1.22.x, scipy 1.8.x, networkx 2.8.x

(changed by @mkoeppe at 2022-08-19 17:21:53)

dimpase · 2022-09-13T14:53:19Z

Comment by @mkoeppe created at 2022-07-03 19:44:39

Last 10 new commits:

e1998da	`Merge #32423`
507fc2e	`build/pkgs/numpy: Update to 1.23.0`
58d62f4	`build/bin/write-dockerfile.sh: ADD src/VERSION.txt`
99f3617	`Merge #34017`
3fab415	`build/pkgs/numpy: Switch to using .tar.gz`
443b3d3	`build/pkgs/numpy/spkg-install.in: Fix 32bit build on x86_64`
9cd5ea6	`Merge #34017`
ee79c2e	`build/pkgs/numpy/spkg-install.in: Fix 32bit build on x86_64 (fixup)`
2534f5a	`build/pkgs/numpy/patches/21891.patch: New`
d87212c	`Merge #32423`

dimpase · 2022-09-13T14:53:22Z

Comment by @mkoeppe created at 2022-07-03 19:44:39

Changing status from new to needs_review.

dimpase · 2022-09-13T14:53:25Z

Comment by @mkoeppe created at 2022-07-04 20:14:00

On debian-stretch-standard (https://github.com/mkoeppe/sage/runs/7184259105?check_suite_focus=true):

In file included from numpy/core/src/common/simd/avx512/avx512.h:75:0,
                   from numpy/core/src/common/simd/simd.h:50,
                   from /sage/local/var/lib/sage/venv-python3.10.3/var/tmp/sage/build/numpy-1.23.0/src/numpy/core/src/npysort/x86-qsort.dispatch.cpp:17,
                   from build/src.linux-x86_64-3.10/numpy/core/src/npysort/x86-qsort.dispatch.avx512_skx.cpp:21:
  numpy/core/src/common/simd/avx512/arithmetic.h: In function 'npy_uint32 npyv_reducemax_u32(npyv_u32)':
  numpy/core/src/common/simd/avx512/arithmetic.h:387:89: error: invalid conversion from 'int' to '_MM_PERM_ENUM' [-fpermissive]
           npyv_u32 a3 = _mm512_max_epu32(a2, _mm512_shuffle_epi32(a2, (1<<6 | 0<<4 | 3<<2 | 2)));
                                                                       ~~~~~~~~~~~~~~~~~~~~^~~~
...
 In file included from build/src.linux-x86_64-3.10/numpy/core/src/npysort/x86-qsort.dispatch.avx512_skx.cpp:21:0:
  /sage/local/var/lib/sage/venv-python3.10.3/var/tmp/sage/build/numpy-1.23.0/src/numpy/core/src/npysort/x86-qsort.dispatch.cpp: In function 'npy_int partition_vec(type_t*, npy_intp, npy_intp, zmm_t, zmm_t, zmm_t*, zmm_t*)':
  /sage/local/var/lib/sage/venv-python3.10.3/var/tmp/sage/build/numpy-1.23.0/src/numpy/core/src/npysort/x86-qsort.dispatch.cpp:654:64: error: there are no arguments to '_knot_mask16' that depend on a template parameter, so a declaration of '_knot_mask16' must be available [-fpermissive]
       vtype::mask_compressstoreu(arr + left, _knot_mask16(gt_mask), curr_vec);
                                                                  ^

(regression from numpy 1.22.x). Reported at numpy/numpy#21920

dimpase · 2022-09-13T14:53:28Z

Comment by @mkoeppe created at 2022-07-06 01:55:00

Changing status from needs_review to needs_work.

dimpase · 2022-09-13T14:53:33Z

Comment by git created at 2022-07-09 02:33:50

Branch pushed to git repo; I updated commit sha1. New commits:

4cce3ef	`Merge tag '9.7.beta4' into t/34110/numpy_1_23`
8f5860a	`build/pkgs/numpy: Update to 1.23.1`

dimpase · 2022-09-13T14:53:36Z

Comment by @mkoeppe created at 2022-07-27 16:20:29

ubuntu-trusty-toolchain-gcc_9 (https://github.com/mkoeppe/sage/runs/7532140899?check_suite_focus=true) and other ubuntu releases

sage -t --random-seed=291926986539572225544641036716487640141 src/sage/matrix/matrix_double_dense.pyx
**********************************************************************
File "src/sage/matrix/matrix_double_dense.pyx", line 3642, in sage.matrix.matrix_double_dense.Matrix_double_dense.exp
Failed example:
    A.exp()  # tol 1e-15
Expected:
    [51.968956198705044  74.73656456700327]
    [112.10484685050491 164.07380304920997]
Got:
    [ 51.96895619870499  74.73656456700321]
    [112.10484685050481 164.07380304920983]
Tolerance exceeded in 1 of 4:
    51.968956198705044 vs 51.96895619870499, tolerance 2e-15 > 1e-15
**********************************************************************
File "src/sage/matrix/matrix_double_dense.pyx", line 3655, in sage.matrix.matrix_double_dense.Matrix_double_dense.exp
Failed example:
    A.exp()   # tol 1e-15
Expected:
    [51.968956198705044  74.73656456700327]
    [112.10484685050491 164.07380304920997]
Got:
    [ 51.96895619870499  74.73656456700321]
    [112.10484685050481 164.07380304920983]
Tolerance exceeded in 1 of 4:
    51.968956198705044 vs 51.96895619870499, tolerance 2e-15 > 1e-15
**********************************************************************

sage -t --random-seed=291926986539572225544641036716487640141 src/sage/symbolic/constants_c_impl.pxi
**********************************************************************
File "src/sage/symbolic/constants_c_impl.pxi", line 164, in sage.symbolic.constants_c_impl.E.__pow__
Failed example:
    e^A  # rel tol 1e-15
Expected:
    [51.968956198705044  74.73656456700327]
    [112.10484685050491 164.07380304920997]
Got:
    [ 51.96895619870499  74.73656456700321]
    [112.10484685050481 164.07380304920983]
Tolerance exceeded in 1 of 4:
    51.968956198705044 vs 51.96895619870499, tolerance 2e-15 > 1e-15

dimpase · 2022-09-13T14:53:39Z

Comment by git created at 2022-07-29 00:36:03

Branch pushed to git repo; I updated commit sha1. New commits:

7aec01a	`src/sage/matrix/matrix_double_dense.pyx, src/sage/symbolic/constants_c_impl.pxi: Increase tolerances for RDF matrix exp`

dimpase · 2022-09-13T14:53:42Z

Comment by git created at 2022-07-29 21:17:25

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

dimpase · 2022-09-13T14:53:45Z

Comment by @mkoeppe created at 2022-08-09 20:52:11

Replying to [comment:4 mkoeppe]:

On debian-stretch-standard

This platform is dropped in #34266, I've set it as a dependency

dimpase · 2022-09-13T14:53:48Z

Comment by @mkoeppe created at 2022-08-09 20:52:11

Changing status from needs_work to needs_review.

dimpase · 2022-09-13T14:53:53Z

Comment by jhpalmieri created at 2022-08-25 23:21:51

On OS X + various homebrew packages, I am getting two doctest failures:

File "src/sage/modules/vector_double_dense.pyx", line 405, in sage.modules.vector_double_dense.Vector_double_dense.norm
Failed example:
    v.norm(p=6)
Expected:
    8.744039097...
Got:
    doctest:warning
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/bin/sage-runtests", line 154, in <module>
        err = DC.run()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/control.py", line 1384, in run
        self.run_doctests()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/control.py", line 1059, in run_doctests
        self.dispatcher.dispatch()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2021, in dispatch
        self.parallel_dispatch()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 1916, in parallel_dispatch
        w.start()  # This might take some time
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2190, in start
        super().start()
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/process.py", line 121, in start
        self._popen = self._Popen(self)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 224, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 277, in _Popen
        return Popen(process_obj)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py", line 19, in __init__
        self._launch(process_obj)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py", line 71, in _launch
        code = process_obj._bootstrap(parent_sentinel=child_r)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
        self.run()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2162, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2492, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2544, in _run
        result = runner.run(test)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 866, in run
        return self._run(test, compileflags, out)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.modules.vector_double_dense.Vector_double_dense.norm[3]>", line 1, in <module>
        v.norm(p=Integer(6))
      File "<__array_function__ internals>", line 180, in norm
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/numpy/linalg/linalg.py", line 2566, in norm
        ret **= reciprocal(ord, dtype=ret.dtype)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/warnings.py", line 109, in _showwarnmsg
        sw(msg.message, msg.category, msg.filename, msg.lineno,
    :
    RuntimeWarning: invalid value encountered in reciprocal
    8.744039097709175
**********************************************************************
1 item had failures:
   1 of  24 in sage.modules.vector_double_dense.Vector_double_dense.norm
    [103 tests, 1 failure, 1.05 s]
sage -t --random-seed=328052423492298536457904078933829346088 src/sage/modules/free_module_element.pyx
**********************************************************************
File "src/sage/modules/free_module_element.pyx", line 1677, in sage.modules.free_module_element.FreeModuleElement.norm
Failed example:
    v.norm(5)
Expected:
    3.077384885394063
Got:
    doctest:warning
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/bin/sage-runtests", line 154, in <module>
        err = DC.run()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/control.py", line 1384, in run
        self.run_doctests()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/control.py", line 1059, in run_doctests
        self.dispatcher.dispatch()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2021, in dispatch
        self.parallel_dispatch()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 1916, in parallel_dispatch
        w.start()  # This might take some time
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2190, in start
        super().start()
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/process.py", line 121, in start
        self._popen = self._Popen(self)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 224, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 277, in _Popen
        return Popen(process_obj)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py", line 19, in __init__
        self._launch(process_obj)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py", line 71, in _launch
        code = process_obj._bootstrap(parent_sentinel=child_r)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
        self.run()
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2162, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2492, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 2544, in _run
        result = runner.run(test)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 866, in run
        return self._run(test, compileflags, out)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/src/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.modules.free_module_element.FreeModuleElement.norm[7]>", line 1, in <module>
        v.norm(Integer(5))
      File "<__array_function__ internals>", line 180, in norm
      File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.7.beta8/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/numpy/linalg/linalg.py", line 2566, in norm
        ret **= reciprocal(ord, dtype=ret.dtype)
      File "/usr/local/Cellar/python`@`3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/warnings.py", line 109, in _showwarnmsg
        sw(msg.message, msg.category, msg.filename, msg.lineno,
    :
    RuntimeWarning: invalid value encountered in reciprocal
    3.077384885394063
**********************************************************************
1 item had failures:
   1 of  24 in sage.modules.free_module_element.FreeModuleElement.norm
    [1079 tests, 1 failure, 9.35 s]
----------------------------------------------------------------------
sage -t --random-seed=328052423492298536457904078933829346088 src/sage/modules/vector_double_dense.pyx  # 1 doctest failed
sage -t --random-seed=328052423492298536457904078933829346088 src/sage/modules/free_module_element.pyx  # 1 doctest failed

dimpase · 2022-09-13T14:53:56Z

Comment by git created at 2022-08-26 00:45:45

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

fdb7764	`build/pkgs/numpy: Update to 1.23.0`
09066c8	`build/pkgs/numpy: Switch to using .tar.gz`
5b0f244	`build/pkgs/numpy: Update to 1.23.1`
d4ff77d	`build/pkgs/numpy: Update to 1.23.2`

dimpase · 2022-09-13T14:53:59Z

Comment by @mkoeppe created at 2022-08-26 00:46:09

Haven't built this in a while, but there's already 1.23.2

dimpase · 2022-09-13T14:54:02Z

Comment by @mkoeppe created at 2022-08-26 04:32:22

Just built it on my Mac (with openblas from current homebrew), and I see these failures too.

dimpase · 2022-09-13T14:54:05Z

Comment by git created at 2022-09-13 02:00:29

Branch pushed to git repo; I updated commit sha1. New commits:

ecda67e	`Merge tag '9.7.rc1' into t/34110/numpy_1_23`
bccc17d	`build/pkgs/numpy: Update to 1.23.3`

dimpase · 2022-09-13T14:54:08Z

Comment by gh-dimpase created at 2022-09-13 08:59:53

test, please ignore

dimpase added enhancement New feature or request major packages: standard labels Sep 13, 2022

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

numpy 1.23.x #26

numpy 1.23.x #26

dimpase commented Sep 13, 2022 •

edited

Loading

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

numpy 1.23.x #26

numpy 1.23.x #26

Comments

dimpase commented Sep 13, 2022 • edited Loading

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022

dimpase commented Sep 13, 2022 •

edited

Loading