Summary: | dev-python/pandas-2.0.3: tests fail on arm with MemoryError | ||
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Product: | Gentoo Linux | Reporter: | Sam James <sam> |
Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | python |
Priority: | Normal | Keywords: | TESTFAILURE |
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
See Also: |
https://github.com/pandas-dev/pandas/issues/54391 https://github.com/pandas-dev/pandas/issues/54396 https://bugs.debian.org/790925 https://bugs.gentoo.org/show_bug.cgi?id=914199 |
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Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Bug Depends on: | |||
Bug Blocks: | 911347 |
Description
Sam James
![]() ![]() ![]() ![]() build.log: https://dev.gentoo.org/~sam/bugs/gentoo/pandas-2.0.3-bug911660-arm-log.xz This is the 'arm32-testing' container on jiji. With fewer jobs, I get further and get UB: https://github.com/pandas-dev/pandas/issues/54391. (In reply to Sam James from comment #2) > With fewer jobs, I get further and get UB: > https://github.com/pandas-dev/pandas/issues/54391. log with -j8 + 32-bit time_t issues skipped: https://dev.gentoo.org/~sam/bugs/gentoo/pandas-2.0.3-bug911660-arm-log-2.xz FAILED pandas/tests/io/parser/test_c_parser_only.py::test_float_precision_options[c_high] - assert 243.164 == 243.16400000000002 FAILED pandas/tests/io/parser/test_c_parser_only.py::test_float_precision_options[c_low] - assert 243.164 == 243.16400000000002 FAILED pandas/tests/io/pytables/test_append.py::test_append_frame_column_oriented FAILED pandas/tests/io/pytables/test_store.py::test_select_filter_corner FAILED pandas/tests/io/sas/test_byteswap.py::test_int_byteswap[True-uint64] FAILED pandas/tests/io/sas/test_byteswap.py::test_int_byteswap[False-uint64] FAILED pandas/tests/io/sas/test_byteswap.py::test_float_byteswap[True-float64] FAILED pandas/tests/io/sas/test_byteswap.py::test_float_byteswap[False-float64] The byteswap failures are covered in the upstream bug I filed (https://github.com/pandas-dev/pandas/issues/54391). Ignoring those too, that means we have: FAILED pandas/tests/io/parser/test_c_parser_only.py::test_float_precision_options[c_high] - assert 243.164 == 243.16400000000002 FAILED pandas/tests/io/parser/test_c_parser_only.py::test_float_precision_options[c_low] - assert 243.164 == 243.16400000000002 FAILED pandas/tests/io/pytables/test_append.py::test_append_frame_column_oriented FAILED pandas/tests/io/pytables/test_store.py::test_select_filter_corner ... and ... pandas/tests/io/pytables/test_store.py::test_select_filter_corner Fatal Python error: Bus error I think we can probably safely assume test_append_frame_column_oriented is the same (the log is a mess b/c paralle). > FAILED > pandas/tests/io/pytables/test_append.py::test_append_frame_column_oriented pandas/_libs/algos.c:172405:173: runtime error: load of misaligned address 0x056a1dd9 for type 'const __pyx_t_5numpy_float64_t', which requires 8 byte alignment 0x056a1dd9: note: pointer points here 00 00 00 41 07 2c e2 69 91 c3 ef 3f 3b 18 13 11 66 2e e9 bf 93 05 1d b4 60 cd 03 40 34 84 74 9e ^ Fatal Python error: Bus error Thread 0xf6dcb420 (most recent call first): File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 474 in read File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 507 in from_io File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 1049 in _thread_receiver File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 296 in run File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 361 in _perform_spawn Current thread 0xf7bcc020 (most recent call first): File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/array_algos/take.py", line 162 in _take_nd_ndarray File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/array_algos/take.py", line 117 in take_nd File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/internals/blocks.py", line 945 in take_nd File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/internals/managers.py", line 748 in <listcomp> File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/internals/managers.py", line 747 in reindex_indexer File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/internals/managers.py", line 963 in take File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/generic.py", line 3932 in _take File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/generic.py", line 3948 in _take_with_is_copy File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/indexing.py", line 1123 in _getbool_axis File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/indexing.py", line 1325 in _getitem_axis File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/core/indexing.py", line 1103 in __getitem__ File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/io/pytables.py", line 4103 in process_filter File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/io/pytables.py", line 4123 in process_axes File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/io/pytables.py", line 4579 in read File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/io/pytables.py", line 850 in func File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/io/pytables.py", line 1937 in get_result File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/io/pytables.py", line 866 in select File "/var/tmp/portage/dev-python/pandas-2.0.3/work/pandas-2.0.3-python3_11/install/usr/lib/python3.11/site-packages/pandas/tests/io/pytables/test_append.py", line 285 in test_append_frame_column_oriented [...] > FAILED pandas/tests/io/pytables/test_store.py::test_select_filter_corner > > ... and ... > > pandas/tests/io/pytables/test_store.py::test_select_filter_corner Fatal > Python error: Bus error > pandas/_libs/algos.c:172405:17 3: runtime error: load of misaligned address 0x0708f763 for type 'const __pyx_t_5numpy_float64_t', which requires 8 byte alignment 0x0708f763: note: pointer points here 00 20 20 30 7f 17 9e 9f b3 20 e6 3f 65 44 21 ce 7b f1 ea bf 21 62 1c ea 6a 4f e6 bf 4f ab 7c 7f ^ Fatal Python error: Bus error Thread 0xf6ffb420 (most recent call first): File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 474 in read File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 507 in from_io File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 1049 in _thread_receiver File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 296 in run File "/usr/lib/python3.11/site-packages/execnet/gateway_base.py", line 361 in _perform_spawn [...] Reported the other two as https://github.com/pandas-dev/pandas/issues/54396. That just leaves the precision ones. The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ef513ae9a7ed27ce30f5c5567fd13900a447c823 commit ef513ae9a7ed27ce30f5c5567fd13900a447c823 Author: Sam James <sam@gentoo.org> AuthorDate: 2023-08-04 16:16:09 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2023-08-21 06:28:55 +0000 dev-libs/c-blosc2: disable unaligned access Causes SIGBUS on armv7 (at least in jiji's arm32-on-arm64 chroot) in Pandas test suite. Unaligned access is UB anyway. Bug: https://bugs.gentoo.org/911619 Bug: https://bugs.gentoo.org/911660 Bug: https://bugs.gentoo.org/911102 Signed-off-by: Sam James <sam@gentoo.org> ...sc2-2.10.2.ebuild => c-blosc2-2.10.2-r1.ebuild} | 4 +++ ...losc2-2.9.3.ebuild => c-blosc2-2.9.3-r1.ebuild} | 4 +++ .../files/c-blosc2-2.9.3-no-unaligned.patch | 32 ++++++++++++++++++++++ 3 files changed, 40 insertions(+) The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2c8c6679b1a55b9912410bb2ff76b8291c23544d commit 2c8c6679b1a55b9912410bb2ff76b8291c23544d Author: Sam James <sam@gentoo.org> AuthorDate: 2023-08-21 06:32:48 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2023-08-21 06:32:59 +0000 dev-libs/c-blosc: disable unaligned access Causes SIGBUS on armv7 (at least in jiji's arm32-on-arm64 chroot) in Pandas test suite. Unaligned access is UB anyway. Bug: https://bugs.gentoo.org/911660 Signed-off-by: Sam James <sam@gentoo.org> dev-libs/c-blosc/c-blosc-1.21.4-r1.ebuild | 57 ++++++++++++++++++++++ .../files/c-blosc-1.21.4-no-unaligned.patch | 33 +++++++++++++ 2 files changed, 90 insertions(+) The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a1141b6f49501f8bc5ad7cd58d4c15852beb52b6 commit a1141b6f49501f8bc5ad7cd58d4c15852beb52b6 Author: Sam James <sam@gentoo.org> AuthorDate: 2023-08-29 04:55:51 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2023-08-29 04:57:35 +0000 dev-python/pandas: skip known-broken tests Closes: https://bugs.gentoo.org/911660 Signed-off-by: Sam James <sam@gentoo.org> dev-python/pandas/pandas-2.0.3-r1.ebuild | 9 +++++++++ 1 file changed, 9 insertions(+) |