python-scanpy 1.7.2 tests failing with SIGILL

  • Done
  • quality assurance status badge
Details
2 participants
  • Ludovic Courtès
  • Maxim Cournoyer
Owner
unassigned
Submitted by
Ludovic Courtès
Severity
normal
L
L
Ludovic Courtès wrote on 8 Jul 2021 19:53
(address . bug-guix@gnu.org)
8735solmk0.fsf@inria.fr
On an x86_64 machine, I’ve seen this:

Toggle snippet (122 lines)
$ guix build python-scanpy --no-grafts --check

[…]

starting phase `check'
============================= test session starts ==============================
platform linux -- Python 3.8.2, pytest-5.3.5, py-1.8.1, pluggy-0.13.1
rootdir: /tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2
plugins: hypothesis-5.4.1, cov-2.8.1, black-0.3.8
Fatal Python error: Illegal instruction

Current thread 0x00007ffff785c300 (most recent call first):
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 1109 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1042 in _handle_fromlist
File "/gnu/store/368d0i579ga5sbc3mms4bg7bd4lzj6km-python-numcodecs-0.6.4/lib/python3.8/site-packages/numcodecs/__init
__.py", line 45 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/gnu/store/cjclqalblsxf8l6cn1l1r4qmyjab0di3-python-zarr-2.4.0/lib/python3.8/site-packages/zarr/codecs.py", line
3 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/gnu/store/cjclqalblsxf8l6cn1l1r4qmyjab0di3-python-zarr-2.4.0/lib/python3.8/site-packages/zarr/__init__.py", li
ne 3 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 961 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/compat/__i
nit__.py", line 19 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/views.py", line 13 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/aligned_mapping.py", line 13 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/raw.py", line 11 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/_core/anndata.py", line 26 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/lib/python3.8/site-packages/anndata/__init__.py", line 7 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/_utils.py", line 18 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/__init__.py", line 5 in <module>
File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
File "<frozen importlib._bootstrap_external>", line 783 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/tests/conftest.py", line 11 in <module>
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/assertion/rewrite.py", line 143 in exec_module
File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 991 in _find_and_load
File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/local.py", line 701 in pyimport
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/config/__init__.py", line 465 in _importconftest
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/config/__init__.py", line 437 in _getconftestmodules
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/main.py", line 445 in gethookproxy
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/main.py", line 626 in _recurse
File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/common.py", line 425 in <listcomp>
File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/common.py", line 424 in gen
File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/common.py", line 435 in gen
File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/python3.8/site-packages/py/_path/common.py", line 383 in visit
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/main.py", line 545 in _collect
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/main.py", line 504 in collect
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py", line 257 in <lambda>
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py", line 237 in from_call
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py", line 257 in pytest_make_collect_report
File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/callers.py", line 187 in _multicall
File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/manager.py", line 84 in <lambda>
File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/hooks.py", line 286 in __call__
File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py", line 379 in collect_one_node
...
command "pytest" failed with signal 4
builder for `/gnu/store/xdqc4a2xhkiknasj8rk36gl3gr5iswr8-python-scanpy-1.7.2.drv' failed with exit code 1
build of /gnu/store/xdqc4a2xhkiknasj8rk36gl3gr5iswr8-python-scanpy-1.7.2.drv failed

It would seem that one of these dependencies has code using x86_64 ISA
extensions that this particular CPU doesn’t support.

Thoughts?

Ludo’.
M
M
Maxim Cournoyer wrote on 4 Oct 2023 05:41
(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)(address . 49467-done@debbugs.gnu.org)
87mswz2gx5.fsf@gmail.com
Hi Ludo,

Ludovic Courtès <ludovic.courtes@inria.fr> writes:

Toggle quote (23 lines)
> On an x86_64 machine, I’ve seen this:
>
> $ guix build python-scanpy --no-grafts --check
>
> […]
>
> starting phase `check'
> ============================= test session starts ==============================
> platform linux -- Python 3.8.2, pytest-5.3.5, py-1.8.1, pluggy-0.13.1
> rootdir: /tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2
> plugins: hypothesis-5.4.1, cov-2.8.1, black-0.3.8
> Fatal Python error: Illegal instruction
>
> Current thread 0x00007ffff785c300 (most recent call first):
> File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
> File "<frozen importlib._bootstrap_external>", line 1109 in exec_module
> File "<frozen importlib._bootstrap>", line 671 in _load_unlocked
> File "<frozen importlib._bootstrap>", line 975 in _find_and_load_unlocked
> File "<frozen importlib._bootstrap>", line 991 in _find_and_load
> File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
> File "<frozen importlib._bootstrap>", line 1042 in _handle_fromlist
> File "/gnu/store/368d0i579ga5sbc3mms4bg7bd4lzj6km-python-numcodecs-0.6.4/lib/python3.8/site-packages/numcodecs/__init

[...]

Toggle quote (17 lines)
> File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py", line 237 in from_call
> File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py", line 257 in pytest_make_collect_report
> File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/callers.py", line 187 in _multicall
> File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/manager.py", line 84 in <lambda>
> File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/manager.py", line 93 in _hookexec
> File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/lib/python3.8/site-packages/pluggy/hooks.py", line 286 in __call__
> File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/runner.py", line 379 in collect_one_node
> ...
> command "pytest" failed with signal 4
> builder for `/gnu/store/xdqc4a2xhkiknasj8rk36gl3gr5iswr8-python-scanpy-1.7.2.drv' failed with exit code 1
> build of /gnu/store/xdqc4a2xhkiknasj8rk36gl3gr5iswr8-python-scanpy-1.7.2.drv failed
>
> It would seem that one of these dependencies has code using x86_64 ISA
> extensions that this particular CPU doesn’t support.
>
> Thoughts?

I don't reproduce with
/gnu/store/0ch25pmwnxl8vfdwiqz3rk9n4hmmhj39-python-scanpy-1.9.1 on an
old x86_64 CPU (Intel Q6700).

I'm assuming for the best and closing :-)

--
Thanks,
Maxim
Closed
?
Your comment

This issue is archived.

To comment on this conversation send an email to 49467@debbugs.gnu.org

To respond to this issue using the mumi CLI, first switch to it
mumi current 49467
Then, you may apply the latest patchset in this issue (with sign off)
mumi am -- -s
Or, compose a reply to this issue
mumi compose
Or, send patches to this issue
mumi send-email *.patch