Skip to content

CircleCI fails on pypy3 build #18624

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Closed
adrinjalali opened this issue Oct 15, 2020 · 6 comments · Fixed by #18867
Closed

CircleCI fails on pypy3 build #18624

adrinjalali opened this issue Oct 15, 2020 · 6 comments · Fixed by #18867
Labels
Build / CI pypy
Milestone
0.24

Comments

@adrinjalali
Copy link
Member

Several pypy3 builds on circleci have been failing recently, example: https://app.circleci.com/pipelines/github/scikit-learn/scikit-learn/8663/workflows/a0349bb9-2c2f-4334-85f2-c48f09a1a30d/jobs/122623

This is kind of a blocker for the 0.24 release since conda-forge now builds for pypy.

Ping @rth

platform linux -- Python 3.6.9[pypy-7.2.0-final], pytest-6.1.1, py-1.9.0, pluggy-0.13.1
rootdir: /root/project, configfile: setup.cfg
collecting 3 items                                                             Fatal Python error: Segmentation fault

Stack (most recent call first, approximate line numbers):
  File "/root/project/pypy-env/site-packages/numpy/core/_asarray.py", line 16 in asarray
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File "/root/project/sklearn/manifold/_t_sne.py", line 11 in <module>
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File "/root/project/sklearn/manifold/__init__.py", line 1 in <module>
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File "/root/project/sklearn/cluster/_spectral.py", line 2 in <module>
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File "/root/project/sklearn/cluster/__init__.py", line 1 in <module>
  File ???
  File ???
  File ???
  File ???
  File ???
  File ???
  File "/usr/local/lib-python/3/importlib/__init__.py", line 108 in import_module
  File "/root/project/pypy-env/site-packages/_pytest/pathlib.py", line 444 in import_path
  File "/root/project/pypy-env/site-packages/_pytest/doctest.py", line 491 in collect
  File "/root/project/pypy-env/site-packages/_pytest/runner.py", line 340 in <lambda>
  File "/root/project/pypy-env/site-packages/_pytest/runner.py", line 299 in from_call
  File "/root/project/pypy-env/site-packages/_pytest/runner.py", line 339 in pytest_make_collect_report
  File "/root/project/pypy-env/site-packages/pluggy/callers.py", line 157 in _multicall
  File "/root/project/pypy-env/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/root/project/pypy-env/site-packages/pluggy/manager.py", line 90 in _hookexec
  File "/root/project/pypy-env/site-packages/pluggy/hooks.py", line 272 in __call__
  File "/root/project/pypy-env/site-packages/_pytest/runner.py", line 454 in collect_one_node
  File "/root/project/pypy-env/site-packages/_pytest/main.py", line 791 in genitems
  File "/root/project/pypy-env/site-packages/_pytest/main.py", line 571 in perform_collect
  File "/root/project/pypy-env/site-packages/_pytest/main.py", line 322 in pytest_collection
  File "/root/project/pypy-env/site-packages/pluggy/callers.py", line 157 in _multicall
  File "/root/project/pypy-env/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/root/project/pypy-env/site-packages/pluggy/manager.py", line 90 in _hookexec
  File "/root/project/pypy-env/site-packages/pluggy/hooks.py", line 272 in __call__
  File "/root/project/pypy-env/site-packages/_pytest/main.py", line 309 in _main
  File "/root/project/pypy-env/site-packages/_pytest/main.py", line 244 in wrap_session
  File "/root/project/pypy-env/site-packages/_pytest/main.py", line 305 in pytest_cmdline_main
  File "/root/project/pypy-env/site-packages/pluggy/callers.py", line 157 in _multicall
  File "/root/project/pypy-env/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/root/project/pypy-env/site-packages/pluggy/manager.py", line 90 in _hookexec
  File "/root/project/pypy-env/site-packages/pluggy/hooks.py", line 272 in __call__
  File "/root/project/pypy-env/site-packages/_pytest/config/__init__.py", line 130 in main
  File "/root/project/pypy-env/site-packages/_pytest/config/__init__.py", line 180 in console_main
  File "/root/project/pypy-env/site-packages/pytest/__main__.py", line 1 in <module>
  File "/usr/local/lib-python/3/runpy.py", line 62 in _run_code
  File "/usr/local/lib-python/3/runpy.py", line 167 in _run_module_as_main
  File "<builtin>/app_main.py", line 88 in run_toplevel
  File "<builtin>/app_main.py", line 560 in run_command_line
  File "<builtin>/app_main.py", line 862 in entry_point
./build_tools/circle/build_test_pypy.sh: line 46:  7987 Segmentation fault      (core dumped) python -m pytest sklearn/
@adrinjalali adrinjalali added this to the 0.24 milestone Oct 15, 2020
@alfaro96
Copy link
Member

Related with #17994?

@adrinjalali
Copy link
Member Author

yep, that should probably solve this

@cmarmo
Copy link
Contributor

cmarmo commented Oct 29, 2020

I have had a look to the segfaults. For the sake of completness here is the list of the import giving a segfault with pypy:

  • import sklearn.cluster
  • import sklearn.ensemble
  • import sklearn.inspection
  • import sklearn.manifold
  • import sklearn.mixture
  • import sklearn.tree

@cmarmo cmarmo mentioned this issue Oct 29, 2020
Closed
@mattip mattip mentioned this issue Oct 29, 2020
Merged
5 tasks
@ogrisel
Copy link
Member

ogrisel commented Nov 6, 2020

It's possible to reproduce easily with an env dedicated to pypy from conda-forge as follows:

conda create -n pypy -c conda-forge pypy numpy scipy joblib threadpoolctl cython pytest
conda activate pypy
python setup.py develop  # python is an alias for pypy in this env
python -c "import sklearn.cluster"

yields:

Fatal error in cpyext, CPython compatibility layer, calling PyMemoryView_FromObject
Either report a bug or consider not using this particular extension
<OperationError object at 0x564dd9c3d038>
RPython traceback:
  File "pypy_module_cpyext.c", line 5650, in wrapper_second_level__star_1
  File "pypy_module_cpyext_1.c", line 35424, in make_ref
  File "pypy_module_cpyext_2.c", line 10168, in create_ref
  File "pypy_module_cpyext_3.c", line 23729, in memory_attach
  File "pypy_module_cpyext_4.c", line 9653, in fill_Py_buffer
  File "pypy_module_cpyext_1.c", line 41590, in unwrapper__StdObjSpaceConst_SomeInstance_star_1_2
  File "pypy_interpreter.c", line 22498, in BuiltinCodePassThroughArguments0_funcrun
  File "pypy_module__frozen_importlib.c", line 70, in import_with_frames_removed
  File "rpython_rlib_rvmprof.c", line 105, in __vmprof_eval_vmprof
  File "pypy_interpreter_1.c", line 29197, in execute_frame
  File "rpython_jit_metainterp.c", line 8574, in ll_portal_runner__Unsigned_Bool_pypy_interpreter
  File "pypy_module_pypyjit.c", line 181, in portal_7
  File "pypy_interpreter_2.c", line 33958, in handle_bytecode__AccessDirect_None
  File "pypy_interpreter_3.c", line 14663, in dispatch_bytecode__AccessDirect_None
  File "pypy_interpreter_3.c", line 38521, in CALL_FUNCTION__AccessDirect_None
  File "rpython_rlib_rvmprof.c", line 105, in __vmprof_eval_vmprof
  File "pypy_interpreter_1.c", line 29197, in execute_frame
  File "rpython_jit_metainterp.c", line 8574, in ll_portal_runner__Unsigned_Bool_pypy_interpreter
  File "pypy_module_pypyjit.c", line 181, in portal_7
  File "pypy_interpreter_2.c", line 33958, in handle_bytecode__AccessDirect_None
  File "pypy_interpreter_3.c", line 14663, in dispatch_bytecode__AccessDirect_None
  File "pypy_interpreter_3.c", line 38521, in CALL_FUNCTION__AccessDirect_None
  File "rpython_rlib_rvmprof.c", line 105, in __vmprof_eval_vmprof
  File "pypy_interpreter_1.c", line 29197, in execute_frame
  File "rpython_jit_metainterp.c", line 8600, in ll_portal_runner__Unsigned_Bool_pypy_interpreter
  File "rpython_jit_metainterp.c", line 21618, in handle_jitexception_7
Segmentation fault (core dumped)

However if you replace the pypy artifacts generated by this PR:

conda-forge/pypy3.6-feedstock#30 (comment)

then it works:

unzip ~/Downloads/conda_artifacts_linux_64__656edd35-690f-5c53-9ba3-09c10d0bea97.zip
conda install conda_artifacts_linux_64__656edd35-690f-5c53-9ba3-09c10d0bea97/linux-64/pypy3.6-7.3.2-h45e8706_2.tar.bz2
python -c "import sklearn.cluster"

@ogrisel
Copy link
Member

ogrisel commented Nov 6, 2020

I cannot run the full test suite on my laptop: it's too slow and takes too much memory... However, I confirm that with the patched pypy, all the failing imports reported by @cmarmo above pass on in this env.

@ogrisel ogrisel removed the Blocker label Nov 6, 2020
@ogrisel
Copy link
Member

ogrisel commented Nov 6, 2020

I removed the blocker label because I think this will be fixed upstream in the next release of pypy and maybe in a patched release on conda-forge so we do not have to anything here.

@ogrisel ogrisel mentioned this issue Nov 9, 2020
Merged
@ogrisel ogrisel mentioned this issue Nov 19, 2020
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
Build / CI pypy
Projects
None yet
Milestone
0.24
Development

Successfully merging a pull request may close this issue.

MNT use conda-forge for the pypy build on circle ci ogrisel/scikit-learn
4 participants
@ogrisel @cmarmo @adrinjalali @alfaro96