Add a Valgrind build on debug Python 3.9 #2746

YannickJadoul · 2020-12-26T14:15:04Z

Description

Finally, together with @bstaletic, we've finally taken the time and effort to add a build with Valgrind; currently still failing, because of #2742.
We might also need to suppress some Python errors reported by Valgrind, but let's take it step by step.

Things to fix:

Plumb or ignore leaks until things pass.
Shut up warnings coming from the test that are now visible, since we have a debug version of Python.

Things to decide:

Do we just want to run this on Python 3.9 (probably; according to @bstaletic, earlier versions had issues) and on Linux?
Do we want to keep the tests run on debug Python first, before running them again with Valgrind?

Things to tweak in CMake/CI config:

@henryiii, valgrind cmake --build build --target pytest doesn't work (we don't want to run Valgrind on CMake). Do we want to include this into the CMake config? ~~The fact that valgrind python also doesn't work with pyenv (it's bash script wrapper/launcher), and we need to use this $(pyenv which python) doesn't make things simpler either.~~
We can probably cache the built version of pyenv's Python build? It just takes 2 minutes, but still, this would make it faster.
Same for Valgrind, maybe; can we cache this?
There have to be ways to get a cleaner CI config?
We should also check out https://pypi.org/project/pytest-valgrind/

Oh, yes, and:

Undo ed0c494, before merging, ofc. That's just to make the test runs cleaner :-)

Things for follow-up PRs:

This should also be run on the embedded tests.
UBSan, ASan, MSan, TSan, ...?
Revert test_dispatch_issue workarounds and debug and fix the underlying issue.

Closes #2578

Suggested changelog entry:

Added a Valgrind build, checking for leaks and memory-related UB, to CI.

(@henryiii, is this something we actually want to add to add to the changelog?)

This change is

bstaletic · 2020-12-26T14:34:05Z

Do we just want to run this on Python 3.9 (probably; according to @bstaletic, earlier versions had issues) and on Linux?

Valgrind being linux-only answers the latter. As for python 3.9.1 only, it's the cleanest CPython ever, so let's not make our own lives harder than they need to be.

bstaletic · 2020-12-26T18:21:13Z

Do we want to keep the tests run on debug Python first, before running them again with Valgrind?

I really don't see the point. The pytest errors that we currently see in the second run, inside valgrind, is due to multiprocessing.subprocess triggering a valgrind error and subsequently getting its exit code overridden by valgrind. When not overriding the exit codes, all pytest tests pass.

YannickJadoul · 2020-12-26T18:33:08Z

I really don't see the point.

The main idea was that 1) our tests are pretty fast (once compiled) and 2) we don't have any debug build currently, so I thought there was some value in first checking if tests pass, and only then checking Valgrind's output. Maybe once Valgrind is more quiet, it'll be more obvious that Valgrind's output won't mess up the interpretation of the tests too much, though.

YannickJadoul · 2020-12-26T19:41:01Z

We can probably cache the built version of pyenv's Python build? It just takes 2 minutes, but still, this would make it faster.

deadsnakes offers this; we don't need to build anything with pyenv after all! Submitted deadsnakes/action#18 to be able to do this with 3 lines of a GitHub action!

bstaletic · 2020-12-26T19:54:27Z

We should also check out https://pypi.org/project/pytest-valgrind/

Maybe not. While we'd get a complete report after each test, it makes testing the start up and shut down impossible. We have had shutdown related leaks before.

The main idea was that 1) our tests are pretty fast (once compiled) and 2) we don't have any debug build currently, so I thought there was some value in first checking if tests pass, and only then checking Valgrind's output

Alright, let's keep it for now.

.github/workflows/ci.yml

bstaletic · 2020-12-28T02:59:27Z

Shut up warnings coming from the test that are now visible, since we have a debug version of Python;

There's a few distinct warnings:

FutureWarning: pybind11-bound class 'pybind11_tests.factory_constructors.TestFactory3' is using an old-style placement-new
- There's 4 of these, because we have some old-style __init__s and __setstate__s, but all of which seem to be there for testing.
/home/runner/venv-3.9/lib/python3.9/site-packages/pip/_vendor/packaging/version.py:127: DeprecationWarning: Creating a LegacyVersion has been deprecated and will be removed in the next major release
- This is pip using deprecated functionality of packaging that it is vendoring. Nothing to do with pybind11.

henryiii · 2020-12-28T04:13:31Z

I'd like to eventfully move over to running PyTest via CTest instead of CMake. If we do that, then a memcheck target will be generated for us, and we can use CTEST_MEMORYCHECK_SUPPRESSIONS_FILE and such to control the options. Maybe we could make a "memcheck" target that would eventually be the CTest one, or maybe we could keep a manual run for now?

henryiii · 2020-12-28T04:15:01Z

We could add a PYBIND11_TEST_PREFIX_COMMAND option that would add anything as a prefix to the test commands, and we could fill it with the options above. Possibly would work nicely for the C++ targets too?

bstaletic · 2020-12-28T10:13:43Z

we can use CTEST_MEMORYCHECK_SUPPRESSIONS_FILE and such to control the options.

Does that support more than one suppressions file? Right now, we have 3 or 4.

Maybe we could make a "memcheck" target that would eventually be the CTest one, or maybe we could keep a manual run for now?

That should be easy to do.

We could add a PYBIND11_TEST_PREFIX_COMMAND option that would add anything as a prefix to the test commands, and we could fill it with the options above.

Do you mean in addition to the memcheck target?

Possibly would work nicely for the C++ targets too?

It could, yes.

YannickJadoul · 2020-12-28T11:23:07Z

Maybe we could make a "memcheck" target

That could works, yes. I'm getting used to the manual version now as well; it's not as bad as it looks, but still.

We could add a PYBIND11_TEST_PREFIX_COMMAND option that would add anything as a prefix to the test commands, and we could fill it with the options above.

That's more or less what I was thinking, but if feels a bit like a hack.

If it helps to get perspective, fitting in ASAN and UBSAN after this might also become part of the plan.

YannickJadoul · 2020-12-28T13:30:39Z

Btw, I added Reviewable on this. I think this PR will benefit from Reviewable, given the size, given the chance we take some parts out into separate PRs, ...

This change is

YannickJadoul · 2020-12-28T13:54:37Z

There's a few distinct warnings:

FutureWarning: pybind11-bound class 'pybind11_tests.factory_constructors.TestFactory3' is using an old-style placement-new

There's 4 of these, because we have some old-style __init__s and __setstate__s, but all of which seem to be there for testing.

Fixed this one!

/home/runner/venv-3.9/lib/python3.9/site-packages/pip/_vendor/packaging/version.py:127: DeprecationWarning: Creating a LegacyVersion has been deprecated and will be removed in the next major release

This is pip using deprecated functionality of packaging that it is vendoring. Nothing to do with pybind11.

I'm not seeing this in CI, now, though?

bstaletic · 2020-12-28T13:59:05Z

I'm not seeing this in CI, now, though?

On a closer look, that one happens during pip install. Do we care about that?

YannickJadoul · 2020-12-28T14:03:42Z

I'm not seeing this in CI, now, though?

On a closer look, that one happens during pip install. Do we care about that?

Nah, and definitely not in the context of this PR, I'd say. It's also in pip it seems, so ... one of our dependencies?

henryiii · 2021-01-15T13:32:19Z

As long as we run the other parts here (cpptest and such), then we can drop the debug build we have on the other one (or change it).

YannickJadoul · 2021-01-15T13:42:28Z

As long as we run the other parts here (cpptest and such), then we can drop the debug build we have on the other one (or change it).

I was thinking about doing it the other way around, having an few if: statements that also install/run Valgrind in the current 3.9 debug. Let me give that a try, how clean it would be :-)

YannickJadoul · 2021-01-15T14:26:59Z

This seems to be working. Happy with this, @henryiii, @bstaletic?

bstaletic

Sorry for the delay, everyone. I wasn't at home much during the holyday season.

This seems to be working. Happy with this, @henryiii, @bstaletic?

I am.

Reviewed 1 of 4 files at r7, 1 of 5 files at r9, 1 of 3 files at r23, 2 of 3 files at r24, 3 of 6 files at r26, 1 of 4 files at r27, 2 of 3 files at r28, 1 of 2 files at r30, 1 of 1 files at r31.
Reviewable status: all files reviewed, 11 unresolved discussions (waiting on @EricCousineau-TRI, @henryiii, and @YannickJadoul)

.github/workflows/ci.yml, line 207 at r29 (raw file):

Previously, henryiii (Henry Schreiner) wrote…

      working-directory: valgrind
      run: |
        sudo make install
        sudo apt-get update && sudo apt-get install libc6-dbg  # Needed by Valgrind

Done.

include/pybind11/pybind11.h, line 499 at r15 (raw file):

Previously, YannickJadoul (Yannick Jadoul) wrote…

See #2756.

This was fixed, right? If so, please resolve the discussion on Reviewable.

include/pybind11/pybind11.h, line 502 at r19 (raw file):

Previously, YannickJadoul (Yannick Jadoul) wrote…

This can still leak, I have just realized.
It's very annoying that we cannot just have a std::unique_ptr<detail::function_record, void (*)(detail::function_record *)>, with destruct as deleter. The issue is that we cannot do this before all the char *s are strduped, and that 1) is only done in initialize_generic, and 2) the repr calls during strdupcan also throw.

Ditto.

tests/pybind11_tests.h, line 83 at r16 (raw file):

Previously, YannickJadoul (Yannick Jadoul) wrote…

For reference, this was the old code, without py::exec (and thus without requiring <pybind11/eval.h> to be included in pybind11_tests.h and thus in all tests).

@bstaletic slightly prefers this, and I think I do to. However, curious to learn what other reviewers think.

/// Simplified ``with warnigns.catch_warnings()`` wrapper
template <typename F>
void ignoreOldStyleInitWarnings(F &&body) {
    auto message = "pybind11-bound class '.+' is using an old-style placement-new '(?:__init__|__setstate__)' which has been deprecated";
    auto category = py::reinterpret_borrow<py::object>(PyExc_FutureWarning);
    auto warnings = py::module_::import("warnings");
    auto context_mgr = warnings.attr("catch_warnings")();
    context_mgr.attr("__enter__")();
    warnings.attr("filterwarnings")("ignore", py::arg("message")=message, py::arg("category")=category);
    body();
    // Exceptions in `body` not handled; see PEP 343 when these would need to be added
    context_mgr.attr("__exit__")(py::none(), py::none(), py::none());
}

This discussion should be "resolved"/decided. Right?

tests/test_virtual_functions.py, line 254 at r13 (raw file):

Previously, YannickJadoul (Yannick Jadoul) wrote…

Here you go:

=11345== Invalid read of size 1
==11345==    at 0x47CC63: subtype_dealloc (typeobject.c:1343)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x456E22: _Py_DECREF (object.h:430)
==11345==    by 0x456E22: _Py_XDECREF (object.h:497)
==11345==    by 0x456E22: free_keys_object (dictobject.c:598)
==11345==    by 0x456D1D: dictkeys_decref (dictobject.c:333)
==11345==    by 0x456D1D: dict_dealloc (dictobject.c:2026)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x43CBCF: _Py_DECREF (object.h:430)
==11345==    by 0x43CB1B: frame_dealloc (frameobject.c:591)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x51E9E5: _Py_DECREF (object.h:430)
==11345==    by 0x51E9E5: _Py_XDECREF (object.h:497)
==11345==    by 0x51E9E5: tb_dealloc (traceback.c:167)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x432CEA: _Py_DECREF (object.h:430)
==11345==    by 0x432CEA: BaseException_clear (exceptions.c:78)
==11345==    by 0x4342E6: BaseException_dealloc (exceptions.c:88)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x4742E6: _Py_DECREF (object.h:430)
==11345==    by 0x4742E6: _Py_XDECREF (object.h:497)
==11345==    by 0x4742E6: tupledealloc (tupleobject.c:237)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x456CBB: _Py_DECREF (object.h:430)
==11345==    by 0x456CBB: _Py_XDECREF (object.h:497)
==11345==    by 0x456CBB: dict_dealloc (dictobject.c:2018)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x476595: _Py_DECREF (object.h:430)
==11345==    by 0x47F1F1: subtype_clear (typeobject.c:1186)
==11345==    by 0x52E694: delete_garbage (gcmodule.c:1004)
==11345==    by 0x52D806: collect (gcmodule.c:1273)
==11345==    by 0x52D28F: collect_with_callback (gcmodule.c:1387)
==11345==    by 0x52D23C: collect_generations (gcmodule.c:1442)
==11345==    by 0x52CF2A: _PyObject_GC_Alloc (gcmodule.c:2242)
==11345==    by 0x52CE47: _PyObject_GC_Malloc (gcmodule.c:2252)
==11345==  Address 0x77b12b9 is 185 bytes inside a block of size 936 free'd
==11345==    at 0x4C33078: free (vg_replace_malloc.c:538)
==11345==    by 0x467EA2: _PyMem_RawFree (obmalloc.c:127)
==11345==    by 0x468F91: PyObject_Free (obmalloc.c:709)
==11345==    by 0x52D1C0: PyObject_GC_Del (gcmodule.c:2317)
==11345==    by 0x47EFE4: type_dealloc (typeobject.c:3486)
==11345==    by 0xA92DA84: pybind11_meta_dealloc (class.h:231)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0xA9220FB: _Py_DECREF (object.h:430)
==11345==    by 0xA92E6FC: pybind11_object_dealloc (class.h:436)
==11345==    by 0x47CC62: subtype_dealloc (typeobject.c:1337)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x456E22: _Py_DECREF (object.h:430)
==11345==    by 0x456E22: _Py_XDECREF (object.h:497)
==11345==    by 0x456E22: free_keys_object (dictobject.c:598)
==11345==    by 0x456D1D: dictkeys_decref (dictobject.c:333)
==11345==    by 0x456D1D: dict_dealloc (dictobject.c:2026)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x43CBCF: _Py_DECREF (object.h:430)
==11345==    by 0x43CB1B: frame_dealloc (frameobject.c:591)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x51E9E5: _Py_DECREF (object.h:430)
==11345==    by 0x51E9E5: _Py_XDECREF (object.h:497)
==11345==    by 0x51E9E5: tb_dealloc (traceback.c:167)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x432CEA: _Py_DECREF (object.h:430)
==11345==    by 0x432CEA: BaseException_clear (exceptions.c:78)
==11345==    by 0x4342E6: BaseException_dealloc (exceptions.c:88)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x4742E6: _Py_DECREF (object.h:430)
==11345==    by 0x4742E6: _Py_XDECREF (object.h:497)
==11345==    by 0x4742E6: tupledealloc (tupleobject.c:237)
==11345==    by 0x4641AD: _Py_Dealloc (object.c:2209)
==11345==    by 0x456CBB: _Py_DECREF (object.h:430)
==11345==    by 0x456CBB: _Py_XDECREF (object.h:497)
==11345==    by 0x456CBB: dict_dealloc (dictobject.c:2018)
==11345==  Block was alloc'd at
==11345==    at 0x4C31ECB: malloc (vg_replace_malloc.c:307)
==11345==    by 0x467566: _PyMem_RawMalloc (obmalloc.c:99)
==11345==    by 0x468168: PyObject_Malloc (obmalloc.c:685)
==11345==    by 0x52CE7B: _PyObject_GC_Alloc (gcmodule.c:2225)
==11345==    by 0x52CE47: _PyObject_GC_Malloc (gcmodule.c:2252)
==11345==    by 0x47638A: PyType_GenericAlloc (typeobject.c:1047)
==11345==    by 0x479D4A: type_new (typeobject.c:2596)
==11345==    by 0x4799EC: type_call (typeobject.c:1014)
==11345==    by 0x42DE98: _PyObject_MakeTpCall (call.c:191)
==11345==    by 0x42DC17: _PyObject_FastCallDictTstate (call.c:113)
==11345==    by 0x42DA26: PyObject_VectorcallDict (call.c:142)
==11345==    by 0x6567F1: builtin___build_class__ (bltinmodule.c:232)
==11345==    by 0x62B2AC: cfunction_vectorcall_FASTCALL_KEYWORDS (methodobject.c:442)
==11345==    by 0x4D5792: _PyObject_VectorcallTstate (abstract.h:118)
==11345==    by 0x4D5792: PyObject_Vectorcall (abstract.h:127)
==11345==    by 0x4D5792: call_function (ceval.c:5072)
==11345==    by 0x4D5792: _PyEval_EvalFrameDefault (ceval.c:3518)
==11345==    by 0x4CBDF5: _PyEval_EvalFrame (pycore_ceval.h:40)
==11345==    by 0x4CBDF5: _PyEval_EvalCode (ceval.c:4327)
==11345==    by 0x42E767: _PyFunction_Vectorcall (call.c:395)
==11345==    by 0x42F6F7: PyVectorcall_Call (call.c:242)
==11345==    by 0x42F4A9: _PyObject_Call (call.c:265)
==11345==    by 0x42F3F9: PyObject_Call (call.c:292)
==11345==    by 0x4D7B7D: do_call_core (ceval.c:5120)
==11345==    by 0x4D5F24: _PyEval_EvalFrameDefault (ceval.c:3580)
==11345==    by 0x4CBDF5: _PyEval_EvalFrame (pycore_ceval.h:40)
==11345==    by 0x4CBDF5: _PyEval_EvalCode (ceval.c:4327)
==11345==    by 0x42E767: _PyFunction_Vectorcall (call.c:395)
==11345==    by 0x42F7AD: PyVectorcall_Call (call.c:230)
==11345==    by 0x42F4A9: _PyObject_Call (call.c:265)

One free was from within pybind11's metaclass. The other was at shutdown when cpython is cleaning up after itself.

tests/valgrind-numpy-scipy.supp, line 2 at r19 (raw file):

Previously, YannickJadoul (Yannick Jadoul) wrote…

Definitely! I just don't believe either @bstaletic or I have looked further than "this already occurs just importing NumPy, so let's suppress these".

Right. Reporting bugs to CPython and/or NumPy shouldn't block this pull request, however. (As long as they aren't actual blockers.)

YannickJadoul

Reviewable status: all files reviewed, 5 unresolved discussions (waiting on @bstaletic, @EricCousineau-TRI, and @henryiii)

.github/workflows/ci.yml, line 197 at r18 (raw file):

Previously, henryiii (Henry Schreiner) wrote…

Let's pull this into three steps, one that downloads and one that compiles valgrind if the cache misses, and one that (always) installs valgrind. Then we can use working-directory and drop the pushd/popd.

Done by @henryiii

.github/workflows/ci.yml, line 198 at r29 (raw file):

Previously, henryiii (Henry Schreiner) wrote…

Also, technically, I think you could also just cd then not go back, since you don't use the outer directory in the next line

Done by @henryiii

include/pybind11/pybind11.h, line 499 at r15 (raw file):

Previously, bstaletic (Boris Staletic) wrote…

This was fixed, right? If so, please resolve the discussion on Reviewable.

Yes, indeed!

include/pybind11/pybind11.h, line 231 at r19 (raw file):

Previously, YannickJadoul (Yannick Jadoul) wrote…

Hmmm, myes, hadn't thought of that yes. But tocommon.h, then?
If you ask me, I'd only do this when we'd need to (because there's another use case), though?

Let's consider this resolved. If other things need this, we can still move it to common.h at a later point?

include/pybind11/pybind11.h, line 502 at r19 (raw file):

Previously, bstaletic (Boris Staletic) wrote…

Ditto.

Yes, thanks! Cutting out these other PRs has left this in a bit of a weird state :-)

tests/pybind11_tests.h, line 83 at r16 (raw file):

Previously, bstaletic (Boris Staletic) wrote…

This discussion should be "resolved"/decided. Right?

It's fine like this, I think!

tests/test_virtual_functions.py, line 254 at r13 (raw file):

Previously, bstaletic (Boris Staletic) wrote…

One free was from within pybind11's metaclass. The other was at shutdown when cpython is cleaning up after itself.

I'll resolve this, but once the PR gets merged, we'll still revert this one.

YannickJadoul

Reviewable status: all files reviewed, 5 unresolved discussions (waiting on @bstaletic, @EricCousineau-TRI, and @henryiii)

YannickJadoul · 2021-01-15T19:38:52Z

Sorry for the delay, everyone. I wasn't at home much during the holyday season.

Not at all :-) You're the one that keeps telling me "open source, no deadlines" ;-)

bstaletic

Reviewable status: all files reviewed, 4 unresolved discussions (waiting on @EricCousineau-TRI and @henryiii)

bstaletic

Does my approval count?

YannickJadoul · 2021-01-15T20:07:24Z

Yeeeeeeeeeeah. At least the two of us together share a full approval, no? For the things the other has done :-)

This is just CI and CMake anyway, and @henryiii approved, and @EricCousineau-TRI's comments were handled in #2756, so .. let's get Valgrind support for all PRs ;-)

YannickJadoul · 2021-01-15T20:07:49Z

Thanks a lot for all the shared work, @bstaletic! :-)

rwgk · 2021-01-15T20:10:27Z

Congratulations and thanks a lot @YannickJadoul & @bstaletic! This is a game changer for future developments.

YannickJadoul · 2021-01-15T20:11:07Z

Thanks! :-) Let's hope so. Almost forgot (since that's longer ago), but thanks for all your reviews as well, @rwgk!

YannickJadoul · 2021-01-15T20:42:55Z

Follow-up in #2797.

Do we also want to report the leaks to Python/NumPy? We could create an issue until someone feels like it? @EricCousineau-TRI suggested this, and @bstaletic reacted. What do you think?

YannickJadoul changed the title ~~Add a valgrind build on debug Python 3.9~~ Add a Valgrind build on debug Python 3.9 Dec 26, 2020

YannickJadoul force-pushed the valgrind branch 4 times, most recently from 59079c4 to 4889a59 Compare December 26, 2020 19:29

YannickJadoul mentioned this pull request Dec 26, 2020

Allow installation of debug version of Python deadsnakes/action#18

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Merge Valgrind and other deadsnakes builds

8abf0da

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YannickJadoul requested review from bstaletic and henryiii January 15, 2021 19:37

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YannickJadoul merged commit 0f8d5f2 into pybind:master Jan 15, 2021

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github-actions bot added the needs changelog Possibly needs a changelog entry label Jan 15, 2021

YannickJadoul added a commit to YannickJadoul/pybind11 that referenced this pull request Jan 15, 2021

Revert workaround of test_virtual_functions.py from pybind#2746

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Revert workaround of test_virtual_functions.py from #2746 #2797

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Add memory checks to CI (valgrind) FEniCS/dolfinx#1355

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chore: prepare for the 2.6.2 release #2821

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JeanChristopheMorinPerso mentioned this pull request Sep 22, 2022

Dynamic code analysis AcademySoftwareFoundation/OpenTimelineIO#1406

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rwgk mentioned this pull request Feb 10, 2023

FWD pybind11 google/pybind11clif#2746

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Add a Valgrind build on debug Python 3.9 #2746

Add a Valgrind build on debug Python 3.9 #2746

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Add a Valgrind build on debug Python 3.9 #2746

Add a Valgrind build on debug Python 3.9 #2746

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