scikit-hep / scikit-hep/uproot5
test_0927_dont_assume_uproot_in_global_scope_in_TPython_Eval now raises an exception
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- Dominant language
- Python
- Stars
- 270
- Forks
- 102
- Avg merge
- 12h 17m
- Merged PRs (30d)
- 6
Description
It was introduced in #927 to fix a segfault, and now it's producing segfaults again, but probably for a different reason. pytest hides the ROOT error messages, but they are:
*** Break *** segmentation violation
Generating stack trace...
0x00005d42557bf44a in PyUnicode_FromFormatV + 0x88a from python
0x00005d42557edc81 in PyErr_Format + 0xf1 from python
0x00005d42556d6851 in <unknown> from python
0x00005d42557c7c9c in _PyEval_EvalFrameDefault + 0xffc from python
0x00005d425587ea8d in <unknown> from python
0x00005d425587e11f in PyEval_EvalCode + 0x9f from python
0x00005d425589d08a in <unknown> from python
0x00005d4255898c13 in <unknown> from python
0x00005d425588d3c2 in PyRun_StringFlags + 0x62 from python
0x0000724653f49dcd in TPython::Exec(char const*) + 0x3d from /home/jpivarski/miniforge3/lib/libROOTTPython.so.6.32.00
0x0000724653f5609b in <unknown function>
0x0000724665957266 in TBuffer::Expand(int, bool) + 0x76 from /home/jpivarski/miniforge3/lib/python3.11/lib-dynload/../.././libCore.so.6.32
0x000072466526403e in TBufferFile::WriteFastArray(double const*, long long) + 0xbe from /home/jpivarski/miniforge3/lib/libRIO.so
0x0000724665a9496b in TStreamerBase::WriteBuffer(TBuffer&, char*) + 0x2b from /home/jpivarski/miniforge3/lib/python3.11/lib-dynload/../.././libCore.so.6.32
0x00007246654ffb84 in int TStreamerInfo::WriteBufferAux<char**>(TBuffer&, char** const&, TStreamerInfo::TCompInfo* const*, int, int, int, int, int) + 0x6504 from /home/jpivarski/miniforge3/lib/libRIO.so
0x00007246653477e1 in TStreamerInfoActions::GenericWriteAction(TBuffer&, void*, TStreamerInfoActions::TConfiguration const*) + 0x51 from /home/jpivarski/miniforge3/lib/libRIO.so
0x000072466526bf9e in TBufferFile::WriteClassBuffer(TClass const*, void*) + 0x2ae from /home/jpivarski/miniforge3/lib/libRIO.so
0x0000724665a9496b in TStreamerBase::WriteBuffer(TBuffer&, char*) + 0x2b from /home/jpivarski/miniforge3/lib/python3.11/lib-dynload/../.././libCore.so.6.32
0x00007246654ffb84 in int TStreamerInfo::WriteBufferAux<char**>(TBuffer&, char** const&, TStreamerInfo::TCompInfo* const*, int, int, int, int, int) + 0x6504 from /home/jpivarski/miniforge3/lib/libRIO.so
0x00007246653477e1 in TStreamerInfoActions::GenericWriteAction(TBuffer&, void*, TStreamerInfoActions::TConfiguration const*) + 0x51 from /home/jpivarski/miniforge3/lib/libRIO.so
0x000072466526bf9e in TBufferFile::WriteClassBuffer(TClass const*, void*) + 0x2ae from /home/jpivarski/miniforge3/lib/libRIO.so
0x000072466526a69b in TBufferFile::WriteObjectClass(void const*, TClass const*, bool) + 0x1ab from /home/jpivarski/miniforge3/lib/libRIO.so
0x0000724665d32bfe in <unknown> from /home/jpivarski/miniforge3/lib/python3.11/lib-dynload/../../libcppyy_backend.so
0x0000724644f7a356 in <unknown> from /home/jpivarski/miniforge3/lib/python3.11/site-packages/libcppyy.so
0x0000724644f6061a in <unknown> from /home/jpivarski/miniforge3/lib/python3.11/site-packages/libcppyy.so
0x0000724644f607c8 in <unknown> from /home/jpivarski/miniforge3/lib/python3.11/site-packages/libcppyy.so
0x0000724644f60956 in CPyCppyy::CPPMethod::Execute(void*, long, CPyCppyy::CallContext*) + 0x26 from /home/jpivarski/miniforge3/lib/python3.11/site-packages/libcppyy.so
0x0000724644f60ac6 in CPyCppyy::CPPMethod::Call(CPyCppyy::CPPInstance*&, _object* const*, unsigned long, _object*, CPyCppyy::CallContext*) + 0x116 from /home/jpivarski/miniforge3/lib/python3.11/site-packages/libcppyy.so
0x0000724644f689d3 in <unknown> from /home/jpivarski/miniforge3/lib/python3.11/site-packages/libcppyy.so
0x00005d42557d3eac in PyObject_Vectorcall + 0x2c from python
0x00005d42557c73b6 in _PyEval_EvalFrameDefault + 0x716 from python
0x00005d425587ea8d in <unknown> from python
0x00005d425587e11f in PyEval_EvalCode + 0x9f from python
0x00005d425589d08a in <unknown> from python
0x00005d4255898c13 in <unknown> from python
0x00005d425588d3c2 in PyRun_StringFlags + 0x62 from python
0x00005d425588d17c in PyRun_SimpleStringFlags + 0x3c from python
0x00005d42558a7bdf in Py_RunMain + 0x23f from python
0x00005d425586e027 in Py_BytesMain + 0x37 from python
0x0000724667c29d90 in <unknown> from /lib/x86_64-linux-gnu/libc.so.6
0x0000724667c29e40 in __libc_start_main + 0x80 from /lib/x86_64-linux-gnu/libc.so.6
0x00005d425586decd in <unknown> from python
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/jpivarski/irishep/uproot5/tests/test_0927_dont_assume_uproot_in_global_scope_in_TPython_Eval.py", line 14, in test
assert __import__("uproot").from_pyroot(h).values().shape == (1, 1, 1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jpivarski/irishep/uproot5/src/uproot/pyroot.py", line 258, in from_pyroot
buffer = pyroot_to_buffer(obj)
^^^^^^^^^^^^^^^^^^^^^
File "/home/jpivarski/irishep/uproot5/src/uproot/pyroot.py", line 136, in pyroot_to_buffer
message.WriteObject(obj)
cppyy.ll.SegmentationViolation: void TBufferIO::WriteObject(const TObject* obj, Bool_t cacheReuse = kTRUE) =>
SegmentationViolation: segfault in C++; program state was reset
*** Break *** segmentation violation
Generating stack trace...
0x00005d42557aef74 in <unknown> from python
0x00005d42557ae513 in <unknown> from python
0x00005d425587a6fb in <unknown> from python
0x00005d42558ac481 in PyGC_Collect + 0x61 from python
0x00005d425589c01e in Py_FinalizeEx + 0x13e from python
0x00005d42558a7b20 in Py_RunMain + 0x180 from python
0x00005d425586e027 in Py_BytesMain + 0x37 from python
0x0000724667c29d90 in <unknown> from /lib/x86_64-linux-gnu/libc.so.6
0x0000724667c29e40 in __libc_start_main + 0x80 from /lib/x86_64-linux-gnu/libc.so.6
0x00005d425586decd in <unknown> from python
*** Break *** segmentation violation
Generating stack trace...
0x00005d42557aef74 in <unknown> from python
0x00005d42557ae513 in <unknown> from python
0x00005d425587a6fb in <unknown> from python
0x00005d42558ac481 in PyGC_Collect + 0x61 from python
0x00005d425589c01e in Py_FinalizeEx + 0x13e from python
0x00005d42558a7b20 in Py_RunMain + 0x180 from python
0x00005d425586e027 in Py_BytesMain + 0x37 from python
0x0000724667c29d90 in <unknown> from /lib/x86_64-linux-gnu/libc.so.6
0x0000724667c29e40 in __libc_start_main + 0x80 from /lib/x86_64-linux-gnu/libc.so.6
0x00005d425586decd in <unknown> from python
The segfault is somewhere in the TBufferIO::WriteObject call.
This is a blocker: our one test that imports ROOT always fails because of this.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start with tests/test_0927_dont_assume_uproot_in_global_scope_in_TPython_Eval.py and reproduce the failure with pytest. Trace uproot/pyroot.py through pyroot_to_buffer and the TBufferIO::WriteObject call; done means the ROOT-importing test completes without a segmentation violation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp, python
- Domain
- data, testing
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100