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https://issues.apache.org/jira/browse/ARROW-7873?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17040047#comment-17040047
]
Antoine Pitrou commented on ARROW-7873:
---------------------------------------
How did you compile pyodbc? I'm surprised about the following output (from GH
bug you linked to):
{code}
linux-vdso.so.1 (0x00007ffe02bee000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007f246c269000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f246c061000)
libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7
(0x00007f246be57000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f246ba66000)
/lib64/ld-linux-x86-64.so.2 (0x00007f246cd89000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f246b862000)
{code}
> [Python] Segfault in pandas version 1.0.1, read_parquet after creating a
> clickhouse odbc connection
> ---------------------------------------------------------------------------------------------------
>
> Key: ARROW-7873
> URL: https://issues.apache.org/jira/browse/ARROW-7873
> Project: Apache Arrow
> Issue Type: Bug
> Components: Python
> Environment: Ubuntu 18.04
> Reporter: Matt Calder
> Priority: Minor
> Fix For: 1.0.0, 0.16.1
>
> Attachments: foo.pkl, foo.pq
>
>
> [I posted this issue to the pandas
> github|[https://github.com/pandas-dev/pandas/issues/31981]].
> We get a segfault when making a call to pd.read_parquet after having made a
> connection to clickhouse via odbc. Like so,
> {code:python}
> import pyodbc
> import pandas as pd
> con_str =
> f"Driver=libclickhouseodbc.so;url=http://clickhouse/query;timeout=600";
> with pyodbc.connect(con_str, autocommit=True) as con:
> pass
> df = pd.DataFrame({'A': [1,1,1], 'B': ['a', 'b', 'c']})
> df.to_parquet('/tmp/foo.pq')
> # This line core dumps:
> pd.read_parquet('/tmp/foo.pq')
> {code}
> This happens with pandas version 1.0.1 but not with pandas 0.25.3. Here's a
> stacktrace:
> {code:java}
> #0 __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:51
> #1 0x00007ffff7a24801 in __GI_abort () at abort.c:79
> #2 0x00007ffff63c1957 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> #3 0x00007ffff63c7ab6 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> #4 0x00007ffff63c7af1 in std::terminate() () from
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> #5 0x00007ffff63c7d24 in __cxa_throw () from
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> #6 0x00007ffff63c6a52 in __cxa_bad_cast () from
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> #7 0x00007ffff64131ec in std::__cxx11::collate<char> const&
> std::use_facet<std::__cxx11::collate<char> >(std::locale const&) () from
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> #8 0x00007fffbe4b8279 in std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >
> std::__cxx11::regex_traits<char>::transform_primary<char const*>(char const*,
> char const*) const () from /usr/local/lib/libparquet.so.100
> #9 0x00007fffbe4bd71c in
> std::__detail::_BracketMatcher<std::__cxx11::regex_traits<char>, false,
> false>::_M_ready() () from /usr/local/lib/libparquet.so.100
> #10 0x00007fffbe4bda9e in void
> std::__detail::_Compiler<std::__cxx11::regex_traits<char>
> >::_M_insert_character_class_matcher<false, false>() () from
> /usr/local/lib/libparquet.so.100
> #11 0x00007fffbe4c0569 in
> std::__detail::_Compiler<std::__cxx11::regex_traits<char> >::_M_atom() ()
> from /usr/local/lib/libparquet.so.100
> #12 0x00007fffbe4c0ad8 in
> std::__detail::_Compiler<std::__cxx11::regex_traits<char> >::_M_alternative()
> () from /usr/local/lib/libparquet.so.100
> #13 0x00007fffbe4c0a43 in
> std::__detail::_Compiler<std::__cxx11::regex_traits<char> >::_M_alternative()
> () from /usr/local/lib/libparquet.so.100
> #14 0x00007fffbe4c0d1c in
> std::__detail::_Compiler<std::__cxx11::regex_traits<char> >::_M_disjunction()
> () from /usr/local/lib/libparquet.so.100
> #15 0x00007fffbe4c1469 in
> std::__detail::_Compiler<std::__cxx11::regex_traits<char> >::_Compiler(char
> const*, char const*, std::locale const&,
> std::regex_constants::syntax_option_type) () from
> /usr/local/lib/libparquet.so.100
> #16 0x00007fffbe4a93d1 in
> parquet::ApplicationVersion::ApplicationVersion(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&) () from
> /usr/local/lib/libparquet.so.100
> #17 0x00007fffbe4c1c03 in
> parquet::FileMetaData::FileMetaDataImpl::FileMetaDataImpl(void const*,
> unsigned int*, std::shared_ptr<parquet::Decryptor> const&) () from
> /usr/local/lib/libparquet.so.100
> #18 0x00007fffbe4a9e62 in parquet::FileMetaData::FileMetaData(void const*,
> unsigned int*, std::shared_ptr<parquet::Decryptor> const&) () from
> /usr/local/lib/libparquet.so.100
> #19 0x00007fffbe4a9ec2 in parquet::FileMetaData::Make(void const*, unsigned
> int*, std::shared_ptr<parquet::Decryptor> const&) () from
> /usr/local/lib/libparquet.so.100
> #20 0x00007fffbe48acaf in
> parquet::SerializedFile::ParseUnencryptedFileMetadata(std::shared_ptr<arrow::Buffer>
> const&, long, long, std::shared_ptr<arrow::Buffer>*, unsigned int*, unsigned
> int*) () from /usr/local/lib/libparquet.so.100
> #21 0x00007fffbe492d75 in parquet::SerializedFile::ParseMetaData() () from
> /usr/local/lib/libparquet.so.100
> #22 0x00007fffbe48d8f8 in
> parquet::ParquetFileReader::Contents::Open(std::shared_ptr<arrow::io::RandomAccessFile>,
> parquet::ReaderProperties const&, std::shared_ptr<parquet::FileMetaData>) ()
> from /usr/local/lib/libparquet.so.100
> #23 0x00007fffbe48e598 in
> parquet::ParquetFileReader::Open(std::shared_ptr<arrow::io::RandomAccessFile>,
> parquet::ReaderProperties const&, std::shared_ptr<parquet::FileMetaData>) ()
> from /usr/local/lib/libparquet.so.100
> #24 0x00007fffbe3a89bd in
> parquet::arrow::FileReaderBuilder::Open(std::shared_ptr<arrow::io::RandomAccessFile>,
> parquet::ReaderProperties const&, std::shared_ptr<parquet::FileMetaData>) ()
> from /usr/local/lib/libparquet.so.100
> #25 0x00007fffbe7dc348 in
> __pyx_pf_7pyarrow_8_parquet_13ParquetReader_2open(__pyx_obj_7pyarrow_8_parquet_ParquetReader*,
> _object*, int, _object*, __pyx_obj_7pyarrow_8_parquet_FileMetaData*, int) ()
> from
> /usr/local/lib/python3.6/dist-packages/pyarrow-0.15.1.dev539+g8cf0c8e0a-py3.6-linux-x86_64.egg/pyarrow/_parquet.cpython-36m-x86_64-linux-gnu.so
> #26 0x00007fffbe7dcbc9 in
> __pyx_pw_7pyarrow_8_parquet_13ParquetReader_3open(_object*, _object*,
> _object*) () from
> /usr/local/lib/python3.6/dist-packages/pyarrow-0.15.1.dev539+g8cf0c8e0a-py3.6-linux-x86_64.egg/pyarrow/_parquet.cpython-36m-x86_64-linux-gnu.so
> #27 0x000000000050ac25 in _PyCFunction_FastCallDict (kwargs=<optimized out>,
> nargs=<optimized out>, args=<optimized out>, func_obj=<built-in method open
> of pyarrow._parquet.ParquetReader object at remote 0x7fffbfc6b938>) at
> ../Objects/methodobject.c:231
> #28 _PyCFunction_FastCallKeywords (kwnames=<optimized out>, nargs=<optimized
> out>, stack=<optimized out>, func=<optimized out>) at
> ../Objects/methodobject.c:294
> #29 call_function.lto_priv () at ../Python/ceval.c:4851
> #30 0x000000000050d390 in _PyEval_EvalFrameDefault () at
> ../Python/ceval.c:3351
> #31 0x0000000000508245 in PyEval_EvalFrameEx (throwflag=0, f=
> Frame 0x142a818, for file
> /usr/local/lib/python3.6/dist-packages/pyarrow-0.15.1.dev539+g8cf0c8e0a-py3.6-linux-x86_64.egg/pyarrow/parquet.py,
> line 137, in __init__
> (self=<ParquetFile(reader=<pyarrow._parquet.ParquetReader at remote
> 0x7fffbfc6b938>) at remote 0x7fffc4b68cc0>, source='/tmp/foo.pq',
> metadata=None, common_metadata=None, read_dictionary=None, memory_map=False,
> buffer_size=0)) at ../Python/ceval.c:754
> #32 _PyEval_EvalCodeWithName.lto_priv.1836 () at ../Python/ceval.c:4166
> #33 0x0000000000509642 in _PyFunction_FastCallDict () at
> ../Python/ceval.c:5075
> #34 0x0000000000595311 in _PyObject_FastCallDict (kwargs={'metadata': None,
> 'memory_map': False, 'read_dictionary': None, 'common_metadata': None,
> 'buffer_size': 0}, nargs=2, args=0x7fffffffc430, func=<function at remote
> 0x7fffbfc5e378>)
> at ../Objects/abstract.c:2310
> #35 _PyObject_Call_Prepend (kwargs={'metadata': None, 'memory_map': False,
> 'read_dictionary': None, 'common_metadata': None, 'buffer_size': 0},
> args=<optimized out>, obj=<optimized out>, func=<function at remote
> 0x7fffbfc5e378>) at ../Objects/abstract.c:2373
> #36 method_call.lto_priv () at ../Objects/classobject.c:314
> #37 0x000000000054a6ff in PyObject_Call (kwargs={'metadata': None,
> 'memory_map': False, 'read_dictionary': None, 'common_metadata': None,
> 'buffer_size': 0}, args=('/tmp/foo.pq',), func=<method at remote
> 0x7ffff7f67fc8>) at ../Objects/abstract.c:2261
> #38 slot_tp_init () at ../Objects/typeobject.c:6420
> #39 0x0000000000551b81 in type_call.lto_priv () at ../Objects/typeobject.c:915
> ---Type <return> to continue, or q <return> to quit---
> {code}
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