Hi, Could you try building Apache Arrow C++ with -DCMAKE_BUILD_TYPE=Debug and get backtrace again? It will show the source location on segmentation fault.
Thanks, -- kou In <calq9kxa8sh07shuckhka9fuzu2n87tbydlp--aahgcwkfwo...@mail.gmail.com> "C++ Segmentation Fault RecordBatchReader::ReadNext in CentOS only" on Tue, 8 Jun 2021 12:01:27 -0700, Rares Vernica <rvern...@gmail.com> wrote: > Hello, > > We recently migrated our C++ Arrow code from 0.16 to 3.0.0. The code works > fine on Ubuntu, but we get a segmentation fault in CentOS while reading > Arrow Record Batch files. We can successfully read the files from Python or > Ubuntu so the files and the writer are fine. > > We use Record Batch Stream Reader/Writer to read/write data to files. > Sometimes we use GZIP to compress the streams. The migration to 3.0.0 was > pretty straight forward with minimal changes to the code > https://github.com/Paradigm4/bridge/commit/03e896e84230ddb41bfef68cde5ed9b21192a0e9 > We have an extensive test suite and all is good on Ubuntu. On CentOS the > write works OK but we get a segmentation fault during reading from C++. We > can successfully read the files using PyArrow. Moreover, the files written > by CentOS can be successfully read from C++ in Ubuntu. > > Here is the backtrace I got form gdb when the segmentation fault occurred: > > Program received signal SIGSEGV, Segmentation fault. > [Switching to Thread 0x7f548c7fb700 (LWP 2649)] > 0x00007f545c003340 in ?? () > (gdb) bt > #0 0x00007f545c003340 in ?? () > #1 0x00007f54903377ce in arrow::ipc::ArrayLoader::GetBuffer(int, > std::shared_ptr<arrow::Buffer>*) () from /lib64/libarrow.so.300 > #2 0x00007f549034006c in arrow::Status > arrow::VisitTypeInline<arrow::ipc::ArrayLoader>(arrow::DataType const&, > arrow::ipc::ArrayLoader*) () from /lib64/libarrow.so.300 > #3 0x00007f5490340db4 in arrow::ipc::ArrayLoader::Load(arrow::Field > const*, arrow::ArrayData*) () from /lib64/libarrow.so.300 > #4 0x00007f5490318b5b in > arrow::ipc::LoadRecordBatchSubset(org::apache::arrow::flatbuf::RecordBatch > const*, std::shared_ptr<arrow::Schema> const&, std::vector<bool, > std::allocator<bool> > const*, arrow::ipc::DictionaryMemo const*, > arrow::ipc::IpcReadOptions const&, arrow::ipc::MetadataVersion, > arrow::Compression::type, arrow::io::RandomAccessFile*) () from > /lib64/libarrow.so.300 > #5 0x00007f549031952a in > arrow::ipc::LoadRecordBatch(org::apache::arrow::flatbuf::RecordBatch > const*, std::shared_ptr<arrow::Schema> const&, std::vector<bool, > std::allocator<bool> > const&, arrow::ipc::DictionaryMemo const*, > arrow::ipc::IpcReadOptions const&, arrow::ipc::MetadataVersion, > arrow::Compression::type, arrow::io::RandomAccessFile*) () from > /lib64/libarrow.so.300 > #6 0x00007f54903197ce in arrow::ipc::ReadRecordBatchInternal(arrow::Buffer > const&, std::shared_ptr<arrow::Schema> const&, std::vector<bool, > std::allocator<bool> > const&, arrow::ipc::DictionaryMemo const*, > arrow::ipc::IpcReadOptions const&, arrow::io::RandomAccessFile*) () from > /lib64/libarrow.so.300 > #7 0x00007f5490345d9c in > arrow::ipc::RecordBatchStreamReaderImpl::ReadNext(std::shared_ptr<arrow::RecordBatch>*) > () from /lib64/libarrow.so.300 > #8 0x00007f549109b479 in scidb::ArrowReader::readObject > (this=this@entry=0x7f548c7f7d80, > name="index/0", reuse=reuse@entry=true, arrowBatch=std::shared_ptr (empty) > 0x0) at XIndex.cpp:104 > #9 0x00007f549109cb0a in scidb::XIndex::load (this=this@entry=0x7f545c003ab0, > driver=std::shared_ptr (count 3, weak 0) 0x7f545c003e70, query=warning: > RTTI symbol not found for class 'std::_Sp_counted_ptr_inplace<scidb::Query, > std::allocator<scidb::Query>, (__gnu_cxx::_Lock_policy)2>' > warning: RTTI symbol not found for class > 'std::_Sp_counted_ptr_inplace<scidb::Query, std::allocator<scidb::Query>, > (__gnu_cxx::_Lock_policy)2>' > std::shared_ptr (count 7, weak 7) 0x7f546c005330) at XIndex.cpp:286 > > I also tried Arrow 4.0.0. The code compiled just fine and the behavior was > the same, with the same backtrace. > > The code where the segmentation fault occurs is trying to read a GZIP > compressed Record Batch Stream. The file is 144 bytes and has only one > column with three int64 values. > >> file 0 > 0: gzip compressed data, from Unix > >> stat 0 > File: ‘0’ > Size: 144 Blocks: 8 IO Block: 4096 regular file > Device: 10302h/66306d Inode: 33715444 Links: 1 > Access: (0644/-rw-r--r--) Uid: ( 1001/ scidb) Gid: ( 1001/ scidb) > Context: unconfined_u:object_r:user_tmp_t:s0 > Access: 2021-06-08 04:42:28.653548604 +0000 > Modify: 2021-06-08 04:14:14.638927052 +0000 > Change: 2021-06-08 04:40:50.221279208 +0000 > Birth: - > > In [29]: s = pyarrow.input_stream('/tmp/bridge/foo/index/0', > compression='gzip') > In [30]: b = pyarrow.RecordBatchStreamReader(s) > In [31]: t = b.read_all() > In [32]: t.columns > Out[32]: > [<pyarrow.lib.ChunkedArray object at 0x7fefb5a552b0> > [ > [ > 0, > 5, > 10 > ] > ]] > > I removed the GZIP compression in both the writer and the reader but the > issue persists. So I don't think it is because of the compression. > > Here is the ldd on the library file which contains the reader and writers > that use the Arrow library. It is built on a CentOS 7 with the g++ 4.9.2 > compiler. > >> ldd libbridge.so > linux-vdso.so.1 => (0x00007fffe4f10000) > libarrow.so.300 => /lib64/libarrow.so.300 (0x00007f8a38908000) > libaws-cpp-sdk-s3.so => /opt/aws/lib64/libaws-cpp-sdk-s3.so > (0x00007f8a384b3000) > libm.so.6 => /lib64/libm.so.6 (0x00007f8a381b1000) > librt.so.1 => /lib64/librt.so.1 (0x00007f8a37fa9000) > libdl.so.2 => /lib64/libdl.so.2 (0x00007f8a37da5000) > libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f8a37a9e000) > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f8a37888000) > libc.so.6 => /lib64/libc.so.6 (0x00007f8a374ba000) > libcrypto.so.10 => /lib64/libcrypto.so.10 (0x00007f8a37057000) > libssl.so.10 => /lib64/libssl.so.10 (0x00007f8a36de5000) > libbrotlienc.so.1 => /lib64/libbrotlienc.so.1 (0x00007f8a36b58000) > libbrotlidec.so.1 => /lib64/libbrotlidec.so.1 (0x00007f8a3694b000) > libbrotlicommon.so.1 => /lib64/libbrotlicommon.so.1 (0x00007f8a3672b000) > libutf8proc.so.1 => /lib64/libutf8proc.so.1 (0x00007f8a3647b000) > libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f8a3626b000) > liblz4.so.1 => /lib64/liblz4.so.1 (0x00007f8a3605c000) > libsnappy.so.1 => /lib64/libsnappy.so.1 (0x00007f8a35e56000) > libz.so.1 => /lib64/libz.so.1 (0x00007f8a35c40000) > libzstd.so.1 => /lib64/libzstd.so.1 (0x00007f8a3593a000) > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f8a3571e000) > /lib64/ld-linux-x86-64.so.2 (0x00007f8a39b67000) > libaws-cpp-sdk-core.so => /opt/aws/lib64/libaws-cpp-sdk-core.so > (0x00007f8a35413000) > libaws-c-event-stream.so.0unstable => > /opt/aws/lib64/libaws-c-event-stream.so.0unstable (0x00007f8a3520b000) > libaws-c-common.so.0unstable => /opt/aws/lib64/libaws-c-common.so.0unstable > (0x00007f8a34fd9000) > libaws-checksums.so => /opt/aws/lib64/libaws-checksums.so > (0x00007f8a34dce000) > libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x00007f8a34b81000) > libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00007f8a34898000) > libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00007f8a34694000) > libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00007f8a34461000) > libcurl.so.4 => /opt/curl/lib/libcurl.so.4 (0x00007f8a341ea000) > libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x00007f8a33fda000) > libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00007f8a33dd6000) > libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f8a33bbc000) > libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f8a33995000) > libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f8a33733000) > >> /opt/rh/devtoolset-3/root/usr/bin/g++ --version > g++ (GCC) 4.9.2 20150212 (Red Hat 4.9.2-6) > > Do all of these ring any bells? > > Thank you! > Rares
