So this particular toolchain mix seems to be broken, does everything work if you compile Arrow, the plugin, and the core database with devtoolset-3? I think the weak link is Arrow C++ compiled with a non-devtoolset compiler toolchain. If there were the package maintainer bandwidth, having both devtoolset-gcc and system-gcc pre-built RPMs would be potentially interesting (but there are so many devtoolsets, which one should you use?).
On Thu, Jun 10, 2021 at 6:04 PM Rares Vernica <rvern...@gmail.com> wrote: > > Yes, the pre-built binaries are the official RPM packages. > > I recompilled 4.0.1 with the default gcc-g++ from CentOS 7 and Debug flag. > The segmentation fault occurred. See below for the backtrace. > > Please note that the SciDB database as well as the Plug-in where the Arrow > library is used are compiled with g++ from devtoolset-3. Maybe this problem > is due to the different versions of the g++ compiler being used... > > Also note that the code path that writes Arrow files work fine, it is just > the path that reads the files that breaks. > > > g++ --version > g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44) > > Program received signal SIGSEGV, Segmentation fault. > [Switching to Thread 0x7fae877fe700 (LWP 16783)] > 0x00007fae8eb1e000 in ?? () > (gdb) bt > #0 0x00007fae8eb1e000 in ?? () > #1 0x00007fae906bd4d0 in arrow::ipc::ArrayLoader::ReadBuffer > (this=0x7fae877fa090, offset=0, length=24, out=0x7fae5c004010) at > /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:163 > #2 0x00007fae906bd7b8 in arrow::ipc::ArrayLoader::GetBuffer > (this=0x7fae877fa090, buffer_index=1, out=0x7fae5c004010) at > /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:199 > #3 0x00007fae906cbfa7 in > arrow::ipc::ArrayLoader::LoadPrimitive<arrow::Int64Type> > (this=0x7fae877fa090, type_id=arrow::Type::INT64) at > /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:241 > #4 0x00007fae906c72c7 in arrow::ipc::ArrayLoader::Visit<arrow::Int64Type> > (this=0x7fae877fa090, type=...) at > /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:300 > #5 0x00007fae906c2bbc in arrow::VisitTypeInline<arrow::ipc::ArrayLoader> > (type=..., visitor=0x7fae877fa090) at > /apache-arrow-4.0.1/cpp/src/arrow/visitor_inline.h:89 > #6 0x00007fae906bd545 in arrow::ipc::ArrayLoader::LoadType > (this=0x7fae877fa090, type=...) at > /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:166 > #7 0x00007fae906bd5f0 in arrow::ipc::ArrayLoader::Load > (this=0x7fae877fa090, field=0x7fae5c004e38, out=0x7fae5c003f88) at > /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:176 > #8 0x00007fae906b1a92 in arrow::ipc::LoadRecordBatchSubset > (metadata=0x7fae8ea140f4, schema=std::shared_ptr (count 2, weak 0) > 0x7fae5c004ea8, inclusion_mask=0x0, context=..., file=0x7fae5c003e50) > at /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:481 > #9 0x00007fae906b24e7 in arrow::ipc::LoadRecordBatch > (metadata=0x7fae8ea140f4, schema=std::shared_ptr (count 2, weak 0) > 0x7fae5c004ea8, inclusion_mask=std::vector<bool> of length 0, capacity 0, > context=..., file=0x7fae5c003e50) > at /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:532 > #10 0x00007fae906b35f3 in arrow::ipc::ReadRecordBatchInternal > (metadata=..., schema=std::shared_ptr (count 2, weak 0) 0x7fae5c004ea8, > inclusion_mask=std::vector<bool> of length 0, capacity 0, context=..., > file=0x7fae5c003e50) > at /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:630 > #11 0x00007fae906bee31 in arrow::ipc::RecordBatchStreamReaderImpl::ReadNext > (this=0x7fae5c007508, batch=0x7fae877face0) at > /apache-arrow-4.0.1/cpp/src/arrow/ipc/reader.cc:837 > #12 0x00007fae912b7349 in scidb::ArrowReader::readObject > (this=this@entry=0x7fae877fad80, > name="index/0", reuse=reuse@entry=true, arrowBatch=std::shared_ptr (empty) > 0x0) at XIndex.cpp:104 > #13 0x00007fae912b89da in scidb::XIndex::load (this=this@entry=0x7fae5c000c00, > driver=std::shared_ptr (count 3, weak 0) 0x7fae5c003d50, 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) 0x7fae680022d0) at XIndex.cpp:284 > > The plug-in code (i.e., XIndex.cpp) is from here > https://github.com/Paradigm4/bridge/tree/arrow3 > > Thanks! > Rares > > On Wed, Jun 9, 2021 at 9:53 PM Sutou Kouhei <k...@clear-code.com> wrote: > > > Hi, > > > > > Then I went back to the pre-built binaries for 3.0.0 and 4.0.0 from JFrog > > > and the issue reappeared. I can only infer that it has to do with the way > > > the pre-built binaries are generated... > > > > The pre-built binaries are the official RPM packages, right? > > > > They are built with the default gcc-g++ package not g++ from > > devtoolset-3. This may be related. Could you try building > > your program with the default gcc-g++ package? > > > > > > Thanks, > > -- > > kou > > > > In <calq9kxaxnyayqohuj3n0cknrbp6wbtxvj2pog7hcb0icy2r...@mail.gmail.com> > > "Re: C++ Segmentation Fault RecordBatchReader::ReadNext in CentOS only" > > on Wed, 9 Jun 2021 21:39:04 -0700, > > Rares Vernica <rvern...@gmail.com> wrote: > > > > > I got the apache-arrow-4.0.1 source and compiled it with the Debug flag. > > No > > > segmentation fault occurred. I then removed the Debug flag and still no > > > segmentation fault. I then tried the 4.0.0 source. Still no issues. > > > Finally, I tried the 3.0.0 source and still no issues. > > > > > > Then I went back to the pre-built binaries for 3.0.0 and 4.0.0 from JFrog > > > and the issue reappeared. I can only infer that it has to do with the way > > > the pre-built binaries are generated... > > > > > > Here is how I compiled the Arrow sources on my CentOS 7. > > > > > > release$ cmake3 -DARROW_WITH_ZLIB=ON > > > -DCMAKE_C_COMPILER=/opt/rh/devtoolset-3/root/usr/bin/gcc > > > -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-3/root/usr/bin/g++ .. > > > > > > Thanks, > > > Rares > > > > > > On Tue, Jun 8, 2021 at 5:37 PM Sutou Kouhei <k...@clear-code.com> wrote: > > > > > >> 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 > > >> > >
