[arrow] Linker errors with arrow[parquet] #22552

diehard2 · 2022-01-16T19:29:56Z

Parquet libraries are not linking correctly.

Environment

OS: CentOS 8
Compiler: GCC 10/12

To Reproduce
The following Docker image will replicate the issue. Just cd into parque_test/build and run scl enable gcc-toolset-10 bash && cmake --build. It appears to not be linking to thrift, lz4, and brotli. The gcc 10 toolset is required due to an error build boost math with the base install. I see the same behavior on a more complicated docker image that uses gcc 12. Sorry, the code blocks on here don't seem to be working

FROM centos:latest

RUN yum update -y && yum install -y initscripts;

RUN yum group install -y "Development Tools"

RUN yum install -y git cmake gcc-toolset-10 emacs


RUN mkdir parquet_test && cd parquet_test && git config --global http.sslverify "false" && git clone https://github.com/microsoft/vcpkg && ./vcpkg/bootstrap-vcpkg.sh

RUN cd parquet_test && SNIPPET="{\"name\": \"versions-test\",\"version\": \"1.0.0\",\"dependencies\": [\"arrow\"], \"builtin-baseline\": \"39b17cf84c8b389d5800775eaa61e279610c3f33\"}" && echo $SNIPPET > "vcpkg.json"
RUN cd parquet_test && SNIPPET="#include \"arrow/api.h\" \n #include \"parquet/metadata.h\" \n \
    int main(){auto pool = arrow::default_memory_pool(); parquet::FileMetaData* foo; foo->num_columns(); return 0;} \n " && echo -e $SNIPPET > "main.cxx" && mkdir build

RUN cd parquet_test && SNIPPET="cmake_minimum_required(VERSION 3.20) \n \
            set(CMAKE_TOOLCHAIN_FILE \${CMAKE_CURRENT_SOURCE_DIR}/vcpkg/scripts/buildsystems/vcpkg.cmake CACHE STRING \"Vcpkg toolchain file\")  \n \
            project(test) \n \
            find_package(Arrow CONFIG REQUIRED) \n \
            find_package(Parquet CONFIG REQUIRED) \n \
            include_directories(\${ARROW_INCLUDE_DIR}) \n \
            add_executable(test main.cxx) \n \
            target_link_libraries(test PRIVATE \${PARQUET_LIBRARIES} \${ARROW_LIBRARIES}) \n " && echo -e $SNIPPET > "CMakeLists.txt" \
            && scl enable gcc-toolset-10 "cd build && cmake .."

Failure logs

opt/rh/gcc-toolset-10/root/usr/bin/ld: vcpkg_installed/x64-linux/debug/lib/libparquet.a(metadata.cc.o): in function `apache::thrift::transport::TMemoryBuffer::TMemoryBuffer(unsigned char*, unsigned int, apache::thrift::transport::TMemoryBuffer::MemoryPolicy)':
/parquet_test/build/vcpkg_installed/x64-linux/include/thrift/transport/TBufferTransports.h:526: undefined reference to `vtable for apache::thrift::transport::TMemoryBuffer'
/opt/rh/gcc-toolset-10/root/usr/bin/ld: /parquet_test/build/vcpkg_installed/x64-linux/include/thrift/transport/TBufferTransports.h:529: undefined reference to `typeinfo for apache::thrift::transport::TTransportException'
/opt/rh/gcc-toolset-10/root/usr/bin/ld: /parquet_test/build/vcpkg_installed/x64-linux/include/thrift/transport/TBufferTransports.h:543: undefined reference to `typeinfo for apache::thrift::transport::TTransportException'
/opt/rh/gcc-toolset-10/root/usr/bin/ld: vcpkg_installed/x64-linux/debug/lib/libparquet.a(metadata.cc.o): in function `unsigned int apache::thrift::transport::readAll<apache::thrift::transport::TTransport>(apache::thrift::transport::TTransport&, unsigned char*, unsigned int)':   
/parquet_test/build/vcpkg_installed/x64-linux/include/thrift/transport/TTransport.h:43: undefined reference to `typeinfo for apache::thrift::transport::TTransportException'
/opt/rh/gcc-toolset-10/root/usr/bin/ld: vcpkg_installed/x64-linux/debug/lib/libparquet.a(metadata.cc.o): in function `unsigned int apache::thrift::transport::readAll<apache::thrift::transport::TBufferBase>(apache::thrift::transport::TBufferBase&, unsigned char*, unsigned int)': 
/parquet_test/build/vcpkg_installed/x64-linux/include/thrift/transport/TTransport.h:43: undefined reference to `typeinfo for apache::thrift::transport::TTransportException'
/opt/rh/gcc-toolset-10/root/usr/bin/ld: vcpkg_installed/x64-linux/debug/lib/libparquet.a(metadata.cc.o): in function `apache::thrift::protocol::TProtocolFactory::TProtocolFactory()':
/parquet_test/build/vcpkg_installed/x64-linux/include/thrift/protocol/TProtocol.h:600: undefined reference to `vtable for apache::thrift::protocol::TProtocolFactory'
/opt/rh/gcc-toolset-10/root/usr/bin/ld: vcpkg_installed/x64-linux/debug/lib/libparquet.a(metadata.cc.o): in function `std::shared_ptr<apache::thrift::transport::TMemoryBuffer> std::dynamic_pointer_cast<apache::thrift::transport::TMemoryBuffer, apache::thrift::transport::TTransport>(std::shared_ptr<apache::thrift::transport::TTransport> const&)':
/opt/rh/gcc-toolset-10/root/usr/include/c++/10/bits/shared_ptr.h:602: undefined reference to `typeinfo for apache::thrift::transport::TMemoryBuffer'

etc
Additional context
Add any other context about the problem here.

The text was updated successfully, but these errors were encountered:

JackBoosY · 2022-01-18T08:08:50Z

Is port arrow[parquet] instead of Parquet [Arrow]?

JackBoosY · 2022-01-18T08:17:26Z

Confirmed, this issue exists in the latest master branch with the following code:

#include "arrow/api.h"
#include "parquet/metadata.h"

int main(){
    auto pool = arrow::default_memory_pool();
    parquet::FileMetaData* foo;
    foo->num_columns();
    return 0;
}

find_package(Arrow CONFIG REQUIRED)
find_package(Parquet CONFIG REQUIRED)
include_directories(${ARROW_INCLUDE_DIR})
add_executable(test main.cxx)
target_link_libraries(test PRIVATE ${PARQUET_LIBRARIES} ${ARROW_LIBRARIES})

root@usr:/home/usr/work/test# nm ../vcpkg/packages/arrow_x64-linux/lib/libparquet.a | grep TTransportException
0000000000000000 W _ZN6apache6thrift9transport19TTransportExceptionD0Ev
0000000000000000 W _ZN6apache6thrift9transport19TTransportExceptionD1Ev
0000000000000000 W _ZN6apache6thrift9transport19TTransportExceptionD2Ev
0000000000000000 n _ZN6apache6thrift9transport19TTransportExceptionD5Ev
                 U _ZTIN6apache6thrift9transport19TTransportExceptionE
                 U _ZTVN6apache6thrift9transport19TTransportExceptionE
0000000000000000 W _ZN6apache6thrift9transport19TTransportExceptionD0Ev
0000000000000000 W _ZN6apache6thrift9transport19TTransportExceptionD1Ev
0000000000000000 W _ZN6apache6thrift9transport19TTransportExceptionD2Ev
0000000000000000 n _ZN6apache6thrift9transport19TTransportExceptionD5Ev
                 U _ZTIN6apache6thrift9transport19TTransportExceptionE
                 U _ZTVN6apache6thrift9transport19TTransportExceptionE
0000000000000000 W _ZN6apache6thrift9transport19TTransportExceptionD0Ev
0000000000000000 W _ZN6apache6thrift9transport19TTransportExceptionD1Ev
0000000000000000 W _ZN6apache6thrift9transport19TTransportExceptionD2Ev
0000000000000000 n _ZN6apache6thrift9transport19TTransportExceptionD5Ev
                 U _ZTIN6apache6thrift9transport19TTransportExceptionE
                 U _ZTVN6apache6thrift9transport19TTransportExceptionE

JackBoosY · 2022-01-18T08:19:15Z

cc @ianmcook @philjdf @@isaacbrodsky

diehard2 · 2022-03-04T17:08:05Z

I'm still seeing this issue with the new 7.0 Arrow port and port-version 1. Its unusable in it's current state. I tried linking in Thrift directly using vcpkg, but there's no information how to do that anywhere online that I can find and nothing in the port provides a helpful hint.

@LilyWangLL @ianmcook (sorry for the tags, but wanted to get this some visibility)

Thomas1664 · 2022-04-07T08:13:06Z

@diehard2 @JackBoosY PR #23423 should have fixed the issue

JackBoosY · 2022-04-07T09:43:03Z

@diehard2 Can you double confirm that?

diehard2 · 2022-04-08T19:21:34Z

Hi @JackBoosY @Thomas1664 thanks for the follow-up! Same errors as before. I can't figure anyway to make this useable. New docker setup showing the issues is below. Similar to the one above, but its using almalinux since CentOS 8 went to a stream. Any help here would be greatly appreciated. (sorry, I can't get the code block to render correctly)

FROM almalinux:latest

RUN yum update -y && yum install -y initscripts;

RUN yum group install -y "Development Tools"

RUN yum install -y git cmake gcc-toolset-10 emacs perl-IPC-Cmd kernel-devel


RUN mkdir parquet_test && cd parquet_test && git config --global http.sslverify "false" && git clone https://github.com/microsoft/vcpkg && ./vcpkg/bootstrap-vcpkg.sh

RUN cd parquet_test && SNIPPET="{\"name\": \"versions-test\",\"version\": \"1.0.0\",\"dependencies\": [\"arrow\"], \"builtin-baseline\": \"d72783cb3aeddfd667861caef1060e54ca6fa7a9\"}" && echo $SNIPPET > "vcpkg.json"
RUN cd parquet_test && SNIPPET="#include \"arrow/api.h\" \n #include \"parquet/metadata.h\" \n \
    int main(){auto pool = arrow::default_memory_pool(); parquet::FileMetaData* foo; foo->num_columns(); return 0;} \n " && echo -e $SNIPPET > "main.cxx" && mkdir build

RUN cd parquet_test && SNIPPET="cmake_minimum_required(VERSION 3.20) \n \
            set(CMAKE_TOOLCHAIN_FILE \${CMAKE_CURRENT_SOURCE_DIR}/vcpkg/scripts/buildsystems/vcpkg.cmake CACHE STRING \"Vcpkg toolchain file\")  \n \
            project(test) \n \
            find_package(Arrow CONFIG REQUIRED) \n \
            find_package(Parquet CONFIG REQUIRED) \n \
            include_directories(\${ARROW_INCLUDE_DIR}) \n \
            add_executable(test main.cxx) \n \
            target_link_libraries(test PRIVATE \${PARQUET_LIBRARIES} \${ARROW_LIBRARIES}) \n " && echo -e $SNIPPET > "CMakeLists.txt" 

WORKDIR /parquet_test/buiild

RUN source scl_source enable gcc-toolset-10 && cmake .. 
RUN source scl_source enable gcc-toolset-10 && make

diehard2 · 2022-04-09T15:17:33Z

@JackBoosY @Thomas1664 here's a docker build that shows I can successfully use a manually built version of the libraries (granted, they're dynamic). Hope this helps

FROM almalinux:latest

RUN yum update -y && yum install -y initscripts;

RUN yum group install -y "Development Tools"

RUN yum install -y git gcc-toolset-10 emacs perl-IPC-Cmd kernel-devel
RUN dnf install -y wget yum-utils && dnf config-manager --set-enabled powertools && yum install -y openssl-devel ninja-build

RUN wget https://github.com/Kitware/CMake/releases/download/v3.22.1/cmake-3.22.1.tar.gz && tar xf cmake-3.22.1.tar.gz && cd cmake-3.22.1 && \
        ./configure && make -j 12 && make install

RUN git clone https://github.com/apache/arrow.git && cd arrow && git checkout e90472e35b40f58b17d408438bb8de1641bfe6ef && \
     git submodule update --init && cd cpp/ && mkdir build && cd build && cmake .. --preset ninja-release-flight -DARROW_WITH_RE2=ON -DARROW_PARQUET=ON && ninja && ninja install


RUN mkdir parquet_test && cd parquet_test && git config --global http.sslverify "false" && git clone https://github.com/microsoft/vcpkg && ./vcpkg/bootstrap-vcpkg.sh

RUN cd parquet_test && SNIPPET="{\"name\": \"versions-test\",\"version\": \"1.0.0\",\"dependencies\": [\"arrow\"], \"builtin-baseline\": \"d72783cb3aeddfd667861caef1060e54ca6fa7a9\"}" && echo $SNIPPET > "vcpkg.json"
RUN cd parquet_test && SNIPPET="#include \"arrow/api.h\" \n #include \"parquet/metadata.h\" \n \
    int main(){auto pool = arrow::default_memory_pool(); parquet::FileMetaData* foo; foo->num_columns(); return 0;} \n " && echo -e $SNIPPET > "main.cxx" && mkdir build


RUN cd parquet_test && SNIPPET="cmake_minimum_required(VERSION 3.20) \n \
            set(CMAKE_TOOLCHAIN_FILE \${CMAKE_CURRENT_SOURCE_DIR}/vcpkg/scripts/buildsystems/vcpkg.cmake CACHE STRING \"Vcpkg toolchain file\")  \n \
            set(CMAKE_SKIP_BUILD_RPATH FALSE) \n \
            set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) \n \
            set(CMAKE_BUILD_RPATH "/usr/local/lib64") \n \
            project(test) \n \
            find_package(Arrow PATHS /usr/local CONFIG REQUIRED) \n \
            find_package(Parquet PATHS /usr/local CONFIG REQUIRED) \n \
            include_directories(\${ARROW_INCLUDE_DIR}) \n \
            add_executable(test main.cxx) \n \
            target_link_libraries(test PRIVATE arrow parquet) \n " && echo -e $SNIPPET > "CMakeLists.txt" 


WORKDIR /parquet_test/build

RUN source scl_source enable gcc-toolset-10 && cmake ..
RUN source scl_source enable gcc-toolset-10 && make


RUN cd /parquet_test && rm -rf build && SNIPPET="cmake_minimum_required(VERSION 3.20) \n \
            set(CMAKE_TOOLCHAIN_FILE \${CMAKE_CURRENT_SOURCE_DIR}/vcpkg/scripts/buildsystems/vcpkg.cmake CACHE STRING \"Vcpkg toolchain file\")  \n \
            project(test) \n \
            find_package(Arrow CONFIG REQUIRED) \n \
            find_package(Parquet CONFIG REQUIRED) \n \
            include_directories(\${ARROW_INCLUDE_DIR}) \n \
            add_executable(test main.cxx) \n \
            target_link_libraries(test PRIVATE \${PARQUET_LIBRARIES} \${ARROW_LIBRARIES}) \n " && echo -e $SNIPPET > "CMakeLists.txt" 

WORKDIR /parquet_test/build

RUN source scl_source enable gcc-toolset-10 && cmake ..

RUN source scl_source enable gcc-toolset-10 && make

moria97 · 2022-07-17T15:19:41Z

Still facing link errors with vcpkg installed arrow. Error disappears when I use a self built arrow.

assignUser · 2022-08-09T13:35:40Z

I was still able to reproduce this issue with 9.0.0, it is caused by PARQUET_REQUIRE_ENCRYPTION enabled by the parquet feature (missing from your manual build)

kou · 2022-08-10T22:19:34Z

I tried #22552 (comment) (that is based on Apache Arrow 7.0.0).

The following dependencies are missed from link command line:

vcpkg_installed/x64-linux/debug/lib/libthriftd.a
vcpkg_installed/x64-linux/debug/lib/liblz4d.a
vcpkg_installed/x64-linux/debug/lib/libbrotli{enc,dec,common}-static.a

It seems that thrift::thrift, lz4::lz4 and unofficial::brotli::brotli{enc,dec,common}-static are missed in arrow_static dependencies:

$ grep INTERFACE_LINK_LIBRARIES vcpkg_installed/x64-linux/share/arrow/ArrowTargets.cmake 
  INTERFACE_LINK_LIBRARIES "OpenSSL::Crypto;OpenSSL::SSL;BZip2::BZip2;Snappy::snappy;ZLIB::ZLIB;zstd::libzstd_static;re2::re2;Threads::Threads;rt;\$<LINK_ONLY:>"

I'm not sure that this is a problem in Apache Arrow's CMake configuration or patches in vcpkg.

kou · 2022-08-10T22:28:34Z

The following patch for Apache Arrow may fix the vcpkg_installed/x64-linux/debug/lib/libthriftd.a (PARQUET_REQUIRE_ENCRYPTION) case:

diff --git a/cpp/src/parquet/CMakeLists.txt b/cpp/src/parquet/CMakeLists.txt
index 542fa5bc08..88f270b6b1 100644
--- a/cpp/src/parquet/CMakeLists.txt
+++ b/cpp/src/parquet/CMakeLists.txt
@@ -221,6 +221,8 @@ if(NOT PARQUET_MINIMAL_DEPENDENCY)
   set(PARQUET_STATIC_LINK_LIBS ${PARQUET_STATIC_LINK_LIBS} thrift::thrift)
 endif(NOT PARQUET_MINIMAL_DEPENDENCY)
 
+set(PARQUET_STATIC_INTERFACE_INSTALL_LIBS ${PARQUET_STATIC_LINK_LIBS})
+
 if(CXX_LINKER_SUPPORTS_VERSION_SCRIPT)
   set(PARQUET_SHARED_LINK_FLAGS
       "-Wl,--version-script=${CMAKE_CURRENT_SOURCE_DIR}/symbols.map")
@@ -244,7 +246,9 @@ add_arrow_lib(parquet
               SHARED_PRIVATE_LINK_LIBS
               ${PARQUET_SHARED_PRIVATE_LINK_LIBS}
               STATIC_LINK_LIBS
-              ${PARQUET_STATIC_LINK_LIBS})
+              ${PARQUET_STATIC_LINK_LIBS}
+              STATIC_INSTALL_INTERFACE_LIBS
+              ${PARQUET_STATIC_INSTALL_INTERFACE_LIBS})
 
 if(WIN32 AND NOT (ARROW_TEST_LINKAGE STREQUAL "static"))
   add_library(parquet_test_support STATIC

JackBoosY · 2022-08-11T07:29:25Z

@kou Can you please provide the related official patch / PR link?

assignUser · 2022-08-11T14:12:05Z

@kou with your patch and 9.0.0 it looks like only thirf::thrift is still missing? thrift::thrift is added to PARQUET_STATIC_LINK_LIB though...

"OpenSSL::Crypto;OpenSSL::SSL;unofficial::brotli::brotlienc;unofficial::brotli::brotlidec;unofficial::brotli::brotlicommon;BZip2::BZip2;lz4::lz4;Snappy::snappy;ZLIB::ZLIB;zstd::libzstd_static;re2::re2;Threads::Threads;rt;\$<LINK_ONLY:>"

The linking issue also still exists :( I don't understand why this only happens with PARQUET_REQUIRE_ENCRYPTION as this only adds some sources (which don't use thrift according to grep).

parquet_static needs Thrift because cpp/src/parquet/thrift_internal.h uses Thrift. See also: microsoft/vcpkg#22552 (comment) We can test this by the following command lines: $ cd cpp/examples/parquet/parquet_arrow $ export Arrow_DIR=${ARROW_INSTALL_PREFIX}/lib/cmake/arrow $ export Parquet_DIR=${ARROW_INSTALL_PREFIX}/lib/cmake/arrow $ cmake -S . -B build -DPARQUET_LINK_SHARED=OFF $ cmake --build build --verbose I also noticed that OpenTelemetry related dependencies are also missed because I usually use -DARROW_WITH_OPENTELEMETRY=ON option for Apache Arrow development. The problem is also fixed in this.

kou · 2022-08-12T02:22:48Z

@JackBoosY I've created it: apache/arrow#13863

kou · 2022-08-12T02:36:20Z

@assignUser Sorry. My patch had a typo: PARQUET_STATIC_INTERFACE_INSTALL_LIBS should have been PARQUET_STATIC_INSTALL_INTERFACE_LIBS.

This may not be related to PARQUET_REQUIRE_ENCRYPTION. I can reproduce the missing libthrift.a with my local build without PARQUET_REQUIRE_ENCRYPTION. (Note that I'm not using vcpkg on my local build environment.)

parquet_static needs Thrift because cpp/src/parquet/thrift_internal.h uses Thrift. See also: microsoft/vcpkg#22552 (comment) We can test this by the following command lines: $ cd cpp/examples/parquet/parquet_arrow $ export Arrow_DIR=${ARROW_INSTALL_PREFIX}/lib/cmake/arrow $ export Parquet_DIR=${ARROW_INSTALL_PREFIX}/lib/cmake/arrow $ cmake -S . -B build -DPARQUET_LINK_SHARED=OFF $ cmake --build build --verbose I also noticed that OpenTelemetry related dependencies are also missed because I usually use -DARROW_WITH_OPENTELEMETRY=ON option for Apache Arrow development. The problem is also fixed in this.

parquet_static needs Thrift because cpp/src/parquet/thrift_internal.h uses Thrift. See also: microsoft/vcpkg#22552 (comment) We can test this by the following command lines: $ cd cpp/examples/parquet/parquet_arrow $ export Arrow_DIR=${ARROW_INSTALL_PREFIX}/lib/cmake/arrow $ export Parquet_DIR=${ARROW_INSTALL_PREFIX}/lib/cmake/arrow $ cmake -S . -B build -DPARQUET_LINK_SHARED=OFF $ cmake --build build --verbose I also noticed that OpenTelemetry related dependencies are also missed because I usually use -DARROW_WITH_OPENTELEMETRY=ON option for Apache Arrow development. The problem is also fixed in this. Authored-by: Sutou Kouhei <[email protected]> Signed-off-by: Sutou Kouhei <[email protected]>

…3863) parquet_static needs Thrift because cpp/src/parquet/thrift_internal.h uses Thrift. See also: microsoft/vcpkg#22552 (comment) We can test this by the following command lines: $ cd cpp/examples/parquet/parquet_arrow $ export Arrow_DIR=${ARROW_INSTALL_PREFIX}/lib/cmake/arrow $ export Parquet_DIR=${ARROW_INSTALL_PREFIX}/lib/cmake/arrow $ cmake -S . -B build -DPARQUET_LINK_SHARED=OFF $ cmake --build build --verbose I also noticed that OpenTelemetry related dependencies are also missed because I usually use -DARROW_WITH_OPENTELEMETRY=ON option for Apache Arrow development. The problem is also fixed in this. Authored-by: Sutou Kouhei <[email protected]> Signed-off-by: Sutou Kouhei <[email protected]>

JackBoosY self-assigned this Jan 17, 2022

JackBoosY changed the title ~~Linker errors with Parquet [Arrow]~~ Linker errors with arrow[parquet] Jan 18, 2022

JackBoosY changed the title ~~Linker errors with arrow[parquet]~~ [arrow] Linker errors with arrow[parquet] Jan 18, 2022

JackBoosY added the category:port-bug The issue is with a library, which is something the port should already support label Jan 18, 2022

JackBoosY added the requires:more-information This Issue requires more information to solve label Apr 7, 2022

JackBoosY removed the requires:more-information This Issue requires more information to solve label Apr 11, 2022

diehard2 mentioned this issue Aug 5, 2022

[arrow] Update Arrow to 9.0.0 #26187

Merged

kou mentioned this issue Aug 12, 2022

ARROW-17394: [C++][Parquet] Fix parquet_static dependencies apache/arrow#13863

Merged

JackBoosY added the depends:upstream-changes Waiting on a change to the upstream project label Aug 12, 2022

JackBoosY removed the depends:upstream-changes Waiting on a change to the upstream project label Aug 15, 2022

JackBoosY removed their assignment Aug 15, 2022

JackBoosY assigned JackBoosY and Adela0814 Aug 15, 2022

JavierMatosD closed this as completed in #26187 Aug 16, 2022

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[arrow] Linker errors with arrow[parquet] #22552

[arrow] Linker errors with arrow[parquet] #22552

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[arrow] Linker errors with arrow[parquet] #22552

[arrow] Linker errors with arrow[parquet] #22552

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