Cannot build cquery on Ubuntu, undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12'

[jamescookmd]

master at 32005b79018cdfc50262bfdb54d24ffafa19b88d

Follow build instructions at https://github.com/cquery-project/cquery/wiki/Building-cquery

jamescook@jamescook:/w/cquery2/build (master)$ cmake --build .
...<normal build>...
[100%] Linking CXX executable cquery
/usr/bin/ld: CMakeFiles/cquery.dir/src/platform_posix.cc.o: undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12'
//lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
CMakeFiles/cquery.dir/build.make:2384: recipe for target 'cquery' failed
make[2]: *** [cquery] Error 1
CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/cquery.dir/all' failed
make[1]: *** [CMakeFiles/cquery.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

After chatting with jacobdufault we tried changing CMakeLists.txt like this:

 # Enable threading support
+set(CMAKE_THREAD_PREFER_PTHREAD ON)
 set(THREADS_PREFER_PTHREAD_FLAG ON)
 find_package(Threads REQUIRED)
 target_link_libraries(cquery PRIVATE Threads::Threads)

Which didn't help, same error.

jamescook@jamescook:/w/cquery2 (master)$ uname -a
Linux <redacted> 4.9.0-7-amd64 #1 SMP Debian 4.9.110-1 (2018-07-05) x86_64 GNU/Linux

jamescook@jamescook:/w/cquery2 (master)$ cmake --version
cmake version 3.9.0

jamescook@jamescook:/w/cquery2 (master)$ ldd --version
ldd (Debian GLIBC 2.24-12) 2.24

[jacobdufault]

@DaanDeMeyer, @bstaletic any thoughts?

[DaanDeMeyer]

https://github.com/kronihias/mcfx/issues/1 This issue seems similar and was fixed by changing the linking order although I'm not sure what we'd have to change in CMake.

I do remember @bstaletic mentioning a CMake bug where Threads did not work if C wasn't specified as a project language but if I remember correctly that was fixed in an earlier version of CMake.

Can you you compile with -DCMAKE_VERBOSE_MAKEFILE=ON and post the output? The pthreads flag should be in there somewhere.

[jamescookmd]

I don't see a pthread flag below.

jamescook@jamescook:/w/cquery2/build (master)$ cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=release -DCMAKE_EXPORT_COMPILE_COMMANDS=YES -DCMAKE_VERBOSE_MAKEFILE=ON -- Using downloaded Clang -- Clang already downloaded -- Configuring done -- Generating done -- Build files have been written to: /w/cquery2/build jamescook@jamescook:/w/cquery2/build (master)$ cmake --build . /usr/bin/cmake -H/w/cquery2 -B/w/cquery2/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /w/cquery2/build/CMakeFiles /w/cquery2/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/w/cquery2/build' make -f third_party/reproc/CMakeFiles/reproc.dir/build.make third_party/reproc/CMakeFiles/reproc.dir/depend make[2]: Entering directory '/w/cquery2/build' cd /w/cquery2/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /w/cquery2 /w/cquery2/third_party/reproc /w/cquery2/build /w/cquery2/build/third_party/reproc /w/cquery2/build/third_party/reproc/CMakeFiles/reproc.dir/DependInfo.cmake --color= make[2]: Leaving directory '/w/cquery2/build' make -f third_party/reproc/CMakeFiles/reproc.dir/build.make third_party/reproc/CMakeFiles/reproc.dir/build make[2]: Entering directory '/w/cquery2/build' [ 1%] Linking CXX static library lib/libreproc.a cd /w/cquery2/build/third_party/reproc && /usr/bin/cmake -P CMakeFiles/reproc.dir/cmake_clean_target.cmake cd /w/cquery2/build/third_party/reproc && /usr/bin/cmake -E cmake_link_script CMakeFiles/reproc.dir/link.txt --verbose=1 /usr/bin/ar qc lib/libreproc.a CMakeFiles/reproc.dir/src/c/common.c.o CMakeFiles/reproc.dir/src/c/posix/fork.c.o CMakeFiles/reproc.dir/src/c/posix/pipe.c.o CMakeFiles/reproc.dir/src/c/posix/reproc.c.o CMakeFiles/reproc.dir/src/c/posix/process.c.o CMakeFiles/reproc.dir/src/cpp/reproc.cpp.o CMakeFiles/reproc.dir/src/cpp/error.cpp.o /usr/bin/ranlib lib/libreproc.a make[2]: Leaving directory '/w/cquery2/build' [ 8%] Built target reproc make -f CMakeFiles/cquery.dir/build.make CMakeFiles/cquery.dir/depend make[2]: Entering directory '/w/cquery2/build' cd /w/cquery2/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /w/cquery2 /w/cquery2 /w/cquery2/build /w/cquery2/build /w/cquery2/build/CMakeFiles/cquery.dir/DependInfo.cmake --color= make[2]: Leaving directory '/w/cquery2/build' make -f CMakeFiles/cquery.dir/build.make CMakeFiles/cquery.dir/build make[2]: Entering directory '/w/cquery2/build' [ 9%] Linking CXX executable cquery /usr/bin/cmake -E cmake_link_script CMakeFiles/cquery.dir/link.txt --verbose=1 /usr/bin/c++ -O3 -DNDEBUG -rdynamic CMakeFiles/cquery.dir/third_party/siphash.cc.o CMakeFiles/cquery.dir/third_party/pugixml/src/pugixml.cpp.o CMakeFiles/cquery.dir/src/c_cpp_properties.cc.o CMakeFiles/cquery.dir/src/cache_manager.cc.o CMakeFiles/cquery.dir/src/clang_complete.cc.o CMakeFiles/cquery.dir/src/clang_cursor.cc.o CMakeFiles/cquery.dir/src/clang_format.cc.o CMakeFiles/cquery.dir/src/clang_index.cc.o CMakeFiles/cquery.dir/src/clang_indexer.cc.o CMakeFiles/cquery.dir/src/clang_system_include_extractor.cc.o CMakeFiles/cquery.dir/src/clang_translation_unit.cc.o CMakeFiles/cquery.dir/src/clang_utils.cc.o CMakeFiles/cquery.dir/src/code_complete_cache.cc.o CMakeFiles/cquery.dir/src/command_line.cc.o CMakeFiles/cquery.dir/src/compiler.cc.o CMakeFiles/cquery.dir/src/diagnostics_engine.cc.o CMakeFiles/cquery.dir/src/file_consumer.cc.o CMakeFiles/cquery.dir/src/file_contents.cc.o CMakeFiles/cquery.dir/src/file_types.cc.o CMakeFiles/cquery.dir/src/fuzzy_match.cc.o CMakeFiles/cquery.dir/src/iindexer.cc.o CMakeFiles/cquery.dir/src/import_manager.cc.o CMakeFiles/cquery.dir/src/import_pipeline.cc.o CMakeFiles/cquery.dir/src/include_complete.cc.o CMakeFiles/cquery.dir/src/method.cc.o CMakeFiles/cquery.dir/src/lex_utils.cc.o CMakeFiles/cquery.dir/src/lsp.cc.o CMakeFiles/cquery.dir/src/lsp_diagnostic.cc.o CMakeFiles/cquery.dir/src/match.cc.o CMakeFiles/cquery.dir/src/message_handler.cc.o CMakeFiles/cquery.dir/src/options.cc.o CMakeFiles/cquery.dir/src/platform_posix.cc.o CMakeFiles/cquery.dir/src/platform_win.cc.o CMakeFiles/cquery.dir/src/platform.cc.o CMakeFiles/cquery.dir/src/position.cc.o CMakeFiles/cquery.dir/src/project.cc.o CMakeFiles/cquery.dir/src/query_utils.cc.o CMakeFiles/cquery.dir/src/query.cc.o CMakeFiles/cquery.dir/src/queue_manager.cc.o CMakeFiles/cquery.dir/src/recorder.cc.o CMakeFiles/cquery.dir/src/semantic_highlight_symbol_cache.cc.o CMakeFiles/cquery.dir/src/serializer.cc.o CMakeFiles/cquery.dir/src/standard_includes.cc.o CMakeFiles/cquery.dir/src/task.cc.o CMakeFiles/cquery.dir/src/test.cc.o CMakeFiles/cquery.dir/src/third_party_impl.cc.o CMakeFiles/cquery.dir/src/threaded_queue.cc.o CMakeFiles/cquery.dir/src/timer.cc.o CMakeFiles/cquery.dir/src/timestamp_manager.cc.o CMakeFiles/cquery.dir/src/type_printer.cc.o CMakeFiles/cquery.dir/src/utils.cc.o CMakeFiles/cquery.dir/src/work_thread.cc.o CMakeFiles/cquery.dir/src/working_files.cc.o CMakeFiles/cquery.dir/src/messages/cquery_base.cc.o CMakeFiles/cquery.dir/src/messages/cquery_call_hierarchy.cc.o CMakeFiles/cquery.dir/src/messages/cquery_callers.cc.o CMakeFiles/cquery.dir/src/messages/cquery_did_view.cc.o CMakeFiles/cquery.dir/src/messages/cquery_file_info.cc.o CMakeFiles/cquery.dir/src/messages/cquery_freshen_index.cc.o CMakeFiles/cquery.dir/src/messages/cquery_index_file.cc.o CMakeFiles/cquery.dir/src/messages/cquery_inheritance_hierarchy.cc.o CMakeFiles/cquery.dir/src/messages/cquery_vars.cc.o CMakeFiles/cquery.dir/src/messages/cquery_wait.cc.o CMakeFiles/cquery.dir/src/messages/exit.cc.o CMakeFiles/cquery.dir/src/messages/initialize.cc.o CMakeFiles/cquery.dir/src/messages/shutdown.cc.o CMakeFiles/cquery.dir/src/messages/text_document_code_action.cc.o CMakeFiles/cquery.dir/src/messages/text_document_code_lens.cc.o CMakeFiles/cquery.dir/src/messages/text_document_completion.cc.o CMakeFiles/cquery.dir/src/messages/text_document_definition.cc.o CMakeFiles/cquery.dir/src/messages/text_document_did_change.cc.o CMakeFiles/cquery.dir/src/messages/text_document_did_close.cc.o CMakeFiles/cquery.dir/src/messages/text_document_did_open.cc.o CMakeFiles/cquery.dir/src/messages/text_document_did_save.cc.o CMakeFiles/cquery.dir/src/messages/text_document_document_highlight.cc.o CMakeFiles/cquery.dir/src/messages/text_document_document_link.cc.o CMakeFiles/cquery.dir/src/messages/text_document_document_symbol.cc.o CMakeFiles/cquery.dir/src/messages/text_document_formatting.cc.o CMakeFiles/cquery.dir/src/messages/text_document_hover.cc.o CMakeFiles/cquery.dir/src/messages/text_document_implementation.cc.o CMakeFiles/cquery.dir/src/messages/text_document_range_formatting.cc.o CMakeFiles/cquery.dir/src/messages/text_document_references.cc.o CMakeFiles/cquery.dir/src/messages/text_document_rename.cc.o CMakeFiles/cquery.dir/src/messages/text_document_signature_help.cc.o CMakeFiles/cquery.dir/src/messages/text_document_type_definition.cc.o CMakeFiles/cquery.dir/src/messages/workspace_did_change_configuration.cc.o CMakeFiles/cquery.dir/src/messages/workspace_did_change_watched_files.cc.o CMakeFiles/cquery.dir/src/messages/workspace_execute_command.cc.o CMakeFiles/cquery.dir/src/messages/workspace_symbol.cc.o -o cquery -Wl,-rpath,/w/cquery2/build/clang+llvm-6.0.1-x86_64-linux-gnu-ubuntu-14.04/lib: third_party/reproc/lib/libreproc.a clang+llvm-6.0.1-x86_64-linux-gnu-ubuntu-14.04/lib/libclang.so -ldl /usr/bin/ld: CMakeFiles/cquery.dir/src/platform_posix.cc.o: undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12' //lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status CMakeFiles/cquery.dir/build.make:2387: recipe for target 'cquery' failed make[2]: *** [cquery] Error 1 make[2]: Leaving directory '/w/cquery2/build' CMakeFiles/Makefile2:102: recipe for target 'CMakeFiles/cquery.dir/all' failed make[1]: *** [CMakeFiles/cquery.dir/all] Error 2 make[1]: Leaving directory '/w/cquery2/build' Makefile:132: recipe for target 'all' failed make: *** [all] Error 2

[DaanDeMeyer]

Does it work if you add the pthread flag explicitly? (set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread") should do the trick

[jamescookmd]

Yes, explicitly adding -pthread makes it link.

[bstaletic]

I wonder what's the output of nm ./cquery | grep pthread_setname_np. For me that's:

                 U pthread_setname_np@@GLIBC_2.12

What it says is, there is no fixed memory address offset for the symbol because the symbol is Undefined. In other words, the symbol should be resolved at load time when the loader loads some shared object - in this case libpthread.so.

So, if all of this is correct, ldd cquery should tell us that there is a need to link against libpthread.so:

	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fd3438e6000)

Lastly, -pthread should have been in the flags, but it also should have appeared in the cmake configuration step:

-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes

[jamescookmd]

After building with the workaround above I get the same thing as you:

jamescook@jamescook:/w/cquery2/build (master)$ nm ./cquery | grep pthread_setname_np U pthread_setname_np@@GLIBC_2.12 jamescook@jamescook:/w/cquery2/build (master)$ ldd cquery linux-vdso.so.1 (0x00007ffef9e9a000) libclang.so.6 => /w/cquery2/build/clang+llvm-6.0.1-x86_64-linux-gnu-ubuntu-14.04/lib/libclang.so.6 (0x00007f734786c000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f7347668000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f73472e3000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f7346fdf000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f7346dc7000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f7346baa000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f734680b000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f73465f1000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f73463e9000) libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 (0x00007f73461bf000) /lib64/ld-linux-x86-64.so.2 (0x00007f734ba93000)

[bstaletic]

Alright, so what is the output of cmake configuration without the explicit -pthread?

[jamescookmd]

Sorry, which command do you want me to run?

On Wed, Aug 22, 2018 at 10:06 AM Boris Staletic [email protected] wrote:

Alright, so what is the output of cmake configuration without the explicit -pthread?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cquery-project/cquery/issues/782#issuecomment-415105884, or mute the thread https://github.com/notifications/unsubscribe-auth/AcGfMM5fmhicVJbRz1SwyFmOQp-eE_93ks5uTY-kgaJpZM4WGTNj .

[DaanDeMeyer]

Try changing the project call to project(cquery LANGUAGES C CXX)

[bstaletic]

@DaanDeMeyer That bug was fixed in cmake 3.4. @jamescookmd The one before cmake --build. Probably just cmake .., but in a clean build directory.

[jamescookmd]

After reverting the workaround (the explicit -pthread):

jamescook@jamescook:/w/cquery2 (master)$ git stash save Saved working directory and index state WIP on master: 32005b79 Check if LOGURU_STACKTRACES is allowed jamescook@jamescook:/w/cquery2 (master)$ git status On branch master Your branch is up to date with 'origin/master'.

nothing to commit, working tree clean jamescook@jamescook:/w/cquery2 (master)$ mkdir build2 && cd build2 jamescook@jamescook:/w/cquery2/build2 (master)$ cmake .. -- The CXX compiler identification is GNU 7.3.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting build type to 'Release' as none was specified. -- Using downloaded Clang -- Downloading Clang 6.0.1 (https://releases.llvm.org/6.0.1/clang+llvm-6.0.1-x86_64-linux-gnu-ubuntu-14.04.tar.xz) ... -- Extracting downloaded Clang with CMake built-in tar ... -- The C compiler identification is GNU 7.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Looking for pipe2 -- Looking for pipe2 - found -- Found Clang: /w/cquery2/build2/clang+llvm-6.0.1-x86_64-linux-gnu-ubuntu-14.04/lib/libclang.so (found suitable version "6.0.1", minimum required is "6.0.0") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE
-- Configuring done -- Generating done -- Build files have been written to: /w/cquery2/build2

[bstaletic]

From your output:

-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE

Which is missing the crucial step that is:

-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes

I wonder if you could properly configure ycmd. For the purpose of this issue, forget the ycmd installation guide. Just run cmake /path/to/ycmd/cpp.