See also: https://gitlab.kitware.com/cmake/cmake/merge_requests/207
https://gitlab.kitware.com/cmake/cmake/issues/17483 (looks semi-related) Ray Donnelly, who filed those issues, maintains the Anaconda compiler toolchain -- so you are in good company hitting this issue. It looks like some conda recipes explicitly define INSTALL_RPATH, likely for this reason: https://github.com/AnacondaRecipes/vtk-feedstock/blob/791a1db9026fa2c81d171c38835b512adf221794/recipe/build.sh#L30 On Mon, Aug 13, 2018 at 11:54 AM Isaiah Norton <isaiah.nor...@gmail.com> wrote: > The RPATH is not included when using Anaconda because CMake considers the > Anaconda lib path to be an implicit link directory (as reported by the > compiler). Look at `$build_dir/CMakeFiles/CMakeOutput.log` in the section > about "implicit link info". > > The simplest work-around is to set BUILD_RPATH manually, and possibly also > INSTALL_RPATH, depending on what conda-build's fixup routine expects. > > For example, adding this line near the top of your example CMakeList fixed > the resulting binary, at least in the build directory: > > set(CMAKE_BUILD_RPATH "$ENV{CONDA_PREFIX}/lib") > > > On Fri, Aug 10, 2018 at 5:55 PM Sebastián Mancilla <smanc...@jlab.org> > wrote: > >> I am trying to use Conda as a package manager for isolated C++ development >> environments. But unfortunately, when using CMake with the >> Anaconda-provided >> compilers [1] (which are used to compile the binary packages in the >> Anaconda >> repositories), things do not work as expected. >> >> I have a small test case available here [2], with an executable calling a >> shared library and a third-party dependency installed with Conda. >> >> [1]: >> https://conda.io/docs/user-guide/tasks/build-packages/compiler-tools.html >> [2]: https://gist.github.com/smancill/b28ca07ac11fdf285b4d559545a1630b >> >> -------------------------------------------------- >> >> First, when using the system compiler, all works fine (but I am not sure >> of the >> binary compatibility with the Conda packages, that's why I want to use the >> Anaconda compilers): >> >> # create the environment and install XercesC >> $ conda create -n test-system xerces-c >> ... >> environment location: >> /Users/smancill/.local/share/miniconda3/envs/test-system >> ... >> The following NEW packages will be INSTALLED: >> >> icu: 58.2-h4b95b61_1 >> libcxx: 4.0.1-h579ed51_0 >> libcxxabi: 4.0.1-hebd6815_0 >> xerces-c: 3.2.1-h44e365a_0 >> ... >> >> # activate the environment >> $ conda activate test-system >> >> $ mkdir build-osx-system >> $ cd build-osx-system >> $ cmake -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX >> -DCMAKE_PREFIX_PATH=$CONDA_PREFIX .. >> -- The CXX compiler identification is AppleClang 9.0.0.9000039 >> -- Check for working CXX compiler: /usr/bin/c++ >> -- Check for working CXX compiler: /usr/bin/c++ -- works >> ... >> -- Found XercesC: >> /Users/smancill/.local/share/miniconda3/envs/test-system/lib/libxerces-c.dylib >> (found version "3.2.1") >> -- Configuring done >> -- Generating done >> -- Build files have been written to: >> /Users/smancill/src/conda-test/build-osx-system >> >> $ make -j1 VERBOSE=1 >> ... >> [100%] Linking CXX executable bar >> /usr/local/bin/cmake -E cmake_link_script CMakeFiles/bar.dir/link.txt >> --verbose=1 >> /usr/bin/c++ -isysroot >> /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk >> -mmacosx-version-min=10.12 -Wl,-search_paths_first >> -Wl,-headerpad_max_install_names CMakeFiles/bar.dir/bar.cpp.o -o bar >> -Wl,-rpath,/Users/smancill/src/conda-test/build-osx-system >> -Wl,-rpath,/Users/smancill/.local/share/miniconda3/envs/test-system/lib >> libfoo.dylib >> /Users/smancill/.local/share/miniconda3/envs/test-system/lib/libxerces-c.dylib >> ... >> >> The build directory (~/src/conda-test/build-osx-system) and the conda >> environment lib directory (~/.local/share/miniconda3/envs/test-system/lib) >> are correctly added to the RPATH in the build tree by the link command: >> >> $ ./bar >> Hello, world! >> >> $ otool -L ./bar >> ./bar: >> @rpath/libfoo.dylib (compatibility version 1.0.0, current version >> 0.0.0) >> @rpath/libxerces-c-3.2.dylib (compatibility version 0.0.0, >> current version 0.0.0) >> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current >> version 400.9.0) >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current >> version 1252.0.0) >> >> $ otool -l ./bar | grep -A2 LC_RPATH >> cmd LC_RPATH >> cmdsize 56 >> path /Users/smancill/src/conda-test/build-osx-system (offset >> 12) >> -- >> cmd LC_RPATH >> cmdsize 80 >> path >> /Users/smancill/.local/share/miniconda3/envs/test-system/lib (offset 12) >> >> If I install the binary, it fails because I haven't configured CMake to >> set the install RPATH: >> >> $ make install >> ... >> Install the project... >> -- Install configuration: "" >> -- Installing: >> /Users/smancill/.local/share/miniconda3/envs/test-system/lib/libfoo.dylib >> -- Installing: >> /Users/smancill/.local/share/miniconda3/envs/test-system/include/foo.hpp >> -- Installing: >> /Users/smancill/.local/share/miniconda3/envs/test-system/bin/bar >> >> $ bar >> dyld: Library not loaded: @rpath/libfoo.dylib >> Referenced from: >> /Users/smancill/.local/share/miniconda4/envs/test-system/bin/bar >> Reason: image not found >> [1] 84611 abort bar >> >> $ otool -L $CONDA_PREFIX/bin/bar >> /Users/smancill/.local/share/miniconda3/envs/test-system/bin/bar: >> @rpath/libfoo.dylib (compatibility version 0.0.0, current version >> 0.0.0) >> @rpath/libxerces-c-3.2.dylib (compatibility version 0.0.0, >> current version 0.0.0) >> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current >> version 400.9.0) >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current >> version 1252.0.0) >> >> $ otool -l $CONDA_PREFIX/bin/bar | grep -A2 LC_RPATH >> # empty >> >> # deactivate the environment to start again >> $ conda deactivate >> >> The same can be observed on Linux. Everything works as it should. >> >> -------------------------------------------------- >> >> If I try to use Anaconda compilers on macOS, the build RPATH is not set >> properly anymore: >> >> # create the environment and install the Anaconda compiler for macOS, >> and XercesC >> $ conda create -n test-conda clangxx_osx-64 xerces-c >> ... >> environment location: >> /Users/smancill/.local/share/miniconda3/envs/test-conda >> ... >> The following NEW packages will be INSTALLED: >> >> cctools: 895-h7512d6f_0 >> clang: 4.0.1-h662ec87_0 >> clang_osx-64: 4.0.1-h1ce6c1d_11 >> clangxx: 4.0.1-hc9b4283_0 >> clangxx_osx-64: 4.0.1-h22b1bf0_11 >> compiler-rt: 4.0.1-h5487866_0 >> icu: 58.2-h4b95b61_1 >> ld64: 274.2-h7c2db76_0 >> libcxx: 4.0.1-h579ed51_0 >> libcxxabi: 4.0.1-hebd6815_0 >> llvm: 4.0.1-hc748206_0 >> llvm-lto-tapi: 4.0.1-h6701bc3_0 >> xerces-c: 3.2.1-h44e365a_0 >> ... >> >> # activate the environment (which sets the variables to use the >> Anaconda compiler) >> $ conda activate test-conda >> >> $ mkdir build-osx-conda >> $ cd build-osx-conda >> $ cmake -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX >> -DCMAKE_PREFIX_PATH=$CONDA_PREFIX .. >> -- The CXX compiler identification is Clang 4.0.1 >> -- Check for working CXX compiler: >> /Users/smancill/.local/share/miniconda3/envs/test-conda/bin/x86_64-apple-darwin13.4.0-clang++ >> -- Check for working CXX compiler: >> /Users/smancill/.local/share/miniconda3/envs/test-conda/bin/x86_64-apple-darwin13.4.0-clang++ >> -- works >> ... >> -- Found XercesC: >> /Users/smancill/.local/share/miniconda3/envs/test-conda/lib/libxerces-c.dylib >> (found version "3.2.1") >> -- Configuring done >> -- Generating done >> -- Build files have been written to: >> /Users/smancill/src/conda-test/build-osx-conda >> >> $ make -j1 VERBOSE=1 >> ... >> [100%] Linking CXX executable bar >> /usr/local/bin/cmake -E cmake_link_script CMakeFiles/bar.dir/link.txt >> --verbose=1 >> >> /Users/smancill/.local/share/miniconda3/envs/test-conda/bin/x86_64-apple-darwin13.4.0-clang++ >> -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE >> -fstack-protector-strong -O2 -pipe -stdlib=libc++ >> -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isysroot >> /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk >> -mmacosx-version-min=10.12 -Wl,-search_paths_first >> -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names >> -Wl,-dead_strip_dylibs CMakeFiles/bar.dir/bar.cpp.o -o bar >> -Wl,-rpath,/Users/smancill/src/conda-test/build-osx-conda libfoo.dylib >> /Users/smancill/.local/share/miniconda3/envs/test-conda/lib/libxerces-c.dylib >> ... >> >> You can see that the environment lib path is not added to the RPATH by >> the link command, >> which in turns result in the executable not running from the build tree >> anymore: >> >> $ ./bar >> dyld: Library not loaded: @rpath/libxerces-c-3.2.dylib >> Referenced from: >> /Users/smancill/src/conda-test/build-osx-conda/./bar >> Reason: image not found >> [1] 89350 abort ./bar >> >> $ otool -L ./bar >> ./bar: >> @rpath/libfoo.dylib (compatibility version 0.0.0, current version >> 0.0.0) >> @rpath/libxerces-c-3.2.dylib (compatibility version 0.0.0, >> current version 0.0.0) >> @rpath/libc++.1.dylib (compatibility version 1.0.0, current >> version 1.0.0) >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current >> version 1252.0.0) >> >> $ otool -l ./bar | grep -A2 LC_RPATH >> cmd LC_RPATH >> cmdsize 56 >> path /Users/smancill/src/conda-test/build-osx-conda (offset 12) >> >> # deactivate the environment >> $ conda deactivate >> >> -------------------------------------------------- >> >> If I try the Anaconda compilers on Linux, there are strange results too: >> >> # create the environment and install the Anaconda compiler for Linux, >> and XercesC >> $ conda create -n test-conda gxx_linux-64 xerces-c >> ... >> environment location: /home/vagrant/miniconda3/envs/test-conda >> ... >> The following NEW packages will be INSTALLED: >> >> binutils_impl_linux-64: 2.28.1-had2808c_3 >> binutils_linux-64: 7.2.0-had2808c_27 >> gcc_impl_linux-64: 7.2.0-habb00fd_3 >> gcc_linux-64: 7.2.0-h550dcbe_27 >> gxx_impl_linux-64: 7.2.0-hdf63c60_3 >> gxx_linux-64: 7.2.0-h550dcbe_27 >> icu: 58.2-h9c2bf20_1 >> libgcc-ng: 7.2.0-hdf63c60_3 >> libstdcxx-ng: 7.2.0-hdf63c60_3 >> xerces-c: 3.2.1-hac72e42_0 >> >> # activate the environment (which sets the variables to use the >> Anaconda compiler) >> $ conda activate test-conda >> >> $ mkdir build-linux-conda >> $ cd build-linux-conda >> $ cmake -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX >> -DCMAKE_PREFIX_PATH=$CONDA_PREFIX .. >> -- The CXX compiler identification is GNU 7.2.0 >> -- Check for working CXX compiler: >> /home/vagrant/miniconda3/envs/test-conda/bin/x86_64-conda_cos6-linux-gnu-c++ >> -- Check for working CXX compiler: >> /home/vagrant/miniconda3/envs/test-conda/bin/x86_64-conda_cos6-linux-gnu-c++ >> -- works >> ... >> -- Found XercesC: >> /home/vagrant/miniconda3/envs/test-conda/lib/libxerces-c.so (found version >> "3.2.1") >> -- Configuring done >> -- Generating done >> -- Build files have been written to: >> /vagrant/conda-test/build-linux-conda >> >> $ make -j1 VERBOSE=1 >> ... >> [100%] Linking CXX executable bar >> /usr/bin/cmake -E cmake_link_script CMakeFiles/bar.dir/link.txt >> --verbose=1 >> >> /home/vagrant/miniconda3/envs/test-conda/bin/x86_64-conda_cos6-linux-gnu-c++ >> -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona >> -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 >> -pipe -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now >> CMakeFiles/bar.dir/bar.cpp.o -o bar libfoo.so >> /home/vagrant/miniconda3/envs/test-conda/lib/libxerces-c.so >> -Wl,-rpath,/vagrant/conda-test/build-linux-conda:/home/vagrant/miniconda3/envs/test-conda/lib: >> ... >> >> You can see that the environment lib path is added to the RPATH by the >> link >> command (unlike macOS): >> >> $ ./bar >> Hello World! >> >> But when inspecting the dependencies, the environment lib path appears >> twice: >> >> $ readelf -d ./bar >> ... >> 0x0000000000000001 (NEEDED) Shared library: [libfoo.so] >> 0x0000000000000001 (NEEDED) Shared library: [ >> libxerces-c-3.2.so] >> 0x0000000000000001 (NEEDED) Shared library: >> [libstdc++.so.6] >> 0x0000000000000001 (NEEDED) Shared library: >> [libgcc_s.so.1] >> 0x0000000000000001 (NEEDED) Shared library: [libc.so.6] >> 0x000000000000000f (RPATH) Library rpath: >> [/home/vagrant/miniconda3/envs/test-conda/lib:/vagrant/conda-test/build-linux-conda:/home/vagrant/miniconda3/envs/test-conda/lib:] >> ... >> >> Which is wrong. Now the build tree binary will pick first any old version >> of >> the foo library installed in the environment instead of the version in the >> build tree. >> >> It seems that the Anaconda toolchain is setting the environment lib path >> into >> the RPATH by its own. It is also set when installing the binaries, even >> when >> CMake is not configured to set the install RPATH: >> >> $ make install >> ... >> Install the project... >> -- Install configuration: "" >> -- Installing: /home/vagrant/miniconda3/envs/test-conda/lib/libfoo.so >> -- Installing: >> /home/vagrant/miniconda3/envs/test-conda/include/foo.hpp >> -- Installing: /home/vagrant/miniconda3/envs/test-conda/bin/bar >> -- Set runtime path of >> "/home/vagrant/miniconda3/envs/test-conda/bin/bar" to "" >> >> $ bar >> Hello World! >> >> $ readelf -d $CONDA_PREFIX/bin/bar >> ... >> 0x0000000000000001 (NEEDED) Shared library: [libfoo.so] >> 0x0000000000000001 (NEEDED) Shared library: [ >> libxerces-c-3.2.so] >> 0x0000000000000001 (NEEDED) Shared library: >> [libstdc++.so.6] >> 0x0000000000000001 (NEEDED) Shared library: >> [libgcc_s.so.1] >> 0x0000000000000001 (NEEDED) Shared library: [libc.so.6] >> 0x000000000000000f (RPATH) Library rpath: >> [/home/vagrant/miniconda3/envs/test-conda/lib] >> ... >> >> # deactivate the environment >> $ conda deactivate >> >> -------------------------------------------------- >> >> TL;DR I cannot get CMake and the Anaconda compilers and packages working >> correctly. >> >> - On macOS, the Conda environment library path is not added to the build >> RPATH. >> - On Linux, the Conda environment library path is always added to the >> RPATH >> (in both build and install) independently of CMake. >> >> Any advice or workarounds? >> >> -- >> Sebastian Mancilla >> -- >> >> Powered by www.kitware.com >> >> Please keep messages on-topic and check the CMake FAQ at: >> http://www.cmake.org/Wiki/CMake_FAQ >> >> Kitware offers various services to support the CMake community. For more >> information on each offering, please visit: >> >> CMake Support: http://cmake.org/cmake/help/support.html >> CMake Consulting: http://cmake.org/cmake/help/consulting.html >> CMake Training Courses: http://cmake.org/cmake/help/training.html >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Follow this link to subscribe/unsubscribe: >> https://cmake.org/mailman/listinfo/cmake >> >
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