[CMake] Issues trying to use the Anaconda compiler tools with CMake
Sebastián Mancilla
smancill at jlab.org
Wed Aug 15 10:33:08 EDT 2018
I cannot use conda-build if I am developing. Consider that I will be
editing the sources, compiling and running tests constantly. Going through
the conda-build process every time I need to check some changes would be
too much overhead. conda-build does a lot of things, it creates multiple
new environments, and the build.sh script may run some commands that I only
need when packaging.
Am I getting conda-build wrong? Is there some kind of development mode?
Also, the "tests" listed in the meta.yaml run with the installed version of
the package. I need to run the unit tests. But unit tests are discouraged
from being run in the build.sh script, to avoid extra CPU time in the CI
servers when building the package (per conda-forge docs).
It would be great if CMake would not filter $CONDA_PREFIX from the build
RPATH.
Well, I just doing this as experiment. I really think that using Conda for
C++ development has a lot of potential, although it doesn't seem to have a
lot of traction. Almost no clear results in Google, (but plenty of "Conda
for Python" ofc). It seems to me that the main purpose of C++ packages is
to be called from some Python/R code.
Just to clarify, I am pointing to distribute packages to people that would
not only run the binaries. They will write some hundred lines of the
ugliest C++ code that they will want to compile against the packages, and
run from their tree ./my-code and get results. They don't need to create a
package for that, they just want to compile and run the code. Also some of
them would want to develop new packages to be part of the meta
distribution, so that's why I am trying to figure out how to do C++
development within a Conda environment.
P.S. I checked gcc_impl_linux-64. I see I would need to set CC, CXX, LD by
hand. Also, no clang_impl_osx-64 package.
El mié., 15 de ago. de 2018 a la(s) 07:44, Ray Donnelly (
mingw.android at gmail.com) escribió:
> Hi Sebastián,
>
> Without having time to properly go through this, I feel I should
> correct some technical inaccuracies, but *all* of your issues can be
> sidestepped by using conda-build. Installation and RPATHs are always
> very tricky for projects to get right so we side step any issues here
> by running post-build fixups on these things. We ensure RPATHs have
> the opportunity to add our own, uniquify them (I think!), and make
> them fully relative on macOS and Linux.
>
> WRT RPATHs being added or not, we set LDFLAGs for RPATHs the linker
> activation script *when run under conda-build*. If you want to fake
> that so you get the exact same flags that are used to compile our
> packages do: CONDA_BUILD=1 conda activate envname. If you don't set
> CONDA_BUILD=1 then it'll set all flags *except* -I${PREFIX}/include,
> -L${PREFIX}/lib and -Wl,-rpath,${PREFIX}/lib.
>
> If you want to use our compilers in their completely 'raw' form (of
> course you could unset LDFLAGS, CFLAGS, CPPFLAGS too), then install
> e.g. gcc_impl_linux-64 instead of gcc_linux-64 which really are
> helpers for interfacing the raw compilers with conda-build (and
> setting good default compilation flags for security and performance
> reasons).
>
> You mentioned using [DY]LD_LIBRARY_PATH, I would caution no one to do
> this ever outside of development workflows. FWIW, we run into lots of
> trouble with LD_LIBRARY_PATH and I am *firmly* in the camp that
> LD_LIBRARY_PATH is harmful (i.e. never use it systematically) and I am
> utterly convinced that DT_RUNPATH is a huge mistake. We actually
> consider detection of DT_RUNPATH in any of our DSOs or exes an error
> condition and only allow DT_RPATH. We just had so many bugs due to the
> wrong libs being used by end users due to this, for example there is
> no way a Qt application linked against our Qt libs is going to be
> happy with some random system Qt library that's been interposed.
>
> For macOS, you should also set CONDA_BUILD_SYSROOT=<somewhere that
> macOS 10.9, 10.10 or 10.11 SDK> (depending on the macOS version you
> want to target). These old SDKs can be gotten from old Xcode builds
> and also on github. Unfortunately the compilers are not compatible
> with the new .tbd file format used in newer SDKs and by the newest
> Apple system linker and the source to enable that has not been
> released yet (there have been no new source drops for Apple's ld64 in
> a while).
>
> But please, just use conda-build! While we try to keep them working in
> as many situations as we can, these tools are primarily focussed
> around conda-build and the technical decisions we make with respect to
> them will be from that perspective.
>
> Hope this helps some?
>
> Fri, Aug 10, 2018 at 10:48 PM, Sebastián Mancilla <smancill at 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://urldefense.proofpoint.com/v2/url?u=https-3A__conda.io_docs_user-2Dguide_tasks_build-2Dpackages_compiler-2Dtools.html&d=DwIFaQ&c=lz9TcOasaINaaC3U7FbMev2lsutwpI4--09aP8Lu18s&r=8hmSv9ww5s9qu3iT8h5WMi8-YcKXaJvelxT3fMih7S4&m=yJC8JYc6vz5iLZ9uvPSIL0hSyOCRBucgCWXee5u73nk&s=9ibJ6jRrwBMZIKheWzEMloZyY7BC5CuzHHPAKWlL37Q&e=
> > [2]:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__gist.github.com_smancill_b28ca07ac11fdf285b4d559545a1630b&d=DwIFaQ&c=lz9TcOasaINaaC3U7FbMev2lsutwpI4--09aP8Lu18s&r=8hmSv9ww5s9qu3iT8h5WMi8-YcKXaJvelxT3fMih7S4&m=yJC8JYc6vz5iLZ9uvPSIL0hSyOCRBucgCWXee5u73nk&s=kyMaMU1dzC_OC1KzWIrkZoymXxkiWxELh37yJ4vd028&e=
> >
> > --------------------------------------------------
> >
> > 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:
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cmake.org_Wiki_CMake-5FFAQ&d=DwIFaQ&c=lz9TcOasaINaaC3U7FbMev2lsutwpI4--09aP8Lu18s&r=8hmSv9ww5s9qu3iT8h5WMi8-YcKXaJvelxT3fMih7S4&m=yJC8JYc6vz5iLZ9uvPSIL0hSyOCRBucgCWXee5u73nk&s=GdelxyoZgjgUDZpZLYDRX5TB7K8bnH7ivyB0EBiNAoQ&e=
> >
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> >
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--
Sebastian Mancilla Matta
CCTVal, UTFSM
Valparaíso, Chile
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