Closed gabor1 closed 3 years ago
I have also tried python setup install
and that seems to fail somewhere else:
docker:librascal$ python setup.py install
--------------------------------------------------------------------------------
-- Trying "Ninja" generator
--------------------------------
---------------------------
----------------------
-----------------
------------
-------
--
Not searching for unused variables given on the command line.
CMake Error: CMake was unable to find a build program corresponding to "Ninja". CMAKE_MAKE_PROGRAM is not set. You probably need to select a different build tool.
-- Configuring incomplete, errors occurred!
See also "/gabor/git-repos/librascal/_cmake_test_compile/build/CMakeFiles/CMakeOutput.log".
--
-------
------------
-----------------
----------------------
---------------------------
--------------------------------
-- Trying "Ninja" generator - failure
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-- Trying "Unix Makefiles" generator
--------------------------------
---------------------------
----------------------
-----------------
------------
-------
--
Not searching for unused variables given on the command line.
-- The C compiler identification is GNU 8.3.0
-- 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
-- The CXX compiler identification is GNU 8.3.0
-- 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
-- Configuring done
-- Generating done
-- Build files have been written to: /gabor/git-repos/librascal/_cmake_test_compile/build
--
-------
------------
-----------------
----------------------
---------------------------
--------------------------------
-- Trying "Unix Makefiles" generator - success
--------------------------------------------------------------------------------
Configuring Project
Working directory:
/gabor/git-repos/librascal/_skbuild/linux-x86_64-3.7/cmake-build
Command:
cmake /gabor/git-repos/librascal -G 'Unix Makefiles' -DCMAKE_INSTALL_PREFIX:PATH=/gabor/git-repos/librascal/_skbuild/linux-x86_64-3.7/cmake-install -DPYTHON_EXECUTABLE:FILEPATH=/usr/local/bin/python -DPYTHON_VERSION_STRING:STRING=3.7.10 -DPYTHON_INCLUDE_DIR:PATH=/usr/local/include/python3.7m -DPYTHON_LIBRARY:FILEPATH=/usr/local/lib/libpython3.7m.so -DSKBUILD:BOOL=TRUE -DCMAKE_MODULE_PATH:PATH=/usr/local/lib/python3.7/site-packages/skbuild/resources/cmake -DINSTALL_PATH:STRING=/gabor/git-repos/librascal/_skbuild/linux-x86_64-3.7/cmake-install -DBUILD_EXAMPLES:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release
-- Build type is: Release
-- The CXX compiler identification is GNU 8.3.0
-- 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
-- Downloading wigxjpf
-- Downloading Eigen3
-- Eigen3 3.3.4
-- Found PythonInterp: /usr/local/bin/python (found suitable version "3.7.10", minimum required is "3")
-- Found PythonLibs: /usr/local/lib/libpython3.7m.so
-- Downloading pybind11
-- pybind11 v2.3.0
-- Installation ROOT: /gabor/git-repos/librascal/_skbuild/linux-x86_64-3.7/cmake-install
-- The project is built using scikit-build
-- cpplint parser: /usr/local/bin/cpplint
-- The optional clang-format auto formatter has not been found. For more information see https://clang.llvm.org/docs/ClangFormat.html
-- BLACK auto formatter: /usr/local/bin/black
-- Configuring done
-- Generating done
-- Build files have been written to: /gabor/git-repos/librascal/_skbuild/linux-x86_64-3.7/cmake-build
Scanning dependencies of target rascal
[ 5%] Building CXX object src/CMakeFiles/rascal.dir/rascal/utils/json_io.cc.o
[ 10%] Building CXX object src/CMakeFiles/rascal.dir/rascal/utils/units.cc.o
[ 15%] Building CXX object src/CMakeFiles/rascal.dir/rascal/utils/utils.cc.o
[ 20%] Building CXX object src/CMakeFiles/rascal.dir/rascal/utils/sparsify_fps.cc.o
[ 25%] Building CXX object src/CMakeFiles/rascal.dir/rascal/math/bessel.cc.o
[ 30%] Building CXX object src/CMakeFiles/rascal.dir/rascal/math/hyp1f1.cc.o
[ 35%] Building CXX object src/CMakeFiles/rascal.dir/rascal/math/interpolator.cc.o
[ 40%] Building CXX object src/CMakeFiles/rascal.dir/rascal/math/gauss_legendre.cc.o
[ 45%] Building CXX object src/CMakeFiles/rascal.dir/rascal/math/spherical_harmonics.cc.o
[ 50%] Building CXX object src/CMakeFiles/rascal.dir/rascal/structure_managers/structure_manager_lammps.cc.o
[ 55%] Building CXX object src/CMakeFiles/rascal.dir/rascal/structure_managers/structure_manager_centers.cc.o
[ 60%] Building CXX object src/CMakeFiles/rascal.dir/rascal/representations/calculator_base.cc.o
[ 65%] Linking CXX shared library librascal.so
[ 65%] Built target rascal
Scanning dependencies of target _rascal
[ 70%] Building CXX object bindings/CMakeFiles/_rascal.dir/bind_py_module.cc.o
[ 75%] Building CXX object bindings/CMakeFiles/_rascal.dir/bind_py_structure_manager.cc.o
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [bindings/CMakeFiles/_rascal.dir/build.make:76: bindings/CMakeFiles/_rascal.dir/bind_py_structure_manager.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:918: bindings/CMakeFiles/_rascal.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/skbuild/setuptools_wrap.py", line 589, in setup
cmkr.make(make_args, env=env)
File "/usr/local/lib/python3.7/site-packages/skbuild/cmaker.py", line 507, in make
os.path.abspath(CMAKE_BUILD_DIR())))
An error occurred while building with CMake.
Command:
cmake --build . --target install --config Release --
Source directory:
/gabor/git-repos/librascal
Working directory:
/gabor/git-repos/librascal/_skbuild/linux-x86_64-3.7/cmake-build
Please see CMake's output for more information.
docker:librascal$
do you by any chance have a built docker in which I can run librascal? I really just need to be able to run a notebook for the chemistry rev regression manuscript...
The error looks like the compiler gets killed by the OS while building librascal.
Can you have a look if the compiler is using more memory than available inside your docker container? I never had a proper look at memory requirements while building librascal, but this could be the culprit. The code builds fine on my machine with 16 GB of RAM, but I'm sure 4-8GB should be more than enough.
do you by any chance have a built docker in which I can run librascal?
I don't think so. As far as I know, most of the core developers are not using docker for day to day operations, instead we usually install librascal in virtual environments.
The code builds fine on my machine with 16 GB of RAM, but I'm sure 4-8GB should be more than enough.
As an other data point, the code build fine inside docker on the CI, and have 4 GB of RAM available there. Another possible culprit could be that the container is running out of disk space to store compiled code.
thanks. I increased the memory, and python setup.py install
now worked. pip install .
still didn't work, it gave this error, but maybe it's just conflicting with my attempts at using setup.py
-- Build files have been written to: /tmp/pip-req-build-k_cc1382/_cmake_test_compile/build
CMake Error: The current CMakeCache.txt directory /tmp/pip-req-build-k_cc1382/_skbuild/linux-x86_64-3.7/cmake-build/CMakeCache.txt is different than the directory /gabor/git-repos/librascal/_skbuild/linux-x86_64-3.7/cmake-build where CMakeCache.txt was created. This may result in binaries being created in the wrong place. If you are not sure, reedit the CMakeCache.txt
CMake Error: The source "/tmp/pip-req-build-k_cc1382/CMakeLists.txt" does not match the source "/gabor/git-repos/librascal/CMakeLists.txt" used to generate cache. Re-run cmake with a different source directory.
File "/tmp/pip-build-env-jc3by0cz/overlay/lib/python3.7/site-packages/skbuild/setuptools_wrap.py", line 586, in setup
languages=cmake_languages
File "/tmp/pip-build-env-jc3by0cz/overlay/lib/python3.7/site-packages/skbuild/cmaker.py", line 240, in configure
os.path.abspath(CMAKE_BUILD_DIR())))
Yes, the pip install error is indeed related to the other build attempts. You can make it go away by removing /gabor/git-repos/librascal/_skbuild/
hi!
newbie question (first time installation). I'm trying to install librascal into the quip docker. python requirements went in fine, but then
pip install .
resulted in this. any suggestions?