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qcscine / sparrow

https://scine.ethz.ch
BSD 3-Clause "New" or "Revised" License
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Problem with Python Bingins #20

Closed ProkopHapala closed 1 year ago

ProkopHapala commented 1 year ago

I was following manual run CMake with -DSCINE_BUILD_PYTHON_BINDINGS=ON

but the python libraries are in different dirctory, in manula is this

export PYTHONPATH=$PYTHONPATH:<source code directory>/install/lib/python<version>/site-packages

but in reality it is here:

export PYTHONPATH=$PYTHONPATH:<source code directory>/install/local/lib/python<version>/site-packages

However the bigger problem is that there is no python binding for scine_utilities therefoere I get this error

prokop@DesktopGTX3060:~/git_SW/sparrow/build/install/local/lib/python3.10/dist-packages$ python
Python 3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scine_sparrow
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/prokop/git_SW/sparrow/build/install/local/lib/python3.10/dist-packages/scine_sparrow/__init__.py", line 7, in <module>
    import scine_utilities as utils
ModuleNotFoundError: No module named 'scine_utilities'
>>> import scine_utilities
weymutht commented 1 year ago

Thanks a lot for giving Sparrow a try! The location where the Python packages are installed depends on your exact setup. Do you find the Utilities Python package when executing find ~/git_SW/sparrow/ -name scine_utilities?

ProkopHapala commented 1 year ago

find ~/git_SW/sparrow/ -name scine_utilities returns nothing

but I can see there in /sparrow/build there are

/build/scine-utils-os-build
/build/scine-utils-os-download
/build/scine-utils-os-src
/build/scine-core-src
/build/scine-core-build
/build/scine-core-download
weymutht commented 1 year ago

When the Python package for the Utilities hasn't been built at all, something went wrong during the compilation. However, to properly investigate this, we'll need some more information. Could you maybe post the output of a CMake?

As a quick workaround, you can also install the precompiled Python package from PyPI: pip install scine-utilities.

ProkopHapala commented 1 year ago

For some reason I cannot install it with pip neighter

prokop@DesktopGTX3060:~$ pip install scine-utilities
Defaulting to user installation because normal site-packages is not writeable
ERROR: Could not find a version that satisfies the requirement scine-utilities (from versions: none)
ERROR: No matching distribution found for scine-utilities
weymutht commented 1 year ago

What Python version are you using? Please note that currently, we only provide precompiled packages for Python 3.6, 3.7, and 3.8.

ProkopHapala commented 1 year ago

output form cmake according to manual

prokop@DesktopGTX3060:~/git_SW/sparrow/build$ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../install ..
-- The C compiler identification is GNU 11.3.0
-- The CXX compiler identification is GNU 11.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at dev/cmake/ComponentSetup.cmake:61 (message):
  You are compiling Scine components with an architecture-specific ISA:
  -march=native.  Linking together libraries with mismatched architecture
  build flags can cause problems, in particular with Eigen.  Watch out!
Call Stack (most recent call first):
  CMakeLists.txt:29 (scine_setup_component)

Cloning into 'scine-utils-os-src'...
HEAD is now at f198b18 Release 6.0.0
Submodule 'dev' (https://github.com/qcscine/development-utils.git) registered for path 'dev'
Cloning into '/home/prokop/git_SW/sparrow/build/scine-utils-os-src/dev'...
Cloning into 'scine-core-src'...
HEAD is now at f26e6c7 Release 4.0.2
Submodule 'dev' (https://github.com/qcscine/development-utils.git) registered for path 'dev'
Cloning into '/home/prokop/git_SW/sparrow/build/scine-core-src/dev'...
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system filesystem 
-- GTest and GMock were not found in your PATH, they are being downloaded.
Cloning into 'googletest-src'...
HEAD is now at 703bd9ca Googletest export
CMake Deprecation Warning at build/googletest-src/CMakeLists.txt:4 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googletest/CMakeLists.txt:56 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- Found PythonInterp: /usr/bin/python (found version "3.10.6") 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- GTest and GMock sources were downloaded.
-- Doxygen not found - Documentation for Core will not be built.
-- Scine::Core was not found in your PATH, so it was downloaded.
Cloning into 'yamlcpp-src'...
HEAD is now at 9a36242 Update version to 0.6.3.
-- Performing Test FLAG_WEXTRA
-- Performing Test FLAG_WEXTRA - Success
-- yaml-cpp was not found in your PATH, so it was downloaded.
Cloning into 'irc-src'...
HEAD is now at 6d5c7c3 Merge pull request #48 from jargonzombies/fix-target-eigen-incls
-- Performing Test WALL_SUPPORTED
-- Performing Test WALL_SUPPORTED - Success
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.58.0")  
-- Eigen3 version: 3.4.0
-- IRC was not found in your PATH, so it was downloaded.
Cloning into 'lbfgspp-src'...
HEAD is now at 7fea82a Merge pull request #24 from steinmig/add-cmake
-- Eigen3 version: 3.4.0
-- LBFGSB was not found in your PATH, so it was downloaded.
-- Could NOT find MKL (missing: MKL_INCLUDE_DIRS) 
-- Found LAPACKE for use with Eigen3
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: filesystem system 
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Doxygen not found - Documentation for UtilsOS will not be built.
-- Scine::UtilsOS was not found in your PATH, so it was downloaded.
Cloning into 'cereal-src'...
HEAD is now at 51cbda5 Merge branch 'develop' for release 1.2.2
CMake Deprecation Warning at build/cereal-src/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Warning (dev) at build/cereal-src/CMakeLists.txt:2 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
    cereal_VERSION
    cereal_VERSION_MAJOR
    cereal_VERSION_MINOR
    cereal_VERSION_PATCH
    cereal_VERSION_TWEAK
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Cereal was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: program_options filesystem 
-- Doxygen not found - Documentation for Sparrow will not be built.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/prokop/git_SW/sparrow/build
prokop@DesktopGTX3060:~/git_SW/sparrow/build$
ProkopHapala commented 1 year ago

What Python version are you using? Please note that currently, we only provide precompiled packages for Python 3.6, 3.7, and 3.8.

prokop@DesktopGTX3060:~/git_SW/sparrow/build$ python --version
Python 3.10.6
ProkopHapala commented 1 year ago

This is after I add python -DSCINE_BUILD_PYTHON_BINDINGS=ON

prokop@DesktopGTX3060:~/git_SW/sparrow/build$ cmake -DSCINE_BUILD_PYTHON_BINDINGS=ON  -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../install ..
CMake Warning at dev/cmake/ComponentSetup.cmake:61 (message):
  You are compiling Scine components with an architecture-specific ISA:
  -march=native.  Linking together libraries with mismatched architecture
  build flags can cause problems, in particular with Eigen.  Watch out!
Call Stack (most recent call first):
  CMakeLists.txt:29 (scine_setup_component)

-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system filesystem 
-- GTest and GMock were not found in your PATH, they are being downloaded.
CMake Deprecation Warning at build/googletest-src/CMakeLists.txt:4 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googletest/CMakeLists.txt:56 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- GTest and GMock sources were downloaded.
-- Doxygen not found - Documentation for Core will not be built.
-- Scine::Core was not found in your PATH, so it was downloaded.
-- yaml-cpp was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.58.0")  
-- Eigen3 version: 3.4.0
-- IRC was not found in your PATH, so it was downloaded.
-- Eigen3 version: 3.4.0
-- LBFGSB was not found in your PATH, so it was downloaded.
-- Could NOT find MKL (missing: MKL_INCLUDE_DIRS) 
-- Found LAPACKE for use with Eigen3
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: filesystem system 
Cloning into 'pybind11-src'...
HEAD is now at 8de7772c chore: prepare for the 2.6.2 release (#2821)
-- pybind11 v2.6.2 
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/CMakeDependentOption.cmake:84 (message):
  Policy CMP0127 is not set: cmake_dependent_option() supports full Condition
  Syntax.  Run "cmake --help-policy CMP0127" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
  build/pybind11-src/CMakeLists.txt:98 (cmake_dependent_option)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Pybind11 was not found in your PATH, so it was downloaded.
-- Targets to copy for python bindings: Scine::Core;Scine::UtilsOS
-- Could NOT find PY_pybind11_stubgen (missing: PY_PYBIND11_STUBGEN) 
-- Not generating typechecking stubs for python package as pybind11-stubgen was not found
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for UtilsOS will not be built.
-- Scine::UtilsOS was not found in your PATH, so it was downloadedprokop@DesktopGTX3060:~/git_SW/sparrow/build$ cmake -DSCINE_BUILD_PYTHON_BINDINGS=ON  -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../install ..
CMake Warning at dev/cmake/ComponentSetup.cmake:61 (message):
  You are compiling Scine components with an architecture-specific ISA:
  -march=native.  Linking together libraries with mismatched architecture
  build flags can cause problems, in particular with Eigen.  Watch out!
Call Stack (most recent call first):
  CMakeLists.txt:29 (scine_setup_component)

-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system filesystem 
-- GTest and GMock were not found in your PATH, they are being downloaded.
CMake Deprecation Warning at build/googletest-src/CMakeLists.txt:4 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googletest/CMakeLists.txt:56 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- GTest and GMock sources were downloaded.
-- Doxygen not found - Documentation for Core will not be built.
-- Scine::Core was not found in your PATH, so it was downloaded.
-- yaml-cpp was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.58.0")  
-- Eigen3 version: 3.4.0
-- IRC was not found in your PATH, so it was downloaded.
-- Eigen3 version: 3.4.0
-- LBFGSB was not found in your PATH, so it was downloaded.
-- Could NOT find MKL (missing: MKL_INCLUDE_DIRS) 
-- Found LAPACKE for use with Eigen3
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: filesystem system 
Cloning into 'pybind11-src'...
HEAD is now at 8de7772c chore: prepare for the 2.6.2 release (#2821)
-- pybind11 v2.6.2 
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/CMakeDependentOption.cmake:84 (message):
  Policy CMP0127 is not set: cmake_dependent_option() supports full Condition
  Syntax.  Run "cmake --help-policy CMP0127" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
  build/pybind11-src/CMakeLists.txt:98 (cmake_dependent_option)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Pybind11 was not found in your PATH, so it was downloaded.
-- Targets to copy for python bindings: Scine::Core;Scine::UtilsOS
-- Could NOT find PY_pybind11_stubgen (missing: PY_PYBIND11_STUBGEN) 
-- Not generating typechecking stubs for python package as pybind11-stubgen was not found
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for UtilsOS will noprokop@DesktopGTX3060:~/git_SW/sparrow/build$ cmake -DSCINE_BUILD_PYTHON_BINDINGS=ON  -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../install ..
CMake Warning at dev/cmake/ComponentSetup.cmake:61 (message):
  You are compiling Scine components with an architecture-specific ISA:
  -march=native.  Linking together libraries with mismatched architecture
  build flags can cause problems, in particular with Eigen.  Watch out!
Call Stack (most recent call first):
  CMakeLists.txt:29 (scine_setup_component)

-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system filesystem 
-- GTest and GMock were not found in your PATH, they are being downloaded.
CMake Deprecation Warning at build/googletest-src/CMakeLists.txt:4 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googletest/CMakeLists.txt:56 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- GTest and GMock sources were downloaded.
-- Doxygen not found - Documentation for Core will not be built.
-- Scine::Core was not found in your PATH, so it was downloaded.
-- yaml-cpp was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.58.0")  
-- Eigen3 version: 3.4.0
-- IRC was not found in your PATH, so it was downloaded.
-- Eigen3 version: 3.4.0
-- LBFGSB was not found in your PATH, so it was downloaded.
-- Could NOT find MKL (missing: MKL_INCLUDE_DIRS) 
-- Found LAPACKE for use with Eigen3
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: filesystem system 
Cloning into 'pybind11-src'...
HEAD is now at 8de7772c chore: prepare for the 2.6.2 release (#2821)
-- pybind11 v2.6.2 
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/CMakeDependentOption.cmake:84 (message):
  Policy CMP0127 is not set: cmake_dependent_option() supports full Condition
  Syntax.  Run "cmake --help-policy CMP0127" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
  build/pybind11-src/CMakeLists.txt:98 (cmake_dependenprokop@DesktopGTX3060:~/git_SW/sparrow/build$ cmake -DSCINE_BUILD_PYTHON_BINDINGS=ON  -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../install ..
CMake Warning at dev/cmake/ComponentSetup.cmake:61 (message):
  You are compiling Scine components with an architecture-specific ISA:
  -march=native.  Linking together libraries with mismatched architecture
  build flags can cause problems, in particular with Eigen.  Watch out!
Call Stack (most recent call first):
  CMakeLists.txt:29 (scine_setup_component)

-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system filesystem 
-- GTest and GMock were not found in your PATH, they are being downloaded.
CMake Deprecation Warning at build/googletest-src/CMakeLists.txt:4 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googletest/CMakeLists.txt:56 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- GTest and GMock sources were downloaded.
-- Doxygen not found - Documentation for Core will not be built.
-- Scine::Core was not found in your PATH, so it was downloaded.
-- yaml-cpp was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.58.0")  
-- Eigen3 version: 3.4.0
-- IRC was not found in your PATH, so it was downloaded.
-- Eigen3 version: 3.4.0
-- LBFGSB was not found in your PATH, so it was downloaded.
-- Could NOT find MKL (missing: MKL_INCLUDE_DIRS) 
-- Found LAPACKE for use with Eigen3
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: filesystem system 
Cloning into 'pybind11-src'...
HEAD is now at 8de7772c chore: prepare for the 2.6.2 release (#2821)
-- pybind11 v2.6.2 
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/CMakeDependentOption.cmake:84 (message):
  Policy CMP0127 is not set: cmake_dependent_option() supports full Condition
  Syntax.  Run "cmake --help-policy CMP0127" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
  build/pybind11-src/CMakeLists.txt:98 (cmake_dependent_option)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Pybind11 was not found in your PATH, so it was downloaded.
-- Targets to copy for python bindings: Scine::Core;Scine::UtilsOS
-- Could NOT find PY_pybind11_stubgen (missing: PY_PYBIND11_STUBGEN) 
-- Not generating typechecking stubs for python package as pybind11-stubgen was not found
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for UtilsOS will not be built.
-- Scine::UtilsOS was not found in your PATH, so it was downloaded.
CMake Deprecation Warning at build/cereal-src/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Warning (dev) at build/cereal-src/CMakeLists.txt:2 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
    cereal_VERSION
    cereal_VERSION_MAJOR
    cereal_VERSION_MINOR
    cereal_VERSION_PATCH
    cereal_VERSION_TWEAK
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Cereal was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: program_options filesystem 
-- Targets to copy for python bindings: Sparrow;Scine::UtilsOS
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for Sparrow will not be built.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/prokop/git_SW/sparrow/build
prokop@DesktopGTX3060:~/git_SW/sparrow/build$ 
prokop@DesktopGTX3060:~/git_SW/sparrow/build$ cmake -DSCINE_BUILD_PYTHON_BINDINGS=ON  -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../install ..
CMake Warning at dev/cmake/ComponentSetup.cmake:61 (message):
  You are compiling Scine components with an architecture-specific ISA:
  -march=native.  Linking together libraries with mismatched architecture
  build flags can cause problems, in particular with Eigen.  Watch out!
Call Stack (most recent call first):
  CMakeLists.txt:29 (scine_setup_component)

-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system filesystem 
-- GTest and GMock were not found in your PATH, they are being downloaded.
CMake Deprecation Warning at build/googletest-src/CMakeLists.txt:4 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googletest/CMakeLists.txt:56 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- GTest and GMock sources were downloaded.
-- Doxygen not found - Documentation for Core will not be built.
-- Scine::Core was not found in your PATH, so it was downloaded.
-- yaml-cpp was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.58.0")  
-- Eigen3 version: 3.4.0
-- IRC was not found in your PATH, so it was downloaded.
-- Eigen3 version: 3.4.0
-- LBFGSB was not found in your PATH, so it was downloaded.
-- Could NOT find MKL (missing: MKL_INCLUDE_DIRS) 
-- Found LAPACKE for use with Eigen3
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: filesystem system 
Cloning into 'pybind11-src'...
HEAD is now at 8de7772c chore: prepare for the 2.6.2 release (#2821)
-- pybind11 v2.6.2 
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/CMakeDependentOption.cmake:84 (message):
  Policy CMP0127 is not set: cmake_dependent_option() supports full Condition
  Syntax.  Run "cmake --help-policy CMP0127" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
  build/pybind11-src/CMakeLists.txt:98 (cmake_dependent_option)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Pybind11 was not found in your PATH, so it was downloaded.
-- Targets to copy for python bindings: Scine::Core;Scine::UtilsOS
-- Could NOT find PY_pybind11_stubgen (missing: PY_PYBIND11_STUBGEN) 
-- Not generating typechecking stubs for python package as pybind11-stubgen was not found
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for UtilsOS will not be built.
-- Scine::UtilsOS was not found in your PATH, so it was dowprokop@DesktopGTX3060:~/git_SW/sparrow/build$ cmake -DSCINE_BUILD_PYTHON_BINDINGS=ON  -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../install ..
CMake Warning at dev/cmake/ComponentSetup.cmake:61 (message):
  You are compiling Scine components with an architecture-specific ISA:
  -march=native.  Linking together libraries with mismatched architecture
  build flags can cause problems, in particular with Eigen.  Watch out!
Call Stack (most recent call first):
  CMakeLists.txt:29 (scine_setup_component)

-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system filesystem 
-- GTest and GMock were not found in your PATH, they are being downloaded.
CMake Deprecation Warning at build/googletest-src/CMakeLists.txt:4 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest-src/googletest/CMakeLists.txt:56 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

-- GTest and GMock sources were downloaded.
-- Doxygen not found - Documentation for Core will not be built.
-- Scine::Core was not found in your PATH, so it was downloaded.
-- yaml-cpp was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.58.0")  
-- Eigen3 version: 3.4.0
-- IRC was not found in your PATH, so it was downloaded.
-- Eigen3 version: 3.4.0
-- LBFGSB was not found in your PATH, so it was downloaded.
-- Could NOT find MKL (missing: MKL_INCLUDE_DIRS) 
-- Found LAPACKE for use with Eigen3
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: filesystem system 
Cloning into 'pybind11-src'...
HEAD is now at 8de7772c chore: prepare for the 2.6.2 release (#2821)
-- pybind11 v2.6.2 
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/CMakeDependentOption.cmake:84 (message):
  Policy CMP0127 is not set: cmake_dependent_option() supports full Condition
  Syntax.  Run "cmake --help-policy CMP0127" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
  build/pybind11-src/CMakeLists.txt:98 (cmake_dependent_option)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Pybind11 was not found in your PATH, so it was downloaded.
-- Targets to copy for python bindings: Scine::Core;Scine::UtilsOS
-- Could NOT find PY_pybind11_stubgen (missing: PY_PYBIND11_STUBGEN) 
-- Not generating typechecking stubs for python package as pybind11-stubgen was not found
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for UtilsOS will not be built.
-- Scine::UtilsOS was not found in your PATH, so it was downloaded.
CMake Deprecation Warning at build/cereal-src/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Warning (dev) at build/cereal-src/CMakeLists.txt:2 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
    cereal_VERSION
    cereal_VERSION_MAJOR
    cereal_VERSION_MINOR
    cereal_VERSION_PATCH
    cereal_VERSION_TWEAK
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Cereal was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: program_options filesystem 
-- Targets to copy for python bindings: Sparrow;Scine::UtilsOS
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for Sparrow will not be built.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/prokop/git_SW/sparrow/build
prokop@DesktopGTX3060:~/git_SW/sparrow/build$ 
nloaded.
CMake Deprecation Warning at build/cereal-src/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Warning (dev) at build/cereal-src/CMakeLists.txt:2 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
    cereal_VERSION
    cereal_VERSION_MAJOR
    cereal_VERSION_MINOR
    cereal_VERSION_PATCH
    cereal_VERSION_TWEAK
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Cereal was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: program_options filesystem 
-- Targets to copy for python bindings: Sparrow;Scine::UtilsOS
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for Sparrow will not be built.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/prokop/git_SW/sparrow/build
prokop@DesktopGTX3060:~/git_SW/sparrow/build$ 
t_option)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Pybind11 was not found in your PATH, so it was downloaded.
-- Targets to copy for python bindings: Scine::Core;Scine::UtilsOS
-- Could NOT find PY_pybind11_stubgen (missing: PY_PYBIND11_STUBGEN) 
-- Not generating typechecking stubs for python package as pybind11-stubgen was not found
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for UtilsOS will not be built.
-- Scine::UtilsOS was not found in your PATH, so it was downloaded.
CMake Deprecation Warning at build/cereal-src/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Warning (dev) at build/cereal-src/CMakeLists.txt:2 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
    cereal_VERSION
    cereal_VERSION_MAJOR
    cereal_VERSION_MINOR
    cereal_VERSION_PATCH
    cereal_VERSION_TWEAK
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Cereal was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: program_options filesystem 
-- Targets to copy for python bindings: Sparrow;Scine::UtilsOS
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for Sparrow will not be built.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/prokop/git_SW/sparrow/build
prokop@DesktopGTX3060:~/git_SW/sparrow/build$ 
t be built.
-- Scine::UtilsOS was not found in your PATH, so it was downloaded.
CMake Deprecation Warning at build/cereal-src/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Warning (dev) at build/cereal-src/CMakeLists.txt:2 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
    cereal_VERSION
    cereal_VERSION_MAJOR
    cereal_VERSION_MINOR
    cereal_VERSION_PATCH
    cereal_VERSION_TWEAK
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Cereal was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: program_options filesystem 
-- Targets to copy for python bindings: Sparrow;Scine::UtilsOS
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for Sparrow will not be built.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/prokop/git_SW/sparrow/build
prokop@DesktopGTX3060:~/git_SW/sparrow/build$ 
.
CMake Deprecation Warning at build/cereal-src/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.

CMake Warning (dev) at build/cereal-src/CMakeLists.txt:2 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
    cereal_VERSION
    cereal_VERSION_MAJOR
    cereal_VERSION_MINOR
    cereal_VERSION_PATCH
    cereal_VERSION_TWEAK
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Cereal was not found in your PATH, so it was downloaded.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: program_options filesystem 
-- Targets to copy for python bindings: Sparrow;Scine::UtilsOS
-- Could NOT find PY_sphinx (missing: PY_SPHINX) 
-- Sphinx python package not found, cannot build python documentation
-- Doxygen not found - Documentation for Sparrow will not be built.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/prokop/git_SW/sparrow/build
prokop@DesktopGTX3060:~/git_SW/sparrow/build$
weymutht commented 1 year ago

Do you get any error during compilation?

ProkopHapala commented 1 year ago

No, no error.

This is output form make install

prokop@DesktopGTX3060:~/git_SW/sparrow/build$ sudo make install
[sudo] password for prokop: 
Consolidate compiler generated dependencies of target Core
[  0%] Built target Core
Consolidate compiler generated dependencies of target yaml-cpp
[  6%] Built target yaml-cpp
Consolidate compiler generated dependencies of target UtilsOS
[ 37%] Built target UtilsOS
Consolidate compiler generated dependencies of target Sparrow
[ 57%] Built target Sparrow
Consolidate compiler generated dependencies of target gtest
[ 57%] Built target gtest
Consolidate compiler generated dependencies of target gtest_main
[ 57%] Built target gtest_main
Consolidate compiler generated dependencies of target gmock
[ 57%] Built target gmock
Consolidate compiler generated dependencies of target Sparrow_tests
[ 63%] Built target Sparrow_tests
Consolidate compiler generated dependencies of target SparrowApp
[ 64%] Built target SparrowApp
Consolidate compiler generated dependencies of target RealTimeSpectroscopy
[ 65%] Built target RealTimeSpectroscopy
Consolidate compiler generated dependencies of target RTSpectroscopyDriver
[ 66%] Built target RTSpectroscopyDriver
Consolidate compiler generated dependencies of target UtilsOSModule
[ 68%] Built target UtilsOSModule
Consolidate compiler generated dependencies of target UtilsOS_tests
[ 87%] Built target UtilsOS_tests
Consolidate compiler generated dependencies of target scine_utilities
[ 96%] Built target scine_utilities
Consolidate compiler generated dependencies of target SampleModule
[ 96%] Built target SampleModule
Consolidate compiler generated dependencies of target CoreTests
[ 96%] Built target CoreTests
Consolidate compiler generated dependencies of target gmock_main
[ 97%] Built target gmock_main
Consolidate compiler generated dependencies of target parse
[ 98%] Built target parse
Consolidate compiler generated dependencies of target sandbox
[ 99%] Built target sandbox
Consolidate compiler generated dependencies of target read
[ 99%] Built target read
Consolidate compiler generated dependencies of target Embed
[100%] Built target Embed
Install the project...
-- Install configuration: "Release"
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Technical
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Technical/StrongType.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Technical/ScopedLocale.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Technical/UniqueIdentifier.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Technical/CloneInterface.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Dftd3
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Dftd3/Dftd3Atom.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Dftd3/Dftd3ReferencePairs.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Dftd3/Dftd3Parameters.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Dftd3/Dftd3.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/CalculatorBasics
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/CalculatorBasics/Results.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/CalculatorBasics/PropertyList.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/CalculatorBasics/CalculationRoutines.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/CalculatorBasics/ResultsAutoCompleter.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/CalculatorBasics/TestCalculator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/CalculatorBasics/StatesHandler.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/ChemicalFileFormats
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/ChemicalFileFormats/FormattedStreamHandler.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/ChemicalFileFormats/OpenBabelStreamHandler.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/ChemicalFileFormats/ChemicalFileHandler.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/ChemicalFileFormats/PdbStreamHandler.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/ChemicalFileFormats/XyzStreamHandler.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/ChemicalFileFormats/MolStreamHandler.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/Yaml.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/FilesystemHelpers.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/Regex.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/NativeFilenames.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/FormattedString.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/TurbomoleMinimalBasisfile.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/IOExceptions.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/MolecularTrajectoryIO.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/IO/FormattedIOUtils.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Solvation
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Solvation/MolecularSurface.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Solvation/RandomIndexGenerator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Solvation/ImplicitSolvation.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Solvation/SoluteSolventComplex.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Solvation/SurfaceSite.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/MathUtils.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/Tensor33.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/AtomicSecondDerivativeCollection.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/DerivOrderEnum.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/LinearSumAssignment.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/FullSecondDerivativeCollection.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines/LinearInterpolator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines/GeneratorUtils.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines/BSplineBasis.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines/ControlPolygonGenerator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines/Generator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines/Exceptions.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines/LooseEndsPenalizedLeastSquaresGenerator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines/Coefficients.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Math/BSplines/FixedEndsPenalizedLeastSquares.h
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-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/TurbomoleState.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/TurbomoleFiles.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/TurbomoleHelper.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/OrbitalSteering
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/OrbitalSteering/TurbomoleOrbitalFileReader.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/OrbitalSteering/TurbomoleOrbitalFileWriter.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/OrbitalSteering/TurbomoleOrbitalSteerer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/OrbitalSteering/TurbomoleOrbitalsMetaInformation.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/OrbitalSteering/TurbomoleNumberStringConverter.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/TurbomoleInputFileCreator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/TurbomoleMainOutputParser.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/TurbomoleCalculator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/Turbomole/TurbomoleCalculatorSettings.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/ExternalQC/ExternalProgram.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/GeometryOptimization.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/UnitCellGeometryOptimizer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/AfirConvergenceCheck.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/NtOptimizer2Settings.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/AfirOptimizerBase.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/IrcOptimizer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/NtOptimizer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/QmmmGeometryOptimizer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/CoordinateSystem.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/GeometryOptimizer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/NtOptimizer2.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/AfirOptimizerSettings.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/AfirOptimizer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/GeometryOptimization/NtOptimizerSettings.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Settings.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Constants.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/GeometryUtilities.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/ElementInfo.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/PeriodicSystem.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/AtomCollection.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/StructuralCompletion.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/ElementTypes.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/ElementData.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/Atom.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/Utilities
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/Utilities/Properties.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/Utilities/Distances.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/Utilities/Manipulations.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/Utilities/Transformations.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/FormulaGenerator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Geometry/InternalCoordinates.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/ConvergenceCheck.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/HessianBased
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/HessianBased/Bofill.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/HessianBased/NewtonRaphson.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/HessianBased/EigenvectorFollowing.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/LeastSquares
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/LeastSquares/LevenbergMarquardt.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/LeastSquares/UpdateFunctionManagerBase.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/GradientBased
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/GradientBased/SteepestDescent.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/GradientBased/Gdiis.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/GradientBased/Lbfgs.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/GradientBased/Dimer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/GradientBased/Bfgs.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/GradientBased/GradientBasedCheck.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Utils/Optimizer/Optimizer.h
-- Installing: /home/prokop/git_SW/sparrow/install/lib/libutilsos.so
-- Set runtime path of "/home/prokop/git_SW/sparrow/install/lib/libutilsos.so" to "$ORIGIN/../lib:$ORIGIN"
-- Installing: /home/prokop/git_SW/sparrow/install/lib/utilsos.module.so
-- Set runtime path of "/home/prokop/git_SW/sparrow/install/lib/utilsos.module.so" to "$ORIGIN/../lib:$ORIGIN"
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineUtilsOS/ScineUtilsOSConfig.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineUtilsOS/ScineUtilsOSConfigVersion.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineUtilsOS/ScineUtilsOSTargets.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineUtilsOS/ScineUtilsOSTargets-release.cmake
Processing ./scine-utils-os-build/src/Utils
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from scine-utilities==6.0.0) (1.21.5)
Requirement already satisfied: scipy in /usr/lib/python3/dist-packages (from scine-utilities==6.0.0) (1.8.0)
Building wheels for collected packages: scine-utilities
  Building wheel for scine-utilities (setup.py): started
  Building wheel for scine-utilities (setup.py): finished with status 'done'
  Created wheel for scine-utilities: filename=scine_utilities-6.0.0-cp310-cp310-linux_x86_64.whl size=8014476 sha256=84575373fe8217f24d0bdd7b8a05a1e606eaa4ae3820baee0b2d66a3c9281917
  Stored in directory: /tmp/pip-ephem-wheel-cache-lo07yuao/wheels/12/c8/85/40540a7dea50775d71183d4f22c305f080a1a31ad102468e06
Successfully built scine-utilities
Installing collected packages: scine-utilities
Successfully installed scine-utilities-6.0.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

[notice] A new release of pip is available: 23.0.1 -> 23.1
[notice] To update, run: python -m pip install --upgrade pip
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/ModuleManager.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/ExportControl.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/Log.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/Exceptions.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/Module.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/BaseClasses
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/BaseClasses/ObjectWithStructure.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/BaseClasses/StateHandableObject.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/BaseClasses/ObjectWithLog.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/Interfaces
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/Interfaces/CalculatorWithReference.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/Interfaces/Calculator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/Interfaces/WavefunctionOutputGenerator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/Interfaces/MMParametrizer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/Interfaces/ObjectWithOrbitals.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Scine/Core/DerivedModule.h
-- Installing: /home/prokop/git_SW/sparrow/install/lib/libcore.so
-- Set runtime path of "/home/prokop/git_SW/sparrow/install/lib/libcore.so" to "$ORIGIN/../lib:$ORIGIN"
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineCore/ScineCoreConfig.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineCore/ScineCoreConfigVersion.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineCore/ScineCoreTargets.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineCore/ScineCoreTargets-release.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/libyaml-cpp.a
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/null.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/emitter.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/emittermanip.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/emitfromevents.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/emitterdef.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/emitterstyle.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/traits.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/ostream_wrapper.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/parser.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/exceptions.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/eventhandler.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/binary.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/stlemitter.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/contrib
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/contrib/graphbuilder.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/contrib/anchordict.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/emit.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/type.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/convert.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/impl.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/node.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail/memory.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail/bool_type.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail/node_data.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail/impl.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail/node.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail/iterator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail/node_ref.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail/iterator_fwd.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/detail/node_iterator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/iterator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/parse.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/node/ptr.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/yaml.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/mark.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/anchor.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/yaml-cpp/dll.h
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/yaml-cpp/yaml-cpp-config.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/yaml-cpp/yaml-cpp-config-version.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/yaml-cpp/yaml-cpp-targets.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/yaml-cpp/yaml-cpp-targets-release.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/pkgconfig/yaml-cpp.pc
-- Up-to-date: /home/prokop/git_SW/sparrow/install/include
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/conversion.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/constants.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/plugins
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/plugins/eigen
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/plugins/eigen/Matrix_initializer_list.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/plugins/eigen/LICENSE
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/periodic_table.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/mathtools.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/transformation.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/wilson.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/irc.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/linalg.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/connectivity.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/io.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/atom.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/libirc/molecule.h
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/irc/irc-targets.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/irc/irc-config.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/irc/irc-config-version.cmake
-- Up-to-date: /home/prokop/git_SW/sparrow/install/include
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp/LineSearchBracketing.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp/Param.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp/SubspaceMin.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp/LineSearchBacktracking.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp/BFGSMat.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp/LineSearchMoreThuente.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp/BKLDLT.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp/Cauchy.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSpp/LineSearchNocedalWright.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGS.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LBFGSB.h
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/lbfgspp/lbfgspp-targets.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/lbfgspp/lbfgspp-config.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/lbfgspp/lbfgspp-config-version.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/share/cmake/cereal/cereal-config.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/deque.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/complex.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/vector.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/list.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/base_class.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/array.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/unordered_set.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/polymorphic.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/utility.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/forward_list.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/concepts
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/concepts/pair_associative_container.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/boost_variant.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/unordered_map.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/bitset.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/common.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/string.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/map.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/valarray.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/stack.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/queue.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/memory.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/chrono.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/functional.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/tuple.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/types/set.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidxml
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidxml/rapidxml_iterators.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidxml/rapidxml.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidxml/rapidxml_utils.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidxml/rapidxml_print.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidxml/license.txt
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidxml/manual.html
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/base64.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/error
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/error/en.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/error/error.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/writer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/stream.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/fwd.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/pointer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/encodings.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/prettywriter.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/memorybuffer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/memorystream.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/rapidjson.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/istreamwrapper.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/reader.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/filereadstream.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/allocators.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/diyfp.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/dtoa.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/meta.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/stack.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/regex.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/biginteger.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/swap.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/strfunc.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/pow10.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/itoa.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/strtod.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/internal/ieee754.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/schema.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/msinttypes
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/msinttypes/inttypes.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/msinttypes/stdint.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/document.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/encodedstream.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/filewritestream.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/stringbuffer.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/external/rapidjson/ostreamwrapper.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/access.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/cereal.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/macros.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/details
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/details/helpers.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/details/polymorphic_impl.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/details/polymorphic_impl_fwd.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/details/static_object.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/details/traits.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/details/util.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/archives
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/archives/adapters.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/archives/json.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/archives/portable_binary.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/archives/xml.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/include/cereal/archives/binary.hpp
-- Installing: /home/prokop/git_SW/sparrow/install/lib/sparrow.module.so
-- Set runtime path of "/home/prokop/git_SW/sparrow/install/lib/sparrow.module.so" to ""
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineSparrow/ScineSparrowConfig.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineSparrow/ScineSparrowConfigVersion.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineSparrow/ScineSparrowTargets.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/cmake/ScineSparrow/ScineSparrowTargets-release.cmake
-- Installing: /home/prokop/git_SW/sparrow/install/lib/libRealTimeSpectroscopy.a
-- Installing: /home/prokop/git_SW/sparrow/install/include/SpectroscopySettings.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/IRCalculator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/IntensitiesCalculator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/UvVisCalculator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Spectrum.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/LineWidthGenerator.h
-- Installing: /home/prokop/git_SW/sparrow/install/include/Observers.h
Processing ./src/Sparrow
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: scine-sparrow
  Building wheel for scine-sparrow (setup.py): started
  Building wheel for scine-sparrow (setup.py): finished with status 'done'
  Created wheel for scine-sparrow: filename=scine_sparrow-3.1.0-cp310-cp310-linux_x86_64.whl size=27086852 sha256=f2b01149c26eb9f2e54abf38496ef37979b8244c574f29bbded4a3dcbb5b2d55
  Stored in directory: /tmp/pip-ephem-wheel-cache-bmt7igg0/wheels/5f/b6/20/096bd1ea82d195cd1bd31fb2ae72e9ee7a1fec70b477f2f4c9
Successfully built scine-sparrow
Installing collected packages: scine-sparrow
Successfully installed scine-sparrow-3.1.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

[notice] A new release of pip is available: 23.0.1 -> 23.1
[notice] To update, run: python -m pip install --upgrade pip
-- Installing: /home/prokop/git_SW/sparrow/install/bin/sparrow
-- Set runtime path of "/home/prokop/git_SW/sparrow/install/bin/sparrow" to "$ORIGIN:$ORIGIN/../lib"
prokop@DesktopGTX3060:~/git_SW/sparrow/build$ pw
pw: command not found
prokop@DesktopGTX3060:~/git_SW/sparrow/build$ pwd
/home/prokop/git_SW/sparrow/build
prokop@DesktopGTX3060:~/git_SW/sparrow/build$ export PATH=$PATH:/home/prokop/git_SW/sparrow/build/install/bin
ProkopHapala commented 1 year ago

After repeating the whole process (compiling from scrath), I have both python packages there

prokop@DesktopGTX3060:~/git_SW/sparrow/install/local/lib/python3.10/dist-packages$ ls
scine_sparrow  scine_sparrow-3.1.0.dist-info  scine_utilities  scine_utilities-6.0.0.dist-info

Now I can import it

prokop@DesktopGTX3060:~/git_SW/sparrow/install/local/lib/python3.10/dist-packages$ echo $PYTHONPATH
:/home/prokop/git_SW/sparrow/install/local/lib/python3.10/site-packages
prokop@DesktopGTX3060:~/git_SW/sparrow/install/local/lib/python3.10/dist-packages$ python
Python 3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scine_sparrow
>>> import scine_utilities as su
>>>

Not sure what was the problem ... sorry to bother

weymutht commented 1 year ago

As you can see from this output, the Utilities package has been created successfully:

Building wheels for collected packages: scine-utilities
  Building wheel for scine-utilities (setup.py): started
  Building wheel for scine-utilities (setup.py): finished with status 'done'
  Created wheel for scine-utilities: filename=scine_utilities-6.0.0-cp310-cp310-linux_x86_64.whl size=8014476 sha256=84575373fe8217f24d0bdd7b8a05a1e606eaa4ae3820baee0b2d66a3c9281917
  Stored in directory: /tmp/pip-ephem-wheel-cache-lo07yuao/wheels/12/c8/85/40540a7dea50775d71183d4f22c305f080a1a31ad102468e06
Successfully built scine-utilities
Installing collected packages: scine-utilities
Successfully installed scine-utilities-6.0.0

Can you find it now in the install folder?

weymutht commented 1 year ago

You were just a little bit faster than me :smile:

Great to hear that it's now working!