-- ************************************************************************** -- Starting configuration of Amber version 20.0.0... -- CMake Version: 3.18.0 -- For how to use this build system, please read this wiki: -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake -- For a list of important CMake variables, check here: -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options -- ************************************************************************** -- Amber source not found, only building AmberTools CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) -- Miniconda is installed in the build directory! -- Found perl make: /usr/bin/make -- Perl modules well be installed to AMBERHOME/lib/perl -- Running updater... -- >>> Preparing to apply updates... please wait. -- >>> No new updates available for AmberTools 20 -- Updater done. If you want to install updates, then set the APPLY_UPDATES variable to true. -- Checking whether to use built-in libraries... -- Unable to locate MKL_HOME for your system. To use MKL, set MKL_HOME to point to your MKL installation location. CMake Warning (dev) at /applications/CMake.app/Contents/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message): The package name passed to `find_package_handle_standard_args` (OpenMP_C) does not match the name of the calling package (OpenMPFixed). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args) cmake/hanjianwei/FindMKL.cmake:194 (find_package) cmake/3rdPartyTools.cmake:221 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) (found version "1.0") CMake Warning (dev) at /applications/CMake.app/Contents/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message): The package name passed to `find_package_handle_standard_args` (OpenMP_CXX) does not match the name of the calling package (OpenMPFixed). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args) cmake/hanjianwei/FindMKL.cmake:194 (find_package) cmake/3rdPartyTools.cmake:221 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) (found version "1.0") CMake Warning (dev) at /applications/CMake.app/Contents/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message): The package name passed to `find_package_handle_standard_args` (OpenMP_Fortran) does not match the name of the calling package (OpenMPFixed). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args) cmake/hanjianwei/FindMKL.cmake:194 (find_package) cmake/3rdPartyTools.cmake:221 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_INTEL_THREADING_LIBRARY MKL_CORE_LIBRARY OpenMP_C_FOUND) -- Cannot search for FFTW Fortran headers because the serial headers were not found -- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS FFTW_INCLUDES_SERIAL FFTW_FORTRAN_WORKS) -- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 = NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 = NetCDF_LIBRARIES_F77-NOTFOUND) -- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 = NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 = NetCDF_LIBRARIES_F90-NOTFOUND) -- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES NetCDF_INCLUDES) -- Could NOT find xblas. Please set XBLAS_LIBRARY to point to libxblas.a. -- A library with BLAS API found. -- A library with LAPACK API found. -- The ARPACK library was not found. Please set ARPACK_LIBRARY to point to it. (missing: ARPACK_LIBRARY ARPACK_WORKS) -- Could not find some or all of the five main APBS libraries. Please set APBS_GENERIC_LIB, APBS_ROUTINES_LIB, APBS_PMGC_LIB, APBS_MG_LIB, and APBS_MALOC_LIB to point to the correct libraries (missing: APBS_API_LIB APBS_ROUTINES_LIB APBS_MG_LIB APBS_PMGC_LIB APBS_GENERIC_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES) Unable to find any JVMs matching version "(null)". No Java runtime present, try --request to install. CMake Warning (dev) at /applications/CMake.app/Contents/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message): The package name passed to `find_package_handle_standard_args` (JNI) does not match the name of the calling package (JNIFixed). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/patched-cmake-modules/FindJNIFixed.cmake:323 (FIND_PACKAGE_HANDLE_STANDARD_ARGS) cmake/FindPUPIL.cmake:19 (find_package) cmake/3rdPartyTools.cmake:368 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could not find some or all of the four PUPIL libraries. Please set PUPIL_MAIN_LIB, PUPIL_BLIND_LIB, and PUPIL_TIME_LIB to point to the correct libraries (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB) -- Could not find lio. If you want to use it, set LIO_HOME to point to a built lio source directory. -- Checking for perl module Chemistry::Mol -- Checking for perl module Chemistry::Mol - failed -- Failed to find Perl modules: Chemistry::Mol (missing: PERLMODULES_CHEMISTRY_MOL_MODULE) -- Found Boost: /usr/local/lib/cmake/Boost-1.72.0/BoostConfig.cmake (found version "1.72.0") found components: thread system program_options iostreams regex timer chrono filesystem graph -- Performing Test BOOST_SUPPORTS_COMPRESSION -- Performing Test BOOST_SUPPORTS_COMPRESSION - Success -- The following libraries were found on your system, but are not being used: boost -- This is because the Amber devs have frequently seen broken installs of these libraries causing trouble. -- To tell Amber to link to these libraries, you can select individual ones using -DFORCE_EXTERNAL_LIBS=. -- Alternatively, you can request that Amber link to all libraries it finds using -DTRUST_SYSTEM_LIBS=TRUE. -- Cannot find PLUMED. You will still be able to load it at runtime. If you want to link it at build time, set PLUMED_ROOT to where you installed it. CMake Error at cmake/LibraryUtils.cmake:75 (message): Could not determine whether "/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libbz2.tbd" is a static or shared library, it does not have a known suffix. Call Stack (most recent call first): cmake/LibraryTracking.cmake:40 (get_lib_type) cmake/LibraryTracking.cmake:196 (using_external_library) cmake/3rdPartyTools.cmake:956 (import_libraries) CMakeLists.txt:194 (include) -- Configuring incomplete, errors occurred! See also "/applications/amber20_src/build/CMakeFiles/CMakeOutput.log". See also "/applications/amber20_src/build/CMakeFiles/CMakeError.log".