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-- ************************************************************************** -- Starting configuration of Amber version 20.0.0... -- CMake Version: 3.22.0 -- 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 found, building AmberTools and Amber 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 -- [1;34mRunning updater... [0m -- >>> Preparing to apply updates... please wait. -- >>> No new updates available for AmberTools 21 -- >>> No new updates available for Amber 20 -- [1;34mUpdater done. If you want to install updates, then set the APPLY_UPDATES variable to true. [0m -- 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-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (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:219 (find_package) CMakeLists.txt:191 (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-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (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:219 (find_package) CMakeLists.txt:191 (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-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (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:219 (find_package) CMakeLists.txt:191 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_Fortran: -fopenmp -- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_INTEL_THREADING_LIBRARY MKL_CORE_LIBRARY OpenMP_C_FOUND MKL_WORKS MKL_FORTRAN_WORKS) -- 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 (missing: XBLAS_LIBRARY XBLAS_C_WORKS XBLAS_FORTRAN_WORKS) -- 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) The operation couldn’t be completed. Unable to locate a Java Runtime. Please visit http://www.java.com for information on installing Java. -- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH) -- Could NOT find PUPIL (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB JNI_FOUND PUPIL_WORKS) -- Could NOT find LIO (missing: LIO_G2G_LIBRARY LIO_AMBER_LIBRARY LIO_WORKS) -- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5") -- 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) -- Could NOT find Boost (missing: Boost_INCLUDE_DIR thread system program_options iostreams regex timer chrono filesystem graph) -- Could NOT find MBX (missing: MBX_DIR) -- Could not find MBX. To locate it, add its install dir to the prefix path. -- Could NOT find tng_io (missing: tng_io_DIR) -- Could not find tng_io. To locate it, add its install dir to the prefix path. -- 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. -- Generating amber source scripts -- Configuring subdirs... -- FFTW: compiler supports stack alignment: FALSE CMake Error at /Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface.cmake:391 (message): The Fortran compiler: /usr/local/bin/gfortran and the C compiler: /usr/bin/clang failed to compile a simple test project using both languages. The output was: Change Dir: /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC Run Build Command(s):/usr/bin/make -f Makefile VerifyFortranC && /Applications/CMake.app/Contents/bin/cmake -S/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify -B/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC --check-build-system CMakeFiles/Makefile.cmake 0 /Library/Developer/CommandLineTools/usr/bin/make -f CMakeFiles/Makefile2 VerifyFortranC /Applications/CMake.app/Contents/bin/cmake -S/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify -B/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC --check-build-system CMakeFiles/Makefile.cmake 0 /Applications/CMake.app/Contents/bin/cmake -E cmake_progress_start /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC/CMakeFiles 5 /Library/Developer/CommandLineTools/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/VerifyFortranC.dir/all /Library/Developer/CommandLineTools/usr/bin/make -f CMakeFiles/VerifyFortran.dir/build.make CMakeFiles/VerifyFortran.dir/depend cd /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC && /Applications/CMake.app/Contents/bin/cmake -E cmake_depends "Unix Makefiles" /Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify /Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC/CMakeFiles/VerifyFortran.dir/DependInfo.cmake Scanning dependencies of target VerifyFortran /Library/Developer/CommandLineTools/usr/bin/make -f CMakeFiles/VerifyFortran.dir/build.make CMakeFiles/VerifyFortran.dir/build [ 20%] Building Fortran object CMakeFiles/VerifyFortran.dir/VerifyFortran.f.o /usr/local/bin/gfortran -I/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk -c /Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify/VerifyFortran.f -o CMakeFiles/VerifyFortran.dir/VerifyFortran.f.o [ 40%] Linking Fortran static library libVerifyFortran.a /Applications/CMake.app/Contents/bin/cmake -P CMakeFiles/VerifyFortran.dir/cmake_clean_target.cmake /Applications/CMake.app/Contents/bin/cmake -E cmake_link_script CMakeFiles/VerifyFortran.dir/link.txt --verbose=1 /usr/bin/ar qc libVerifyFortran.a CMakeFiles/VerifyFortran.dir/VerifyFortran.f.o /usr/bin/ranlib libVerifyFortran.a [ 40%] Built target VerifyFortran /Library/Developer/CommandLineTools/usr/bin/make -f CMakeFiles/VerifyFortranC.dir/build.make CMakeFiles/VerifyFortranC.dir/depend cd /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC && /Applications/CMake.app/Contents/bin/cmake -E cmake_depends "Unix Makefiles" /Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify /Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC /Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC/CMakeFiles/VerifyFortranC.dir/DependInfo.cmake /Library/Developer/CommandLineTools/usr/bin/make -f CMakeFiles/VerifyFortranC.dir/build.make CMakeFiles/VerifyFortranC.dir/build [ 60%] Building C object CMakeFiles/VerifyFortranC.dir/main.c.o /usr/bin/clang -I/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC -Wall -Wno-unused-function -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk -MD -MT CMakeFiles/VerifyFortranC.dir/main.c.o -MF CMakeFiles/VerifyFortranC.dir/main.c.o.d -o CMakeFiles/VerifyFortranC.dir/main.c.o -c /Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify/main.c [ 80%] Building C object CMakeFiles/VerifyFortranC.dir/VerifyC.c.o /usr/bin/clang -I/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC -Wall -Wno-unused-function -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk -MD -MT CMakeFiles/VerifyFortranC.dir/VerifyC.c.o -MF CMakeFiles/VerifyFortranC.dir/VerifyC.c.o.d -o CMakeFiles/VerifyFortranC.dir/VerifyC.c.o -c /Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify/VerifyC.c [100%] Linking C executable VerifyFortranC /Applications/CMake.app/Contents/bin/cmake -E cmake_link_script CMakeFiles/VerifyFortranC.dir/link.txt --verbose=1 /usr/bin/clang -Wall -Wno-unused-function -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/VerifyFortranC.dir/main.c.o CMakeFiles/VerifyFortranC.dir/VerifyC.c.o -o VerifyFortranC -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib libVerifyFortran.a -lgfortran -lgcc_ext.10.5 -lgcc -lquadmath -lm -lgcc_ext.10.5 -lgcc ld: warning: ignoring file /usr/local/gfortran/lib/libgcc_ext.10.5.dylib, missing required architecture arm64 in file /usr/local/gfortran/lib/libgcc_ext.10.5.dylib (1 slices) ld: warning: ignoring file libVerifyFortran.a, building for macOS-arm64 but attempting to link with file built for macOS-x86_64 ld: warning: ignoring file /usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0/libgcc.a, building for macOS-arm64 but attempting to link with file built for macOS-x86_64 ld: warning: ignoring file /usr/local/gfortran/lib/libgfortran.dylib, building for macOS-arm64 but attempting to link with file built for macOS-x86_64 ld: warning: ignoring file /usr/local/gfortran/lib/libquadmath.dylib, building for macOS-arm64 but attempting to link with file built for macOS-x86_64 Undefined symbols for architecture arm64: "_VerifyFortran", referenced from: _main in main.c.o ld: symbol(s) not found for architecture arm64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[3]: *** [VerifyFortranC] Error 1 make[2]: *** [CMakeFiles/VerifyFortranC.dir/all] Error 2 make[1]: *** [CMakeFiles/VerifyFortranC.dir/rule] Error 2 make: *** [VerifyFortranC] Error 2 Call Stack (most recent call first): AmberTools/src/fftw-3.3/CMakeLists.txt:420 (FortranCInterface_VERIFY) -- Configuring incomplete, errors occurred! See also "/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/CMakeOutput.log". See also "/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/CMakeError.log". -- Brandon J. Orzolek *Pronouns: *he/him, they/them Ph.D. Candidate, University of Pennsylvania Department of Chemistry _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Nov 16 2021 - 17:30:02 PST