andriy@andriy-Precision-Tower-5810:~/amber24_src/build$ ./run_cmake -- ************************************************************************** -- Starting configuration of Amber version 24.0.0... -- CMake Version: 3.28.3 -- 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 -- Miniconda is installed in the build directory! CMake Warning (dev) at cmake/PythonBuildConfig.cmake:13 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:121 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonLibs: /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/libpython3.12.so -- 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 24 -- >>> No new updates available for Amber 24 -- 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 /usr/share/cmake-3.28/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:233 (find_package) CMakeLists.txt:218 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find OpenMP_C (missing: OpenMP_pthread_LIBRARY) CMake Warning (dev) at /usr/share/cmake-3.28/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:233 (find_package) CMakeLists.txt:218 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find OpenMP_CXX (missing: OpenMP_pthread_LIBRARY) CMake Warning (dev) at /usr/share/cmake-3.28/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:233 (find_package) CMakeLists.txt:218 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find OpenMP_Fortran (missing: OpenMP_pthread_LIBRARY) -- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY OpenMP_C_FOUND MKL_WORKS MKL_FORTRAN_WORKS) -- hints given to look for KMMD in DIR: -- found KMMD?: KMMD_LIB-NOTFOUND -- found INCLUDES?: -- Did not find an external KMMD library, should be able to use bundled. If you have a custom version then set the path with -DKMMD_DIR (missing: KMMD_LIB) -- 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 Protobuf (missing: Protobuf_LIBRARIES Protobuf_INCLUDE_DIR) -- Could NOT find XBLAS (missing: XBLAS_LIBRARY XBLAS_C_WORKS XBLAS_FORTRAN_WORKS) -- A library with BLAS API not found. Please specify library location. -- LAPACK requires BLAS -- A library with LAPACK API not found. Please specify library location. -- 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, APBS_MC_LIB, APBS_FEM_LIB, UMFPACK_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_FEM_LIB APBS_MC_LIB UMFPACK_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES) -- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 AWT JVM) -- 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 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. -- 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. -- KMMD not added to 3RDPARTY_SUBDIRS : -- : ucpp-1.3;fftw-3.3 -- 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... CMake Deprecation Warning at AmberTools/src/fftw-3.3/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- FFTW: compiler supports stack alignment: TRUE CMake Warning (dev) at AmberTools/src/netcdf-4.6.1/CMakeLists.txt:40 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): AmberTools/src/netcdf-4.6.1/CMakeLists.txt:42 (getuname) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at AmberTools/src/netcdf-4.6.1/CMakeLists.txt:40 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): AmberTools/src/netcdf-4.6.1/CMakeLists.txt:43 (getuname) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at AmberTools/src/netcdf-4.6.1/CMakeLists.txt:40 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): AmberTools/src/netcdf-4.6.1/CMakeLists.txt:44 (getuname) This warning is for project developers. Use -Wno-dev to suppress it. -- Found bash: /usr/bin/bash CMake Warning (dev) at AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:37 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:39 (getuname) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:37 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:40 (getuname) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:37 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:41 (getuname) This warning is for project developers. Use -Wno-dev to suppress it. -- netcdf-fortran: Detected TS29113 support in Fortran compiler CMake Deprecation Warning at AmberTools/src/nlopt/CMakeLists.txt:15 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- NLopt version 2.7.1 CMake Warning (dev) at AmberTools/src/nlopt/CMakeLists.txt:314 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at AmberTools/src/nlopt/CMakeLists.txt:315 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonLibs: /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/libpython3.12.so (Required is exact version "3.11.9") CMake Warning (dev) at AmberTools/src/nlopt/cmake/FindNumPy.cmake:45 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): AmberTools/src/nlopt/CMakeLists.txt:316 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find Guile (missing: GUILE_EXECUTABLE GUILE_ROOT_DIR GUILE_INCLUDE_DIRS GUILE_LIBRARIES) -- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR) -- Could NOT find Octave (missing: OCTAVE_EXECUTABLE OCTAVE_ROOT_DIR OCTAVE_INCLUDE_DIRS OCTAVE_LIBRARIES) -- Could NOT find Matlab (missing: Matlab_INCLUDE_DIRS Matlab_MEX_LIBRARY Matlab_MEX_EXTENSION Matlab_ROOT_DIR Matlab_MX_LIBRARY MX_LIBRARY MAIN_PROGRAM) (found version "NOTFOUND") CMake Warning at /usr/share/cmake-3.28/Modules/CPack.cmake:507 (message): CPack.cmake has already been included!! Call Stack (most recent call first): AmberTools/src/nlopt/CMakeLists.txt:368 (include) -- Reticulating splines... CMake Deprecation Warning at AmberTools/src/cpptraj/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Found C++11 support: cxx_std_11 CMake Deprecation Warning at AmberTools/src/cphstats/CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning at src/pmemd/src/xray/CMakeLists.txt:25 (message): PMEMD_XRAY_CPU_FFT_BACKEND=NONE disables xray functionality of `pmemd` executable -- KMMD_LIB: kmmd If you can't see the following build report, then you need to turn off COLOR_CMAKE_MESSAGES -- ************************************************************************** -- Build Report -- Compiler Flags: -- C No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -O0 -- C Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -O3 -mtune=native -- -- CXX No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O0 -- CXX Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native -- -- Fortran No-Opt: -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -fallow-argument-mismatch -fno-inline-arg-packing -O0 -- Fortran Optimized: -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -fallow-argument-mismatch -fno-inline-arg-packing -O3 -mtune=native -- -- 3rd Party Libraries -- ---building bundled: ----------------------------------------------------- -- blas - for fundamental linear algebra calculations -- lapack - for fundamental linear algebra calculations -- arpack - for fundamental linear algebra calculations -- ucpp - used as a preprocessor for the NAB compiler -- netcdf - for creating trajectory data files -- netcdf-fortran - for creating trajectory data files from Fortran -- fftw - used to do Fourier transforms very quickly -- xblas - used for high-precision linear algebra calculations -- boost - C++ support library -- kmmd - Machine-learning molecular dynamics -- tng_io - enables GROMACS tng trajectory input in cpptraj -- nlopt - used to perform nonlinear optimizations -- perlmol - chemistry library used by FEW -- ---using installed: ------------------------------------------------------ -- readline - enables an interactive terminal in cpptraj -- zlib - for various compression and decompression tasks -- libbz2 - for bzip2 compression in cpptraj -- libm - for fundamental math routines if they are not contained in the C library -- ---disabled: ------------------------------------------------ -- c9x-complex - used as a support library on systems that do not have C99 complex.h support -- protobuf - protocol buffers library, used for communication with external software in QM/MM -- lio - used by Sander to run certain QM routines on the GPU -- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver -- pupil - used by Sander as an alternate user interface -- plumed - used as an alternate MD backend for Sander -- mkl - alternate implementation of lapack and blas that is tuned for speed -- mbx - computes energies and forces for pmemd with the MB-pol model -- libtorch - enables libtorch C++ library for tensor computation and dynamic neural networks -- Features: -- MPI: OFF -- MVAPICH2-GDR for GPU-GPU comm.: OFF -- OpenMP: OFF -- CUDA: OFF -- Build Shared Libraries: ON -- Build GUI Interfaces: OFF -- Build Python Programs: ON -- -Python Interpreter: Internal Miniconda (version 3.11) -- Build Perl Programs: ON -- Build configuration: RELEASE -- Target Processor: x86_64 -- Build Documentation: ON -- Sander Variants: normal LES API LES-API -- Install location: /home/andriy/amber24/ -- Installation of Tests: ON -- Compilers: -- C: GNU 13.2.0 (/usr/bin/gcc) -- CXX: GNU 13.2.0 (/usr/bin/g++) -- Fortran: GNU 13.2.0 (/usr/bin/gfortran) -- Building Tools: -- addles ambpdb antechamber cew cifparse cphstats cpptraj emil etc fe-toolkit few gbnsr6 gem.pmemd kmmd leap lib mdgx mm_pbsa mmpbsa_py moft nabc ndiff-2.00 nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit parmed pbsa pdb4amber pmemd pymsmt pysander pytraj quick reduce rism sander saxs sebomd sff sqm xray xtalutil -- NOT Building Tools: -- tcpb-cpp - BUILD_TCPB is not enabled -- tcpb-cpp/pytcpb - BUILD_TCPB is not enabled -- reaxff_puremd - BUILD_REAXFF_PUREMD is not enabled -- gpu_utils - Requires CUDA -- ************************************************************************** -- Environment resource files are provided to set the proper environment -- variables to use AMBER and AmberTools. This is required to run any Python -- programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj) -- -- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the -- /home/andriy/amber24//amber.sh file in your shell. Consider adding the line -- test -f /home/andriy/amber24//amber.sh && source /home/andriy/amber24//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /home/andriy/amber24//amber.csh file in your shell. Consider adding the line -- test -f /home/andriy/amber24//amber.csh && source /home/andriy/amber24//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /home/andriy/amber24/ -- Configuring done (5.9s) -- Generating done (0.8s) -- Build files have been written to: /home/andriy/amber24_src/build If errors are reported, search for 'CMake Error' in the cmake.log file. If the cmake build report looks OK, you should now do the following: make install source /home/andriy/amber24/amber.sh Consider adding the last line to your login startup script, e.g. ~/.bashrc