-- ************************************************************************** -- 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 -- ************************************************************************** -- Setting C compiler to gcc -- Setting CXX compiler to g++ -- Setting Fortran compiler to gfortran -- Amber source found, building AmberTools and Amber -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- The Fortran compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/cray/pe/gcc/12.2.0/snos/bin/gcc - 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: /opt/cray/pe/gcc/12.2.0/snos/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /opt/cray/pe/gcc/12.2.0/snos/bin/gfortran - skipped -- Testing if stdlib.h can be included... -- Testing if stdlib.h can be included... yes CMake Error at cmake/FindHipCUDA.cmake:706 (string): string sub-command REGEX, mode REPLACE needs at least 6 arguments total to command. Call Stack (most recent call first): cmake/CudaConfig.cmake:179 (find_package) CMakeLists.txt:119 (include) CMake Error at cmake/FindHipCUDA.cmake:707 (string): string sub-command REGEX, mode REPLACE needs at least 6 arguments total to command. Call Stack (most recent call first): cmake/CudaConfig.cmake:179 (find_package) CMakeLists.txt:119 (include) -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found cufft as roc::rocfft -- Adding hip::hipfft to cufft -- Found cublas as roc::rocblas -- Adding roc::hipblas to cublas -- Found curand as roc::rocrand -- Adding hip::hiprand to curand -- Found cusparse as roc::rocsparse -- Adding roc::hipsparse to cusparse -- Found cusolver as roc::rocsolver -- Found hip::hipcub: adding to CUDA_INCLUDE_DIRS -- Found roc::rocthrust: adding to CUDA_INCLUDE_DIRS CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (CUDA) does not match the name of the calling package (HipCUDA). 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/FindHipCUDA.cmake:1038 (find_package_handle_standard_args) cmake/CudaConfig.cmake:179 (find_package) CMakeLists.txt:119 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found CUDA: /opt/rocm-6.2.4 (found version ".") -- Found system Anaconda at /lustre/orion/bip174/proj-shared/miniconda3. It will be used as a Python interpereter, and for additional shared libraries.To disable this, set -DUSE_CONDA_LIBS=FALSE.To use Amber's internal Minconda instead, set DOWNLOAD_MINICONDA to TRUE. To use a different Anaconda install, activate it, delete the build dir, and rerun CMake. To change the Python interpreter in use to a different one inside Anaconda, set the PYTHON_EXECUTABLE variable to point to it. CMake Warning (dev) at cmake/PythonInterpreterConfig.cmake:120 (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:120 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /lustre/orion/bip174/proj-shared/miniconda3/bin/python3.12 (found version "3.12.2") -- Python version 3.12 -- OK 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: /lustre/orion/bip174/proj-shared/miniconda3/lib/libpython3.12.so (found version "3.12.2") -- Checking for Python package numpy -- found -- Checking for Python package scipy -- found -- Checking for Python package matplotlib -- found -- Checking for Python package setuptools -- found -- Checking for Python package tkinter -- found -- Checking for Python package distutils.sysconfig -- found -- Python relative site-packages location: /lib/python3.12/site-packages -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Found BISON: /usr/bin/bison (found version "3.0.4") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found Perl: /usr/bin/perl (found version "5.26.1") -- Found perl make: /usr/bin/make -- Perl modules well be installed to AMBERHOME/lib/perl -- Checking for updates... -- >>> Checking for available patches online. This may take a few seconds... -- >>> Available AmberTools 24 patches: -- >>> No patches available -- >>> Available Amber 24 patches: -- >>> No patches available -- Updating succeeded! APPLY_UPDATES has been disabled. -- Checking whether to use built-in libraries... -- Looking for complex.h -- Looking for complex.h - found -- Looking for rl_initialize in libreadline.so -- Looking for rl_initialize in libreadline.so - found -- Found Readline: /lustre/orion/bip174/proj-shared/miniconda3/include -- 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/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) (found version "4.5") CMake Warning (dev) at /usr/share/cmake/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) (found version "4.5") CMake Warning (dev) at /usr/share/cmake/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) (found version "4.5") -- Performing Test SUPPORTS_NO_AS_NEEDED -- Performing Test SUPPORTS_NO_AS_NEEDED - Success -- Performing Test CMath_LINKS_WITHOUT_M -- Performing Test CMath_LINKS_WITHOUT_M - Failed -- Performing Test CMath_LINKS_WITH_M -- Performing Test CMath_LINKS_WITH_M - Success -- Found CMath: /usr/lib64/libm.so -- Looking for sgemm in -Wl,--no-as-needed libmkl_core.so libmkl_gnu_thread.so libmkl_intel_lp64.so libdl.a libm.so -- Looking for sgemm in -Wl,--no-as-needed libmkl_core.so libmkl_gnu_thread.so libmkl_intel_lp64.so libdl.a libm.so - not found -- Detailed information about why this check failed can be found in /lustre/orion/bip174/proj-shared/amber24_src/build/CMakeFiles/CMakeError.log -- Looking for sgemm in -Wl,--no-as-needed libmkl_core.so libmkl_gnu_thread.so libmkl_gf_lp64.so libdl.a libm.so -- Looking for sgemm in -Wl,--no-as-needed libmkl_core.so libmkl_gnu_thread.so libmkl_gf_lp64.so libdl.a libm.so - not found -- Detailed information about why this check failed can be found in /lustre/orion/bip174/proj-shared/amber24_src/build/CMakeFiles/CMakeError.log -- Could NOT find MKL (missing: 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) -- Looking for fftw_execute in libfftw3.so -- Looking for fftw_execute in libfftw3.so - found -- Looking for fftw_cleanup in libfftw3.so -- Looking for fftw_cleanup in libfftw3.so - found -- Found FFTW: /opt/cray/pe/fftw/3.3.10.10/x86_trento/lib/libfftw3.so -- 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) -- Found Protobuf: /lustre/orion/bip174/proj-shared/miniconda3/lib/libprotobuf.so (found version "5.29.3") -- 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) -- Found JNI: /usr/lib64/jvm/java-11-openjdk-11/include found components: AWT JVM -- Could NOT find PUPIL (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB 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") -- Found ZLIB: /lustre/orion/bip174/proj-shared/miniconda3/lib/libz.so (found version "1.2.13") -- Found BZip2: /lustre/orion/bip174/proj-shared/miniconda3/lib/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Checking for perl module Chemistry::Mol -- Checking for perl module Chemistry::Mol - found at /lustre/orion/world-shared/stf006/ngoav/amber22/lib/perl/Chemistry/Mol.pm -- Checking for perl module ExtUtils::MakeMaker -- Checking for perl module ExtUtils::MakeMaker - found at /usr/lib/perl5/5.26.1/ExtUtils/MakeMaker.pm -- Found PerlModules: TRUE CMake Warning (dev) at cmake/3rdPartyTools.cmake:547 (find_package): Policy CMP0144 is not set: find_package uses upper-case _ROOT variables. Run "cmake --help-policy CMP0144" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Environment variable BOOST_ROOT is set to: /sw/frontier/spack-envs/cpe24.11-cpu/opt/rocmcc-6.2.4/boost-1.85.0-zk6zz2yv4o2szmssya5yp3aufn6b2p6z For compatibility, find_package is ignoring the variable, but code in a .cmake module might still use it. Call Stack (most recent call first): CMakeLists.txt:218 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /sw/frontier/spack-envs/cpe24.11-cpu/opt/rocmcc-6.2.4/boost-1.85.0-zk6zz2yv4o2szmssya5yp3aufn6b2p6z/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found version "1.85.0") found components: thread system program_options iostreams regex timer chrono filesystem graph -- Looking for boost::system::system_error() in libboost_thread.so.1.85.0 libboost_system.so.1.85.0 libboost_program_options.so.1.85.0 libboost_iostreams.so.1.85.0 libboost_regex.so.1.85.0 libboost_timer.so.1.85.0 libboost_chrono.so.1.85.0 libboost_atomic.so.1.85.0 libboost_filesystem.so.1.85.0 libboost_regex.so.1.85.0 libboost_graph.so.1.85.0 -- Looking for boost::system::system_error() in libboost_thread.so.1.85.0 libboost_system.so.1.85.0 libboost_program_options.so.1.85.0 libboost_iostreams.so.1.85.0 libboost_regex.so.1.85.0 libboost_timer.so.1.85.0 libboost_chrono.so.1.85.0 libboost_atomic.so.1.85.0 libboost_filesystem.so.1.85.0 libboost_regex.so.1.85.0 libboost_graph.so.1.85.0 - not found -- Detailed information about why this check failed can be found in /lustre/orion/bip174/proj-shared/amber24_src/build/CMakeFiles/CMakeError.log CMake Warning at cmake/CheckBoostWorks.cmake:30 (message): The boost library Boost::system cannot be linked. This could be due to an incompatible compiler, STL, or ABI. Call Stack (most recent call first): cmake/3rdPartyTools.cmake:557 (check_boost_works) CMakeLists.txt:218 (include) -- Could NOT find NCCL (missing: NCCL_INCLUDE_DIR) -- 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. -- Could NOT find nlopt (missing: nlopt_LIBRARY nlopt_INCLUDE_DIR) -- Could not find nlopt. To locate it, add its install dir to the prefix path. -- Did not find external nlopt -- KMMD not added to 3RDPARTY_SUBDIRS : -- : -- 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. -- Performing Test SUPPORTS_WNO_UNUSED_LOCAL_TYPEDEFS -- Performing Test SUPPORTS_WNO_UNUSED_LOCAL_TYPEDEFS - Success -- Looking for mkstemp -- Looking for mkstemp - found -- Building the GTI version of pmemd.cuda -- Generating amber source scripts -- Configuring subdirs... 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. -- Performing Test LIBTOOL_HAS_NO_UNDEFINED -- Performing Test LIBTOOL_HAS_NO_UNDEFINED - Success -- Performing Test CC_HAS_WCONVERSION -- Performing Test CC_HAS_WCONVERSION - Success -- Performing Test CC_HAS_SHORTEN_64_32 -- Performing Test CC_HAS_SHORTEN_64_32 - Failed -- Looking for math.h -- Looking for math.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for alloca.h -- Looking for alloca.h - found -- Looking for malloc.h -- Looking for malloc.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for getopt.h -- Looking for getopt.h - found -- Looking for locale.h -- Looking for locale.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stdio.h -- Looking for stdio.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for stdarg.h -- Looking for stdarg.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for signal.h -- Looking for signal.h - found -- Looking for sys/param.h -- Looking for sys/param.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for sys/mman.h -- Looking for sys/mman.h - found -- Looking for sys/resource.h -- Looking for sys/resource.h - found -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for pstdint.h -- Looking for pstdint.h - found -- Looking for endian.h -- Looking for endian.h - found -- Looking for BaseTsd.h -- Looking for BaseTsd.h - not found -- Looking for stddef.h -- Looking for stddef.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for winsock2.h -- Looking for winsock2.h - not found -- Looking for ftw.h -- Looking for ftw.h - found -- Looking for libgen.h -- Looking for libgen.h - found -- Looking for isfinite -- Looking for isfinite - found -- Looking for isnan -- Looking for isnan - found -- Looking for isinf -- Looking for isinf - found -- Looking for st_blksize -- Looking for st_blksize - not found -- Looking for alloca -- Looking for alloca - found -- Looking for snprintf -- Looking for snprintf - found -- Check size of char -- Check size of char - done -- Check size of double -- Check size of double - done -- Check size of float -- Check size of float - done -- Check size of int -- Check size of int - done -- Check size of uint -- Check size of uint - done -- Check size of schar -- Check size of schar - failed -- Check size of long -- Check size of long - done -- Check size of long long -- Check size of long long - done -- Check size of unsigned long long -- Check size of unsigned long long - done -- Check size of off_t -- Check size of off_t - done -- Check size of off64_t -- Check size of off64_t - done -- Check size of short -- Check size of short - done -- Check size of ushort -- Check size of ushort - done -- Check size of _Bool -- Check size of _Bool - done -- Check size of size_t -- Check size of size_t - done -- Check size of ssize_t -- Check size of ssize_t - done -- Check size of __int64 -- Check size of __int64 - failed -- Check size of int64_t -- Check size of int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Check size of unsigned char -- Check size of unsigned char - done -- Check size of unsigned short int -- Check size of unsigned short int - done -- Check size of unsigned int -- Check size of unsigned int - done -- Check size of long long -- Check size of long long - done -- Check size of unsigned long long -- Check size of unsigned long long - done -- Looking for fsync -- Looking for fsync - found -- Looking for strlcat -- Looking for strlcat - found -- Looking for strdup -- Looking for strdup - found -- Looking for strndup -- Looking for strndup - found -- Looking for strtoll -- Looking for strtoll - found -- Looking for strtoull -- Looking for strtoull - found -- Looking for mktemp -- Looking for mktemp - found -- Looking for random -- Looking for random - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for MPI_Comm_f2c -- Looking for MPI_Comm_f2c - not found -- Looking for memmove -- Looking for memmove - found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for getrlimit -- Looking for getrlimit - found -- Looking for _filelengthi64 -- Looking for _filelengthi64 - not found -- Looking for mremap -- Looking for mremap - found -- 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 -- Check size of signed char -- Check size of signed char - done -- Detecting Fortran/C Interface -- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling -- Verifying Fortran/C Compiler Compatibility -- Verifying Fortran/C Compiler Compatibility - Success -- Looking for fpu_control.h -- Looking for fpu_control.h - found -- NLopt version 2.8.0 -- Looking for time.h -- Looking for time.h - found -- Looking for getpid -- Looking for getpid - found -- Looking for syscall -- Looking for syscall - found -- Looking for isinf -- Looking for isinf - found -- Looking for isnan -- Looking for isnan - found -- Looking for qsort_r -- Looking for qsort_r - found -- Looking for time -- Looking for time - found -- Looking for copysign -- Looking for copysign - found -- Looking for getopt -- Looking for getopt - found -- Check size of uint32_t -- Check size of uint32_t - done -- Check size of unsigned long -- Check size of unsigned long - done -- Looking for sqrt in m -- Looking for sqrt in m - found -- Looking for fpclassify -- Looking for fpclassify - TRUE -- Performing Test HAVE_THREAD_LOCAL_STORAGE -- Performing Test HAVE_THREAD_LOCAL_STORAGE - Success -- Performing Test HAVE_THREAD_LOCAL_STORAGE -- Performing Test HAVE_THREAD_LOCAL_STORAGE - Failed -- Looking for __cplusplus -- Looking for __cplusplus - found CMake Warning at /usr/share/cmake/Modules/CPack.cmake:507 (message): CPack.cmake has already been included!! Call Stack (most recent call first): AmberTools/src/nlopt/CMakeLists.txt:383 (include) -- Reticulating splines... -- Looking for sscanf -- Looking for sscanf - found -- Check size of long double -- Check size of long double - done 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. -- Set CUDA PIC flag -fPIC -- Found C++11 support: cxx_std_11 -- Looking for getline -- Looking for getline - found -- Performing Test SUPPORTS_WNO_UNUSED_RESULT -- Performing Test SUPPORTS_WNO_UNUSED_RESULT - Success -- Looking for backtrace -- Looking for backtrace - found 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. -- Looking for sys/dir.h -- Looking for sys/dir.h - found -- Looking for dirent.h -- Looking for dirent.h - found -- Looking for pwd.h -- Looking for pwd.h - found -- Looking for stdbool.h -- Looking for stdbool.h - found -- Looking for Windows.h -- Looking for Windows.h - not found -- Looking for X11/Xmd.h -- Looking for X11/Xmd.h - found -- Looking for toupper -- Looking for toupper - found -- Looking for tolower -- Looking for tolower - found -- Check size of BOOL -- Check size of BOOL - done 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 -- netcdf - for creating trajectory data files -- netcdf-fortran - for creating trajectory data files from Fortran -- 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 -- ---using installed: ------------------------------------------------------ -- ucpp - used as a preprocessor for the NAB compiler -- fftw - used to do Fourier transforms very quickly -- 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 -- perlmol - chemistry library used by FEW -- ---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 -- nccl - NVIDIA parallel GPU communication library -- Features: -- MPI: OFF -- MVAPICH2-GDR for GPU-GPU comm.: OFF -- OpenMP: OFF -- CUDA: ON -- NCCL: OFF -- Build Shared Libraries: ON -- Build GUI Interfaces: ON -- Build Python Programs: ON -- -Python Interpreter: /lustre/orion/bip174/proj-shared/miniconda3/bin/python3.12 (version 3.12) -- Build Perl Programs: ON -- Build configuration: RELEASE -- Target Processor: x86_64 -- Build Documentation: ON -- Sander Variants: normal LES API LES-API -- Install location: /lustre/orion/bip174/proj-shared/amber24/ -- Installation of Tests: ON -- Compilers: --  C: GNU 12.2.0 (/opt/cray/pe/gcc/12.2.0/snos/bin/gcc) --  CXX: GNU 12.2.0 (/opt/cray/pe/gcc/12.2.0/snos/bin/g++) --  Fortran: GNU 12.2.0 (/opt/cray/pe/gcc/12.2.0/snos/bin/gfortran) -- Building Tools: -- addles ambpdb antechamber cifparse cphstats cpptraj emil etc fe-toolkit few gbnsr6 gem.pmemd gpu_utils 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 reduce rism sander saxs sebomd sff sqm xray xtalutil -- NOT Building Tools: -- quick - BUILD_QUICK is not enabled -- cew - BUILD_QUICK is not enabled -- tcpb-cpp - BUILD_TCPB is not enabled -- tcpb-cpp/pytcpb - BUILD_TCPB is not enabled -- reaxff_puremd - BUILD_REAXFF_PUREMD is not enabled -- ************************************************************************** -- 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 -- /lustre/orion/bip174/proj-shared/amber24//amber.sh file in your shell. Consider adding the line -- test -f /lustre/orion/bip174/proj-shared/amber24//amber.sh && source /lustre/orion/bip174/proj-shared/amber24//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /lustre/orion/bip174/proj-shared/amber24//amber.csh file in your shell. Consider adding the line -- test -f /lustre/orion/bip174/proj-shared/amber24//amber.csh && source /lustre/orion/bip174/proj-shared/amber24//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /lustre/orion/bip174/proj-shared/amber24/ -- Configuring incomplete, errors occurred!