-- ************************************************************************** -- Starting configuration of Amber version 24.0.0... -- CMake Version: 3.25.1 -- 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 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- The Fortran compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/martis-e@univ-nantes.fr/.guix-profile/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: /home/martis-e@univ-nantes.fr/.guix-profile/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: /home/martis-e@univ-nantes.fr/.guix-profile/bin/gfortran - skipped -- Testing if stdlib.h can be included... -- Testing if stdlib.h can be included... yes -- Found MPI_C: /home/martis-e@univ-nantes.fr/.guix-profile/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /home/martis-e@univ-nantes.fr/.guix-profile/lib/libmpi.so (found version "3.1") -- Found MPI_Fortran: /home/martis-e@univ-nantes.fr/.guix-profile/lib/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI C Compiler: /home/martis-e@univ-nantes.fr/.guix-profile/bin/mpicc -- MPI CXX Compiler: /home/martis-e@univ-nantes.fr/.guix-profile/bin/mpicxx -- MPI Fortran Compiler: /home/martis-e@univ-nantes.fr/.guix-profile/bin/mpif90 -- If these are not the correct MPI wrappers, then set MPI__COMPILER to the correct wrapper and reconfigure. -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found CUDA: /home/martis-e@univ-nantes.fr/.guix-profile (found version "11.7") -- CUDA version 11.7 detected -- Configuring for SM3.5, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1, SM7.0, SM7.5 and SM8.0 -- Checking CUDA and GNU versions -- compatible -- Found PythonInterp: /usr/local/bin/python (found version "3.6.8") -- Python version 3.6 -- OK -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Found FLEX: /home/martis-e@univ-nantes.fr/.guix-profile/bin/flex (found version "2.6.4") -- Found BISON: /home/martis-e@univ-nantes.fr/.guix-profile/bin/bison (found version "3.8.2") -- Found X11: /home/martis-e@univ-nantes.fr/.guix-profile/include -- Looking for XOpenDisplay in /home/martis-e@univ-nantes.fr/.guix-profile/lib/libX11.so;/home/martis-e@univ-nantes.fr/.guix-profile/lib/libXext.so -- Looking for XOpenDisplay in /home/martis-e@univ-nantes.fr/.guix-profile/lib/libX11.so;/home/martis-e@univ-nantes.fr/.guix-profile/lib/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: /home/martis-e@univ-nantes.fr/.guix-profile/bin/perl (found version "5.36.0") -- Found perl make: /home/martis-e@univ-nantes.fr/.guix-profile/bin/make -- Perl modules well be installed to AMBERHOME/lib/perl -- Running updater... NoInternetAccess: Cannot connect to https://ambermd.org -- >>> Preparing to apply updates... please wait. -- Failed to check for updates! If you need to supply additional arguments to the updater you can call the /home/martis-e@univ-nantes.fr/tmp/amber24_src/update_amber script directly. -- 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: /home/martis-e@univ-nantes.fr/.guix-profile/include CMake Warning (dev) at /gnu/store/g8aclbqfmaywpn8l2xg545dhyy0b20c9-cmake-3.25.1/share/cmake-3.25/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:220 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_C: -fopenmp (found version "4.5") CMake Warning (dev) at /gnu/store/g8aclbqfmaywpn8l2xg545dhyy0b20c9-cmake-3.25.1/share/cmake-3.25/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:220 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_CXX: -fopenmp (found version "4.5") CMake Warning (dev) at /gnu/store/g8aclbqfmaywpn8l2xg545dhyy0b20c9-cmake-3.25.1/share/cmake-3.25/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:220 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_Fortran: -fopenmp (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: /home/martis-e@univ-nantes.fr/.guix-profile/lib/libm.so -- Looking for sgemm in -Wl,--no-as-needed libmkl_core.so libmkl_gnu_thread.so libmkl_intel_lp64.so libdl.a -fopenmp libgomp.so libpthread.so libm.so -- Looking for sgemm in -Wl,--no-as-needed libmkl_core.so libmkl_gnu_thread.so libmkl_intel_lp64.so libdl.a -fopenmp libgomp.so libpthread.so libm.so - not found -- Detailed information about why this check failed can be found in /home/martis-e@univ-nantes.fr/tmp/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 -fopenmp libgomp.so libpthread.so libm.so -- Looking for sgemm in -Wl,--no-as-needed libmkl_core.so libmkl_gnu_thread.so libmkl_gf_lp64.so libdl.a -fopenmp libgomp.so libpthread.so libm.so - not found -- Detailed information about why this check failed can be found in /home/martis-e@univ-nantes.fr/tmp/amber24_src/build/CMakeFiles/CMakeError.log -- Could NOT find MKL (missing: 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 -- Cannot find FFTW Fortran headers - FFTW_INCLUDES_MPI-NOTFOUND/fftw3-mpi.f03 is missing -- Could NOT find FFTW (missing: FFTW_LIBRARY_MPI FFTW_INCLUDES_MPI FFTW_MPI_WORKS) -- Looking for nc_strerror in netcdf -- Looking for nc_strerror in netcdf - found -- Performing Test NetCDF_F90_WORKS -- Performed Test NetCDF_F90_WORKS - Success -- Found NetCDF: 1 found components: F77 F90 -- Could NOT find Protobuf (missing: Protobuf_LIBRARIES Protobuf_INCLUDE_DIR) -- Could NOT find XBLAS (missing: XBLAS_LIBRARY XBLAS_C_WORKS XBLAS_FORTRAN_WORKS) -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- A library with BLAS API found. -- Looking for Fortran cheev -- Looking for Fortran cheev - 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 PnetCDF (missing: PnetCDF_LIBRARY PnetCDF_INCLUDE_DIR PnetCDF_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) -- 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") -- Found ZLIB: /home/martis-e@univ-nantes.fr/.guix-profile/lib/libz.so (found version "1.2.13") -- Found BZip2: /home/martis-e@univ-nantes.fr/.guix-profile/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 - failed -- Checking for perl module ExtUtils::MakeMaker -- Checking for perl module ExtUtils::MakeMaker - found at /gnu/store/pj0960mg004ra45kmmla79vpffjy0qrj-perl-5.36.0/lib/perl5/5.36.0/ExtUtils/MakeMaker.pm -- 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 NCCL (missing: NCCL_INCLUDE_DIR NCCL_LIBRARY) -- 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. -- 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. -- 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... -- Performing Test SUPPORTS_SSE_FLAG -- Performing Test SUPPORTS_SSE_FLAG - Success -- Looking for alloca.h -- Looking for alloca.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- Looking for libintl.h -- Looking for libintl.h - found -- Looking for malloc.h -- Looking for malloc.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for limits.h -- Looking for limits.h - found -- Looking for c_asm.h -- Looking for c_asm.h - not found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for stdarg.h -- Looking for stdarg.h - found -- Looking for float.h -- Looking for float.h - found -- Looking for intrinsics.h -- Looking for intrinsics.h - not found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for mach/mach_time.h -- Looking for mach/mach_time.h - not found -- Looking for sys/sysctl.h -- Looking for sys/sysctl.h - not found -- Looking for altivec.h -- Looking for altivec.h - not found -- Looking for alloca -- Looking for alloca - found -- Looking for vprintf -- Looking for vprintf - found -- Looking for BSDgettimeofday -- Looking for BSDgettimeofday - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for gethrtime -- Looking for gethrtime - not found -- Looking for read_real_time -- Looking for read_real_time - not found -- Looking for time_base_to_time -- Looking for time_base_to_time - not found -- Looking for sqrt -- Looking for sqrt - found -- Looking for memset -- Looking for memset - found -- Looking for _mm_malloc -- Looking for _mm_malloc - not found -- Looking for _mm_free -- Looking for _mm_free - not found -- Looking for clock_gettime -- Looking for clock_gettime - found -- Looking for mach_absolute_time -- Looking for mach_absolute_time - not found -- Looking for sysctl -- Looking for sysctl - not found -- Looking for abort -- Looking for abort - found -- Looking for snprintf -- Looking for snprintf - found -- Looking for drand48 -- Looking for drand48 - found -- Looking for memalign -- Looking for memalign - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for sinl -- Looking for sinl - found -- Looking for cosl -- Looking for cosl - found -- Looking for tanl -- Looking for tanl - found -- Looking for drand48 -- Looking for drand48 - found -- Looking for srand48 -- Looking for srand48 - found -- Looking for memalign -- Looking for memalign - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for sinl -- Looking for sinl - found -- Looking for cosl -- Looking for cosl - found -- Looking for isnan -- Looking for isnan - found -- 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 long -- Check size of long - done -- Check size of long long -- Check size of long long - done -- Check size of long double -- Check size of long double - done -- Check size of unsigned int -- Check size of unsigned int - done -- Check size of unsigned long -- Check size of unsigned long - done -- Check size of unsigned long long -- Check size of unsigned long long - done -- Check size of ptrdiff_t -- Check size of ptrdiff_t - done -- Check size of size_t -- Check size of size_t - done -- Check size of uintptr_t -- Check size of uintptr_t - done -- Check size of hrtime_t -- Check size of hrtime_t - failed -- Check size of MPI_Fint -- Check size of MPI_Fint - done -- Check size of fftw_r2r_kind -- Check size of fftw_r2r_kind - done -- Performing Test SUPPORTS_PREFERRED_STACK_BOUNDARY -- Performing Test SUPPORTS_PREFERRED_STACK_BOUNDARY - Success -- Performing Test SUPPORTS_MALIGN_DOUBLE -- Performing Test SUPPORTS_MALIGN_DOUBLE - Success -- FFTW: compiler supports stack alignment: TRUE -- Performing Test HAVE_TICK_COUNTER -- Performing Test HAVE_TICK_COUNTER - Success -- 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 -- Looking for MPI_MODE_RDWR -- Looking for MPI_MODE_RDWR - found -- Looking for MPI_COMBINER_DUP -- Looking for MPI_COMBINER_DUP - not found -- Looking for MPI_COMBINER_DUP as #define or enum -- Looking for MPI_COMBINER_DUP as #define or enum - found -- Looking for MPI_COMBINER_HVECTOR_INTEGER -- Looking for MPI_COMBINER_HVECTOR_INTEGER - not found -- Looking for MPI_COMBINER_HVECTOR_INTEGER as #define or enum -- Looking for MPI_COMBINER_HVECTOR_INTEGER as #define or enum - not found -- Looking for MPI_COMBINER_HINDEXED_INTEGER -- Looking for MPI_COMBINER_HINDEXED_INTEGER - not found -- Looking for MPI_COMBINER_HINDEXED_INTEGER as #define or enum -- Looking for MPI_COMBINER_HINDEXED_INTEGER as #define or enum - not found -- Looking for MPI_COMBINER_SUBARRAY -- Looking for MPI_COMBINER_SUBARRAY - not found -- Looking for MPI_COMBINER_SUBARRAY as #define or enum -- Looking for MPI_COMBINER_SUBARRAY as #define or enum - found -- Looking for MPI_COMBINER_DARRAY -- Looking for MPI_COMBINER_DARRAY - not found -- Looking for MPI_COMBINER_DARRAY as #define or enum -- Looking for MPI_COMBINER_DARRAY as #define or enum - found -- Looking for MPI_COMBINER_RESIZED -- Looking for MPI_COMBINER_RESIZED - not found -- Looking for MPI_COMBINER_RESIZED as #define or enum -- Looking for MPI_COMBINER_RESIZED as #define or enum - found -- Looking for MPI_COMBINER_STRUCT_INTEGER -- Looking for MPI_COMBINER_STRUCT_INTEGER - not found -- Looking for MPI_COMBINER_STRUCT_INTEGER as #define or enum -- Looking for MPI_COMBINER_STRUCT_INTEGER as #define or enum - not found -- Looking for MPI_COMBINER_INDEXED_BLOCK -- Looking for MPI_COMBINER_INDEXED_BLOCK - not found -- Looking for MPI_COMBINER_INDEXED_BLOCK as #define or enum -- Looking for MPI_COMBINER_INDEXED_BLOCK as #define or enum - found -- Looking for MPI_COMBINER_F90_REAL -- Looking for MPI_COMBINER_F90_REAL - not found -- Looking for MPI_COMBINER_F90_REAL as #define or enum -- Looking for MPI_COMBINER_F90_REAL as #define or enum - found -- Looking for MPI_COMBINER_F90_INTEGER -- Looking for MPI_COMBINER_F90_INTEGER - not found -- Looking for MPI_COMBINER_F90_INTEGER as #define or enum -- Looking for MPI_COMBINER_F90_INTEGER as #define or enum - found -- Looking for MPI_COMBINER_F90_COMPLEX -- Looking for MPI_COMBINER_F90_COMPLEX - not found -- Looking for MPI_COMBINER_F90_COMPLEX as #define or enum -- Looking for MPI_COMBINER_F90_COMPLEX as #define or enum - found -- Looking for MPI_CHARACTER -- Looking for MPI_CHARACTER - found -- Looking for MPI_REAL -- Looking for MPI_REAL - found -- Looking for MPI_INTEGER -- Looking for MPI_INTEGER - found -- Looking for MPI_DOUBLE_PRECISION -- Looking for MPI_DOUBLE_PRECISION - found -- Looking for MPI_INTEGER1 -- Looking for MPI_INTEGER1 - found -- Looking for MPI_INTEGER2 -- Looking for MPI_INTEGER2 - found -- Looking for MPI_INTEGER4 -- Looking for MPI_INTEGER4 - found -- Looking for MPI_INTEGER8 -- Looking for MPI_INTEGER8 - found -- Looking for MPI_INTEGER16 -- Looking for MPI_INTEGER16 - not found -- Looking for MPI_INTEGER16 as #define or enum -- Looking for MPI_INTEGER16 as #define or enum - not found -- Looking for MPI_REAL4 -- Looking for MPI_REAL4 - found -- Looking for MPI_REAL8 -- Looking for MPI_REAL8 - found -- Looking for MPI_REAL16 -- Looking for MPI_REAL16 - found -- Looking for MPI_COMPLEX8 -- Looking for MPI_COMPLEX8 - found -- Looking for MPI_COMPLEX16 -- Looking for MPI_COMPLEX16 - found -- Looking for MPI_COMPLEX32 -- Looking for MPI_COMPLEX32 - found -- Looking for MPI_UB -- Looking for MPI_UB - not found -- Looking for MPI_UB as #define or enum -- Looking for MPI_UB as #define or enum - not found -- Looking for MPI_LB -- Looking for MPI_LB - not found -- Looking for MPI_LB as #define or enum -- Looking for MPI_LB as #define or enum - not found -- Looking for strerror -- Looking for strerror - found -- Looking for MPI_Request_get_status -- Looking for MPI_Request_get_status - found -- Looking for MPI_Type_dup -- Looking for MPI_Type_dup - found -- Looking for MPI_Info_dup -- Looking for MPI_Info_dup - found -- Check size of ssize_t -- Check size of ssize_t - done -- Check size of uchar -- Check size of uchar - failed -- Check size of MPI_Offset -- Check size of MPI_Offset - failed -- Check size of short -- Check size of short - done -- Check size of off_t -- Check size of off_t - done -- Check size of ((struct stat*)0)->st_blksize -- Check size of ((struct stat*)0)->st_blksize - failed -- Check size of signed char -- Check size of signed char - done -- Looking for mpio.h -- Looking for mpio.h - not found -- Looking for inttypes.h -- Looking for inttypes.h - found -- NLopt version 2.7.1 -- Looking for getopt.h -- Looking for getopt.h - found -- 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 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 -- 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 -- Performing Test SUPPORTS_STDCXX11 -- Performing Test SUPPORTS_STDCXX11 - Success -- Found PythonLibs: /usr/lib64/libpython3.6m.so (found suitable exact version "3.6.8") -- Could NOT find NumPy (missing: NUMPY_INCLUDE_DIRS) -- Found Guile: /home/martis-e@univ-nantes.fr/.guix-profile/bin/guile (found version "3.0.9") -- Found SWIG: /home/martis-e@univ-nantes.fr/.guix-profile/bin/swig (found version "4.1.1") -- Performing Test UNDEFINED_SYMBOLS_ALLOWED - Failed -- Found Octave: /home/martis-e@univ-nantes.fr/.guix-profile/bin/octave (found version "9.1.0") -- 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 /gnu/store/g8aclbqfmaywpn8l2xg545dhyy0b20c9-cmake-3.25.1/share/cmake-3.25/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... -- Looking for sscanf -- Looking for sscanf - found -- Set CUDA PIC flag --compiler-options -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 -- Looking for sys/param.h -- Looking for sys/param.h - found -- 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 -- Check size of _Bool -- Check size of _Bool - done -- 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: ----------------------------------------------------- -- arpack - for fundamental linear algebra calculations -- ucpp - used as a preprocessor for the NAB compiler -- 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 -- pnetcdf - used by cpptraj for parallel trajectory output -- perlmol - chemistry library used by FEW -- ---using installed: ------------------------------------------------------ -- blas - for fundamental linear algebra calculations -- lapack - for fundamental linear algebra calculations -- netcdf - for creating trajectory data files -- netcdf-fortran - for creating trajectory data files from Fortran -- 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 -- nccl - NVIDIA parallel GPU communication library -- Features: -- MPI: ON -- MVAPICH2-GDR for GPU-GPU comm.: OFF -- OpenMP: OFF -- CUDA: ON -- NCCL: OFF -- Build Shared Libraries: ON -- Build GUI Interfaces: ON -- Build Python Programs: OFF -- -Python Interpreter: /usr/local/bin/python (version 3.6) -- Build Perl Programs: ON -- Build configuration: RELEASE -- Target Processor: x86_64 -- Build Documentation: ON -- Sander Variants: normal LES API LES-API MPI LES-MPI -- Install location: /home/martis-e@univ-nantes.fr/bin/amber/24/ -- Installation of Tests: OFF -- Compilers: --  C: GNU 11.3.0 (/home/martis-e@univ-nantes.fr/.guix-profile/bin/gcc) --  CXX: GNU 11.3.0 (/home/martis-e@univ-nantes.fr/.guix-profile/bin/g++) --  Fortran: GNU 11.3.0 (/home/martis-e@univ-nantes.fr/.guix-profile/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 moft nabc ndiff-2.00 nfe-umbrella-slice nmode nmr_aux paramfit pbsa pdb4amber pmemd reduce rism sander saxs sebomd sff sqm xray xtalutil -- NOT Building Tools: -- pysander - Python programs are disabled -- pytraj - Python programs are disabled -- pymsmt - Python programs are disabled -- mmpbsa_py - Python programs are disabled -- parmed - Python programs are disabled -- packmol_memgen - Python programs are disabled -- tcpb-cpp/pytcpb - Python programs are disabled -- quick - BUILD_QUICK is not enabled -- cew - BUILD_QUICK is not enabled -- tcpb-cpp - 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 -- /home/martis-e@univ-nantes.fr/bin/amber/24//amber.sh file in your shell. Consider adding the line -- test -f /home/martis-e@univ-nantes.fr/bin/amber/24//amber.sh && source /home/martis-e@univ-nantes.fr/bin/amber/24//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /home/martis-e@univ-nantes.fr/bin/amber/24//amber.csh file in your shell. Consider adding the line -- test -f /home/martis-e@univ-nantes.fr/bin/amber/24//amber.csh && source /home/martis-e@univ-nantes.fr/bin/amber/24//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /home/martis-e@univ-nantes.fr/bin/amber/24/ -- Configuring done -- Generating done -- Build files have been written to: /home/martis-e@univ-nantes.fr/tmp/amber24_src/build