-- ************************************************************************** -- Starting configuration of Amber version 20.0.0... -- CMake Version: 3.19.3 -- 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 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- The Fortran compiler identification is GNU 4.8.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/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: /usr/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: /usr/bin/gfortran - skipped -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 - yes -- Testing if stdlib.h can be included... -- Testing if stdlib.h can be included... yes -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found CUDA: /opt/cuda-11.3 (found version "11.3") -- Found PythonInterp: /share/apps/amber20_src/miniconda/bin/python3.8 (found version "3.8.5") -- Python version 3.8 -- OK -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Found FLEX: /usr/bin/flex (found version "2.5.37") -- 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 "5.16.3") -- 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 21 -- >>> No new updates available for Amber 20 -- Updater done. If you want to install updates, then set the APPLY_UPDATES variable to true. -- Checking whether to use built-in libraries... -- Looking for complex.h -- Looking for complex.h - found CMake Warning (dev) at /share/apps/cmake-3.19.3/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:426 (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:213 (find_package) CMakeLists.txt:190 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_C: -fopenmp (found version "3.1") CMake Warning (dev) at /share/apps/cmake-3.19.3/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:426 (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:213 (find_package) CMakeLists.txt:190 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_CXX: -fopenmp (found version "3.1") CMake Warning (dev) at /share/apps/cmake-3.19.3/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:426 (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:213 (find_package) CMakeLists.txt:190 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_Fortran: -fopenmp (found version "3.1") -- 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.so -lpthread -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.so -lpthread -fopenmp libgomp.so libpthread.so libm.so - found -- Looking for sgemm in -Wl,--no-as-needed libmkl_core.so libmkl_gnu_thread.so libmkl_gf_lp64.so libdl.so -lpthread -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.so -lpthread -fopenmp libgomp.so libpthread.so libm.so - found -- Found MKL: /home/jinfeng/intel/oneapi/mkl/2021.3.0/lib/intel64/libmkl_intel_lp64.so -- Looking for fftw_execute in libfftw3.a -- Looking for fftw_execute in libfftw3.a - found -- Looking for fftw_cleanup in libfftw3.a -- Looking for fftw_cleanup in libfftw3.a - found -- Found FFTW: /usr/local/lib/libfftw3.a -- 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) -- 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 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) -- Found JNI: /usr/lib/jvm/java-1.8.0-openjdk/jre/lib/amd64/libjawt.so -- 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: /usr/lib64/libz.so (found version "1.2.7") -- Found BZip2: /usr/lib64/libbz2.so (found version "1.0.6") -- 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 /usr/share/perl5/vendor_perl/ExtUtils/MakeMaker.pm -- Failed to find Perl modules: Chemistry::Mol (missing: PERLMODULES_CHEMISTRY_MOL_MODULE) -- Found Boost: /usr/local/lib/cmake/Boost-1.73.0/BoostConfig.cmake (found version "1.73.0") found components: thread system program_options iostreams regex timer chrono filesystem graph -- Looking for boost::system::system_error() in -lpthread libboost_thread.so.1.73.0 libboost_system.so.1.73.0 libboost_program_options.so.1.73.0 libboost_iostreams.so.1.73.0 libboost_regex.so.1.73.0 libboost_chrono.so.1.73.0 libboost_timer.so.1.73.0 libboost_chrono.so.1.73.0 libboost_filesystem.so.1.73.0 libboost_regex.so.1.73.0 libboost_graph.so.1.73.0 -- Looking for boost::system::system_error() in -lpthread libboost_thread.so.1.73.0 libboost_system.so.1.73.0 libboost_program_options.so.1.73.0 libboost_iostreams.so.1.73.0 libboost_regex.so.1.73.0 libboost_chrono.so.1.73.0 libboost_timer.so.1.73.0 libboost_chrono.so.1.73.0 libboost_filesystem.so.1.73.0 libboost_regex.so.1.73.0 libboost_graph.so.1.73.0 - found -- Looking for boost::iostreams::bzip2_decompressor() and boost::iostreams::gzip_decompressor() in -lpthread libboost_thread.so.1.73.0 libboost_system.so.1.73.0 libboost_program_options.so.1.73.0 libboost_iostreams.so.1.73.0 libboost_regex.so.1.73.0 libboost_chrono.so.1.73.0 libboost_timer.so.1.73.0 libboost_chrono.so.1.73.0 libboost_filesystem.so.1.73.0 libboost_regex.so.1.73.0 libboost_graph.so.1.73.0 -- Looking for boost::iostreams::bzip2_decompressor() and boost::iostreams::gzip_decompressor() in -lpthread libboost_thread.so.1.73.0 libboost_system.so.1.73.0 libboost_program_options.so.1.73.0 libboost_iostreams.so.1.73.0 libboost_regex.so.1.73.0 libboost_chrono.so.1.73.0 libboost_timer.so.1.73.0 libboost_chrono.so.1.73.0 libboost_filesystem.so.1.73.0 libboost_regex.so.1.73.0 libboost_graph.so.1.73.0 - found -- Could NOT find MBX (missing: MBX_DIR) -- Could not find MBX. To locate it, add its install dir to the prefix path. -- The following libraries were found on your system, but are not being used: mkl boost -- This is because the Amber devs have frequently seen broken installs of these libraries causing trouble. -- To tell Amber to link to these libraries, you can select individual ones using -DFORCE_EXTERNAL_LIBS=. -- Alternatively, you can request that Amber link to all libraries it finds using -DTRUST_SYSTEM_LIBS=TRUE. -- Cannot find PLUMED. You will still be able to load it at runtime. If you want to link it at build time, set PLUMED_ROOT to where you installed it. -- Performing Test SUPPORTS_WNO_UNUSED_LOCAL_TYPEDEFS -- Performing Test SUPPORTS_WNO_UNUSED_LOCAL_TYPEDEFS - Success -- Looking for mkstemp -- Looking for mkstemp - found -- Generating amber source scripts -- Configuring subdirs... -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- 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 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/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 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 - not 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 -- 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 -- Reticulating splines... -- Looking for sscanf -- Looking for sscanf - found -- Looking for stat -- Looking for stat - found -- Check size of long double -- Check size of long double - done -- 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/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 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 -O0 -- C Optimized:   -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -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 -O0 -- Fortran Optimized:  -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O3 -mtune=native -- -- 3rd Party Libraries -- ---building bundled: ----------------------------------------------------- -- 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 -- perlmol - chemistry library used by FEW -- ---using installed: ------------------------------------------------------ -- blas - for fundamental linear algebra calculations -- lapack - for fundamental linear algebra calculations -- ucpp - used as a preprocessor for the NAB compiler -- fftw - used to do Fourier transforms very quickly -- 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 -- 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 -- Features: -- MPI: OFF -- OpenMP: OFF -- CUDA: OFF -- Build Shared Libraries: ON -- Build GUI Interfaces: ON -- Build Python Programs: OFF -- -Python Interpreter: /share/apps/amber20_src/miniconda/bin/python3.8 (version 3.8) -- Build Perl Programs: ON -- Build configuration: RELEASE -- Target Processor: x86_64 -- Build Documentation: OFF -- Sander Variants: normal LES API LES-API -- Install location: /home/jinfeng/soft/amber20/ -- Installation of Tests: OFF -- Compilers: --  C: GNU 4.8.5 (/usr/bin/gcc) --  CXX: GNU 4.8.5 (/usr/bin/g++) --  Fortran: GNU 4.8.5 (/usr/bin/gfortran) -- Building Tools: -- addles amberlite ambpdb antechamber cifparse cphstats cpptraj emil etc few gbnsr6 gem.pmemd leap lib mdgx mm_pbsa moft nab ndiff-2.00 nfe-umbrella-slice nmode nmr_aux paramfit pbsa pdb4amber pmemd pymsmt python_site_packages reduce rism sander saxs sebomd sff sqm xray xtalutil -- NOT Building Tools: -- pysander - Python programs are disabled -- pytraj - Python programs are disabled -- mmpbsa_py - Python programs are disabled -- parmed - Python programs are disabled -- packmol_memgen - Python programs are disabled -- quick - BUILD_QUICK 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/jinfeng/soft/amber20//amber.sh file in your shell. Consider adding the line -- test -f /home/jinfeng/soft/amber20//amber.sh && source /home/jinfeng/soft/amber20//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /home/jinfeng/soft/amber20//amber.csh file in your shell. Consider adding the line -- test -f /home/jinfeng/soft/amber20//amber.csh && source /home/jinfeng/soft/amber20//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /home/jinfeng/soft/amber20/ -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: FORCE_INTERNAL_LIBRARIES MINICONDA_USE_PY3 -- Build files have been written to: /home/jinfeng/soft/amber20_src/build