-- ************************************************************************** -- Starting configuration of Amber version 20.0.0... -- CMake Version: 3.17.2 -- 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 not found, only building AmberTools -- MPI C Compiler: /home/drewaight/anaconda3/bin/mpicc -- MPI CXX Compiler: /home/drewaight/anaconda3/bin/mpicxx -- MPI Fortran Compiler: /home/drewaight/anaconda3/bin/mpif90 -- If these are not the correct MPI wrappers, then set MPI__COMPILER to the correct wrapper and reconfigure. -- CUDA version 10.2 detected -- Configuring for SM3.0, SM3.5, SM3.7, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1 and SM7.0 -- Miniconda is installed in the build directory! -- 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 20 -- 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/local/cmake-3.17.2/Modules/FindPackageHandleStandardArgs.cmake:272 (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:221 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_C: -fopenmp CMake Warning (dev) at /usr/local/cmake-3.17.2/Modules/FindPackageHandleStandardArgs.cmake:272 (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:221 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_CXX: -fopenmp CMake Warning (dev) at /usr/local/cmake-3.17.2/Modules/FindPackageHandleStandardArgs.cmake:272 (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:221 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_Fortran: -fopenmp -- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS FFTW_FORTRAN_WORKS FFTW_LIBRARY_MPI FFTW_MPI_WORKS) -- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 = NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 = NetCDF_LIBRARIES_F77-NOTFOUND) -- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 = NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 = NetCDF_LIBRARIES_F90-NOTFOUND) -- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES NetCDF_INCLUDES) -- Could NOT find xblas. Please set XBLAS_LIBRARY to point to libxblas.a. -- 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) CMake Warning (dev) at /usr/local/cmake-3.17.2/Modules/FindPackageHandleStandardArgs.cmake:272 (message): The package name passed to `find_package_handle_standard_args` (PnetCDF_C) does not match the name of the calling package (PnetCDF). 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/FindPnetCDF.cmake:273 (find_package_handle_standard_args) cmake/FindPnetCDF.cmake:396 (find_package_component) cmake/3rdPartyTools.cmake:339 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PnetCDF_C (missing: PnetCDF_C_LIBRARY PnetCDF_C_INCLUDE_DIR) -- 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) CMake Warning (dev) at /usr/local/cmake-3.17.2/Modules/FindPackageHandleStandardArgs.cmake:272 (message): The package name passed to `find_package_handle_standard_args` (JNI) does not match the name of the calling package (JNIFixed). 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/FindJNIFixed.cmake:323 (FIND_PACKAGE_HANDLE_STANDARD_ARGS) cmake/FindPUPIL.cmake:19 (find_package) cmake/3rdPartyTools.cmake:368 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH) -- Could not find the Java development libraries, so PUPIL can't be used. (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB) -- Could not find lio. If you want to use it, set LIO_HOME to point to a built lio source directory. -- Found PLUMED, linking to it at build time. -- Found ZLIB: /home/drewaight/anaconda3/lib/libz.so (found version "1.2.11") -- Found BZip2: /home/drewaight/anaconda3/lib/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- 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/drewaight/anaconda3/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/libm.so -- Checking for Python package mpi4py -- not 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 /home/drewaight/anaconda3/lib/5.26.2/ExtUtils/MakeMaker.pm -- Failed to find Perl modules: Chemistry::Mol (missing: PERLMODULES_CHEMISTRY_MOL_MODULE) -- Found Boost: /usr/include (found version "1.65.1") found components: thread system program_options iostreams regex timer chrono filesystem graph date_time atomic -- Performing Test BOOST_SUPPORTS_COMPRESSION -- Performing Test BOOST_SUPPORTS_COMPRESSION - Success -- The following libraries were found on your system, but are not being used: boost mkl -- 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. -- 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 - 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 - 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 -- Check if the system is big endian -- Searching 16 bit integer -- 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 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 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/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 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 -- Check size of char -- Check size of char - done -- Check size of uint -- Check size of uint - done -- Check size of schar -- Check size of schar - failed -- 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 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 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 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: /bin/bash -- netcdf-fortran: Detected TS29113 support in Fortran compiler -- Check size of signed char -- Check size of signed char - done -- 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 - 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 - 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 - 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 - 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 - found -- Looking for MPI_LB -- Looking for MPI_LB - 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 ((struct stat*)0)->st_blksize -- Check size of ((struct stat*)0)->st_blksize - failed -- Looking for mpio.h -- Looking for mpio.h - found -- Reticulating splines... -- Looking for sscanf -- Looking for sscanf - found -- Looking for stat -- Looking for stat - found -- 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:  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drewaight/anaconda3/include -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -O0 -- C Optimized:  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drewaight/anaconda3/include -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native -- -- CXX No-Opt:  -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drewaight/anaconda3/include -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O0 -- CXX Optimized:  -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drewaight/anaconda3/include -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 -- 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 -- mpi4py - MPI support library for MMPBSA.py -- 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 -- readline - used for the console functionality of cpptraj -- zlib - for various compression and decompression tasks -- libbz2 - for bzip2 compression in cpptraj -- plumed - used as an alternate MD backend for Sander -- 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 -- mkl - alternate implementation of lapack and blas that is tuned for speed -- Features: -- MPI: ON -- OpenMP: OFF -- CUDA: ON -- NCCL: OFF -- Build Shared Libraries: ON -- Build GUI Interfaces: ON -- Build Python Programs: ON -- -Python Interpreter: Internal Miniconda (version 3.7) -- Build Perl Programs: ON -- Build configuration: RELEASE -- Target Processor: x86_64 -- Build Documentation: OFF -- Sander Variants: normal LES API LES-API MPI LES-MPI -- Install location: /usr/local/amber20/ -- Installation of Tests: ON -- Compilers: --  C: GNU 7.5.0 (/usr/bin/gcc) --  CXX: GNU 7.5.0 (/usr/bin/g++) --  Fortran: GNU 7.5.0 (/usr/bin/gfortran) -- Building Tools: -- addles amberlite ambpdb antechamber cifparse cphstats cpptraj emil etc few gbnsr6 gem.pmemd leap lib mdgx mm_pbsa mmpbsa_py moft nab ndiff-2.00 nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit parmed pbsa pdb4amber pymsmt pysander pytraj reduce rism sander saxs sebomd sff sqm xray xtalutil -- NOT Building Tools: -- quick - In-development programs are disabled. -- pymdgx - In-development programs are disabled. -- gpu_utils - Not included in AmberTools -- pmemd - Not included in AmberTools -- ************************************************************************** -- 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 -- /usr/local/amber20//amber.sh file in your shell. Consider adding the line -- test -f /usr/local/amber20//amber.sh && source /usr/local/amber20//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /usr/local/amber20//amber.csh file in your shell. Consider adding the line -- test -f /usr/local/amber20//amber.csh && source /usr/local/amber20//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /usr/local/amber20/ -- Configuring done -- Generating done -- Build files have been written to: /usr/local/amber20_src/build