-- ************************************************************************** -- Starting configuration of Amber version 22.0.0... -- CMake Version: 3.16.3 -- 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 9.4.0 -- The CXX compiler identification is GNU 9.4.0 -- The Fortran compiler identification is GNU 9.4.0 -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/g++ -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working Fortran compiler: /usr/bin/gfortran -- Check for working Fortran compiler: /usr/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- 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 CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) -- Downloading Python 3 Miniconda -- Detected Linux OS. Downloading the Linux installer -- Using 64 bit miniconda Downloading http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -> /tank/amber/amber/amber22/amber22_src/build/CMakeFiles/miniconda/download/Miniconda3-latest-Linux-x86_64.sh 0.6% ### 4.6% ############ 16.8% ####################### 32.1% ################################# 47.2% ############################################# 62.7% ######################################################## 78.2% ################################################################### 93.8% ######################################################################## 100.0% Installing Miniconda Python. PREFIX=/tank/amber/amber/amber22/amber22_src/build/CMakeFiles/miniconda/install Unpacking payload ... 0%| | 0/49 [00:00 3.4.4-h6a678d5_0 requests 2.28.1-py310h06a4308_1 --> 2.29.0-py310h06a4308_0 sqlite 3.41.1-h5eee18b_0 --> 3.41.2-h5eee18b_0 xz 5.2.10-h5eee18b_1 --> 5.4.2-h5eee18b_0 Downloading and Extracting Packages Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Requirement already satisfied: pip in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (23.0.1) Collecting pip Using cached pip-23.1.2-py3-none-any.whl (2.1 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 23.0.1 Uninstalling pip-23.0.1: Successfully uninstalled pip-23.0.1 Successfully installed pip-23.1.2 Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /tank/amber/amber/amber22/amber22_src/build/CMakeFiles/miniconda/install added / updated specs: - nomkl The following packages will be downloaded: package | build ---------------------------|----------------- blas-1.0 | openblas 46 KB nomkl-3.0 | 0 46 KB ------------------------------------------------------------ Total: 91 KB The following NEW packages will be INSTALLED: blas pkgs/main/linux-64::blas-1.0-openblas nomkl pkgs/main/linux-64::nomkl-3.0-0 Downloading and Extracting Packages blas-1.0 | 46 KB | | 0% nomkl-3.0 | 46 KB | | 0%  nomkl-3.0 | 46 KB | ###5 | 35%  blas-1.0 | 46 KB | ###5 | 35% nomkl-3.0 | 46 KB | ########## | 100%  blas-1.0 | 46 KB | ########## | 100%  Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /tank/amber/amber/amber22/amber22_src/build/CMakeFiles/miniconda/install added / updated specs: - f90nml The following packages will be downloaded: package | build ---------------------------|----------------- ca-certificates-2023.5.7 | hbcca054_0 145 KB conda-forge certifi-2023.5.7 | pyhd8ed1ab_0 149 KB conda-forge conda-23.3.1 | py310hff52083_0 941 KB conda-forge python_abi-3.10 | 2_cp310 4 KB conda-forge ------------------------------------------------------------ Total: 1.2 MB The following NEW packages will be INSTALLED: f90nml conda-forge/noarch::f90nml-1.4.3-pyhd8ed1ab_0 python_abi conda-forge/linux-64::python_abi-3.10-2_cp310 The following packages will be UPDATED: ca-certificates pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2023.5.7-hbcca054_0 certifi pkgs/main/linux-64::certifi-2022.12.7~ --> conda-forge/noarch::certifi-2023.5.7-pyhd8ed1ab_0 The following packages will be SUPERSEDED by a higher-priority channel: conda pkgs/main::conda-23.3.1-py310h06a4308~ --> conda-forge::conda-23.3.1-py310hff52083_0 Downloading and Extracting Packages python_abi-3.10 | 4 KB | | 0% certifi-2023.5.7 | 149 KB | | 0%  conda-23.3.1 | 941 KB | | 0%  ca-certificates-2023 | 145 KB | | 0%  ca-certificates-2023 | 145 KB | #1 | 11%  python_abi-3.10 | 4 KB | ########## | 100% python_abi-3.10 | 4 KB | ########## | 100% ca-certificates-2023 | 145 KB | ########## | 100%  conda-23.3.1 | 941 KB | 1 | 2%  certifi-2023.5.7 | 149 KB | # | 11%  certifi-2023.5.7 | 149 KB | ########## | 100%  conda-23.3.1 | 941 KB | ########## | 100%  conda-23.3.1 | 941 KB | ########## | 100%     Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /tank/amber/amber/amber22/amber22_src/build/CMakeFiles/miniconda/install added / updated specs: - pandas The following packages will be downloaded: package | build ---------------------------|----------------- libgfortran-ng-11.2.0 | h00389a5_1 20 KB numpy-1.24.3 | py310hac523dd_0 11 KB ------------------------------------------------------------ Total: 31 KB The following NEW packages will be INSTALLED: bottleneck pkgs/main/linux-64::bottleneck-1.3.5-py310ha9d4c09_0 libgfortran-ng pkgs/main/linux-64::libgfortran-ng-11.2.0-h00389a5_1 libgfortran5 pkgs/main/linux-64::libgfortran5-11.2.0-h1234567_1 libopenblas pkgs/main/linux-64::libopenblas-0.3.21-h043d6bf_0 numexpr pkgs/main/linux-64::numexpr-2.8.4-py310h757a811_1 numpy pkgs/main/linux-64::numpy-1.24.3-py310hac523dd_0 numpy-base pkgs/main/linux-64::numpy-base-1.24.3-py310h375b286_0 pandas pkgs/main/linux-64::pandas-1.5.3-py310h1128e8f_0 python-dateutil pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0 pytz pkgs/main/linux-64::pytz-2022.7-py310h06a4308_0 The following packages will be SUPERSEDED by a higher-priority channel: ca-certificates conda-forge::ca-certificates-2023.5.7~ --> pkgs/main::ca-certificates-2023.01.10-h06a4308_0 certifi conda-forge/noarch::certifi-2023.5.7-~ --> pkgs/main/linux-64::certifi-2022.12.7-py310h06a4308_0 conda conda-forge::conda-23.3.1-py310hff520~ --> pkgs/main::conda-23.3.1-py310h06a4308_0 Downloading and Extracting Packages numpy-1.24.3 | 11 KB | | 0% libgfortran-ng-11.2. | 20 KB | | 0%  numpy-1.24.3 | 11 KB | ########## | 100% libgfortran-ng-11.2. | 20 KB | ########## | 100%  libgfortran-ng-11.2. | 20 KB | ########## | 100%   Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /tank/amber/amber/amber22/amber22_src/build/CMakeFiles/miniconda/install added / updated specs: - conda-build - cython=0.29 - ipython - notebook - numpy - pytest - scipy The following packages will be downloaded: package | build ---------------------------|----------------- typing-extensions-4.5.0 | py310h06a4308_0 9 KB ------------------------------------------------------------ Total: 9 KB The following NEW packages will be INSTALLED: anyio pkgs/main/linux-64::anyio-3.5.0-py310h06a4308_0 appdirs pkgs/main/noarch::appdirs-1.4.4-pyhd3eb1b0_0 argon2-cffi pkgs/main/noarch::argon2-cffi-21.3.0-pyhd3eb1b0_0 argon2-cffi-bindi~ pkgs/main/linux-64::argon2-cffi-bindings-21.2.0-py310h7f8727e_0 asttokens pkgs/main/noarch::asttokens-2.0.5-pyhd3eb1b0_0 attrs pkgs/main/linux-64::attrs-22.1.0-py310h06a4308_0 backcall pkgs/main/noarch::backcall-0.2.0-pyhd3eb1b0_0 beautifulsoup4 pkgs/main/linux-64::beautifulsoup4-4.12.2-py310h06a4308_0 bleach pkgs/main/noarch::bleach-4.1.0-pyhd3eb1b0_0 chardet pkgs/main/linux-64::chardet-4.0.0-py310h06a4308_1003 comm pkgs/main/linux-64::comm-0.1.2-py310h06a4308_0 conda-build 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transaction: ...working... done Collecting matplotlib Downloading matplotlib-3.7.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 31.9 MB/s eta 0:00:00 Collecting contourpy>=1.0.1 (from matplotlib) Downloading contourpy-1.0.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (300 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 300.3/300.3 kB 20.3 MB/s eta 0:00:00 Collecting cycler>=0.10 (from matplotlib) Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB) Collecting fonttools>=4.22.0 (from matplotlib) Downloading fonttools-4.39.4-py3-none-any.whl (1.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 32.8 MB/s eta 0:00:00 Collecting kiwisolver>=1.0.1 (from matplotlib) Downloading kiwisolver-1.4.4-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 47.2 MB/s eta 0:00:00 Requirement already satisfied: numpy>=1.20 in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (from matplotlib) (1.24.3) Requirement already satisfied: packaging>=20.0 in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (from matplotlib) (23.0) Collecting pillow>=6.2.0 (from matplotlib) Downloading Pillow-9.5.0-cp310-cp310-manylinux_2_28_x86_64.whl (3.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 68.4 MB/s eta 0:00:00 Collecting pyparsing>=2.3.1 (from matplotlib) Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 13.5 MB/s eta 0:00:00 Requirement already satisfied: python-dateutil>=2.7 in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (from matplotlib) (2.8.2) Requirement already satisfied: six>=1.5 in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib) (1.16.0) Installing collected packages: pyparsing, pillow, kiwisolver, fonttools, cycler, contourpy, matplotlib Successfully installed contourpy-1.0.7 cycler-0.11.0 fonttools-4.39.4 kiwisolver-1.4.4 matplotlib-3.7.1 pillow-9.5.0 pyparsing-3.0.9 Will remove 9 (1.3 MB) tarball(s). Will remove 1 index cache(s). Will remove 9 (5.2 MB) package(s). There are no tempfile(s) to remove. There are no logfile(s) to remove. -- Miniconda install successful! -- Found PythonLibs: /tank/amber/amber/amber22/amber22_src/build/CMakeFiles/miniconda/install/lib/libpython3.10.so (found version "3.10.10") -- 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/python3.10/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 "3.5.1") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/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 "5.30.0") -- 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 22 -- >>> No new updates available for Amber 22 -- 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 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 -- Looking for complex.h -- Looking for complex.h - found -- Could NOT find Readline (missing: READLINE_INCLUDE_DIR READLINE_WORKS) -- Unable to locate MKL_HOME for your system. To use MKL, set MKL_HOME to point to your MKL installation location. -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- 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: /usr/lib/x86_64-linux-gnu/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 CMake Warning at /tank/amber/amber/amber22/amber22_src/build/CMakeFiles/CMakeTmp/CMakeLists.txt:16 (add_executable): Cannot generate a safe runtime search path for target cmTC_0f412 because files in some directories may conflict with libraries in implicit directories: runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/9 may be hidden by files in: /usr/local/anaconda2/lib Some of these libraries may not be found correctly. -- 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 CMake Warning at /tank/amber/amber/amber22/amber22_src/build/CMakeFiles/CMakeTmp/CMakeLists.txt:16 (add_executable): Cannot generate a safe runtime search path for target cmTC_c9391 because files in some directories may conflict with libraries in implicit directories: runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/9 may be hidden by files in: /usr/local/anaconda2/lib Some of these libraries may not be found correctly. -- 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: /usr/local/anaconda2/lib/libmkl_intel_lp64.so -- 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 -- Cannot search for FFTW Fortran headers because the serial headers were not found -- Could NOT find FFTW (missing: FFTW_INCLUDES_SERIAL FFTW_FORTRAN_WORKS) -- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 = NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 = NetCDF_LIBRARIES_F77-NOTFOUND) -- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 = NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 = NetCDF_LIBRARIES_F90-NOTFOUND) -- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES NetCDF_INCLUDES) -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so;-lpthread (found version "3.6.1") -- 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, 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) -- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH) -- 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: /usr/local/anaconda2/lib/libz.so (found version "1.2.9") -- Found BZip2: /usr/local/anaconda2/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 /usr/share/perl/5.30/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 MBX (missing: MBX_DIR) -- Could not find MBX. To locate it, add its install dir to the prefix path. -- Could NOT find tng_io (missing: tng_io_DIR) -- Could not find tng_io. To locate it, add its install dir to the prefix path. -- The following libraries were found on your system, but are not being used: 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. -- KMMD not added to 3RDPARTY_SUBDIRS : -- : ucpp-1.3;cpptraj/src/readline;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 -- 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 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 -- 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 -- Reticulating splines... -- Looking for sscanf -- Looking for sscanf - found -- Looking for stat -- Looking for stat - found -- 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/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 -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: ----------------------------------------------------- -- blas - for fundamental linear algebra calculations -- lapack - for fundamental linear algebra calculations -- arpack - for fundamental linear algebra calculations -- ucpp - used as a preprocessor for the NAB compiler -- netcdf - for creating trajectory data files -- netcdf-fortran - for creating trajectory data files from Fortran -- fftw - used to do Fourier transforms very quickly -- readline - enables an interactive terminal in cpptraj -- 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 -- perlmol - chemistry library used by FEW -- ---using installed: ------------------------------------------------------ -- 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 -- Features: -- MPI: OFF -- OpenMP: OFF -- CUDA: OFF -- Build Shared Libraries: ON -- Build GUI Interfaces: ON -- Build Python Programs: ON -- -Python Interpreter: Internal Miniconda (version 3.10) -- Build Perl Programs: ON -- Build configuration: RELEASE -- Target Processor: x86_64 -- Build Documentation: OFF -- Sander Variants: normal LES API LES-API -- Install location: /tank/amber/amber/amber22/amber22/ -- Installation of Tests: ON -- Compilers: --  C: GNU 9.4.0 (/usr/bin/gcc) --  CXX: GNU 9.4.0 (/usr/bin/g++) --  Fortran: GNU 9.4.0 (/usr/bin/gfortran) -- Building Tools: -- addles amberlite ambpdb antechamber cifparse cphstats cpptraj emil etc few gbnsr6 gem.pmemd kmmd leap lib mdgx mm_pbsa mmpbsa_py moft nab 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 -- tcpb-cpp - BUILD_TCPB is not enabled -- tcpb-cpp/pytcpb - BUILD_TCPB is not enabled -- reaxff_puremd - BUILD_REAXFF_PUREMD is not enabled -- gpu_utils - Requires CUDA -- ************************************************************************** -- Environment resource files are provided to set the proper environment -- variables to use AMBER and AmberTools. This is required to run any Python -- programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj) -- -- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the -- /tank/amber/amber/amber22/amber22//amber.sh file in your shell. Consider adding the line -- test -f /tank/amber/amber/amber22/amber22//amber.sh && source /tank/amber/amber/amber22/amber22//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /tank/amber/amber/amber22/amber22//amber.csh file in your shell. Consider adding the line -- test -f /tank/amber/amber/amber22/amber22//amber.csh && source /tank/amber/amber/amber22/amber22//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /tank/amber/amber/amber22/amber22/ -- Configuring done -- Generating done -- Build files have been written to: /tank/amber/amber/amber22/amber22_src/build If the cmake build report looks OK, you should now do the following: make install source /tank/amber/amber/amber22/amber22/amber.sh Consider adding the last line to your login startup script, e.g. ~/.bashrc