Output of RunCMake: (base) sks@HP-Z640-Workstation:~/Desktop/SUCHETANA/amber20_src/build$ ./run_cmake -- ************************************************************************** -- Starting configuration of Amber version 20.0.0... -- CMake Version: 3.9.0 -- 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 found, building AmberTools and Amber -- CUDA version 9.0 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 -- >>> 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... -- Could NOT find Readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY READLINE_IS_LINKABLE) -- Could NOT find Termcap (missing: TERMCAP_LIBRARY TERMCAP_INCLUDE_DIR) -- Cannot use internal readline because its dependency (libtermcap/libtinfo/libncurses) was not found. -- 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 OpenMP_CXX: -fopenmp -- Found OpenMP_Fortran: -fopenmp -- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY) -- Cannot search for FFTW Fortran headers because the serial headers were not found -- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS 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) -- Could NOT find xblas. Please set XBLAS_LIBRARY to point to libxblas.a. -- A library with BLAS API 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) -- 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. -- Checking for perl module Chemistry::Mol -- Checking for perl module Chemistry::Mol - found at /home/sks/Desktop/SUCHETANA/amber20/lib/perl/Chemistry/Mol.pm -- Found PerlModules: TRUE CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769 (message): Imported targets not available for Boost version 106501 Call Stack (most recent call first): /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501 (_Boost_MISSING_DEPENDENCIES) cmake/3rdPartyTools.cmake:526 (find_package) CMakeLists.txt:194 (include) CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769 (message): Imported targets not available for Boost version 106501 Call Stack (most recent call first): /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501 (_Boost_MISSING_DEPENDENCIES) cmake/3rdPartyTools.cmake:526 (find_package) CMakeLists.txt:194 (include) CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769 (message): Imported targets not available for Boost version 106501 Call Stack (most recent call first): /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501 (_Boost_MISSING_DEPENDENCIES) cmake/3rdPartyTools.cmake:526 (find_package) CMakeLists.txt:194 (include) CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769 (message): Imported targets not available for Boost version 106501 Call Stack (most recent call first): /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501 (_Boost_MISSING_DEPENDENCIES) cmake/3rdPartyTools.cmake:526 (find_package) CMakeLists.txt:194 (include) CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769 (message): Imported targets not available for Boost version 106501 Call Stack (most recent call first): /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501 (_Boost_MISSING_DEPENDENCIES) cmake/3rdPartyTools.cmake:526 (find_package) CMakeLists.txt:194 (include) CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769 (message): Imported targets not available for Boost version 106501 Call Stack (most recent call first): /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501 (_Boost_MISSING_DEPENDENCIES) cmake/3rdPartyTools.cmake:526 (find_package) CMakeLists.txt:194 (include) CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769 (message): Imported targets not available for Boost version 106501 Call Stack (most recent call first): /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501 (_Boost_MISSING_DEPENDENCIES) cmake/3rdPartyTools.cmake:526 (find_package) CMakeLists.txt:194 (include) CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769 (message): Imported targets not available for Boost version 106501 Call Stack (most recent call first): /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501 (_Boost_MISSING_DEPENDENCIES) cmake/3rdPartyTools.cmake:526 (find_package) CMakeLists.txt:194 (include) CMake Warning at /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:769 (message): Imported targets not available for Boost version 106501 Call Stack (most recent call first): /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:873 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake-3.9/Modules/FindBoost.cmake:1501 (_Boost_MISSING_DEPENDENCIES) cmake/3rdPartyTools.cmake:526 (find_package) CMakeLists.txt:194 (include) -- Boost version: 1.65.1 -- Found the following Boost libraries: -- 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. -- The following libraries were found on your system, but are not being used: 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. -- Building the GTI version of pmemd.cuda -- Generating amber source scripts -- Configuring subdirs... -- FFTW: compiler supports stack alignment: TRUE -- Found bash: /bin/bash -- netcdf-fortran: Detected TS29113 support in Fortran compiler -- Reticulating splines... 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 -- 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 -- ---using installed: ------------------------------------------------------ -- blas - for fundamental linear algebra calculations -- lapack - for fundamental linear algebra calculations -- zlib - for various compression and decompression tasks -- libbz2 - for bzip2 compression in cpptraj -- libm - for fundamental math routines if they are not contained in the C library -- perlmol - chemistry library used by FEW -- ---disabled: ------------------------------------------------ -- c9x-complex - used as a support library on systems that do not have C99 complex.h support -- readline - used for the console functionality of cpptraj -- 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 -- nccl - NVIDIA parallel GPU communication library -- Features: -- MPI: OFF -- 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 -- Install location: /home/sks/Desktop/SUCHETANA/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 gpu_utils 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 - In-development programs are disabled. -- pymdgx - In-development programs are disabled. -- ************************************************************************** -- 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/sks/Desktop/SUCHETANA/amber20//amber.sh file in your shell. Consider adding the line -- test -f /home/sks/Desktop/SUCHETANA/amber20//amber.sh && source /home/sks/Desktop/SUCHETANA/amber20//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /home/sks/Desktop/SUCHETANA/amber20//amber.csh file in your shell. Consider adding the line -- test -f /home/sks/Desktop/SUCHETANA/amber20//amber.csh && source /home/sks/Desktop/SUCHETANA/amber20//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /home/sks/Desktop/SUCHETANA/amber20/ -- Configuring done -- Generating done -- Build files have been written to: /home/sks/Desktop/SUCHETANA/amber20_src/build If the cmake build report looks OK, you should now do the following: make install source /home/sks/Desktop/SUCHETANA/amber20/amber.sh Consider adding the last line to your login startup script, e.g. ~/.bashrc Output of make install: After 74%, this came up: Building NVCC (Device) object AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/cpptraj_cuda_routines_generated_GistCudaSetup.cu.o In file included from /usr/local/cuda-9.0/include/host_config.h:50:0, from /usr/local/cuda-9.0/include/cuda_runtime.h:78, from :0: /usr/local/cuda-9.0/include/crt/host_config.h:119:2: error: #error -- unsupported GNU version! gcc versions later than 6 are not supported! #error -- unsupported GNU version! gcc versions later than 6 are not supported! ^~~~~ CMake Error at cpptraj_cuda_routines_generated_GistCudaSetup.cu.o.RELEASE.cmake:220 (message): Error generating /home/sks/Desktop/SUCHETANA/amber20_src/build/AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir//./cpptraj_cuda_routines_generated_GistCudaSetup.cu.o AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/build.make:84: recipe for target 'AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/cpptraj_cuda_routines_generated_GistCudaSetup.cu.o' failed make[2]: *** [AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/cpptraj_cuda_routines_generated_GistCudaSetup.cu.o] Error 1 CMakeFiles/Makefile2:6010: recipe for target 'AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/all' failed make[1]: *** [AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/all] Error 2 Makefile:151: recipe for target 'all' failed make: *** [all] Error 2