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-- ************************************************************************** -- Starting configuration of Amber version 20.0.0... -- CMake Version: 3.19.1 -- For how to use this build system, please read this wiki: -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake -- For a list of important CMake variables, check here: -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options -- ************************************************************************** -- Amber source found, building AmberTools and Amber -- MPI C Compiler: /usr/local/mpich-3.2.1/bin/mpicc -- MPI CXX Compiler: /usr/local/mpich-3.2.1/bin/mpicxx -- MPI Fortran Compiler: /usr/local/mpich-3.2.1/bin/mpif90 -- If these are not the correct MPI wrappers, then set MPI_<language>_COMPILER to the correct wrapper and reconfigure. -- Found and removed RPATH control flags from MPI flags -- Found and removed RPATH control flags from MPI flags -- Found and removed RPATH control flags from MPI flags -- Found and removed RPATH control flags from MPI flags -- Found and removed RPATH control flags from MPI flags -- Found and removed RPATH control flags from MPI flags -- 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. CMake Warning (dev) at /usr/local/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (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. CMake Warning (dev) at /usr/local/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (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. CMake Warning (dev) at /usr/local/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (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. -- 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 FFTW_LIBRARY_MPI FFTW_INCLUDES_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. -- 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) CMake Warning (dev) at /usr/local/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (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/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (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. -- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5") -- 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. -- 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. -- Generating amber source scripts -- Configuring subdirs... -- FFTW: compiler supports stack alignment: TRUE -- Found bash: /usr/bin/bash -- netcdf-fortran: Detected TS29113 support in Fortran compiler -- Reticulating splines... ** (gedit:1471): WARNING **: 16:05:58.932: Error querying file info: Error when getting information for file “/home/exx/Downloads/amber20_src/build/config.h.tmp”: No such file or directory 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 -- xblas - used for high-precision linear algebra calculations -- boost - C++ support library -- pnetcdf - used by cpptraj for parallel trajectory output -- ---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 -- mpi4py - MPI support library for MMPBSA.py -- 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 -- Features: *-- MPI: OFF -- OpenMP: OFF -- CUDA: OFF * -- Build Shared Libraries: ON -- Build GUI Interfaces: ON -- Build Python Programs: ON -- -Python Interpreter: Internal Miniconda (version 3.8) -- 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: /home/exx/Downloads/amber20/ -- Installation of Tests: ON -- 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 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. -- 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/exx/Downloads/amber20//amber.sh file in your shell. Consider adding the line -- test -f /home/exx/Downloads/amber20//amber.sh && source /home/exx/Downloads/amber20//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /home/exx/Downloads/amber20//amber.csh file in your shell. Consider adding the line -- test -f /home/exx/Downloads/amber20//amber.csh && source /home/exx/Downloads/amber20//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /home/exx/Downloads/amber20/ -- Configuring done -- Generating done -- Build files have been written to: /home/exx/Downloads/amber20_src/build If the cmake build report looks OK, you should now do the following: make install source /home/exx/Downloads/amber20/amber.sh Consider adding the last line to your login startup script, e.g. ~/.bashrc (base) [exx.c107739 build]$ -- Regards, Dr. Vaibhav A. Dixit, Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. AND Assistant Professor, Department of Pharmacy, ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄ Birla Institute of Technology and Sciences Pilani (BITS-Pilani), VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031. India. Phone No. +91 1596 255652, Mob. No. +91-7709129400, Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ ORCID ID: https://orcid.org/0000-0003-4015-2941 http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra P Please consider the environment before printing this e-mail _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Dec 10 2020 - 03:00:02 PST