Hi All,
I am getting an error message while running a file run_cmake. Below the content in the run_cmake and error message
cmake $AMBER_PREFIX/amber20_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
-DCOMPILER=GNU \
-DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
-DINSTALL_TESTS=TRUE \
2>&1 | tee cmake.log
./run_cmake
-- **************************************************************************
-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.8.2
-- 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 found, building AmberTools and Amber
-- Miniconda is installed in the build directory!
-- Found perl make: /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 var iable to true.
-- Checking whether to use built-in libraries...
-- Could NOT find Readline (missing: READLINE_WORKS)
-- Unable to locate MKL_HOME for your system. To use MKL, set MKL_HOME to point to your MKL installation location.
-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY MKL_WORKS MKL_FORTRAN_WORKS)
-- 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 (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.
-- Looking for dsaupd in libarpack.so
-- Looking for dsaupd in libarpack.so - found
-- Looking for arsecond in libarpack.so
-- Looking for arsecond in libarpack.so - not found
-- Detailed information about why this check failed can be found in /data/Amber/amber20_src/build/CMakeFiles/CMakeError.log
-- Found ARPACK: /usr/lib64/libarpack.so
-- 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 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")
-- Checking for perl module Chemistry::Mol
-- Checking for perl module Chemistry::Mol - failed
-- Failed to find Perl modules: Chemistry::Mol (missing: PERLMODULES_CHEMISTRY_MOL_MODULE)
-- Boost version: 1.53.0
-- Found the following Boost libraries:
-- thread
-- system
-- program_options
-- iostreams
-- regex
-- timer
-- chrono
-- filesystem
-- graph
-- date_time
-- atomic
CMake Warning at cmake/3rdPartyTools.cmake:560 (find_package):
Could not find a package configuration file provided by "MBX" (requested
version 0.2.3) with any of the following names:
MBXConfig.cmake
mbx-config.cmake
Add the installation prefix of "MBX" to CMAKE_PREFIX_PATH or set "MBX_DIR"
to a directory containing one of the above files. If "MBX" provides a
separate development package or SDK, be sure it has been installed.
Call Stack (most recent call first):
CMakeLists.txt:191 (include)
-- Could not find MBX. To locate it, add its install dir to the prefix path.
CMake Warning at cmake/3rdPartyTools.cmake:575 (find_package):
Could not find a package configuration file provided by "tng_io" with any
of the following names:
tng_ioConfig.cmake
tng_io-config.cmake
Add the installation prefix of "tng_io" to CMAKE_PREFIX_PATH or set
"tng_io_DIR" to a directory containing one of the above files. If "tng_io"
provides a separate development package or SDK, be sure it has been
installed.
Call Stack (most recent call first):
CMakeLists.txt:191 (include)
-- 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: 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=<names>.
-- Alternatively, you can request that Amber link to all libraries it finds using -DTRUST_SYSTEM_LIBS=TRUE.
-- System arpack is missing the arsecond_ function. That function will be built inside amber
-- 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: /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: -----------------------------------------------------
-- blas - for fundamental linear algebra calculations
-- lapack - 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
-- tng_io - enables GROMACS tng trajectory input in cpptraj
-- perlmol - chemistry library used by FEW
-- ---using installed: ------------------------------------------------------
-- arpack - 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
-- ---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: ON
-- -Python Interpreter: Internal Miniconda (version 3.9)
-- Build Perl Programs: ON
-- Build configuration: RELEASE
-- Target Processor: x86_64
-- Build Documentation: OFF
-- Sander Variants: normal LES API LES-API
-- Install location: /data/Amber/amber20/
-- Installation of Tests: ON
-- Compilers:
-- C: GNU 4.8.5 (/bin/gcc)
-- CXX: GNU 4.8.5 (/bin/g++)
-- Fortran: GNU 4.8.5 (/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 python_site_packages pytraj reduce rism sander saxs sebomd sff sqm xray xtalutil
-- NOT Building Tools:
-- 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
-- /data/Amber/amber20//amber.sh file in your shell. Consider adding the line
-- test -f /data/Amber/amber20//amber.sh && source /data/Amber/amber20//amber.sh
-- to your startup file (e.g., ~/.bashrc)
--
-- If you use a C shell (e.g., csh, tcsh), source the
-- /data/Amber/amber20//amber.csh file in your shell. Consider adding the line
-- test -f /data/Amber/amber20//amber.csh && source /data/Amber/amber20//amber.csh
-- to your startup file (e.g., ~/.cshrc)
--
-- Amber will be installed to /data/Amber/amber20/
-- Configuring done
-- Generating done
-- Build files have been written to: /data/Amber/amber20_src/build
If the cmake build report looks OK, you should now do the following:
make install
source /data/Amber/amber20/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
Regards
Suguna
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Received on Tue Dec 21 2021 - 11:30:02 PST
