Dear Amber,
I'm struggling to install Amber 22 on a Linux running Linux Mint.
The output of cat /etc/os-release is:
NAME="Linux Mint"
VERSION="18.1 (Serena)"
ID=linuxmint
ID_LIKE=ubuntu
PRETTY_NAME="Linux Mint 18.1"
VERSION_ID="18.1"
HOME_URL="
http://www.linuxmint.com/"
SUPPORT_URL="
http://forums.linuxmint.com/"
BUG_REPORT_URL="
http://bugs.launchpad.net/linuxmint/"
VERSION_CODENAME=serena
UBUNTU_CODENAME=xenial
and when I run ./run_cmake from the amber22_src/build directory, I get the following output:
-- **************************************************************************
-- Starting configuration of Amber version 22.0.0...
-- CMake Version: 3.22.2
-- 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
CMake Warning at /home/local/CAMPUS/nngha/apps/cmake/cmake/share/cmake-3.22/Modules/FindCUDA.cmake:1054 (message):
Expecting to find librt for libcudart_static, but didn't find it.
Call Stack (most recent call first):
cmake/CudaConfig.cmake:11 (find_package)
CMakeLists.txt:120 (include)
-- Miniconda is installed in the build directory!
-- Could NOT find X11 (missing: X11_X11_LIB)
Couldn't find the X11 development libraries!
To search for them try the command: locate libXt
On new Fedora install the libXt-devel libXext-devel libX11-devel libICE-devel libSM-devel packages.
On old Fedora install the xorg-x11-devel package.
On RedHat install the XFree86-devel package.
On Ubuntu install the xorg-dev and xserver-xorg packages.
-- 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...
-- 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.
CMake Warning (dev) at /home/local/CAMPUS/nngha/apps/cmake/cmake/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (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:223 (find_package)
CMakeLists.txt:205 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at /home/local/CAMPUS/nngha/apps/cmake/cmake/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (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:223 (find_package)
CMakeLists.txt:205 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at /home/local/CAMPUS/nngha/apps/cmake/cmake/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (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:223 (find_package)
CMakeLists.txt:205 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find CMath (missing: CMath_WORKS)
-- Could NOT find MKL (missing: CMath_FOUND MKL_WORKS MKL_FORTRAN_WORKS)
-- 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)
-- Cannot search for FFTW Fortran headers because the serial headers were not found
-- Could NOT find FFTW (missing: 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 Protobuf (missing: Protobuf_LIBRARIES) (found version "2.6.1")
-- 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")
-- Could NOT find CMath (missing: CMath_WORKS)
-- 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)
-- 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: 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.
-- KMMD not added to 3RDPARTY_SUBDIRS :
-- : cpptraj/src/readline;fftw-3.3
-- Generating amber source scripts
-- Configuring subdirs...
-- Check size of int
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
CMath_LIBRARIES
linked by target "cmTC_31af9" in directory /tank/amber/amber/amber22/amber22_src/build/CMakeFiles/CMakeTmp
CMake Error at /home/local/CAMPUS/nngha/apps/cmake/cmake/share/cmake-3.22/Modules/CheckTypeSize.cmake:139 (try_compile):
Failed to generate test project build system.
Call Stack (most recent call first):
/home/local/CAMPUS/nngha/apps/cmake/cmake/share/cmake-3.22/Modules/CheckTypeSize.cmake:270 (__check_type_size_impl)
cmake/Shorthand.cmake:206 (check_type_size)
AmberTools/src/fftw-3.3/CMakeLists.txt:329 (check_all_types)
-- Configuring incomplete, errors occurred!
See also "/tank/amber/amber/amber22/amber22_src/build/CMakeFiles/CMakeOutput.log".
See also "/tank/amber/amber/amber22/amber22_src/build/CMakeFiles/CMakeError.log".
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
Any help to get beyond that CMath_LIBRARIES problem and any other apparent issues from this output would be welcome.
Many thanks,
Nahoum anthony
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Received on Tue Dec 06 2022 - 07:00:03 PST
