Hello members of the Amber community,
I am currently trying to install Amber22 on Ubuntu 22.04. I ran into a similar issue as mentioned in
http://archive.ambermd.org/202212/0024.html, and, as advised by the reply, I commented out lines 329 (and additionally line 345) in
AmberTools/src/fftw-3.3/api/CMakeLists.txt
However, the installation still had errors. I am posting the output here for clarity. Any advice on how to move forward would be appreciated. Thanks
Output:
-- **************************************************************************
-- Starting configuration of Amber version 22.0.0...
-- CMake Version: 3.22.1
-- 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
-- Miniconda is installed in the build directory!
-- Could NOT find X11 (missing: X11_X11_INCLUDE_PATH 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
-- [1;34mRunning updater...[0m
-- >>> Preparing to apply updates... please wait.
-- >>> No new updates available for AmberTools 22
-- >>> No new updates available for Amber 22
-- [1;34mUpdater done. If you want to install updates, then set the APPLY_UPDATES variable to true.[0m
-- Checking whether to use built-in libraries...
-- Could NOT find Readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY 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 /usr/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 /usr/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 /usr/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: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY 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)
-- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS 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 Protobuf_INCLUDE_DIR)
-- 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 ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR)
-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
-- 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 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.
-- KMMD not added to 3RDPARTY_SUBDIRS :
-- : ucpp-1.3;cpptraj/src/readline;fftw-3.3
-- Generating amber source scripts
-- Configuring subdirs...
-- FFTW: compiler supports stack alignment: TRUE
CMake Error at AmberTools/src/fftw-3.3/api/CMakeLists.txt:10 (math):
math cannot parse the expression: " * 8": syntax error, unexpected
exp_TIMES (2).
-- Found bash: /usr/bin/bash
-- netcdf-fortran: Detected TS29113 support in Fortran compiler
CMake Error at cmake/Shorthand.cmake:96 (if):
if given arguments:
"(" "NOT" "FOUNDANY" ")" "AND" "EQUAL" "1"
Unknown arguments specified
Call Stack (most recent call first):
AmberTools/src/netcdf-fortran-4.4.4/MatchNetcdfFortranTypes.cmake:34 (test)
AmberTools/src/netcdf-fortran-4.4.4/MatchNetcdfFortranTypes.cmake:51 (find_c_type_with_size)
AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:421 (include)
-- Configuring incomplete, errors occurred!
See also "/home/hassan/Downloads/amber22_src/build/CMakeFiles/CMakeOutput.log".
See also "/home/hassan/Downloads/amber22_src/build/CMakeFiles/CMakeError.log".
If the cmake build report looks OK, you should now do the following:
make install
source /home/hassan/Downloads/amber22/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
Prateek Bansal
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Received on Fri Mar 10 2023 - 08:30:02 PST
