Dear Votca users/developers,
I am trying to build votca on my machine using cmake and following the
instructions provided in the README.md file.
Briefly, I get into the master branch directory and create a build
directory and enter it (mkdir build && cd build).
I then run the cmake command as follows:
cmake -DBUILD_CSGAPPS=ON -DFFTW3_INCLUDE_DIR=/apps/FFTW/fftw-3.3.8/include
-DFFTW3_LIBRARY=/apps/FFTW/fftw-3.3.8/lib
-DGROMACS_INCLUDE_DIR=/apps/GROMACS/gromacs-2019.0_tmpi/include
-DGROMACS_LIBRARY=/apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so
-DCMAKE_INSTALL_PREFIX=/apps/VOTCA/votca-wdgromacs/ ..
however I get the following errors which I can't understnd.
Am I missing anything?
Could you please help me to solve the problem?
This is the output of cmake:
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS-Wall
-- Performing Test COMPILER_SUPPORTS-Wall - Success
-- Performing Test COMPILER_SUPPORTS-Wextra
-- Performing Test COMPILER_SUPPORTS-Wextra - Success
-- Performing Test COMPILER_SUPPORTS-Wpedantic
-- Performing Test COMPILER_SUPPORTS-Wpedantic - Success
-- Performing Test COMPILER_SUPPORTS-Wshadow
-- Performing Test COMPILER_SUPPORTS-Wshadow - Success
-- Performing Test COMPILER_SUPPORTS-Wconversion
-- Performing Test COMPILER_SUPPORTS-Wconversion - Success
-- Found Git: /usr/bin/git (found version "2.7.4")
-- Check size of int
-- Check size of int - done
-- Found MKL: /opt/intel/mkl/include
-- 'Intel OpenMP' used for MKL parallelisation
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.58.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Found Eigen3: /usr/local/share/eigen3/cmake
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Checking for module 'fftw3'
-- No package 'fftw3' found
-- Found FFTW3: /apps/FFTW/fftw-3.3.8/lib
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stack
-- Looking for C++ include stack - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Found EXPAT: /usr/lib/x86_64-linux-gnu/libexpat.so (found version
"2.1.0")
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE)
-- txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE
-- Found UnixCommands: /bin/bash
-- Boost version: 1.58.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Found Eigen3: /usr/local/share/eigen3/cmake
-- Found VOTCA_TOOLS:
-- Checking for module 'libgromacs_d'
-- No package 'libgromacs_d' found
-- Checking for module 'libgromacs'
-- Found libgromacs, version 2019
-- Looking for c++ gmx_version in
/apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so
-- Looking for c++ gmx_version in
/apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so - found
-- Looking for c++ gmx_is_single_precision in
/apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so
-- Looking for c++ gmx_is_single_precision in
/apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so - found
-- Looking for c++ gmx_is_double_precision in
/apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so
-- Looking for c++ gmx_is_double_precision in
/apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so - not found
-- Found GROMACS: /apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so
(found suitable version "2019.0", minimum required is "2019")
-- Could NOT find GMX (missing: GMX_EXECUTABLE)
-- Looking for C++ include algorithm
-- Looking for C++ include algorithm - found
-- Looking for C++ include iomanip
-- Looking for C++ include iomanip - found
-- Looking for C++ include numeric
-- Looking for C++ include numeric - found
-- Looking for C++ include cstdlib
-- Looking for C++ include cstdlib - found
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5:
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
(found version "1.8.16") found components: C
-- Could NOT find LMP (missing: LMP_EXECUTABLE)
-- Found VOTCA_CSG:
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.11") found
components: doxygen missing components: dot
-- Could NOT find SPHINX (missing: SPHINX_EXECUTABLE)
CMake Error at /usr/share/llvm-3.8/cmake/LLVMConfig.cmake:178 (include):
include could not find load file:
/usr/share/llvm/cmake/LLVMExports.cmake
Call Stack (most recent call first):
CMakeLists.txt:106 (_find_package)
share/format/CMakeLists.txt:1 (find_package)
CMake Error at /usr/share/llvm-3.8/cmake/LLVMConfig.cmake:181 (include):
include could not find load file:
/usr/share/llvm/cmake/LLVM-Config.cmake
Call Stack (most recent call first):
CMakeLists.txt:106 (_find_package)
share/format/CMakeLists.txt:1 (find_package)
-- The following features have been enabled:
* BUILD_CSGAPPS, Build extra app using csg
* BUILD_MANPAGES, Build manpages (disable for cross-compile)
* INSTALL_RC_FILES, Install votca rc files (VOTCARC.bash etc.)
-- The following OPTIONAL packages have been found:
* Git
Generated version for development version
* MKL
Enables accelerated performance with MKL
* UnixCommands
Used to build manpages
* Doxygen
Needed to build API documentation
* LLVM
Needed for automatic code formatting with clang-format
-- The following RECOMMENDED packages have been found:
* FFTW3
Enables FFT functionality
* PkgConfig
Used to detect fftw package
Used to detect gromacs package
* GROMACS (required version >= 2019)
Used to read/write gromacs data files
* HDF5
Used to read h5md data files
-- The following REQUIRED packages have been found:
* EXPAT
Used for XML parsing
* Boost (required version >= 1.53.0)
Extended C++ libraries
* Eigen3 (required version >= 3.3.0)
C++ vector data structures
* Threads
Used for thread parallelization
-- The following features have been disabled:
* BUILD_XTP, Build xtp module
* BUILD_CSG_MANUAL, Build csg-manual
* ENABLE_TESTING, Enable unit tests
* ENABLE_RPATH_INJECT, Inject rpath into executables
* BUILD_OWN_GROMACS, Build an internal version of gromacs
* ENABLE_REGRESSION_TESTING, Enable regression tests
-- The following OPTIONAL packages have not been found:
* TXT2TAGS
Used to build manpages
* Clang
Needed for automatic code formatting with clang-format
-- Configuring incomplete, errors occurred!
I have attached a cmakeError.log file also
Thank you in advance for your time.
Pragati
--
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Determining if the pthread_create exist failed with the following output:
Change Dir: /home/pragati/software/votca/votca/build/CMakeFiles/CMakeTmp
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/usr/bin/make -f CMakeFiles/cmTC_ef4c7.dir/build.make
CMakeFiles/cmTC_ef4c7.dir/build
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/home/pragati/software/votca/votca/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
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CMakeFiles/cmTC_ef4c7.dir/link.txt --verbose=1
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Change Dir: /home/pragati/software/votca/votca/build/CMakeFiles/CMakeTmp
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