On Wed, May 20, 2020, 23:42 Pragati Sharma <[email protected]> wrote:
> Thanks Christoph, Adding -DCMAKE_DISABLE_FIND_PACKAGE_LLVM=ON. to cmake > worked. but then a new error came in next "make" step. > *make -j8* > Screen output: > > /usr/bin/ld: cannot find -lmkl_core > Seems something is wrong with your mkl installation, just disable the usage with -DCMAKE_DISABLE_FIND_PACKAGE_MKL=on /usr/bin/ld: cannot find /apps/FFTW/fftw-3.3.8/lib: File format not > recognized > The problem is the value of FFTW3_LIBRARY you specified is wrong, it needs to be the location of the library itself. collect2: error: ld returned 1 exit status > tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:618: recipe for > target 'tools/src/libtools/libvotca_tools.so.7' failed > make[2]: *** [tools/src/libtools/libvotca_tools.so.7] Error 1 > CMakeFiles/Makefile2:214: recipe for target > 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed > make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2 > Makefile:129: recipe for target 'all' failed > make: *** [all] Error 2 > > Thank you in advance for your time. > Pragati > > On Wed, May 20, 2020 at 6:15 PM Christoph Junghans <[email protected]> > wrote: > >> On Wed, May 20, 2020 at 6:41 AM Pragati Sharma <[email protected]> >> wrote: >> > >> > 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 >> Something seems to be wrong with your LLVM installation. try to add >> -DCMAKE_DISABLE_FIND_PACKAGE_LLVM=ON. >> >> Christoph >> > 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 >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > You received this message because you are subscribed to the Google >> Groups "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> an email to [email protected]. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/da59f684-c0e1-4088-86af-ec12610ada8f%40googlegroups.com >> . >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to 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