On Fri, May 21, 2021 at 3:51 PM Arash Elahi <[email protected]> wrote: > > Hi All > I'm trying to install VOTCA, but I'm facing errors I couldn't resolve after > days of struggling with this error in the title. > My OS version: Ubuntu 16.04 > My local Gromcas: 2019.3 > I appreciate your helps regarding this issue very much > VOTCA_install$ cmake -Bbuilddir -DBUILD_XTP=OFF -DBUILD_OWN_LIBINT=ON > -DCMAKE_INSTALL_PREFIX=${prefix} ENABLE_TESTING=ON votca If you don't need xtp, you also don't need to build libint.
> -- MKL: Thread Layer(Intel OpenMP) Interface(4-byte Integer) > -- Found Boost: /usr/include (found suitable version "1.58.0", minimum > required is "1.53.0") found components: program_options filesystem system > -- MKL: Thread Layer(Intel OpenMP) Interface(4-byte Integer) > -- Found Eigen3: /usr/lib/cmake/eigen3 > -- Found Boost: /usr/include (found suitable version "1.58.0", minimum > required is "1.53.0") found components: program_options filesystem system > regex > -- Found Eigen3: /usr/lib/cmake/eigen3 > -- Found VOTCA_TOOLS: > -- Checking for module 'libgromacs_d' > -- No package 'libgromacs_d' found > -- Found HDF5: > $HOME/anaconda3/lib/libhdf5_cpp.so;$HOME/anaconda3/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;$HOME/anaconda3/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so > (found version "1.8.17") found components: CXX > -- Could NOT find LMP (missing: LMP_EXECUTABLE) > -- Could NOT find CLANG_FORMAT: Found unsuitable version "6.0.1", but > required is at least "11" (found /opt/moose/llvm-6.0.1/bin/clang-format) > -- The following features have been enabled: > > * BUILD_OWN_LIBINT, Build an internal version of libint > * 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 > * OpenMP > * MKL > Enables accelerated performance with MKL > * TXT2TAGS > Used to build manpages > * UnixCommands > Used to build manpages > * Python (required version >= 3) > Used to build documentation files > * Doxygen > Needed to build API documentation > > -- The following RECOMMENDED packages have been found: > > * PkgConfig > Used to detect gromacs package > * GROMACS (required version >= 2018) > 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 > * ENABLE_TESTING, Enable unit tests > * ENABLE_RPATH_INJECT, Inject rpath into executables > * BUILD_OWN_GROMACS, Build an internal version of gromacs > * BUILD_CSGAPPS, Install extra app using csg > * ENABLE_REGRESSION_TESTING, Enable regression tests > > -- The following OPTIONAL packages have not been found: > > * CLANG_FORMAT (required version >= 11) > > -- Configuring done > -- Generating done > -- Build files have been written to: VOTCA_install/builddir > VOTCA_install$ cmake --build builddir/ --parallel 12 > /usr/bin/ld: > $HOME/Downloads/amber20_src/build/AmberTools/src/boost/stage/lib/libboost_program_options.a(cmdline.o): > relocation R_X86_64_32S against `.rodata' can not be used when making a > shared object; recompile with -fPIC The error message basically says it, you need a shared (or version compiled with -fPIC) of the boost library. If you don't want to compile boost yourself, just try to use spack instead, https://github.com/votca/votca/blob/master/share/doc/INSTALL.rst#spack Christoph > $HOME/Downloads/amber20_src/build/AmberTools/src/boost/stage/lib/libboost_program_options.a: > error adding symbols: Bad value > collect2: error: ld returned 1 exit status > tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:681: recipe for > target 'tools/src/libtools/libvotca_tools.so.2021' failed > make[2]: *** [tools/src/libtools/libvotca_tools.so.2021] Error 1 > CMakeFiles/Makefile2:682: recipe for target > 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed > make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... > checking build system type... x86_64-pc-linux-gnu > checking host system type... x86_64-pc-linux-gnu > checking target system type... x86_64-pc-linux-gnu > Using standard ordering of cartesian Gaussians > Using standard ordering of solid harmonic Gaussians > Will generate standard shell quartet sets > Will generate composite evaluators for multiple integral types > Shell sets will be unrolled up to size 100 > Will generate single evaluator type > Will not generate FMA instructions > Will copy integrals to the buffer > FLOP counter will not be supported > Profiling instrumentation disabled > Will support contracted integrals > checking whether make sets $(MAKE)... yes > checking whether ln -s works... yes > checking for a BSD-compatible install... /usr/bin/install -c > checking whether the C++ compiler works... yes > checking for C++ compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C++ compiler... yes > checking whether mpicxx accepts -g... yes > checking how to run the C++ preprocessor... mpicxx -E > checking for ar... ar > checking for perl... perl > checking for gnutar... no > checking for tar... tar > checking for python... python > checking for doxygen... /opt/moose/doxygen-1.8.14/bin/doxygen > checking for pdflatex... no > checking for pslatex... no > checking for dvips... no > checking for latex... no > checking for latex2html... no > checking for bibtex... no > configure: WARNING: C++ optimization options are not given! For optimum > performance give CXXGENFLAGS or use --with-cxxgen-optflags configure option > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking limits.h usability... yes > checking limits.h presence... yes > checking for limits.h... yes > checking for stdint.h... (cached) yes > checking for posix_memalign... yes > checking CXX for general C++11 support... yes > checking CXX for shared_ptr... yes > checking CXX for std::make_shared and std::allocate_shared... yes > checking CXX for type_traits... yes > checking CXX for array... yes > checking CXXGEN for general C++11 support... yes > checking gmpxx.h usability... no > checking gmpxx.h presence... no > checking for gmpxx.h... no > configure: error: cannot link against GMP C++ library. Please get the latest > GMP with support for C++. It can be obtained at gmplib.org . > CMakeFiles/Libint_build.dir/build.make:91: recipe for target > 'libint/src/Libint_build-stamp/Libint_build-configure' failed > make[2]: *** [libint/src/Libint_build-stamp/Libint_build-configure] Error 1 > CMakeFiles/Makefile2:561: recipe for target 'CMakeFiles/Libint_build.dir/all' > failed > make[1]: *** [CMakeFiles/Libint_build.dir/all] Error 2 > Makefile:135: recipe for target 'all' failed > make: *** [all] Error 2 > > -- > 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/77108190-c3b4-4c91-b7ed-57f876b03606n%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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7CBXqLCsnt25p6kQ7-_9xV-yT35nCURvaVH0UaWPv6-Q%40mail.gmail.com.
