On Tue, Jun 1, 2021 at 11:10 AM Arash Elahi <[email protected]> wrote: > > Thank you dear Christoph for your reply. > Spack was very helpful for the installation, but there's hdf5 inconsistency > when I use smack, when I want to run the csg executables, let's say csg_map. > installing hdf5 locally did not make it work out yet. Is it what I needed to > do? We already know about this issue: https://github.com/votca/csg/issues/684, but haven't fixed it yet, as it is only a warning, so please ignore it for now.
Christoph > Thanks > Best > HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0: > #000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset > major: Invalid arguments to routine > minor: Inappropriate type > HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0: > #000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset > major: Invalid arguments to routine > minor: Inappropriate type > HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0: > #000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset > major: Invalid arguments to routine > minor: Inappropriate type > HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0: > ..... > > > On Friday, May 21, 2021 at 4:55:10 PM UTC-5 Christoph Junghans wrote: >> >> 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/4875b995-8512-4140-a81a-34798f089022n%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/CAHG27e5SW%2BmVXMsUZ0CgP3RicRCNR-kNJDMhfo5WipJATOmsPg%40mail.gmail.com.
