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?
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
>
--
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