Hi Christoph, I really appreciate your input.
Indeed, there was a problem with the boost. I loaded the wrong one. I also unloaded the modules. Now, I have used the one compiled with gcc-8. I overcame the preview error, but now I am getting one when linking the executable csg_gmxtopol. I thought it was related to the fftw libraries, I build it with both fftw-serial(which I think is the one prefered in VOTCA (?)) and fftw-mpi (this is the one it is used in the gromacs installation of the supercomputer), but I got the same error message. Below is the last part of the output for cmake --build builddir --verbose in both cases: *fftw-serial* ...... [ 66%] Linking CXX executable csg_gmxtopol cd /u/forero/src/votca/builddir/csg/src/tools && /u/system/soft/SLE_12/packages/x86_64/cmake/3.15.2/bin/cmake -E cmake_link_script CMakeFiles/csg_gmxtopol.dir/link.txt --verbose=1 /mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/bin/g++ -Wall -Wextra -Wpedantic -Wshadow -Wconversion -O3 -DNDEBUG CMakeFiles/csg_gmxtopol.dir/csg_gmxtopol.cc.o -o csg_gmxtopol -Wl,-rpath,/mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib:/mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64:/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0/3.3.8/lib: ../libcsg/libvotca_csg.a /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a /mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib/libhdf5.so /usr/lib64/libz.so /usr/lib64/libdl.so -lm ../../../tools/src/libtools/libvotca_tools.a /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0 /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0 /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0 /usr/lib64/libexpat.so -lm /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0/3.3.8/lib/libfftw3.so /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0 /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0 /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0 -lpthread /usr/bin/ld: /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(binaryinformation.cpp.o): in function `gmx::printBinaryInformation(gmx::TextWriter*, gmx::IProgramContext const&, gmx::BinaryInformationSettings const&)': binaryinformation.cpp:(.text+0x706): undefined reference to `fftwf_version' collect2: error: ld returned 1 exit status csg/src/tools/CMakeFiles/csg_gmxtopol.dir/build.make:98: recipe for target 'csg/src/tools/csg_gmxtopol' failed gmake[2]: *** [csg/src/tools/csg_gmxtopol] Error 1 gmake[2]: Leaving directory '/cobra/u/forero/src/votca/builddir' CMakeFiles/Makefile2:644: recipe for target 'csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all' failed gmake[1]: *** [csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all] Error 2 gmake[1]: Leaving directory '/cobra/u/forero/src/votca/builddir' Makefile:129: recipe for target 'all' failed gmake: *** [all] Error 2 *fftw-mpi* ..... [ 66%] Linking CXX executable csg_gmxtopol cd /u/forero/src/votca/builddir/csg/src/tools && /u/system/soft/SLE_12/packages/x86_64/cmake/3.15.2/bin/cmake -E cmake_link_script CMakeFiles/csg_gmxtopol.dir/link.txt --verbose=1 /mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/bin/g++ -Wall -Wextra -Wpedantic -Wshadow -Wconversion -O3 -DNDEBUG CMakeFiles/csg_gmxtopol.dir/csg_gmxtopol.cc.o -o csg_gmxtopol -Wl,-rpath,/mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib:/mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64:/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib: ../libcsg/libvotca_csg.a /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a /mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib/libhdf5.so /usr/lib64/libz.so /usr/lib64/libdl.so -lm ../../../tools/src/libtools/libvotca_tools.a /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0 /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0 /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0 /usr/lib64/libexpat.so -lm /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.so /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0 /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0 /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0 -lpthread /usr/bin/ld: /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(binaryinformation.cpp.o): in function `gmx::printBinaryInformation(gmx::TextWriter*, gmx::IProgramContext const&, gmx::BinaryInformationSettings const&)': binaryinformation.cpp:(.text+0x706): undefined reference to `fftwf_version' collect2: error: ld returned 1 exit status csg/src/tools/CMakeFiles/csg_gmxtopol.dir/build.make:98: recipe for target 'csg/src/tools/csg_gmxtopol' failed gmake[2]: *** [csg/src/tools/csg_gmxtopol] Error 1 gmake[2]: Leaving directory '/cobra/u/forero/src/votca/builddir' CMakeFiles/Makefile2:644: recipe for target 'csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all' failed gmake[1]: *** [csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all] Error 2 gmake[1]: Leaving directory '/cobra/u/forero/src/votca/builddir' Makefile:129: recipe for target 'all' failed gmake: *** [all] Error 2 I do not know what else to check. Cheers, Nancy On Saturday, 19 December 2020 at 21:26:16 UTC+1 Christoph Junghans wrote: > On Sat, Dec 19, 2020 at 9:41 AM nancyfor <[email protected]> wrote: > > > > Thanks Christoph, > > > > I have added -DBUILD_SHARED_LIBS=OFF -DBUILD_CSGAPPS=ON -DBUILD_XTP=OFF, > since I want to use the gromacs in the supercomputer. > Hmm, I tried the same locally and it worked. > > The error below usually means your boost was compiled with a compiler > that has a different cxx abi. > Looking at the path of the boost package you are using, it looks like > it was compiled with intel_19.1.1, but you are compiling votca with > gcc-8.4.0. > > I have no good solution, except you could try to not load intel/19.1.1 > impi/2019.7 mkl/2020.1 as you aren't really using any of these. > > Christoph > > > Now the output error for > > > > cmake --build builddir > > > > occurs when linking CXX executable votca_property > > > > here the last lines: (whole --verbose output attached) > > ... > > > cESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x3e): > > undefined reference to > `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, > > std::char_traits<char>, std::allocator<char> >, > std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> > >, std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&>)' > > /usr/bin/ld: ../libtools/libvotca_tools.a(application.cc.o): in function > `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, > > char const* const*)': > > > application.cc:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x1b8): > > undefined reference to > `boost::program_options::to_internal(std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&)' > > /usr/bin/ld: > application.cc:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x277): > > undefined reference to > `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, > > std::char_traits<char>, std::allocator<char> >, > std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> > > > const&)' > > collect2: error: ld returned 1 exit status > > tools/src/tools/CMakeFiles/votca_property.dir/build.make:89: recipe for > target 'tools/src/tools/votca_property' failed > > gmake[2]: *** [tools/src/tools/votca_property] Error 1 > > CMakeFiles/Makefile2:317: recipe for target > 'tools/src/tools/CMakeFiles/votca_property.dir/all' failed > > gmake[1]: *** [tools/src/tools/CMakeFiles/votca_property.dir/all] Error 2 > > Makefile:129: recipe for target 'all' failed > > gmake: *** [all] Error 2 > > > > Cheers, > > Nancy > > On Saturday, 19 December 2020 at 16:22:11 UTC+1 Christoph Junghans wrote: > >> > >> On Sat, Dec 19, 2020 at 8:05 AM nancyfor <[email protected]> wrote: > >> > > >> > Hi Christoph, > >> > > >> > I am using the following command, > >> > > >> > cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ > -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON > -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/ > > -DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a > > -DLIBXC_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/include/ > > -DLIBXC_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/lib/libxc.a > > -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix} > ../votca > >> > > >> > and the configuration show no problems. But when building it, I have > a problem with the linking of the libraries for gromacs, which are in this > cases static, there is not .so libraries available. > >> > > >> > Below is the last part of the output of > >> > cmake --build builddir --verbose > >> > > >> > I have attached the complete output in: > output_verbose_votca_19_12_2020.txt > >> > > >> > I tried to pass the -fPIC option when compiling but I think I am > doing it wrong. How this should be done? > >> > > >> > Best regards, > >> > Nancy > >> > > >> > ... > >> > /usr/bin/ld: > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(merge_sort.c.o): > > relocation R_X86_64_PC32 against symbol `memcpy@@GLIBC_2.14' can not be > used when making a shared object; recompile with -fPIC > >> > /usr/bin/ld: final link failed: nonrepresentable section on output > >> > collect2: error: ld returned 1 exit status > >> > csg/src/libcsg/CMakeFiles/votca_csg.dir/build.make:798: recipe for > target 'csg/src/libcsg/libvotca_csg.so.6' failed > >> > gmake[2]: *** [csg/src/libcsg/libvotca_csg.so.6] Error 1 > >> > gmake[2]: Leaving directory '/cobra/u/forero/src/votca/builddir' > >> > CMakeFiles/Makefile2:590: recipe for target > 'csg/src/libcsg/CMakeFiles/votca_csg.dir/all' failed > >> > gmake[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2 > >> > gmake[1]: Leaving directory '/cobra/u/forero/src/votca/builddir' > >> > Makefile:129: recipe for target 'all' failed > >> > gmake: *** [all] Error 2 > >> This error just means you cannot mix shared (.so) and static (.a) > libraries. > >> > >> You have three options: > >> - rebuild gromacs shared: using -DBUILD_SHARED_LIBS=ON when you build > gromacs > >> - have VOTCA builds its own gromacs: -DBUILD_OWN_GROMACS=ON when > building votca > >> - build VOTCA with static libs: -DBUILD_SHARED_LIBS=OFF when building > votca > >> > >> I see libxc is static, too, so you will have the same issue later when > >> building votca xtp. > >> Options here: > >> - rebuild libxc shared: using --enable-shared when building libxc > >> - build VOTCA with static libs: -DBUILD_SHARED_LIBS=OFF when building > votca > >> - don't build the xtp module (not sure if you need it): > >> -DBUILD_XTP=OFF when building votca > >> > >> Alternatively, you could use spack to install everything, see > >> https://github.com/votca/votca/blob/master/share/doc/INSTALL.rst#spack > >> > >> Christoph > >> > > >> > On Tuesday, 1 December 2020 at 15:20:46 UTC+1 nancyfor wrote: > >> >> > >> >> I think the issue with MKL is related to the gcc version, there is > not module of MKL for gcc-8. > >> >> When I succed, I will let you know. > >> >> Thank you! > >> >> Cheers > >> >> Nancy > >> >> > >> >> On Tuesday, 1 December 2020 at 15:15:11 UTC+1 Christoph Junghans > wrote: > >> >>> > >> >>> On Tue, Dec 1, 2020 at 7:11 AM nancyfor <[email protected]> wrote: > >> >>> > > >> >>> > Hi Christoph > >> >>> > Few minutes ago I was using, > >> >>> > > >> >>> > -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ > >> >>> > > >> >>> > and correctly use GNU 8.4.0 > >> >>> > > >> >>> > However, now there is something related to the > 'MKL_ThreadingLibrary_LINK_LIBRARY-NOTFOUND' > >> >>> Try to compile without MKL for now: > >> >>> -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON, if you aren't using xtp, mkl > >> >>> doesn't gain you much anyhow. > >> >>> > >> >>> Christoph > >> >>> > >> >>> > > >> >>> > this is the output for cmake --build builddir > >> >>> > > >> >>> > Scanning dependencies of target gitversion-xtp > >> >>> > Current git revision is 9b6bbd0 > >> >>> > [ 0%] Built target gitversion-xtp > >> >>> > Scanning dependencies of target gitversion > >> >>> > Current git revision is 9b6bbd0 > >> >>> > [ 0%] Built target gitversion > >> >>> > Scanning dependencies of target votca_tools > >> >>> > [ 1%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o > >> >>> > [ 1%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o > >> >>> > [ 1%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/calculator.cc.o > >> >>> > [ 2%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o > >> >>> > [ 2%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o > >> >>> > [ 2%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o > >> >>> > [ 3%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o > >> >>> > [ 3%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o > >> >>> > [ 3%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/edge.cc.o > >> >>> > [ 4%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/edgecontainer.cc.o > >> >>> > [ 4%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/elements.cc.o > >> >>> > [ 4%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/filesystem.cc.o > >> >>> > [ 5%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/globals.cc.o > >> >>> > [ 5%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o > >> >>> > [ 5%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/graph_bf_visitor.cc.o > >> >>> > [ 6%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/graph_df_visitor.cc.o > >> >>> > [ 6%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/graphalgorithm.cc.o > >> >>> > [ 6%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/graphdistvisitor.cc.o > >> >>> > [ 7%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/graphnode.cc.o > >> >>> > [ 7%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/graphvisitor.cc.o > >> >>> > [ 8%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/histogram.cc.o > >> >>> > [ 8%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/histogramnew.cc.o > >> >>> > [ 8%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o > >> >>> > [ 9%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/linspline.cc.o > >> >>> > [ 9%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/mutex.cc.o > >> >>> > [ 9%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/parcer.cc.o > >> >>> > [ 10%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/property.cc.o > >> >>> > [ 10%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o > >> >>> > [ 10%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o > >> >>> > [ 11%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/reducededge.cc.o > >> >>> > [ 11%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/reducedgraph.cc.o > >> >>> > [ 11%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o > >> >>> > [ 12%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/table.cc.o > >> >>> > [ 12%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o > >> >>> > [ 12%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o > >> >>> > [ 13%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/version.cc.o > >> >>> > gmake[2]: *** No rule to make target > 'MKL_ThreadingLibrary_LINK_LIBRARY-NOTFOUND', needed by > 'tools/src/libtools/libvotca_tools.so.6'. Stop. > >> >>> > CMakeFiles/Makefile2:256: recipe for target > 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed > >> >>> > gmake[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] > Error 2 > >> >>> > Makefile:129: recipe for target 'all' failed > >> >>> > gmake: *** [all] Error 2 > >> >>> > > >> >>> > I have attached the output for cmake --build builddir --verbose > >> >>> > > >> >>> > Thanks > >> >>> > Nancy > >> >>> > > >> >>> > On Tuesday, 1 December 2020 at 14:46:11 UTC+1 Christoph Junghans > wrote: > >> >>> >> > >> >>> >> On Tue, Dec 1, 2020 at 3:00 AM nancyfor <[email protected]> > wrote: > >> >>> >> > > >> >>> >> > Hi Christoph, > >> >>> >> > > >> >>> >> > I thought I was using gcc. I did not change anything on > purpose. So, to be a little bit more consistent, I checked again the gcc > and the boost version that worked together, and include the flag > -DCMAKE_CXX_COMPILER_ID=GNU (is this alright?) Currently I have the > following modules uploaded: > >> >>> >> > > >> >>> >> > mkl/2020.1 > >> >>> >> > gromacs/2019.4 > >> >>> >> > doxygen/1.8 > >> >>> >> > cmake/3.15 > >> >>> >> > clang/10.0 > >> >>> >> > gcc/8 > >> >>> >> > boost/1.66 > >> >>> >> > libxc/4.3.4 > >> >>> >> > fftw-serial/3.3.8 > >> >>> >> > hdf5-serial/1.8.21 > >> >>> >> > > >> >>> >> > Un run the following with the new library paths (I have > attached the CMakeOutput.log and the output from "cmake -Bbuilddir > ../votca" output_cmake_Bbuildir.txt) > >> >>> >> > > >> >>> >> > cmake -Bbuilddir -DCMAKE_CXX_COMPILER_ID=GNU > -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON > -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/ > > -DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a > > -DLIBXC_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/include/ > > -DLIBXC_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/lib/libxc.a > > -DCMAKE_INSTALL_PREFIX=${prefix} ../votca > >> >>> >> > > >> >>> >> > and again when doing > >> >>> >> > cmake --build builddir --verbose > >> >>> >> > I get an error, different from the origina one I mentioned. > The full output is in cmake_verbose.txt > >> >>> >> Thanks, the cmake log says: > >> >>> >> > >> >>> >> The C compiler identification is GNU 4.8.5 > >> >>> >> > >> >>> >> GCC 4.8.5 is unfortunately too old as it misses some C++-11 > features, > >> >>> >> you mentioned a "gcc/8" in your first email, maybe you can try > to use > >> >>> >> that one instead. I guess something like > "-DCMAKE_CXX_COMPILER=g++-8" > >> >>> >> > >> >>> >> Christoph > >> >>> >> > >> >>> >> > >> >>> >> > > >> >>> >> > Thanks > >> >>> >> > Nancy > >> >>> >> > On Monday, 30 November 2020 at 17:08:19 UTC+1 Christoph > Junghans wrote: > >> >>> >> >> > >> >>> >> >> Nancy, > >> >>> >> >> > >> >>> >> >> Are you trying to compile with gcc or icc? > >> >>> >> >> > >> >>> >> >> Could you attach the full output of "cmake -Bbuilddir > ../votca" and > >> >>> >> >> "cmake --build builddir --verbose" (mind the extra > "--verbose" here)? > >> >>> >> >> > >> >>> >> >> Thanks, > >> >>> >> >> > >> >>> >> >> Christoph > >> >>> >> >> > >> >>> >> >> On Mon, Nov 30, 2020 at 8:18 AM nancyfor <[email protected]> > wrote: > >> >>> >> >> > > >> >>> >> >> > Hello everybody, > >> >>> >> >> > > >> >>> >> >> > I am trying to install votca version 1.6.2 in a > supercomputer. After succesffully configure using the following modules: > >> >>> >> >> > > >> >>> >> >> > intel/19.1.1 > >> >>> >> >> > impi/2019.7 > >> >>> >> >> > mkl/2020.1 > >> >>> >> >> > gromacs/2019.4 > >> >>> >> >> > libxc/4.3.4 > >> >>> >> >> > doxygen/1.8 > >> >>> >> >> > cmake/3.15 (version 3.13 incompatible with doxygen 1.8) > >> >>> >> >> > clang/10.0 > >> >>> >> >> > hdf5-serial/1.8.21 > >> >>> >> >> > fftw-serial/3.3.8 > >> >>> >> >> > boost/1.73 > >> >>> >> >> > with gcc version 9.3.0 > >> >>> >> >> > > >> >>> >> >> > and > >> >>> >> >> > > >> >>> >> >> > cmake -Bbuilddir -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON > -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/ > > -DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a > > -DLIBXC_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_10-10.2.0/4.3.4/ > > -DLIBXC_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_10-10.2.0/4.3.4/lib/libxc.a > > -DCMAKE_INSTALL_PREFIX=${prefix} ../votca > >> >>> >> >> > > >> >>> >> >> > However when I try to run > >> >>> >> >> > > >> >>> >> >> > cmake --build builddir > >> >>> >> >> > > >> >>> >> >> > I got the following: > >> >>> >> >> > > >> >>> >> >> > Current git revision is 9b6bbd0 > >> >>> >> >> > [ 0%] Built target gitversion-xtp > >> >>> >> >> > Current git revision is 9b6bbd0 > >> >>> >> >> > [ 0%] Built target gitversion > >> >>> >> >> > [ 0%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o > >> >>> >> >> > In file included from > /u/forero/src/votca/tools/include/votca/tools/property.h:23:0, > >> >>> >> >> > from > /u/forero/src/votca/tools/include/votca/tools/application.h:21, > >> >>> >> >> > from > /u/forero/src/votca/tools/src/libtools/application.cc:19: > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:107:3: error: > ‘unique_ptr’ in namespace ‘std’ does not name a type > >> >>> >> >> > > std::unique_ptr<boost::tokenizer<boost::char_separator<char>>> tok; > >> >>> >> >> > ^ > >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h: > In constructor ‘votca::tools::Tokenizer::Tokenizer(const string&, const > char*)’: > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:50:5: error: > ‘tok’ was not declared in this scope > >> >>> >> >> > tok = > std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str, > >> >>> >> >> > ^ > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:50:11: error: > ‘make_unique’ is not a member of ‘std’ > >> >>> >> >> > tok = > std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str, > >> >>> >> >> > ^ > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:50:73: error: > expected primary-expression before ‘>’ token > >> >>> >> >> > tok = > std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str, > >> >>> >> >> > ^ > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:51:75: warning: > left operand of comma operator has no effect [-Wunused-value] > >> >>> >> >> > sep); > >> >>> >> >> > ^ > >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h: > In member function ‘votca::tools::Tokenizer::iterator > votca::tools::Tokenizer::begin()’: > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:60:29: error: > ‘tok’ was not declared in this scope > >> >>> >> >> > iterator begin() { return tok->begin(); } > >> >>> >> >> > ^ > >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h: > In member function ‘votca::tools::Tokenizer::iterator > votca::tools::Tokenizer::end()’: > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:65:27: error: > ‘tok’ was not declared in this scope > >> >>> >> >> > iterator end() { return tok->end(); } > >> >>> >> >> > ^ > >> >>> >> >> > In file included from > /u/forero/src/votca/tools/include/votca/tools/application.h:21:0, > >> >>> >> >> > from > /u/forero/src/votca/tools/src/libtools/application.cc:19: > >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h: > In constructor ‘votca::tools::Property::Property(const string&, const > string&, const string&)’: > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/property.h:59:7: warning: > declaration of ‘path’ shadows a member of 'this' [-Wshadow] > >> >>> >> >> > : _name(name), _value(value), _path(path) {} > >> >>> >> >> > ^ > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/property.h:59:7: warning: > declaration of ‘value’ shadows a member of 'this' [-Wshadow] > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/property.h:59:7: warning: > declaration of ‘name’ shadows a member of 'this' [-Wshadow] > >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h: > In member function ‘votca::tools::Property& > votca::tools::Property::set(const string&, const string&)’: > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/property.h:248:56: warning: > declaration of ‘value’ shadows a member of 'this' [-Wshadow] > >> >>> >> >> > const std::string &value) { > >> >>> >> >> > ^ > >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h: > In member function ‘votca::tools::Property& > votca::tools::Property::add(const string&, const string&)’: > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/property.h:255:56: warning: > declaration of ‘value’ shadows a member of 'this' [-Wshadow] > >> >>> >> >> > const std::string &value) { > >> >>> >> >> > ^ > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/property.h:256:15: warning: > declaration of ‘path’ shadows a member of 'this' [-Wshadow] > >> >>> >> >> > std::string path = _path; > >> >>> >> >> > ^ > >> >>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h: > In member function ‘void votca::tools::Property::setAttribute(const > string&, const T&)’: > >> >>> >> >> > > /u/forero/src/votca/tools/include/votca/tools/property.h:420:50: warning: > declaration of ‘value’ shadows a member of 'this' [-Wshadow] > >> >>> >> >> > const T &value) { > >> >>> >> >> > ^ > >> >>> >> >> > > tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:75: recipe for > target 'tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o' > failed > >> >>> >> >> > gmake[2]: *** > [tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o] Error 1 > >> >>> >> >> > CMakeFiles/Makefile2:256: recipe for target > 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed > >> >>> >> >> > gmake[1]: *** > [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2 > >> >>> >> >> > Makefile:129: recipe for target 'all' failed > >> >>> >> >> > gmake: *** [all] Error 2 > >> >>> >> >> > > >> >>> >> >> > Does anyone have an idea of what might be the problem. I > tried different combinations of the gcc version and the boost without > success. > >> >>> >> >> > > >> >>> >> >> > Best regards, > >> >>> >> >> > Nancy > >> >>> >> >> > > >> >>> >> >> > > >> >>> >> >> > > >> >>> >> >> > > >> >>> >> >> > > >> >>> >> >> > > >> >>> >> >> > > >> >>> >> >> > -- > >> >>> >> >> > 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/41e71c8f-bef2-4df9-85ae-dcdc81474176n%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/27db68be-a714-4e69-92e0-a990dc90014en%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/6815a3c7-fefc-4d92-b3f5-7703a3e8cbc4n%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/61130d5f-ea2c-4326-9e05-c9ee9186863bn%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/f12d1177-3ac0-493c-b40b-0561c51aa00bn%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/c8c2483f-beac-434e-a33c-877618704c70n%40googlegroups.com.
