On Sat, Dec 19, 2020 at 4:02 PM nancyfor <[email protected]> wrote: > > > 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
fftwf_version() is part of the single-precession version of fftw. VOTCA only depends on the double precision version of fftw. So my guess is that this is a dependency from libgromacs.a, which is most likely single precision. When doing a build with static libraries, you will have to list libgromacs' dependencies in GROMACS_LIBRARY as well, e.g. -DGROMACS_LIBRARY="/path/to/libgromacs.a;/path/to/libfftwf.a" If you are linking against a mpi-enabled version of libgromacs, you might need to add libmpi in there, too. When using shared libraries all the dependency handling is automatic, as dependencies are embedded in the .so files. As a sidenote, VOTCA doesn't really benefit from an mpi-enabled libgromacs as we only use libgromacs to read gromacs file formats. So using a serial version is preferred. Christoph > > 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. -- 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/CAHG27e5ifxsD80DjB-vtvSsOAa-F7sRmHP2P0mmE7h8y6foafQ%40mail.gmail.com.
