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/CAHG27e5kvkbx9svUmcLvmOssYXA2csNg4kWFX1iucbyeJ2-c2A%40mail.gmail.com.
