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/0d934249-b579-4b86-a97f-c3d23855e87en%40googlegroups.com.
