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Trouble compiling run_single_zone

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Anonymous
2018-08-28
2020-10-01

  • Anonymous

    Anonymous - 2018-08-28

    Whenever I try to compile anything in examples/network, I get the error:

    make: *** No rule to make target '../../vendor/wn_matrix.tar.gz', needed by '../../obj/WnMatrix.o'. Stop.

    I'm at revision 587, and I have relevant environment variables NNT_HYDRO_CODE=traj and WN_XML_CHAR=xmlChar running on linux.

    Output from test_versions:

    libxml version 2.9.1
    gsl version 1.16
    Boost version 1.55.0

     

  • Bradley S. Meyer

    Bradley S. Meyer - 2018-08-29

    Thanks for your post. What happens if you type (in the network directory):

    ./examples_make

    Best wishes.

     

  • Anonymous

    Anonymous - 2018-08-29

    ./examples_make
    Updating '.':
    At revision 587.
    make: No rule to make target '../../vendor/wn_matrix.tar.gz', needed by '../../obj/WnMatrix.o'. Stop.
    rm -fr ../../obj
    rm ../../nnt/string_defs.h
    make:     No rule to make target '../../vendor/wn_matrix.tar.gz', needed by '../../obj/WnMatrix.o'. Stop.
    rm -fr ../../obj
    rm ../../nnt/string_defs.h
    rm -fr ../../vendor
    make: *** No rule to make target '../../vendor/wn_matrix.tar.gz', needed by '../../obj/WnMatrix.o'. Stop.
    Make failed. Contact project maintainer.

     

    • Bradley S. Meyer

      Bradley S. Meyer - 2018-08-29

      That's curious. It just worked for me. Are you in a bash shell?

       

  • Anonymous

    Anonymous - 2018-08-29

    yes

     

    • Bradley S. Meyer

      Bradley S. Meyer - 2018-08-29

      Ok. What is the result of

      cd nucnet-tools-code
      ls vendor

      and

      svn diff examples/network/Makefile

      Thanks.

       

  • Anonymous

    Anonymous - 2018-08-29

    ls vendor/
    SPARSKIT2

    svn diff examples/network/Makefile
    doesn't haven't any output

     

  • Bradley S. Meyer

    Bradley S. Meyer - 2018-08-29

    Are you able to download wn_matrix? In particular, what happens if you type (from the directory examples/network)

    wget http://sourceforge.net/projects//wnmatrix/files/wn_matrix/wn_matrix_0.19.tar.gz -O ../../vendor/wn_matrix.tar.gz

    This is all on a single line.

     

  • Bradley S. Meyer

    Bradley S. Meyer - 2018-08-29

    Ok. Let's just try the following in examples/network.

    make clean
    make clean_dist
    make run_single_zone &> log

    You can attach log to your reply.

     

  • Anonymous

    Anonymous - 2018-08-29

    After I run a make clean_all, that wget for wn_matrix, then ./examples_make, I get a slightly different error now:

    Updating '.':
    At revision 587.
    tar xz -C ../../vendor -f ../../vendor/wn_matrix.tar.gz
    g++ -Werror -Wall -Wpointer-arith -Wwrite-strings -fno-common -g -DWN_XML_CHAR=xmlChar -O0 -DNO_OPENMP -Wno-deprecated -DHYDRO_TRAJ xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.32/src -I../../vendor/wn_matrix/0.19/src -I../../vendor/libstatmech/0.10/src -I../../vendor/libnuceq/0.7/src -I../.. -I ../../vendor/wn_sparse_solve/0.6/src -c ../../vendor/wn_matrix/0.19/src/WnMatrix.c -o ../../obj/WnMatrix.o

    wget http://sourceforge.net/projects//libstatmech/files/libstatmech/libstatmech_0.10.tar.gz -O ../../obj/WnMatrix.o

    make: *** No rule to make target '../../vendor/libnucnet.tar.gz', needed by '../../obj/Libnucnet__Nuc.o'. Stop.
    rm -fr ../../obj
    rm ../../nnt/string_defs.h
    tar xz -C ../../vendor -f ../../vendor/wn_matrix.tar.gz
    g++ -Werror -Wall -Wpointer-arith -Wwrite-strings -fno-common -g -DWN_XML_CHAR=xmlChar -O0 -DNO_OPENMP -Wno-deprecated -DHYDRO_TRAJ xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.32/src -I../../vendor/wn_matrix/0.19/src -I../../vendor/libstatmech/0.10/src -I../../vendor/libnuceq/0.7/src -I../.. -I ../../vendor/wn_sparse_solve/0.6/src -c ../../vendor/wn_matrix/0.19/src/WnMatrix.c -o ../../obj/WnMatrix.o

    wget http://sourceforge.net/projects//libstatmech/files/libstatmech/libstatmech_0.10.tar.gz -O ../../obj/WnMatrix.o

    make: No rule to make target '../../vendor/libnucnet.tar.gz', needed by '../../obj/Libnucnet__Nuc.o'. Stop.
    rm -fr ../../obj
    rm ../../nnt/string_defs.h
    rm -fr ../../vendor
    make:     No rule to make target '../../vendor/wn_matrix.tar.gz', needed by '../../obj/WnMatrix.o'. Stop.
    Make failed. Contact project maintainer.

    and run_constant_entropy makes, but the rest fail

     

    • Bradley S. Meyer

      Bradley S. Meyer - 2018-08-29

      Let's try again. Don't do any wget yourself, just type (in examples/network):

      make clean_all
      make run_single_zone &> log

      Attach or print out log.

       

  • Anonymous

    Anonymous - 2018-08-29

    make: *** No rule to make target '../../vendor/wn_matrix.tar.gz', needed by '../../obj/WnMatrix.o'. Stop.

     

  • Bradley S. Meyer

    Bradley S. Meyer - 2018-08-29

    Ok. Please let me know the results of (from the nucnet-tools-code directory)

    svn diff build/*
    g++ -v

     

  • Anonymous

    Anonymous - 2018-08-29

    Index: build/Makefile

    --- build/Makefile (revision 587)
    +++ build/Makefile (working copy)
    @@ -236,29 +236,29 @@
    # Build dependencies.
    #===============================================================================

    -$(VENDORDIR)/wn_matrix.tar.gz:
    - $(WGET) $(WNMATRIX_URL)/wn_matrix_$(WNMATRIX_VERSION).tar.gz -O $@
    +#$(VENDORDIR)/wn_matrix.tar.gz:
    + #$(WGET) $(WNMATRIX_URL)/wn_matrix_$(WNMATRIX_VERSION).tar.gz -O $@

    $(OBJDIR)/WnMatrix.o: $(VENDORDIR)/wn_matrix.tar.gz
    tar xz -C $(VENDORDIR) -f $<
    $(CC) -c $(WNMATRIXDIR)/WnMatrix.c -o $@

    -$(VENDORDIR)/libstatmech.tar.gz:
    - $(WGET) $(LIBSTATMECH_URL)/libstatmech_$(LIBSTATMECH_VERSION).tar.gz -O $@
    +#$(VENDORDIR)/libstatmech.tar.gz:
    + #$(WGET) $(LIBSTATMECH_URL)/libstatmech_$(LIBSTATMECH_VERSION).tar.gz -O $@

    $(OBJDIR)/Libstatmech.o: $(VENDORDIR)/libstatmech.tar.gz
    tar xz -C $(VENDORDIR) -f $<
    $(CC) -c $(LIBSTATMECHDIR)/Libstatmech.c -o $@

    -$(VENDORDIR)/libnuceq.tar.gz:
    - $(WGET) $(LIBNUCEQ_URL)/libnuceq_$(LIBNUCEQ_VERSION).tar.gz -O $@
    +#$(VENDORDIR)/libnuceq.tar.gz:
    + #$(WGET) $(LIBNUCEQ_URL)/libnuceq_$(LIBNUCEQ_VERSION).tar.gz -O $@

    $(OBJDIR)/Libnuceq.o: $(VENDORDIR)/libnuceq.tar.gz $(OBJDIR)/Libnucnet.o
    tar xz -C $(VENDORDIR) -f $<
    $(CC) -c $(LIBNUCEQDIR)/Libnuceq.c -o $@

    -$(VENDORDIR)/libnucnet.tar.gz:
    - $(WGET) $(LIBNUCNET_URL)/libnucnet_$(LIBNUCNET_VERSION).tar.gz -O $@
    +#$(VENDORDIR)/libnucnet.tar.gz:
    + #$(WGET) $(LIBNUCNET_URL)/libnucnet_$(LIBNUCNET_VERSION).tar.gz -O $@

    $(OBJDIR)/Libnucnet__Nuc.o: $(VENDORDIR)/libnucnet.tar.gz $(OBJDIR)/WnMatrix.o
    tar xz -C $(VENDORDIR) -f $<

    g++ -v
    Using built-in specs.
    COLLECT_GCC=/mnt/simulations/nucnettools/mesa-r10398/mesasdk/bin/g++.exec
    COLLECT_LTO_WRAPPER=/mnt/simulations/nucnettools/mesa-r10398/mesasdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/7.2.0/lto-wrapper
    Target: x86_64-pc-linux-gnu
    Configured with: /root/mesasdk-src/gcc/configure CC=gcc --build=x86_64-pc-linux-gnu --prefix=/root/mesasdk --with-gmp=/root/mesasdk --with-mpfr=/root/mesasdk --with-mpc=/root/mesasdk --enable-languages=c,c++,fortran --disable-multilib --disable-nls --disable-libsanitizer --enable-clocale=generic
    Thread model: posix
    gcc version 7.2.0 (GCC)

     

  • Anonymous

    Anonymous - 2018-08-29

    So, I got to looking at that output, and there are some wget lines in build/Makefile that I uncommented. run_single_zone now compiles (which is what I need) but run_entropy fails

     

    • Bradley S. Meyer

      Bradley S. Meyer - 2018-08-29

      Ok, that's progress. What's the error on run_entropy?

       

  • Anonymous

    Anonymous - 2018-08-29

    make run_entropy
    g++ -Werror -Wall -Wpointer-arith -Wwrite-strings -fno-common -g -DWN_XML_CHAR=xmlChar -O0 -DNO_OPENMP -Wno-deprecated -DHYDRO_TRAJ xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.32/src -I../../vendor/wn_matrix/0.19/src -I../../vendor/libstatmech/0.10/src -I../../vendor/libnuceq/0.7/src -I../.. -I ../../vendor/wn_sparse_solve/0.6/src -c -o ../../obj/run_entropy.o run_entropy.cpp
    g++ -Werror -Wall -Wpointer-arith -Wwrite-strings -fno-common -g -DWN_XML_CHAR=xmlChar -O0 -DNO_OPENMP -Wno-deprecated -DHYDRO_TRAJ xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.32/src -I../../vendor/wn_matrix/0.19/src -I../../vendor/libstatmech/0.10/src -I../../vendor/libnuceq/0.7/src -I../.. -I ../../vendor/wn_sparse_solve/0.6/src ../../obj/WnMatrix.o ../../obj/LibnucnetNuc.o ../../obj/LibnucnetReac.o ../../obj/Libnucnet.o ../../obj/Libstatmech.o ../../obj/Libnuceq.o ../../obj/auxiliary.o ../../obj/iter.o ../../obj/math.o ../../obj/two_d_weak_rates.o ../../obj/wrappers.o ../../obj/hydro.o ../../obj/hydro_helper.o ../../obj/matrix_solver.o ../../obj/evolve.o ../../obj/network_limiter.o ../../obj/user_rate_functions.o ../../obj/flow_utilities.o ../../obj/aa522a25.o ../../obj/neutrino_rate_functions.o ../../obj/network_utilities.o ../../obj/rate_modifiers.o ../../obj/screen.o ../../obj/thermo.o ../../obj/nse_corr.o ../../obj/weak_utilities.o ../../obj/remove_duplicate.o ../../obj/run_entropy.o -o ./run_entropy -L/usr/lib/x86_64-linux-gnu/ -lboost_program_options xml2-config --libs gsl-config --libs
    ../../obj/run_entropy.o: In function get_input(int, char**)': /mnt/simulations/nucnettools/nucnet-tools-code/examples/network/run_entropy.cpp:216: undefined reference toboost::program_options::options_description::options_description(std::cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> > const&, unsigned int, unsigned int)'
    ../../obj/run_entropy.o: In function boost::program_options::variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const': /usr/include/boost/program_options/variables_map.hpp:155: undefined reference toboost::program_options::abstract_variables_map::operator const'
    ../../obj/run_entropy.o: In function boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)': /usr/include/boost/program_options/detail/parsers.hpp:43: undefined reference toboost::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&)'
    ../../obj/run_entropy.o: In function boost::program_options::basic_command_line_parser<char>::extra_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/include/boost/program_options/detail/parsers.hpp:77: undefined reference toboost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> >, std::</char></std::pair<std::__cxx11::basic_string<char,></char></std::__cxx11::basic_string<char,></char></std::__cxx11::basic_string<char,></char></char,>    cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> > >, std::cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> > const&>)'
    ../../obj/run_entropy.o: In function 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> > > > boost::program_options::to_internal<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(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&)': /usr/include/boost/program_options/detail/convert.hpp:79: undefined reference toboost::program_options::to_internal(std::</char></char,>    cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> > const&)'
    ../../obj/run_entropy.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x38): undefined reference to boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, 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&, bool) const' ../../obj/run_entropy.o: In functionboost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> >, char>::name() const':
    /usr/include/boost/program_options/detail/value_semantic.hpp:19: undefined reference to boost::program_options::arg[abi:cxx11]' ../../obj/run_entropy.o: In functionboost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> >, char>::xparse(boost::any&, 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&) const':
    /usr/include/boost/program_options/detail/value_semantic.hpp:170: undefined reference to `boost::program_options::validate(boost::any&, 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&, std::</char></std::__cxx11::basic_string<char,></char></std::__cxx11::basic_string<char,></char></std::__cxx11::basic_string<char,></char></std::__cxx11::basic_string<char,></char></std::__cxx11::basic_string<char,></char></std::__cxx11::basic_string<char,>    cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> >, int)'
    collect2: error: ld returned 1 exit status
    Makefile:120: recipe for target 'run_entropy' failed
    make:     ** [run_entropy] Error 1</char></char,></char></char,></char></char,>

     

    • Bradley S. Meyer

      Bradley S. Meyer - 2018-09-01

      This looks like your compiler is not finding the compiled boost program options library. You might look at:

      https://sourceforge.net/u/mbradle/blog/2016/05/using-the-boost-compiled-libraries/

      Best wishes.

       

  • Anonymous

    Anonymous - 2020-08-31

    Dear Prof. Meyer.

    My computer is macOS Catalina Version 10.15.6
    When I install all of necessary libraries except valgrind because this one cannot install on the Version 10.15.6, I think valgrind is not the necessary library. But I encountered some problems which are none business with valgrind. Could you help me?

    When I make run_single_zone, the error is following:

    gzip: (stdin): unexpected end of file
    tar: Child returned status 1
    tar: Error is not recoverable: exiting now
    make: *** [../../obj/WnMatrix.o] Error 2

    I noticed the file ../../vendor wn_matrix.tar.gz is empty, so I download this file and put it in ../../vendor

    After that another error happened, part of the error is following:

    In file included from /opt/local/include/boost/boost/bind/bind.hpp:29,
    from /opt/local/include/boost/boost/bind.hpp:22,
    from ../../nnt/wrappers.hpp:38,
    from ../../nnt/math.h:46,
    from ../../nnt/auxiliary.h:49,
    from ../../nnt/auxiliary.cpp:29:
    /opt/local/include/boost/boost/bind/arg.hpp: In constructor 'boost::arg::arg(const$
    /opt/local/include/boost/boost/bind/arg.hpp:37:22: error: typedef 'T_must_be_placehol$
    37 | typedef char T_must_be_placeholder[ I == is_placeholder<t>::value? 1:$
    | ^~~~~~~~~~~~~~~~~~~~~
    cc1plus: all warnings being treated as errors
    make: *** [../../obj/auxiliary.o]</t>     Error 1

    The full error is in the attachment.

    I have no idea about it, please help me.

    Thanks
    Ertao LI

     
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