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Compiling 'make run_programs'

Getting Help with Nucnet Tools
Anonymous
2016-08-13
2021-03-13
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    Anonymous

    Anonymous - 2016-08-13

    Hello,

    I have installed everything and am trying to compile 'make run_single_zone' and am receiving errors (OS X 10.11.6, XCode 7.3.1). I have seen this blog post and if I compile with clang or gcc I receive similar errors, the last few lines being:

    In file included from ../../nnt/auxiliary.cpp:29:
    In file included from ../../nnt/auxiliary.h:39:
    In file included from /opt/local/include/boost/lexical_cast.hpp:32:
    In file included from /opt/local/include/boost/lexical_cast/try_lexical_convert.hpp:35:
    In file included from /opt/local/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
    /opt/local/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:210:17: error:
    unused typedef 'boost_static_assert_typedef_212'
    [-Werror,-Wunused-local-typedef]
    BOOST_STATIC_ASSERT_MSG(( sizeof(T) <= sizeof(CharT)),
    ^
    /opt/local/include/boost/static_assert.hpp:36:48: note: expanded from macro
    'BOOST_STATIC_ASSERT_MSG'

    define BOOST_STATIC_ASSERT_MSG( B, Msg ) BOOST_STATIC_ASSERT( B )

                                               ^

    /opt/local/include/boost/static_assert.hpp:170:16: note: expanded from macro
    'BOOST_STATIC_ASSERT'
    BOOST_JOIN(boost_static_assert_typedef_, LINE) BOOST_...
    ^
    /opt/local/include/boost/config/suffix.hpp:544:28: note: expanded from macro
    'BOOST_JOIN'

    define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )

                           ^

    /opt/local/include/boost/config/suffix.hpp:545:31: note: expanded from macro
    'BOOST_DO_JOIN'

    define BOOST_DO_JOIN( X, Y ) BOOST_DO_JOIN2(X,Y)

                              ^

    /opt/local/include/boost/config/suffix.hpp:546:32: note: expanded from macro
    'BOOST_DO_JOIN2'

    define BOOST_DO_JOIN2( X, Y ) X##Y

                               ^

    <scratch space="">:116:1: note: expanded from here
    boost_static_assert_typedef_212
    ^
    fatal error: too many errors emitted, stopping now [-ferror-limit=]
    20 errors generated.
    make: *** [../../obj/auxiliary.o] Error 1

    Please let me know what I can do to fix this.

     

    • Bradley S. Meyer

      Bradley S. Meyer - 2016-08-13

      It looks like you are compiling with clang and that clang is not ignoring the warnings as errors. An immediate fix is to change the lines in nucnet-tools-code/build/Makefile from

      ifneq "$(CLANG_TEST)" ""
   CFLAGS+= -Wno-error=unused-local-typedef
 endif

      to

       #ifneq "$(CLANG_TEST)" ""
    CFLAGS+= -Wno-error=unused-local-typedef
 #endif

      and try remaking. That will force clang to use the warning. The make file should be performing the clang test correctly, but maybe there is something off in your installation. If you are using clang, I'd be interested in knowing what the result of

      gcc -v 2>&1 > /dev/null | grep clang

      is. It should give something like

       Apple LLVM version 7.3.0 (clang-703.0.29)

      Another fix is to update boost as in the blog post you note. You don't need to compile the library or change to gcc. Once you've cloned boost, keep clang and type

      export BOOST_DIR=/Users/bradleymeyer/boost

      (of course using your directory for the installed boost instead of mine). Then remake the code. The version of boost you check out with git will have the unused local typedef errors fixed.

      A third point is that gcc should not give this problem. I've not seen gcc complain about the Boost unused local typedefs. You might check that you've carried out the gcc steps carefully. Let me know what you try and how it turns out. Best wishes.

       
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    Anonymous

    Anonymous - 2016-08-15

    Thank you for your assistance and very fast response time! I managed to resolve the issue by removing GC = clang++ from the examples/network/Makefile. I had forgotten to remove it when attempting to find a solution. The code is working fully on my computer now.

     

    • Bradley S. Meyer

      Bradley S. Meyer - 2016-08-15

      Glad to hear it. Yes, that line GC = clang++ was only to get the code to compile the c++ part with clang and the fortran with gfortran. It's probably best for now to compile code that needs both c++ and fortran with GNU gcc only. Again, for mac users who want to use both clang and gcc, for now I recommend the steps in this post.

       
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    Anonymous

    Anonymous - 2016-11-11

    Hello, Brad,
    I have a problem for the make run_entropy as below:
    What is the possible problenm for this?
    Thanks very much.

    network]$ make run_entropy
    tar xz -C ../../vendor -f ../../vendor/wn_matrix.tar.gz
    g++ -Werror -Wall -Wpointer-arith -Wwrite-strings -fshort-enums -fno-common -g -O0 -fopenmp -Wno-deprecated -DHYDRO_EXP_EXPANSION -I/home/zhuang/boost xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/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/0.18/src/WnMatrix.c -o ../../obj/WnMatrix.o
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'int WnMatrixassignElement(WnMatrix, size_t, size_t, double)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:130: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:130: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:131: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:131: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char*, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'int WnMatrix    updateElement(WnMatrix, size_t, size_t, double)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:244: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:244: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:245: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:245: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'int WnMatrixremoveElement(WnMatrix, size_t, size_t)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:282: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:282: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:283: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:283: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char*, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'double WnMatrix    getElement(WnMatrix    , size_t, size_t)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:322: error: invalid conversion from 'const WnChar' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:322: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar, int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:323: error: invalid conversion from 'const WnChar' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:323: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar, int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'WnMatrixLine* WnMatrixgetRow(WnMatrix, size_t)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1044: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1044: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'WnMatrixLine* WnMatrixgetColumn(WnMatrix    , size_t)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1108: error: invalid conversion from 'const WnChar' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1108: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar, int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'xmlDoc WnMatrixCoomakeXmlDocument(WnMatrixCoo, const WnChar)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1903: error: invalid conversion from 'const WnChar' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1903: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar, int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1920: error: invalid conversion from 'const WnChar' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1920: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar, int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1937: error: invalid conversion from 'const WnChar' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:1937: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar, int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'xmlDoc* WnMatrix    CsrmakeXmlDocument(WnMatrixCsr    , const WnChar)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2095: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2095: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2140: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2140: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2157: error: invalid conversion from 'const WnChar    ' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2157: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar    , int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'xmlDoc     WnMatrixYalemakeXmlDocument(WnMatrixYale, const WnChar)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2320: error: invalid conversion from 'const WnChar' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2320: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar, int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2337: error: invalid conversion from 'const WnChar' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2337: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar, int, const char, ...)'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function 'xmlDoc* WnMatrix    make_gsl_vector_xml_document(gsl_vector, const WnChar)':
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2899: error: invalid conversion from 'const WnChar' to 'const char'
    ../../vendor/wn_matrix/0.18/src/WnMatrix.c:2899: error: initializing argument 3 of 'int xmlStrPrintf(xmlChar, int, const char, ...)'
    make: *** [../../obj/WnMatrix.o] Error 1

     

    • Bradley S. Meyer

      Bradley S. Meyer - 2016-11-11

      Thanks for your post. libxml updated their xmlStrPrintf format statement which can cause a conflict depending on how up to date your libxml version is and how it was patched. You should be able to do the following (in bash):

      cd nucnet-tools-code/examples/network/

      export WN_XML_CHAR=xmlChar

      make clean

      make run_entropy

      The environment variable WN_XML_CHAR sets the format string. The possible values are char and xmlChar, and the code usually chooses between them correctly depending on the version of libxml it detects. Sometimes, however, there's a mismatch and you have to set by hand as above. If the above doesn't work, try

      export WN_XML_CHAR=char

      make clean

      make run_entropy

      If one of these works, you can set WN_XML_CHAR in your .bashrc file. I hope this helps. Best wishes.

       
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    Anonymous

    Anonymous - 2016-11-13

    Dear Brad,
    Thanks very mcuh, I have done that as you wrote above and export WN_XML_CHAR=char works for me.
    But another problem come as follows:

    run_entropy.cpp:32:36: error: boost/numeric/odeint.hpp: No such file or directory
    run_entropy.cpp: In function 'int main(int, char)':
    run_entropy.cpp:653: error: 'boost::numeric' has not been declared
    run_entropy.cpp:653: error: expected primary-expression before '>' token
    run_entropy.cpp:653: error: 'stepper' was not declared in this scope
    make:     * [run_entropy] Error 1
    Make failed. Contact project maintainer.

    I tried to reinstall the boost and it still come out with the same error.

    Thanks very much.

     

    • Bradley S. Meyer

      Bradley S. Meyer - 2016-11-13

      I've moved this to a new thread.

       

  • Anonymous

    Anonymous - 2021-01-28

    Hello prof .Bradley S. Meyer
    I have installed everything and am trying to compile 'make run_single_zone' and am receiving errors
    /bin/sh: 1: xsltproc: not found
    tar xz -C ../../vendor -f ../../vendor/wn_matrix.tar.gz
    g++ -Werror -Wall -Wpointer-arith -Wwrite-strings -fno-common -g -O0 -fopenmp -Wno-deprecated -DHYDRO_EXP_EXPANSION xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.40/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/0.7/src -c ../../vendor/wn_matrix/0.19/src/WnMatrix.c -o ../../obj/WnMatrix.o
    /bin/sh: 1: xml2-config: not found
    /bin/sh: 1: gsl-config: not found
    In file included from ../../vendor/wn_matrix/0.19/src/WnMatrix.c:40:0:
    ../../vendor/wn_matrix/0.19/src/WnMatrix.h:49:25: fatal error: libxml/hash.h: No such file or directory
    #include <libxml hash.h="">
    ^
    compilation terminated.
    make: *** [../../obj/WnMatrix.o] Error 1</libxml>

     

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