Re: [Pcsim-users] problems of installing PCSim (Pecevski Dejan)

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Hi Zhicheng,

In the file ${PCSIM_HOME}/scripts/generate_header.py
on line 70 you'll find the following piece of code:
-----------------
o.write( '#include "parser/PCSIMParserEnvironment.h"\n' )
for dir in neuromldir:
     for f in  glob.glob( dir + "/*.h" ):
         if not f in neuromldir_exclude:
             o.write( '#include "%s"\n' % ( os.path.basename(f) ) )
----------------

Remove that, and try recompiling from scratch from a clean environment.

Best,
Dejan

On 11/26/2011 06:16 AM, zhicheng Hou wrote:
> Hi Dejan,
> Thanks for your reply. I followed your advice and there are still some
> errors. When i run  ---$ sudo python build.py -j 2 wipe, it seems ok.
> however when i run  ---sudo python build.py -j 2 install, errors occur
> again:
> the bash said:
>
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D CMAKE_INSTALL_PREFIX:PATH=/home/hou/pcsim/pcsim-0.5.4 -D PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D EXTRA_INSTALL:STRING=NO /home/hou/pcsim/pcsim-0.5.4
> -- The C compiler identification is GNU
> -- The CXX compiler identification is GNU
> -- Check for working C compiler: /usr/bin/gcc
> -- Check for working C compiler: /usr/bin/gcc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
>     Build type   = Release
>     Platform     = linux-i686
>     Make tool    = /usr/bin/make
>     Make command = /usr/bin/make -i
> -- Looking for python executable ...
> -- Found PythonInterp: /usr/bin/python
>     Python executable : /usr/bin/python version 2.6
> -- Looking for python libraries ...
>     Python libraries : /usr/lib/python2.6/config
>     Python includes : /usr/include/python2.6
> -- Looking for doxygen executable ...
>     Doxygen executable : /usr/bin/doxygen
> -- Looking for GCCXML executable ...
>     GCCXML executable : /usr/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc-mt
> BOOST_LIB_SUFFIX_2 IS gcc41-mt
> -- Looking for Boost C++ libraries ... - toolset    = gcc
> -- Looking for Boost C++ libraries ... - lib suffixes = gcc-mt gcc41-mt
>     Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc41-mt.so
>     Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc41-mt.so
>     Boost C++ library boost_date_time :
> /usr/local/lib/libboost_date_time-gcc41-mt.so
>     Boost C++ libraries : /usr/local/lib
>     Boost C++ include path : /usr/local/include/boost-1_34_1
> -- Looking for MPICH2 ...
>     MPICH2 library: /usr/local/lib/libmpich.so
>     MPICH2 include path : /usr/local/include
> -- Looking for GNU Scientific library ...
>     GNU Scientific library : /usr/local/lib/libgsl.so
> -- Looking for Xerces-C library ...
>     Xerces library : /usr/lib/libxerces-c.so
> -- Looking for CppUnit ...
>     CppUnit : /usr/local/lib/libcppunit.so
>     JNI headers : /usr/lib/jvm/java-6-openjdk/include
> -- Checking to see if CXX compiler accepts flag -pthread
> -- Checking to see if CXX compiler accepts flag -pthread - yes
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> /usr/bin/make -j 2 rebuild_cache
> Running CMake to regenerate build system...
>     Build type   = Release
>     Platform     = linux-i686
>     Make tool    = /usr/bin/make
>     Make command = /usr/bin/make -i
>     Python executable : /usr/bin/python version 2.6
>     Python libraries : /usr/lib/python2.6/config
>     Python includes : /usr/include/python2.6
>     Doxygen executable : /usr/bin/doxygen
>     GCCXML executable : /usr/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc-mt
> BOOST_LIB_SUFFIX_2 IS gcc41-mt
>     Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc41-mt.so
>     Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc41-mt.so
>     Boost C++ library boost_date_time :
> /usr/local/lib/libboost_date_time-gcc41-mt.so
>     Boost C++ libraries : /usr/local/lib
>     Boost C++ include path : /usr/local/include/boost-1_34_1
>     MPICH2 library: /usr/local/lib/libmpich.so
>     MPICH2 include path : /usr/local/include
>     GNU Scientific library : /usr/local/lib/libgsl.so
>     Xerces library : /usr/lib/libxerces-c.so
>     CppUnit : /usr/local/lib/libcppunit.so
>     JNI headers : /usr/lib/jvm/java-6-openjdk/include
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
> *******************************************
> *  GENERATING PY++ WRAPPER CPP FILES      *
> *******************************************
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> /usr/bin/make -j 2 generate_code
> [100%] Generating ../../python/pypcsim.h
> [100%] Generating ../../python/pypcsim/pypcsim.indicator.cpp
> /usr/local/lib/python2.6/dist-packages/pygccxml/parser/declarations_cache.py:8:
> DeprecationWarning: the md5 module is deprecated; use hashlib instead
>    import md5
>
> INFO Parsing source file "pypcsim.h" ...
>
> INFO gccxml cmd: /usr/bin/gccxml  --gccxml-cxxflags -pthread
> -fpermissive   -I"." -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simutils"
> -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simcore"
> -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/construction"
> -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml"
> -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simobjects"
> -I"/home/hou/pcsim/pcsim-0.5.4/libxsd"
> -I"/usr/local/include/boost-1_34_1"  -D"MPICH_IGNORE_CXX_SEEK"
> -D"BOOST_HAS_THREADS" -D"BOOST_PYTHON_MAX_ARITY=30"  "pypcsim.h"
> -fxml="/tmp/tmpapqeKv.xml"
> /usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py:152:
> DeprecationWarning: os.popen4 is deprecated.  Use the subprocess
> module.
>    input_, output = os.popen4( command_line )
> Traceback (most recent call last):
>    File "/home/hou/pcsim/pcsim-0.5.4/scripts/generate_boost_python_wrapper_code.py",
> line 143, in<module>
>      encoding = 'utf-8'
>    File "/usr/local/lib/python2.6/dist-packages/pyplusplus/module_builder/builder.py",
> line 90, in __init__
>      , indexing_suite_version)
>    File "/usr/local/lib/python2.6/dist-packages/pyplusplus/module_builder/builder.py",
> line 144, in __parse_declarations
>      decls = reader.read_files( files, compilation_mode )
>    File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/project_reader.py",
> line 225, in read_files
>      return self.__parse_file_by_file(files)
>    File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/project_reader.py",
> line 250, in __parse_file_by_file
>      decls = reader.read_file( header )
>    File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py",
> line 198, in read_file
>      return self.read_gccxml_file( source_file )
>    File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py",
> line 225, in read_gccxml_file
>      raise error
> pygccxml.parser.source_reader.gccxml_runtime_error_t: Error occured
> while running GCC-XML: In file included from
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/parser/xerces/elements.txx:16,
>                   from
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/parser/xerces/elements.hxx:449,
>                   from
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/skeleton/NeuroML_Level3_v1.7.1-pskel.hpp:76,
>                   from
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:11,
>                   from
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:7,
>                   from pypcsim.h:148:
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:
> In member function 'virtual xercesc_3_1::BinInputStream*
> xsd::cxx::xml::sax::std_input_source::makeStream() const':
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:156:
> error: cannot allocate an object of abstract type
> 'xsd::cxx::xml::sax::std_input_stream'
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:25:
> note:   because the following virtual functions are pure within
> 'xsd::cxx::xml::sax::std_input_stream':
> /usr/local/include/xercesc/util/BinInputStream.hpp:67: note: 	virtual
> const XMLCh* xercesc_3_1::BinInputStream::getContentType() const
>
> make[3]: *** [../python/pypcsim/pypcsim.indicator.cpp] Error 1
> make[2]: *** [python/CMakeFiles/generate_python_wrapper_code.dir/all] Error 2
> make[1]: *** [CMakeFiles/generate_code.dir/rule] Error 2
> make: *** [generate_code] Error 2
> BUILD PROCESS FAILED. ERROR = 512
> Command: /usr/bin/make -j 2 generate_code
>
>
> Best Regards
> Hou Zhicheng
>
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-- 
_______________________________________________
Dejan Pecevski, PhD
Institute for Theoretical Computer Science
Graz University of Technology
Inffeldgasse 16b, A-8010 Graz, Austria
Tel. +43 316 873 5849