Re: [Pcsim-users] problems of installing PCSim

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Hi!

Thanks for your reply, i followed your advice but there are still
errors. The bash said:

hou@hou-pc:~/pcsim/pcsim-0.5.4$ sudo python build.py -j 2 install
>>>> 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
   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-gcc34-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc34-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/local/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
>>>> 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-gcc34-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc34-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/local/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
Built target generate_python_wrapper_code
Built target generate_code
>>>> 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-gcc34-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc34-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/local/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
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 install
[  0%] Built target generate_python_wrapper_code
[  0%] Building CXX object pcsim/CMakeFiles/pcsim.dir/neuroml/NeuroMLImporter.o
[  0%] Building CXX object
pcsim/CMakeFiles/pcsim.dir/neuroml/parser/cxxproxy/morphml/CxxProxyCell.o
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:1:50:
error: parser/cxxproxy/morphml/CxxProxyCell.h: No such file or
directory
In file included from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:7,
                 from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:1:
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:11:59:
error: parser/skeleton/NeuroML_Level3_v1.7.1-pskel.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:13:60:
error: parser/implementation/NetworkML_v1.7.1-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:15:58:
error: parser/implementation/MorphML_v1.7.1-pimpl.hpp: No such file or
directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:17:61:
error: parser/implementation/Biophysics_v1.7.1-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:19:60:
error: parser/implementation/ChannelML_v1.7.1-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:21:59:
error: parser/implementation/Metadata_v1.7.1-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:23:57:
error: parser/implementation/NeuroMLLevel3-pimpl.hpp: No such file or
directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:25:55:
error: parser/implementation/Level3Cells-pimpl.hpp: No such file or
directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:27:54:
error: parser/implementation/Level3Cell-pimpl.hpp: No such file or
directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:29:60:
error: parser/implementation/Level3Biophysics-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:9:43:
error: parser/PCSIMParserEnvironment.h: No such file or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:11:
error: ‘cxxproxy’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:
In function ‘bool isPointNeuron()’:
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:14:
error: ‘properties’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:19:
error: ‘properties’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:
At global scope:
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:27:
error: ‘cxxproxy’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:
In function ‘boost::shared_ptr<SimObject> as_SimObjectFactory()’:
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:29:
error: ‘properties’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:36:
error: ‘cxxproxy’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:36:
error: expected `;' before ‘p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:37:
error: ‘p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:44:
error: invalid use of ‘this’ in non-member function
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:44:
error: ‘str’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:45: error:
‘NeuroMLLevel3_pimpl’ in namespace ‘neuroml::schema’ does not name a
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:46: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:46:
warning: ISO C++ forbids declaration of ‘Notes_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:46: error:
expected ‘;’ before ‘Notes_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:47: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:47:
warning: ISO C++ forbids declaration of ‘Properties_pimpl’ with no
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:47: error:
expected ‘;’ before ‘Properties_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:48: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:48:
warning: ISO C++ forbids declaration of ‘Property_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:48: error:
expected ‘;’ before ‘Property_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:49: error:
‘::xml_schema’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:49:
warning: ISO C++ forbids declaration of ‘string_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:49: error:
expected ‘;’ before ‘string_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:50: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:50:
warning: ISO C++ forbids declaration of ‘Annotation_pimpl’ with no
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:50: error:
expected ‘;’ before ‘Annotation_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:51: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:51:
warning: ISO C++ forbids declaration of ‘Group_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:51: error:
expected ‘;’ before ‘Group_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:52: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:52:
warning: ISO C++ forbids declaration of ‘Authors_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:52: error:
expected ‘;’ before ‘Authors_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:53: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:53:
warning: ISO C++ forbids declaration of ‘Person_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:53: error:
expected ‘;’ before ‘Person_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:54: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:54:
warning: ISO C++ forbids declaration of ‘Publication_pimpl’ with no
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:54: error:
expected ‘;’ before ‘Publication_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:55: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:55:
warning: ISO C++ forbids declaration of ‘NeuronDBReference_pimpl’ with
no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:55: error:
expected ‘;’ before ‘NeuronDBReference_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:56: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:56:
warning: ISO C++ forbids declaration of ‘ModelDBReference_pimpl’ with
no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:56: error:
expected ‘;’ before ‘ModelDBReference_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:57: error:
field ‘Level3Cells_p’ has incomplete type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:58: error:
‘Level3Cell_pimpl’ in namespace ‘neuroml::schema’ does not name a type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:59: error:
‘::morphml’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:59:
warning: ISO C++ forbids declaration of ‘cellBody_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:59: error:
expected ‘;’ before ‘cellBody_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:60: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:60:
warning: ISO C++ forbids declaration of ‘Polygon_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:60: error:
expected ‘;’ before ‘Polygon_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:61: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:61:
warning: ISO C++ forbids declaration of ‘Point_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:61: error:
expected ‘;’ before ‘Point_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:62: error:
‘::xml_schema’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:62:
warning: ISO C++ forbids declaration of ‘double_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:62: error:
expected ‘;’ before ‘double_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:63: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:63:
warning: ISO C++ forbids declaration of ‘Polyhedron_pimpl’ with no
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:63: error:
expected ‘;’ before ‘Polyhedron_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:64: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:64:
warning: ISO C++ forbids declaration of ‘polygons_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:64: error:
expected ‘;’ before ‘polygons_p’

...
...

/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:136:
error: ‘DoubleExponentialSynapse_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:137:
error: ‘TimeConstantValueIncZero_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:138:
error: ‘TimeConstantValue_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:139:
error: ‘BlockingSynapse_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:140:
error: ‘Block_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:141:
error: ‘MultiDecaySynapse_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:142:
error: ‘FacDepSynapse_p’ was not declared in this scope
........
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:435:
error: ‘InputSite_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:437:
error: ‘CellIdInNetwork_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:439:
error: ‘all_cells_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:439:
error: ‘percentage_cells_p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:441:
error: ‘Percentage_p’ was not declared in this scope
make[2]: *** [pcsim/CMakeFiles/pcsim.dir/neuroml/parser/cxxproxy/morphml/CxxProxyCell.o]
Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [pcsim/CMakeFiles/pcsim.dir/neuroml/NeuroMLImporter.o] Error 1
make[1]: *** [pcsim/CMakeFiles/pcsim.dir/all] Error 2
make: *** [all] Error 2
BUILD PROCESS FAILED. ERROR = 512
Command: /usr/bin/make -j 2 install

Perhaps you can help me again.
Thank you for your reply again, and any other kind of help is appreciated also.

If there are someone installed it successfully, the experience you
shared will help me a lot! You can tell me your linux distribution
version, gcc version, python version and etc. Thanks in advance.

Best Regards.
Hou Zhicheng.