pcsim-users — List for PCSIM users to help each other and share knowledge.

Re: [Pcsim-users] Building extension modules with construction elements

[Pecevski D. <de...@ig...>]

Hi Chris,

To fix the reported problem, change the lines 330 and 331 in 
pcsim_module_builder.py to:

C.constructors( arg_types = [ "::SimNetwork &", "::SimObjectFactory *", 
"::boost::shared_ptr<Point3DSet>" ], allow_empty = True ).call_policies 
= cp.with_custodian_and_ward(1, 4, cp.default_call_policies())

C.constructors( arg_types = [ "::SimNetwork &", 
"::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> > 
const &", "::SpatialFamilyIDGenerator const &", 
"::boost::shared_ptr<Point3DSet>" ], allow_empty = True ).call_policies 
= cp.with_custodian_and_ward(1, 5, cp.default_call_policies())

While testing this, I also run into problems with undefined references 
for the xerces library. To fix this additional problem you
should change all the TARGET_LINK_LIBRARIES commands in the 
CMakeLists.txt file located in the pcsim extension module root directory
to include the  ${XERCES_LIBS} libraries, i.e.

TARGET_LINK_LIBRARIES(
  ${MYPYPCSIM}   
      ${PCSIM_MODULE_NAME}
      pcsim  
      ${MPI_LIBS}
      ${GSL_LIBS}
      ${BOOST_LIBS}
      ${STLP_LIBS}
)

to

TARGET_LINK_LIBRARIES(
  ${MYPYPCSIM}   
      ${PCSIM_MODULE_NAME}
      pcsim
      ${XERCES_LIBS}     
      ${MPI_LIBS}
      ${GSL_LIBS}
      ${BOOST_LIBS}
      ${STLP_LIBS}
)

and so on.

The fixes I described here will be updated in the repository and 
included in the next PCSIM release.

Cheers,
Dejan

Christopher Nolan wrote:
>
> Hi all,
>
>  
>
> (This is my third attempt sending this email, I believe the address 
> was invalid on previous attempts, so my apologies if this message ends 
> up spamming the list)
>
>  
>
> I'm building an extension module containing a new 
> ConnectionDecisionPredicate, however when I try to build according to 
> the instructions in the extension template README, I've been getting 
> an error.  To make sure it wasn't my code, I created a new extension 
> template, made a copy of the 
> LateralEuclidianDistanceConnectionPredicate, changed its class name 
> etc. to TestEuclidianDistanceConnectionPredicate, and tried to build 
> that as the sole target of the extension.  This build resulted in the 
> same error.  I've pasted the whole build output at the bottom, but in 
> short it is failing at line 332 of pcsim_module_builder.py:
>
>  
>
> C.constructor( arg_types = [ "::SimNetwork &", 
> "::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> > 
> const &", "::SpatialFamilyIDGenerator const &", 
> "::boost::shared_ptr<Point3DSet>" ] ).call_policies = 
> cp.with_custodian_and_ward(1, 5, cp.default_call_policies())
>
>  
>
> Any ideas? (the default template builds without problems)
>
>  
>
> Cheers,
>
> Chris.
>
>  
>
> ---
>
> Build output:
>
>  
>
>    Build type   = Release
>
>    Platform     = linux-unknown
>
>    Make tool    = /usr/bin/make
>
>    Make command = /usr/bin/make -i
>
>    Python executable : /usr/bin/python version 2.5
>
>    Python libraries : /usr/lib/python2.5/config
>
>    Python includes : /usr/include/python2.5
>
>    Doxygen executable : /usr/bin/doxygen
>
>    GCCXML executable : /usr/local/bin/gccxml
>
>    Boost C++ library boost_python : /usr/lib/libboost_python-mt.so
>
>    Boost C++ library boost_thread : /usr/lib/libboost_thread-mt.so
>
>    Boost C++ library boost_date_time : /usr/lib/libboost_date_time-mt.so
>
>    Boost C++ libraries : /usr/lib
>
>    Boost C++ include path : /usr/include
>
>    MPICH2 library: /usr/lib/libmpich.so
>
>    MPICH2 include path : /usr/include
>
>    GNU Scientific library : /usr/lib/libgsl.so
>
>    Xerces library : /usr/lib/libxerces-c.so
>
>    CppUnit : /usr/lib/libcppunit.so
>
> -- Configuring done
>
> -- Generating done
>
> -- Build files have been written to: 
> /home/cnolan/Development/pcsim_ext/test/build
>
> [ 33%] Generating pytest/pytest.main.cpp, pytest/pytest.indicator.cpp
>
>  
>
> INFO Parsing source file 
> "/home/cnolan/Development/pcsim_ext/test/build/pytest.h" ...
>
>  
>
> INFO gccxml cmd: /usr/local/bin/gccxml  --gccxml-cxxflags -pthread   
> -I"." -I"src" -I"/home/cnolan/Development/pcsim-active/pcsim/simutils" 
> -I"/home/cnolan/Development/pcsim-active/pcsim/simcore" 
> -I"/home/cnolan/Development/pcsim-active/pcsim/construction" 
> -I"/home/cnolan/Development/pcsim-active/pcsim/simobjects" 
> -I"/usr/include" -I"/usr/include" -I"/usr/include" 
> -I"/home/cnolan/Development/pcsim-active/python"  
> -D"MPICH_IGNORE_CXX_SEEK" -D"BOOST_HAS_THREADS" 
> -D"BOOST_PYTHON_MAX_ARITY=30"  
> "/home/cnolan/Development/pcsim_ext/test/build/pytest.h" 
> -fxml="/tmp/tmp7uXm-d.xml"
>
>  
>
> INFO GCCXML version - 0.9
>
> /usr/lib/python2.5/site-packages/pygccxml/parser/scanner.py:335: 
> UserWarning: unable to find out array size from expression ""
>
>   warnings.warn( msg )
>
>  
>
> DISABLED warning W1007: The function has more than %d arguments ( %d 
> ). You should adjust BOOST_PYTHON_MAX_ARITY macro. For more DISABLED 
> compilation error W1033: Py++ can not expose unnamed variables 
> DISABLED compilation error W1014: "%s" is not supported. See 
> Boost.Python documentation: http://www.boost.org/libs/python/doc/v2/
>
> DISABLED warning W1043: Py++ created an ugly alias ("%s") for template 
> instantiated class.
>
> DISABLED compilation error W1036: Py++ can not expose pointer to 
> Python immutable member variables. This could be changed in futu 
> DISABLED execution error W1040: The declaration is unexposed, but 
> there are other declarations, which refer to it. This could cau 
> Traceback (most recent call last):
>
>   File 
> "/home/cnolan/Development/pcsim-active/scripts/generate_boost_python_wrapper_code.py", 
> line 192, in <module>
>
>     pypcsim_module.specify_exclusions( M, options)   
>
>   File 
> "/home/cnolan/Development/pcsim-active/python/pcsim_module_builder.py", 
> line 332, in specify_exclusions
>
>     C.constructor( arg_types = [ "::SimNetwork &", 
> "::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> > 
> const &", "::SpatialFamilyIDGenerator const &", 
> "::boost::shared_ptr<Point3DSet>" ] ).call_policies = 
> cp.with_custodian_and_ward(1, 5, cp.default_call_policies())
>
>   File 
> "/usr/lib/python2.5/site-packages/pygccxml/declarations/scopedef.py", 
> line 520, in constructor
>
>     , recursive=recursive )
>
>   File 
> "/usr/lib/python2.5/site-packages/pygccxml/declarations/scopedef.py", 
> line 343, in _find_single
>
>     found = matcher_module.matcher.get_single( matcher, decls, False )
>
>   File 
> "/usr/lib/python2.5/site-packages/pygccxml/declarations/matcher.py", 
> line 79, in get_single
>
>     raise matcher.declaration_not_found_t( decl_matcher )
>
> pygccxml.declarations.matcher.declaration_not_found_t: Unable to find 
> declaration.  matcher: [(decl type==constructor_t) and (arg 0 
> type==::SimNetwork &) and (arg 1 
> type==::std::vector<SimObjectFactory*, 
> std::allocator<SimObjectFactory*> > const &) and (arg 2 
> type==::SpatialFamilyIDGenerator const &) and (arg 3 
> type==::boost::shared_ptr<Point3DSet>)]
>
> make[3]: *** [pytest/pytest.main.cpp] Error 1
>
> make[2]: *** [CMakeFiles/generate_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: make generate_code
>
> >>>> cd /home/cnolan/Development/pcsim_ext/test/build
>
> >>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release ..
>
> >>>> cd /home/cnolan/Development/pcsim_ext/test/build
>
> >>>> make generate_code
>
>  
>
>  
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>   

[Pcsim-users] Building extension modules with construction elements

[Christopher N. <cn...@it...>]

Hi all,

 

(This is my third attempt sending this email, I believe the address was
invalid on previous attempts, so my apologies if this message ends up
spamming the list)

 

I'm building an extension module containing a new
ConnectionDecisionPredicate, however when I try to build according to
the instructions in the extension template README, I've been getting an
error.  To make sure it wasn't my code, I created a new extension
template, made a copy of the
LateralEuclidianDistanceConnectionPredicate, changed its class name etc.
to TestEuclidianDistanceConnectionPredicate, and tried to build that as
the sole target of the extension.  This build resulted in the same
error.  I've pasted the whole build output at the bottom, but in short
it is failing at line 332 of pcsim_module_builder.py:

 

C.constructor( arg_types = [ "::SimNetwork &",
"::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> >
const &", "::SpatialFamilyIDGenerator const &",
"::boost::shared_ptr<Point3DSet>" ] ).call_policies =
cp.with_custodian_and_ward(1, 5, cp.default_call_policies())

 

Any ideas? (the default template builds without problems)

 

Cheers,

Chris.

 

---

Build output:

 

   Build type   = Release

   Platform     = linux-unknown

   Make tool    = /usr/bin/make

   Make command = /usr/bin/make -i

   Python executable : /usr/bin/python version 2.5 

   Python libraries : /usr/lib/python2.5/config

   Python includes : /usr/include/python2.5

   Doxygen executable : /usr/bin/doxygen

   GCCXML executable : /usr/local/bin/gccxml

   Boost C++ library boost_python : /usr/lib/libboost_python-mt.so

   Boost C++ library boost_thread : /usr/lib/libboost_thread-mt.so

   Boost C++ library boost_date_time : /usr/lib/libboost_date_time-mt.so

   Boost C++ libraries : /usr/lib 

   Boost C++ include path : /usr/include 

   MPICH2 library: /usr/lib/libmpich.so

   MPICH2 include path : /usr/include

   GNU Scientific library : /usr/lib/libgsl.so

   Xerces library : /usr/lib/libxerces-c.so

   CppUnit : /usr/lib/libcppunit.so

-- Configuring done

-- Generating done

-- Build files have been written to:
/home/cnolan/Development/pcsim_ext/test/build

[ 33%] Generating pytest/pytest.main.cpp, pytest/pytest.indicator.cpp

 

INFO Parsing source file
"/home/cnolan/Development/pcsim_ext/test/build/pytest.h" ... 

 

INFO gccxml cmd: /usr/local/bin/gccxml  --gccxml-cxxflags -pthread
-I"." -I"src" -I"/home/cnolan/Development/pcsim-active/pcsim/simutils"
-I"/home/cnolan/Development/pcsim-active/pcsim/simcore"
-I"/home/cnolan/Development/pcsim-active/pcsim/construction"
-I"/home/cnolan/Development/pcsim-active/pcsim/simobjects"
-I"/usr/include" -I"/usr/include" -I"/usr/include"
-I"/home/cnolan/Development/pcsim-active/python"
-D"MPICH_IGNORE_CXX_SEEK" -D"BOOST_HAS_THREADS"
-D"BOOST_PYTHON_MAX_ARITY=30"
"/home/cnolan/Development/pcsim_ext/test/build/pytest.h"
-fxml="/tmp/tmp7uXm-d.xml"

 

INFO GCCXML version - 0.9

/usr/lib/python2.5/site-packages/pygccxml/parser/scanner.py:335:
UserWarning: unable to find out array size from expression ""

  warnings.warn( msg )

 

DISABLED warning W1007: The function has more than %d arguments ( %d ).
You should adjust BOOST_PYTHON_MAX_ARITY macro. For more DISABLED
compilation error W1033: Py++ can not expose unnamed variables DISABLED
compilation error W1014: "%s" is not supported. See Boost.Python
documentation: http://www.boost.org/libs/python/doc/v2/

DISABLED warning W1043: Py++ created an ugly alias ("%s") for template
instantiated class.

DISABLED compilation error W1036: Py++ can not expose pointer to Python
immutable member variables. This could be changed in futu DISABLED
execution error W1040: The declaration is unexposed, but there are other
declarations, which refer to it. This could cau Traceback (most recent
call last):

  File
"/home/cnolan/Development/pcsim-active/scripts/generate_boost_python_wra
pper_code.py", line 192, in <module>

    pypcsim_module.specify_exclusions( M, options)    

  File
"/home/cnolan/Development/pcsim-active/python/pcsim_module_builder.py",
line 332, in specify_exclusions

    C.constructor( arg_types = [ "::SimNetwork &",
"::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> >
const &", "::SpatialFamilyIDGenerator const &",
"::boost::shared_ptr<Point3DSet>" ] ).call_policies =
cp.with_custodian_and_ward(1, 5, cp.default_call_policies())

  File
"/usr/lib/python2.5/site-packages/pygccxml/declarations/scopedef.py",
line 520, in constructor

    , recursive=recursive )

  File
"/usr/lib/python2.5/site-packages/pygccxml/declarations/scopedef.py",
line 343, in _find_single

    found = matcher_module.matcher.get_single( matcher, decls, False )

  File
"/usr/lib/python2.5/site-packages/pygccxml/declarations/matcher.py",
line 79, in get_single

    raise matcher.declaration_not_found_t( decl_matcher )

pygccxml.declarations.matcher.declaration_not_found_t: Unable to find
declaration.  matcher: [(decl type==constructor_t) and (arg 0
type==::SimNetwork &) and (arg 1 type==::std::vector<SimObjectFactory*,
std::allocator<SimObjectFactory*> > const &) and (arg 2
type==::SpatialFamilyIDGenerator const &) and (arg 3
type==::boost::shared_ptr<Point3DSet>)]

make[3]: *** [pytest/pytest.main.cpp] Error 1

make[2]: *** [CMakeFiles/generate_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: make generate_code

>>>> cd /home/cnolan/Development/pcsim_ext/test/build

>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release ..

>>>> cd /home/cnolan/Development/pcsim_ext/test/build

>>>> make generate_code

 

 

[Pcsim-users] Building extension modules with construction elements

[Christopher N. <cn...@it...>]

Hi all,

(Resending without the attachment, the first attempt didn't seem to work, apologies if this appears twice)

I'm building an extension module containing a new ConnectionDecisionPredicate, however when I try to build according to the instructions in the extension template README, I've been getting an error.  To make sure it wasn't my code, I created a new extension template, made a copy of the LateralEuclidianDistanceConnectionPredicate, changed its class name etc. to TestEuclidianDistanceConnectionPredicate, and tried to build that as the sole target of the extension.  This build resulted in the same error.  I've pasted the whole build output at the bottom, but in short it is failing at line 332 of pcsim_module_builder.py:

C.constructor( arg_types = [ "::SimNetwork &", "::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> > const &", "::SpatialFamilyIDGenerator const &", "::boost::shared_ptr<Point3DSet>" ] ).call_policies = cp.with_custodian_and_ward(1, 5, cp.default_call_policies())

Any ideas? (the default template builds without problems)

Cheers,
Chris.

---
Build output:

   Build type   = Release
   Platform     = linux-unknown
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.5 
   Python libraries : /usr/lib/python2.5/config
   Python includes : /usr/include/python2.5
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/local/bin/gccxml
   Boost C++ library boost_python : /usr/lib/libboost_python-mt.so
   Boost C++ library boost_thread : /usr/lib/libboost_thread-mt.so
   Boost C++ library boost_date_time : /usr/lib/libboost_date_time-mt.so
   Boost C++ libraries : /usr/lib 
   Boost C++ include path : /usr/include 
   MPICH2 library: /usr/lib/libmpich.so
   MPICH2 include path : /usr/include
   GNU Scientific library : /usr/lib/libgsl.so
   Xerces library : /usr/lib/libxerces-c.so
   CppUnit : /usr/lib/libcppunit.so
-- Configuring done
-- Generating done
-- Build files have been written to: /home/cnolan/Development/pcsim_ext/test/build
[ 33%] Generating pytest/pytest.main.cpp, pytest/pytest.indicator.cpp

INFO Parsing source file "/home/cnolan/Development/pcsim_ext/test/build/pytest.h" ... 

INFO gccxml cmd: /usr/local/bin/gccxml  --gccxml-cxxflags -pthread   -I"." -I"src" -I"/home/cnolan/Development/pcsim-active/pcsim/simutils" -I"/home/cnolan/Development/pcsim-active/pcsim/simcore" -I"/home/cnolan/Development/pcsim-active/pcsim/construction" -I"/home/cnolan/Development/pcsim-active/pcsim/simobjects" -I"/usr/include" -I"/usr/include" -I"/usr/include" -I"/home/cnolan/Development/pcsim-active/python"  -D"MPICH_IGNORE_CXX_SEEK" -D"BOOST_HAS_THREADS" -D"BOOST_PYTHON_MAX_ARITY=30"  "/home/cnolan/Development/pcsim_ext/test/build/pytest.h" -fxml="/tmp/tmp7uXm-d.xml"

INFO GCCXML version - 0.9
/usr/lib/python2.5/site-packages/pygccxml/parser/scanner.py:335: UserWarning: unable to find out array size from expression ""
  warnings.warn( msg )

DISABLED warning W1007: The function has more than %d arguments ( %d ). You should adjust BOOST_PYTHON_MAX_ARITY macro. For more 
DISABLED compilation error W1033: Py++ can not expose unnamed variables
DISABLED compilation error W1014: "%s" is not supported. See Boost.Python documentation: http://www.boost.org/libs/python/doc/v2/
DISABLED warning W1043: Py++ created an ugly alias ("%s") for template instantiated class.
DISABLED compilation error W1036: Py++ can not expose pointer to Python immutable member variables. This could be changed in futu
DISABLED execution error W1040: The declaration is unexposed, but there are other declarations, which refer to it. This could cau
Traceback (most recent call last):
  File "/home/cnolan/Development/pcsim-active/scripts/generate_boost_python_wrapper_code.py", line 192, in <module>
    pypcsim_module.specify_exclusions( M, options)    
  File "/home/cnolan/Development/pcsim-active/python/pcsim_module_builder.py", line 332, in specify_exclusions
    C.constructor( arg_types = [ "::SimNetwork &", "::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> > const &", "::SpatialFamilyIDGenerator const &", "::boost::shared_ptr<Point3DSet>" ] ).call_policies = cp.with_custodian_and_ward(1, 5, cp.default_call_policies())
  File "/usr/lib/python2.5/site-packages/pygccxml/declarations/scopedef.py", line 520, in constructor
    , recursive=recursive )
  File "/usr/lib/python2.5/site-packages/pygccxml/declarations/scopedef.py", line 343, in _find_single
    found = matcher_module.matcher.get_single( matcher, decls, False )
  File "/usr/lib/python2.5/site-packages/pygccxml/declarations/matcher.py", line 79, in get_single
    raise matcher.declaration_not_found_t( decl_matcher )
pygccxml.declarations.matcher.declaration_not_found_t: Unable to find declaration.  matcher: [(decl type==constructor_t) and (arg 0 type==::SimNetwork &) and (arg 1 type==::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> > const &) and (arg 2 type==::SpatialFamilyIDGenerator const &) and (arg 3 type==::boost::shared_ptr<Point3DSet>)]
make[3]: *** [pytest/pytest.main.cpp] Error 1
make[2]: *** [CMakeFiles/generate_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: make generate_code
>>>> cd /home/cnolan/Development/pcsim_ext/test/build
>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release ..
>>>> cd /home/cnolan/Development/pcsim_ext/test/build
>>>> make generate_code

[Pcsim-users] Building extension modules with construction elements

[Christopher N. <cn...@it...>]

   Build type   = Release
   Platform     = linux-unknown
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.5 
   Python libraries : /usr/lib/python2.5/config
   Python includes : /usr/include/python2.5
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/local/bin/gccxml
   Boost C++ library boost_python : /usr/lib/libboost_python-mt.so
   Boost C++ library boost_thread : /usr/lib/libboost_thread-mt.so
   Boost C++ library boost_date_time : /usr/lib/libboost_date_time-mt.so
   Boost C++ libraries : /usr/lib 
   Boost C++ include path : /usr/include 
   MPICH2 library: /usr/lib/libmpich.so
   MPICH2 include path : /usr/include
   GNU Scientific library : /usr/lib/libgsl.so
   Xerces library : /usr/lib/libxerces-c.so
   CppUnit : /usr/lib/libcppunit.so
-- Configuring done
-- Generating done
-- Build files have been written to: /home/cnolan/Development/pcsim_ext/test/build
[ 33%] Generating pytest/pytest.main.cpp, pytest/pytest.indicator.cpp

INFO Parsing source file "/home/cnolan/Development/pcsim_ext/test/build/pytest.h" ... 

INFO gccxml cmd: /usr/local/bin/gccxml  --gccxml-cxxflags -pthread   -I"." -I"src" -I"/home/cnolan/Development/pcsim-active/pcsim/simutils" -I"/home/cnolan/Development/pcsim-active/pcsim/simcore" -I"/home/cnolan/Development/pcsim-active/pcsim/construction" -I"/home/cnolan/Development/pcsim-active/pcsim/simobjects" -I"/usr/include" -I"/usr/include" -I"/usr/include" -I"/home/cnolan/Development/pcsim-active/python"  -D"MPICH_IGNORE_CXX_SEEK" -D"BOOST_HAS_THREADS" -D"BOOST_PYTHON_MAX_ARITY=30"  "/home/cnolan/Development/pcsim_ext/test/build/pytest.h" -fxml="/tmp/tmp7uXm-d.xml"

INFO GCCXML version - 0.9
/usr/lib/python2.5/site-packages/pygccxml/parser/scanner.py:335: UserWarning: unable to find out array size from expression ""
  warnings.warn( msg )

DISABLED warning W1007: The function has more than %d arguments ( %d ). You should adjust BOOST_PYTHON_MAX_ARITY macro. For more 
DISABLED compilation error W1033: Py++ can not expose unnamed variables
DISABLED compilation error W1014: "%s" is not supported. See Boost.Python documentation: http://www.boost.org/libs/python/doc/v2/
DISABLED warning W1043: Py++ created an ugly alias ("%s") for template instantiated class.
DISABLED compilation error W1036: Py++ can not expose pointer to Python immutable member variables. This could be changed in futu
DISABLED execution error W1040: The declaration is unexposed, but there are other declarations, which refer to it. This could cau
Traceback (most recent call last):
  File "/home/cnolan/Development/pcsim-active/scripts/generate_boost_python_wrapper_code.py", line 192, in <module>
    pypcsim_module.specify_exclusions( M, options)    
  File "/home/cnolan/Development/pcsim-active/python/pcsim_module_builder.py", line 332, in specify_exclusions
    C.constructor( arg_types = [ "::SimNetwork &", "::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> > const &", "::SpatialFamilyIDGenerator const &", "::boost::shared_ptr<Point3DSet>" ] ).call_policies = cp.with_custodian_and_ward(1, 5, cp.default_call_policies())
  File "/usr/lib/python2.5/site-packages/pygccxml/declarations/scopedef.py", line 520, in constructor
    , recursive=recursive )
  File "/usr/lib/python2.5/site-packages/pygccxml/declarations/scopedef.py", line 343, in _find_single
    found = matcher_module.matcher.get_single( matcher, decls, False )
  File "/usr/lib/python2.5/site-packages/pygccxml/declarations/matcher.py", line 79, in get_single
    raise matcher.declaration_not_found_t( decl_matcher )
pygccxml.declarations.matcher.declaration_not_found_t: Unable to find declaration.  matcher: [(decl type==constructor_t) and (arg 0 type==::SimNetwork &) and (arg 1 type==::std::vector<SimObjectFactory*, std::allocator<SimObjectFactory*> > const &) and (arg 2 type==::SpatialFamilyIDGenerator const &) and (arg 3 type==::boost::shared_ptr<Point3DSet>)]
make[3]: *** [pytest/pytest.main.cpp] Error 1
make[2]: *** [CMakeFiles/generate_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: make generate_code
>>>> cd /home/cnolan/Development/pcsim_ext/test/build
>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release ..
>>>> cd /home/cnolan/Development/pcsim_ext/test/build
>>>> make generate_code

Re: [Pcsim-users] Editing object properties

[Christopher N. <cn...@it...>]

Hi Dejan,

collectIDs does the trick.  Many thanks.

Cheers,
Chris.


-----Original Message-----
From: pcs...@li...
[mailto:pcs...@li...] On Behalf Of Pecevski
Dejan
Sent: Friday, 19 September 2008 12:57 AM
To: pcs...@li...
Subject: Re: [Pcsim-users] Editing object properties

Hi Chris,

a_b_syn_project = ConnectionsProjection(
    a_nrn_popul, a_b_nrn_popul, a_b_syn_factory,
 
PredicateBasedConnections(EuclidianDistanceConnectionPredicate(a_b_connp
, 20 )),
    collectIDs = True, collectPairs = True )

would do the job.

Notice the collectIDs flag set to true.


Best,
Dejan


Christopher Nolan wrote:
> Hi all,
>
> How can I change the properties of an existing object?  I've created
> some connections with
>
> a_b_syn_project = ConnectionsProjection(
>     a_nrn_popul, a_b_nrn_popul, a_b_syn_factory,
>     PredicateBasedConnections(EuclidianDistanceConnectionPredicate(
> a_b_connp, 20 )),
>     collectPairs = True )
>
> After simulating for some amount of time, I want to change the weights
> of these connections.  I can get the object ids with e.g.
> a_b_syn_project(0), but if I try to get the object handle with
> net.object(a_b_syn_project(0)), python segfaults, so I guess that's
not
> the correct method.
>
> Any ideas?
>
> Cheers,
> Chris.
>
>
>
------------------------------------------------------------------------
-
> This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
> Build the coolest Linux based applications with Moblin SDK & win great
prizes
> Grand prize is a trip for two to an Open Source event anywhere in the
world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>   


------------------------------------------------------------------------
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the
world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Pcsim-users mailing list
Pcs...@li...
https://lists.sourceforge.net/lists/listinfo/pcsim-users

Re: [Pcsim-users] Editing object properties

[Pecevski D. <de...@ig...>]

Hi Chris,

a_b_syn_project = ConnectionsProjection(
    a_nrn_popul, a_b_nrn_popul, a_b_syn_factory,
    PredicateBasedConnections(EuclidianDistanceConnectionPredicate(a_b_connp, 20 )),
    collectIDs = True, collectPairs = True )

would do the job.

Notice the collectIDs flag set to true.


Best,
Dejan


Christopher Nolan wrote:
> Hi all,
>
> How can I change the properties of an existing object?  I've created
> some connections with
>
> a_b_syn_project = ConnectionsProjection(
>     a_nrn_popul, a_b_nrn_popul, a_b_syn_factory,
>     PredicateBasedConnections(EuclidianDistanceConnectionPredicate(
> a_b_connp, 20 )),
>     collectPairs = True )
>
> After simulating for some amount of time, I want to change the weights
> of these connections.  I can get the object ids with e.g.
> a_b_syn_project(0), but if I try to get the object handle with
> net.object(a_b_syn_project(0)), python segfaults, so I guess that's not
> the correct method.
>
> Any ideas?
>
> Cheers,
> Chris.
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>   

[Pcsim-users] Editing object properties

[Christopher N. <cn...@it...>]

Hi all,

How can I change the properties of an existing object?  I've created
some connections with

a_b_syn_project = ConnectionsProjection(
    a_nrn_popul, a_b_nrn_popul, a_b_syn_factory,
    PredicateBasedConnections(EuclidianDistanceConnectionPredicate(
a_b_connp, 20 )),
    collectPairs = True )

After simulating for some amount of time, I want to change the weights
of these connections.  I can get the object ids with e.g.
a_b_syn_project(0), but if I try to get the object handle with
net.object(a_b_syn_project(0)), python segfaults, so I guess that's not
the correct method.

Any ideas?

Cheers,
Chris.

Re: [Pcsim-users] How to make an all-to-all projection

[Natschläger T. <Tho...@sc...>]

Hi:

Actually the RandomConnections with conn_prob = 1 is implemented such that no random generator is called (see file RandomConnections.cpp).
Hence RandomConnections( conn_prob = 1 ) seems a good way to implement a all-to-all connectivity.

Nevertheless it seems a good idea to include a AllToAllConections class in the PCSIM release.

Regards

  -thomas natschlager

-----Original Message-----
From: pcs...@li... on behalf of de...@ig...
Sent: Sat 9/13/2008 10:42 AM
To: pcs...@li...
Subject: Re: [Pcsim-users] How to make an all-to-all projection
 
Hi Mathieu,

Currently this is the only way to create all-to-all connectivity. Off  
course, it's not the optimal way since at each neuron pair a RNG is  
polled to decide whether a connection is to be formed. One can  
implement AllToAllConnectionIterator for this purpose (if it's not  
already there), or else
derive from ConnectionDecisionPredicate a TruePredicate which always  
decides True and then use it with:

proj = ConnectionsProjection( pop1, pop2, StaticSpikingSynapse(),
                               PredicateBasedConnections( TruePredicate() ) )


SimpleAllToAllWiringMethod is not meant for all-to-all connectivity  
projections.
WiringMethod classes are for optimization of connection creations in  
distributed mode for large networks, and are always used with  
ConnectionIterator. The actual logic is contained in the  
ConnectionIterator class.

regards,
Dejan




Quoting Mathieu Dubois <mat...@li...>:

> Hi everybody,
>
> This may seem a dumb question but I don't understand how can I make an
> all-to-all connection from one population to one other (the context is:
> connecting a reservoir to readout neurons).
>
> For the moment, I use a RandomConnections with a probability of 1. This is
> certainly not the best way. I have looked at Class
> SimpleAllToAllWiringMethod but I was unable to use it correctly.
>
> Could anyone provide a working example? I use a modest size reservoir so
> parallelization is not an issue.
>
> Thanks in advance (class AdvanceInfo),
> Mathieu
>
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>



-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Pcsim-users mailing list
Pcs...@li...
https://lists.sourceforge.net/lists/listinfo/pcsim-users

Re: [Pcsim-users] How to make an all-to-all projection

[<de...@ig...>]

Hi Mathieu,

Currently this is the only way to create all-to-all connectivity. Off  
course, it's not the optimal way since at each neuron pair a RNG is  
polled to decide whether a connection is to be formed. One can  
implement AllToAllConnectionIterator for this purpose (if it's not  
already there), or else
derive from ConnectionDecisionPredicate a TruePredicate which always  
decides True and then use it with:

proj = ConnectionsProjection( pop1, pop2, StaticSpikingSynapse(),
                               PredicateBasedConnections( TruePredicate() ) )


SimpleAllToAllWiringMethod is not meant for all-to-all connectivity  
projections.
WiringMethod classes are for optimization of connection creations in  
distributed mode for large networks, and are always used with  
ConnectionIterator. The actual logic is contained in the  
ConnectionIterator class.

regards,
Dejan




Quoting Mathieu Dubois <mat...@li...>:

> Hi everybody,
>
> This may seem a dumb question but I don't understand how can I make an
> all-to-all connection from one population to one other (the context is:
> connecting a reservoir to readout neurons).
>
> For the moment, I use a RandomConnections with a probability of 1. This is
> certainly not the best way. I have looked at Class
> SimpleAllToAllWiringMethod but I was unable to use it correctly.
>
> Could anyone provide a working example? I use a modest size reservoir so
> parallelization is not an issue.
>
> Thanks in advance (class AdvanceInfo),
> Mathieu
>
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>

[Pcsim-users] How to make an all-to-all projection

[Mathieu D. <mat...@li...>]

Hi everybody,

This may seem a dumb question but I don't understand how can I make an
all-to-all connection from one population to one other (the context is:
connecting a reservoir to readout neurons).

For the moment, I use a RandomConnections with a probability of 1. This is
certainly not the best way. I have looked at Class
SimpleAllToAllWiringMethod but I was unable to use it correctly.

Could anyone provide a working example? I use a modest size reservoir so
parallelization is not an issue.

Thanks in advance (class AdvanceInfo),
Mathieu

Re: [Pcsim-users] noisy DA modulated STDP synapses - how to add OU noise to a neuron?

[Robert I. <ri...@gm...>]

Hello Dejan,

Thank you for the information. I added the noise to the neurons in the model
as you pointed out and I got spontaneus activity in the network.

Thank you again.

All the best,
Robert.

On Fri, Aug 29, 2008 at 7:49 AM, Pecevski Dejan <de...@ig...> wrote:

>
> Hi Robert,
>
> the following code will add the corresponding excitatory and inhibitory
> parts of the
> Ornstein-Uhlenbeck Noise in the DARecvCbLifNeuron:
>
> net.mount(OUNoiseSynapse(0.012e-6, 0.003e-6, 2.7e-3, 0.0), neuron_id_array)
> net.mount(OUNoiseSynapse(0.057e-6, 0.0066e-6, 10.5e-3,-75e-3),
> neuron_id_array)
>
> The OUNoiseSynapse if attached/mounted to a neuron injects OU noise in the
> neuron.
>
> cheers!
> Dejan
>
>>
>>
>

Re: [Pcsim-users] noisy DA modulated STDP synapses - how to add OU noise to a neuron?

[Pecevski D. <de...@ig...>]

Robert Ioiart wrote:
> Hello,
>
> I am a newcomer to PCSIM and as exercise I started implementing the 
> simulations from [LegensteinPecevskiMaass2008].
>
> I got stuck when I tried to define the neuron model, let me explain why.
>
> The simulations in [LegensteinPecevskiMaass2008] use LIF neurons with 
> conductance based synapses subjected to short term dynamics and DA 
> modulated STDP.
>
> My first guess was to use the following built-in types:
> DARecvCbLifNeuron - for the neurons
> DAModStdpDynamicCondExpSynapse - for the synapses
>
> The neurons also receive Ornstein-Uhlenbeck noise as conductance 
> input, but I could not find a built-in neuron or synapse model that 
> incorporates all the above mentioned processes AND noise as well.
>
> My best guess at the moment (after studying the c++ class reference 
> and source code) is that in order to have a OU-noisy DARecvCbLifNeuron 
> I have to extend PCSIM by implementing a class that extends both 
> DARecvCbLifNeuron and OUNoiseGenerator and that implements the virtual 
> method conductanceNoiseInput.
> Something like:
>
> class DARecvCbLifOUNoisyNeuron : public DARecvCbLifNeuron, public 
> OUNoiseGenerator
> {
>  
> SIMOBJECT( CbLifNeuron, AdvancePhase::One )
>
> public:
> ...the constructor taking all the parameters...
>
> virtual double conductanceNoiseInput(){
>    OUNoiseGenerator::advance();
>    return OUNoiseGenerator::getValue();
> }
>
> virtual int reset(double dt){
> return (OUNoiseGenerator::reset(dt) || DARecvCbLifNeuron::reset(dt));
> }
>
> virtual int adjust(double dt){
> return (OUNoiseGenerator::adjust(dt) || DARecvCbLifNeuron::adjust(dt));
> }
>
> }//class
>
> Is this the correct aproach? Is there a simpler way to add noise to a 
> neuron?
Hi Robert,

the following code will add the corresponding excitatory and inhibitory 
parts of the
Ornstein-Uhlenbeck Noise in the DARecvCbLifNeuron:

net.mount(OUNoiseSynapse(0.012e-6, 0.003e-6, 2.7e-3, 0.0), neuron_id_array)
net.mount(OUNoiseSynapse(0.057e-6, 0.0066e-6, 10.5e-3,-75e-3), 
neuron_id_array)

The OUNoiseSynapse if attached/mounted to a neuron injects OU noise in 
the neuron.

cheers!
Dejan
>

[Pcsim-users] noisy DA modulated STDP synapses - how to add OU noise to a neuron?

[Robert I. <ri...@gm...>]

Hello,

I am a newcomer to PCSIM and as exercise I started implementing the
simulations from [LegensteinPecevskiMaass2008].

I got stuck when I tried to define the neuron model, let me explain why.

The simulations in [LegensteinPecevskiMaass2008] use LIF neurons with
conductance based synapses subjected to short term dynamics and DA modulated
STDP.

My first guess was to use the following built-in types:
DARecvCbLifNeuron - for the neurons
DAModStdpDynamicCondExpSynapse - for the synapses

The neurons also receive Ornstein-Uhlenbeck noise as conductance input, but
I could not find a built-in neuron or synapse model that incorporates all
the above mentioned processes AND noise as well.

My best guess at the moment (after studying the c++ class reference and
source code) is that in order to have a OU-noisy DARecvCbLifNeuron I have to
extend PCSIM by implementing a class that extends both DARecvCbLifNeuron and
OUNoiseGenerator and that implements the virtual method
conductanceNoiseInput.
Something like:

class DARecvCbLifOUNoisyNeuron : public DARecvCbLifNeuron, public
OUNoiseGenerator
{

SIMOBJECT( CbLifNeuron, AdvancePhase::One )

public:
...the constructor taking all the parameters...

virtual double conductanceNoiseInput(){
   OUNoiseGenerator::advance();
   return OUNoiseGenerator::getValue();
}

virtual int reset(double dt){
return (OUNoiseGenerator::reset(dt) || DARecvCbLifNeuron::reset(dt));
}

virtual int adjust(double dt){
return (OUNoiseGenerator::adjust(dt) || DARecvCbLifNeuron::adjust(dt));
}

}//class

Is this the correct aproach? Is there a simpler way to add noise to a
neuron?


References:
[1] R. Legenstein, D. Pecevski, and W. Maass.* A learning theory for
reward-modulated spike-timing-dependent plasticity with application to
biofeedback*. PLoS Computational Biology, 2008. in press.


Thank you in advance.

Kind regards,
Robert.

Re: [Pcsim-users] Compiling 0.5.1

[Christopher N. <cn...@it...>]

Thanks Thomas,

> Yes your you are quite right: One has to install
> 
> xerces-c (http://xerces.apache.org/xerces-c/; I use version libxerces-c.so.270 which was preinstalled on my openSUSE 10.2) and 
> 
> XSD (http://www.codesynthesis.com/products/xsd/; the XSD runtime is a header-only library and does not require compilation)
> 

This XSD install was the one I was missing, the SVN version is
compiling happily now, however the 0.5.1 package has a new error:

Scanning dependencies of target pypcsim
[100%] [100%] Building CXX object
python/CMakeFiles/pypcsim.dir/pypcsim/warning_preventer.o
Building CXX object python/CMakeFiles/pypcsim.dir/pypcsim/pypcsim.main.o
/home/cnolan/Development/pypcsim-0.5.1/python/pypcsim/pypcsim.main.cpp:11:47: error: pypcsim/AdaptiveStepSolver.pypp.hpp: No such file or directory
...
and these missing file errors continue for a while.

I noticed the classes that were failing due to the XSD error were from a
NeuroML package, is any of this NeuroML integration functional right
now?

Cheers,
Chris.

Re: [Pcsim-users] Compiling 0.5.1

[Natschläger T. <Tho...@sc...>]

Dear Chris! 

Yes your you are quite right: One has to install

xerces-c (http://xerces.apache.org/xerces-c/; I use version libxerces-c.so.270 which was preinstalled on my openSUSE 10.2) and 

XSD (http://www.codesynthesis.com/products/xsd/; the XSD runtime is a header-only library and does not require compilation)

in order to compile the new version (compilation requires some XSD header files, linking requires libcerxes-c).


It is my fault not having documented this. I will fix this during the next days.

Regards

  -thomas natschlaeger


-----Original Message-----
From: pcs...@li... [mailto:pcs...@li...] On Behalf Of Christopher Nolan
Sent: Dienstag, 22. Juli 2008 14:10
To: pcs...@li...
Subject: [Pcsim-users] Compiling 0.5.1

Hey,

I've tried to recompile using both the packaged 0.5.1 version and the SVN version, and both are producing XSD runtime version mismatch errors, which I assume is something to do with the new xerces dependency.  Is there a particular version of xerces I'm supposed to have?

Cheers,
Chris.


-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Pcsim-users mailing list
Pcs...@li...
https://lists.sourceforge.net/lists/listinfo/pcsim-users

[Pcsim-users] Compiling 0.5.1

[Christopher N. <cn...@it...>]

Hey,

I've tried to recompile using both the packaged 0.5.1 version and the
SVN version, and both are producing XSD runtime version mismatch errors,
which I assume is something to do with the new xerces dependency.  Is
there a particular version of xerces I'm supposed to have?

Cheers,
Chris.

Re: [Pcsim-users] plot

[Mathieu D. <mat...@li...>]

Hello Dejan,

I wanted to use a ConnectionsProjection because I would like to make a 
function which look more or less like this:
plot(net, subpopulations, connections, subpop_style, connection_style)
This way it is easy to assign one style to each population (for instance 
input neurons in blue, liquid neurons in red and so on) and to each type 
of connections (also I think this is the best to describe a network).

Thank you for your help.
I will continue to work on this those days and keep you in touch.

Mathieu
Pecevski Dejan wrote:
> Mathieu Dubois wrote:
>> I want to build (and plot) the same LSM than in [1] (very similar to 
>> the one given in the Circuit-Tool tutorial).
>> I have created the liquid neurons as a spatial population with 2 
>> families:
>> liquid_nrn_popul = SpatialFamilyPopulation( net, [ exc_nrn_factory, 
>> inh_nrn_factory ], RatioBasedFamilies( EXC_INH_Ratio  ), 
>> CuboidIntegerGrid3D(LIQUID_SIZE, LIQUID_ORIGIN) );
>> so I can make the connections inside the liquid with a 
>> ConnectionsProjection and draw those synapses with the help you gave me.
>>
>> But for connecting (for instance) the input neurons to the liquid I 
>> use net.connect (as in the examples) so I cannot use a 
>> ConnectionsProjection (each input neuron is connected to the three 
>> liquid neurons at the same altitude).
>>   
> It's not clear to me why you want  to use a ConnectionsProjection?
> If I understood correctly, the connection map from input to the liquid is
> predefined, you already know which neurons to connect in the plot, so you
> probably don't need this to get the presynaptic and postsynaptic 
> neuron pairs.
>
> If you want to get the parameters of the synapses you can achieve this 
> with
> the synapses IDs.
>
> When you execute
>
> syn_id = net.connect( pre_nrn_id, post_nrn_id, StaticSpikingSynapse() )
>
> for example, then the output of net.connect is the id of the synapse 
> created.
> Now you can get this synapse with
>
> net.object(syn_id)
>
> regards,
> Dejan
>> I think that I can define a new sub-population in the liquid with the 
>> function subset (and therefore  use a ConnectionsProjection) but I 
>> cannot figure out how to do that with the online help.
>>   So my question is: How to define a subpopulation?
>>   
> You can define a new population by giving a list of IDs of the 
> simobjects:
>
> ---------------
>
> exz_nrn_popul = SimObjectPopulation(net, lifmodel, int( nNeurons *  
> Frac_EXC ) );
> inh_nrn_popul = SimObjectPopulation(net, lifmodel, nNeurons - 
> exz_nrn_popul.size() );
>
> all_nrn_popul = SimObjectPopulation(net, 
> list(exz_nrn_popul.idVector()) + list(inh_nrn_popul.idVector()));
>
> print "Created", exz_nrn_popul.size(), "exz and", 
> inh_nrn_popul.size(), "inh neurons";
> ------------
> See example : 
> http://www.lsm.tugraz.at/pcsim/examples/cuba_model_populations.py
>
> You can extract the ids of the neurons in the liquid that the input 
> neurons connect to, with
> id = liquid_popul.getIdAt( 3,4,5 ).packed()
>
> make a python list of these ids
> and then call
>
> new_popul = SimObjectPopulation( net, id_list )
>
> And then you can create the wanted projections between populations.
>
> I hope that's helpful.
>
> regards, Dejan
>
>> Thanks in advance,
>> Mathieu
>>
>> [1] "Imitation Learning with spiking networks and real-world 
>> devices", H. Burgsteiner, Engineering Applications of AI, 19, 
>> 741-752, 2006
>>
>>   
>

Re: [Pcsim-users] mpdroot problem

[Pecevski D. <de...@ig...>]

Fontaine Bertrand wrote:
>
> When I run python setup.py, at the end I get an error relaled to mpdroot:
>
> Running tests: mpiexec -l -np 4 
> /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test
> mpdroot: perror msg: Connection refused
> >>>> cd /home/Berti/Desktop/pypcsim-0.5.0/_build/bin
> >>>> mpiexec -l -np 4 
> /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test
> mpiexec_MyPC: mpd_uncaught_except_tb handling:
>   exceptions.KeyError: 'cmd'
>     /usr/local/bin/mpiexec  257  mpiexec
>         elif msg['cmd'] != 'response_get_mpdrun_values':
>     /usr/local/bin/mpiexec  1423  ?
>         mpiexec()
> BUILD PROCESS FAILED. ERROR = 256
> Command: mpiexec -l -np 4 
> /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test
>
>
> if I type mpdboot -n 1 directly after I have
> mpdboot_MyPC (handle_mpd_output 385): failed to handshake with mpd on 
> MyPC; recvd output={}
>

Kill all mpd.py processes.

Then run

mpdboot -n 1

and afterwards

mpiexec -l -np 4 /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test


You can also try the following:
Kill all mpd.py processes and run

mpdboot -n 1
mpdtrace -l

or run mpdboot -n 1 twice

to see what happens.

When an active client process tries to connect with a client socket to 
the mpd server, it fails.
This will confirm that the problem is with mpich2.

Dejan
>
>
> If I kill python2.4 /usr/local/bin/mpd.py
>
> it works but if I rerun the test, it  gives the same error.
>

[Pcsim-users] mpdroot problem

[Fontaine B. <ber...@ua...>]

When I run python setup.py, at the end I get an error relaled to mpdroot:

Running tests: mpiexec -l -np 4 /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test
mpdroot: perror msg: Connection refused
>>>> cd /home/Berti/Desktop/pypcsim-0.5.0/_build/bin
>>>> mpiexec -l -np 4 /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test
mpiexec_MyPC: mpd_uncaught_except_tb handling:
  exceptions.KeyError: 'cmd'
    /usr/local/bin/mpiexec  257  mpiexec
        elif msg['cmd'] != 'response_get_mpdrun_values':
    /usr/local/bin/mpiexec  1423  ?
        mpiexec()
BUILD PROCESS FAILED. ERROR = 256
Command: mpiexec -l -np 4 /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test


if I type mpdboot -n 1 directly after I have 
mpdboot_MyPC (handle_mpd_output 385): failed to handshake with mpd on MyPC; recvd output={}

If I kill python2.4 /usr/local/bin/mpd.py

it works but if I rerun the test, it  gives the same error.

Re: [Pcsim-users] plot

[Pecevski D. <de...@ig...>]

Mathieu Dubois wrote:
> I want to build (and plot) the same LSM than in [1] (very similar to the 
> one given in the Circuit-Tool tutorial).
> I have created the liquid neurons as a spatial population with 2 families:
> liquid_nrn_popul = SpatialFamilyPopulation( net, [ exc_nrn_factory, 
> inh_nrn_factory ], RatioBasedFamilies( EXC_INH_Ratio  ), 
> CuboidIntegerGrid3D(LIQUID_SIZE, LIQUID_ORIGIN) );
> so I can make the connections inside the liquid with a 
> ConnectionsProjection and draw those synapses with the help you gave me.
>
> But for connecting (for instance) the input neurons to the liquid I use 
> net.connect (as in the examples) so I cannot use a ConnectionsProjection 
> (each input neuron is connected to the three liquid neurons at the same 
> altitude).
>   
It's not clear to me why you want  to use a ConnectionsProjection?
If I understood correctly, the connection map from input to the liquid is
predefined, you already know which neurons to connect in the plot, so you
probably don't need this to get the presynaptic and postsynaptic neuron 
pairs.

If you want to get the parameters of the synapses you can achieve this with
the synapses IDs.

When you execute

syn_id = net.connect( pre_nrn_id, post_nrn_id, StaticSpikingSynapse() )

for example, then the output of net.connect is the id of the synapse 
created.
Now you can get this synapse with

net.object(syn_id)

regards,
Dejan
> I think that I can define a new sub-population in the liquid with the 
> function subset (and therefore  use a ConnectionsProjection) but I 
> cannot figure out how to do that with the online help.
>   
> So my question is: How to define a subpopulation?
>   
You can define a new population by giving a list of IDs of the simobjects:

---------------

exz_nrn_popul = SimObjectPopulation(net, lifmodel, int( nNeurons *  Frac_EXC ) );
inh_nrn_popul = SimObjectPopulation(net, lifmodel, nNeurons - exz_nrn_popul.size() );

all_nrn_popul = SimObjectPopulation(net, list(exz_nrn_popul.idVector()) + list(inh_nrn_popul.idVector()));

print "Created", exz_nrn_popul.size(), "exz and", inh_nrn_popul.size(), "inh neurons";
------------
See example : http://www.lsm.tugraz.at/pcsim/examples/cuba_model_populations.py

You can extract the ids of the neurons in the liquid that the input neurons connect to, with 

id = liquid_popul.getIdAt( 3,4,5 ).packed()

make a python list of these ids 

and then call

new_popul = SimObjectPopulation( net, id_list )

And then you can create the wanted projections between populations.

I hope that's helpful.

regards, 
Dejan

> Thanks in advance,
> Mathieu
>
> [1] "Imitation Learning with spiking networks and real-world devices", 
> H. Burgsteiner, Engineering Applications of AI, 19, 741-752, 2006
>
>   

Re: [Pcsim-users] Almost installed Pcsim

[Pecevski D. <de...@ig...>]

Hi Fontaine,

Can you run the command
 
mpdboot -n 1

on the machine and see what happens?

If this fails, then the problem is in mpich2, it looks like the mpich2 
client is unable to access the server port
of the process deamon.

If this succeeds, then run again

python setup.py install

and see what happens.

Can you briefly describe what kind of problems you had during installation?
Maybe we can fix some of these problems in future releases, if they 
occurred because of the Pcsim build process.

regards,
Dejan

P.S. Please could you subscribe and send further questions on the 
pcsim-users mailing list on sourceforge?
       http://sourceforge.net/mail/?group_id=159322
       I'm forwarding this message also to the list.



Fontaine Bertrand wrote:
>
>
> Hello,
>
> it's me again. I tried further the installation and I'm very close to 
> have it completed. I run the pyhton setup.py install without problems 
> (after a lot of problems) and the beginning of the test runs ok until 
> I get an mpd error. I really think I'm almost there so any help would 
> be welcome.
>
> Thank you very much
>
> Bertrand Fontaine
>
> MyPC:/home/Berti/Desktop/pypcsim-0.5.0 # python setup.py test
> running test
> >>>> cd /home/Berti/Desktop/pypcsim-0.5.0/_build
> >>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D 
> CMAKE_INSTALL_PREFIX:PATH=/home/Berti/Desktop/pypcsim-0.5.0 -D 
> PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D 
> EXTRA_INSTALL:STRING=NO /home/Berti/Desktop/pypcsim-0.5.0
>    Build type   = Release
>    Platform     = linux-x86_64
>    Make tool    = /usr/bin/gmake
>    Make command = /usr/bin/gmake -i
>    Python executable : /usr/bin/python version 2.4
>    Python libraries : /usr/lib64/python2.4/config
>    Python includes : /usr/include/python2.4
> -- Looking for doxygen...
> -- Looking for doxygen... - found /usr/bin/doxygen
> -- Looking for dot tool...
> -- Looking for dot tool... - found /usr/bin/dot
>    Doxygen executable : /usr/bin/doxygen
>    GCCXML executable : /usr/local/bin/gccxml
>    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
>    CppUnit : /usr/local/lib/libcppunit.so
> -- Configuring done
> -- Generating done
> -- Build files have been written to: 
> /home/Berti/Desktop/pypcsim-0.5.0/_build
> >>>> cd /home/Berti/Desktop/pypcsim-0.5.0/_build
> >>>> /usr/bin/gmake -j 2 rebuild_cache
> Running CMake to regenerate build system...
>    Build type   = Release
>    Platform     = linux-x86_64
>    Make tool    = /usr/bin/gmake
>    Make command = /usr/bin/gmake -i
>    Python executable : /usr/bin/python version 2.4
>    Python libraries : /usr/lib64/python2.4/config
>    Python includes : /usr/include/python2.4
> -- Looking for doxygen...
> -- Looking for doxygen... - found /usr/bin/doxygen
> -- Looking for dot tool...
> -- Looking for dot tool... - found /usr/bin/dot
>    Doxygen executable : /usr/bin/doxygen
>    GCCXML executable : /usr/local/bin/gccxml
>    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
>    CppUnit : /usr/local/lib/libcppunit.so
> -- Configuring done
> -- Generating done
> -- Build files have been written to: 
> /home/Berti/Desktop/pypcsim-0.5.0/_build
> *******************************************
> *  GENERATING PY++ WRAPPER CPP FILES      *
> *******************************************
> >>>> cd /home/Berti/Desktop/pypcsim-0.5.0/_build
> >>>> /usr/bin/gmake -j 2 generate_code
> [100%] Built target generate_python_wrapper_code
> [100%] Built target generate_code
> *******************************************
>   BUILDING all
> *******************************************
> >>>> cd /home/Berti/Desktop/pypcsim-0.5.0/_build
> >>>> /usr/bin/gmake -j 2 rebuild_cache
> Running CMake to regenerate build system...
>    Build type   = Release
>    Platform     = linux-x86_64
>    Make tool    = /usr/bin/gmake
>    Make command = /usr/bin/gmake -i
>    Python executable : /usr/bin/python version 2.4
>    Python libraries : /usr/lib64/python2.4/config
>    Python includes : /usr/include/python2.4
> -- Looking for doxygen...
> -- Looking for doxygen... - found /usr/bin/doxygen
> -- Looking for dot tool...
> -- Looking for dot tool... - found /usr/bin/dot
>    Doxygen executable : /usr/bin/doxygen
>    GCCXML executable : /usr/local/bin/gccxml
>    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
>    CppUnit : /usr/local/lib/libcppunit.so
> -- Configuring done
> -- Generating done
> -- Build files have been written to: 
> /home/Berti/Desktop/pypcsim-0.5.0/_build
> >>>> cd /home/Berti/Desktop/pypcsim-0.5.0/_build
> >>>> /usr/bin/gmake -i -j 2
> [  1%] Built target generate_python_wrapper_code
> [ 30%] Built target pcsim
> [ 41%] Built target pcsim_test
> [100%] Built target pypcsim
> test_pcsim
> Running tests: mpiexec -l -np 4 
> /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test
> mpdboot_MyPC (handle_mpd_output 385): failed to handshake with mpd on 
> MyPC; recvd output={}
>
> >>>> cd /home/Berti/Desktop/pypcsim-0.5.0/_build/bin
> >>>> mpiexec -l -np 4 
> /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test
> mpiexec_MyPC: mpd_uncaught_except_tb handling:
>   exceptions.KeyError: 'cmd'
>     /usr/local/bin/mpiexec  257  mpiexec
>         elif msg['cmd'] != 'response_get_mpdrun_values':
>     /usr/local/bin/mpiexec  1423  ?
>         mpiexec()
> BUILD PROCESS FAILED. ERROR = 256
> Command: mpiexec -l -np 4 
> /home/Berti/Desktop/pypcsim-0.5.0/_build/bin/pcsim_test
>

Re: [Pcsim-users] plot

[Natschläger T. <Tho...@sc...>]

Hi Mathieu,

please have a look at the example

http://www.lsm.tugraz.at/pcsim/examples/spatial_inh_exc_populations.py

(which is also included in the distribution) which shows how to use a *population of input neurons* connected via a ConnectionProjection to the pool of neurons.
This will allow you to access the individual connections.

Best Regards

  -thomas (natschlaeger)


-----Original Message-----
From: Mathieu Dubois [mailto:mat...@li...]
Sent: Thu 6/26/2008 6:03 PM
To: pcs...@li...
Cc: Natschläger Thomas
Subject: Re: [Pcsim-users] plot
 
Hi Thomas, Hi Dejan,

Thank you very much for the helpful information. I'm close to get the 
kind of plot that I want.

Nevertheless, I still have some problems. Let me explain.

I want to build (and plot) the same LSM than in [1] (very similar to the 
one given in the Circuit-Tool tutorial).
I have created the liquid neurons as a spatial population with 2 families:
liquid_nrn_popul = SpatialFamilyPopulation( net, [ exc_nrn_factory, 
inh_nrn_factory ], RatioBasedFamilies( EXC_INH_Ratio  ), 
CuboidIntegerGrid3D(LIQUID_SIZE, LIQUID_ORIGIN) );
so I can make the connections inside the liquid with a 
ConnectionsProjection and draw those synapses with the help you gave me.

But for connecting (for instance) the input neurons to the liquid I use 
net.connect (as in the examples) so I cannot use a ConnectionsProjection 
(each input neuron is connected to the three liquid neurons at the same 
altitude).

I think that I can define a new sub-population in the liquid with the 
function subset (and therefore  use a ConnectionsProjection) but I 
cannot figure out how to do that with the online help.

So my question is: How to define a subpopulation?

Thanks in advance,
Mathieu

[1] "Imitation Learning with spiking networks and real-world devices", 
H. Burgsteiner, Engineering Applications of AI, 19, 741-752, 2006

Natschläger Thomas wrote:
> Hi Mathieu,
>
> please find attached an example which shows how to extract such information.
>
> Regards
>
>   -thomas natschlaeger
>
>
> -----Original Message-----
> From: pcs...@li... on behalf of Mathieu Dubois
> Sent: Tue 6/24/2008 6:20 PM
> To: pcs...@li...
> Subject: [Pcsim-users] plot
>  
> Hi,
>
> I would like to plot the networks created with pcsim (with Gnuplot.py).
>
> I know how to access the neurons (in fact the sub-populations created  
> with SpatialSimObjectPopulation) but I don't know how to access the 
> synapses in the network.
> Furthermore how can I find the source and the destination of a synapse?
>
> Thanks in advance,
> Mathieu
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>
>
>   

Re: [Pcsim-users] plot

[Mathieu D. <mat...@li...>]

Hi Thomas, Hi Dejan,

Thank you very much for the helpful information. I'm close to get the 
kind of plot that I want.

Nevertheless, I still have some problems. Let me explain.

I want to build (and plot) the same LSM than in [1] (very similar to the 
one given in the Circuit-Tool tutorial).
I have created the liquid neurons as a spatial population with 2 families:
liquid_nrn_popul = SpatialFamilyPopulation( net, [ exc_nrn_factory, 
inh_nrn_factory ], RatioBasedFamilies( EXC_INH_Ratio  ), 
CuboidIntegerGrid3D(LIQUID_SIZE, LIQUID_ORIGIN) );
so I can make the connections inside the liquid with a 
ConnectionsProjection and draw those synapses with the help you gave me.

But for connecting (for instance) the input neurons to the liquid I use 
net.connect (as in the examples) so I cannot use a ConnectionsProjection 
(each input neuron is connected to the three liquid neurons at the same 
altitude).

I think that I can define a new sub-population in the liquid with the 
function subset (and therefore  use a ConnectionsProjection) but I 
cannot figure out how to do that with the online help.

So my question is: How to define a subpopulation?

Thanks in advance,
Mathieu

[1] "Imitation Learning with spiking networks and real-world devices", 
H. Burgsteiner, Engineering Applications of AI, 19, 741-752, 2006

Natschläger Thomas wrote:
> Hi Mathieu,
>
> please find attached an example which shows how to extract such information.
>
> Regards
>
>   -thomas natschlaeger
>
>
> -----Original Message-----
> From: pcs...@li... on behalf of Mathieu Dubois
> Sent: Tue 6/24/2008 6:20 PM
> To: pcs...@li...
> Subject: [Pcsim-users] plot
>  
> Hi,
>
> I would like to plot the networks created with pcsim (with Gnuplot.py).
>
> I know how to access the neurons (in fact the sub-populations created  
> with SpatialSimObjectPopulation) but I don't know how to access the 
> synapses in the network.
> Furthermore how can I find the source and the destination of a synapse?
>
> Thanks in advance,
> Mathieu
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>
>
>   

Re: [Pcsim-users] plot

[Natschläger T. <Tho...@sc...>]

Hi Mathieu,

please find attached an example which shows how to extract such information.

Regards

  -thomas natschlaeger


-----Original Message-----
From: pcs...@li... on behalf of Mathieu Dubois
Sent: Tue 6/24/2008 6:20 PM
To: pcs...@li...
Subject: [Pcsim-users] plot
 
Hi,

I would like to plot the networks created with pcsim (with Gnuplot.py).

I know how to access the neurons (in fact the sub-populations created  
with SpatialSimObjectPopulation) but I don't know how to access the 
synapses in the network.
Furthermore how can I find the source and the destination of a synapse?

Thanks in advance,
Mathieu

-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php
_______________________________________________
Pcsim-users mailing list
Pcs...@li...
https://lists.sourceforge.net/lists/listinfo/pcsim-users

Re: [Pcsim-users] plot

[Pecevski D. <de...@ig...>]

Mathieu Dubois wrote:
> Hi,
>
> I would like to plot the networks created with pcsim (with Gnuplot.py).
>
> I know how to access the neurons (in fact the sub-populations created  
> with SpatialSimObjectPopulation) but I don't know how to access the 
> synapses in the network.
>   
The neurons and synapses are treated the same in pcsim, they are both 
inherited from SimObject base class.
If you use populations and projections to construct your model, then

syn_handle = projection_handle.object(i)

gives you the python handle of the synapse with index i in the projection.
To access the synapses and presynaptic and postsynaptic neurons of 
synapses you must construct the projection by
setting the arguments collectIDs and collectPairs to true in the 
constructor, e.g.:

----------

n_exz_syn_project = ConnectionsProjection( exz_nrn_popul, all_nrn_popul, 
                                            StaticSpikingSynapse( W=Wexc, tau=5e-3, delay=1e-3 ),                                               
                                            RandomConnections( conn_prob = ConnP ), 
                                            SimpleAllToAllWiringMethod(net),
                                            collectIDs = True, collectPairs = True )
-------


> Furthermore how can I find the source and the destination of a synapse?
>   

With

pre_post_pair  = projection_handle.prePostPair(i)

you can get the tuple with the id-s of the presynaptic and postsynaptic 
neurons the synapse connects.

You can access these neurons with

net.object(pre_post_pair[0])

etc.

cheers,
Dejan
> Thanks in advance,
> Mathieu
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>