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From: Adrian M. W. <am...@in...> - 2010-11-17 16:45:35
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I've just had cause to build PCSIM on OpenSuse 11.2 once again. Although this used to work, I now get the errors quoted below, the key line being "error: '__builtin_fpclassify' was not declared in this scope". This looks like this bug here: http://www.vtk.org/Bug/view.php?id=10141 so I'm hoping that using the latest gccxml will fix it. I'll let you know what happens! Adrian > ******************************************* > * GENERATING PY++ WRAPPER CPP FILES * > ******************************************* >>>>> cd /usr/src/packages/BUILD/pcsim-0.5.4/_build >>>>> /usr/bin/gmake -j 2 generate_code > gmake[1]: Entering directory `/usr/src/packages/BUILD/pcsim-0.5.4/_build' > gmake[2]: Entering directory `/usr/src/packages/BUILD/pcsim-0.5.4/_build' > gmake[3]: Entering directory `/usr/src/packages/BUILD/pcsim-0.5.4/_build' > gmake[4]: Entering directory `/usr/src/packages/BUILD/pcsim-0.5.4/_build' > Generating ../../python/pypcsim.h > Generating ../../python/pypcsim/pypcsim.indicator.cpp > /usr/lib/python2.6/site-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/local/bin/gccxml --gccxml-cxxflags -pthread -fpermissive -I"." -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/simutils" -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/simcore" -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/construction" -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/neuroml" -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/simobjects" -I"/usr/src/packages/BUILD/pcsim-0.5.4/libxsd" -D"MPICH_IGNORE_CXX_SEEK" -D"BOOST_HAS_THREADS" -D"BOOST_PYTHON_MAX_ARITY=30" "pypcsim.h" -fxml="/tmp/tmprVfQbS.xml" > /usr/lib/python2.6/site-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 "/usr/src/packages/BUILD/pcsim-0.5.4/scripts/generate_boost_python_wrapper_code.py", line 143, in <module> > encoding = 'utf-8' > File "/usr/lib/python2.6/site-packages/pyplusplus/module_builder/builder.py", line 90, in __init__ > , indexing_suite_version) > File "/usr/lib/python2.6/site-packages/pyplusplus/module_builder/builder.py", line 144, in __parse_declarations > decls = reader.read_files( files, compilation_mode ) > File "/usr/lib/python2.6/site-packages/pygccxml/parser/project_reader.py", line 225, in read_files > return self.__parse_file_by_file(files) > File "/usr/lib/python2.6/site-packages/pygccxml/parser/project_reader.py", line 250, in __parse_file_by_file > decls = reader.read_file( header ) > File "/usr/lib/python2.6/site-packages/pygccxml/parser/source_reader.py", line 198, in read_file > return self.read_gccxml_file( source_file ) > File "/usr/lib/python2.6/site-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 pypcsim.h:165: > /usr/include/c++/4.4/cmath: In function 'typename __gnu_cxx::__enable_if<std::__is_arithmetic<_Tp>::__value, int>::__type std::fpclassify(_Tp) [with _Tp = float]': > /usr/include/boost/functional/hash/detail/hash_float.hpp:172: instantiated from 'size_t boost::hash_detail::float_hash_value(T) [with T = float]' > /usr/include/boost/functional/hash/hash.hpp:304: instantiated from here > /usr/include/c++/4.4/cmath:501: error: '__builtin_fpclassify' was not declared in this scope > /usr/include/c++/4.4/cmath: In function 'typename __gnu_cxx::__enable_if<std::__is_arithmetic<_Tp>::__value, int>::__type std::fpclassify(_Tp) [with _Tp = double]': > /usr/include/boost/functional/hash/detail/hash_float.hpp:172: instantiated from 'size_t boost::hash_detail::float_hash_value(T) [with T = double]' > /usr/include/boost/functional/hash/hash.hpp:309: instantiated from here > /usr/include/c++/4.4/cmath:501: error: '__builtin_fpclassify' was not declared in this scope > /usr/include/c++/4.4/cmath: In function 'typename __gnu_cxx::__enable_if<std::__is_arithmetic<_Tp>::__value, int>::__type std::fpclassify(_Tp) [with _Tp = long double]': > /usr/include/boost/functional/hash/detail/hash_float.hpp:172: instantiated from 'size_t boost::hash_detail::float_hash_value(T) [with T = long double]' > /usr/include/boost/functional/hash/hash.hpp:314: instantiated from here > /usr/include/c++/4.4/cmath:501: error: '__builtin_fpclassify' was not declared in this scope > -- Adrian M. Whatley Institute of Neuroinformatics, University of Zurich and ETH Zurich Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. Phone: +41 44 635 3067 Fax: +41 44 635 3053 Email: am...@in... WWW: http://www.ini.uzh.ch/~amw/ |
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From: Pecevski D. <de...@ig...> - 2010-04-01 15:35:19
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Hi Edmund, The features of saving and loading a network specification and/or network state are not supported in PCSIM in the current version. You can retrieve all the information about the network specification/state by accessing all the neurons, synapses and connection pairs from the populations and projections, and retrieving their parameters/state variables. Then having this information in Python, you can pickle it. Regards, Dejan e c wrote: > Hello all, > > Does anyone know if there is any function to save / load a network > with all its connections and parameters? Say I have a neuron > population with all its connections already initialized. I have tried > to pickle the object population but that doesn't seem to work... > > Edmund > > > ------------------------------------------------------------------------ > New Email names for you! > <http://sg.rd.yahoo.com/sg/mail/domainchoice/mail/signature/*http://mail.promotions.yahoo.com/newdomains/sg/> > > Get the Email name you've always wanted on the new @ymail and @rocketmail. > Hurry before someone else does! > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ------------------------------------------------------------------------ > > _______________________________________________ > Pcsim-users mailing list > Pcs...@li... > https://lists.sourceforge.net/lists/listinfo/pcsim-users > -- _______________________________________________ Dejan Pecevski Institute for Theoretical Computer Science Graz University of Technology Inffeldgasse 16b, A-8010 Graz, Austria Tel. +43 316 873 5849 |
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From: e c <ila...@ya...> - 2010-04-01 09:25:21
|
Hello all,
Does anyone know if there is any function to save / load a network with all its connections and parameters? Say I have a neuron population with all its connections already initialized. I have tried to pickle the object population but that doesn't seem to work...
Edmund
Get your new Email address!
Grab the Email name you've always wanted before someone else does!
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|
From: Christopher N. <cn...@it...> - 2010-02-18 05:16:14
|
Hey all,
Just a quick one, to use the standalone save / read functions of
pypcsimplus.Parameters, I've had to change a couple of very simple
things in the source:
1. In saveInH5File(...), the openFile command has open for read ('r')
instead of write ('w').
2. In readFromH5File(...), I've changed all self.__openFile uses to
local variables (i.e. openedFile = False) to avoid the __openedFile
element trying to override a non-existent element of the same name when
passing to an Experiment or Model.
Cheers,
Chris.
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From: Pecevski D. <de...@ig...> - 2009-11-19 10:31:26
|
Hi Daniel, If you use exactly the recommended versions for all the dependent packages, then since there is a compile error in the generated code, it's possible that the generated code of the boost.python library version 1.34.1 is not compatible with the new version of gcc you are using. Boost.python is using advanced template meta-programming C++ techniques so it's not impossible that it requires features of the compiler that are realized slightly differently between versions. We are using gcc 4.1.2. Do you have the possibility to try to compile with another older version of gcc? regards, Dejan Daniel Krieg wrote: > Hi, > > I'm trying to compile pypcsim 0.5.4. I have sticked strictly to the > versions and compile options mentioned in the dependencies. > I get an error when compiling the files generated by the py++. The same > error occurs when I compile from the current svn files. > gcc version: 4.3.3 > python version: 2.6 > > Thanks, > Daniel > > >>>>> /usr/bin/make -j 2 >>>>> > pypcsim > > [ 0%] Built target > generate_python_wrapper_code > > [ 56%] Built target > pcsim > > [ 56%] [ 56%] Building CXX object > python/CMakeFiles/pypcsim.dir/pypcsim/PredicateBasedConnections.pypp.o > > Building CXX object > python/CMakeFiles/pypcsim.dir/pypcsim/HHNeuronTraubMiles91.pypp.o > > In file included from > /usr/include/c++/4.3/ext/hash_map:64, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/pcsim_hash.h:21, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SpikeSender.h:6, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/ODESystemBasedSpikingNeuron.h:16, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/HHNeuronTraubMiles91.h:4, > > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:4: > > /usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning > This file includes at least one deprecated or antiquated header which > may be removed without further notice at a future date. Please use a > non-deprecated interface with equivalent functionality instead. For a > listing of replacement headers and interfaces, consult the file > backward_warning.h. To disable this warning use > -Wno-deprecated. > In file included from > /usr/include/c++/4.3/ext/hash_map:64, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/pcsim_hash.h:21, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/construction/Point3DSet.h:19, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/construction/SpatialSimObjectPopulation.h:15, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/construction/PredicateBasedConnections.h:15, > > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:4: > > /usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning > This file includes at least one deprecated or antiquated header which > may be removed without further notice at a future date. Please use a > non-deprecated interface with equivalent functionality instead. For a > listing of replacement headers and interfaces, consult the file > backward_warning.h. To disable this warning use > -Wno-deprecated. > In file included from > /home/krieg/software/include/boost-1_34_1/boost/python/class.hpp:29, > > from > /home/krieg/software/include/boost-1_34_1/boost/python.hpp:18, > > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:3: > > /home/krieg/software/include/boost-1_34_1/boost/python/detail/def_helper.hpp:192: > warning: declaration of ‘typename > boost::python::detail::keyword_extract<boost::tuples::tuple<const T1&, > const T2&, const T3&, const T4&, boost::python::default_call_policies, > boost::python::detail::keywords<0ul>, const char*, void > (boost::python::detail::not_specified::*)(), boost::tuples::null_type, > boost::tuples::null_type> >::result_type > boost::python::detail::def_helper<T1, T2, T3, T4>::keywords() > const’ > > /home/krieg/software/include/boost-1_34_1/boost/python/args_fwd.hpp:35: > warning: changes meaning of ‘keywords’ from ‘struct > boost::python::detail::keywords<0ul>’ > > In file included from > /home/krieg/software/include/boost-1_34_1/boost/python/class.hpp:29, > > from > /home/krieg/software/include/boost-1_34_1/boost/python.hpp:18, > > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:3: > > /home/krieg/software/include/boost-1_34_1/boost/python/detail/def_helper.hpp:192: > warning: declaration of ‘typename > boost::python::detail::keyword_extract<boost::tuples::tuple<const T1&, > const T2&, const T3&, const T4&, boost::python::default_call_policies, > boost::python::detail::keywords<0ul>, const char*, void > (boost::python::detail::not_specified::*)(), boost::tuples::null_type, > boost::tuples::null_type> >::result_type > boost::python::detail::def_helper<T1, T2, T3, T4>::keywords() > const’ > > /home/krieg/software/include/boost-1_34_1/boost/python/args_fwd.hpp:35: > warning: changes meaning of ‘keywords’ from ‘struct > boost::python::detail::keywords<0ul>’ > > In file included from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian_io.hpp:12, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/conversion.hpp:23, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:21, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomDistribution.h:18, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/construction/ConnectionIterator.h:14, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/construction/PredicateBasedConnections.h:14, > > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:4: > > /home/krieg/software/include/boost-1_34_1/boost/date_time/date_facet.hpp:560: > warning: declaration of ‘void > boost::date_time::date_input_facet<date_type, CharT, > InItrT>::special_values_parser(boost::date_time::special_values_parser<date_type, > charT>)’ > /home/krieg/software/include/boost-1_34_1/boost/date_time/special_values_parser.hpp:34: > warning: changes meaning of ‘special_values_parser’ from ‘class > boost::date_time::special_values_parser<date_type, > charT>’ > > In file included from > /home/krieg/software/include/boost-1_34_1/boost/token_iterator.hpp:24, > > from > /home/krieg/software/include/boost-1_34_1/boost/tokenizer.hpp:20, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/date_parsing.hpp:14, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/parsers.hpp:13, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:34, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomDistribution.h:18, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/construction/ConnectionIterator.h:14, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/construction/PredicateBasedConnections.h:14, > > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:4: > > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In > member function ‘bool > boost::offset_separator::operator()(InputIterator&, InputIterator, > Token&)’: > > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:338: > warning: suggest explicit curly brackets to avoid ambiguous > ‘else’ > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In > member function ‘bool boost::char_separator<Char, > Traits>::operator()(InputIterator&, InputIterator, > Token&)’: > > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:451: > warning: suggest explicit curly brackets to avoid ambiguous > ‘else’ > In file included from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian_io.hpp:12, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/conversion.hpp:23, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:21, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SimObject.h:56, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/ODESystemBasedSpikingNeuron.h:17, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/HHNeuronTraubMiles91.h:4, > > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:4: > > /home/krieg/software/include/boost-1_34_1/boost/date_time/date_facet.hpp:560: > warning: declaration of ‘void > boost::date_time::date_input_facet<date_type, CharT, > InItrT>::special_values_parser(boost::date_time::special_values_parser<date_type, > charT>)’ > /home/krieg/software/include/boost-1_34_1/boost/date_time/special_values_parser.hpp:34: > warning: changes meaning of ‘special_values_parser’ from ‘class > boost::date_time::special_values_parser<date_type, > charT>’ > > In file included from > /home/krieg/software/include/boost-1_34_1/boost/token_iterator.hpp:24, > > from > /home/krieg/software/include/boost-1_34_1/boost/tokenizer.hpp:20, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/date_parsing.hpp:14, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/parsers.hpp:13, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:34, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12, > > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SimObject.h:56, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/ODESystemBasedSpikingNeuron.h:17, > > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/HHNeuronTraubMiles91.h:4, > > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:4: > > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In > member function ‘bool > boost::offset_separator::operator()(InputIterator&, InputIterator, > Token&)’: > > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:338: > warning: suggest explicit curly brackets to avoid ambiguous > ‘else’ > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In > member function ‘bool boost::char_separator<Char, > Traits>::operator()(InputIterator&, InputIterator, > Token&)’: > > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:451: > warning: suggest explicit curly brackets to avoid ambiguous > ‘else’ > /home/krieg/software/include/boost-1_34_1/boost/python/converter/implicit.hpp: > In static member function ‘static void > boost::python::converter::implicit<Source, Target>::construct(PyObject*, > boost::python::converter::rvalue_from_python_stage1_data*) [with Source > = boost::shared_ptr<ConnectionDecisionPredicate>, Target = > PredicateBasedConnections]’: > > /home/krieg/software/include/boost-1_34_1/boost/python/implicit.hpp:21: > instantiated from ‘void > boost::python::implicitly_convertible(boost::type<Target>*, > boost::type<Target>*) [with Source = > boost::shared_ptr<ConnectionDecisionPredicate>, Target = > PredicateBasedConnections]’ > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:19: > instantiated from here > /home/krieg/software/include/boost-1_34_1/boost/python/converter/implicit.hpp:34: > warning: unused variable ‘convertible’ > [ 56%] Building CXX object > python/CMakeFiles/pypcsim.dir/pypcsim/StaticNMDAAlphaSynapse.pypp.o > > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp: > At global scope: > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp: > In instantiation of ‘boost::detail::is_polymorphic_imp1<SimNetwork>::d1’: > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:56: > instantiated from ‘const bool > boost::detail::is_polymorphic_imp1<SimNetwork>::value’ > > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:91: > instantiated from ‘const bool > boost::detail::is_polymorphic_imp<SimNetwork>::value’ > > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:96: > instantiated from ‘boost::is_polymorphic<SimNetwork>’ > /home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:55: > instantiated from ‘PyObject* boost::python::to_python_indirect<T, > MakeHolder>::execute(const U&, mpl_::false_) const [with U = SimNetwork, > T = SimNetwork&, MakeHolder = > boost::python::detail::make_reference_holder]’ > /home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:37: > instantiated from ‘PyObject* boost::python::to_python_indirect<T, > MakeHolder>::operator()(const U&) const [with U = SimNetwork, T = > SimNetwork&, MakeHolder = > boost::python::detail::make_reference_holder]’ > /home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:224: > instantiated from ‘static PyObject* > boost::python::converter::detail::reference_arg_to_python<T>::get_object(T&) > [with T = > SimNetwork]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:229: > instantiated from > ‘boost::python::converter::detail::reference_arg_to_python<T>::reference_arg_to_python(T&) > [with T = > SimNetwork]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:256: > instantiated from > ‘boost::python::converter::arg_to_python<T>::arg_to_python(const T&) > [with T = > boost::reference_wrapper<SimNetwork>]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/override.hpp:138: > instantiated from ‘boost::python::detail::method_result > boost::python::override::operator()(const A0&, const A1&, const A2&, > const A3&) const [with A0 = boost::python::pointer_wrapper<SimObject*>, > A1 = boost::reference_wrapper<const SimObject::ID>, A2 = > boost::reference_wrapper<const SimObject::ID>, A3 = > boost::reference_wrapper<SimNetwork>]’ > > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:219: > instantiated from here > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:28: > error: invalid use of incomplete type ‘struct SimNetwork’ > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7: > error: forward declaration of ‘struct > SimNetwork’ > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp: > In instantiation of ‘boost::detail::is_polymorphic_imp1<SimNetwork>::d2’: > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:56: > instantiated from ‘const bool > boost::detail::is_polymorphic_imp1<SimNetwork>::value’ > > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:91: > instantiated from ‘const bool > boost::detail::is_polymorphic_imp<SimNetwork>::value’ > > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:96: > instantiated from ‘boost::is_polymorphic<SimNetwork>’ > /home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:55: > instantiated from ‘PyObject* boost::python::to_python_indirect<T, > MakeHolder>::execute(const U&, mpl_::false_) const [with U = SimNetwork, > T = SimNetwork&, MakeHolder = > boost::python::detail::make_reference_holder]’ > /home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:37: > instantiated from ‘PyObject* boost::python::to_python_indirect<T, > MakeHolder>::operator()(const U&) const [with U = SimNetwork, T = > SimNetwork&, MakeHolder = > boost::python::detail::make_reference_holder]’ > /home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:224: > instantiated from ‘static PyObject* > boost::python::converter::detail::reference_arg_to_python<T>::get_object(T&) > [with T = > SimNetwork]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:229: > instantiated from > ‘boost::python::converter::detail::reference_arg_to_python<T>::reference_arg_to_python(T&) > [with T = > SimNetwork]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:256: > instantiated from > ‘boost::python::converter::arg_to_python<T>::arg_to_python(const T&) > [with T = > boost::reference_wrapper<SimNetwork>]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/override.hpp:138: > instantiated from ‘boost::python::detail::method_result > boost::python::override::operator()(const A0&, const A1&, const A2&, > const A3&) const [with A0 = boost::python::pointer_wrapper<SimObject*>, > A1 = boost::reference_wrapper<const SimObject::ID>, A2 = > boost::reference_wrapper<const SimObject::ID>, A3 = > boost::reference_wrapper<SimNetwork>]’ > > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:219: > instantiated from here > /home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:40: > error: invalid use of incomplete type ‘struct SimNetwork’ > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7: > error: forward declaration of ‘struct > SimNetwork’ > /home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp: In > function ‘boost::python::type_info boost::python::type_id() [with T = > const volatile > SimNetwork&]’: > > /home/krieg/software/include/boost-1_34_1/boost/python/converter/registered.hpp:87: > instantiated from ‘const boost::python::converter::registration& > boost::python::converter::detail::registry_lookup2(T& (*)()) [with T = > const volatile > SimNetwork]’ > /home/krieg/software/include/boost-1_34_1/boost/python/converter/registered.hpp:94: > instantiated from ‘const boost::python::converter::registration& > boost::python::converter::detail::registry_lookup1(boost::type<Target>) > [with T = const volatile > SimNetwork&]’ > /home/krieg/software/include/boost-1_34_1/boost/python/converter/registered.hpp:105: > instantiated from ‘const boost::python::converter::registration& > boost::python::converter::detail::registered_base<const volatile > SimNetwork&>::converters’ > > /home/krieg/software/include/boost-1_34_1/boost/python/object/make_ptr_instance.hpp:45: > instantiated from ‘static PyTypeObject* > boost::python::objects::make_ptr_instance<T, > Holder>::get_class_object_impl(const volatile U*) [with U = SimNetwork, > T = SimNetwork, Holder = > boost::python::objects::pointer_holder<SimNetwork*, > SimNetwork>]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/object/make_ptr_instance.hpp:30: > instantiated from ‘static PyTypeObject* > boost::python::objects::make_ptr_instance<T, > Holder>::get_class_object(const Ptr&) [with Ptr = SimNetwork*, T = > SimNetwork, Holder = boost::python::objects::pointer_holder<SimNetwork*, > SimNetwork>]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/object/make_instance.hpp:26: > instantiated from ‘static PyObject* > boost::python::objects::make_instance_impl<T, Holder, > Derived>::execute(Arg&) [with Arg = SimNetwork*, T = SimNetwork, Holder > = boost::python::objects::pointer_holder<SimNetwork*, SimNetwork>, > Derived = boost::python::objects::make_ptr_instance<SimNetwork, > boost::python::objects::pointer_holder<SimNetwork*, SimNetwork> > >> ]’ >> > /home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:96: > instantiated from ‘static PyObject* > boost::python::detail::make_reference_holder::execute(T*) [with T = > SimNetwork]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:60: > instantiated from ‘PyObject* boost::python::to_python_indirect<T, > MakeHolder>::execute(const U&, mpl_::false_) const [with U = SimNetwork, > T = SimNetwork&, MakeHolder = > boost::python::detail::make_reference_holder]’ > /home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:37: > instantiated from ‘PyObject* boost::python::to_python_indirect<T, > MakeHolder>::operator()(const U&) const [with U = SimNetwork, T = > SimNetwork&, MakeHolder = > boost::python::detail::make_reference_holder]’ > /home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:224: > instantiated from ‘static PyObject* > boost::python::converter::detail::reference_arg_to_python<T>::get_object(T&) > [with T = > SimNetwork]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:229: > instantiated from > ‘boost::python::converter::detail::reference_arg_to_python<T>::reference_arg_to_python(T&) > [with T = > SimNetwork]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:256: > instantiated from > ‘boost::python::converter::arg_to_python<T>::arg_to_python(const T&) > [with T = > boost::reference_wrapper<SimNetwork>]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/override.hpp:138: > instantiated from ‘boost::python::detail::method_result > boost::python::override::operator()(const A0&, const A1&, const A2&, > const A3&) const [with A0 = boost::python::pointer_wrapper<SimObject*>, > A1 = boost::reference_wrapper<const SimObject::ID>, A2 = > boost::reference_wrapper<const SimObject::ID>, A3 = > boost::reference_wrapper<SimNetwork>]’ > > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:219: > instantiated from here > /home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp:88: > error: invalid use of incomplete type ‘struct > SimNetwork’ > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7: > error: forward declaration of ‘struct > SimNetwork’ > /home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp: In > function ‘boost::python::type_info boost::python::type_id() [with T = > SimNetwork]’: > /home/krieg/software/include/boost-1_34_1/boost/python/object/pointer_holder.hpp:137: > instantiated from ‘void* boost::python::objects::pointer_holder<Pointer, > Value>::holds(boost::python::type_info, bool) [with Pointer = > SimNetwork*, Value = > SimNetwork]’ > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:666: > instantiated from here > /home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp:88: > error: invalid use of incomplete type ‘struct > SimNetwork’ > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7: > error: forward declaration of ‘struct > SimNetwork’ > /home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp: In > function ‘boost::python::type_info boost::python::type_id() [with T = > SimNetwork&]’: > > /home/krieg/software/include/boost-1_34_1/boost/python/detail/signature.hpp:80: > instantiated from ‘static const > boost::python::detail::signature_element* > boost::python::detail::signature_arity<5u>::impl<Sig>::elements() [with > Sig = boost::mpl::vector6<void, HHNeuronTraubMiles91_wrapper&, > SimObject*, const SimObject::ID&, const SimObject::ID&, > SimNetwork&>]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/detail/caller.hpp:208: > instantiated from ‘static const > boost::python::detail::signature_element* > boost::python::detail::caller_arity<5u>::impl<F, Policies, > Sig>::signature() [with F = void > (HHNeuronTraubMiles91_wrapper::*)(SimObject*, const SimObject::ID&, > const SimObject::ID&, SimNetwork&), Policies = > boost::python::default_call_policies, Sig = boost::mpl::vector6<void, > HHNeuronTraubMiles91_wrapper&, SimObject*, const SimObject::ID&, const > SimObject::ID&, > SimNetwork&>]’ > > /home/krieg/software/include/boost-1_34_1/boost/python/object/py_function.hpp:48: > instantiated from ‘const boost::python::detail::signature_element* > boost::python::objects::caller_py_function_impl<Caller>::signature() > const [with Caller = boost::python::detail::caller<void > (HHNeuronTraubMiles91_wrapper::*)(SimObject*, const SimObject::ID&, > const SimObject::ID&, SimNetwork&), > boost::python::default_call_policies, boost::mpl::vector6<void, > HHNeuronTraubMiles91_wrapper&, SimObject*, const SimObject::ID&, const > SimObject::ID&, SimNetwork&> > >> ]’ >> > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:666: > instantiated from here > /home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp:88: > error: invalid use of incomplete type ‘struct > SimNetwork’ > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7: > error: forward declaration of ‘struct > SimNetwork’ > make[3]: *** > [python/CMakeFiles/pypcsim.dir/pypcsim/HHNeuronTraubMiles91.pypp.o] > Error 1 > make[3]: *** Waiting for unfinished > jobs.... > > In file included from > /home/krieg/software/include/boost-1_34_1/boost/python/class.hpp:29, > > from > /home/krieg/software/include/boost-1_34_1/boost/python.hpp:18, > > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/StaticNMDAAlphaSynapse.pypp.cpp:3: > > /home/krieg/software/include/boost-1_34_1/boost/python/detail/def_helper.hpp:192: > warning: declaration of ‘typename > boost::python::detail::keyword_extract<boost::tuples::tuple<const T1&, > const T2&, const T3&, const T4&, boost::python::default_call_policies, > boost::python::detail::keywords<0ul>, const char*, void > (boost::python::detail::not_specified::*)(), boost::tuples::null_type, > boost::tuples::null_type> >::result_type > boost::python::detail::def_helper<T1, T2, T3, T4>::keywords() > const’ > > /home/krieg/software/include/boost-1_34_1/boost/python/args_fwd.hpp:35: > warning: changes meaning of ‘keywords’ from ‘struct > boost::python::detail::keywords<0ul>’ > In file included from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian_io.hpp:12, > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/conversion.hpp:23, > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:21, > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12, > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24, > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15, > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SimObject.h:56, > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/GenericDynamicSpikingSynapse.h:4, > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/NMDASynapse.h:8, > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/StaticNMDAAlphaSynapse.pypp.cpp:4: > /home/krieg/software/include/boost-1_34_1/boost/date_time/date_facet.hpp:560: > warning: declaration of ‘void > boost::date_time::date_input_facet<date_type,CharT, > InItrT>::special_values_parser(boost::date_time::special_values_parser<date_type, > charT>)’ > /home/krieg/software/include/boost-1_34_1/boost/date_time/special_values_parser.hpp:34: > warning: changes meaning of ‘special_values_parser’ from ‘class > boost::date_time::special_values_parser<date_type, charT>’ > In file included from > /home/krieg/software/include/boost-1_34_1/boost/token_iterator.hpp:24, > from > /home/krieg/software/include/boost-1_34_1/boost/tokenizer.hpp:20, > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/date_parsing.hpp:14, > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/parsers.hpp:13, > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:34, > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12, > from > /home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24, > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15, > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SimObject.h:56, > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/GenericDynamicSpikingSynapse.h:4, > from > /home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/NMDASynapse.h:8, > from > /home/krieg/software/source/pcsim-0.5.4/python/pypcsim/StaticNMDAAlphaSynapse.pypp.cpp:4: > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In > member function ‘bool > boost::offset_separator::operator()(InputIterator&, InputIterator, Token&)’: > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:338: > warning: suggest explicit curly brackets to avoid ambiguous ‘else’ > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In > member function ‘bool boost::char_separator<Char, > Traits>::operator()(InputIterator&, InputIterator, Token&)’: > /home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:451: > warning: suggest explicit curly brackets to avoid ambiguous ‘else’ > make[2]: *** [python/CMakeFiles/pypcsim.dir/all] Error 2 > make[1]: *** [python/CMakeFiles/pypcsim.dir/rule] Error 2 > make: *** [pypcsim] Error 2 > BUILD PROCESS FAILED. ERROR = 512 > Command: /usr/bin/make -j 2 pypcsim > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Pcsim-users mailing list > Pcs...@li... > https://lists.sourceforge.net/lists/listinfo/pcsim-users > -- _______________________________________________ Dejan Pecevski Institute for Theoretical Computer Science Graz University of Technology Inffeldgasse 16b, A-8010 Graz, Austria Tel. +43 316 873 5849 |
|
From: Daniel K. <kr...@fi...> - 2009-11-18 10:20:50
|
Hi,
I'm trying to compile pypcsim 0.5.4. I have sticked strictly to the
versions and compile options mentioned in the dependencies.
I get an error when compiling the files generated by the py++. The same
error occurs when I compile from the current svn files.
gcc version: 4.3.3
python version: 2.6
Thanks,
Daniel
>>>> /usr/bin/make -j 2
pypcsim
[ 0%] Built target
generate_python_wrapper_code
[ 56%] Built target
pcsim
[ 56%] [ 56%] Building CXX object
python/CMakeFiles/pypcsim.dir/pypcsim/PredicateBasedConnections.pypp.o
Building CXX object
python/CMakeFiles/pypcsim.dir/pypcsim/HHNeuronTraubMiles91.pypp.o
In file included from
/usr/include/c++/4.3/ext/hash_map:64,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/pcsim_hash.h:21,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SpikeSender.h:6,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/ODESystemBasedSpikingNeuron.h:16,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/HHNeuronTraubMiles91.h:4,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:4:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning
This file includes at least one deprecated or antiquated header which
may be removed without further notice at a future date. Please use a
non-deprecated interface with equivalent functionality instead. For a
listing of replacement headers and interfaces, consult the file
backward_warning.h. To disable this warning use
-Wno-deprecated.
In file included from
/usr/include/c++/4.3/ext/hash_map:64,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/pcsim_hash.h:21,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/construction/Point3DSet.h:19,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/construction/SpatialSimObjectPopulation.h:15,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/construction/PredicateBasedConnections.h:15,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:4:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: warning: #warning
This file includes at least one deprecated or antiquated header which
may be removed without further notice at a future date. Please use a
non-deprecated interface with equivalent functionality instead. For a
listing of replacement headers and interfaces, consult the file
backward_warning.h. To disable this warning use
-Wno-deprecated.
In file included from
/home/krieg/software/include/boost-1_34_1/boost/python/class.hpp:29,
from
/home/krieg/software/include/boost-1_34_1/boost/python.hpp:18,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:3:
/home/krieg/software/include/boost-1_34_1/boost/python/detail/def_helper.hpp:192:
warning: declaration of ‘typename
boost::python::detail::keyword_extract<boost::tuples::tuple<const T1&,
const T2&, const T3&, const T4&, boost::python::default_call_policies,
boost::python::detail::keywords<0ul>, const char*, void
(boost::python::detail::not_specified::*)(), boost::tuples::null_type,
boost::tuples::null_type> >::result_type
boost::python::detail::def_helper<T1, T2, T3, T4>::keywords()
const’
/home/krieg/software/include/boost-1_34_1/boost/python/args_fwd.hpp:35:
warning: changes meaning of ‘keywords’ from ‘struct
boost::python::detail::keywords<0ul>’
In file included from
/home/krieg/software/include/boost-1_34_1/boost/python/class.hpp:29,
from
/home/krieg/software/include/boost-1_34_1/boost/python.hpp:18,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:3:
/home/krieg/software/include/boost-1_34_1/boost/python/detail/def_helper.hpp:192:
warning: declaration of ‘typename
boost::python::detail::keyword_extract<boost::tuples::tuple<const T1&,
const T2&, const T3&, const T4&, boost::python::default_call_policies,
boost::python::detail::keywords<0ul>, const char*, void
(boost::python::detail::not_specified::*)(), boost::tuples::null_type,
boost::tuples::null_type> >::result_type
boost::python::detail::def_helper<T1, T2, T3, T4>::keywords()
const’
/home/krieg/software/include/boost-1_34_1/boost/python/args_fwd.hpp:35:
warning: changes meaning of ‘keywords’ from ‘struct
boost::python::detail::keywords<0ul>’
In file included from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian_io.hpp:12,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/conversion.hpp:23,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:21,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomDistribution.h:18,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/construction/ConnectionIterator.h:14,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/construction/PredicateBasedConnections.h:14,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:4:
/home/krieg/software/include/boost-1_34_1/boost/date_time/date_facet.hpp:560:
warning: declaration of ‘void
boost::date_time::date_input_facet<date_type, CharT,
InItrT>::special_values_parser(boost::date_time::special_values_parser<date_type,
charT>)’
/home/krieg/software/include/boost-1_34_1/boost/date_time/special_values_parser.hpp:34:
warning: changes meaning of ‘special_values_parser’ from ‘class
boost::date_time::special_values_parser<date_type,
charT>’
In file included from
/home/krieg/software/include/boost-1_34_1/boost/token_iterator.hpp:24,
from
/home/krieg/software/include/boost-1_34_1/boost/tokenizer.hpp:20,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/date_parsing.hpp:14,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/parsers.hpp:13,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:34,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomDistribution.h:18,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/construction/ConnectionIterator.h:14,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/construction/PredicateBasedConnections.h:14,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:4:
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In
member function ‘bool
boost::offset_separator::operator()(InputIterator&, InputIterator,
Token&)’:
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:338:
warning: suggest explicit curly brackets to avoid ambiguous
‘else’
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In
member function ‘bool boost::char_separator<Char,
Traits>::operator()(InputIterator&, InputIterator,
Token&)’:
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:451:
warning: suggest explicit curly brackets to avoid ambiguous
‘else’
In file included from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian_io.hpp:12,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/conversion.hpp:23,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:21,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SimObject.h:56,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/ODESystemBasedSpikingNeuron.h:17,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/HHNeuronTraubMiles91.h:4,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:4:
/home/krieg/software/include/boost-1_34_1/boost/date_time/date_facet.hpp:560:
warning: declaration of ‘void
boost::date_time::date_input_facet<date_type, CharT,
InItrT>::special_values_parser(boost::date_time::special_values_parser<date_type,
charT>)’
/home/krieg/software/include/boost-1_34_1/boost/date_time/special_values_parser.hpp:34:
warning: changes meaning of ‘special_values_parser’ from ‘class
boost::date_time::special_values_parser<date_type,
charT>’
In file included from
/home/krieg/software/include/boost-1_34_1/boost/token_iterator.hpp:24,
from
/home/krieg/software/include/boost-1_34_1/boost/tokenizer.hpp:20,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/date_parsing.hpp:14,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/parsers.hpp:13,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:34,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SimObject.h:56,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/ODESystemBasedSpikingNeuron.h:17,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/HHNeuronTraubMiles91.h:4,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:4:
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In
member function ‘bool
boost::offset_separator::operator()(InputIterator&, InputIterator,
Token&)’:
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:338:
warning: suggest explicit curly brackets to avoid ambiguous
‘else’
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In
member function ‘bool boost::char_separator<Char,
Traits>::operator()(InputIterator&, InputIterator,
Token&)’:
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:451:
warning: suggest explicit curly brackets to avoid ambiguous
‘else’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/implicit.hpp:
In static member function ‘static void
boost::python::converter::implicit<Source, Target>::construct(PyObject*,
boost::python::converter::rvalue_from_python_stage1_data*) [with Source
= boost::shared_ptr<ConnectionDecisionPredicate>, Target =
PredicateBasedConnections]’:
/home/krieg/software/include/boost-1_34_1/boost/python/implicit.hpp:21:
instantiated from ‘void
boost::python::implicitly_convertible(boost::type<Target>*,
boost::type<Target>*) [with Source =
boost::shared_ptr<ConnectionDecisionPredicate>, Target =
PredicateBasedConnections]’
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/PredicateBasedConnections.pypp.cpp:19:
instantiated from here
/home/krieg/software/include/boost-1_34_1/boost/python/converter/implicit.hpp:34:
warning: unused variable ‘convertible’
[ 56%] Building CXX object
python/CMakeFiles/pypcsim.dir/pypcsim/StaticNMDAAlphaSynapse.pypp.o
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:
At global scope:
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:
In instantiation of ‘boost::detail::is_polymorphic_imp1<SimNetwork>::d1’:
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:56:
instantiated from ‘const bool
boost::detail::is_polymorphic_imp1<SimNetwork>::value’
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:91:
instantiated from ‘const bool
boost::detail::is_polymorphic_imp<SimNetwork>::value’
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:96:
instantiated from ‘boost::is_polymorphic<SimNetwork>’
/home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:55:
instantiated from ‘PyObject* boost::python::to_python_indirect<T,
MakeHolder>::execute(const U&, mpl_::false_) const [with U = SimNetwork,
T = SimNetwork&, MakeHolder =
boost::python::detail::make_reference_holder]’
/home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:37:
instantiated from ‘PyObject* boost::python::to_python_indirect<T,
MakeHolder>::operator()(const U&) const [with U = SimNetwork, T =
SimNetwork&, MakeHolder =
boost::python::detail::make_reference_holder]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:224:
instantiated from ‘static PyObject*
boost::python::converter::detail::reference_arg_to_python<T>::get_object(T&)
[with T =
SimNetwork]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:229:
instantiated from
‘boost::python::converter::detail::reference_arg_to_python<T>::reference_arg_to_python(T&)
[with T =
SimNetwork]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:256:
instantiated from
‘boost::python::converter::arg_to_python<T>::arg_to_python(const T&)
[with T =
boost::reference_wrapper<SimNetwork>]’
/home/krieg/software/include/boost-1_34_1/boost/python/override.hpp:138:
instantiated from ‘boost::python::detail::method_result
boost::python::override::operator()(const A0&, const A1&, const A2&,
const A3&) const [with A0 = boost::python::pointer_wrapper<SimObject*>,
A1 = boost::reference_wrapper<const SimObject::ID>, A2 =
boost::reference_wrapper<const SimObject::ID>, A3 =
boost::reference_wrapper<SimNetwork>]’
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:219:
instantiated from here
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:28:
error: invalid use of incomplete type ‘struct SimNetwork’
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7:
error: forward declaration of ‘struct
SimNetwork’
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:
In instantiation of ‘boost::detail::is_polymorphic_imp1<SimNetwork>::d2’:
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:56:
instantiated from ‘const bool
boost::detail::is_polymorphic_imp1<SimNetwork>::value’
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:91:
instantiated from ‘const bool
boost::detail::is_polymorphic_imp<SimNetwork>::value’
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:96:
instantiated from ‘boost::is_polymorphic<SimNetwork>’
/home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:55:
instantiated from ‘PyObject* boost::python::to_python_indirect<T,
MakeHolder>::execute(const U&, mpl_::false_) const [with U = SimNetwork,
T = SimNetwork&, MakeHolder =
boost::python::detail::make_reference_holder]’
/home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:37:
instantiated from ‘PyObject* boost::python::to_python_indirect<T,
MakeHolder>::operator()(const U&) const [with U = SimNetwork, T =
SimNetwork&, MakeHolder =
boost::python::detail::make_reference_holder]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:224:
instantiated from ‘static PyObject*
boost::python::converter::detail::reference_arg_to_python<T>::get_object(T&)
[with T =
SimNetwork]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:229:
instantiated from
‘boost::python::converter::detail::reference_arg_to_python<T>::reference_arg_to_python(T&)
[with T =
SimNetwork]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:256:
instantiated from
‘boost::python::converter::arg_to_python<T>::arg_to_python(const T&)
[with T =
boost::reference_wrapper<SimNetwork>]’
/home/krieg/software/include/boost-1_34_1/boost/python/override.hpp:138:
instantiated from ‘boost::python::detail::method_result
boost::python::override::operator()(const A0&, const A1&, const A2&,
const A3&) const [with A0 = boost::python::pointer_wrapper<SimObject*>,
A1 = boost::reference_wrapper<const SimObject::ID>, A2 =
boost::reference_wrapper<const SimObject::ID>, A3 =
boost::reference_wrapper<SimNetwork>]’
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:219:
instantiated from here
/home/krieg/software/include/boost-1_34_1/boost/type_traits/is_polymorphic.hpp:40:
error: invalid use of incomplete type ‘struct SimNetwork’
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7:
error: forward declaration of ‘struct
SimNetwork’
/home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp: In
function ‘boost::python::type_info boost::python::type_id() [with T =
const volatile
SimNetwork&]’:
/home/krieg/software/include/boost-1_34_1/boost/python/converter/registered.hpp:87:
instantiated from ‘const boost::python::converter::registration&
boost::python::converter::detail::registry_lookup2(T& (*)()) [with T =
const volatile
SimNetwork]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/registered.hpp:94:
instantiated from ‘const boost::python::converter::registration&
boost::python::converter::detail::registry_lookup1(boost::type<Target>)
[with T = const volatile
SimNetwork&]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/registered.hpp:105:
instantiated from ‘const boost::python::converter::registration&
boost::python::converter::detail::registered_base<const volatile
SimNetwork&>::converters’
/home/krieg/software/include/boost-1_34_1/boost/python/object/make_ptr_instance.hpp:45:
instantiated from ‘static PyTypeObject*
boost::python::objects::make_ptr_instance<T,
Holder>::get_class_object_impl(const volatile U*) [with U = SimNetwork,
T = SimNetwork, Holder =
boost::python::objects::pointer_holder<SimNetwork*,
SimNetwork>]’
/home/krieg/software/include/boost-1_34_1/boost/python/object/make_ptr_instance.hpp:30:
instantiated from ‘static PyTypeObject*
boost::python::objects::make_ptr_instance<T,
Holder>::get_class_object(const Ptr&) [with Ptr = SimNetwork*, T =
SimNetwork, Holder = boost::python::objects::pointer_holder<SimNetwork*,
SimNetwork>]’
/home/krieg/software/include/boost-1_34_1/boost/python/object/make_instance.hpp:26:
instantiated from ‘static PyObject*
boost::python::objects::make_instance_impl<T, Holder,
Derived>::execute(Arg&) [with Arg = SimNetwork*, T = SimNetwork, Holder
= boost::python::objects::pointer_holder<SimNetwork*, SimNetwork>,
Derived = boost::python::objects::make_ptr_instance<SimNetwork,
boost::python::objects::pointer_holder<SimNetwork*, SimNetwork>
>]’
/home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:96:
instantiated from ‘static PyObject*
boost::python::detail::make_reference_holder::execute(T*) [with T =
SimNetwork]’
/home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:60:
instantiated from ‘PyObject* boost::python::to_python_indirect<T,
MakeHolder>::execute(const U&, mpl_::false_) const [with U = SimNetwork,
T = SimNetwork&, MakeHolder =
boost::python::detail::make_reference_holder]’
/home/krieg/software/include/boost-1_34_1/boost/python/to_python_indirect.hpp:37:
instantiated from ‘PyObject* boost::python::to_python_indirect<T,
MakeHolder>::operator()(const U&) const [with U = SimNetwork, T =
SimNetwork&, MakeHolder =
boost::python::detail::make_reference_holder]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:224:
instantiated from ‘static PyObject*
boost::python::converter::detail::reference_arg_to_python<T>::get_object(T&)
[with T =
SimNetwork]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:229:
instantiated from
‘boost::python::converter::detail::reference_arg_to_python<T>::reference_arg_to_python(T&)
[with T =
SimNetwork]’
/home/krieg/software/include/boost-1_34_1/boost/python/converter/arg_to_python.hpp:256:
instantiated from
‘boost::python::converter::arg_to_python<T>::arg_to_python(const T&)
[with T =
boost::reference_wrapper<SimNetwork>]’
/home/krieg/software/include/boost-1_34_1/boost/python/override.hpp:138:
instantiated from ‘boost::python::detail::method_result
boost::python::override::operator()(const A0&, const A1&, const A2&,
const A3&) const [with A0 = boost::python::pointer_wrapper<SimObject*>,
A1 = boost::reference_wrapper<const SimObject::ID>, A2 =
boost::reference_wrapper<const SimObject::ID>, A3 =
boost::reference_wrapper<SimNetwork>]’
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:219:
instantiated from here
/home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp:88:
error: invalid use of incomplete type ‘struct
SimNetwork’
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7:
error: forward declaration of ‘struct
SimNetwork’
/home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp: In
function ‘boost::python::type_info boost::python::type_id() [with T =
SimNetwork]’:
/home/krieg/software/include/boost-1_34_1/boost/python/object/pointer_holder.hpp:137:
instantiated from ‘void* boost::python::objects::pointer_holder<Pointer,
Value>::holds(boost::python::type_info, bool) [with Pointer =
SimNetwork*, Value =
SimNetwork]’
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:666:
instantiated from here
/home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp:88:
error: invalid use of incomplete type ‘struct
SimNetwork’
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7:
error: forward declaration of ‘struct
SimNetwork’
/home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp: In
function ‘boost::python::type_info boost::python::type_id() [with T =
SimNetwork&]’:
/home/krieg/software/include/boost-1_34_1/boost/python/detail/signature.hpp:80:
instantiated from ‘static const
boost::python::detail::signature_element*
boost::python::detail::signature_arity<5u>::impl<Sig>::elements() [with
Sig = boost::mpl::vector6<void, HHNeuronTraubMiles91_wrapper&,
SimObject*, const SimObject::ID&, const SimObject::ID&,
SimNetwork&>]’
/home/krieg/software/include/boost-1_34_1/boost/python/detail/caller.hpp:208:
instantiated from ‘static const
boost::python::detail::signature_element*
boost::python::detail::caller_arity<5u>::impl<F, Policies,
Sig>::signature() [with F = void
(HHNeuronTraubMiles91_wrapper::*)(SimObject*, const SimObject::ID&,
const SimObject::ID&, SimNetwork&), Policies =
boost::python::default_call_policies, Sig = boost::mpl::vector6<void,
HHNeuronTraubMiles91_wrapper&, SimObject*, const SimObject::ID&, const
SimObject::ID&,
SimNetwork&>]’
/home/krieg/software/include/boost-1_34_1/boost/python/object/py_function.hpp:48:
instantiated from ‘const boost::python::detail::signature_element*
boost::python::objects::caller_py_function_impl<Caller>::signature()
const [with Caller = boost::python::detail::caller<void
(HHNeuronTraubMiles91_wrapper::*)(SimObject*, const SimObject::ID&,
const SimObject::ID&, SimNetwork&),
boost::python::default_call_policies, boost::mpl::vector6<void,
HHNeuronTraubMiles91_wrapper&, SimObject*, const SimObject::ID&, const
SimObject::ID&, SimNetwork&>
>]’
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/HHNeuronTraubMiles91.pypp.cpp:666:
instantiated from here
/home/krieg/software/include/boost-1_34_1/boost/python/type_id.hpp:88:
error: invalid use of incomplete type ‘struct
SimNetwork’
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/AdvanceInfo.h:7:
error: forward declaration of ‘struct
SimNetwork’
make[3]: ***
[python/CMakeFiles/pypcsim.dir/pypcsim/HHNeuronTraubMiles91.pypp.o]
Error 1
make[3]: *** Waiting for unfinished
jobs....
In file included from
/home/krieg/software/include/boost-1_34_1/boost/python/class.hpp:29,
from
/home/krieg/software/include/boost-1_34_1/boost/python.hpp:18,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/StaticNMDAAlphaSynapse.pypp.cpp:3:
/home/krieg/software/include/boost-1_34_1/boost/python/detail/def_helper.hpp:192:
warning: declaration of ‘typename
boost::python::detail::keyword_extract<boost::tuples::tuple<const T1&,
const T2&, const T3&, const T4&, boost::python::default_call_policies,
boost::python::detail::keywords<0ul>, const char*, void
(boost::python::detail::not_specified::*)(), boost::tuples::null_type,
boost::tuples::null_type> >::result_type
boost::python::detail::def_helper<T1, T2, T3, T4>::keywords()
const’
/home/krieg/software/include/boost-1_34_1/boost/python/args_fwd.hpp:35:
warning: changes meaning of ‘keywords’ from ‘struct
boost::python::detail::keywords<0ul>’
In file included from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian_io.hpp:12,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/conversion.hpp:23,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:21,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SimObject.h:56,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/GenericDynamicSpikingSynapse.h:4,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/NMDASynapse.h:8,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/StaticNMDAAlphaSynapse.pypp.cpp:4:
/home/krieg/software/include/boost-1_34_1/boost/date_time/date_facet.hpp:560:
warning: declaration of ‘void
boost::date_time::date_input_facet<date_type,CharT,
InItrT>::special_values_parser(boost::date_time::special_values_parser<date_type,
charT>)’
/home/krieg/software/include/boost-1_34_1/boost/date_time/special_values_parser.hpp:34:
warning: changes meaning of ‘special_values_parser’ from ‘class
boost::date_time::special_values_parser<date_type, charT>’
In file included from
/home/krieg/software/include/boost-1_34_1/boost/token_iterator.hpp:24,
from
/home/krieg/software/include/boost-1_34_1/boost/tokenizer.hpp:20,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/date_parsing.hpp:14,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/parsers.hpp:13,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/gregorian/gregorian.hpp:34,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/time_formatters.hpp:12,
from
/home/krieg/software/include/boost-1_34_1/boost/date_time/posix_time/posix_time.hpp:24,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simutils/RandomEngine.h:15,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simcore/SimObject.h:56,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/GenericDynamicSpikingSynapse.h:4,
from
/home/krieg/software/source/pcsim-0.5.4/pcsim/simobjects/NMDASynapse.h:8,
from
/home/krieg/software/source/pcsim-0.5.4/python/pypcsim/StaticNMDAAlphaSynapse.pypp.cpp:4:
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In
member function ‘bool
boost::offset_separator::operator()(InputIterator&, InputIterator, Token&)’:
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:338:
warning: suggest explicit curly brackets to avoid ambiguous ‘else’
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp: In
member function ‘bool boost::char_separator<Char,
Traits>::operator()(InputIterator&, InputIterator, Token&)’:
/home/krieg/software/include/boost-1_34_1/boost/token_functions.hpp:451:
warning: suggest explicit curly brackets to avoid ambiguous ‘else’
make[2]: *** [python/CMakeFiles/pypcsim.dir/all] Error 2
make[1]: *** [python/CMakeFiles/pypcsim.dir/rule] Error 2
make: *** [pypcsim] Error 2
BUILD PROCESS FAILED. ERROR = 512
Command: /usr/bin/make -j 2 pypcsim
|
|
From: Sergiy V. <vs...@ho...> - 2009-09-16 17:31:48
|
_________________________________________________________________ With Windows Live, you can organize, edit, and share your photos. http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx |
|
From: Pecevski D. <de...@ig...> - 2009-07-24 07:47:56
|
Please ignore the previous message, it was intended for another mailing list. regards, Dejan Pecevski Dejan wrote: > The pycluster is free to be used again. > > Rgds, > Dejan > > Pecevski Dejan wrote: > >> Hi all, >> >> As I can see nobody uses currently the pycluster. I would like to >> start another round of benchmark tests for >> PCSIM for which I will need the whole pycluster dedicated for the tests. >> If there is not any notice from you I will start the tests in 10 >> minutes from now. >> >> Please do not run any new jobs on the pycluster until I announce that >> the tests are finished. >> They will last approximately 2 days. >> >> The other clusters can be freely used. >> >> regards, >> Dejan >> >> > > > -- _______________________________________________ Dejan Pecevski Institute for Theoretical Computer Science Graz University of Technology Inffeldgasse 16b, A-8010 Graz, Austria Tel. +43 316 873 5849 |
|
From: Pecevski D. <de...@ig...> - 2009-07-24 07:44:24
|
The pycluster is free to be used again. Rgds, Dejan Pecevski Dejan wrote: > Hi all, > > As I can see nobody uses currently the pycluster. I would like to > start another round of benchmark tests for > PCSIM for which I will need the whole pycluster dedicated for the tests. > If there is not any notice from you I will start the tests in 10 > minutes from now. > > Please do not run any new jobs on the pycluster until I announce that > the tests are finished. > They will last approximately 2 days. > > The other clusters can be freely used. > > regards, > Dejan > -- _______________________________________________ Dejan Pecevski Institute for Theoretical Computer Science Graz University of Technology Inffeldgasse 16b, A-8010 Graz, Austria Tel. +43 316 873 5849 |
|
From: Nabeelah A. <nab...@uq...> - 2009-07-23 02:02:36
|
#ifndef _GENERICMEANFIRERATESYNAPSE_H_
#define _GENERICMEANFIRERATESYNAPSE_H_
#include "SimObject.h"
#include "GenericStaticSpikingSynapse.h"
#include "GenericCurrentBasedSpikingSynapse.h"
#include "ExponentialDecaySpikeResponse.h"
template<class BaseSyn>
class GenericMeanFireRateSynapse : public BaseSyn
{
public:
// The learning rate of the synapse.
double learningRate;
// The desired firing rate of the postsynaptic neuron (in Hertz).
double desiredFiringRate;
// The connection type.
// Inhibitory if connType == -1
// Excitatory if connType == 1
int connType;
GenericMeanFireRateSynapse(double learningRate = 0.1,
double desiredFiringRate = 3):
learningRate(learningRate), desiredFiringRate(desiredFiringRate)
{
/* Need to redefine constructor for any classes created
* using this template. */
};
virtual ~GenericMeanFireRateSynapse()
{ /* NOOP */ };
virtual int spikeHit( spikeport_t port, SpikeEvent const& spike ) {
int retval = BaseSyn::spikeHit(port, spike);
return retval;
};
virtual int reset( double dt ) {
int retval = BaseSyn::reset(dt);
// Determine whether this is an inhibitory or excitatory synapse.
if (BaseSyn::W > 0) {
connType = 1;
} else if (BaseSyn::W < 0) {
connType = -1;
}
return retval;
};
};
#endif /* _GENERICMEANFIRERATESYNAPSE_H_ */
|
|
From: Nabeelah A. <nab...@uq...> - 2009-07-23 01:16:04
|
#ifndef _MFRSTATICSPIKINGSYNAPSE_H_
#define _MFRSTATICSPIKINGSYNAPSE_H_
#include "GenericMeanFireRateSynapse.h"
#include "GenericStaticSpikingSynapse.h"
#include "GenericCurrentBasedSpikingSynapse.h"
#include "ExponentialDecaySpikeResponse.h"
class MFRStaticSpikingSynapse : public GenericMeanFireRateSynapse< GenericStaticSpikingSynapse<
GenericCurrentBasedSpikingSynapse< ExponentialDecaySpikeResponse > > >
{
SIMOBJECT( MFRStaticSpikingSynapse, AdvancePhase::SpikeDriven )
public:
MFRStaticSpikingSynapse(
const float W = 1e-9,
const float tau = 3e-3,
const float delay = 2e-4,
const double learningRate = 0.1,
const double desiredFiringRate = 3
)
{
this->W = W;
this->tau = tau;
this->delay = delay;
this->learningRate = learningRate;
this->desiredFiringRate = desiredFiringRate;
};
};
#endif /* _MFRSTATICSPIKINGSYNAPSE_H_ */
|
|
From: Pecevski D. <de...@ig...> - 2009-07-21 08:33:30
|
Hi Nabeelah,
Can you send me the code of both GenericTestSynapse and
TestStaticSpikingSynapse?
regards,
Dejan
Nabeelah Ali wrote:
> Hello (again),
>
> So now that creating synapses works perfectly, I wanted to create a
> template class that I could create other synapses from,
> i.e.
> template<class BaseSyn>
> class GenericTestSynapse : public BaseSyn
> {
> /* SNIP */
> };
>
> and then create a synapse from it:
> class TestStaticSpikingSynapse : public GenericTestSynapse<
> GenericStaticSpikingSynapse< GenericCurrentBasedSpikingSynapse<
> ExponentialDecaySpikeResponse > > >
> {
> SIMOBJECT( TestStaticSpikingSynapse, AdvancePhase::SpikeDriven )
> /* SNIP */
> };
>
> I tried implementing both the template class GenericTestSynapse and
> TestStaticSpikingSynapse through the extension module, however, I get
> a long string of errors when I try to use TestStaticSpikingSynapse in
> a python model:
> File "GenericClassTest.py", line 89, in <module>
> net2.connect (inp_nrn2, n2, inp_s2)
> Boost.Python.ArgumentError: Python argument types in
> SimNetwork.connect(SingleThreadNetwork, long, long,
> TestStaticSpikingSynapse)
> did not match C++ signature:
> connect(SimNetwork {lvalue}, std::vector<long long,
> std::allocator<long long
> > > src, std::vector<long long, std::allocator<long long> > dst,
> SimObjectFactor
> y model, ConnectionIterator {lvalue} decider, bool collect=False)
> connect(SimNetwork {lvalue}, std::vector<long long,
> std::allocator<long long
> > > src, std::vector<long long, std::allocator<long long> > dst,
> ConnectionItera
> tor {lvalue} decider)
> connect(SimNetwork {lvalue}, std::vector<long long,
> std::allocator<long long
> > > src, std::vector<long long, std::allocator<long long> > dst, Time
> delay)
> connect(SimNetwork {lvalue}, long long src, long long dst,
> SimObjectFactory
> connector)
> etc etc.
>
> However, if I put the GenericTestSynapse class into the /simobjects
> directory of my PCSIM install, edit CMakeLists.txt to include it, and
> then do a clean install of PCSIM, my TestSpikingSynapse (still
> implemented through the extension module) works perfectly.
>
> Is there something I'm doing wrong or is it not possible to implement
> template classes with the extension module?
>
> Thanks,
> Nabeelah
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> This is your chance to win up to $100,000 in prizes! For a limited time,
> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full prize
> details at: http://p.sf.net/sfu/Challenge
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>
--
_______________________________________________
Dejan Pecevski
Institute for Theoretical Computer Science
Graz University of Technology
Inffeldgasse 16b, A-8010 Graz, Austria
Tel. +43 316 873 5849
|
|
From: Nabeelah A. <nab...@uq...> - 2009-07-21 00:55:29
|
Hello (again),
So now that creating synapses works perfectly, I wanted to create a template class that I could create other synapses from,
i.e.
template<class BaseSyn>
class GenericTestSynapse : public BaseSyn
{
/* SNIP */
};
and then create a synapse from it:
class TestStaticSpikingSynapse : public GenericTestSynapse< GenericStaticSpikingSynapse< GenericCurrentBasedSpikingSynapse< ExponentialDecaySpikeResponse > > >
{
SIMOBJECT( TestStaticSpikingSynapse, AdvancePhase::SpikeDriven )
/* SNIP */
};
I tried implementing both the template class GenericTestSynapse and TestStaticSpikingSynapse through the extension module, however, I get a long string of errors when I try to use TestStaticSpikingSynapse in a python model:
File "GenericClassTest.py", line 89, in <module>
net2.connect (inp_nrn2, n2, inp_s2)
Boost.Python.ArgumentError: Python argument types in
SimNetwork.connect(SingleThreadNetwork, long, long, TestStaticSpikingSynapse)
did not match C++ signature:
connect(SimNetwork {lvalue}, std::vector<long long, std::allocator<long long
> > src, std::vector<long long, std::allocator<long long> > dst, SimObjectFactor
y model, ConnectionIterator {lvalue} decider, bool collect=False)
connect(SimNetwork {lvalue}, std::vector<long long, std::allocator<long long
> > src, std::vector<long long, std::allocator<long long> > dst, ConnectionItera
tor {lvalue} decider)
connect(SimNetwork {lvalue}, std::vector<long long, std::allocator<long long
> > src, std::vector<long long, std::allocator<long long> > dst, Time delay)
connect(SimNetwork {lvalue}, long long src, long long dst, SimObjectFactory
connector)
etc etc.
However, if I put the GenericTestSynapse class into the /simobjects directory of my PCSIM install, edit CMakeLists.txt to include it, and then do a clean install of PCSIM, my TestSpikingSynapse (still implemented through the extension module) works perfectly.
Is there something I'm doing wrong or is it not possible to implement template classes with the extension module?
Thanks,
Nabeelah
|
|
From: Nabeelah A. <nab...@uq...> - 2009-07-19 23:56:55
|
Hi Dejan, I've checked out the latest version and it now works perfectly. Thanks for the prompt fix and the explanation! Regards, Nabeelah |
|
From: Pecevski D. <de...@ig...> - 2009-07-17 09:08:51
|
Hi Nabeelah, The problem that you reported occurs while downcasting of objects within the extension module C++ code, which are created from classes defined in the main PCSIM library. If the class defined in the main pcsim library has multiple inheritance, like in the case of LifNeuron (inherited from LifNeuronBase and CurrentInputTarget) then it seems that the downcasting to CurrentInputTarget doesn't work properly. Whether the class is defined through templates or not should not make any difference. I've changed the code so that the downcasting always occurs in the main PCSIM library, checkout the latest revision from the repository. If you want to implement your own synapse, for downcasting use the functions downcastCurrentInputTarget and downcastConductanceInputTarget. See how it is done in GenericCurrentBasedSpikingSynapse for an example. regards, Dejan Miss Nabeelah Ali wrote: > Hi all, > > I am creating a new synapse class as an extension, however I cannot > use any synapses that I've > created and compiled from the extension module. > > > In fact, I cannot even use the DynamicCurrSquareSynapse that is > provided as an example. When I attempt to use it in a Python program, > for example, this: > > net = SingleThreadNetwork() > inp_nrn = net.create(SpikingInputNeuron([some input spike times here])) > syn = DynamicCurrSquareSynapse # This runs. > out_nrn = net.create(LifNeuron()) > net.connect(inp_nrn, out_nrn, syn) # Gives a runtime error. > > The error I consistently get from net.connect() is: > Unidentifiable C++ exception > > Neurons I create with the extension module work correctly, however. I > experimented with creating different synapse types, and I only get > this error if the synapse is based off templates. So, for example, the > synapse I wanted to create was based off: > > GenericCurrentBasedSpikingSynase<ExponentialDecaySpikeResponse> > > and this synapse gives me the same unidentifiable C++ exception. > > > If I don't use templates to create a synapse, then the synapse will > compile and not give any errors when I try to use it in a Python > script, however it doesn't seem to connect properly to the > postsynaptic neuron: it won't inject current into it. I've attached my > 'experimental' synapse type that I was using to test whether I could > get any synapse to work correctly (because any template-based synapse > gives me errors, I just copied code from the templates and created a > class that directly derives from ExponentialDecaySpikeResponse). > > Any ideas? > > Thanks, > Nabeelah > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. See full prize > details at: http://p.sf.net/sfu/Challenge > ------------------------------------------------------------------------ > > _______________________________________________ > Pcsim-users mailing list > Pcs...@li... > https://lists.sourceforge.net/lists/listinfo/pcsim-users > -- _______________________________________________ Dejan Pecevski Institute for Theoretical Computer Science Graz University of Technology Inffeldgasse 16b, A-8010 Graz, Austria Tel. +43 316 873 5849 |
|
From: Mathieu D. <mat...@li...> - 2009-05-29 08:37:07
|
Hello again, Apparently the LinearPoissonNeuron model can emit spikes at a given rate... Thanks, Mathieu Mathieu Dubois wrote: > Hello, > > I may be wrong but I think that you can not change the rate of a > PoissonInputNeuron during the simulation, right? > > This is because the isi_gen > <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/classPoissonInputNeuron.html#1962f2e4e38db1362e1c040a4f30583f> > field (which generates the distribution of inter-spikes intervals) is > set once in the reset() method. > > Is there a way to change that? > > Thanks in advance, > Mathieu > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://www.creativitycat.com > _______________________________________________ > Pcsim-users mailing list > Pcs...@li... > https://lists.sourceforge.net/lists/listinfo/pcsim-users > |
|
From: Mathieu D. <mat...@li...> - 2009-05-25 15:35:59
|
Hello, I may be wrong but I think that you can not change the rate of a PoissonInputNeuron during the simulation, right? This is because the isi_gen <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/classPoissonInputNeuron.html#1962f2e4e38db1362e1c040a4f30583f> field (which generates the distribution of inter-spikes intervals) is set once in the reset() method. Is there a way to change that? Thanks in advance, Mathieu |
|
From: Mathieu D. <mat...@li...> - 2009-05-25 14:29:44
|
Hello,
Mathieu Dubois wrote:
> Hello PCSIMers,
>
> I would like some advice on the best way to construct the reservoir of
> an LSM.
>
> In the standard LSM literature, the weights of the intra-reservoir
> synapses are drawn from a Gamma distribution with parameters depending
> on the type of neurons connected (up to now I was using constant
> weights but I would like to see if using those weights increase
> performance).
> I have found the BndGammaDistribution object in PCSIM and the relevant
> parameters in [1].
>
> The problem is: how can I generate negative weights within the liquid
> (to connect an inhibitory neuron to another neuron)?
> The Gamma distribution returns positive numbers so I have to do this
> by hand.
>
> I have looked into the (matlab) circuit toolbox and found the code:
> if synpar.W > 0
> synpar.W = sign(synpar.W) * bnd_gammarnd(abs(synpar.W), sh(1),
> abs(6*synpar.W), 1, m, 'exz A');
> else
> synpar.W = sign(synpar.W) * bnd_gammarnd(abs(synpar.W), sh(1),
> abs(6*synpar.W), 1, m, 'inh A');
> end
>
> Under PCSIM, I use 4 SimObjectVariationFactory (one for each type of
> synapse: EE, EI, IE, II) and 4 ConnectionsProjection. Only the IE and
> II weights have to be negative. I was thinking at using the
> setFieldScale method in SimObjectPopulation. For instance for the II
> connections this would give:
>
> liquid_syn[INH][INH] =
> ConnectionsProjection(self.liquid_sub_populs[INH],
> self.liquid_sub_populs[INH], syn_factory,
> PredicateBasedConnections(EuclidianDistanceConnectionPredicate(C[INH][INH],
> lambda_conn)))
> tmp_pop = SimObjectPopulation( liquid_syn[INH][INH].idVector() );
> tmp_pop.setFieldScale("W", -1);
I just wanted to say that I have tested this method and this seems to
work (I have gamma-distributed negative weights).
Mathieu
|
|
From: Pecevski D. <de...@ig...> - 2009-05-08 09:05:10
|
Hi Chris, The reason why the templates that are used as parameters in another template need to be included in the file holding the definition of the particular template is related to the way Py++ generates code and some optimizations that we made in order to speed-up the compilation of py++ generated files. However, in the newer versions of Py++ (0.9.0 and above) additional flexibility was added that allows one to specify the include files for each exported declaration separately during the code generation process. I've used this new feature to fix the reported problem with the inclusion of the files. You can check out the fixed version from the repository. Cheers, Dejan Chris Nolan wrote: > Hi all, > > I've just been writing a new synapse class, and ran in to a few > templating issues. I appreciate the flexibility of the Generic* design, > however I'm having problems with it and the current PCSIM / python build > system. > > I created a new generic synapse type, originally intending to have it > substitute the GenericStaticSpikingSynapse in a few of my own custom > synapse classes. However it seems that when building the python > objects, they require explicit #includes of the classes that will be > passed as template parameters. For those classes that are being passed > as template parameters to my class, e.g. > > typedef GenericMySpikingSynapse< GenericCurrentBasedSpikingSynapse< > ExponentialDecaySpikeResponse > > GenericMySpikingSynapseType > > I can just include the appropriate headers in my class header, which is > not elegant, but is a workaround. However the next step is problematic, > as I want to use my class as a template parameter to existing classes, > e.g. > > typedef GenericFroemkeDanStdpSynapse< GenericEachPairStdpSynapse< > GenericMySpikingSynapseType > > GenericMyFroemkeDanStdpSynapseType > > so I need to add my class header to existing framework class headers, > which starts to get quite messy. > > Now I realise that you (the designers that is) undoubtedly know all > this, as you've done that very thing in your own classes. I guess my > question is, is there any nicer workaround anyone can think of than > modifying the existing objects, or are there any build system / > structural changes happening that will alleviate this problem? I don't > understand the complete python <-> c++ architecture, so I'm not sure how > deep the problem lies. > > Cheers, > Chris. > > > ------------------------------------------------------------------------------ > Register Now & Save for Velocity, the Web Performance & Operations > Conference from O'Reilly Media. Velocity features a full day of > expert-led, hands-on workshops and two days of sessions from industry > leaders in dedicated Performance & Operations tracks. Use code vel09scf > and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf > _______________________________________________ > Pcsim-users mailing list > Pcs...@li... > https://lists.sourceforge.net/lists/listinfo/pcsim-users > -- _______________________________________________ Dejan Pecevski Institute for Theoretical Computer Science Graz University of Technology Inffeldgasse 16b, A-8010 Graz, Austria Tel. +43 316 873 5849 |
|
From: Mathieu D. <mat...@li...> - 2009-05-06 16:21:32
|
Hello PCSIMers,
I would like some advice on the best way to construct the reservoir of
an LSM.
In the standard LSM literature, the weights of the intra-reservoir
synapses are drawn from a Gamma distribution with parameters depending
on the type of neurons connected (up to now I was using constant weights
but I would like to see if using those weights increase performance).
I have found the BndGammaDistribution object in PCSIM and the relevant
parameters in [1].
The problem is: how can I generate negative weights within the liquid
(to connect an inhibitory neuron to another neuron)?
The Gamma distribution returns positive numbers so I have to do this by
hand.
I have looked into the (matlab) circuit toolbox and found the code:
if synpar.W > 0
synpar.W = sign(synpar.W) * bnd_gammarnd(abs(synpar.W), sh(1),
abs(6*synpar.W), 1, m, 'exz A');
else
synpar.W = sign(synpar.W) * bnd_gammarnd(abs(synpar.W), sh(1),
abs(6*synpar.W), 1, m, 'inh A');
end
Under PCSIM, I use 4 SimObjectVariationFactory (one for each type of
synapse: EE, EI, IE, II) and 4 ConnectionsProjection. Only the IE and II
weights have to be negative. I was thinking at using the setFieldScale
method in SimObjectPopulation. For instance for the II connections this
would give:
liquid_syn[INH][INH] =
ConnectionsProjection(self.liquid_sub_populs[INH],
self.liquid_sub_populs[INH], syn_factory,
PredicateBasedConnections(EuclidianDistanceConnectionPredicate(C[INH][INH],
lambda_conn)))
tmp_pop = SimObjectPopulation( liquid_syn[INH][INH].idVector() );
tmp_pop.setFieldScale("W", -1);
However I'm not sure this is correct or if it is the best way.
Any advice?
Thanks in advance,
Mathieu
[1] W. Maass, T. Natschläger, and H. Markram. Real-time computing
without stable states: A new framework for neural computation based on
perturbations <http://www.igi.tugraz.at/Abstracts/MaassETAL:01a>. Neural
Computation, 14(11):2531-2560, 2002. (PDF
<http://www.igi.tugraz.at/maass/psfiles/130.pdf>, 886 KB). (hum, you
probably know this one )
|
|
From: Chris N. <cn...@it...> - 2009-05-01 14:48:22
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Hi all, I've just been writing a new synapse class, and ran in to a few templating issues. I appreciate the flexibility of the Generic* design, however I'm having problems with it and the current PCSIM / python build system. I created a new generic synapse type, originally intending to have it substitute the GenericStaticSpikingSynapse in a few of my own custom synapse classes. However it seems that when building the python objects, they require explicit #includes of the classes that will be passed as template parameters. For those classes that are being passed as template parameters to my class, e.g. typedef GenericMySpikingSynapse< GenericCurrentBasedSpikingSynapse< ExponentialDecaySpikeResponse > > GenericMySpikingSynapseType I can just include the appropriate headers in my class header, which is not elegant, but is a workaround. However the next step is problematic, as I want to use my class as a template parameter to existing classes, e.g. typedef GenericFroemkeDanStdpSynapse< GenericEachPairStdpSynapse< GenericMySpikingSynapseType > > GenericMyFroemkeDanStdpSynapseType so I need to add my class header to existing framework class headers, which starts to get quite messy. Now I realise that you (the designers that is) undoubtedly know all this, as you've done that very thing in your own classes. I guess my question is, is there any nicer workaround anyone can think of than modifying the existing objects, or are there any build system / structural changes happening that will alleviate this problem? I don't understand the complete python <-> c++ architecture, so I'm not sure how deep the problem lies. Cheers, Chris. |
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From: Pecevski D. <de...@ig...> - 2009-04-29 07:05:33
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Hi, > > Mathieu Dubois wrote: >>> However, I have noted this, and we will consider to change this in >>> the future. >>> >> OK. One reason for that is that I have written some simple functions >> to get some properties of the network. For instance a function to >> list which neurons (identified by their local indexes in the >> population) are connected by a ConnectionsProjection (see attachment). >> As the ConnectionsProjection itself doesn't store information about >> the populations it connects I have to pass those populations as >> arguments. >> As an aside this could probably be done via NeuroML but I have never >> used it. >>> Thank you for your suggestions. >>> >> I have seen a "Feature Request" on the SourceForge page. Would that >> help if I submit those suggestions here? Yes, you can do that. regards, Dejan > -- _______________________________________________ Dejan Pecevski Institute for Theoretical Computer Science Graz University of Technology Inffeldgasse 16b, A-8010 Graz, Austria Tel. +43 316 873 5849 |
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From: Mathieu D. <mat...@li...> - 2009-04-27 10:45:48
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Hi Dejan, Thanks for the answer. > >> Hello PCSIMers, >> >> Sorry to bother you again but I was wondering why ConnectionsProjection >> doesn't inherit from SimObjectPopulation? >> >> I ask the question because I often want to create recorders for a whole >> ConnectionsProjection (for instance to record the psr). With a >> SimObjectPopulation, it's easy: the record method is here for that. But >> AFAIK there is no equivalent method in ConnectionsProjection. So I often >> have to create a population from a ConnectionsProjection with something >> like syn_popul = SimObjectPopulation( proj.idVector() ). >> >> > The is not any strong reason why ConnectionsProjection does not > inherit from SimObjectPopulation. There is a difference in the > behavior of ConnectionsProjection in distributed modes of simulation > that does not conform to the definition of the SimObjectPopulation, > like for example, it's possible to specify collectIDs = false, > in the ConnectionsProjection which saves memory by not storing > the ids of the synapses. Also in some distributed construction algorithms, > a ConnectionsProjection instance on one MPI node stores the IDs of the > synapses > that are located on the particular node, whereas a SimObjectPopulation > in distributed > mode is expected to hold the all IDs of SimObjects over all nodes. > Nevertheless, in spite of these differences which can be explicitly > pointed out in the documentation > in order to avoid confusion and reconciled with error messages in the > interface if the IDs are not present > in the projection, it should be in principle possible to make > ConnectionsProjection inherit from SimObjectPopulation, > and we have considered it. It's not done since other things had higher > priority. > For recording variables from synapses I also create a > SimObjectPopulation from the ID vector of synapses. > It's possible that the interface is extended with this feature in the > future. > OK. I'll continue to use the SimObjectPopulation trick (I have probably borrowed it from an example :). I'll be happy to test this feature in a future release. >> Also why ConnectionsProjection doesn't store information about the >> source and destination populations? Therefore we could write something >> like proj.getSourcePopulation (which again could be useful in my case). >> >> > This is also a possibility that is not yet implemented. Usually in a > script when you create a ConnectionsProjection, > you can keep the python references to both source and dest. populations > that you can use afterwards, therefore we > didn't consider it important or necessary to add it so far. > However, I have noted this, and we will consider to change this in the > future. > OK. One reason for that is that I have written some simple functions to get some properties of the network. For instance a function to list which neurons (identified by their local indexes in the population) are connected by a ConnectionsProjection (see attachment). As the ConnectionsProjection itself doesn't store information about the populations it connects I have to pass those populations as arguments. As an aside this could probably be done via NeuroML but I have never used it. > Thank you for your suggestions. > I have seen a "Feature Request" on the SourceForge page. Would that help if I submit those suggestions here? Best regards, Mathieu |
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From: Pecevski D. <de...@ig...> - 2009-04-23 14:03:02
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Hi Mathieu, Mathieu Dubois wrote: > Hello PCSIMers, > > Sorry to bother you again but I was wondering why ConnectionsProjection > doesn't inherit from SimObjectPopulation? > > I ask the question because I often want to create recorders for a whole > ConnectionsProjection (for instance to record the psr). With a > SimObjectPopulation, it's easy: the record method is here for that. But > AFAIK there is no equivalent method in ConnectionsProjection. So I often > have to create a population from a ConnectionsProjection with something > like syn_popul = SimObjectPopulation( proj.idVector() ). > The is not any strong reason why ConnectionsProjection does not inherit from SimObjectPopulation. There is a difference in the behavior of ConnectionsProjection in distributed modes of simulation that does not conform to the definition of the SimObjectPopulation, like for example, it's possible to specify collectIDs = false, in the ConnectionsProjection which saves memory by not storing the ids of the synapses. Also in some distributed construction algorithms, a ConnectionsProjection instance on one MPI node stores the IDs of the synapses that are located on the particular node, whereas a SimObjectPopulation in distributed mode is expected to hold the all IDs of SimObjects over all nodes. Nevertheless, in spite of these differences which can be explicitly pointed out in the documentation in order to avoid confusion and reconciled with error messages in the interface if the IDs are not present in the projection, it should be in principle possible to make ConnectionsProjection inherit from SimObjectPopulation, and we have considered it. It's not done since other things had higher priority. For recording variables from synapses I also create a SimObjectPopulation from the ID vector of synapses. It's possible that the interface is extended with this feature in the future. > Also why ConnectionsProjection doesn't store information about the > source and destination populations? Therefore we could write something > like proj.getSourcePopulation (which again could be useful in my case). > This is also a possibility that is not yet implemented. Usually in a script when you create a ConnectionsProjection, you can keep the python references to both source and dest. populations that you can use afterwards, therefore we didn't consider it important or necessary to add it so far. However, I have noted this, and we will consider to change this in the future. Thank you for your suggestions. best, Dejan > I don't criticize PCSIM's API, it's wonderful. I was just asking the > question. Maybe I am missing something? > > Thanks, > Mathieu > > ------------------------------------------------------------------------------ > Stay on top of everything new and different, both inside and > around Java (TM) technology - register by April 22, and save > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. > 300 plus technical and hands-on sessions. Register today. > Use priority code J9JMT32. http://p.sf.net/sfu/p > _______________________________________________ > Pcsim-users mailing list > Pcs...@li... > https://lists.sourceforge.net/lists/listinfo/pcsim-users > -- _______________________________________________ Dejan Pecevski Institute for Theoretical Computer Science Graz University of Technology Inffeldgasse 16b, A-8010 Graz, Austria Tel. +43 316 873 5849 |
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From: Mathieu D. <mat...@li...> - 2009-04-23 11:50:23
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Hello PCSIMers, Sorry to bother you again but I was wondering why ConnectionsProjection doesn't inherit from SimObjectPopulation? I ask the question because I often want to create recorders for a whole ConnectionsProjection (for instance to record the psr). With a SimObjectPopulation, it's easy: the record method is here for that. But AFAIK there is no equivalent method in ConnectionsProjection. So I often have to create a population from a ConnectionsProjection with something like syn_popul = SimObjectPopulation( proj.idVector() ). Also why ConnectionsProjection doesn't store information about the source and destination populations? Therefore we could write something like proj.getSourcePopulation (which again could be useful in my case). I don't criticize PCSIM's API, it's wonderful. I was just asking the question. Maybe I am missing something? Thanks, Mathieu |
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