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

Re: [Pcsim-users] Some clarifications

[Natschläger T. <Tho...@sc...>]

 
Hi Mathieu!

>
> Let's begin with AnalogInputNeuron::addAnalogValue(double v).
> Suppose that I call addAnalogValue(5). Will the output remain constant 
> until the next call to addAnalogValue or will it be equal to 5 for only 
> one simulation step?
>

AnalogInputNeuron simply holds a list of values and a current index into this list.
At reset() the index is set to 0 and Vm = values[index].
At each call to advance(), i.e. at each time-step, the index is incremented by one and Vm = values[index].
If index is to large Vm is "clamped" to its current value.
addAnalogValue(double v) does nothing more than adding v to the the end of the list of values.
Hence whether a call addAnalogValue(v) immediately influences Vm depends on the state
(i.e. on the value of index) of the input neuron.

>
> I would also like some help about SimNetwork::simulate(Time const & T) 
> (sounds crazy but I'm no longer sure of anything).
> If I call simulate(Time.ms(25)) will the simulation advance by 25 ms or 
> stop to 25 ms? More precisely, if I use simulate(Time.ms(25)) in a loop 
> will the simulation advance by 25 ms at each step or will it stick to 25 ms?

If you use simulate(Time.ms(25)) in a loop  the simulation advance by 25 ms at each step.
You need to call reset explicitly to set t=0ms.

>
> In fact I'm trying to use both PCSIM and webots 
> (http://www.cyberbotics.com/) for my experiment. Webots simulate the 
> robot and its environment and PCSIM is used to simulate the neural 
> network controlling the robot. Sensors values are injected from webots 
> to the network and the motor values are read from the network and sent 
> back to webots.
> I'm facing difficulties (the code runs but I have strange values on the 
> khepera sensors). Does anyone have some experience on this?
>

People at IGI (http://www.igi.tugraz.at/) are also using Webots but I do not know wether they use it in combination with PCSIM.
So maybe they can help you (at least a former college, Harald Burgsteiner, did something similar with CSIM - not PCSIM - and
real Khepera).

Regards

  -Thomas Natschläger

[Pcsim-users] Some clarifications

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

Hi everybody,

I just would like some clarifications about some PCSIM functions.

Let's begin with AnalogInputNeuron::addAnalogValue(double v).
Suppose that I call addAnalogValue(5). Will the output remain constant 
until the next call to addAnalogValue or will it be equal to 5 for only 
one simulation step?

I would also like some help about SimNetwork::simulate(Time const & T) 
(sounds crazy but I'm no longer sure of anything).
If I call simulate(Time.ms(25)) will the simulation advance by 25 ms or 
stop to 25 ms? More precisely, if I use simulate(Time.ms(25)) in a loop 
will the simulation advance by 25 ms at each step or will it stick to 25 ms?

In fact I'm trying to use both PCSIM and webots 
(http://www.cyberbotics.com/) for my experiment. Webots simulate the 
robot and its environment and PCSIM is used to simulate the neural 
network controlling the robot. Sensors values are injected from webots 
to the network and the motor values are read from the network and sent 
back to webots.
I'm facing difficulties (the code runs but I have strange values on the 
khepera sensors). Does anyone have some experience on this?

Thanks in advance,
Mathieu

Re: [Pcsim-users] How to make a field recordable?

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

Hello Dejan,

Under Python I would like to invoke getLinearInput like this:

inp_pop  = SimObjectPopulation(net, inp_model, 1);
nrn_pop  = SpatialSimObjectPopulation(net, , CuboidIntegerGrid3D(SIZE,
ORIGIN));
syn_proj = ConnectionsProjection(inp_pop, nrn_pop, syn_model,
RandomConnections(1.0));

N = 5;
for i in range(N):
  net.advance( i );
  print "Linear input: ", net.object(nrn_pop[0]).getLinearInput();


I get the following error:
ArgumentError: Python argument types in

     SquashingNeuron.getLinearInput(SquashingNeuron)

did not match C++ signature:

     getLinearInput(SquashingNeuron {lvalue})

Please find attached the code. Compilation is fine (though some warnings)
and the C++ unit test are passed (though the call to getLinearInput()
seems to return wrong values). I have tried to write a PyUnit test but I
don't know how to launch it.
There is a simple python test: launch test_SquashingNeuron.py (the error
message comes when executing this file).

Thank you so much.
Mathieu

> Hi,
>
> Mathieu Dubois wrote:
>> However, I would like to create a member function double
>> getLinearInput(void) that returns the value of the member "linear_input"
>> (in the same vein as getAnalogOutput()). How do I have to declare it?
>>
>> I have tried the following declaration double getLinearInput(void) {
>> return this->linear_input;}; (see attachments) but when I try to use it
>> I get the following error:
>>
>> ArgumentError: Python argument types in
>>
>>     SquashingNeuron.getLinearInput(SquashingNeuron)
>>
>> did not match C++ signature:
>>
>>     getLinearInput(SquashingNeuron {lvalue})
>>
>>
>> I have seen that AnalogPointNeuron::getAnalogOutput is declared as
>> follows:
>>
>> virtual double
>> <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/classdouble.html>
>> getAnalogOutput
>> <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/classAnalogPointNeuron.html#a6e02306ef9cd057f844615691b9293f>
>> (analog_port_id_t
>> <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/globaldefinitions_8h.html#40dfc683bdf73c81c9c73726fc834feb>
>> port=0) const
>>
> How do you invoke the getLinearInput function from Python?
> You can try the virtual keyword, but I'm not sure that causes the problem.
>
> rgds,
> Dejan
>>
>> Is it necessary to declare the function virtual (I'm not a C++ expert :)
>> ?
>>
>> Thank you again & sorry for the trouble,
>> Mathieu
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
>> easily build your RIAs with Flex Builder, the Eclipse(TM)based
>> development
>> software that enables intelligent coding and step-through debugging.
>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>> _______________________________________________
>> 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
>
>
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>

Re: [Pcsim-users] How to make a field recordable?

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

Hi,

Mathieu Dubois wrote:
> However, I would like to create a member function double 
> getLinearInput(void) that returns the value of the member "linear_input" 
> (in the same vein as getAnalogOutput()). How do I have to declare it?
>
> I have tried the following declaration double getLinearInput(void) { 
> return this->linear_input;}; (see attachments) but when I try to use it 
> I get the following error:
>
> ArgumentError: Python argument types in
>
>     SquashingNeuron.getLinearInput(SquashingNeuron)
>
> did not match C++ signature:
>
>     getLinearInput(SquashingNeuron {lvalue})
>
>
> I have seen that AnalogPointNeuron::getAnalogOutput is declared as follows:
>
> virtual double <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/classdouble.html> getAnalogOutput <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/classAnalogPointNeuron.html#a6e02306ef9cd057f844615691b9293f> (analog_port_id_t <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/globaldefinitions_8h.html#40dfc683bdf73c81c9c73726fc834feb> port=0) const
>   
How do you invoke the getLinearInput function from Python?
You can try the virtual keyword, but I'm not sure that causes the problem.

rgds,
Dejan
>
> Is it necessary to declare the function virtual (I'm not a C++ expert :) ?
>
> Thank you again & sorry for the trouble,
> Mathieu
>
>   
>
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> 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

Re: [Pcsim-users] pcsim installation problems

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

Hi Roman,

You should use PCSIM on a Linux system, since we haven't tested it yet 
on Windows.

Based on your output, there is possibly some problem with the state of 
your build system.
You can try the following on the installation where you have reported 
the pcsim_install_output_txt :

remove the _build directory in PCSIM's home:

rm -rf _build

then run:

python build.py wipe

then:

python build.py -j 2 install

Note that you have to have the boost 1.34.1 version installed. A newer 
version doesn't work.

If you have further questions about PCSIM, please post them on the 
sourceforge mailing list

http://sourceforge.net/mailarchive/forum.php?forum_name=pcsim-users

so that other users can benefit from the discussion.

Cheers,
Dejan


Roman Bauer wrote:
>
> Dear Mr. Pecevski,
>
>  
>
> I started my PhD this year at the Institute of Neuroinformatics in 
> Zürich this year, and want to use PCSIM (pcsim-0.5.4) for simulating 
> some neural network models. However, I'm having some problems 
> installing it, and I'd be very gratefull for some help or tipps where 
> to look at if you don't mind...
>
>  
>
> python setup.py install does yield errors, as some pypp.hpp files are 
> not found (see the attached output file "pcsim_install_output_txt"). I 
> installed the dependencies as described in 
> "HowTo-Install-PCSIM-Dependencies-Linux" and have been struggling with 
> this (on two different machines, 32 bit and 64 bit, with the same 
> problem) for some time, do you know where the problem could be?  I 
> installed gccxml from
>
> cvs -d :pserver:an...@ww...:/cvsroot/GCC_XML co gccxml
>
> and pygccxml-0.9.5 and Py++0.9.5.
>
>  
>
> On windows, I tried to follow the guide 
> "HowTo-Install-PCSIM-Dependencies-Windows", but at point 9) I don't 
> understand from where exactly to copy the files   bin\release\*    and 
>  bin\gccxml_config  from (into %PCSIMDEVENV%\gccxml-0.7.0\bin).
>
>  
>
> I also tried to install it on cygwin, however it seems like the gcc 
> --pthread option is not supported there, which is probably why 
> installing the thread part of pcsim does not succeed 
> (cygwin_install_output.dat).
>
>  
>
> Thanks a lot for your suggestions,
>
>  
>
> Roman Bauer
>
> ------------------------------------------------------------------------
>
> running install
> running build
> running build_clib
> building 'pcsim' library
>    Build type   = Release
>    Platform     = linux-i686
>    Make tool    = /usr/bin/gmake
>    Make command = /usr/bin/gmake -i
>    Python executable : /usr/local/bin/python version 2.4 
>    Python libraries : /usr/local/lib/python2.4/config
>    Python includes : /usr/local/include/python2.4
>    Doxygen executable : /usr/bin/doxygen
>    GCCXML executable : /usr/local/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc43-mt
> BOOST_LIB_SUFFIX_2 IS gcc43-mt-1_34_1
> boost_python-gcc43-mt
>    Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc43-mt.so
> boost_thread-gcc43-mt
>    Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc43-mt.so
> boost_date_time-gcc43-mt
>    Boost C++ library boost_date_time : /usr/local/lib/libboost_date_time-gcc43-mt.so
>    Boost C++ libraries : /usr/local/lib 
>    Boost C++ include path : /usr/local/include/boost-1_34_1 
>    MPICH2 library: /usr/local/lib/libmpich.so
>    MPICH2 include path : /usr/local/include
>    GNU Scientific library : /usr/local/lib/libgsl.so
>    Xerces library : /usr/lib/libxerces-c.so
>    CppUnit : /usr/lib/libcppunit.so
> $JAVA_EXECUTABLE
> $JNI_INCLUDE_PATH_CAND
>    JNI headers : /usr/lib/jvm/java-1.6.0-sun-1.6.0/include
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/roman/packages/pcsim-0.5.4/_build
> Running CMake to regenerate build system...
>    Build type   = Release
>    Platform     = linux-i686
>    Make tool    = /usr/bin/gmake
>    Make command = /usr/bin/gmake -i
>    Python executable : /usr/local/bin/python version 2.4 
>    Python libraries : /usr/local/lib/python2.4/config
>    Python includes : /usr/local/include/python2.4
>    Doxygen executable : /usr/bin/doxygen
>    GCCXML executable : /usr/local/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc43-mt
> BOOST_LIB_SUFFIX_2 IS gcc43-mt-1_34_1
> boost_python-gcc43-mt
>    Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc43-mt.so
> boost_thread-gcc43-mt
>    Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc43-mt.so
> boost_date_time-gcc43-mt
>    Boost C++ library boost_date_time : /usr/local/lib/libboost_date_time-gcc43-mt.so
>    Boost C++ libraries : /usr/local/lib 
>    Boost C++ include path : /usr/local/include/boost-1_34_1 
>    MPICH2 library: /usr/local/lib/libmpich.so
>    MPICH2 include path : /usr/local/include
>    GNU Scientific library : /usr/local/lib/libgsl.so
>    Xerces library : /usr/lib/libxerces-c.so
>    CppUnit : /usr/lib/libcppunit.so
> $JAVA_EXECUTABLE
> $JNI_INCLUDE_PATH_CAND
>    JNI headers : /usr/lib/jvm/java-1.6.0-sun-1.6.0/include
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/roman/packages/pcsim-0.5.4/_build
> [100%] Built target pcsim
>   
>>>>> cd /home/roman/packages/pcsim-0.5.4/_build
>>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D CMAKE_INSTALL_PREFIX:PATH=/home/roman/packages/pcsim-0.5.4 -D PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D EXTRA_INSTALL:STRING=NO /home/roman/packages/pcsim-0.5.4
>>>>> cd /home/roman/packages/pcsim-0.5.4/_build
>>>>> /usr/bin/gmake -j 2 rebuild_cache
>>>>>           
> *******************************************
>   BUILDING pcsim 
> *******************************************
>   
>>>>> cd /home/roman/packages/pcsim-0.5.4/_build
>>>>> /usr/bin/gmake -j 2 pcsim
>>>>>           
> Finished in 10 secs.
> running build_ext
> building 'pypcsim' python module
> Built target generate_python_wrapper_code
> Built target generate_code
> Running CMake to regenerate build system...
>    Build type   = Release
>    Platform     = linux-i686
>    Make tool    = /usr/bin/gmake
>    Make command = /usr/bin/gmake -i
>    Python executable : /usr/local/bin/python version 2.4 
>    Python libraries : /usr/local/lib/python2.4/config
>    Python includes : /usr/local/include/python2.4
>    Doxygen executable : /usr/bin/doxygen
>    GCCXML executable : /usr/local/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc43-mt
> BOOST_LIB_SUFFIX_2 IS gcc43-mt-1_34_1
> boost_python-gcc43-mt
>    Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc43-mt.so
> boost_thread-gcc43-mt
>    Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc43-mt.so
> boost_date_time-gcc43-mt
>    Boost C++ library boost_date_time : /usr/local/lib/libboost_date_time-gcc43-mt.so
>    Boost C++ libraries : /usr/local/lib 
>    Boost C++ include path : /usr/local/include/boost-1_34_1 
>    MPICH2 library: /usr/local/lib/libmpich.so
>    MPICH2 include path : /usr/local/include
>    GNU Scientific library : /usr/local/lib/libgsl.so
>    Xerces library : /usr/lib/libxerces-c.so
>    CppUnit : /usr/lib/libcppunit.so
> $JAVA_EXECUTABLE
> $JNI_INCLUDE_PATH_CAND
>    JNI headers : /usr/lib/jvm/java-1.6.0-sun-1.6.0/include
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/roman/packages/pcsim-0.5.4/_build
> [  0%] Built target generate_python_wrapper_code
> [ 98%] Built target pcsim
> [ 98%] Building CXX object python/CMakeFiles/pypcsim.dir/pypcsim/pypcsim.main.o
> In file included from /usr/include/c++/4.3/ext/hash_map:64,
>                  from /home/roman/packages/pcsim-0.5.4/pcsim/simutils/pcsim_hash.h:21,
>                  from /home/roman/packages/pcsim-0.5.4/pcsim/simcore/SingleThreadAnalogMsgDispatcher.h:9,
>                  from /home/roman/packages/pcsim-0.5.4/pcsim/simcore/SingleThreadNetwork.h:14,
>                  from /home/roman/packages/pcsim-0.5.4/python/pypcsim.h:6,
>                  from /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:9:
> /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.
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:11:47: error: pypcsim/AdaptiveStepSolver.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:13:40: error: pypcsim/AdvanceInfo.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:15:55: error: pypcsim/AlphaFunctionSpikeResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:17:55: error: pypcsim/AlphaInfiniteSpikeResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:19:46: error: pypcsim/AnalogDelayObject.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:21:50: error: pypcsim/AnalogDelayedRecorder.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:23:46: error: pypcsim/AnalogInputNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:25:56: error: pypcsim/AnalogLevelBasedInputNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:27:46: error: pypcsim/AnalogPointNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:29:43: error: pypcsim/AnalogRecorder.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:31:42: error: pypcsim/AnalogSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:33:62: error: pypcsim/AttributeConnObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:35:61: error: pypcsim/AttributePopObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:37:65: error: pypcsim/AugmentedConnectionDecisionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:39:55: error: pypcsim/AugmentedSpatialPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:41:50: error: pypcsim/BernoulliDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:43:49: error: pypcsim/BinomialDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:45:49: error: pypcsim/BndGammaDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:47:50: error: pypcsim/BndNormalDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:49:47: error: pypcsim/CauchyDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:51:43: error: pypcsim/CbExIzhiNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:53:41: error: pypcsim/CbIzhiNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:55:40: error: pypcsim/CbLifNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:57:45: error: pypcsim/CbRhythmicNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:59:50: error: pypcsim/CbStaticAnalogSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:61:41: error: pypcsim/CbaEIFNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:63:48: error: pypcsim/ClippedDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:65:50: error: pypcsim/CoBaSyn_AlphaFunction.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:67:54: error: pypcsim/CoBaSyn_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:69:53: error: pypcsim/CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:71:51: error: pypcsim/CoBaSyn_GABA_BResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:73:55: error: pypcsim/CoBaSyn_GABA_BResponseNest.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:75:54: error: pypcsim/CoBaSyn_GABA_BResponseODE.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:77:52: error: pypcsim/CoBaSyn_OUNoiseResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:79:56: error: pypcsim/CompositeNeuron_CbLifNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:81:57: error: pypcsim/CompositeNeuron_CbaEIFNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:83:54: error: pypcsim/CompositeNeuron_LifNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:85:58: error: pypcsim/ConductanceBasedAnalogSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:87:51: error: pypcsim/ConductanceInputTarget.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:89:46: error: pypcsim/ConnObjectFactory.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:91:53: error: pypcsim/ConnObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:93:121: error: pypcsim/ConnObjectValueGeneratorSpecialization_AugmentedSpatialPopulation_AugmentedSpatialPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:95:107: error: pypcsim/ConnObjectValueGeneratorSpecialization_SimObjectPopulation_SimObjectPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:97:115: error: pypcsim/ConnObjectValueGeneratorSpecialization_SpatialFamilyPopulation_SpatialFamilyPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:99:121: error: pypcsim/ConnObjectValueGeneratorSpecialization_SpatialSimObjectPopulation_SpatialSimObjectPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:101:56: error: pypcsim/ConnectionDecisionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:103:124: error: pypcsim/ConnectionDecisionPredicateSpecialization_AugmentedSpatialPopulation_AugmentedSpatialPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:105:110: error: pypcsim/ConnectionDecisionPredicateSpecialization_SimObjectPopulation_SimObjectPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:107:118: error: pypcsim/ConnectionDecisionPredicateSpecialization_SpatialFamilyPopulation_SpatialFamilyPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:109:124: error: pypcsim/ConnectionDecisionPredicateSpecialization_SpatialSimObjectPopulation_SpatialSimObjectPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:111:47: error: pypcsim/ConnectionIterator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:113:50: error: pypcsim/ConnectionsProjection.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:115:43: error: pypcsim/ConstantNumber.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:117:50: error: pypcsim/CuBaSyn_AlphaFunction.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:119:50: error: pypcsim/CuBaSyn_AlphaInfinite.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:121:54: error: pypcsim/CuBaSyn_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:123:53: error: pypcsim/CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:125:48: error: pypcsim/CuBaSyn_SquarePulse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:127:55: error: pypcsim/CuboidGridObjectPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:129:48: error: pypcsim/CuboidIntegerGrid3D.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:131:54: error: pypcsim/CurrentBasedAnalogSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:133:47: error: pypcsim/CurrentInputTarget.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:135:59: error: pypcsim/DAModStdpDynamicCondExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:137:60: error: pypcsim/DAModStdpDynamicCondExpSynapse2.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:139:59: error: pypcsim/DAModStdpDynamicCurrExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:141:60: error: pypcsim/DAModStdpDynamicCurrExpSynapse2.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:143:56: error: pypcsim/DAModStdpSquarePulseSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:145:57: error: pypcsim/DAModStdpSquarePulseSynapse2.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:147:58: error: pypcsim/DAModStdpStaticCondExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:149:59: error: pypcsim/DAModStdpStaticCondExpSynapse2.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:151:58: error: pypcsim/DAModulatedDynamicStdpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:153:59: error: pypcsim/DAModulatedDynamicStdpSynapse2.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:155:130: error: pypcsim/DAModulatedSTDPSynapse2_FroemkeDanStdpSynapse_EachPairStdpSynapse_DynamicSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:157:130: error: pypcsim/DAModulatedSTDPSynapse2_FroemkeDanStdpSynapse_EachPairStdpSynapse_DynamicSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:159:129: error: pypcsim/DAModulatedSTDPSynapse2_FroemkeDanStdpSynapse_EachPairStdpSynapse_StaticSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:161:129: error: pypcsim/DAModulatedSTDPSynapse2_FroemkeDanStdpSynapse_EachPairStdpSynapse_StaticSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:163:124: error: pypcsim/DAModulatedSTDPSynapse2_FroemkeDanStdpSynapse_EachPairStdpSynapse_StaticSyn_CuBaSyn_SquarePulse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:165:129: error: pypcsim/DAModulatedSTDPSynapse_FroemkeDanStdpSynapse_EachPairStdpSynapse_DynamicSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:167:129: error: pypcsim/DAModulatedSTDPSynapse_FroemkeDanStdpSynapse_EachPairStdpSynapse_DynamicSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:169:128: error: pypcsim/DAModulatedSTDPSynapse_FroemkeDanStdpSynapse_EachPairStdpSynapse_StaticSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:171:128: error: pypcsim/DAModulatedSTDPSynapse_FroemkeDanStdpSynapse_EachPairStdpSynapse_StaticSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:173:123: error: pypcsim/DAModulatedSTDPSynapse_FroemkeDanStdpSynapse_EachPairStdpSynapse_StaticSyn_CuBaSyn_SquarePulse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:175:57: error: pypcsim/DAModulatedStaticStdpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:177:58: error: pypcsim/DAModulatedStaticStdpSynapse2.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:179:46: error: pypcsim/DARecvCbLifNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:181:44: error: pypcsim/DARecvLifNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:183:54: error: pypcsim/DARecvLinearPoissonNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:185:58: error: pypcsim/DegreeDistributionConnections.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:187:38: error: pypcsim/DelayCond.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:189:44: error: pypcsim/DelayCondAndSyn.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:191:58: error: pypcsim/DistributedMultiThreadNetwork.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:193:47: error: pypcsim/DistributedNetwork.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:195:59: error: pypcsim/DistributedSingleThreadNetwork.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:197:56: error: pypcsim/DistributedSyncWiringMethod.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:199:49: error: pypcsim/DistributionStrategy.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:201:45: error: pypcsim/DopamineReceiver.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:203:59: error: pypcsim/DoubleExponentialSpikeResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:205:52: error: pypcsim/DynamicCondAlphaSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:207:56: error: pypcsim/DynamicCondDoubleExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:209:50: error: pypcsim/DynamicCondExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:211:52: error: pypcsim/DynamicCurrAlphaSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:213:56: error: pypcsim/DynamicCurrDoubleExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:215:50: error: pypcsim/DynamicCurrExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:217:49: error: pypcsim/DynamicGABAAlphaBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:219:52: error: pypcsim/DynamicGABAAlphaSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:221:53: error: pypcsim/DynamicGABADoubleExpBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:223:56: error: pypcsim/DynamicGABADoubleExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:225:47: error: pypcsim/DynamicGABAExpBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:227:50: error: pypcsim/DynamicGABAExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:229:54: error: pypcsim/DynamicGlutamateAlphaBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:231:57: error: pypcsim/DynamicGlutamateAlphaSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:233:58: error: pypcsim/DynamicGlutamateDoubleExpBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:235:61: error: pypcsim/DynamicGlutamateDoubleExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:237:52: error: pypcsim/DynamicGlutamateExpBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:239:55: error: pypcsim/DynamicGlutamateExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:241:61: error: pypcsim/DynamicHomeostaticCurrentSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:243:54: error: pypcsim/DynamicHomeostaticSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:245:51: error: pypcsim/DynamicIzhiStdpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:247:52: error: pypcsim/DynamicNMDAAlphaSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:249:56: error: pypcsim/DynamicNMDADoubleExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:251:50: error: pypcsim/DynamicNMDAExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:253:53: error: pypcsim/DynamicNonLinGABAExpBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:255:56: error: pypcsim/DynamicNonLinGABAExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:257:50: error: pypcsim/DynamicSpikingSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:259:54: error: pypcsim/DynamicStdpCondExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:261:47: error: pypcsim/DynamicStdpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:263:61: error: pypcsim/DynamicSyn_CoBaSyn_AlphaFunction.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:265:65: error: pypcsim/DynamicSyn_CoBaSyn_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:267:64: error: pypcsim/DynamicSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:269:61: error: pypcsim/DynamicSyn_CuBaSyn_AlphaFunction.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:271:65: error: pypcsim/DynamicSyn_CuBaSyn_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:273:64: error: pypcsim/DynamicSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:275:65: error: pypcsim/DynamicSyn_NMDASynapse_AlphaFunction.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:277:69: error: pypcsim/DynamicSyn_NMDASynapse_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:279:68: error: pypcsim/DynamicSyn_NMDASynapse_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:281:84: error: pypcsim/EachPairStdpSynapse_DynamicSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:283:84: error: pypcsim/EachPairStdpSynapse_DynamicSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:285:83: error: pypcsim/EachPairStdpSynapse_StaticSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:287:83: error: pypcsim/EachPairStdpSynapse_StaticSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:289:78: error: pypcsim/EachPairStdpSynapse_StaticSyn_CuBaSyn_SquarePulse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:291:63: error: pypcsim/EuclideanDistanceRandomConnections.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:293:65: error: pypcsim/EuclidianDistanceConnectionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:295:40: error: pypcsim/EvLifNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:297:41: error: pypcsim/ExIzhiNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:299:45: error: pypcsim/ExIzhiNeuronBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:301:58: error: pypcsim/ExponentialDecaySpikeResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:303:52: error: pypcsim/ExponentialDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:305:57: error: pypcsim/FacetsHWDepressionExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:307:54: error: pypcsim/FacetsHWDepressionSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:309:80: error: pypcsim/FacetsHWDepressionSynapse_CoBaSyn_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:311:79: error: pypcsim/FacetsHWDepressionSynapse_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:313:59: error: pypcsim/FacetsHWFacilitationExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:315:56: error: pypcsim/FacetsHWFacilitationSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:317:82: error: pypcsim/FacetsHWFacilitationSynapse_CoBaSyn_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:319:81: error: pypcsim/FacetsHWFacilitationSynapse_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:321:59: error: pypcsim/FamilyConnObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:323:64: error: pypcsim/FamilyIdConnectionDecisionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:325:58: error: pypcsim/FamilyPopObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:327:48: error: pypcsim/FiniteSpikeResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:329:44: error: pypcsim/FixedStepSolver.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:331:106: error: pypcsim/FroemkeDanStdpSynapse_EachPairStdpSynapse_DynamicSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:333:106: error: pypcsim/FroemkeDanStdpSynapse_EachPairStdpSynapse_DynamicSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:335:105: error: pypcsim/FroemkeDanStdpSynapse_EachPairStdpSynapse_StaticSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:337:105: error: pypcsim/FroemkeDanStdpSynapse_EachPairStdpSynapse_StaticSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:339:100: error: pypcsim/FroemkeDanStdpSynapse_EachPairStdpSynapse_StaticSyn_CuBaSyn_SquarePulse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:341:105: error: pypcsim/FroemkeDanStdpSynapse_OnePairStdpSynapse_DynamicSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:343:104: error: pypcsim/FroemkeDanStdpSynapse_OnePairStdpSynapse_StaticSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:345:54: error: pypcsim/GABASynapse_AlphaFunction.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:347:58: error: pypcsim/GABASynapse_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:349:57: error: pypcsim/GABASynapse_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:351:43: error: pypcsim/GABA_BResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:353:47: error: pypcsim/GABA_BResponseNest.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:355:46: error: pypcsim/GABA_BResponseODE.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:357:42: error: pypcsim/GABA_BSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:359:46: error: pypcsim/GABA_BSynapseNest.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:361:45: error: pypcsim/GABA_BSynapseODE.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:363:47: error: pypcsim/Gamma2Distribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:365:46: error: pypcsim/GammaDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:367:42: error: pypcsim/GaussianNoise.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:369:50: error: pypcsim/GeometricDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:371:59: error: pypcsim/GlutamateSynapse_AlphaFunction.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:373:63: error: pypcsim/GlutamateSynapse_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:375:62: error: pypcsim/GlutamateSynapse_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:377:40: error: pypcsim/GridPoint3D.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:379:39: error: pypcsim/GslStepper.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:381:43: error: pypcsim/GslStepperType.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:383:38: error: pypcsim/HHINeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:385:37: error: pypcsim/HHNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:387:49: error: pypcsim/HHNeuronTraubMiles91.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:389:51: error: pypcsim/HomDynGlutamateExpBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:391:54: error: pypcsim/HomDynGlutamateExpSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:393:83: error: pypcsim/HomeostaticSynapse_DynamicSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:395:83: error: pypcsim/HomeostaticSynapse_DynamicSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:397:82: error: pypcsim/HomeostaticSynapse_StaticSyn_CoBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:399:82: error: pypcsim/HomeostaticSynapse_StaticSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:401:50: error: pypcsim/InfiniteSpikeResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:403:39: error: pypcsim/IzhiNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:405:43: error: pypcsim/IzhiNeuronBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:407:47: error: pypcsim/LIFCondAlphaNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:409:45: error: pypcsim/LIFCondExpNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:411:47: error: pypcsim/LIFCurrAlphaNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:413:45: error: pypcsim/LIFCurrExpNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:415:48: error: pypcsim/LaggedFibonacci1279.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:417:49: error: pypcsim/LaggedFibonacci19937.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:419:48: error: pypcsim/LaggedFibonacci2281.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:421:49: error: pypcsim/LaggedFibonacci23209.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:423:48: error: pypcsim/LaggedFibonacci3217.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:425:48: error: pypcsim/LaggedFibonacci4423.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:427:49: error: pypcsim/LaggedFibonacci44497.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:429:47: error: pypcsim/LaggedFibonacci607.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:431:48: error: pypcsim/LaggedFibonacci9689.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:433:51: error: pypcsim/LateralDelayCondAndSyn.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:435:72: error: pypcsim/LateralEuclidianDistanceConnectionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:437:75: error: pypcsim/LateralLongRangeOrientationConnectionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:439:38: error: pypcsim/LifNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:441:42: error: pypcsim/LifNeuronBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:443:41: error: pypcsim/LinearNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:445:48: error: pypcsim/LinearPoissonNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:447:50: error: pypcsim/LogNormalDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:449:42: error: pypcsim/MPICommHandle.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:451:50: error: pypcsim/MersenneTwister11213b.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:453:49: error: pypcsim/MersenneTwister19937.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:455:47: error: pypcsim/MultiThreadNetwork.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:457:54: error: pypcsim/MultipleOutputSpikeSender.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:459:54: error: pypcsim/NMDASynapse_AlphaFunction.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:461:58: error: pypcsim/NMDASynapse_DoubleExponential.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:463:57: error: pypcsim/NMDASynapse_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:465:44: error: pypcsim/NeuroMLImporter.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:467:63: error: pypcsim/NonLinGABASynapse_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:469:47: error: pypcsim/NormalDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:471:38: error: pypcsim/ODESystem.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:473:56: error: pypcsim/ODESystemBasedSpikingNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:475:40: error: pypcsim/OUGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:477:44: error: pypcsim/OUNoiseResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:479:43: error: pypcsim/OUNoiseSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:481:83: error: pypcsim/OnePairStdpSynapse_DynamicSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:483:82: error: pypcsim/OnePairStdpSynapse_StaticSyn_CuBaSyn_ExponentialDecay.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:485:49: error: pypcsim/OneToOneWiringMethod.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:487:43: error: pypcsim/OnlineAverager.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:489:53: error: pypcsim/OnlineHistogramGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:491:51: error: pypcsim/PCSIMParserEnvironment.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:493:58: error: pypcsim/PlainConnObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:495:61: error: pypcsim/PlainConnectionDecisionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:497:57: error: pypcsim/PlainPopObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:499:39: error: pypcsim/Point3DSet.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:501:46: error: pypcsim/Point3DSetSpliter.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:503:43: error: pypcsim/Point3D_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:505:48: error: pypcsim/PoissonDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:507:47: error: pypcsim/PoissonInputNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:509:54: error: pypcsim/PopObjectAttributeFactory.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:511:45: error: pypcsim/PopObjectFactory.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:513:52: error: pypcsim/PopObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:515:93: error: pypcsim/PopObjectValueGeneratorSpecialization_AugmentedSpatialPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:517:86: error: pypcsim/PopObjectValueGeneratorSpecialization_SimObjectPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:519:90: error: pypcsim/PopObjectValueGeneratorSpecialization_SpatialFamilyPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:521:93: error: pypcsim/PopObjectValueGeneratorSpecialization_SpatialSimObjectPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:523:58: error: pypcsim/PositionBased2dValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:525:54: error: pypcsim/PredicateBasedConnections.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:527:67: error: pypcsim/PyAugmentedConnectionDecisionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:529:58: error: pypcsim/PyConnectionDecisionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:531:44: error: pypcsim/PySimObjectBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:533:44: error: pypcsim/PySimObjectStub.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:535:45: error: pypcsim/QuadDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:537:82: error: pypcsim/RandDistBoostImpl_boost_bernoulli_distribution_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:539:85: error: pypcsim/RandDistBoostImpl_boost_binomial_distribution_int_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:541:79: error: pypcsim/RandDistBoostImpl_boost_cauchy_distribution_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:543:84: error: pypcsim/RandDistBoostImpl_boost_exponential_distribution_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:545:78: error: pypcsim/RandDistBoostImpl_boost_gamma_distribution_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:547:86: error: pypcsim/RandDistBoostImpl_boost_geometric_distribution_int_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:549:82: error: pypcsim/RandDistBoostImpl_boost_lognormal_distribution_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:551:79: error: pypcsim/RandDistBoostImpl_boost_normal_distribution_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:553:84: error: pypcsim/RandDistBoostImpl_boost_poisson_distribution_int_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:555:81: error: pypcsim/RandDistBoostImpl_boost_triangle_distribution_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:557:72: error: pypcsim/RandDistBoostImpl_boost_uniform_real_double.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:559:99: error: pypcsim/RandEngBoostImpl_boost_random_lagged_fibonacci_01_double_48_1279u_418u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:561:101: error: pypcsim/RandEngBoostImpl_boost_random_lagged_fibonacci_01_double_48_19937u_9842u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:563:100: error: pypcsim/RandEngBoostImpl_boost_random_lagged_fibonacci_01_double_48_2281u_1252u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:565:102: error: pypcsim/RandEngBoostImpl_boost_random_lagged_fibonacci_01_double_48_23209u_13470u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:567:99: error: pypcsim/RandEngBoostImpl_boost_random_lagged_fibonacci_01_double_48_3217u_576u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:569:100: error: pypcsim/RandEngBoostImpl_boost_random_lagged_fibonacci_01_double_48_4423u_2098u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:571:102: error: pypcsim/RandEngBoostImpl_boost_random_lagged_fibonacci_01_double_48_44497u_21034u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:573:98: error: pypcsim/RandEngBoostImpl_boost_random_lagged_fibonacci_01_double_48_607u_273u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:575:100: error: pypcsim/RandEngBoostImpl_boost_random_lagged_fibonacci_01_double_48_9689u_5502u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:577:160: error: pypcsim/RandEngBoostImpl_boost_random_mersenne_twister_unsigned_int_32_351_175_19_3433795303u_11_7_834054912u_15_4293197824u_17_2742893714u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:579:161: error: pypcsim/RandEngBoostImpl_boost_random_mersenne_twister_unsigned_int_32_624_397_31_2567483615u_11_7_2636928640u_15_4022730752u_18_3346425566u.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:581:46: error: pypcsim/RandomConnections.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:583:47: error: pypcsim/RandomDistribution.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:585:41: error: pypcsim/RandomEngine.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:587:55: error: pypcsim/RandomFixNumberConnections.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:589:47: error: pypcsim/RatioBasedFamilies.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:591:46: error: pypcsim/RatioBasedSpliter.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:593:70: error: pypcsim/RetinotopicOrientationConnectionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:595:43: error: pypcsim/RhythmicNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:597:47: error: pypcsim/RhythmicNeuronBase.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:599:40: error: pypcsim/RungeKutta2.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:601:40: error: pypcsim/RungeKutta4.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:603:38: error: pypcsim/SimEngine.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:605:39: error: pypcsim/SimNetwork.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:607:38: error: pypcsim/SimObject.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:609:50: error: pypcsim/SimObjectArrayFactory.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:611:48: error: pypcsim/SimObjectAttributes.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:613:45: error: pypcsim/SimObjectFactory.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:615:48: error: pypcsim/SimObjectPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:617:54: error: pypcsim/SimObjectVariationFactory.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:619:41: error: pypcsim/SimParameter.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:621:43: error: pypcsim/SimProgressBar.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:623:64: error: pypcsim/SimilarAttributeConnectionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:625:55: error: pypcsim/SimpleAllToAllWiringMethod.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:627:56: error: pypcsim/SimpleScalingSpikingSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:629:52: error: pypcsim/SingleOutputSpikeSender.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:631:48: error: pypcsim/SingleThreadNetwork.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:633:35: error: pypcsim/Solver.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:635:60: error: pypcsim/SpatialConnObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:637:63: error: pypcsim/SpatialConnectionDecisionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:639:53: error: pypcsim/SpatialFamilyIDGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:641:52: error: pypcsim/SpatialFamilyPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:643:59: error: pypcsim/SpatialPopObjectValueGenerator.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:645:55: error: pypcsim/SpatialSimObjectPopulation.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:647:54: error: pypcsim/SphereConnectionPredicate.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:649:39: error: pypcsim/SpikeEvent.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:651:40: error: pypcsim/SpikeSender.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:653:53: error: pypcsim/SpikeTimeDelayedRecorder.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:655:46: error: pypcsim/SpikeTimeRecorder.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:657:47: error: pypcsim/SpikingInputNeuron.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:659:53: error: pypcsim/SquarePulseSpikeResponse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:661:52: error: pypcsim/StaticAnaSyn_CoBaAnaSyn.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:663:52: error: pypcsim/StaticAnaSyn_CuBaAnaSyn.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:665:48: error: pypcsim/StaticAnalogSynapse.pypp.hpp: No such file or directory
> /home/roman/packages/pcsim-0.5.4/python/pypcsim/pypcsim.main.cpp:667:51: error: pypcsim/StaticCondAlphaSynapse.pypp.hpp: No such ...
 
[truncated message content]

Re: [Pcsim-users] How to make a field recordable?

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

[Sorry I forgot to send the response to the list]

Hi Dejan,

Thanks to your remark I have realised my error! In a previous version I 
used "linear_sum" and wrote the python with this name. I later changed 
the C++ member to "linear_input" but not the python code. It was a 
stupid mistake :(

I have updated the code and I can now record the field.

However, I would like to create a member function double 
getLinearInput(void) that returns the value of the member "linear_input" 
(in the same vein as getAnalogOutput()). How do I have to declare it?

I have tried the following declaration double getLinearInput(void) { 
return this->linear_input;}; (see attachments) but when I try to use it 
I get the following error:

ArgumentError: Python argument types in

    SquashingNeuron.getLinearInput(SquashingNeuron)

did not match C++ signature:

    getLinearInput(SquashingNeuron {lvalue})


I have seen that AnalogPointNeuron::getAnalogOutput is declared as follows:

virtual double <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/classdouble.html> getAnalogOutput <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/classAnalogPointNeuron.html#a6e02306ef9cd057f844615691b9293f> (analog_port_id_t <http://www.lsm.tugraz.at/pcsim/cppclassreference/html/globaldefinitions_8h.html#40dfc683bdf73c81c9c73726fc834feb> port=0) const


Is it necessary to declare the function virtual (I'm not a C++ expert :) ?

Thank you again & sorry for the trouble,
Mathieu

Pecevski Dejan wrote:
> Hi Mathieu,
>
> I've looked at your code.
> Do you mean the linear_input public member in the SquashingNeuron 
> function, instead of linear_sum?
> Did you try the linear_input member or linear_sum?
>
> regards,
> Dejan
>
>
> Mathieu Dubois wrote:
>> Hi everybody,
>>
>> I'm developing a small PCSIM extension (I have carefully followed the 
>> steps in the HowTo).
>>
>> I want to define a new class SquashingNeuron which derives from 
>> LinearNeuron. At each step it should sum the synaptic inputs (like 
>> LinearNeuron) and apply a squashing function.
>>
>> The implementation is straightforward (see attachments). Compilation 
>> & tests went fine.
>>
>> However (for debugging purpose) I would like to be able to record the 
>> "linear_sum" public member (which is the linear sum of synaptic 
>> inputs - result of LinearNeuron::advance(...) see code).
>>
>> When I try this I get the following error message:
>>
>> RuntimeError: PCSIM::Exception in function SimObject::findField: 
>> SquashingNeuron has no field named linear_sum
>>
>> Is there something wrong with my code or do I have to do something to 
>> turn a C++ public member into a PCSIM field?
>>
>> Interested readers will recognize the kind of squashing function used 
>> in the p-delta learning rule... which is what I would like to implement.
>>
>> Thanks in advance,
>> Mathieu
>> ------------------------------------------------------------------------
>>
>> #include "SquashingNeuron.h"
>>
>> // SquashingNeuron::SquashingNeuron(): rho(DEFAULT_RHO) {
>> // }
>>
>> SquashingNeuron::SquashingNeuron(double rho): rho(rho) {
>> }
>>
>> int SquashingNeuron::advance(AdvanceInfo const & info) {
>>     LinearNeuron::advance(info);
>>     linear_input = this->Vm;
>>     if (linear_input < -this->rho) {
>>         this->Vm = POSITIVE_OUTPUT;
>>     }
>>     if ((linear_input >= -this->rho) && (linear_input <= this->rho)) {
>>          this->Vm = linear_input/this->rho;
>>     }
>>     if (linear_input > this->rho) {
>>         this->Vm = NEGATIVE_OUTPUT;
>>     }
>>     return 0;
>> }
>>   
>> ------------------------------------------------------------------------
>>
>> #ifndef SQUASHINGNEURON_H_
>> #define SQUASHINGNEURON_H_
>>
>> #include "LinearNeuron.h"
>>
>> #define POSITIVE_OUTPUT (1)
>> #define NEGATIVE_OUTPUT (-1)
>>
>> #define DEFAULT_RHO (0.25)
>>
>> class SquashingNeuron : public LinearNeuron
>> {
>>
>>     SIMOBJECT( SquashingNeuron, AdvancePhase::Two )
>>
>> public:
>> //     SquashingNeuron();
>>     SquashingNeuron(double rho = DEFAULT_RHO);
>>
>>     int advance(AdvanceInfo const &);
>>
>>     double linear_input;
>>
>> protected:
>>     double rho;
>> };
>>
>> #endif /*SQUASHINGNEURON_H_*/
>>   
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
>> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
>> software that enables intelligent coding and step-through debugging.
>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> 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
>   
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>   

Re: [Pcsim-users] How to make a field recordable?

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

Hi Mathieu,

I've looked at your code.
Do you mean the linear_input public member in the SquashingNeuron 
function, instead of linear_sum?
Did you try the linear_input member or linear_sum?

regards,
Dejan


Mathieu Dubois wrote:
> Hi everybody,
>
> I'm developing a small PCSIM extension (I have carefully followed the 
> steps in the HowTo).
>
> I want to define a new class SquashingNeuron which derives from 
> LinearNeuron. At each step it should sum the synaptic inputs (like 
> LinearNeuron) and apply a squashing function.
>
> The implementation is straightforward (see attachments). Compilation & 
> tests went fine.
>
> However (for debugging purpose) I would like to be able to record the 
> "linear_sum" public member (which is the linear sum of synaptic inputs 
> - result of LinearNeuron::advance(...) see code).
>
> When I try this I get the following error message:
>
> RuntimeError: PCSIM::Exception in function SimObject::findField: 
> SquashingNeuron has no field named linear_sum
>
> Is there something wrong with my code or do I have to do something to 
> turn a C++ public member into a PCSIM field?
>
> Interested readers will recognize the kind of squashing function used 
> in the p-delta learning rule... which is what I would like to implement.
>
> Thanks in advance,
> Mathieu
> ------------------------------------------------------------------------
>
> #include "SquashingNeuron.h"
>
> // SquashingNeuron::SquashingNeuron(): rho(DEFAULT_RHO) {
> // }
>
> SquashingNeuron::SquashingNeuron(double rho): rho(rho) {
> }
>
> int SquashingNeuron::advance(AdvanceInfo const & info) {
>     LinearNeuron::advance(info);
>     linear_input = this->Vm;
>     if (linear_input < -this->rho) {
>         this->Vm = POSITIVE_OUTPUT;
>     }
>     if ((linear_input >= -this->rho) && (linear_input <= this->rho)) {
>          this->Vm = linear_input/this->rho;
>     }
>     if (linear_input > this->rho) {
>         this->Vm = NEGATIVE_OUTPUT;
>     }
>     return 0;
> }
>   
> ------------------------------------------------------------------------
>
> #ifndef SQUASHINGNEURON_H_
> #define SQUASHINGNEURON_H_
>
> #include "LinearNeuron.h"
>
> #define POSITIVE_OUTPUT (1)
> #define NEGATIVE_OUTPUT (-1)
>
> #define DEFAULT_RHO (0.25)
>
> class SquashingNeuron : public LinearNeuron
> {
>
>     SIMOBJECT( SquashingNeuron, AdvancePhase::Two )
>
> public:
> //     SquashingNeuron();
>     SquashingNeuron(double rho = DEFAULT_RHO);
>
>     int advance(AdvanceInfo const &);
>
>     double linear_input;
>
> protected:
>     double rho;
> };
>
> #endif /*SQUASHINGNEURON_H_*/
>   
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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

[Pcsim-users] How to make a field recordable?

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

Hi everybody,

I'm developing a small PCSIM extension (I have carefully followed the 
steps in the HowTo).

I want to define a new class SquashingNeuron which derives from 
LinearNeuron. At each step it should sum the synaptic inputs (like 
LinearNeuron) and apply a squashing function.

The implementation is straightforward (see attachments). Compilation & 
tests went fine.

However (for debugging purpose) I would like to be able to record the 
"linear_sum" public member (which is the linear sum of synaptic inputs - 
result of LinearNeuron::advance(...) see code).

When I try this I get the following error message:

RuntimeError: PCSIM::Exception in function SimObject::findField: SquashingNeuron has no field named linear_sum

Is there something wrong with my code or do I have to do something to 
turn a C++ public member into a PCSIM field?

Interested readers will recognize the kind of squashing function used in 
the p-delta learning rule... which is what I would like to implement.

Thanks in advance,
Mathieu

[Pcsim-users] Errors with PCSIM 0.5.4

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

Hi everybody,

I have recently decided to update my version of PCSIM from 0.5.0 to 
0.5.4 (because I switched from Ubuntu 8.04 to 8.10).

First I also had the same Java path problem that Christopher Nolan 
reported a few months ago. I fixed it with a ugly little hack in 
config.cmake.

After some troubles with mpich2 I succeeded in compiling PCSIM 0.5.4 
correctly. Nevertheless I have some errors when running tests. Here is 
the output of the failing test:

0:                                                                                              

0: ##Failure Location unknown## : Error                                                         

0: Test name: NeuroMLImporterTest::test_skeleton                                                

0: uncaught exception of type N3xsd3cxx6parser7parsingIcEE                                      

0: - instance document parsing failed                                                           

0:                                                                                              

0: Failures !!!                                                                                 

0: Run: 129   Failure total: 1   Failures: 0   Errors: 1 

[ LOT OF SUCCESSFUL TESTS]

0: Done with tests: local=0, mpi-tests=1

BUILD PROCESS FAILED. ERROR = 65280

Command: mpiexec -l -np 4 /usr/local/src/pcsim-0.5.4/_build/bin/pcsim_test


Apparently all the MPI test are passed and it's an error with the 
NeuroML features of PCSIM.

First question: Can it be related to the Java Path problem? Can it be fixed?

Second question: I don't need the NeuroML features. Is it safe to ignore 
the error and continue (happy) working with PCSIM?

Thanks in advance,
Mathieu

[Pcsim-users] fixed spike pattern stimulus

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

Hi,

Thank you Dejan for clarifying what net.reset() does exactly.

Actually what I am trying to do is present a fixed spike pattern stimulus to
the network repeatedly while having plasticity enabled in the network. The
only way I can think of to represent the fixed spike pattern is with neurons
of SpikingInputNeuron class.
The way I go about it now is:
- reset the network
- repeat N times
   - run simulation for 1 sec ( stimulus is 0.5 sec)
   - save the weights of all the plastic synapses
   - reset network
   - restore the weights of the plastic synapses

Is there a more natural way from pypcsim's perspective to "train" a network
with a fixed spiking pattern then saving weights and resetting the network?
More precisely is there any functionality for declaring repetitive or cyclic
stimuli?

Thanks again for the prompt answers.

Regards,
Robert.

Re: [Pcsim-users] question regarding net.reset()

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

Hi Robert,

The net.reset() initializes the weights of plastic synapses according to 
their initial weight value set at their creation.
Notice the two weight parameters inside the plastic synapses Winit, and W.
W is the weight that is evolving over time due to plasticity. Winit 
represents the initial value of the weight.

At net.reset(), W = Winit is executed.

regards,
Dejan


Robert Ioiart wrote:
> Hi,
>
> After running a simulation in which synapses are plastic, I call 
> net.reset(). In this situation are the weights of the synapses reset 
> according to the parameters given during their creation 
> (distributions, etc), or just the simulation time is reset and no 
> parameters of the network are changed?
>
> Thank you.
> Robert.
>
>
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
> -Strategies to boost innovation and cut costs with open source participation
> -Receive a $600 discount off the registration fee with the source code: SFAD
> http://p.sf.net/sfu/XcvMzF8H
> ------------------------------------------------------------------------
>
> _______________________________________________
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> 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

[Pcsim-users] question regarding net.reset()

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

Hi,

After running a simulation in which synapses are plastic, I call
net.reset(). In this situation are the weights of the synapses reset
according to the parameters given during their creation (distributions,
etc), or just the simulation time is reset and no parameters of the network
are changed?

Thank you.
Robert.

[Pcsim-users] Java paths in config.cmake

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

Hey all,

The cache variable JAVA_EXECUTABLE appears to be set when I run the
build process (somewhere in cmake, not in my shell environment), thus my
JAVA_HOME location is never picked up.  Unfortunately the preset value
is to /usr/bin/java, which is just a symbolic link to the actual Java
path, thus the attempt to find "jni.h" fails.

I'm currently working around the problem by modifying the name of the
cache variable used in config.cmake.

Distribution: Ubuntu 8.10 (Intrepid)

Another note, since my upgrade to ubuntu 8.10 and hence gcc 4.3.2, I've
had to add the -fpermissive option to the gcc options in config.cmake to
compile PCSIM.

Cheers,
Chris.

Re: [Pcsim-users] problem with xerces in Ubuntu 8.04

[Grzegorz M. W. <gmw...@gm...>]

Hi!

Thank you Thomas. Unfortunately this didn't work, however, after
trying all combinantions I found (as I suppose) a bug in the file
./cppunittests/CMakeLists.txt there is in the 16th line

${XERCES-LIBS}

and should be

${XERCES_LIBS}

with dash and without hyphen :-))))

I know, I would never find it without your seuggestion concerning the
sequence of linking librarier. Thank you!!!!!

After making the change the build is successful. I am very, very happy...

Best regards to all pcsim users,
Grzegorz




On Thu, Dec 11, 2008 at 8:33 AM, Natschläger Thomas
<Tho...@sc...> wrote:
> Hi!
>
> If I remember correctly a college of mine here at SCCG has already encountered the problem. The fix was to change the order of lib's against we link. So we tried to find a proper oder of
>
> TARGET_LINK_LIBRARIES( pcsim_test
>  pcsim
>   ${XERCES_LIBS}
>  ${MPI_LIBS}
>  ${GSL_LIBS}
>  ${CPPUNIT_LIBS}
>  ${BOOST_THREAD}
>  ${BOOST_DATETIME}
>  ${STLP_LIBS}
> )
>
> If I remember correctly we put ${XERCES_LIBS} more towards the end of that list in
> cppunit/CMakeLists.txt
> python/CMakeLists.txt
> java/CMakeLists.txt
>
>
> I hope this helps. We have to check this more thoroughly.
>
> -thomas natschlaeger
>
>
> ________________________________
>
> Von: Grzegorz M. Wojcik [mailto:gmw...@gm...]
> Gesendet: Mi 12/10/2008 6:19
> An: pcs...@li...
> Betreff: [Pcsim-users] problem with xerces in Ubuntu 8.04
>
>
>
> Hello!
>
> I came across serious problem when trying to compile pcsim on Ubuntu
> 8.04 Hardy Heron. I receive some errors concerning xerces-c, I suppose
> in same the end of my compilation process. They look like:
>
> NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_710XMLRefInfoD0Ev[xercesc_2_7::XMLRefInfo::~XMLRefInfo()]+0x35):
> undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
>
> with very often repeating phrase: undefined reference to `xercesc_2_7
>
> I have libxerces-c v. 2.7.0 located in /usr/lib (I think it is typical
> location).
>
> I was trying with no result doing the following things:
>
> 1) Telling the linker where libxerces is located.
> 2) libxerces 2.8
> 3) libxerces 3.0
> 4) compiling libxerces of all above versions from te scratch by the
> same compiler I compile pcsim
>
> To make matters worse (or better) when I run python setup.py test - a
> lot of tests end up with a positive 'OK' message.
>
> Do you have any ideas?
>
> best regards,
>
> Grzegorz
>
> P.S. Here is the whole set of error messages:
>
>
> [ 63%] Building CXX object
> python/CMakeFiles/pypcsim.dir/pypcsim/CuBaSyn_AlphaFunction.pypp.o
> [ 63%] Building CXX object
> cppunittests/CMakeFiles/pcsim_test.dir/HHNeuronTraubMiles91Test.o
> [ 64%] Building CXX object
> python/CMakeFiles/pypcsim.dir/pypcsim/SpatialSimObjectPopulation.pypp.o
> [ 64%] Building CXX object cppunittests/CMakeFiles/pcsim_test.dir/commonUtils.o
> Linking CXX executable ../bin/pcsim_test
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
> `xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
> const&)':
> NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_714DefaultHandler10fatalErrorERKNS_17SAXParseExceptionE[xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
> const&)]+0x2b): undefined reference to
> `xercesc_2_7::SAXParseException::SAXParseException(xercesc_2_7::SAXParseException
> const&)'
> NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_714DefaultHandler10fatalErrorERKNS_17SAXParseExceptionE[xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
> const&)]+0x4b): undefined reference to
> `xercesc_2_7::SAXParseException::~SAXParseException()'
> NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_714DefaultHandler10fatalErrorERKNS_17SAXParseExceptionE[xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
> const&)]+0x50): undefined reference to `typeinfo for
> xercesc_2_7::SAXParseException'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
> `xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()':
> NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713DTDEntityDeclD0Ev[xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()]+0xc):
> undefined reference to `xercesc_2_7::XMLEntityDecl::~XMLEntityDecl()'
> NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713DTDEntityDeclD0Ev[xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()]+0x14):
> undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
> `xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()':
> NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713DTDEntityDeclD1Ev[xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()]+0xc):
> undefined reference to `xercesc_2_7::XMLEntityDecl::~XMLEntityDecl()'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
> `xercesc_2_7::XMLRefInfo::~XMLRefInfo()':
> NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_710XMLRefInfoD0Ev[xercesc_2_7::XMLRefInfo::~XMLRefInfo()]+0x35):
> undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
> `xercesc_2_7::XMLAttDefList::~XMLAttDefList()':
> NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713XMLAttDefListD0Ev[xercesc_2_7::XMLAttDefList::~XMLAttDefList()]+0xc):
> undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_710XMLRefInfoE[vtable
> for xercesc_2_7::XMLRefInfo]+0x20): undefined reference to
> `xercesc_2_7::XMLRefInfo::isSerializable() const'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_710XMLRefInfoE[vtable
> for xercesc_2_7::XMLRefInfo]+0x28): undefined reference to
> `xercesc_2_7::XMLRefInfo::serialize(xercesc_2_7::XSerializeEngine&)'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_710XMLRefInfoE[vtable
> for xercesc_2_7::XMLRefInfo]+0x30): undefined reference to
> `xercesc_2_7::XMLRefInfo::getProtoType() const'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713DTDEntityDeclE[vtable
> for xercesc_2_7::DTDEntityDecl]+0x20): undefined reference to
> `xercesc_2_7::DTDEntityDecl::isSerializable() const'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713DTDEntityDeclE[vtable
> for xercesc_2_7::DTDEntityDecl]+0x28): undefined reference to
> `xercesc_2_7::DTDEntityDecl::serialize(xercesc_2_7::XSerializeEngine&)'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713DTDEntityDeclE[vtable
> for xercesc_2_7::DTDEntityDecl]+0x30): undefined reference to
> `xercesc_2_7::DTDEntityDecl::getProtoType() const'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713XMLAttDefListE[vtable
> for xercesc_2_7::XMLAttDefList]+0x20): undefined reference to
> `xercesc_2_7::XMLAttDefList::isSerializable() const'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713XMLAttDefListE[vtable
> for xercesc_2_7::XMLAttDefList]+0x28): undefined reference to
> `xercesc_2_7::XMLAttDefList::serialize(xercesc_2_7::XSerializeEngine&)'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713XMLAttDefListE[vtable
> for xercesc_2_7::XMLAttDefList]+0x30): undefined reference to
> `xercesc_2_7::XMLAttDefList::getProtoType() const'
> CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTIN11xercesc_2_713DTDEntityDeclE[typeinfo
> for xercesc_2_7::DTDEntityDecl]+0x10): undefined reference to
> `typeinfo for xercesc_2_7::XMLEntityDecl'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::SAX2XMLReaderImpl::SAX2XMLReaderImpl(xercesc_2_7::MemoryManager*,
> xercesc_2_7::XMLGrammarPool*)'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLUni::fgXercesValidationErrorAsFatal'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMemory::operator delete(void*,
> xercesc_2_7::MemoryManager*)'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLUni::fgSAX2CoreValidation'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::SAXParseException::SAXParseException(unsigned
> short const*, unsigned short const*, unsigned short const*, long,
> long, xercesc_2_7::MemoryManager*)'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::SAXParseException::getPublicId() const'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::SAXParseException::getSystemId() const'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLUni::fgSAX2CoreNameSpacePrefixes'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLUni::fgXercescDefaultLocale'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLUni::fgXercesSchema'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLUni::fgXercesSchemaFullChecking'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLPlatformUtils::Terminate()'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::SAXParseException::getColumnNumber() const'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::SchemaSymbols::fgURI_XSI'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLUni::fgXercesSchemaExternalSchemaLocation'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLPlatformUtils::fgMemoryManager'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMemory::operator new(unsigned long,
> xercesc_2_7::MemoryManager*)'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLUni::fgSAX2CoreNameSpaces'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLPlatformUtils::Initialize(char const*,
> char const*, xercesc_2_7::PanicHandler*, xercesc_2_7::MemoryManager*,
> bool)'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::SchemaSymbols::fgXSI_TYPE'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::SAXParseException::getLineNumber() const'
> /home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
> reference to `xercesc_2_7::XMLUni::fgXercesSchemaExternalNoNameSpaceSchemaLocation'
> collect2: ld returned 1 exit status
>
> --
> gmwojcik
>
> Registered Linux User #388348
> ----------------------------------------------------------------
>     PER ASPERA AD ASTRA
> ----------------------------------------------------------------
>
> ------------------------------------------------------------------------------
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>
>
>



-- 
gmwojcik

Registered Linux User #388348
----------------------------------------------------------------
     PER ASPERA AD ASTRA
----------------------------------------------------------------

Re: [Pcsim-users] problem with xerces in Ubuntu 8.04

[Natschläger T. <Tho...@sc...>]

Hi!
 
If I remember correctly a college of mine here at SCCG has already encountered the problem. The fix was to change the order of lib's against we link. So we tried to find a proper oder of
 
TARGET_LINK_LIBRARIES( pcsim_test
  pcsim
   ${XERCES_LIBS}
  ${MPI_LIBS}
  ${GSL_LIBS}
  ${CPPUNIT_LIBS} 
  ${BOOST_THREAD} 
  ${BOOST_DATETIME}
  ${STLP_LIBS}
)

If I remember correctly we put ${XERCES_LIBS} more towards the end of that list in
cppunit/CMakeLists.txt
python/CMakeLists.txt
java/CMakeLists.txt

 
I hope this helps. We have to check this more thoroughly.
 
-thomas natschlaeger
 

________________________________

Von: Grzegorz M. Wojcik [mailto:gmw...@gm...]
Gesendet: Mi 12/10/2008 6:19
An: pcs...@li...
Betreff: [Pcsim-users] problem with xerces in Ubuntu 8.04



Hello!

I came across serious problem when trying to compile pcsim on Ubuntu
8.04 Hardy Heron. I receive some errors concerning xerces-c, I suppose
in same the end of my compilation process. They look like:

NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_710XMLRefInfoD0Ev[xercesc_2_7::XMLRefInfo::~XMLRefInfo()]+0x35):
undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'

with very often repeating phrase: undefined reference to `xercesc_2_7

I have libxerces-c v. 2.7.0 located in /usr/lib (I think it is typical
location).

I was trying with no result doing the following things:

1) Telling the linker where libxerces is located.
2) libxerces 2.8
3) libxerces 3.0
4) compiling libxerces of all above versions from te scratch by the
same compiler I compile pcsim

To make matters worse (or better) when I run python setup.py test - a
lot of tests end up with a positive 'OK' message.

Do you have any ideas?

best regards,

Grzegorz

P.S. Here is the whole set of error messages:


[ 63%] Building CXX object
python/CMakeFiles/pypcsim.dir/pypcsim/CuBaSyn_AlphaFunction.pypp.o
[ 63%] Building CXX object
cppunittests/CMakeFiles/pcsim_test.dir/HHNeuronTraubMiles91Test.o
[ 64%] Building CXX object
python/CMakeFiles/pypcsim.dir/pypcsim/SpatialSimObjectPopulation.pypp.o
[ 64%] Building CXX object cppunittests/CMakeFiles/pcsim_test.dir/commonUtils.o
Linking CXX executable ../bin/pcsim_test
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
const&)':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_714DefaultHandler10fatalErrorERKNS_17SAXParseExceptionE[xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
const&)]+0x2b): undefined reference to
`xercesc_2_7::SAXParseException::SAXParseException(xercesc_2_7::SAXParseException
const&)'
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_714DefaultHandler10fatalErrorERKNS_17SAXParseExceptionE[xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
const&)]+0x4b): undefined reference to
`xercesc_2_7::SAXParseException::~SAXParseException()'
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_714DefaultHandler10fatalErrorERKNS_17SAXParseExceptionE[xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
const&)]+0x50): undefined reference to `typeinfo for
xercesc_2_7::SAXParseException'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713DTDEntityDeclD0Ev[xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()]+0xc):
undefined reference to `xercesc_2_7::XMLEntityDecl::~XMLEntityDecl()'
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713DTDEntityDeclD0Ev[xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()]+0x14):
undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713DTDEntityDeclD1Ev[xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()]+0xc):
undefined reference to `xercesc_2_7::XMLEntityDecl::~XMLEntityDecl()'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::XMLRefInfo::~XMLRefInfo()':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_710XMLRefInfoD0Ev[xercesc_2_7::XMLRefInfo::~XMLRefInfo()]+0x35):
undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::XMLAttDefList::~XMLAttDefList()':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713XMLAttDefListD0Ev[xercesc_2_7::XMLAttDefList::~XMLAttDefList()]+0xc):
undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_710XMLRefInfoE[vtable
for xercesc_2_7::XMLRefInfo]+0x20): undefined reference to
`xercesc_2_7::XMLRefInfo::isSerializable() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_710XMLRefInfoE[vtable
for xercesc_2_7::XMLRefInfo]+0x28): undefined reference to
`xercesc_2_7::XMLRefInfo::serialize(xercesc_2_7::XSerializeEngine&)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_710XMLRefInfoE[vtable
for xercesc_2_7::XMLRefInfo]+0x30): undefined reference to
`xercesc_2_7::XMLRefInfo::getProtoType() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713DTDEntityDeclE[vtable
for xercesc_2_7::DTDEntityDecl]+0x20): undefined reference to
`xercesc_2_7::DTDEntityDecl::isSerializable() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713DTDEntityDeclE[vtable
for xercesc_2_7::DTDEntityDecl]+0x28): undefined reference to
`xercesc_2_7::DTDEntityDecl::serialize(xercesc_2_7::XSerializeEngine&)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713DTDEntityDeclE[vtable
for xercesc_2_7::DTDEntityDecl]+0x30): undefined reference to
`xercesc_2_7::DTDEntityDecl::getProtoType() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713XMLAttDefListE[vtable
for xercesc_2_7::XMLAttDefList]+0x20): undefined reference to
`xercesc_2_7::XMLAttDefList::isSerializable() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713XMLAttDefListE[vtable
for xercesc_2_7::XMLAttDefList]+0x28): undefined reference to
`xercesc_2_7::XMLAttDefList::serialize(xercesc_2_7::XSerializeEngine&)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713XMLAttDefListE[vtable
for xercesc_2_7::XMLAttDefList]+0x30): undefined reference to
`xercesc_2_7::XMLAttDefList::getProtoType() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTIN11xercesc_2_713DTDEntityDeclE[typeinfo
for xercesc_2_7::DTDEntityDecl]+0x10): undefined reference to
`typeinfo for xercesc_2_7::XMLEntityDecl'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAX2XMLReaderImpl::SAX2XMLReaderImpl(xercesc_2_7::MemoryManager*,
xercesc_2_7::XMLGrammarPool*)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesValidationErrorAsFatal'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMemory::operator delete(void*,
xercesc_2_7::MemoryManager*)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgSAX2CoreValidation'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::SAXParseException(unsigned
short const*, unsigned short const*, unsigned short const*, long,
long, xercesc_2_7::MemoryManager*)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::getPublicId() const'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::getSystemId() const'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgSAX2CoreNameSpacePrefixes'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercescDefaultLocale'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesSchema'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesSchemaFullChecking'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLPlatformUtils::Terminate()'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::getColumnNumber() const'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SchemaSymbols::fgURI_XSI'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesSchemaExternalSchemaLocation'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLPlatformUtils::fgMemoryManager'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMemory::operator new(unsigned long,
xercesc_2_7::MemoryManager*)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgSAX2CoreNameSpaces'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLPlatformUtils::Initialize(char const*,
char const*, xercesc_2_7::PanicHandler*, xercesc_2_7::MemoryManager*,
bool)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SchemaSymbols::fgXSI_TYPE'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::getLineNumber() const'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesSchemaExternalNoNameSpaceSchemaLocation'
collect2: ld returned 1 exit status

--
gmwojcik

Registered Linux User #388348
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[Pcsim-users] problem with xerces in Ubuntu 8.04

[Grzegorz M. W. <gmw...@gm...>]

Hello!

I came across serious problem when trying to compile pcsim on Ubuntu
8.04 Hardy Heron. I receive some errors concerning xerces-c, I suppose
in same the end of my compilation process. They look like:

NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_710XMLRefInfoD0Ev[xercesc_2_7::XMLRefInfo::~XMLRefInfo()]+0x35):
undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'

with very often repeating phrase: undefined reference to `xercesc_2_7

I have libxerces-c v. 2.7.0 located in /usr/lib (I think it is typical
location).

I was trying with no result doing the following things:

1) Telling the linker where libxerces is located.
2) libxerces 2.8
3) libxerces 3.0
4) compiling libxerces of all above versions from te scratch by the
same compiler I compile pcsim

To make matters worse (or better) when I run python setup.py test - a
lot of tests end up with a positive 'OK' message.

Do you have any ideas?

best regards,

Grzegorz

P.S. Here is the whole set of error messages:


[ 63%] Building CXX object
python/CMakeFiles/pypcsim.dir/pypcsim/CuBaSyn_AlphaFunction.pypp.o
[ 63%] Building CXX object
cppunittests/CMakeFiles/pcsim_test.dir/HHNeuronTraubMiles91Test.o
[ 64%] Building CXX object
python/CMakeFiles/pypcsim.dir/pypcsim/SpatialSimObjectPopulation.pypp.o
[ 64%] Building CXX object cppunittests/CMakeFiles/pcsim_test.dir/commonUtils.o
Linking CXX executable ../bin/pcsim_test
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
const&)':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_714DefaultHandler10fatalErrorERKNS_17SAXParseExceptionE[xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
const&)]+0x2b): undefined reference to
`xercesc_2_7::SAXParseException::SAXParseException(xercesc_2_7::SAXParseException
const&)'
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_714DefaultHandler10fatalErrorERKNS_17SAXParseExceptionE[xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
const&)]+0x4b): undefined reference to
`xercesc_2_7::SAXParseException::~SAXParseException()'
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_714DefaultHandler10fatalErrorERKNS_17SAXParseExceptionE[xercesc_2_7::DefaultHandler::fatalError(xercesc_2_7::SAXParseException
const&)]+0x50): undefined reference to `typeinfo for
xercesc_2_7::SAXParseException'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713DTDEntityDeclD0Ev[xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()]+0xc):
undefined reference to `xercesc_2_7::XMLEntityDecl::~XMLEntityDecl()'
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713DTDEntityDeclD0Ev[xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()]+0x14):
undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713DTDEntityDeclD1Ev[xercesc_2_7::DTDEntityDecl::~DTDEntityDecl()]+0xc):
undefined reference to `xercesc_2_7::XMLEntityDecl::~XMLEntityDecl()'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::XMLRefInfo::~XMLRefInfo()':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_710XMLRefInfoD0Ev[xercesc_2_7::XMLRefInfo::~XMLRefInfo()]+0x35):
undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o: In function
`xercesc_2_7::XMLAttDefList::~XMLAttDefList()':
NeuroMLImporterTest.cpp:(.text._ZN11xercesc_2_713XMLAttDefListD0Ev[xercesc_2_7::XMLAttDefList::~XMLAttDefList()]+0xc):
undefined reference to `xercesc_2_7::XMemory::operator delete(void*)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_710XMLRefInfoE[vtable
for xercesc_2_7::XMLRefInfo]+0x20): undefined reference to
`xercesc_2_7::XMLRefInfo::isSerializable() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_710XMLRefInfoE[vtable
for xercesc_2_7::XMLRefInfo]+0x28): undefined reference to
`xercesc_2_7::XMLRefInfo::serialize(xercesc_2_7::XSerializeEngine&)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_710XMLRefInfoE[vtable
for xercesc_2_7::XMLRefInfo]+0x30): undefined reference to
`xercesc_2_7::XMLRefInfo::getProtoType() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713DTDEntityDeclE[vtable
for xercesc_2_7::DTDEntityDecl]+0x20): undefined reference to
`xercesc_2_7::DTDEntityDecl::isSerializable() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713DTDEntityDeclE[vtable
for xercesc_2_7::DTDEntityDecl]+0x28): undefined reference to
`xercesc_2_7::DTDEntityDecl::serialize(xercesc_2_7::XSerializeEngine&)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713DTDEntityDeclE[vtable
for xercesc_2_7::DTDEntityDecl]+0x30): undefined reference to
`xercesc_2_7::DTDEntityDecl::getProtoType() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713XMLAttDefListE[vtable
for xercesc_2_7::XMLAttDefList]+0x20): undefined reference to
`xercesc_2_7::XMLAttDefList::isSerializable() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713XMLAttDefListE[vtable
for xercesc_2_7::XMLAttDefList]+0x28): undefined reference to
`xercesc_2_7::XMLAttDefList::serialize(xercesc_2_7::XSerializeEngine&)'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTVN11xercesc_2_713XMLAttDefListE[vtable
for xercesc_2_7::XMLAttDefList]+0x30): undefined reference to
`xercesc_2_7::XMLAttDefList::getProtoType() const'
CMakeFiles/pcsim_test.dir/NeuroMLImporterTest.o:(.rodata._ZTIN11xercesc_2_713DTDEntityDeclE[typeinfo
for xercesc_2_7::DTDEntityDecl]+0x10): undefined reference to
`typeinfo for xercesc_2_7::XMLEntityDecl'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAX2XMLReaderImpl::SAX2XMLReaderImpl(xercesc_2_7::MemoryManager*,
xercesc_2_7::XMLGrammarPool*)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesValidationErrorAsFatal'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMemory::operator delete(void*,
xercesc_2_7::MemoryManager*)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgSAX2CoreValidation'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::SAXParseException(unsigned
short const*, unsigned short const*, unsigned short const*, long,
long, xercesc_2_7::MemoryManager*)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::getPublicId() const'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::getSystemId() const'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgSAX2CoreNameSpacePrefixes'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercescDefaultLocale'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesSchema'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesSchemaFullChecking'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLPlatformUtils::Terminate()'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::getColumnNumber() const'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SchemaSymbols::fgURI_XSI'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesSchemaExternalSchemaLocation'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLPlatformUtils::fgMemoryManager'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMemory::operator new(unsigned long,
xercesc_2_7::MemoryManager*)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgSAX2CoreNameSpaces'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLPlatformUtils::Initialize(char const*,
char const*, xercesc_2_7::PanicHandler*, xercesc_2_7::MemoryManager*,
bool)'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SchemaSymbols::fgXSI_TYPE'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::SAXParseException::getLineNumber() const'
/home/gmwojcik/install/pypcsim-0.5.2/_build/lib/libpcsim.so: undefined
reference to `xercesc_2_7::XMLUni::fgXercesSchemaExternalNoNameSpaceSchemaLocation'
collect2: ld returned 1 exit status

-- 
gmwojcik

Registered Linux User #388348
----------------------------------------------------------------
     PER ASPERA AD ASTRA
----------------------------------------------------------------

Re: [Pcsim-users] Problem with spike senders

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

Hi Dejan,

On Fri, 2008-11-14 at 09:09 +0100, Pecevski Dejan wrote:
> Hi Chris,
> 
> No unfortunately there is not any switch for this purpose. One could
> play around with the cmake files to achieve this functionality.
> 
> Another workaround would be to compile a blank  sim object  in the main 
> pcsim
> code, which is derived from SimObject and SingleOutputSpikeSender, (e.g.
> SOSpikeSenderSimObject). Then you can derive in the extension module from
> SOSpikeSenderSimObject class and implement your custom sim object. The
> extension module build should work when you don't use multiple inheritance
> in the extension classes.
> 

Excellent thought there, that workaround is doing the trick.  Many
thanks once again.

Cheers,
Chris.

Re: [Pcsim-users] Problem with spike senders

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

Hi Chris,

Christopher Nolan wrote:
> Hi Dejan,
>
> Thanks for that reply, I'm compiling in the main source tree without a
> problem.  The only issue now is the compilation time; it takes quite
> some time to compile/link every time I make quite minor changes,
> particularly if I turn debug symbols on.
>
> I don't suppose there is a switch in the build scripts to compile static
> versions of the libpcsim.so and pypcsim.so and include these static
> versions in my extension build (then loading up only my extension
> library in python)?
>   
No unfortunately there is not any switch for this purpose. One could
play around with the cmake files to achieve this functionality.

Another workaround would be to compile a blank  sim object  in the main 
pcsim
code, which is derived from SimObject and SingleOutputSpikeSender, (e.g.
SOSpikeSenderSimObject). Then you can derive in the extension module from
SOSpikeSenderSimObject class and implement your custom sim object. The
extension module build should work when you don't use multiple inheritance
in the extension classes.

Cheers,
Dejan

Re: [Pcsim-users] Problem with spike senders

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

Hi Chris,

Christopher Nolan wrote:
> I've taken a bit more of a look at this, and it seems that the problem
> is in attempting to use runtime type information across shared module
> boundaries.  The dynamic_cast works for calls within libpcsim, and also
> works if called within an extension module, but extension classes
> derived from libpcsim classes cannot be correctly examined by the
> libpcsim library. 
I've looked a this, there seems to be a problem with the RTTI across 
separate c++ libraries, but in relation with multiple inheritance 
classes.  SimObjects that are defined in the extension and are derived 
just from one Simobject class defined in libpcsim work fine, like in the 
pcsim extension template example. When the extension SimObjects are 
derived from multiple classes, like in your case (SimObject and 
SingleOutputSpikeSener), or they are derived from another class that is 
defined within the extension module it doesn't seem to work, probably 
because in this case, for reasons not clear to me currently, the 
compiler puts another typeinfo RTTI signature  for the  parent classes 
(SpikeSender) in the extension module, or doesn't handle correctly the 
setup of the virtual tables of the newly defined extension class. I need 
to investigate this a bit further.
>  I've worked around the issue for the moment by
> changing SingleThreadNetwork line 170 from:
>
> SpikeSender *ss = dynamic_cast<SpikeSender*>( src_obj );
>
> to:
>
> SpikeSender *ss =
> static_cast<SpikeSender*>( dynamic_cast<void*>( src_obj ) );
>
> and similarly in the MultiThreadNetwork class.  I'm not particularly
> sure of the rules for pointer casting in class hierarchies, but as far
> as I understand it, the dynamic_cast<void*> may not operate correctly if
> the start of the derived (extension) class is not the same as the start
> of the SimObject* class?
>   
dynamic_cast<void *> here will give the pointer to the top of the class, 
that is the pointer to first class the sim object inherits from (we are 
not using any virtual inheritance), which in case of the TestSpikeSender 
is SimObject. Simply casting it to SpikeSender should not be safe since 
the void * pointer doesn't point to the SpikeSender part of the 
TestSpikeSender object.

I've run a simple example to test this in C++:

--------------
SpikingInputNeuron nrn;
SpikingInputNeuron *nrn_p = &nrn;
SimObject *obj_p = &nrn;
SpikeSender *sndr_p = &nrn;
cerr << "        nrn ptr=" << nrn_p << endl;
cerr << "        obj ptr=" << obj_p << endl;
cerr << " spk sender ptr=" << sndr_p <<  endl;
SpikeSender * dyn_sndr_p = dynamic_cast<SpikeSender *>(obj_p);
SpikeSender * st_sndr_p = static_cast<SpikeSender *>(dynamic_cast<void 
*>(obj_p));
cerr << " dyn sender ptr=" << dyn_sndr_p <<  endl;
cerr << "  st sender ptr=" << st_sndr_p <<  endl;
--------------

and the output was:

---------------------------
               nrn ptr=0x7fff7d125490
                obj ptr=0x7fff7d125490
  spk sender ptr=0x7fff7d125498
  dyn sender ptr=0x7fff7d125498
     st sender ptr=0x7fff7d125490
---------------------------

You can see that the dynamic_cast from SimObject and the static_cast 
from void do not return the same pointer.

The following articles explains further the matter:
http://carcino.gen.nz/tech/cpp/multiple_inheritance_this.php#static_cast_cant_downcast
http://www.phpcompiler.org/articles/virtualinheritance.html

Until we find out an appropriate solution, you could compile your custom 
class together within the main pcsim code.

Cheers,
Dejan

Re: [Pcsim-users] Problem with spike senders

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

I've taken a bit more of a look at this, and it seems that the problem
is in attempting to use runtime type information across shared module
boundaries.  The dynamic_cast works for calls within libpcsim, and also
works if called within an extension module, but extension classes
derived from libpcsim classes cannot be correctly examined by the
libpcsim library.  I've worked around the issue for the moment by
changing SingleThreadNetwork line 170 from:

SpikeSender *ss = dynamic_cast<SpikeSender*>( src_obj );

to:

SpikeSender *ss =
static_cast<SpikeSender*>( dynamic_cast<void*>( src_obj ) );

and similarly in the MultiThreadNetwork class.  I'm not particularly
sure of the rules for pointer casting in class hierarchies, but as far
as I understand it, the dynamic_cast<void*> may not operate correctly if
the start of the derived (extension) class is not the same as the start
of the SimObject* class?

Cheers,
Chris.


On Wed, 2008-10-29 at 13:02 +1000, Christopher Nolan wrote:
> Hi,
> 
> I've tried to create a new spike source in an external module.  When
> trying to connect the output of the new SpikeSender to spiking synapses
> or spike recorders, I get the exception
> 
> <type 'exceptions.RuntimeError'>: PCSIM::ConstructionException in
> function SingleThreadNetwork::addSpikeMessage: Specified simulation
> object ((n=0,e=
> 
> occurring in:
> 
> void SingleThreadNetwork::_addSpikeMessage_(const SimObject::ID &sender,
> const port_t out, const SimObject::ID &receiver, const port_t in_port,
> const Time &delay)
> 
> It appears as though the dynamic_cast on line 170 of
> SingleThreadNetwork.cpp is returning null, however I can achieve a naive
> cast:
> 
> (SpikeSender*) src_obj
> 
> in a debugger and call the appropriate SpikeSender members (so the
> object is the right type).
> 
> I've simplified the class and tested that the problem still occurs; the
> simplified version is attached along with a python script that produces
> the error.  Any thoughts would be most appreciated.
> 
> Cheers,
> Chris.
> 
> 

[Pcsim-users] Problem with spike senders

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

Hi,

I've tried to create a new spike source in an external module.  When
trying to connect the output of the new SpikeSender to spiking synapses
or spike recorders, I get the exception

<type 'exceptions.RuntimeError'>: PCSIM::ConstructionException in
function SingleThreadNetwork::addSpikeMessage: Specified simulation
object ((n=0,e=

occurring in:

void SingleThreadNetwork::_addSpikeMessage_(const SimObject::ID &sender,
const port_t out, const SimObject::ID &receiver, const port_t in_port,
const Time &delay)

It appears as though the dynamic_cast on line 170 of
SingleThreadNetwork.cpp is returning null, however I can achieve a naive
cast:

(SpikeSender*) src_obj

in a debugger and call the appropriate SpikeSender members (so the
object is the right type).

I've simplified the class and tested that the problem still occurs; the
simplified version is attached along with a python script that produces
the error.  Any thoughts would be most appreciated.

Cheers,
Chris.

Re: [Pcsim-users] how to enable DA modulated STDP in simulation?

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

Thank you Dejan,

The example you attached is very helpful.
Thanks again for the quick reply.

Regards,
Robert.

On Mon, Oct 13, 2008 at 10:17 AM, Pecevski Dejan <de...@ig...>wrote:

>  Hi Robert,
>
> Please find attached an example for Dopamine modulated STDP with comments
> explaining the parts of the model.
>
> regards,
> Dejan
>
> Robert Ioiart wrote:
>
> Dear all,
>
> I would like to create a simulation that uses DA modulated STDP but I
> couldn't figure out from the documentation how to enable it. For example how
> can one modulate plasticity by DA release that is proportional to the firing
> rate of a particular neuron.
>
> Does anyone have an example where synapses are subject to DA modulated
> STDP?
>
>
> Thank you in advance.
>
> Regards,
> Robert.
>
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>
>

Re: [Pcsim-users] how to enable DA modulated STDP in simulation?

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

Hi Robert,

Please find attached an example for Dopamine modulated STDP with 
comments explaining the parts of the model.

regards,
Dejan

Robert Ioiart wrote:
> Dear all,
>
> I would like to create a simulation that uses DA modulated STDP but I 
> couldn't figure out from the documentation how to enable it. For 
> example how can one modulate plasticity by DA release that is 
> proportional to the firing rate of a particular neuron.
>
> Does anyone have an example where synapses are subject to DA modulated 
> STDP?
>
>
> Thank you in advance.
>
> Regards,
> Robert.
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ------------------------------------------------------------------------
>
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> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>   

[Pcsim-users] how to enable DA modulated STDP in simulation?

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

Dear all,

I would like to create a simulation that uses DA modulated STDP but I
couldn't figure out from the documentation how to enable it. For example how
can one modulate plasticity by DA release that is proportional to the firing
rate of a particular neuron.

Does anyone have an example where synapses are subject to DA modulated STDP?


Thank you in advance.

Regards,
Robert.

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

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

Hi Dejan,

Many thanks, that's working now (without me removing the constructor
completely).

Cheers,
Chris.