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

Re: [Pcsim-users] How to use pylsm?

[Sam <zg...@gm...>]

Is the email list still active?

On Tue, Mar 17, 2015 at 10:15 PM, Sam <zg...@gm...> wrote:

> I am a newbie, so pardon me for such a basic question.
>
> I would like to use LSM for classification of spatial temporal data. In
> the pylsm folder, there are some .py scripts but no documentation. Could
> someone walk me through how to run a Hello World example, including data
> generation, training and readout? Thanks a lot!
>

[Pcsim-users] How to use pylsm?

[Sam <zg...@gm...>]

I am a newbie, so pardon me for such a basic question.

I would like to use LSM for classification of spatial temporal data. In the
pylsm folder, there are some .py scripts but no documentation. Could
someone walk me through how to run a Hello World example, including data
generation, training and readout? Thanks a lot!

[Pcsim-users] noob advice

[Jason C. <jas...@gm...>]

Hi everyone,

I hope that there are still people subscribed to this list.
I have become fascinated as a neuroscience B.Sc and masters candidate in
comp sci with the liquid state machine.
I have been reading about it for some time now, and have looked through the
example on http://www.lsm.tugraz.at/pcsim/examples/index.html

What I'm trying to do is to transform some data from an EEG Headset into
something that the PCSIM framework will accept.
Here is a teeny,tiny sample of the data I have :
4375    4190    4399    4658    4080    4256    4194    4138    4582
4281    4311    4424    4260    4219    1658    1662
4368    4181    4391    4650    4072    4254    4191    4135    4572
4272    4304    4421    4263    4218    1657    1662
4365    4173    4389    4643    4067    4253    4192    4135    4564
4264    4292    4414    4243    4213    1657    1661
That is three lines of the 16 channels I have data for, each line a time
point.
Can I take this data an input it into an analogInputNeuron directly?
or
Do I have to create a program to transform it into spike times for a
spikingInputNeuron?

Any help would be greatly appreciated, Thanks


Jason Cummer

204a61736f6e2043756d6d657220

Re: [Pcsim-users] install pcsim

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

Hi Robert,

In the file /pcsim/HowTos/HowTo-Install-PCSIM-Dependencies-Linux.txt
you can find also the versions of all packages that we use to install pcsim.
When it says >= 1.34.1 this means that you should use version 1.34.1.
In some of the packages the version is contained in the name of the 
.tar.gz file
that we used in the step by step command instructions to compile and 
install the package.

On our system the g++ version is 4.1.2.

Best,
Dejan

On 11/04/2012 08:52, Robert H. Fujii wrote:
> Hello Dr. Pecevski,
> Thank you for your reply. Could you let me know
> the exact versions of all "known to work" dependent software ?
> If necessary, please also include information about the g++ version and the
> version of any other software that is not included in your "HCWTO: Installation
> of software packages needed to build PCSIM under LINUX".
>
> I will install all the dependencies again.
>
> Regards,
> Robert
>


-- 
_______________________________________________
Dejan Pecevski, Ph.D.
Institute for Theoretical Computer Science
Graz University of Technology
Inffeldgasse 16b, A-8010 Graz, Austria
Tel. +43 316 873 5849

Re: [Pcsim-users] install pcsim

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

Hi Robert,

You are using probably using a newer version of the g++ compiler, 
therefore some errors occur.

You should be able to fix the errors within the CircularQueue.h file by 
adding the following header at the beginning of the file, after #include 
<iostream>:

#include <cstring>


The reason for the errors occuring in the ThreadPool.cpp seem to be that 
you are using a different version of the boost library (probably the 
already installed linux package).
You should follow the build instructions in the how-to directory, and 
install the correct versions of all libraries specified there.
Otherwise PCSIM is not guaranteed to work.

Best,
Dejan


On 06/04/2012 15:16, robert fujii wrote:
> Dear Dr. Pecevski,
> Thank you for your assistance.  The ElementTree problem is fixed but now
> I am running into some other ones related to pcsim/simutils.
> Sorry to say I am a bit in the dark at the moment.
> Best regards,
> Robert
>
>
>
> -- Generating done
> -- Build files have been written to: /usr/local/pypcsim-0.5.0/_build
> >>>> cd /usr/local/pypcsim-0.5.0/_build
> >>>> /usr/bin/make -j 2 install
> [  1%] Built target generate_python_wrapper_code
> Scanning dependencies of target pcsim
> [  1%] [  2%] Building CXX object 
> pcsim/CMakeFiles/pcsim.dir/simutils/ThreadPool.o
> Building CXX object pcsim/CMakeFiles/pcsim.dir/simutils/CircularQueue.o
> In file included from 
> /usr/local/pypcsim-0.5.0/pcsim/simutils/CircularQueue.cpp:1:
> /usr/local/pypcsim-0.5.0/pcsim/simutils/CircularQueue.h: In member 
> function ‘void CircularQueue<T>::putArray(double*, int)’:
> /usr/local/pypcsim-0.5.0/pcsim/simutils/CircularQueue.h:114: error: 
> there are no arguments to ‘memcpy’ that depend on a template 
> parameter, so a declaration of ‘memcpy’ must be available
> /usr/local/pypcsim-0.5.0/pcsim/simutils/CircularQueue.h:114: note: (if 
> you use ‘-fpermissive’, G++ will accept your code, but allowing the 
> use of an undeclared name is deprecated)
> /usr/local/pypcsim-0.5.0/pcsim/simutils/CircularQueue.h:115: error: 
> there are no arguments to ‘memcpy’ that depend on a template 
> parameter, so a declaration of ‘memcpy’ must be available
> /usr/local/pypcsim-0.5.0/pcsim/simutils/CircularQueue.h:118: error: 
> there are no arguments to ‘memcpy’ that depend on a template 
> parameter, so a declaration of ‘memcpy’ must be available
> make[2]: *** [pcsim/CMakeFiles/pcsim.dir/simutils/CircularQueue.o] Error 1
> make[2]: *** Waiting for unfinished jobs....
> /usr/local/pypcsim-0.5.0/pcsim/simutils/ThreadPool.cpp:52: error: 
> expected constructor, destructor, or type conversion before ‘<’ token
> /usr/local/pypcsim-0.5.0/pcsim/simutils/ThreadPool.cpp: In constructor 
> ‘ThreadPool::ThreadPool(int)’:
> /usr/local/pypcsim-0.5.0/pcsim/simutils/ThreadPool.cpp:70: error: 
> ‘function0’ is not a member of ‘boost’
> /usr/local/pypcsim-0.5.0/pcsim/simutils/ThreadPool.cpp:70: error: 
> expected primary-expression before ‘void’
> /usr/local/pypcsim-0.5.0/pcsim/simutils/ThreadPool.cpp:70: error: 
> expected ‘;’ before ‘void’
> /usr/local/pypcsim-0.5.0/pcsim/simutils/ThreadPool.cpp:71: error: ‘f’ 
> was not declared in this scope
> make[2]: *** [pcsim/CMakeFiles/pcsim.dir/simutils/ThreadPool.o] Error 1
> make[1]: *** [pcsim/CMakeFiles/pcsim.dir/all] Error 2
> make: *** [all] Error 2
> BUILD PROCESS FAILED. ERROR = 512
> Command: /usr/bin/make -j 2 install
>
>


-- 
_______________________________________________
Dejan Pecevski, Ph.D.
Institute for Theoretical Computer Science
Graz University of Technology
Inffeldgasse 16b, A-8010 Graz, Austria
Tel. +43 316 873 5849

Re: [Pcsim-users] install pcsim

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

Hi Robert,

It looks like you do not have installed  the python package ElementTree.

You can find it here:
http://effbot.org/zone/element-index.htm

or maybe there is a linux package for that.

regards,
Dejan

On 04/06/2012 11:25 AM, robert fujii wrote:
> Dear Dr. Pecevski - It looks like I was able to correct the mpich2 
> problem;
> what I did is to complie the mpich2 source code (mpich2-1.4.1p1) 
> myself instead of
> using  "apt-get install mpich2".
> The installation of pcsim seems to be almost complete; however error 
> messages
> have appeared and I don't know how to resolve them. Thank you for your 
> time and patience.
>
> Best regards,
> Robert
>
>
> Running CMake to regenerate build system...
>    Build type   = Release
>    Platform     = linux-i686
>    Make tool    = /usr/bin/make
>    Make command = /usr/bin/make -i
>    Python executable : /usr/bin/python version 2.6
>    Python libraries : /usr/lib/python2.6/config
>    Python includes : /usr/include/python2.6
>    Doxygen executable : /usr/local/bin/doxygen
>    GCCXML executable : /usr/local/bin/gccxml
>    Boost C++ library boost_python : /usr/lib/libboost_python.so
>    Boost C++ library boost_thread : /usr/lib/libboost_thread-mt.so
>    Boost C++ library boost_date_time : /usr/lib/libboost_date_time-mt.so
>    Boost C++ libraries : /usr/lib
>    Boost C++ include path : /usr/include
>    MPICH2 library: /usr/lib/libmpich.so
>    MPICH2 include path : /usr/local/mpich2-1.4.1p1/src/include
>    GNU Scientific library : /usr/local/lib/libgsl.so
>    CppUnit : /usr/local/lib/libcppunit.so
> -- Configuring done
> CMake Warning (dev) at cppunittests/CMakeLists.txt:8 (ADD_EXECUTABLE):
>   Policy CMP0003 should be set before this line.  Add code such as
>
>     if(COMMAND cmake_policy)
>       cmake_policy(SET CMP0003 NEW)
>     endif(COMMAND cmake_policy)
>
>   as early as possible but after the most recent call to
>   cmake_minimum_required or cmake_policy(VERSION).  This warning appears
>   because target "pcsim_test" links to some libraries for which the linker
>   must search:
>
>     mpich, mpichcxx, gsl, gslcblas, cppunit, dl
>
>   and other libraries with known full path:
>
>     /usr/local/pypcsim-0.5.0/_build/lib/libpcsim.so
>
>   CMake is adding directories in the second list to the linker search 
> path in
>   case they are needed to find libraries from the first list (for 
> backwards
>   compatibility with CMake 2.4).  Set policy CMP0003 to OLD or NEW to 
> enable
>   or disable this behavior explicitly.  Run "cmake --help-policy 
> CMP0003" for
>   more information.
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> -- Generating done
> -- Build files have been written to: /usr/local/pypcsim-0.5.0/_build
> >>>> cd /usr/local/pypcsim-0.5.0/_build
> >>>> /usr/bin/make -j 2 install
> [  1%] Built target generate_python_wrapper_code
> [  1%] Generating ../../pcsim/RegisterSimObjects.cpp, 
> ../../pcsim/register_fields_includes.h, 
> ../../pcsim/register_fields_calls.h, 
> ../../pcsim/register.indicator.cpp, 
> ../../pcsim/pcsimSimObjectRegistrator.h
> Traceback (most recent call last):
>   File 
> "/usr/local/pypcsim-0.5.0/scripts/generate_simobject_registry_code.py", line 
> 3, in <module>
>     from elementtree import ElementTree
> ImportError: No module named elementtree
> make[2]: *** [../pcsim/RegisterSimObjects.cpp] Error 1
> make[1]: *** [pcsim/CMakeFiles/pcsim.dir/all] Error 2
> make: *** [all] Error 2
> BUILD PROCESS FAILED. ERROR = 512
> Command: /usr/bin/make -j 2 install
>
>


-- 
_______________________________________________
Dejan Pecevski, PhD
Institute for Theoretical Computer Science
Graz University of Technology
Inffeldgasse 16b, A-8010 Graz, Austria
Tel. +43 316 873 5849

Re: [Pcsim-users] install pcsim

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

On 4/5/2012 9:28 AM, Dejan Pecevski wrote:
> Hi Robert,
>
> Instead of executing:
>
> python setup.py install
>
> try to execute:
>
> python build.py -j 2 install
>
> Regards,
> Dejan
>
> On 4/5/2012 2:42 AM, robert fujii wrote:
>> Hello - I have  first successfully (I believe) installed all the 
>> necessary
>> dependencies for PCSIM. Then I tried to install PCSIM but I got the 
>> following
>> messages.  Please let me know what is causing the problem(s).
>> I am using Ubuntu 10.04.
>>
>> Thank you.
>> Robert
>>
>>
>> root@ubuntu:/usr/local/pypcsim-0.5.0# python setup.py install
>> running install
>> Traceback (most recent call last):
>>   File "setup.py", line 425, in <module>
>>     libraries     = [ 'pcsim' ] )
>>   File "/usr/lib/python2.6/distutils/core.py", line 152, in setup
>>     dist.run_commands()
>>   File "/usr/lib/python2.6/distutils/dist.py", line 975, in run_commands
>>     self.run_command(cmd)
>>   File "/usr/lib/python2.6/distutils/dist.py", line 994, in run_command
>>     cmd_obj.ensure_finalized()
>>   File "/usr/lib/python2.6/distutils/cmd.py", line 117, in 
>> ensure_finalized
>>     self.finalize_options()
>>   File "setup.py", line 215, in finalize_options
>>     _install.finalize_options(self)
>>   File "/usr/lib/python2.6/distutils/command/install.py", line 301, 
>> in finalize_options
>>     if self.user and (self.prefix or self.exec_prefix or self.home or
>>   File "/usr/lib/python2.6/distutils/cmd.py", line 112, in __getattr__
>>     raise AttributeError, attr
>> AttributeError: user
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Better than sec? Nothing is better than sec when it comes to
>> monitoring Big Data applications. Try Boundary one-second
>> resolution app monitoring today. Free.
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>>
>>
>> _______________________________________________
>> Pcsim-users mailing list
>> Pcs...@li...
>> https://lists.sourceforge.net/lists/listinfo/pcsim-users
>
>
> -- 
> _______________________________________________
> Dejan Pecevski, Ph.D.
> Institute for Theoretical Computer Science
> Graz University of Technology
> Inffeldgasse 16b, A-8010 Graz, Austria
> Tel. +43 316 873 5849


-- 
_______________________________________________
Dejan Pecevski, Ph.D.
Institute for Theoretical Computer Science
Graz University of Technology
Inffeldgasse 16b, A-8010 Graz, Austria
Tel. +43 316 873 5849

[Pcsim-users] install pcsim

[robert f. <fu...@u-...>]

Hello - I have  first successfully (I believe) installed all the necessary
dependencies for PCSIM. Then I tried to install PCSIM but I got the
following
messages.  Please let me know what is causing the problem(s).
I am using Ubuntu 10.04.

Thank you.
Robert


root@ubuntu:/usr/local/pypcsim-0.5.0# python setup.py install
running install
Traceback (most recent call last):
  File "setup.py", line 425, in <module>
    libraries     = [ 'pcsim' ] )
  File "/usr/lib/python2.6/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/usr/lib/python2.6/distutils/dist.py", line 975, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python2.6/distutils/dist.py", line 994, in run_command
    cmd_obj.ensure_finalized()
  File "/usr/lib/python2.6/distutils/cmd.py", line 117, in ensure_finalized
    self.finalize_options()
  File "setup.py", line 215, in finalize_options
    _install.finalize_options(self)
  File "/usr/lib/python2.6/distutils/command/install.py", line 301, in
finalize_options
    if self.user and (self.prefix or self.exec_prefix or self.home or
  File "/usr/lib/python2.6/distutils/cmd.py", line 112, in __getattr__
    raise AttributeError, attr
AttributeError: user

[Pcsim-users] knoppixpcsim

[Robert H. F. <fu...@u-...>]

Hello - I have downloaded the knoppixpcsim iso
image and burned it onto a DVD.  I am unable to boot
from the DVD; is there something I have overlooked ?

Thank you.
R. Fujii

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

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

Hi Zhicheng,

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

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

Best,
Dejan



On 11/26/2011 06:16 AM, zhicheng Hou wrote:
> Hi Dejan,
> Thanks for your reply. I followed your advice and there are still some
> errors. When i run  ---$ sudo python build.py -j 2 wipe, it seems ok.
> however when i run  ---sudo python build.py -j 2 install, errors occur
> again:
> the bash said:
>
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D CMAKE_INSTALL_PREFIX:PATH=/home/hou/pcsim/pcsim-0.5.4 -D PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D EXTRA_INSTALL:STRING=NO /home/hou/pcsim/pcsim-0.5.4
> -- The C compiler identification is GNU
> -- The CXX compiler identification is GNU
> -- Check for working C compiler: /usr/bin/gcc
> -- Check for working C compiler: /usr/bin/gcc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
>     Build type   = Release
>     Platform     = linux-i686
>     Make tool    = /usr/bin/make
>     Make command = /usr/bin/make -i
> -- Looking for python executable ...
> -- Found PythonInterp: /usr/bin/python
>     Python executable : /usr/bin/python version 2.6
> -- Looking for python libraries ...
>     Python libraries : /usr/lib/python2.6/config
>     Python includes : /usr/include/python2.6
> -- Looking for doxygen executable ...
>     Doxygen executable : /usr/bin/doxygen
> -- Looking for GCCXML executable ...
>     GCCXML executable : /usr/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc-mt
> BOOST_LIB_SUFFIX_2 IS gcc41-mt
> -- Looking for Boost C++ libraries ... - toolset    = gcc
> -- Looking for Boost C++ libraries ... - lib suffixes = gcc-mt gcc41-mt
>     Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc41-mt.so
>     Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc41-mt.so
>     Boost C++ library boost_date_time :
> /usr/local/lib/libboost_date_time-gcc41-mt.so
>     Boost C++ libraries : /usr/local/lib
>     Boost C++ include path : /usr/local/include/boost-1_34_1
> -- Looking for MPICH2 ...
>     MPICH2 library: /usr/local/lib/libmpich.so
>     MPICH2 include path : /usr/local/include
> -- Looking for GNU Scientific library ...
>     GNU Scientific library : /usr/local/lib/libgsl.so
> -- Looking for Xerces-C library ...
>     Xerces library : /usr/lib/libxerces-c.so
> -- Looking for CppUnit ...
>     CppUnit : /usr/local/lib/libcppunit.so
>     JNI headers : /usr/lib/jvm/java-6-openjdk/include
> -- Checking to see if CXX compiler accepts flag -pthread
> -- Checking to see if CXX compiler accepts flag -pthread - yes
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> /usr/bin/make -j 2 rebuild_cache
> Running CMake to regenerate build system...
>     Build type   = Release
>     Platform     = linux-i686
>     Make tool    = /usr/bin/make
>     Make command = /usr/bin/make -i
>     Python executable : /usr/bin/python version 2.6
>     Python libraries : /usr/lib/python2.6/config
>     Python includes : /usr/include/python2.6
>     Doxygen executable : /usr/bin/doxygen
>     GCCXML executable : /usr/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc-mt
> BOOST_LIB_SUFFIX_2 IS gcc41-mt
>     Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc41-mt.so
>     Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc41-mt.so
>     Boost C++ library boost_date_time :
> /usr/local/lib/libboost_date_time-gcc41-mt.so
>     Boost C++ libraries : /usr/local/lib
>     Boost C++ include path : /usr/local/include/boost-1_34_1
>     MPICH2 library: /usr/local/lib/libmpich.so
>     MPICH2 include path : /usr/local/include
>     GNU Scientific library : /usr/local/lib/libgsl.so
>     Xerces library : /usr/lib/libxerces-c.so
>     CppUnit : /usr/local/lib/libcppunit.so
>     JNI headers : /usr/lib/jvm/java-6-openjdk/include
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
> *******************************************
> *  GENERATING PY++ WRAPPER CPP FILES      *
> *******************************************
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> /usr/bin/make -j 2 generate_code
> [100%] Generating ../../python/pypcsim.h
> [100%] Generating ../../python/pypcsim/pypcsim.indicator.cpp
> /usr/local/lib/python2.6/dist-packages/pygccxml/parser/declarations_cache.py:8:
> DeprecationWarning: the md5 module is deprecated; use hashlib instead
>    import md5
>
> INFO Parsing source file "pypcsim.h" ...
>
> INFO gccxml cmd: /usr/bin/gccxml  --gccxml-cxxflags -pthread
> -fpermissive   -I"." -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simutils"
> -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simcore"
> -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/construction"
> -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml"
> -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simobjects"
> -I"/home/hou/pcsim/pcsim-0.5.4/libxsd"
> -I"/usr/local/include/boost-1_34_1"  -D"MPICH_IGNORE_CXX_SEEK"
> -D"BOOST_HAS_THREADS" -D"BOOST_PYTHON_MAX_ARITY=30"  "pypcsim.h"
> -fxml="/tmp/tmpapqeKv.xml"
> /usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py:152:
> DeprecationWarning: os.popen4 is deprecated.  Use the subprocess
> module.
>    input_, output = os.popen4( command_line )
> Traceback (most recent call last):
>    File "/home/hou/pcsim/pcsim-0.5.4/scripts/generate_boost_python_wrapper_code.py",
> line 143, in<module>
>      encoding = 'utf-8'
>    File "/usr/local/lib/python2.6/dist-packages/pyplusplus/module_builder/builder.py",
> line 90, in __init__
>      , indexing_suite_version)
>    File "/usr/local/lib/python2.6/dist-packages/pyplusplus/module_builder/builder.py",
> line 144, in __parse_declarations
>      decls = reader.read_files( files, compilation_mode )
>    File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/project_reader.py",
> line 225, in read_files
>      return self.__parse_file_by_file(files)
>    File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/project_reader.py",
> line 250, in __parse_file_by_file
>      decls = reader.read_file( header )
>    File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py",
> line 198, in read_file
>      return self.read_gccxml_file( source_file )
>    File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py",
> line 225, in read_gccxml_file
>      raise error
> pygccxml.parser.source_reader.gccxml_runtime_error_t: Error occured
> while running GCC-XML: In file included from
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/parser/xerces/elements.txx:16,
>                   from
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/parser/xerces/elements.hxx:449,
>                   from
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/skeleton/NeuroML_Level3_v1.7.1-pskel.hpp:76,
>                   from
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:11,
>                   from
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:7,
>                   from pypcsim.h:148:
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:
> In member function 'virtual xercesc_3_1::BinInputStream*
> xsd::cxx::xml::sax::std_input_source::makeStream() const':
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:156:
> error: cannot allocate an object of abstract type
> 'xsd::cxx::xml::sax::std_input_stream'
> /home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:25:
> note:   because the following virtual functions are pure within
> 'xsd::cxx::xml::sax::std_input_stream':
> /usr/local/include/xercesc/util/BinInputStream.hpp:67: note: 	virtual
> const XMLCh* xercesc_3_1::BinInputStream::getContentType() const
>
> make[3]: *** [../python/pypcsim/pypcsim.indicator.cpp] Error 1
> make[2]: *** [python/CMakeFiles/generate_python_wrapper_code.dir/all] Error 2
> make[1]: *** [CMakeFiles/generate_code.dir/rule] Error 2
> make: *** [generate_code] Error 2
> BUILD PROCESS FAILED. ERROR = 512
> Command: /usr/bin/make -j 2 generate_code
>
>
> Best Regards
> Hou Zhicheng
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users


-- 
_______________________________________________
Dejan Pecevski, PhD
Institute for Theoretical Computer Science
Graz University of Technology
Inffeldgasse 16b, A-8010 Graz, Austria
Tel. +43 316 873 5849

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

[zhicheng H. <zhi...@gm...>]

Hi Dejan,
Thanks for your reply. I followed your advice and there are still some
errors. When i run  ---$ sudo python build.py -j 2 wipe, it seems ok.
however when i run  ---sudo python build.py -j 2 install, errors occur
again:
the bash said:

>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D CMAKE_INSTALL_PREFIX:PATH=/home/hou/pcsim/pcsim-0.5.4 -D PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D EXTRA_INSTALL:STRING=NO /home/hou/pcsim/pcsim-0.5.4
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
-- Looking for python executable ...
-- Found PythonInterp: /usr/bin/python
   Python executable : /usr/bin/python version 2.6
-- Looking for python libraries ...
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
-- Looking for doxygen executable ...
   Doxygen executable : /usr/bin/doxygen
-- Looking for GCCXML executable ...
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
-- Looking for Boost C++ libraries ... - toolset    = gcc
-- Looking for Boost C++ libraries ... - lib suffixes = gcc-mt gcc41-mt
   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc41-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc41-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc41-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
-- Looking for MPICH2 ...
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
-- Looking for GNU Scientific library ...
   GNU Scientific library : /usr/local/lib/libgsl.so
-- Looking for Xerces-C library ...
   Xerces library : /usr/lib/libxerces-c.so
-- Looking for CppUnit ...
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Checking to see if CXX compiler accepts flag -pthread
-- Checking to see if CXX compiler accepts flag -pthread - yes
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 rebuild_cache
Running CMake to regenerate build system...
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.6
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc41-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc41-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc41-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
   GNU Scientific library : /usr/local/lib/libgsl.so
   Xerces library : /usr/lib/libxerces-c.so
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
*******************************************
*  GENERATING PY++ WRAPPER CPP FILES      *
*******************************************
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 generate_code
[100%] Generating ../../python/pypcsim.h
[100%] Generating ../../python/pypcsim/pypcsim.indicator.cpp
/usr/local/lib/python2.6/dist-packages/pygccxml/parser/declarations_cache.py:8:
DeprecationWarning: the md5 module is deprecated; use hashlib instead
  import md5

INFO Parsing source file "pypcsim.h" ...

INFO gccxml cmd: /usr/bin/gccxml  --gccxml-cxxflags -pthread
-fpermissive   -I"." -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simutils"
-I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simcore"
-I"/home/hou/pcsim/pcsim-0.5.4/pcsim/construction"
-I"/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml"
-I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simobjects"
-I"/home/hou/pcsim/pcsim-0.5.4/libxsd"
-I"/usr/local/include/boost-1_34_1"  -D"MPICH_IGNORE_CXX_SEEK"
-D"BOOST_HAS_THREADS" -D"BOOST_PYTHON_MAX_ARITY=30"  "pypcsim.h"
-fxml="/tmp/tmpapqeKv.xml"
/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py:152:
DeprecationWarning: os.popen4 is deprecated.  Use the subprocess
module.
  input_, output = os.popen4( command_line )
Traceback (most recent call last):
  File "/home/hou/pcsim/pcsim-0.5.4/scripts/generate_boost_python_wrapper_code.py",
line 143, in <module>
    encoding = 'utf-8'
  File "/usr/local/lib/python2.6/dist-packages/pyplusplus/module_builder/builder.py",
line 90, in __init__
    , indexing_suite_version)
  File "/usr/local/lib/python2.6/dist-packages/pyplusplus/module_builder/builder.py",
line 144, in __parse_declarations
    decls = reader.read_files( files, compilation_mode )
  File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/project_reader.py",
line 225, in read_files
    return self.__parse_file_by_file(files)
  File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/project_reader.py",
line 250, in __parse_file_by_file
    decls = reader.read_file( header )
  File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py",
line 198, in read_file
    return self.read_gccxml_file( source_file )
  File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py",
line 225, in read_gccxml_file
    raise error
pygccxml.parser.source_reader.gccxml_runtime_error_t: Error occured
while running GCC-XML: In file included from
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/parser/xerces/elements.txx:16,
                 from
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/parser/xerces/elements.hxx:449,
                 from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/skeleton/NeuroML_Level3_v1.7.1-pskel.hpp:76,
                 from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:11,
                 from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:7,
                 from pypcsim.h:148:
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:
In member function 'virtual xercesc_3_1::BinInputStream*
xsd::cxx::xml::sax::std_input_source::makeStream() const':
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:156:
error: cannot allocate an object of abstract type
'xsd::cxx::xml::sax::std_input_stream'
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:25:
note:   because the following virtual functions are pure within
'xsd::cxx::xml::sax::std_input_stream':
/usr/local/include/xercesc/util/BinInputStream.hpp:67: note: 	virtual
const XMLCh* xercesc_3_1::BinInputStream::getContentType() const

make[3]: *** [../python/pypcsim/pypcsim.indicator.cpp] Error 1
make[2]: *** [python/CMakeFiles/generate_python_wrapper_code.dir/all] Error 2
make[1]: *** [CMakeFiles/generate_code.dir/rule] Error 2
make: *** [generate_code] Error 2
BUILD PROCESS FAILED. ERROR = 512
Command: /usr/bin/make -j 2 generate_code


Best Regards
Hou Zhicheng

Re: [Pcsim-users] problems of installing PCSim

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

Hi Zhicheng ,

Always before trying a new build, try first to clean all your previous 
compiled and generated files,
and compile from a clean environment. The following command does that:

python build.py -j 2 wipe

In order to avoid compiling the neuroml functionality, you can try the 
following:

1. In the file ${PCSIM_HOME}/pcsim/CMakeLists.txt
     on the line 271 there should be the following statement:
-------------------------------------------------------
SET( PCSIM_SOURCES ${SIMUTILS_SOURCES}
             ${SIMCORE_SOURCES}
             ${CONSTRUCTION_SOURCES}
             ${NEUROML_SOURCES}
             ${SIMOBJECT_SOURCES}
             ${SIM_OBJ_REG_CPP}
             CACHE INTERNAL "Sources for core pcsim library" )
-------------------------------------------------------

    Remove the '${NEUROML_SOURCES}' text from this statement (which is 
on the fourth line).

2. In the file ${PCSIM_HOME}/python/pcsim_module_builder.py
     on line 35 there should be a long statement of the form:
-------------------------------
     simcore_classes = [ 'SimEngine',
                                          'SimParameter',
                                           ...
                                           ...
                                          
'ConnObjectValueGeneratorSpecialization<AugmentedSpatialPopulation, 
AugmentedSpatialPopulation>',
                                          'NeuroMLImporter',
                                          'PCSIMParserEnvironment',
                                          ...
                                          ...
                                          ]
-------------------------------

Remove in this python list the 'NeuroMLImporter' element, i.e. the part:
-----------------------------------
                                          
'ConnObjectValueGeneratorSpecialization<AugmentedSpatialPopulation, 
AugmentedSpatialPopulation>',
                                          'NeuroMLImporter',
                                          'PCSIMParserEnvironment',
------------------------------------
should be
------------------------------------
                                       
'ConnObjectValueGeneratorSpecialization<AugmentedSpatialPopulation, 
AugmentedSpatialPopulation>',
                                       'PCSIMParserEnvironment',
------------------------------------

This should enable compiling PCSIM without NeuroML. Hope this solves 
your problem.

Best regards,
Dejan

On 11/21/2011 10:26 AM, 厚之成 wrote:
> Hi!
>
> Thanks for your reply, i followed your advice but there are still
> errors. The bash said:
>
>
> hou@hou-pc:~/pcsim/pcsim-0.5.4$ sudo python build.py -j 2 install
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D CMAKE_INSTALL_PREFIX:PATH=/home/hou/pcsim/pcsim-0.5.4 -D PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D EXTRA_INSTALL:STRING=NO /home/hou/pcsim/pcsim-0.5.4
>     Build type   = Release
>     Platform     = linux-i686
>     Make tool    = /usr/bin/make
>     Make command = /usr/bin/make -i
>     Python executable : /usr/bin/python version 2.6
>     Python libraries : /usr/lib/python2.6/config
>     Python includes : /usr/include/python2.6
>     Doxygen executable : /usr/bin/doxygen
>     GCCXML executable : /usr/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc-mt
> BOOST_LIB_SUFFIX_2 IS gcc41-mt
>     Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc34-mt.so
>     Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so
>     Boost C++ library boost_date_time :
> /usr/local/lib/libboost_date_time-gcc34-mt.so
>     Boost C++ libraries : /usr/local/lib
>     Boost C++ include path : /usr/local/include/boost-1_34_1
>     MPICH2 library: /usr/local/lib/libmpich.so
>     MPICH2 include path : /usr/local/include
>     GNU Scientific library : /usr/local/lib/libgsl.so
>     Xerces library : /usr/local/lib/libxerces-c.so
>     CppUnit : /usr/local/lib/libcppunit.so
>     JNI headers : /usr/lib/jvm/java-6-openjdk/include
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> /usr/bin/make -j 2 rebuild_cache
> Running CMake to regenerate build system...
>     Build type   = Release
>     Platform     = linux-i686
>     Make tool    = /usr/bin/make
>     Make command = /usr/bin/make -i
>     Python executable : /usr/bin/python version 2.6
>     Python libraries : /usr/lib/python2.6/config
>     Python includes : /usr/include/python2.6
>     Doxygen executable : /usr/bin/doxygen
>     GCCXML executable : /usr/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc-mt
> BOOST_LIB_SUFFIX_2 IS gcc41-mt
>     Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc34-mt.so
>     Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so
>     Boost C++ library boost_date_time :
> /usr/local/lib/libboost_date_time-gcc34-mt.so
>     Boost C++ libraries : /usr/local/lib
>     Boost C++ include path : /usr/local/include/boost-1_34_1
>     MPICH2 library: /usr/local/lib/libmpich.so
>     MPICH2 include path : /usr/local/include
>     GNU Scientific library : /usr/local/lib/libgsl.so
>     Xerces library : /usr/local/lib/libxerces-c.so
>     CppUnit : /usr/local/lib/libcppunit.so
>     JNI headers : /usr/lib/jvm/java-6-openjdk/include
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
> *******************************************
> *  GENERATING PY++ WRAPPER CPP FILES      *
> *******************************************
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> /usr/bin/make -j 2 generate_code
> Built target generate_python_wrapper_code
> Built target generate_code
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> /usr/bin/make -j 2 rebuild_cache
> Running CMake to regenerate build system...
>     Build type   = Release
>     Platform     = linux-i686
>     Make tool    = /usr/bin/make
>     Make command = /usr/bin/make -i
>     Python executable : /usr/bin/python version 2.6
>     Python libraries : /usr/lib/python2.6/config
>     Python includes : /usr/include/python2.6
>     Doxygen executable : /usr/bin/doxygen
>     GCCXML executable : /usr/bin/gccxml
> BOOST_LIB_SUFFIX IS gcc-mt
> BOOST_LIB_SUFFIX_2 IS gcc41-mt
>     Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc34-mt.so
>     Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so
>     Boost C++ library boost_date_time :
> /usr/local/lib/libboost_date_time-gcc34-mt.so
>     Boost C++ libraries : /usr/local/lib
>     Boost C++ include path : /usr/local/include/boost-1_34_1
>     MPICH2 library: /usr/local/lib/libmpich.so
>     MPICH2 include path : /usr/local/include
>     GNU Scientific library : /usr/local/lib/libgsl.so
>     Xerces library : /usr/local/lib/libxerces-c.so
>     CppUnit : /usr/local/lib/libcppunit.so
>     JNI headers : /usr/lib/jvm/java-6-openjdk/include
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>>> /usr/bin/make -j 2 install
> [  0%] Built target generate_python_wrapper_code
> [  0%] Building CXX object pcsim/CMakeFiles/pcsim.dir/neuroml/NeuroMLImporter.o
> [  0%] Building CXX object
> pcsim/CMakeFiles/pcsim.dir/neuroml/parser/cxxproxy/morphml/CxxProxyCell.o
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:1:50:
> error: parser/cxxproxy/morphml/CxxProxyCell.h: No such file or
> directory
> In file included from
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:7,
>                   from
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:1:
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:11:59:
> error: parser/skeleton/NeuroML_Level3_v1.7.1-pskel.hpp: No such file
> or directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:13:60:
> error: parser/implementation/NetworkML_v1.7.1-pimpl.hpp: No such file
> or directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:15:58:
> error: parser/implementation/MorphML_v1.7.1-pimpl.hpp: No such file or
> directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:17:61:
> error: parser/implementation/Biophysics_v1.7.1-pimpl.hpp: No such file
> or directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:19:60:
> error: parser/implementation/ChannelML_v1.7.1-pimpl.hpp: No such file
> or directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:21:59:
> error: parser/implementation/Metadata_v1.7.1-pimpl.hpp: No such file
> or directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:23:57:
> error: parser/implementation/NeuroMLLevel3-pimpl.hpp: No such file or
> directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:25:55:
> error: parser/implementation/Level3Cells-pimpl.hpp: No such file or
> directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:27:54:
> error: parser/implementation/Level3Cell-pimpl.hpp: No such file or
> directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:29:60:
> error: parser/implementation/Level3Biophysics-pimpl.hpp: No such file
> or directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:9:43:
> error: parser/PCSIMParserEnvironment.h: No such file or directory
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:11:
> error: ‘cxxproxy’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:
> In function ‘bool isPointNeuron()’:
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:14:
> error: ‘properties’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:19:
> error: ‘properties’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:
> At global scope:
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:27:
> error: ‘cxxproxy’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:
> In function ‘boost::shared_ptr<SimObject>  as_SimObjectFactory()’:
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:29:
> error: ‘properties’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:36:
> error: ‘cxxproxy’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:36:
> error: expected `;' before ‘p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:37:
> error: ‘p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:44:
> error: invalid use of ‘this’ in non-member function
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:44:
> error: ‘str’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:45: error:
> ‘NeuroMLLevel3_pimpl’ in namespace ‘neuroml::schema’ does not name a
> type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:46: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:46:
> warning: ISO C++ forbids declaration of ‘Notes_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:46: error:
> expected ‘;’ before ‘Notes_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:47: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:47:
> warning: ISO C++ forbids declaration of ‘Properties_pimpl’ with no
> type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:47: error:
> expected ‘;’ before ‘Properties_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:48: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:48:
> warning: ISO C++ forbids declaration of ‘Property_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:48: error:
> expected ‘;’ before ‘Property_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:49: error:
> ‘::xml_schema’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:49:
> warning: ISO C++ forbids declaration of ‘string_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:49: error:
> expected ‘;’ before ‘string_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:50: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:50:
> warning: ISO C++ forbids declaration of ‘Annotation_pimpl’ with no
> type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:50: error:
> expected ‘;’ before ‘Annotation_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:51: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:51:
> warning: ISO C++ forbids declaration of ‘Group_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:51: error:
> expected ‘;’ before ‘Group_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:52: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:52:
> warning: ISO C++ forbids declaration of ‘Authors_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:52: error:
> expected ‘;’ before ‘Authors_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:53: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:53:
> warning: ISO C++ forbids declaration of ‘Person_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:53: error:
> expected ‘;’ before ‘Person_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:54: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:54:
> warning: ISO C++ forbids declaration of ‘Publication_pimpl’ with no
> type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:54: error:
> expected ‘;’ before ‘Publication_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:55: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:55:
> warning: ISO C++ forbids declaration of ‘NeuronDBReference_pimpl’ with
> no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:55: error:
> expected ‘;’ before ‘NeuronDBReference_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:56: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:56:
> warning: ISO C++ forbids declaration of ‘ModelDBReference_pimpl’ with
> no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:56: error:
> expected ‘;’ before ‘ModelDBReference_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:57: error:
> field ‘Level3Cells_p’ has incomplete type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:58: error:
> ‘Level3Cell_pimpl’ in namespace ‘neuroml::schema’ does not name a type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:59: error:
> ‘::morphml’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:59:
> warning: ISO C++ forbids declaration of ‘cellBody_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:59: error:
> expected ‘;’ before ‘cellBody_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:60: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:60:
> warning: ISO C++ forbids declaration of ‘Polygon_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:60: error:
> expected ‘;’ before ‘Polygon_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:61: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:61:
> warning: ISO C++ forbids declaration of ‘Point_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:61: error:
> expected ‘;’ before ‘Point_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:62: error:
> ‘::xml_schema’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:62:
> warning: ISO C++ forbids declaration of ‘double_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:62: error:
> expected ‘;’ before ‘double_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:63: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:63:
> warning: ISO C++ forbids declaration of ‘Polyhedron_pimpl’ with no
> type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:63: error:
> expected ‘;’ before ‘Polyhedron_p’
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:64: error:
> ‘::metadata’ has not been declared
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:64:
> warning: ISO C++ forbids declaration of ‘polygons_pimpl’ with no type
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:64: error:
> expected ‘;’ before ‘polygons_p’
>
> ...
> ...
>
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:136:
> error: ‘DoubleExponentialSynapse_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:137:
> error: ‘TimeConstantValueIncZero_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:138:
> error: ‘TimeConstantValue_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:139:
> error: ‘BlockingSynapse_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:140:
> error: ‘Block_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:141:
> error: ‘MultiDecaySynapse_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:142:
> error: ‘FacDepSynapse_p’ was not declared in this scope
> ........
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:435:
> error: ‘InputSite_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:437:
> error: ‘CellIdInNetwork_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:439:
> error: ‘all_cells_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:439:
> error: ‘percentage_cells_p’ was not declared in this scope
> /home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:441:
> error: ‘Percentage_p’ was not declared in this scope
> make[2]: *** [pcsim/CMakeFiles/pcsim.dir/neuroml/parser/cxxproxy/morphml/CxxProxyCell.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[2]: *** [pcsim/CMakeFiles/pcsim.dir/neuroml/NeuroMLImporter.o] Error 1
> make[1]: *** [pcsim/CMakeFiles/pcsim.dir/all] Error 2
> make: *** [all] Error 2
> BUILD PROCESS FAILED. ERROR = 512
> Command: /usr/bin/make -j 2 install
>
> Perhaps you can help me again.
> Thank you for your reply again, and any other kind of help is appreciated also.
>
> If there are someone installed it successfully, the experience you
> shared will help me a lot! You can tell me your linux distribution
> version, gcc version, python version and etc. Thanks in advance.
>
> Best Regards.
> Hou Zhicheng.
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> Pcsim-users mailing list
> Pcs...@li...
> https://lists.sourceforge.net/lists/listinfo/pcsim-users


-- 
_______________________________________________
Dejan Pecevski, PhD
Institute for Theoretical Computer Science
Graz University of Technology
Inffeldgasse 16b, A-8010 Graz, Austria
Tel. +43 316 873 5849

Re: [Pcsim-users] problems of installing PCSim

[厚之成 <zhi...@gm...>]

Hi!

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


hou@hou-pc:~/pcsim/pcsim-0.5.4$ sudo python build.py -j 2 install
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D CMAKE_INSTALL_PREFIX:PATH=/home/hou/pcsim/pcsim-0.5.4 -D PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D EXTRA_INSTALL:STRING=NO /home/hou/pcsim/pcsim-0.5.4
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.6
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc34-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc34-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
   GNU Scientific library : /usr/local/lib/libgsl.so
   Xerces library : /usr/local/lib/libxerces-c.so
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 rebuild_cache
Running CMake to regenerate build system...
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.6
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc34-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc34-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
   GNU Scientific library : /usr/local/lib/libgsl.so
   Xerces library : /usr/local/lib/libxerces-c.so
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
*******************************************
*  GENERATING PY++ WRAPPER CPP FILES      *
*******************************************
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 generate_code
Built target generate_python_wrapper_code
Built target generate_code
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 rebuild_cache
Running CMake to regenerate build system...
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.6
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc34-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc34-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
   GNU Scientific library : /usr/local/lib/libgsl.so
   Xerces library : /usr/local/lib/libxerces-c.so
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 install
[  0%] Built target generate_python_wrapper_code
[  0%] Building CXX object pcsim/CMakeFiles/pcsim.dir/neuroml/NeuroMLImporter.o
[  0%] Building CXX object
pcsim/CMakeFiles/pcsim.dir/neuroml/parser/cxxproxy/morphml/CxxProxyCell.o
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:1:50:
error: parser/cxxproxy/morphml/CxxProxyCell.h: No such file or
directory
In file included from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:7,
                 from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.cpp:1:
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:11:59:
error: parser/skeleton/NeuroML_Level3_v1.7.1-pskel.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:13:60:
error: parser/implementation/NetworkML_v1.7.1-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:15:58:
error: parser/implementation/MorphML_v1.7.1-pimpl.hpp: No such file or
directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:17:61:
error: parser/implementation/Biophysics_v1.7.1-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:19:60:
error: parser/implementation/ChannelML_v1.7.1-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:21:59:
error: parser/implementation/Metadata_v1.7.1-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:23:57:
error: parser/implementation/NeuroMLLevel3-pimpl.hpp: No such file or
directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:25:55:
error: parser/implementation/Level3Cells-pimpl.hpp: No such file or
directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:27:54:
error: parser/implementation/Level3Cell-pimpl.hpp: No such file or
directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:29:60:
error: parser/implementation/Level3Biophysics-pimpl.hpp: No such file
or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:9:43:
error: parser/PCSIMParserEnvironment.h: No such file or directory
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:11:
error: ‘cxxproxy’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:
In function ‘bool isPointNeuron()’:
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:14:
error: ‘properties’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:19:
error: ‘properties’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:
At global scope:
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:27:
error: ‘cxxproxy’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:
In function ‘boost::shared_ptr<SimObject> as_SimObjectFactory()’:
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:29:
error: ‘properties’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:36:
error: ‘cxxproxy’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:36:
error: expected `;' before ‘p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:37:
error: ‘p’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:44:
error: invalid use of ‘this’ in non-member function
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/cxxproxy/morphml/CxxProxyCell.cpp:44:
error: ‘str’ was not declared in this scope
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:45: error:
‘NeuroMLLevel3_pimpl’ in namespace ‘neuroml::schema’ does not name a
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:46: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:46:
warning: ISO C++ forbids declaration of ‘Notes_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:46: error:
expected ‘;’ before ‘Notes_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:47: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:47:
warning: ISO C++ forbids declaration of ‘Properties_pimpl’ with no
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:47: error:
expected ‘;’ before ‘Properties_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:48: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:48:
warning: ISO C++ forbids declaration of ‘Property_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:48: error:
expected ‘;’ before ‘Property_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:49: error:
‘::xml_schema’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:49:
warning: ISO C++ forbids declaration of ‘string_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:49: error:
expected ‘;’ before ‘string_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:50: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:50:
warning: ISO C++ forbids declaration of ‘Annotation_pimpl’ with no
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:50: error:
expected ‘;’ before ‘Annotation_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:51: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:51:
warning: ISO C++ forbids declaration of ‘Group_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:51: error:
expected ‘;’ before ‘Group_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:52: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:52:
warning: ISO C++ forbids declaration of ‘Authors_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:52: error:
expected ‘;’ before ‘Authors_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:53: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:53:
warning: ISO C++ forbids declaration of ‘Person_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:53: error:
expected ‘;’ before ‘Person_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:54: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:54:
warning: ISO C++ forbids declaration of ‘Publication_pimpl’ with no
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:54: error:
expected ‘;’ before ‘Publication_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:55: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:55:
warning: ISO C++ forbids declaration of ‘NeuronDBReference_pimpl’ with
no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:55: error:
expected ‘;’ before ‘NeuronDBReference_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:56: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:56:
warning: ISO C++ forbids declaration of ‘ModelDBReference_pimpl’ with
no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:56: error:
expected ‘;’ before ‘ModelDBReference_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:57: error:
field ‘Level3Cells_p’ has incomplete type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:58: error:
‘Level3Cell_pimpl’ in namespace ‘neuroml::schema’ does not name a type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:59: error:
‘::morphml’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:59:
warning: ISO C++ forbids declaration of ‘cellBody_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:59: error:
expected ‘;’ before ‘cellBody_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:60: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:60:
warning: ISO C++ forbids declaration of ‘Polygon_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:60: error:
expected ‘;’ before ‘Polygon_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:61: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:61:
warning: ISO C++ forbids declaration of ‘Point_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:61: error:
expected ‘;’ before ‘Point_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:62: error:
‘::xml_schema’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:62:
warning: ISO C++ forbids declaration of ‘double_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:62: error:
expected ‘;’ before ‘double_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:63: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:63:
warning: ISO C++ forbids declaration of ‘Polyhedron_pimpl’ with no
type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:63: error:
expected ‘;’ before ‘Polyhedron_p’
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:64: error:
‘::metadata’ has not been declared
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:64:
warning: ISO C++ forbids declaration of ‘polygons_pimpl’ with no type
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:64: error:
expected ‘;’ before ‘polygons_p’

...
...

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

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

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

Best Regards.
Hou Zhicheng.

Re: [Pcsim-users] problems of installing PCSim

[Natschläger T. <Tho...@sc...>]

Hi!

 

If you do not need to use the NeuroML feature probably the easiest way to solve is to go to the top level CMakeLists.txt and remove

 

               "${PCSIM_SOURCE_DIR}/pcsim/neuroml"

                "${PCSIM_SOURCE_DIR}/libxsd"

 

from the INCLUDE_DIRECTORIES.

 

Best Regards

 

    Thomas Natschläger

 

 

From: 厚之成 [mailto:zhi...@gm...] 
Sent: Sonntag, 20. November 2011 13:12
To: pcs...@li...
Subject: [Pcsim-users] problems of installing PCSim

 

Hello all,

i want to install the PCSim 0.5.4 in my ubuntu 10.04, but some problems happened.  i have replace the gcc by gcc 4.1.3 and install all the dependence.  when i run python build.py -j 2 install(my python version is 2.6.5), the bash said:

 

>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build

>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D CMAKE_INSTALL_PREFIX:PATH=/home/hou/pcsim/pcsim-0.5.4 -D PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D EXTRA_INSTALL:STRING=NO /home/hou/pcsim/pcsim-0.5.4

   Build type   = Release

   Platform     = linux-i686

   Make tool    = /usr/bin/make

   Make command = /usr/bin/make -i

   Python executable : /usr/bin/python version 2.6 

   Python libraries : /usr/lib/python2.6/config

   Python includes : /usr/include/python2.6

   Doxygen executable : /usr/bin/doxygen

   GCCXML executable : /usr/bin/gccxml

BOOST_LIB_SUFFIX IS gcc-mt

BOOST_LIB_SUFFIX_2 IS gcc41-mt

   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc34-mt.so

   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so

   Boost C++ library boost_date_time : /usr/local/lib/libboost_date_time-gcc34-mt.so

   Boost C++ libraries : /usr/local/lib 

   Boost C++ include path : /usr/local/include/boost-1_34_1 

   MPICH2 library: /usr/local/lib/libmpich.so

   MPICH2 include path : /usr/local/include

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

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

   CppUnit : /usr/local/lib/libcppunit.so

   JNI headers : /usr/lib/jvm/java-6-openjdk/include

-- Configuring done

-- Generating done

-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build

>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build

>>>> /usr/bin/make -j 2 rebuild_cache

Running CMake to regenerate build system...

   Build type   = Release

   Platform     = linux-i686

   Make tool    = /usr/bin/make

   Make command = /usr/bin/make -i

   Python executable : /usr/bin/python version 2.6 

   Python libraries : /usr/lib/python2.6/config

   Python includes : /usr/include/python2.6

   Doxygen executable : /usr/bin/doxygen

   GCCXML executable : /usr/bin/gccxml

BOOST_LIB_SUFFIX IS gcc-mt

BOOST_LIB_SUFFIX_2 IS gcc41-mt

   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc34-mt.so

   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so

   Boost C++ library boost_date_time : /usr/local/lib/libboost_date_time-gcc34-mt.so

   Boost C++ libraries : /usr/local/lib 

   Boost C++ include path : /usr/local/include/boost-1_34_1 

   MPICH2 library: /usr/local/lib/libmpich.so

   MPICH2 include path : /usr/local/include

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

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

   CppUnit : /usr/local/lib/libcppunit.so

   JNI headers : /usr/lib/jvm/java-6-openjdk/include

-- Configuring done

-- Generating done

-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build

*******************************************

*  GENERATING PY++ WRAPPER CPP FILES      *

*******************************************

>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build

>>>> /usr/bin/make -j 2 generate_code

Built target generate_python_wrapper_code

Built target generate_code

>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build

>>>> /usr/bin/make -j 2 rebuild_cache

Running CMake to regenerate build system...

   Build type   = Release

   Platform     = linux-i686

   Make tool    = /usr/bin/make

   Make command = /usr/bin/make -i

   Python executable : /usr/bin/python version 2.6 

   Python libraries : /usr/lib/python2.6/config

   Python includes : /usr/include/python2.6

   Doxygen executable : /usr/bin/doxygen

   GCCXML executable : /usr/bin/gccxml

BOOST_LIB_SUFFIX IS gcc-mt

BOOST_LIB_SUFFIX_2 IS gcc41-mt

   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc34-mt.so

   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc34-mt.so

   Boost C++ library boost_date_time : /usr/local/lib/libboost_date_time-gcc34-mt.so

   Boost C++ libraries : /usr/local/lib 

   Boost C++ include path : /usr/local/include/boost-1_34_1 

   MPICH2 library: /usr/local/lib/libmpich.so

   MPICH2 include path : /usr/local/include

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

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

   CppUnit : /usr/local/lib/libcppunit.so

   JNI headers : /usr/lib/jvm/java-6-openjdk/include

-- Configuring done

-- Generating done

-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build

>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build

>>>> /usr/bin/make -j 2 install

[  0%] Built target generate_python_wrapper_code

[  0%] [  0%] Building CXX object pcsim/CMakeFiles/pcsim.dir/neuroml/NeuroMLImporter.o

Building CXX object pcsim/CMakeFiles/pcsim.dir/neuroml/parser/skeleton/offset-pskel.o

/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx: In member function ‘virtual xercesc_3_1::BinInputStream* xsd::cxx::xml::sax::std_input_source::makeStream() const’:

/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:156: error: cannot allocate an object of abstract type ‘xsd::cxx::xml::sax::std_input_stream’

/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:25: note:   because the following virtual functions are pure within ‘xsd::cxx::xml::sax::std_input_stream’:

/usr/local/include/xercesc/util/BinInputStream.hpp:67: note:           virtual const XMLCh* xercesc_3_1::BinInputStream::getContentType() const

make[2]: *** [pcsim/CMakeFiles/pcsim.dir/neuroml/parser/skeleton/offset-pskel.o] Error 1

make[2]: *** Waiting for unfinished jobs....

/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx: In member function ‘virtual xercesc_3_1::BinInputStream* xsd::cxx::xml::sax::std_input_source::makeStream() const’:

/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:156: error: cannot allocate an object of abstract type ‘xsd::cxx::xml::sax::std_input_stream’

/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:25: note:   because the following virtual functions are pure within ‘xsd::cxx::xml::sax::std_input_stream’:

/usr/local/include/xercesc/util/BinInputStream.hpp:67: note:           virtual const XMLCh* xercesc_3_1::BinInputStream::getContentType() const

make[2]: *** [pcsim/CMakeFiles/pcsim.dir/neuroml/NeuroMLImporter.o] Error 1

make[1]: *** [pcsim/CMakeFiles/pcsim.dir/all] Error 2

make: *** [all] Error 2

BUILD PROCESS FAILED. ERROR = 512

Command: /usr/bin/make -j 2 install

 

i don't know how to solve it and searching help.

 

any kind of help is very appreciated!

 

Regards,

Hou Zhicheng

 

 

[Pcsim-users] problems of installing PCSim

[厚之成 <zhi...@gm...>]

Hello all,
i want to install the PCSim 0.5.4 in my ubuntu 10.04, but some problems
happened.  i have replace the gcc by gcc 4.1.3 and install all the
dependence.  when i run python build.py -j 2 install(my python version is
2.6.5), the bash said:

>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D
CMAKE_INSTALL_PREFIX:PATH=/home/hou/pcsim/pcsim-0.5.4 -D
PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D
EXTRA_INSTALL:STRING=NO /home/hou/pcsim/pcsim-0.5.4
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.6
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
   Boost C++ library boost_python :
/usr/local/lib/libboost_python-gcc34-mt.so
   Boost C++ library boost_thread :
/usr/local/lib/libboost_thread-gcc34-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc34-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
   GNU Scientific library : /usr/local/lib/libgsl.so
   Xerces library : /usr/local/lib/libxerces-c.so
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 rebuild_cache
Running CMake to regenerate build system...
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.6
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
   Boost C++ library boost_python :
/usr/local/lib/libboost_python-gcc34-mt.so
   Boost C++ library boost_thread :
/usr/local/lib/libboost_thread-gcc34-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc34-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
   GNU Scientific library : /usr/local/lib/libgsl.so
   Xerces library : /usr/local/lib/libxerces-c.so
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
*******************************************
*  GENERATING PY++ WRAPPER CPP FILES      *
*******************************************
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 generate_code
Built target generate_python_wrapper_code
Built target generate_code
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 rebuild_cache
Running CMake to regenerate build system...
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.6
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
   Boost C++ library boost_python :
/usr/local/lib/libboost_python-gcc34-mt.so
   Boost C++ library boost_thread :
/usr/local/lib/libboost_thread-gcc34-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc34-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
   GNU Scientific library : /usr/local/lib/libgsl.so
   Xerces library : /usr/local/lib/libxerces-c.so
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 install
[  0%] Built target generate_python_wrapper_code
[  0%] [  0%] Building CXX object
pcsim/CMakeFiles/pcsim.dir/neuroml/NeuroMLImporter.o
Building CXX object
pcsim/CMakeFiles/pcsim.dir/neuroml/parser/skeleton/offset-pskel.o
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx: In
member function ‘virtual xercesc_3_1::BinInputStream*
xsd::cxx::xml::sax::std_input_source::makeStream() const’:
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:156:
error: cannot allocate an object of abstract type
‘xsd::cxx::xml::sax::std_input_stream’
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:25:
note:   because the following virtual functions are pure within
‘xsd::cxx::xml::sax::std_input_stream’:
/usr/local/include/xercesc/util/BinInputStream.hpp:67: note: virtual const
XMLCh* xercesc_3_1::BinInputStream::getContentType() const
make[2]: ***
[pcsim/CMakeFiles/pcsim.dir/neuroml/parser/skeleton/offset-pskel.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx: In
member function ‘virtual xercesc_3_1::BinInputStream*
xsd::cxx::xml::sax::std_input_source::makeStream() const’:
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:156:
error: cannot allocate an object of abstract type
‘xsd::cxx::xml::sax::std_input_stream’
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:25:
note:   because the following virtual functions are pure within
‘xsd::cxx::xml::sax::std_input_stream’:
/usr/local/include/xercesc/util/BinInputStream.hpp:67: note: virtual const
XMLCh* xercesc_3_1::BinInputStream::getContentType() const
make[2]: *** [pcsim/CMakeFiles/pcsim.dir/neuroml/NeuroMLImporter.o] Error 1
make[1]: *** [pcsim/CMakeFiles/pcsim.dir/all] Error 2
make: *** [all] Error 2
BUILD PROCESS FAILED. ERROR = 512
Command: /usr/bin/make -j 2 install

i don't know how to solve it and searching help.

any kind of help is very appreciated!

Regards,
Hou Zhicheng

[Pcsim-users] PCSIM development

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

Hi all,

I've noticed that there have been no commits on the PCSIM repository for quite some time, is PCSIM still under development?

Cheers,
Chris.

Re: [Pcsim-users] Installing pcsim

[Natschläger T. <Tho...@sc...>]

Dear Martin,

there is the branch http://pcsim.svn.sourceforge.net/viewvc/pcsim/branches/newbuild/ which should work with much more recent libs.
However its is mainly tested on Windows ...

Regards

   -thomas natschläger


-----Original Message-----
From: Martin Kleinschrodt [mailto:mar...@ph...]
Sent: Wed 18.05.2011 15:39
To: pcs...@li...
Subject: [Pcsim-users] Installing pcsim
 
Hello fellow pcsim-users!

I am trying to install pcsim on ubuntu 11.04 and am having some difficulties. I am running into one compilation error after the other. If I fix one the next one pops up. I expect this is due to pcsim depending on some outdated versions of certain libraries. Has anyone managed to get pcsim running on a newer linux distro? If so could you please send me a list of the libraries you used and any other tweaks that helped you getting it to run?

Any kind of help is very appreciated!

Kind regards,
Martin

Re: [Pcsim-users] Installing pcsim

[Yaroslav H. <sf...@on...>]

Hi Martin,

have a look at the previous thread
http://sourceforge.net/mailarchive/message.php?msg_id=26673916

it would indeed be cool if someone contributes allowing pcsim to build
with recent versions of the dependencies.  Then we could progress with
making it available as a part of NeuroDebian (and official
Debian/Ubuntu).  According to our just initiated survey PCSIM is used
out there! ;)  FWIW here is the announcement if you want to
participate/see results:

    We invite you to participate in a survey on software usage and computing
    environments in neuroscience research. It will take no more than five
    minutes to fill it out. Immediately after sending your answers you will
    get to see a summary of how other participants have responded before.
    This data will eventually be made available to software vendors and
    distributors to determine advantages and issue of popular computing
    environments in neuroscience research.

    Learn about what fellow neuroscientists are doing to address their computing
    demands -- take the survey!

        http://goo.gl/euIMc

Sorry for a shameless plug ;)

Cheers,

On Wed, 18 May 2011, Martin Kleinschrodt wrote:
>    I am trying to install pcsim on ubuntu 11.04 and am having some
>    difficulties. I am running into one compilation error after the other.
>    If I fix one the next one pops up. I expect this is due to pcsim
>    depending on some outdated versions of certain libraries. Has anyone
>    managed to get pcsim running on a newer linux distro? If so could you
>    please send me a list of the libraries you used and any other tweaks
>    that helped you getting it to run?
>    Any kind of help is very appreciated!
-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic

[Pcsim-users] Installing pcsim

[Martin K. <mar...@ph...>]

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
  <head>

    <meta http-equiv="content-type" content="text/html; charset=ISO-8859-15">
  </head>
  <body text="#000000" bgcolor="#ffffff">
    Hello fellow pcsim-users!<br>
    <br>
    I am trying to install pcsim on ubuntu 11.04 and am having some
    difficulties. I am running into one compilation error after the
    other. If I fix one the next one pops up. I expect this is due to
    pcsim depending on some outdated versions of certain libraries. Has
    anyone managed to get pcsim running on a newer linux distro? If so
    could you please send me a list of the libraries you used and any
    other tweaks that helped you getting it to run?<br>
    <br>
    Any kind of help is very appreciated!<br>
    <br>
    Kind regards,<br>
    Martin<br>
  </body>
</html>

Re: [Pcsim-users] pcsim -> Debian: build issues; externals depends versions question

[Yaroslav H. <sf...@on...>]

ah, almost forgot ;)

if you ever decide/need to test/debug/develop on a Linux platform, and
Debian in particular, I would recommend using our Virtual Appliance for
VirtualBox:

http://neuro.debian.net/vm.html

should be quite easy to setup and get all dependencies by simply
selecting them in a package manager and clicking 'apply' ;)

N.B. besides pyplusplus, which I will look into packaging after
initial build of pcsim succeeds

On Tue, 30 Nov 2010, Yaroslav Halchenko wrote:

> > > actually there is already a branch in the SVN (see http://pcsim.svn.sourceforge.net/viewvc/pcsim/branches/newbuild/) where we are updating PCSIM to be compatible with current versions of the dependencies and to work under Windows. However this branch is not yet ready for release and as we are short of resources it may take a few weeks until this will happen.

> > > Best Regards

> > >    Thomas Natschläger
-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic

Re: [Pcsim-users] pcsim -> Debian: build issues; externals depends versions question

[Yaroslav H. <sf...@on...>]

On Tue, 30 Nov 2010, Yaroslav Halchenko wrote:
> no problem -- a few weeks sounds like a good schedule.  Meanwhile I will
> have a look at the newbuild branch which I already cloned but since
> changes were lots I decided to check first the most "recent" release
> first.

Please have a look at the attached patch... sorry for it being somewhat
a mess, but I wonder if pcsim builds from newbuild (rev 269 as of
2010-08-03 04:55:27 - the last commit I see) no problem?  or may
be something was forgotten to be committed? ;-)

I had to move many definitions from private/protected into public
(included in the attached patch) just to proceed forward to catch real
"compatibility" issues (also listed/embedded in the patch).

More comments are in the patch description

Cheers,

> > actually there is already a branch in the SVN (see http://pcsim.svn.sourceforge.net/viewvc/pcsim/branches/newbuild/) where we are updating PCSIM to be compatible with current versions of the dependencies and to work under Windows. However this branch is not yet ready for release and as we are short of resources it may take a few weeks until this will happen.

> > Best Regards

> >    Thomas Natschläger
-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic

Re: [Pcsim-users] pcsim -> Debian: build issues; externals depends versions question

[Yaroslav H. <sf...@on...>]

Hi Thomas,

Thanks for the reply!

no problem -- a few weeks sounds like a good schedule.  Meanwhile I will
have a look at the newbuild branch which I already cloned but since
changes were lots I decided to check first the most "recent" release
first.

Cheers

On Tue, 30 Nov 2010, Natschläger Thomas wrote:

> Dear  Yaroslav Halchenko,

> actually there is already a branch in the SVN (see http://pcsim.svn.sourceforge.net/viewvc/pcsim/branches/newbuild/) where we are updating PCSIM to be compatible with current versions of the dependencies and to work under Windows. However this branch is not yet ready for release and as we are short of resources it may take a few weeks until this will happen.

> Best Regards

>    Thomas Natschläger

-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic

Re: [Pcsim-users] pcsim -> Debian: build issues; externals depends versions question

[Natschläger T. <Tho...@sc...>]

Dear  Yaroslav Halchenko,

actually there is already a branch in the SVN (see http://pcsim.svn.sourceforge.net/viewvc/pcsim/branches/newbuild/) where we are updating PCSIM to be compatible with current versions of the dependencies and to work under Windows. However this branch is not yet ready for release and as we are short of resources it may take a few weeks until this will happen.

Best Regards

   Thomas Natschläger

-----Original Message-----
From: Yaroslav Halchenko [mailto:sf...@on...] 
Sent: Dienstag, 30. November 2010 03:27
To: pcs...@li...
Subject: [Pcsim-users] pcsim -> Debian: build issues;externals depends versions question

Dear PCSIM Author(s),

NB uff.. had to repost few times (subscribe, gzip attachement)... but hopefully this time

Thanks for the project.  PyNN author (Andrew Davison) kindly suggested me to look into packaging of pcsim for Debian since it is quite often a problematic endeavor for non-IT savy neuro-users; so here I am
;-)

I have approached initial building/packaging of pcsim 0.5.4 and ran into a build failure(s) which, most probably, is due to versioned depends.
Since I am building on a Debian (primarily squeeze) and against Debian-available versions I have boost 1.42 (not the advised
1.34.1) and pygccxml 1.0.0 (not mandated 0.9.5).

So the question first: are there plans/WiP toward supporting newer versions of those externals?  If no, I might, unfortunately, need to wait for that compatibility before being able to make pcsim readily available for Debian/Ubuntu users.

And here is one of the build failures:
(git)novo:~/deb/perspect/pcsim[debian-release]_build
$> make 2>&1 | tee build.log
[ 88%] Built target pcsim
Linking CXX executable ../bin/pcsim_test
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o: In function `DistributedMultiThreadNetworkTest::doSpikeExchangeTest()':
DistributedMultiThreadNetworkTest.cpp:(.text+0x714c): undefined reference to `SpikingInputNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x718c): undefined reference to `SpikeTimeRecorder::type'
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o: In function `DistributedMultiThreadNetworkTest::test_addObject_roundrobin()':
DistributedMultiThreadNetworkTest.cpp:(.text+0x83b8): undefined reference to `LifNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x84c3): undefined reference to `LifNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x85dc): undefined reference to `LifNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x86fe): undefined reference to `LifNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x8820): undefined reference to `LifNeuron::type'
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o:DistributedMultiThreadNetworkTest.cpp:(.text+0x8942): more undefined references to `LifNeuron::type' follow
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o: In function `ExponentialDecaySpikeResponse::setObjectTypeID(unsigned char)':
DistributedMultiThreadNetworkTest.cpp:(.text._ZN29ExponentialDecaySpikeResponse15setObjectTypeIDEh[ExponentialDecaySpikeResponse::setObjectTypeID(unsigned char)]+0x3): undefined reference to `ExponentialDecaySpikeResponse::type'
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o: In function `ExponentialDecaySpikeResponse::setSimObjectInformation(SimObjectInformation*)':
DistributedMultiThreadNetworkTest.cpp:(.text._ZN29ExponentialDecaySpikeResponse23setSimObjectInformationEP20SimObjectInformation[ExponentialDecaySpikeResponse::setSimObjectInformation(SimObjectInformation*)]+0x3): undefined reference to `ExponentialDecaySpikeResponse::simObjectInfo'
...
full output in the attached build.log

Thank you in advance for the reply.


--
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic

[Pcsim-users] pcsim -> Debian: build issues; externals depends versions question

[Yaroslav H. <sf...@on...>]

Dear PCSIM Author(s),

NB uff.. had to repost few times (subscribe, gzip attachement)... but
hopefully this time

Thanks for the project.  PyNN author (Andrew Davison) kindly suggested
me to look into packaging of pcsim for Debian since it is quite
often a problematic endeavor for non-IT savy neuro-users; so here I am
;-)

I have approached initial building/packaging of pcsim 0.5.4 and ran into
a build failure(s) which, most probably, is due to versioned depends.
Since I am building on a Debian (primarily squeeze) and against
Debian-available versions I have boost 1.42 (not the advised
1.34.1) and pygccxml 1.0.0 (not mandated 0.9.5).

So the question first: are there plans/WiP toward supporting newer versions of
those externals?  If no, I might, unfortunately, need to wait for that
compatibility before being able to make pcsim readily available for
Debian/Ubuntu users.

And here is one of the build failures:
(git)novo:~/deb/perspect/pcsim[debian-release]_build
$> make 2>&1 | tee build.log
[ 88%] Built target pcsim
Linking CXX executable ../bin/pcsim_test
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o: In function `DistributedMultiThreadNetworkTest::doSpikeExchangeTest()':
DistributedMultiThreadNetworkTest.cpp:(.text+0x714c): undefined reference to `SpikingInputNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x718c): undefined reference to `SpikeTimeRecorder::type'
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o: In function `DistributedMultiThreadNetworkTest::test_addObject_roundrobin()':
DistributedMultiThreadNetworkTest.cpp:(.text+0x83b8): undefined reference to `LifNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x84c3): undefined reference to `LifNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x85dc): undefined reference to `LifNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x86fe): undefined reference to `LifNeuron::type'
DistributedMultiThreadNetworkTest.cpp:(.text+0x8820): undefined reference to `LifNeuron::type'
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o:DistributedMultiThreadNetworkTest.cpp:(.text+0x8942): more undefined references to `LifNeuron::type' follow
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o: In function `ExponentialDecaySpikeResponse::setObjectTypeID(unsigned char)':
DistributedMultiThreadNetworkTest.cpp:(.text._ZN29ExponentialDecaySpikeResponse15setObjectTypeIDEh[ExponentialDecaySpikeResponse::setObjectTypeID(unsigned char)]+0x3): undefined reference to `ExponentialDecaySpikeResponse::type'
CMakeFiles/pcsim_test.dir/DistributedMultiThreadNetworkTest.o: In function `ExponentialDecaySpikeResponse::setSimObjectInformation(SimObjectInformation*)':
DistributedMultiThreadNetworkTest.cpp:(.text._ZN29ExponentialDecaySpikeResponse23setSimObjectInformationEP20SimObjectInformation[ExponentialDecaySpikeResponse::setSimObjectInformation(SimObjectInformation*)]+0x3): undefined reference to `ExponentialDecaySpikeResponse::simObjectInfo'
...
full output in the attached build.log

Thank you in advance for the reply.


-- 
=------------------------------------------------------------------=
Keep in touch                                     www.onerussian.com
Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic

Re: [Pcsim-users] /usr/include/c++/4.4/cmath:501: error: '__builtin_fpclassify' was not declared in this scope

[Adrian M. W. <am...@in...>]

Using gccxml newly exported from its CVS repository enables me to get
further. PCSIM build is now progressing...

On 17/11/10 17:26, Adrian M. Whatley wrote:
> I've just had cause to build PCSIM on OpenSuse 11.2 once again. Although
> this used to work, I now get the errors quoted below, the key line being
> "error: '__builtin_fpclassify' was not declared in this scope".
> 
> This looks like this bug here: http://www.vtk.org/Bug/view.php?id=10141
> so I'm hoping that using the latest gccxml will fix it.
> 
> I'll let you know what happens!
> 
> Adrian
> 
> 
>> *******************************************                                                                                                                                     
>> *  GENERATING PY++ WRAPPER CPP FILES      *                                                                                                                                     
>> *******************************************                                                                                                                                     
>>>>>> cd /usr/src/packages/BUILD/pcsim-0.5.4/_build                                                                                                                              
>>>>>> /usr/bin/gmake -j 2 generate_code                                                                                                                                          
>> gmake[1]: Entering directory `/usr/src/packages/BUILD/pcsim-0.5.4/_build'                                                                                                       
>> gmake[2]: Entering directory `/usr/src/packages/BUILD/pcsim-0.5.4/_build'                                                                                                       
>> gmake[3]: Entering directory `/usr/src/packages/BUILD/pcsim-0.5.4/_build'                                                                                                       
>> gmake[4]: Entering directory `/usr/src/packages/BUILD/pcsim-0.5.4/_build'                                                                                                       
>> Generating ../../python/pypcsim.h                                                                                                                                               
>> Generating ../../python/pypcsim/pypcsim.indicator.cpp                                                                                                                           
>> /usr/lib/python2.6/site-packages/pygccxml/parser/declarations_cache.py:8: DeprecationWarning: the md5 module is deprecated; use hashlib instead                                 
>>   import md5                                                                                                                                                                    
>>
>> INFO Parsing source file "pypcsim.h" ... 
>>
>> INFO gccxml cmd: /usr/local/bin/gccxml  --gccxml-cxxflags -pthread -fpermissive   -I"." -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/simutils" -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/simcore" -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/construction" -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/neuroml" -I"/usr/src/packages/BUILD/pcsim-0.5.4/pcsim/simobjects" -I"/usr/src/packages/BUILD/pcsim-0.5.4/libxsd"  -D"MPICH_IGNORE_CXX_SEEK" -D"BOOST_HAS_THREADS" -D"BOOST_PYTHON_MAX_ARITY=30"  "pypcsim.h" -fxml="/tmp/tmprVfQbS.xml"                                                                                                                                                                            
>> /usr/lib/python2.6/site-packages/pygccxml/parser/source_reader.py:152: DeprecationWarning: os.popen4 is deprecated.  Use the subprocess module.                                 
>>   input_, output = os.popen4( command_line )                                                                                                                                    
>> Traceback (most recent call last):                                                                                                                                              
>>   File "/usr/src/packages/BUILD/pcsim-0.5.4/scripts/generate_boost_python_wrapper_code.py", line 143, in <module>                                                               
>>     encoding = 'utf-8'                                                                                                                                                          
>>   File "/usr/lib/python2.6/site-packages/pyplusplus/module_builder/builder.py", line 90, in __init__                                                                            
>>     , indexing_suite_version)                                                                                                                                                   
>>   File "/usr/lib/python2.6/site-packages/pyplusplus/module_builder/builder.py", line 144, in __parse_declarations                                                               
>>     decls = reader.read_files( files, compilation_mode )                                                                                                                        
>>   File "/usr/lib/python2.6/site-packages/pygccxml/parser/project_reader.py", line 225, in read_files                                                                            
>>     return self.__parse_file_by_file(files)                                                                                                                                     
>>   File "/usr/lib/python2.6/site-packages/pygccxml/parser/project_reader.py", line 250, in __parse_file_by_file                                                                  
>>     decls = reader.read_file( header )                                                                                                                                          
>>   File "/usr/lib/python2.6/site-packages/pygccxml/parser/source_reader.py", line 198, in read_file                                                                              
>>     return self.read_gccxml_file( source_file )                                                                                                                                 
>>   File "/usr/lib/python2.6/site-packages/pygccxml/parser/source_reader.py", line 225, in read_gccxml_file                                                                       
>>     raise error                                                                                                                                                                 
>> pygccxml.parser.source_reader.gccxml_runtime_error_t: Error occured while running GCC-XML: In file included from pypcsim.h:165:                                                 
>> /usr/include/c++/4.4/cmath: In function 'typename __gnu_cxx::__enable_if<std::__is_arithmetic<_Tp>::__value, int>::__type std::fpclassify(_Tp) [with _Tp = float]':
>> /usr/include/boost/functional/hash/detail/hash_float.hpp:172:   instantiated from 'size_t boost::hash_detail::float_hash_value(T) [with T = float]'
>> /usr/include/boost/functional/hash/hash.hpp:304:   instantiated from here
>> /usr/include/c++/4.4/cmath:501: error: '__builtin_fpclassify' was not declared in this scope
>> /usr/include/c++/4.4/cmath: In function 'typename __gnu_cxx::__enable_if<std::__is_arithmetic<_Tp>::__value, int>::__type std::fpclassify(_Tp) [with _Tp = double]':
>> /usr/include/boost/functional/hash/detail/hash_float.hpp:172:   instantiated from 'size_t boost::hash_detail::float_hash_value(T) [with T = double]'
>> /usr/include/boost/functional/hash/hash.hpp:309:   instantiated from here
>> /usr/include/c++/4.4/cmath:501: error: '__builtin_fpclassify' was not declared in this scope
>> /usr/include/c++/4.4/cmath: In function 'typename __gnu_cxx::__enable_if<std::__is_arithmetic<_Tp>::__value, int>::__type std::fpclassify(_Tp) [with _Tp = long double]':
>> /usr/include/boost/functional/hash/detail/hash_float.hpp:172:   instantiated from 'size_t boost::hash_detail::float_hash_value(T) [with T = long double]'
>> /usr/include/boost/functional/hash/hash.hpp:314:   instantiated from here
>> /usr/include/c++/4.4/cmath:501: error: '__builtin_fpclassify' was not declared in this scope
>>
> 


-- 
Adrian M. Whatley
Institute of Neuroinformatics,
University of Zurich and ETH Zurich
Winterthurerstrasse 190,
CH-8057 Zurich, Switzerland.
Phone: +41 44 635 3067		Fax: +41 44 635 3053
Email: am...@in...	WWW: http://www.ini.uzh.ch/~amw/