[SciPy-user] Eigenvalues of the Floquet matrix

Nils Wagner nwagner@iam.uni-stuttgart...
Mon Mar 16 12:18:11 CDT 2009


On Mon, 16 Mar 2009 11:00:26 -0400
  Rob Clewley <rob.clewley@gmail.com> wrote:
>>>
>>> It would be really nice to have a setup.py ;-)
> 
> I know, I'm trying to pay somebody this spring to write 
>me one!
> 
>> /home/nwagner/local/lib64/python2.6/site-packages/Pyrex/Compiler/Errors.py:17:
>> DeprecationWarning: BaseException.message has been
>> deprecated as of Python 2.6
> 
> OK, for a start PyDSTool has not been tested at all on 
>Python 2.6. I
> just haven't been able to keep up! If there's any chance 
>you can also
> have 2.4.3 or 2.5 on your system then that would be the 
>easiest thing
> to do. I know that people have installed successfully 
>recently from
> SVN on Python 2.5. Maybe I need to post a clear 
>disclaimer on my
> webpage since Python 2.6 has become so common.
> 
>> Error occurred in generating Radau system
>> (while moving library extension modules to CWD)
>> <type 'exceptions.TypeError'> cannot concatenate 'str' 
>>and
>> 'int' objects
>> Traceback (most recent call last):
>>   File "seyranian-PyDSTool.py", line 43, in <module>
>>     osc = Generator.Radau_ODEsystem(DSargs)
>>   File
>> "/home/nwagner/svn/PyDSTool/PyDSTool/Generator/Radau_ODEsystem.py",
>> line 545, in __init__
>>     self.compileLib()
>>   File
>> "/home/nwagner/svn/PyDSTool/PyDSTool/Generator/Radau_ODEsystem.py",
>> line 991, in compileLib
>>     raise RuntimeError
>> RuntimeError
>>
>>
>> Any idea ?
> 
> I don't have a clue right now.
> 
> The list of test failures you sent me is pretty 
>catastrophic, which
> makes me suspect the problem is something basic in 
>python that has
> changed between 2.5 and 2.6 that is at the heart of 
>every one of the
> tests.
> 
> And/or it's something to do with Pyrex getting involved 
>for the legacy
> ODE solvers. I don't know why the pyrex compiler is 
>being invoked,
> because it should be gcc. Can you look at the wiki 
>GettingStarted page
> (Section 1.4.5.) on getting C integrators set up on 
>Linux and tell me
> if you've set up SWIG and set the CC environment 
>variable?
> 
> -Rob
> _______________________________________________
> SciPy-user mailing list
> SciPy-user@scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-user


Hi Rob,

the entries I found in 
/usr/lib64/python2.6/config/Makefile

CC=             gcc -pthread
CXX=            g++
MAINCC=         $(CC)
LINKCC=         $(PURIFY) $(MAINCC)
AR=             ar
RANLIB=         ranlib
SVNVERSION=     echo exported
  
swig -version

SWIG Version 1.3.36

Compiled with g++ [x86_64-suse-linux-gnu]
Please see http://www.swig.org for reporting bugs and 
further information

echo $CC is currently empty.

How do I set the environmental variable ?

Cheers,

       Nils


Here is the new output of run_all_tests.py

Summary:
Basic PyDSTool functions: appears to work on your system
Map related modules: appears to work on your system
VODE related modules: appears to work on your system
Symbolic differentiation module: appears to work on your 
system
Parameter estimation module: appears to be broken on your 
system
PyCont: appears to be broken on your system
Dopri ODE systems: appears to be broken on your system
Radau ODE systems: appears to be broken on your system
Parameter estimation module with external compilers: 
appears to work on your system
PyCont interface to AUTO: appears to be broken on your 
system




python -i pest_test2.py
/home/nwagner/local/lib64/python2.6/site-packages/Pyrex/Compiler/Errors.py:17: 
DeprecationWarning: BaseException.message has been 
deprecated as of Python 2.6
   self.message = message
[ 0.05714896  0.20918955  0.58088371]
[  3.60595823e-01+0.j  -2.29878191e-17+0.j 
  6.16263995e-02+0.j]
[ 0.06162640+0.j  0.36059582+0.j]
Generating non-uniform samples from HH orbit...
... done
HH spike time found at  8.43278894472
Traceback (most recent call last):
   File "pest_test2.py", line 127, in <module>
     verbose=True)
   File 
"/home/nwagner/svn/PyDSTool/PyDSTool/Toolbox/ParamEst.py", 
line 1215, in run
     int(verbose))
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/scipy/optimize/optimize.py", 
line 1199, in fminbound
     fx = func(x,*args)
   File 
"/home/nwagner/svn/PyDSTool/PyDSTool/Toolbox/ParamEst.py", 
line 354, in residual
     r = self._res_fn(p, extra_args)
   File 
"/home/nwagner/svn/PyDSTool/PyDSTool/Toolbox/ParamEst.py", 
line 416, in _res_fn
     return pest.evaluate()[0]
   File 
"/home/nwagner/svn/PyDSTool/PyDSTool/Toolbox/ParamEst.py", 
line 813, in evaluate
     res = self.context.residual(self.testModel)
   File "/home/nwagner/svn/PyDSTool/PyDSTool/MProject.py", 
line 1019, in residual
     self.evaluate(model)
   File "/home/nwagner/svn/PyDSTool/PyDSTool/MProject.py", 
line 1003, in evaluate
     new_result = test_mi(ref_mi)
   File "/home/nwagner/svn/PyDSTool/PyDSTool/MProject.py", 
line 1282, in evaluate
     target.get_test_traj(force=force)
   File "/home/nwagner/svn/PyDSTool/PyDSTool/MProject.py", 
line 1374, in get_test_traj
     self.compute_traj()
   File "/home/nwagner/svn/PyDSTool/PyDSTool/MProject.py", 
line 1360, in compute_traj
     self.model.compute(trajname=self._trajname, 
force=True)
   File "/home/nwagner/svn/PyDSTool/PyDSTool/Model.py", 
line 2449, in compute
     MI, swRules)
   File "/home/nwagner/svn/PyDSTool/PyDSTool/Model.py", 
line 2064, in _findTrajInitiator
     self.verboselevel)
   File "/home/nwagner/svn/PyDSTool/PyDSTool/Model.py", 
line 2885, in findTrajInitiator
     dxdt = dict(MI.Rhs(t, icdict, pardict))
   File "/home/nwagner/svn/PyDSTool/PyDSTool/MProject.py", 
line 1209, in Rhs
     return self.model.Rhs(t, xdict, pdict)
   File "/home/nwagner/svn/PyDSTool/PyDSTool/Model.py", 
line 1646, in Rhs
     'norm': self._normord})
   File "/home/nwagner/svn/PyDSTool/PyDSTool/Points.py", 
line 124, in __init__
     datalist.append(coorddict[c][0])
IndexError: invalid index to scalar variable.




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