[SciPy-user] Eigenvalues of the Floquet matrix

[Nils Wagner]

On Wed, 18 Mar 2009 11:48:09 -0400
  Rob Clewley <rob.clewley at gmail.com> wrote:
> Nils,
> 
>> possible that it's not a 2.5 vs. 2.6 issue after all. 
>>Could it be
>> something about your 64 bit platform? Are the standard 
>>libraries all
>> slightly different somehow? The segfault is coming from
>> lib64/libpython2.5.so. What version of gcc are you 
>>running? Based on
>> past experience I recommend 3.1 but 3.3 may also work. I 
>>will try to
>> do some research about getting DLLs working via SWIG on 
>>64 bit
>> platforms to see if there are known problems.
> 
> I think there *is* a problem trying to link the 32 bit 
>code with 64
> bit libraries. Check out 31.2.7 of
> 
> http://www.swig.org/Doc1.3/Python.html#Python_nn11
> 
> I think we need to add the compiler option to link to 
>the 32 bit
> libraries. On line 937 of Generator/Radau_ODEsystem.py 
>you should have
> 
>         extra_compile_args=['-w', '-D__RADAU__']
> 
> According to the instructions on the SWIG page, you can 
>add '-m32' at
> the beginning of this list and see if Radau now runs. If 
>it does, find
> the equivalent line in Dopri_ODEsystem.py (just text 
>search for
> extra_compile_args) and add it there too.
> 
> Let me know what happens!
> -Rob
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-user
  
Rob,

I have checked PyDSTool on different machines using
both, python2.5 and python2.6.

Now I have added the option '-m32'.

The segfault vanished.

Cheers,

            Nils

Another issue

python 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.