[SciPy-user] Eigenvalues of the Floquet matrix

Rob Clewley rob.clewley@gmail....
Mon Mar 16 13:26:18 CDT 2009


> Here is the new output of run_all_tests.py
>
> 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

Good so far.

> PyCont: appears to be broken on your system

I'd like to see the specific errors raised by any of this group.

> Dopri ODE systems: appears to be broken on your system
> Radau ODE systems: appears to be broken on your system
> PyCont interface to AUTO: appears to be broken on your system

See below.

> Parameter estimation module: appears to be broken on your system
> Parameter estimation module with external compilers: appears to work on your system

Weird that the parameter estimation doesn't work with vode but it
claims that it does with the external compilers.
I'd like to see a specific error raised by the first of these groups.

>>
>>> 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
>>>
>
> The problem persists
>
> Error occurred in generating Radau system

Yes, let's fix Dopri first on simple examples before we get in to
Radau. In my experience, Dopri is easier to get working than Radau, as
Dopri requires gcc while Radau requires gfortran. Typically, systems
have gcc set up OK but often need more work for gfortran. So can you
check that gfortran --version works? Also, what are your gcc and
gfortran versions? Sometimes there have been problems with gcc being
too new (also noted on the GettingStarted page somewhere)

> (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
>

Can you get a traceback on the TypeError exception? Maybe by
commenting out the raising of that RuntimeError that I raise?

Do any of the Dopri tests run? e.g. interp_dopri_test.py? The
run_all_tests report says some of them don't run, but I'd like to be
sure if any of them do. In particular, I'd like to see exactly what
part is failing. Is it the compilation of the DLL or something that
happens while the DLL is being used?

> python -i pest_test2.py

[SNIP]

File "/home/nwagner/svn/PyDSTool/PyDSTool/MProject.py",
line 1209, in Rhs
    return self.model.Rhs(t, xdict, pdict)

[SNIP]

> line 124, in __init__
>     datalist.append(coorddict[c][0])
> IndexError: invalid index to scalar variable.

Looks like the RHS function isn't working. Could you run this script
in pdb or a debugger, or at least put in some print statements here to
show me what t, xdict and pdict are when Rhs is called. And then,
inside Points, what coorddict and c are? This might be another Python
2.6 issue because there is some funky magic used to create some class
methods dynamically.


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