[SciPy-user] Eigenvalues of the Floquet matrix

Nils Wagner nwagner at iam.uni-stuttgart.de
Mon Mar 16 14:30:01 EDT 2009 

On Mon, 16 Mar 2009 14:26:18 -0400
  Rob Clewley <rob.clewley at gmail.com> wrote:
>> 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.
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-user

Here is the output of interp_dopri_test.py

gdb python
GNU gdb (GDB; openSUSE 11.1) 6.8.50.20081120-cvs
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and 
redistribute it.
There is NO WARRANTY, to the extent permitted by law. 
 Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
For bug reporting instructions, please see:
<http://bugs.opensuse.org/>...
(no debugging symbols found)
(gdb) run interp_dopri_test.py
Starting program: /usr/bin/python interp_dopri_test.py
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
[Thread debugging using libthread_db enabled]
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
/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]
-------- Test: InterpolateTable
names for variables: xnames =  ['x1', 'x2']
timeData =  [  0.  11.  20.  30.]
x1data =  [ 10.2  -1.4   4.1   6. ]
x2data =  [ 0.1   0.01  0.4  -0.8 ]
interptable.variables['x1'](0.4) =  9.77818181818

itabletraj(11, ['x1']) =  x1:  -1.4  (preferred syntax)

-------- Test: ODE system


Information for Contents

algparams:
     init_step: 0.02
checklevel: 2
fnspecs:
     auxval1: ([t, x], if(x>100,2*cos(10*t/pi),-0.5))
     auxval2: ([x], x/2)
ics:
     w: 30.0
     y: 80
inputs: Variable x1(t)
name: ODEtest
pars:
     a: 2
     k: 1
tdata: [0, 10]
tdomain: [0, 20]
varspecs:
     w: 100 -(1+a)*w*heav(0.2-sin(t+1)) -2*x1 
-k*auxval1(t, w)*auxval2(y)
     y: 50 - (w/100)*y
xdomain:
     w: [0, 340]
     y: [0, 150]


Integrating...

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff7b14cab in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.6.so.1.0
(gdb) bt
#0  0x00007ffff7b14cab in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.6.so.1.0
#1  0x00007ffff7b1b6c0 in PyEval_EvalCodeEx () from 
/usr/lib64/libpython2.6.so.1.0
#2  0x00007ffff7b14f24 in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.6.so.1.0
#3  0x00007ffff7b1b6c0 in PyEval_EvalCodeEx () from 
/usr/lib64/libpython2.6.so.1.0
#4  0x00007ffff7b14f24 in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.6.so.1.0
#5  0x00007ffff7b1b6c0 in PyEval_EvalCodeEx () from 
/usr/lib64/libpython2.6.so.1.0
#6  0x00007ffff7b13822 in PyEval_EvalCode () from 
/usr/lib64/libpython2.6.so.1.0
#7  0x00007ffff7b34b13 in ?? () from 
/usr/lib64/libpython2.6.so.1.0
#8  0x00007ffff7b34bca in PyRun_FileExFlags () from 
/usr/lib64/libpython2.6.so.1.0
#9  0x00007ffff7b3550d in PyRun_SimpleFileExFlags () from 
/usr/lib64/libpython2.6.so.1.0
#10 0x00007ffff7b40dba in Py_Main () from 
/usr/lib64/libpython2.6.so.1.0
#11 0x00007ffff6e94586 in __libc_start_main () from 
/lib64/libc.so.6
#12 0x00000000004006e9 in _start ()
  
Nils

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