[SciPy-user] integrate.odeint problem

Johann Rohwer jr@sun.ac...
Mon Feb 16 07:47:52 CST 2009

Hi Peter

Try increasing the parameter mxstep (default is 500) in the odeint 
function call to a higher value (such as 1000 or 3000). We are using 
SciPy's odeint in our Python based systems biology simulation 
software PySCeS (http://pysces.sf.net) and have found quite regularly 
for biological models that an mxstep value of 500 is insufficient. 
Incidentally, when PySCeS encounters this situation, it automatically 
increments the mxstep value and re-simulates....

In general, we have been able to get good agreement with PySCeS and 
Jarnac simulating the same model, so I'd be surprised if this does 
not fix it. 


On Monday, 16 February 2009, Peter Cimermančič wrote:
> Hi!
> Using 60 differential equations, I am trying to simulate some
> biological process. After running the script, I've got next
> message:
> lsoda-- at current t (=r1), mxstep (=i1) steps
>        taken on this call before reaching tout
>        In above message, I1 =                  500
>        In above message, R1 = 0.857...E+01
> Excess work done on this call (Perhaps wrong Dfun type).
> Run with full_output = 1 to get quantitative information.
> After running with full_output = 1, additional information was:
> KeyError: 0.
> The same equations and parameters were run in Jarnac (simulation
> software) and I've got correct results, assuming equations and
> parameters are right. What else could go wrong to produce above
> error message?
> Thank you in advance,
> Peter

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