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Andrew Miller wrote:
> Shane Blackett wrote:
>> Hopefully your maximum step size and your tabulation step size are much
>> larger than the step size sometimes used by the adaptive integrator.
>> Here forcing results to come back at a fixed spacing forces you not to
>> capture this signal properly in your graphs. This seems really
>> unfortunate, you may have correctly integrated a complicated action
>> potential and then you draw a graph which completely misses it! This
>> seems really bad. Isn't it much better is to concentrate your line
>> segments in your graph in exactly the same places where the adaptive
>> step size system found your solution to be complicated?
>>
> I have been looking into alternative approaches for choosing which
> points to send, taking the general idea behind Shane's suggestion (since
> providing the integrator is the point behind the first release, this is
> essential). When we find a good method, it would be useful to put that
> into some other type of metadata specification (probably not the
> simulation metadata) so that similar results can be reproduced.

Does this kind of information belong in the graph metadata? I guess you
can look at the simulation metadata as describing how a certain set of
data can be generated from a model and the graph metadata as one way to
represent such data (or sets of data). Then software is free to combine
both the simulation metadata and graph metadata in order to determine
how to perform a simulation (or set of simulations) and present the
results in such a way as to meet the requirements of both sets of metadata.

> I also noticed that we do not have any way to specify error control
> parameters. I guess that this is genuinely simulation metadata, although
> unfortunately it is somewhat dependent on the error control method
> chosen. Are there any objections to leaving this out of the metadata
> used for the first release of PCEnv? (it currently only extracts the
> bound variable starting and ending time points). The CIS supports a
> maximum step size, although it isn't on the UI now (the flow is
> currently metadata => UI => CIS, although I could add hidden state to
> pass through the UI if it was useful).

I think it makes sense to leave error control out for the first release.
While error control is an important piece of simulation metadata, I
generally find that all the models I work with will at least run and
produce consistent results with a reasonable default error tolerance. I
think there are quite a few issues to think through in terms of
specifying the error control to be used in a given simulation. The
actual error control used in most standard integration packages
available is generally pretty internal to the package and only exposed
via the user being able to specify relative and absolute tolerances
either as scalars or vectors. So error control will probably always be
tied to the integrator you choose to use, which has already been dropped
from the requirements for the first release of PCEnv.

If with the above comments you are saying the PCEnv provides no way for
the user to control the maximum step size used in the integration, then
I think such functionality is definitely required as that is one of the
main parameters in determining the success of a model's integration. If,
on the other hand, you're just saying the the user can control it but it
won't be read from the model metadata then I guess that is ok for the
first release of PCEnv.


Andre.

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• [cellml-discussion] Summary of simulation metadata meeting, David Nickerson, 09/07/2006
  • [cellml-discussion] Summary of simulation metadata meeting, Andrew Miller, 09/08/2006

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