MATLAB: Simulation stop criteria for simfunctions and sbiofit

maximumwallclockSimBiology

Hello,

A few questions that are related to each other:

Does the 'MaximumWallClock' property (https://www.mathworks.com/help/simbio/ref/maximumwallclock.html) apply only to 'sbiosimulate', or also to simfunctions and 'sbiofit'?
If it does apply to simfunctions, would the specification of output times in the call of the simfunction override the MaximumWallClock setting, as suggested to be the case for 'sbiosimulate' in the link above?
If the 'MaximumWallClock' property is used in 'sbiofit', what is the objective function value assigned to a failed simulation?

Thank you,

Abed

Best Answer

Hi Abed,

Interesting questions -

Yes, most settings are inherited from the active configset. The most notable exceptions are the states and sensitivities that get logged, and the stop time/output times. So, MaximumWallClock should apply to all simulations for both SimFunction and sbiofit simulations.
As always, the simulation runs until any of the stop criteria are met. So there’s no concept of “overruling.” If a simulation takes longer than the maximumWallClock time, simulation results are returned for whatever output times have been reached.
Sbiofit detects when a simulation ends early and returns an objective function value of Inf, so that the optimizer will reject this condition as an optimum. Using a maximumWallClock time for sbiofit is generally a good idea to avoid the ODE solver getting stuck on implausible simulation results.

Best,

Sietse

Related Solutions

MATLAB: Using MaximumWallClock in a loop

There is no built-in flag but you could exclude any simulation for which the final time step does not equal your stop-time. Let me know if that answers your question.

MATLAB: Stopping simulation early on event

Hi Abed,

Interesting question. The only way an event can stop a simulation early is if the event errors. sbiofit would handle such a siutation by returning Inf for the objective function value. Since you mentioned fitting, I generally recommend setting MaximumWallClock during fitting to ensure that things don't get stuck if a fit encounters a bad parameter value that results in a really long running simulation.

Ok, back to a simulation that errors. The only tricky thing with that is creating an event that is compatible with SimBiology's acceleration (that is, with the subset of the MATLAB language that can be used for code generation). Here's an example of modifying the Lotka-Volterra model to end early due to an event:

First, save the following function to myfunction.m:

function time = myfunction(time)
if time >= 0
    error("Ending simulation at time " + time);
end

Then, execute the following:

sbioloadproject('lotka');
threshold = m1.addparameter('threshold',1e6);
m1.addevent('y1 > threshold', 'z = myfunction(time)');
sbioaccelerate(m1);         % Ensure this model can be accelerated
simdata = sbiosimulate(m1); % Runs to completion
threshold.Value = 1e3;
simdata = sbiosimulate(m1); % Simulation errors

Best Answer

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MATLAB: Using MaximumWallClock in a loop

MATLAB: Stopping simulation early on event

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