I have investigated this over the past few days and haven't managed to
solve the issue yet.
Just so you have a better idea of what modifications I am trying to implement-
I am trying to move all individuals of a subpopulation from one group of
nodes to another group of nodes. There is one trigger event per relevant
edge specified in the pajek graph.
As you know "When removing the triggers generated by my pajek graph,
the scenario runs normally. However, when the triggers are included in
the scenario, progress on the simulation control remains at 0% for a while
and then this error appears (see email below)." This is when using
the stochastic solver.
This is what I have found so far from following your suggestions:
* When I run the scenario using a deterministic solver,
it will run and complete a simulation. However, the triggers do not appear
to be implemented.
* I have further tested this with other smaller scenarios
and it does seem that triggers are not implemented with the deterministic
solver, whether you use absolute migration rates or not. However, the stochastic
solver does work on these smaller scenarios.
* Despite the stochastic solver working on the smaller scenarios,
I can never seem to get all of the subpopulation to move- there is always
a 0.99 (2dp) of an individual left, whether I use absolute migration rates
or not and when trying different values for the rates.
Let me know if you have any suggestions. I would rather not send my project
to the whole of STEM DEV, but if you would like to take a look at it then
let me know and I can send it to you. We can continue correspondence over
STEM DEV, so that others will be able to see how we solve the issue.
Thank you for all your help,
Emily Nixon PhD Student
School of Biological Sciences University of Bristol Bristol Life Sciences Building 24 Tyndall Avenue Bristol BS8 1TQ Tel +44 (0)117 394 1389 ________________________________ From: stem-dev-bounces@xxxxxxxxxxx <stem-dev-bounces@xxxxxxxxxxx>
on behalf of James Kaufman <jhkauf@xxxxxxxxxx> Sent: 28 January 2019 17:19:28 To: stem-dev@xxxxxxxxxxx Subject: Re: [stem-dev] stem-dev Digest, Vol 117, Issue 7
Hi Emily, The error is appearing in the BinomialDistribution code which is part of
the stochastic solver (not part of triggers/predicates/modifiers). Could you please test your scenario (including the triggers) using a deterministic
IF that passes then the problem is not triggers but most likely the convergence
theshold setting in the stochastic solver (which can cause also an apparant
OutOfRangeExceptioncan also indicate a problem with the epi model itself.
values in a compartment should never go below zero so please double check
all of your transitions and rates....
Finally, what is the modification you are triggering? Could this be causing
a compartment value to go negative? IF you are forcing a discontinous movement
of population you may not be able to use any integrating solver as there
could be a problem getting convergence around the discontinuity. If that's
the issue you need to make sure your modifier logic never causes a negative
From: stem-dev-request@xxxxxxxxxxx To: stem-dev@xxxxxxxxxxx Date: 01/28/2019 09:00 AM Subject: stem-dev Digest, Vol 117, Issue 7 Sent by: stem-dev-bounces@xxxxxxxxxxx ________________________________
Send stem-dev mailing list submissions to stem-dev@xxxxxxxxxxx
Message: 1 Date: Mon, 28 Jan 2019 16:36:21 +0000 From: Emily Nixon <emily.nixon@xxxxxxxxxxxxx> To: developer mailing list STEM <stem-dev@xxxxxxxxxxx> Subject: [stem-dev] Out of range error when using triggers Message-ID: <VI1PR0601MB2352807807A3AB21510AD868BF960@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>
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I was wondering if anyone knew what might be causing the error below when
I run my scenario "Jan19"?
When removing the triggers generated by my pajek graph, the scenario runs
normally. However, when the triggers are included in the scenario, progress
on the simulation control remains at 0% for a while and then this error
An internal error occurred during "Jan19" org.apache.commons.math3.exception.OutOfRangeException: -0.045 out of [0,
1] range at org.apache.commons.math3.distribution.BinomialDistribution.<init>(BinomialDistribution.java:75) at org.eclipse.stem.core.math.BinomialDistributionUtil.fastPickFromBinomialDist(BinomialDistributionUtil.java:76) at org.eclipse.stem.solvers.stochastic.impl.StandardStochasticImpl.step(StandardStochasticImpl.java:228) at org.eclipse.stem.core.scenario.impl.ScenarioImpl.step(ScenarioImpl.java:395) at org.eclipse.stem.jobs.simulation.Simulation.run(Simulation.java:313) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54)
I've had a go at troubleshooting this for a while and have run out of ideas
of what to try next to get it to work.
If anyone has any ideas of what the issue might be, then please let me
know and I will try to investigate further!