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Re: [stem-dev] stem-dev Digest, Vol 116, Issue 2

Hi Emily,
As we discussed on the call we will be happy to debug this once we have merged the STEM 4 branch back to head.
The fact that you see this running locally (with a large external data file) with GUI suggests we should check you scenario configuration. Maybe you could upload an archive of a non-confidential scenario that shows the bug. That would help us find the issue most quickly.

From:        stem-dev-request@xxxxxxxxxxx
To:        stem-dev@xxxxxxxxxxx
Date:        12/06/2018 09:00 AM
Subject:        stem-dev Digest, Vol 116, Issue 2
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Today's Topics:

  1. STEM CALL TODAY: Error Log for my Items for Participants
     section (Emily Nixon)


Message: 1
Date: Thu, 6 Dec 2018 16:55:12 +0000
From: Emily Nixon <emily.nixon@xxxxxxxxxxxxx>
To: developer mailing list STEM <stem-dev@xxxxxxxxxxx>
Subject: [stem-dev] STEM CALL TODAY: Error Log for my Items for
                Participants                 section
Content-Type: text/plain; charset="iso-8859-1"


For those on the STEM call today, I just wanted to send some error logs that I would like to discuss during my items for participants section, as it is much easier if you can see these in front of you during the call.

Looking forward to talking soon.

Best wishes,


I have a scenario which runs on my PC, but will not run on a supercomputer. I am testing this scenario on the supercomputer because it is similar to another scenario that I need to run on there (that is too big to run on my PC).

I need to have an external data source to initialise the data in both scenarios and I need to ultimately be running them headless and not on the GUI of the supercomputer. I could only get the test scenario with an infector that doesn't use an external data source to work and only on the GUI, not when running headless.

When running the test scenario headless on a supercomputer (that works when run on the STEM GUI on the supercomputer) I get this error:

!ENTRY org.eclipse.stem.core 4 0 2018-12-06 16:34:20.924 !MESSAGE decorateGraph() not implemented in "null" of type "org.eclipse.stem.core.model.impl.NodeDecoratorImpl" Error creating simulation for URI platform:/resource/GBJune2018/scenarios/FrenchcomparisonDiseaseInitialzer.scenario java.lang.UnsupportedOperationException at org.eclipse.stem.core.model.impl.DecoratorImpl.decorateGraph( at org.eclipse.stem.core.model.impl.ModelImpl.invokeNodeDecorators( at org.eclipse.stem.core.model.impl.ModelImpl.getCanonicalGraph( at org.eclipse.stem.core.model.impl.ModelImpl.getCanonicalGraph( at org.eclipse.stem.core.scenario.impl.ScenarioImpl.initialize( at at org.eclipse.stem.ui.headless.HeadlessSimulationRunner.runScenarios( at org.eclipse.stem.ui.headless.Headles at org.eclipse.stem.ui.headless.HeadlessLauncher.launch( at org.eclipse.stem.core.common.presentation.CoreEditorAdvisor$Application.start( at at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication( at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start( at at at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke( at sun.reflect.DelegatingMethodAccessorImpl.invoke( at java.lang.reflect.Method.invoke( at org.eclips
e.equinox.launcher.Main.invokeFramework( at org.eclipse.equinox.launcher.Main.basicRun( at at org.eclipse.equinox.launcher.Main.main(

On the STEM GUI on the supercomputer (which is using STEM version Milestone 3.0.0M5) I can't seem to get infectors to work when they initialise from an external file:

java.lang.ClassCastException: org.eclipse.emf.ecore.util.BasicInternalEList cannot be cast to org.eclipse.emf.ecore.EStructuralFeature$Setting at org.eclipse.emf.ecore.impl.BasicEObjectImpl.eSetting( at org.eclipse.emf.ecore.util.EcoreUtil$Copier.getTarget( at org.eclipse.emf.ecore.util.EcoreUtil$Copier.copyContainment( at org.eclipse.emf.ecore.util.EcoreUtil$Copier.copy( at org.eclipse.emf.ecore.util.EcoreUtil.copy( at org.eclipse.stem.core.scenario.impl.ScenarioImpl.initialize( at at$ at

I can't seem to get external disease initializers to work either on the STEM GUI on the supercomputer:

java.lang.NullPointerException at org.eclipse.stem.diseasemodels.standard.impl.ExternalDataSourceDiseaseInitializerImpl.getCompartmentValues( at org.eclipse.stem.diseasemodels.standard.impl.ExternalDataSourceDiseaseInitializerImpl.decorateGraph( at org.eclipse.stem.core.scenario.impl.ScenarioImpl.initialize( at at$ at

Emily Nixon
PhD Student


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Tel +44 (0)117 394 1389
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