| Re: [stem-dev] stem-dev Digest, Vol 116, Issue 2 |
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Hi Jamie,
Thank you very much for offering to look at a example scenario, however, I've now managed to fix the problem with the external disease initialiser which seems to be working now in the GUI on a similar project. I think it may have been a problem with the way I edited the files in the recorded simulations file that I was using and/or with the location of the recorded simulations file that I wanted to use.
However, I am still having problems running it headless. I've been testing it on various machines, versions of STEM and using different project and I still get the same error. As you've said, after the STEM 4 branch has been merged it would be great if you were able to debug this.
Thank you so much for your help.
Best wishes,
Emily
Emily Nixon
PhD Student Demonstrator 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: 10 December 2018 18:26:50 To: stem-dev@xxxxxxxxxxx Subject: 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 Sent by: stem-dev-bounces@xxxxxxxxxxx Send stem-dev mailing list submissions to stem-dev@xxxxxxxxxxx To subscribe or unsubscribe via the World Wide Web, visit https://www.eclipse.org/mailman/listinfo/stem-dev or, via email, send a message with subject or body 'help' to stem-dev-request@xxxxxxxxxxx You can reach the person managing the list at stem-dev-owner@xxxxxxxxxxx When replying, please edit your Subject line so it is more specific than "Re: Contents of stem-dev digest..." 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 Message-ID: <VI1PR0601MB2352ED91162647E0377B7162BFA90@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx> Content-Type: text/plain; charset="iso-8859-1" Hi, 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, Emily 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(DecoratorImpl.java:276) at org.eclipse.stem.core.model.impl.ModelImpl.invokeNodeDecorators(ModelImpl.java:483) at org.eclipse.stem.core.model.impl.ModelImpl.getCanonicalGraph(ModelImpl.java:234) at org.eclipse.stem.core.model.impl.ModelImpl.getCanonicalGraph(ModelImpl.java:212) at org.eclipse.stem.core.scenario.impl.ScenarioImpl.initialize(ScenarioImpl.java:560) at org.eclipse.stem.jobs.simulation.SimulationManager.createSimulation(SimulationManager.java:326) at org.eclipse.stem.ui.headless.HeadlessSimulationRunner.runScenarios(HeadlessSimulationRunner.java:175) at org.eclipse.stem.ui.headless.Headles sSimulationRunner.run(HeadlessSimulationRunner.java:90) at org.eclipse.stem.ui.headless.HeadlessLauncher.launch(HeadlessLauncher.java:107) at org.eclipse.stem.core.common.presentation.CoreEditorAdvisor$Application.start(CoreEditorAdvisor.java:409) at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:380) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:235) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.eclips e.equinox.launcher.Main.invokeFramework(Main.java:648) at org.eclipse.equinox.launcher.Main.basicRun(Main.java:603) at org.eclipse.equinox.launcher.Main.run(Main.java:1465) at org.eclipse.equinox.launcher.Main.main(Main.java:1438) On the STEM GUI on the supercomputer (which is using STEM version Milestone 3.0.0M5) I can't seem to get infectors to work when they initialise from an external file: java.lang.ClassCastException: org.eclipse.emf.ecore.util.BasicInternalEList cannot be cast to org.eclipse.emf.ecore.EStructuralFeature$Setting at org.eclipse.emf.ecore.impl.BasicEObjectImpl.eSetting(BasicEObjectImpl.java:1596) at org.eclipse.emf.ecore.util.EcoreUtil$Copier.getTarget(EcoreUtil.java:562) at org.eclipse.emf.ecore.util.EcoreUtil$Copier.copyContainment(EcoreUtil.java:587) at org.eclipse.emf.ecore.util.EcoreUtil$Copier.copy(EcoreUtil.java:490) at org.eclipse.emf.ecore.util.EcoreUtil.copy(EcoreUtil.java:357) at org.eclipse.stem.core.scenario.impl.ScenarioImpl.initialize(ScenarioImpl.java:622) at org.eclipse.stem.jobs.simulation.SimulationManager.createSimulation(SimulationManager.java:326) at org.eclipse.stem.jobs.simulation.SimulationManager$2.run(SimulationManager.java:393) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54) 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(ExternalDataSourceDiseaseInitializerImpl.java:439) at org.eclipse.stem.diseasemodels.standard.impl.ExternalDataSourceDiseaseInitializerImpl.decorateGraph(ExternalDataSourceDiseaseInitializerImpl.java:323) at org.eclipse.stem.core.scenario.impl.ScenarioImpl.initialize(ScenarioImpl.java:633) at org.eclipse.stem.jobs.simulation.SimulationManager.createSimulation(SimulationManager.java:326) at org.eclipse.stem.jobs.simulation.SimulationManager$2.run(SimulationManager.java:393) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54) Emily Nixon PhD Student Demonstrator School of Biological Sciences University of Bristol Bristol Life Sciences Building 24 Tyndall Avenue Bristol BS8 1TQ Tel +44 (0)117 394 1389 -------------- next part -------------- An HTML attachment was scrubbed... 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