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We observed this exception in our product. !ENTRY org.eclipse.core.resources 4 2 2020-08-04 16:06:06.305 !MESSAGE Problems occurred when invoking code from plug-in: "org.eclipse.core.resources". !STACK 0 java.util.ConcurrentModificationException at java.util.HashMap$HashIterator.nextNode(HashMap.java:1442) at java.util.HashMap$KeyIterator.next(HashMap.java:1466) at org.eclipse.jdt.internal.core.JavaModelManager.secondaryTypesRemoving(JavaModelManager.java:5115) at org.eclipse.jdt.internal.core.DeltaProcessor.updateIndex(DeltaProcessor.java:2838) at org.eclipse.jdt.internal.core.DeltaProcessor.updateIndex(DeltaProcessor.java:2780) at org.eclipse.jdt.internal.core.DeltaProcessor.updateCurrentDeltaAndIndex(DeltaProcessor.java:2596) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2313) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2363) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2363) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2363) at org.eclipse.jdt.internal.core.DeltaProcessor.processResourceDelta(DeltaProcessor.java:1964) at org.eclipse.jdt.internal.core.DeltaProcessor.resourceChanged(DeltaProcessor.java:2138) at org.eclipse.jdt.internal.core.DeltaProcessingState.resourceChanged(DeltaProcessingState.java:477) at org.eclipse.core.internal.events.NotificationManager$1.run(NotificationManager.java:305) at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:45) at org.eclipse.core.internal.events.NotificationManager.notify(NotificationManager.java:295) at org.eclipse.core.internal.events.NotificationManager.broadcastChanges(NotificationManager.java:158) at org.eclipse.core.internal.resources.Workspace.broadcastPostChange(Workspace.java:379) at org.eclipse.core.internal.resources.Workspace.endOperation(Workspace.java:1502) at org.eclipse.core.internal.resources.Resource.delete(Resource.java:780) at org.eclipse.xtext.builder.BuilderParticipant.cleanOutput(BuilderParticipant.java:495) I can reproduce a race condition with breakpoints, when adding secondary types and clean building. I see the following concurrent stack traces while debugging: "Java indexing" #47 daemon prio=4 os_prio=0 tid=0x00007ffff3e95000 nid=0x192ff at breakpoint[0x00007fff8729b000] java.lang.Thread.State: RUNNABLE at org.eclipse.jdt.internal.core.JavaModelManager.secondaryTypeAdding(JavaModelManager.java:4807) at org.eclipse.jdt.internal.core.search.indexing.AbstractIndexer.addTypeDeclaration(AbstractIndexer.java:235) at org.eclipse.jdt.internal.core.search.indexing.AbstractIndexer.addClassDeclaration(AbstractIndexer.java:50) at org.eclipse.jdt.internal.core.search.indexing.SourceIndexer.indexResolvedDocument(SourceIndexer.java:227) at org.eclipse.jdt.internal.core.search.JavaSearchParticipant.indexResolvedDocument(JavaSearchParticipant.java:84) at org.eclipse.jdt.internal.core.search.indexing.IndexManager.indexResolvedDocument(IndexManager.java:558) at org.eclipse.jdt.internal.core.search.indexing.IndexManager$1.execute(IndexManager.java:1080) at org.eclipse.jdt.internal.core.search.processing.JobManager.run(JobManager.java:401) at java.lang.Thread.run(Thread.java:748) "Worker-27: Updating workspace" #509 prio=5 os_prio=0 tid=0x000055555666d800 nid=0x2bd1f at breakpoint[0x00007fff8adc0000] java.lang.Thread.State: RUNNABLE at org.eclipse.jdt.internal.core.JavaModelManager.secondaryTypesRemoving(JavaModelManager.java:5124) at org.eclipse.jdt.internal.core.DeltaProcessor.updateIndex(DeltaProcessor.java:2838) at org.eclipse.jdt.internal.core.DeltaProcessor.updateIndex(DeltaProcessor.java:2780) at org.eclipse.jdt.internal.core.DeltaProcessor.updateCurrentDeltaAndIndex(DeltaProcessor.java:2596) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2313) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2363) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2363) at org.eclipse.jdt.internal.core.DeltaProcessor.processResourceDelta(DeltaProcessor.java:1964) at org.eclipse.jdt.internal.core.DeltaProcessor.resourceChanged(DeltaProcessor.java:2138) at org.eclipse.jdt.internal.core.DeltaProcessingState.resourceChanged(DeltaProcessingState.java:477) at org.eclipse.core.internal.events.NotificationManager$1.run(NotificationManager.java:305) at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:45) at org.eclipse.core.internal.events.NotificationManager.notify(NotificationManager.java:295) at org.eclipse.core.internal.events.NotificationManager.broadcastChanges(NotificationManager.java:158) at org.eclipse.core.internal.resources.Workspace.broadcastPostChange(Workspace.java:379) at org.eclipse.core.internal.resources.Workspace.endOperation(Workspace.java:1502) at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2308) at org.eclipse.core.internal.events.NotificationManager$NotifyJob.run(NotificationManager.java:44) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63) So far I cannot reproduce this with pure JDT. The clean build in JDT seems to result in calling "JavaModelManager.secondaryTypesRemoving()" only with "cleanIndexCache = false". I'm guessing our xtext-based build does cleaning up differently (it generates Java code, in the exception stack trace above it cleans up what it generated, including secondary types it generated).
Simeon, could you please provide stack based on master / I-build? Should be possible if you use e4x branch. The stack trace seem to be from 4.12 Eclipse.
Here is a stack trace from a newer build: java.util.ConcurrentModificationException at java.base/java.util.HashMap$HashIterator.nextNode(HashMap.java:1493) at java.base/java.util.HashMap$KeyIterator.next(HashMap.java:1516) at org.eclipse.jdt.internal.core.JavaModelManager.secondaryTypesRemoving(JavaModelManager.java:5100) at org.eclipse.jdt.internal.core.DeltaProcessor.updateIndex(DeltaProcessor.java:2855) at org.eclipse.jdt.internal.core.DeltaProcessor.updateIndex(DeltaProcessor.java:2797) at org.eclipse.jdt.internal.core.DeltaProcessor.updateCurrentDeltaAndIndex(DeltaProcessor.java:2613) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2330) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2380) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2380) at org.eclipse.jdt.internal.core.DeltaProcessor.processResourceDelta(DeltaProcessor.java:1981) at org.eclipse.jdt.internal.core.DeltaProcessor.resourceChanged(DeltaProcessor.java:2155) at org.eclipse.jdt.internal.core.DeltaProcessingState.resourceChanged(DeltaProcessingState.java:477) at org.eclipse.core.internal.events.NotificationManager$1.run(NotificationManager.java:305) at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:45) at org.eclipse.core.internal.events.NotificationManager.notify(NotificationManager.java:295) at org.eclipse.core.internal.events.NotificationManager.broadcastChanges(NotificationManager.java:158) at org.eclipse.core.internal.resources.Workspace.broadcastPostChange(Workspace.java:380) at org.eclipse.core.internal.resources.Workspace.endOperation(Workspace.java:1502) at org.eclipse.core.internal.resources.InternalWorkspaceJob.run(InternalWorkspaceJob.java:49) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)
New Gerrit change created: https://git.eclipse.org/r/c/jdt/eclipse.jdt.core/+/170198
OK, got feedback from Christian on how to reproduce in pure JDT (which didn't occur to me). 1. Set JDT core breakpoints as follows: 1.1. at line "indexedSecondaryTypes.put((IFile) resource, allTypes);" in JavaModelManager.secondaryTypeAdding(String, char[], char[]) 1.2. at line "IFile cachedFile = cachedFiles.next();" in JavaModelManager.secondaryTypesRemoving(IFile, boolean) 2. Debug Eclipse in a clean workspace. 3. Create a Java project. 4. Create 2 classes "Test1" and "Test2". 5. Add a secondary type in Test1.java: class Test1Secondary { } 6. Add a secondary type in Test2.java: class Test2Secondary { } 7. Observe breakpoint hit in secondaryTypeAdding(), resume *once*, observe another breakpoint hit (due to the 2nd secondary type). 8. From the Package Explorer, delete Test1.java and Test2.java. 9. Observe a breakpoint hit in secondaryTypesRemoving(). 10. Resume the thread suspended at in secondaryTypeAdding(). 11. Resume the thread suspended at secondaryTypesRemoving(), observe exception in the log: !ENTRY org.eclipse.core.resources 4 2 2020-10-02 10:56:30.934 !MESSAGE Problems occurred when invoking code from plug-in: "org.eclipse.core.resources". !STACK 0 java.util.ConcurrentModificationException at java.base/java.util.HashMap$HashIterator.nextNode(HashMap.java:1493) at java.base/java.util.HashMap$KeyIterator.next(HashMap.java:1516) at org.eclipse.jdt.internal.core.JavaModelManager.secondaryTypesRemoving(JavaModelManager.java:5100) at org.eclipse.jdt.internal.core.DeltaProcessor.updateIndex(DeltaProcessor.java:2855) at org.eclipse.jdt.internal.core.DeltaProcessor.updateCurrentDeltaAndIndex(DeltaProcessor.java:2613) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2330) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2380) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2380) at org.eclipse.jdt.internal.core.DeltaProcessor.traverseDelta(DeltaProcessor.java:2380) at org.eclipse.jdt.internal.core.DeltaProcessor.processResourceDelta(DeltaProcessor.java:1981) at org.eclipse.jdt.internal.core.DeltaProcessor.resourceChanged(DeltaProcessor.java:2155) at org.eclipse.jdt.internal.core.DeltaProcessingState.resourceChanged(DeltaProcessingState.java:477) at org.eclipse.core.internal.events.NotificationManager$1.run(NotificationManager.java:305) at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:45) at org.eclipse.core.internal.events.NotificationManager.notify(NotificationManager.java:295) at org.eclipse.core.internal.events.NotificationManager.broadcastChanges(NotificationManager.java:158) at org.eclipse.core.internal.resources.Workspace.broadcastPostChange(Workspace.java:380) at org.eclipse.core.internal.resources.Workspace.checkpoint(Workspace.java:575) at org.eclipse.ltk.core.refactoring.PerformChangeOperation.lambda$0(PerformChangeOperation.java:263) at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2292) at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2317) at org.eclipse.ltk.core.refactoring.PerformChangeOperation.executeChange(PerformChangeOperation.java:295) at org.eclipse.ltk.internal.ui.refactoring.UIPerformChangeOperation.executeChange(UIPerformChangeOperation.java:94) at org.eclipse.ltk.core.refactoring.PerformChangeOperation.run(PerformChangeOperation.java:219) at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2292) at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2317) at org.eclipse.ltk.internal.ui.refactoring.WorkbenchRunnableAdapter.run(WorkbenchRunnableAdapter.java:89) at org.eclipse.jface.operation.ModalContext$ModalContextThread.run(ModalContext.java:122)
Gerrit change https://git.eclipse.org/r/c/jdt/eclipse.jdt.core/+/170198 was merged to [master]. Commit: http://git.eclipse.org/c/jdt/eclipse.jdt.core.git/commit/?id=e59811a5cf43566d5300a91fc0b632e557a64348
Simeon, how are things in your setup? I know you provided the fix. Anyway, if you can confirm things are good, can you mark this one as verified? TIA!
I've checked with the reproduction steps from comment 4, the problem is fixed (we no longer iterate over the collection during removal; the collection is also now synchronized).
