Parallel Chunk Loop crashes with "LocalToolExecutor: Error in stream gobbler."

lars20070 · September 5, 2018, 6:58am

The workflow below crashes with “LocalToolExecutor: Error in stream gobbler.” See screenshot and Log below. The workflow is nearly identical to the one in issue crash in Parallel Chunk End (multiple port) Only the “Parallel Chunk End (multiport)” was in replaced by the simpler “Parallel Chunk End”. The example workflow and input data were provided with the previous issue.

gist.github.com

https://gist.github.com/lars20070/0f5b372d6069395d5296f3f38eef0044

KnimeErrorLog

2018-09-04 18:10:10,792 : DEBUG : main : Node : Virtual Start : 0:54:1 : clean output ports.
2018-09-04 18:10:10,792 : DEBUG : KNIME-Workflow-Notifier : WorkflowEditor :  :  : Workflow event triggered: WorkflowEvent [type=NODE_REMOVED;node=0;old=(WFM) Parallel Chunks 0:54 (IDLE);new=null;timestamp=04-Sep-2018 18:10:10]
2018-09-04 22:16:54,322 : WARN  : pool-2-thread-1 : KNIMEApplication$4 :  :  : Potential deadlock in AWT Event Queue detected. Full thread dump will follow as debug output.
2018-09-04 22:16:54,322 : WARN  : pool-1-thread-1 : KNIMEApplication$3 :  :  : Potential deadlock in SWT Display thread detected. Full thread dump will follow as debug output.
2018-09-04 22:16:54,325 : DEBUG : pool-1-thread-1 : KNIMEApplication$3 :  :  : "AWT-EventQueue-0" Id=2648 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@2d72a840
	at sun.misc.Unsafe.park(Native Method)
	-  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@2d72a840
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
	at java.awt.EventQueue.getNextEvent(EventQueue.java:554)

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AlexanderFillbrunn · September 5, 2018, 7:18am

Hi,
The class LocalToolExecutor is a part of the Generic KNIME Nodes plugin by the OpenMS and SeqAn guys. The error occurs in one of their nodes and the Parallel Chunk Loop End just reports that one of the nodes within the loop crashed. You have to check the content of the meta node created by the chunk loop start for errors.
Kind regards
Alexander

lars20070 · September 5, 2018, 9:19am

In a second run, the crash was not reproducible. Workflow did execute alright.

system · September 12, 2018, 9:19am

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