[Freefluo-users] Problems Executing Workflow with Implicit Iteration

[Tim T. <tim...@ed...>]

Hi,

I posted this to the taverna hackers mailing list a while ago with no  
response. Apologies for cross-posting but I was hoping I may have  
more luck here as from what I can tell the issue is more closely tied  
to freefluo.

I am using Taverna to build and execute a workflow which uses  
implicit iteration. In this workflow i specify an array of Strings as  
input to a nested workflow which accepts a String as input. The array  
is of size 200 so it should iterate 200 times. I have run this  
workflow numerous times using the same services and data sets each  
time. With each invocation it iterates a seemingly random number of  
times before stating the workflow has completed successfully.

I run Taverna from the command line in linux. Just before the  
workflow dies I see the following error written to the terminal (see  
below). It seems as though the freefluo enactment engine is having  
some issues with threading. Anyone else encounter this problem? Any  
known work-arounds or fixes?


Thanks,

Tim

Exception in thread "Thread-1171"  
java.lang.ArrayIndexOutOfBoundsException
         at java.lang.System.arraycopy(Native Method)
         at java.util.ArrayList.toArray(ArrayList.java:305)
         at org.embl.ebi.escience.scufl.ScuflModel.getProcessors 
(ScuflModel.java:341)
         at org.embl.ebi.escience.scufl.Processor.<init> 
(Processor.java:492)
         at  
org.embl.ebi.escience.scuflworkers.beanshell.BeanshellProcessor.<init> 
(BeanshellProcessor.java:38)
         at  
org.embl.ebi.escience.scuflworkers.beanshell.BeanshellXMLHandler.loadPro 
cessorFromXML(BeanshellXMLHandler.java:91)
         at  
org.embl.ebi.escience.scuflworkers.ProcessorHelper.loadProcessorFromXML( 
ProcessorHelper.java:416)
         at  
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run 
(XScuflParser.java:446)
Exception in thread "Thread-1175"  
java.lang.ArrayIndexOutOfBoundsException
         at java.lang.System.arraycopy(Native Method)
         at java.util.ArrayList.toArray(ArrayList.java:305)
         at org.embl.ebi.escience.scufl.ScuflModel.getProcessors 
(ScuflModel.java:341)
         at org.embl.ebi.escience.scufl.Processor.<init> 
(Processor.java:492)
         at  
org.embl.ebi.escience.scuflworkers.java.LocalServiceProcessor.<init> 
(LocalServiceProcessor.java:46)
         at  
org.embl.ebi.escience.scuflworkers.java.LocalServiceXMLHandler.loadProce 
ssorFromXML(LocalServiceXMLHandler.java:60)
         at  
org.embl.ebi.escience.scuflworkers.ProcessorHelper.loadProcessorFromXML( 
ProcessorHelper.java:416)
         at  
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run 
(XScuflParser.java:446)
text/plain
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ERROR                                      2006-01-25 14:46:24,897  
(uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser: 
82) - Serious error compiling workflow.
org.embl.ebi.escience.scufl.UnknownProcessorException: Unable to  
locate processor with name 'FuzzPath1'
         at org.embl.ebi.escience.scufl.ScuflModel.locateProcessor 
(ScuflModel.java:587)
         at org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate 
(ScuflModel.java:561)
         at org.embl.ebi.escience.scufl.DataConstraint.<init> 
(DataConstraint.java:32)
         at org.embl.ebi.escience.scufl.parser.XScuflParser.populate 
(XScuflParser.java:369)
         at org.embl.ebi.escience.scufl.parser.XScuflParser.populate 
(XScuflParser.java:85)
         at  
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p 
arse(TavernaScuflModelParser.java:78)
         at uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile 
(EngineImpl.java:128)
         at  
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy. 
compileWorkflow(FreefluoEnactorProxy.java:100)
         at  
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy. 
compileWorkflow(FreefluoEnactorProxy.java:91)
         at  
org.embl.ebi.escience.scuflworkers.workflow.WorkflowTask.execute 
(WorkflowTask.java:97)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:462)
at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:407)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:329)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingle 
Iteration(ProcessorTask.java:878)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access 
$000(ProcessorTask.java:88)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run 
(ProcessorTask.java:690)
ERROR                                      2006-01-25 14:46:24,898  
(uk.ac.soton.itinnovation.freefluo.main.EngineImpl:147) - Serio
us error compiling workflow.
java.lang.RuntimeException: Serious error compiling workflow.
         at  
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p 
arse(TavernaScuflModelParser.java:83)
         at uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile 
(EngineImpl.java:128)
         at  
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy. 
compileWorkflow(FreefluoEnactorProxy.java:100)
         at  
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy. 
compileWorkflow(FreefluoEnactorProxy.java:91)
         at  
org.embl.ebi.escience.scuflworkers.workflow.WorkflowTask.execute 
(WorkflowTask.java:97)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:462)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:407)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:329)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingle 
Iteration(ProcessorTask.java:878)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access 
$000(ProcessorTask.java:88)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run 
(ProcessorTask.java:690)
Caused by: org.embl.ebi.escience.scufl.UnknownProcessorException:  
Unable to locate processor with name 'FuzzPath1'
         at org.embl.ebi.escience.scufl.ScuflModel.locateProcessor 
(ScuflModel.java:587)
         at org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate 
(ScuflModel.java:561)
         at org.embl.ebi.escience.scufl.DataConstraint.<init> 
(DataConstraint.java:32)
         at org.embl.ebi.escience.scufl.parser.XScuflParser.populate 
(XScuflParser.java:369)
         at org.embl.ebi.escience.scufl.parser.XScuflParser.populate 
(XScuflParser.java:85)
         at  
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p 
arse(TavernaScuflModelParser.java:78)
         ... 10 more
java.lang.RuntimeException: Serious error compiling workflow.
         at uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile 
(EngineImpl.java:148)
         at  
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy. 
compileWorkflow(FreefluoEnactorProxy.java:100)
         at  
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy. 
compileWorkflow(FreefluoEnactorProxy.java:91)
         at  
org.embl.ebi.escience.scuflworkers.workflow.WorkflowTask.execute 
(WorkflowTask.java:97)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:462)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:407)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:329)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingle 
Iteration(ProcessorTask.java:878)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access 
$000(ProcessorTask.java:88)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run 
(ProcessorTask.java:690)
Caused by: java.lang.RuntimeException: Serious error compiling workflow.
         at  
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p 
arse(TavernaScuflModelParser.java:83)
         at uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile 
(EngineImpl.java:128)
         ... 9 more
Caused by: org.embl.ebi.escience.scufl.UnknownProcessorException:  
Unable to locate processor with name 'FuzzPath1'
         at org.embl.ebi.escience.scufl.ScuflModel.locateProcessor 
(ScuflModel.java:587)
         at org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate 
(ScuflModel.java:561)
         at org.embl.ebi.escience.scufl.DataConstraint.<init> 
(DataConstraint.java:32)
         at org.embl.ebi.escience.scufl.parser.XScuflParser.populate 
(XScuflParser.java:369)
         at org.embl.ebi.escience.scufl.parser.XScuflParser.populate 
(XScuflParser.java:85)
         at  
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p 
arse(TavernaScuflModelParser.java:78)
         ... 10 more
java.lang.IllegalStateException: Can't overwrite cause
         at java.lang.Throwable.initCause(Throwable.java:320)
         at  
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy. 
compileWorkflow(FreefluoEnactorProxy.java:116)
         at  
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy. 
compileWorkflow(FreefluoEnactorProxy.java:91)
         at  
org.embl.ebi.escience.scuflworkers.workflow.WorkflowTask.execute 
(WorkflowTask.java:97)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:462)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:407)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:329)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingle 
Iteration(ProcessorTask.java:878)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access 
$000(ProcessorTask.java:88)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run 
(ProcessorTask.java:690)
Thread[Thread-326,6,main] completed
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