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From "Shinyoung Ahn (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (AIRAVATA-821) Airavata do not execute applications in parallel
Date Tue, 30 Apr 2013 07:46:16 GMT

    [ https://issues.apache.org/jira/browse/AIRAVATA-821?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13645355#comment-13645355
] 

Shinyoung Ahn commented on AIRAVATA-821:
----------------------------------------

Hi Lahiru! 
I test the trunk version for parallel execution. it seems work in parallel
but I got another errors such like
-----------------------------------------------------------------------------------------------------------
<ns:sendingFault infoModelVersion="2.6"
  xmlns:ns="http://airavata.apache.org/schemas/wft/2011/08">
  <ns:notificationSource ns:serviceID="Workflow1_4f539794-77e4-46dd-b9a9-01b2ebdd7bdb"
ns:workflowID="Workflow1_4f539794-77e4-46dd-b9a9-01b2ebdd7bdb" ns:workflowNodeID="bwa_aln_bwd_invoke"
ns:experimentID="Workflow1_4f539794-77e4-46dd-b9a9-01b2ebdd7bdb" />
  <ns:timestamp>2013-04-30T16:37:00.525+09:00</ns:timestamp>
  <ns:description>Error in retrieving results</ns:description>
  <ns:annotation />
  <ns:receiver ns:serviceID="Workflow1_4f539794-77e4-46dd-b9a9-01b2ebdd7bdb" ns:workflowID="Workflow1_4f539794-77e4-46dd-b9a9-01b2ebdd7bdb"
ns:workflowNodeID="bwa_aln_bwd_invoke" />
</ns:sendingFault>
--------------------------------------------------------------------------------------------------------------
<ns:invokingServiceFailed infoModelVersion="2.6"
  xmlns:ns="http://airavata.apache.org/schemas/wft/2011/08">
  <ns:notificationSource ns:serviceID="Workflow1_4f539794_77e4_46dd_b9a9_01b2ebdd7bdb"
ns:experimentID="Workflow1_4f539794-77e4-46dd-b9a9-01b2ebdd7bdb" />
  <ns:timestamp>2013-04-30T16:37:00.548+09:00</ns:timestamp>
  <ns:description>Error while invoking provider org.apache.airavata.gfac.provider.impl.LocalProvider
dispose method.: org.apache.airavata.gfac.GFacException: Error while invoking provider org.apache.airavata.gfac.provider.impl.LocalProvider
dispose method.</ns:description>
  <ns:annotation>
    <stackTrace>org.apache.airavata.gfac.GFacException: Error while invoking provider
org.apache.airavata.gfac.provider.impl.LocalProvider dispose method.
	at org.apache.airavata.gfac.GFacAPI.disposeProvider(GFacAPI.java:102)
	at org.apache.airavata.gfac.GFacAPI.schedule(GFacAPI.java:72)
	at org.apache.airavata.gfac.GFacAPI.submitJob(GFacAPI.java:53)
	at org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:332)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:698)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:517)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.access$000(WorkflowInterpreter.java:88)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter$1.run(WorkflowInterpreter.java:195)
Caused by: org.apache.airavata.gfac.provider.GFacProviderException: Error in retrieving results
	at org.apache.airavata.gfac.provider.impl.LocalProvider.dispose(LocalProvider.java:140)
	at org.apache.airavata.gfac.GFacAPI.disposeProvider(GFacAPI.java:100)
	... 7 more
Caused by: java.lang.NullPointerException
	at org.apache.airavata.gfac.utils.OutputUtils.fillOutputFromStdout(OutputUtils.java:56)
	at org.apache.airavata.gfac.provider.impl.LocalProvider.dispose(LocalProvider.java:134)
	... 8 more
</stackTrace>
  </ns:annotation>
  <ns:receiver ns:serviceID="bwa_aln_bwd_invoke" ns:workflowID="Workflow1_4f539794_77e4_46dd_b9a9_01b2ebdd7bdb"
ns:workflowTimestep="0" ns:workflowNodeID="bwa_aln_bwd_invoke" />
  <ns:failure>
    <ns:trace xsi:type="xs:string" xmlns:xs="http://www.w3.org/2001/XMLSchema"
      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
      xmlns:ns="http://airavata.apache.org/schemas/wft/2011/08">org.apache.airavata.gfac.GFacException:
Error while invoking provider org.apache.airavata.gfac.provider.impl.LocalProvider dispose
method.
	at org.apache.airavata.gfac.GFacAPI.disposeProvider(GFacAPI.java:102)
	at org.apache.airavata.gfac.GFacAPI.schedule(GFacAPI.java:72)
	at org.apache.airavata.gfac.GFacAPI.submitJob(GFacAPI.java:53)
	at org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:332)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:698)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:517)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.access$000(WorkflowInterpreter.java:88)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter$1.run(WorkflowInterpreter.java:195)
Caused by: org.apache.airavata.gfac.provider.GFacProviderException: Error in retrieving results
	at org.apache.airavata.gfac.provider.impl.LocalProvider.dispose(LocalProvider.java:140)
	at org.apache.airavata.gfac.GFacAPI.disposeProvider(GFacAPI.java:100)
	... 7 more
Caused by: java.lang.NullPointerException
	at org.apache.airavata.gfac.utils.OutputUtils.fillOutputFromStdout(OutputUtils.java:56)
	at org.apache.airavata.gfac.provider.impl.LocalProvider.dispose(LocalProvider.java:134)
	... 8 more
</ns:trace>
  </ns:failure>
</ns:invokingServiceFailed>
----------------------------------------------------------------------------------------------------------------------------------------------
<ns:invokingServiceFailed infoModelVersion="2.6"
  xmlns:ns="http://airavata.apache.org/schemas/wft/2011/08">
  <ns:notificationSource ns:serviceID="Workflow1_4f539794_77e4_46dd_b9a9_01b2ebdd7bdb"
ns:experimentID="Workflow1_4f539794-77e4-46dd-b9a9-01b2ebdd7bdb" />
  <ns:timestamp>2013-04-30T16:37:00.647+09:00</ns:timestamp>
  <ns:description>Error while invoking provider org.apache.airavata.gfac.provider.impl.LocalProvider
dispose method.: org.apache.airavata.gfac.GFacException: Error while invoking provider org.apache.airavata.gfac.provider.impl.LocalProvider
dispose method.</ns:description>
  <ns:annotation>
    <stackTrace>org.apache.airavata.gfac.GFacException: Error while invoking provider
org.apache.airavata.gfac.provider.impl.LocalProvider dispose method.
	at org.apache.airavata.gfac.GFacAPI.disposeProvider(GFacAPI.java:102)
	at org.apache.airavata.gfac.GFacAPI.schedule(GFacAPI.java:72)
	at org.apache.airavata.gfac.GFacAPI.submitJob(GFacAPI.java:53)
	at org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:332)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:698)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:517)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.access$000(WorkflowInterpreter.java:88)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter$1.run(WorkflowInterpreter.java:195)
Caused by: org.apache.airavata.gfac.provider.GFacProviderException: Error in retrieving results
	at org.apache.airavata.gfac.provider.impl.LocalProvider.dispose(LocalProvider.java:140)
	at org.apache.airavata.gfac.GFacAPI.disposeProvider(GFacAPI.java:100)
	... 7 more
Caused by: java.lang.NullPointerException
	at org.apache.airavata.gfac.utils.OutputUtils.fillOutputFromStdout(OutputUtils.java:56)
	at org.apache.airavata.gfac.provider.impl.LocalProvider.dispose(LocalProvider.java:134)
	... 8 more
</stackTrace>
  </ns:annotation>
  <ns:receiver ns:serviceID="bwa_aln_fwd_invoke" ns:workflowID="Workflow1_4f539794_77e4_46dd_b9a9_01b2ebdd7bdb"
ns:workflowTimestep="0" ns:workflowNodeID="bwa_aln_fwd_invoke" />
  <ns:failure>
    <ns:trace xsi:type="xs:string" xmlns:xs="http://www.w3.org/2001/XMLSchema"
      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
      xmlns:ns="http://airavata.apache.org/schemas/wft/2011/08">org.apache.airavata.gfac.GFacException:
Error while invoking provider org.apache.airavata.gfac.provider.impl.LocalProvider dispose
method.
	at org.apache.airavata.gfac.GFacAPI.disposeProvider(GFacAPI.java:102)
	at org.apache.airavata.gfac.GFacAPI.schedule(GFacAPI.java:72)
	at org.apache.airavata.gfac.GFacAPI.submitJob(GFacAPI.java:53)
	at org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:332)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:698)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:517)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.access$000(WorkflowInterpreter.java:88)
	at org.apache.airavata.xbaya.interpretor.WorkflowInterpreter$1.run(WorkflowInterpreter.java:195)
Caused by: org.apache.airavata.gfac.provider.GFacProviderException: Error in retrieving results
	at org.apache.airavata.gfac.provider.impl.LocalProvider.dispose(LocalProvider.java:140)
	at org.apache.airavata.gfac.GFacAPI.disposeProvider(GFacAPI.java:100)
	... 7 more
Caused by: java.lang.NullPointerException
	at org.apache.airavata.gfac.utils.OutputUtils.fillOutputFromStdout(OutputUtils.java:56)
	at org.apache.airavata.gfac.provider.impl.LocalProvider.dispose(LocalProvider.java:134)
	... 8 more
</ns:trace>
  </ns:failure>
</ns:invokingServiceFailed>
-----------------------------------------------------------------------------------------------------------
Would you check these error messages?

Shinyoung
                
> Airavata do not execute applications in parallel
> ------------------------------------------------
>
>                 Key: AIRAVATA-821
>                 URL: https://issues.apache.org/jira/browse/AIRAVATA-821
>             Project: Airavata
>          Issue Type: Bug
>         Environment: 
>            Reporter: Shinyoung Ahn
>
> I draw my workflow and executed the workflow as follows. 
> bwa_aln_fwd_invoke and bwa_aln_bwd_invoke do not have dependency. 
> I can expect bwa_aln_fwd_invoke and bwa_aln_bwd_invoke should run in parallel. 
> But bwa_aln_fwd_invoke and bwa_aln_bwd_invoke do not run in parallel, they run serially
> I didn’t configure any HPC configuration for the web service.
> refer the next mail for details
> 1) http://markmail.org/search/+list:org.apache.airavata.users#query:%20list%3Aorg.apache.airavata.users+page:1+mid:whfcv3nkhgqcwt3g+state:results

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