[Swift-devel] null pointer exception from nested loops

Ian Foster foster at anl.gov
Tue Mar 17 17:22:07 CDT 2009 

I wasn't sure if this ran without Swift--with just Falkon


On Mar 17, 2009, at 5:05 PM, Michael Wilde wrote:

> Not quite sure what you're asking, Ian.
>
> The latest tests have been on BGP w/ Falkon.
> Earlier tests were on other clusters.
>
> The scripts has grown in last week or so, on BGP, and grew some more  
> today to explore some new science code algorithm questions.
>
> Its not yet running at full desired scale on the BGP; we are now  
> scaling up carefully so as not to impact other users.
>
> This is a test case for the "cio" work as well.
>
> - Mike
>
>
> On 3/17/09 4:26 PM, Ian Foster wrote:
>> Just curious, is the whole thing working with just Falkon?
>> On Mar 17, 2009, at 4:25 PM, Michael Wilde wrote:
>>> The log contains this just before the NPE, including the  
>>> suspicious message: WARN  FlowNode Ex098:
>>>
>>> Thats giving me a clue as to the offending statements.
>>>
>>> ---
>>>
>>> 2009-03-17 16:20:34,723-0500 INFO  AbstractDataNode Adding handle  
>>> listener "F/org.griphyn.vdl.mapping.DataNode identifier tag:benc at ci.uchicago.edu 
>>> ,2008:swift:dataset:20090\
>>> 317-1620-e1n1bz3g:720000000071 type SecSeq with no value at  
>>> dataset=secseq path=[0] (not closed)" to  
>>> "org.griphyn.vdl.mapping.DataNode identifier tag:benc at ci.uchicago.edu 
>>> ,\
>>> 2008:swift:dataset:20090317-1620-e1n1bz3g:720000000071 type SecSeq  
>>> with no value at dataset=secseq path=[0] (not closed)"
>>> 2009-03-17 16:20:34,724-0500 INFO  AbstractDataNode closed  
>>> org.griphyn.vdl.mapping.RootDataNode identifier tag:benc at ci.uchicago.edu 
>>> ,2008:swift:dataset:20090317-1620-e1n1bz\
>>> 3g:720000000092 type string value=s/@DIT@/10/ dataset=unnamed  
>>> SwiftScript value (closed)
>>> 2009-03-17 16:20:34,724-0500 INFO  AbstractDataNode ROOTPATH  
>>> dataset=tag:benc at ci.uchicago.edu,2008:swift:dataset:20090317-1620- 
>>> e1n1bz3g:720000000092 path=$
>>> 2009-03-17 16:20:34,724-0500 INFO  AbstractDataNode VALUE  
>>> dataset=tag:benc at ci.uchicago.edu,2008:swift:dataset:20090317-1620- 
>>> e1n1bz3g:720000000092 VALUE=s/@DIT@/10/
>>> 2009-03-17 16:20:34,725-0500 INFO  AbstractDataNode closed  
>>> org.griphyn.vdl.mapping.RootDataNode identifier tag:benc at ci.uchicago.edu 
>>> ,2008:swift:dataset:20090317-1620-e1n1bz\
>>> 3g:720000000093 type string value=s/@TUI@/1/ dataset=unnamed  
>>> SwiftScript value (closed)
>>> 2009-03-17 16:20:34,725-0500 INFO  AbstractDataNode ROOTPATH  
>>> dataset=tag:benc at ci.uchicago.edu,2008:swift:dataset:20090317-1620- 
>>> e1n1bz3g:720000000093 path=$
>>> 2009-03-17 16:20:34,725-0500 INFO  AbstractDataNode VALUE  
>>> dataset=tag:benc at ci.uchicago.edu,2008:swift:dataset:20090317-1620- 
>>> e1n1bz3g:720000000093 VALUE=s/@TUI@/1/
>>> 2009-03-17 16:20:34,726-0500 INFO  AbstractDataNode closed  
>>> org.griphyn.vdl.mapping.RootDataNode identifier tag:benc at ci.uchicago.edu 
>>> ,2008:swift:dataset:20090317-1620-e1n1bz\
>>> 3g:720000000094 type string value=params.tloop dataset=unnamed  
>>> SwiftScript value (closed)
>>> 2009-03-17 16:20:34,726-0500 INFO  AbstractDataNode ROOTPATH  
>>> dataset=tag:benc at ci.uchicago.edu,2008:swift:dataset:20090317-1620- 
>>> e1n1bz3g:720000000094 path=$
>>> 2009-03-17 16:20:34,726-0500 INFO  AbstractDataNode VALUE  
>>> dataset=tag:benc at ci.uchicago.edu,2008:swift:dataset:20090317-1620- 
>>> e1n1bz3g:720000000094 VALUE=params.tloop
>>> 2009-03-17 16:20:34,727-0500 WARN  FlowNode Ex098
>>> java.lang.NullPointerException
>>>       at  
>>> org 
>>> .griphyn.vdl.karajan.lib.VDLFunction.leafFileName(VDLFunction.java: 
>>> 285)
>>>       at  
>>> org.griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java: 
>>> 201)
>>>       at  
>>> org.griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java: 
>>> 182)
>>>       at  
>>> org 
>>> .griphyn 
>>> .vdl.karajan.lib.swiftscript.FileName.function(FileName.java:19)
>>>       at  
>>> org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:67)
>>>
>>>
>>>
>>> On 3/17/09 4:17 PM, Michael Wilde wrote:
>>>> It seems not related to scale or Falkon.
>>>> It occurs when running on localhost (but on bgp) and when I cut  
>>>> all the loops down to a single iteration.
>>>> I'm still debugging.
>>>> On 3/17/09 4:07 PM, Michael Wilde wrote:
>>>>> I just expanded my oops protein folding script to add another  
>>>>> level of parameter sweep. This script is getting pretty complex  
>>>>> now (at least, for a swift script).
>>>>>
>>>>> I got the following npe on my first two tries. Im going to start  
>>>>> debugging, but any clues as to the cause would be helpful.
>>>>>
>>>>> The outer loops are:
>>>>>
>>>>> main()
>>>>> {
>>>>> string protein[] = readData(@arg("plist"));
>>>>> string startTemp[] = ["10","20"];
>>>>> string tempUpdate[] = ["1","2","3"];
>>>>>
>>>>> foreach p in protein {
>>>>>   foreach st in startTemp {
>>>>>     foreach tu in tempUpdate {
>>>>>       doRoundSet(p,st,tu);
>>>>>     }
>>>>>   }
>>>>> }
>>>>> }
>>>>>
>>>>> There are two levels of inner loops further down below  
>>>>> doRoundSet().
>>>>>
>>>>> The script, output, command line args and log are in:
>>>>> http://ww.ci.uchicago.edu/~wilde/swift3.tar.gz
>>>>>
>>>>> I suspect it will take a while to narrow the cause to a simpler  
>>>>> test case thats easy tp reproduce without a lot of setup.
>>>>>
>>>>> I'll try on a vanilla swift on local execution; this is on bgp  
>>>>> with Falkon.
>>>>>
>>>>> Thanks.
>>>>>
>>>>> -- 
>>>>>
>>>>> ...
>>>>> Progress:  uninitialized:1 Selecting site:2
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 7
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 2
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 8
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 0
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 5
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 9
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 1
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 6
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 3
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 4
>>>>> Ex098
>>>>> java.lang.NullPointerException
>>>>>   at  
>>>>> org 
>>>>> .griphyn 
>>>>> .vdl.karajan.lib.VDLFunction.leafFileName(VDLFunction.java:285)
>>>>>   at  
>>>>> org 
>>>>> .griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java: 
>>>>> 201)
>>>>>   at  
>>>>> org 
>>>>> .griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java: 
>>>>> 182)
>>>>>   at  
>>>>> org 
>>>>> .griphyn 
>>>>> .vdl.karajan.lib.swiftscript.FileName.function(FileName.java:19)
>>>>>   at  
>>>>> org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:67)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow 
>>>>> .nodes 
>>>>> .AbstractSequentialWithArguments 
>>>>> .childCompleted(AbstractSequentialWithArguments.java:192)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java: 
>>>>> 332)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.events.EventBus.send(EventBus.java: 
>>>>> 125)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:176)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:296)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow 
>>>>> .nodes.functions.AbstractFunction.post(AbstractFunction.java:46)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java: 
>>>>> 51)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.nodes.Sequential.executeChildren(Sequential.java:27)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow 
>>>>> .nodes 
>>>>> .functions 
>>>>> .AbstractFunction.executeChildren(AbstractFunction.java:40)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java: 
>>>>> 63)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:233)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java: 
>>>>> 278)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java: 
>>>>> 391)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java: 
>>>>> 329)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.FlowElementWrapper.event(FlowElementWrapper.java:227)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.events.EventBus.send(EventBus.java: 
>>>>> 125)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.events.EventWorker.run(EventWorker.java:69)
>>>>> Execution failed:
>>>>>   java.lang.NullPointerException
>>>>>   at  
>>>>> org 
>>>>> .griphyn 
>>>>> .vdl.karajan.lib.VDLFunction.leafFileName(VDLFunction.java:285)
>>>>>   at  
>>>>> org 
>>>>> .griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java: 
>>>>> 201)
>>>>>   at  
>>>>> org 
>>>>> .griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java: 
>>>>> 182)
>>>>>   at  
>>>>> org 
>>>>> .griphyn 
>>>>> .vdl.karajan.lib.swiftscript.FileName.function(FileName.java:19)
>>>>>   at  
>>>>> org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:67)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow 
>>>>> .nodes 
>>>>> .AbstractSequentialWithArguments 
>>>>> .childCompleted(AbstractSequentialWithArguments.java:192)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java: 
>>>>> 332)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.events.EventBus.send(EventBus.java: 
>>>>> 125)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:176)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:296)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow 
>>>>> .nodes.functions.AbstractFunction.post(AbstractFunction.java:46)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java: 
>>>>> 51)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.nodes.Sequential.executeChildren(Sequential.java:27)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow 
>>>>> .nodes 
>>>>> .functions 
>>>>> .AbstractFunction.executeChildren(AbstractFunction.java:40)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java: 
>>>>> 63)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:233)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java: 
>>>>> 278)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java: 
>>>>> 391)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java: 
>>>>> 329)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.FlowElementWrapper.event(FlowElementWrapper.java:227)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.events.EventBus.send(EventBus.java: 
>>>>> 125)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.events.EventWorker.run(EventWorker.java:69)
>>>>>
>>>>> Ex098
>>>>> java.lang.NullPointerException
>>>>>   at  
>>>>> org 
>>>>> .griphyn 
>>>>> .vdl.karajan.lib.VDLFunction.leafFileName(VDLFunction.java:285)
>>>>>   at  
>>>>> org 
>>>>> .griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java: 
>>>>> 201)
>>>>>   at  
>>>>> org 
>>>>> .griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java: 
>>>>> 182)
>>>>>   at  
>>>>> org 
>>>>> .griphyn 
>>>>> .vdl.karajan.lib.swiftscript.FileName.function(FileName.java:19)
>>>>>   at  
>>>>> org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:67)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow 
>>>>> .nodes 
>>>>> .AbstractSequentialWithArguments 
>>>>> .childCompleted(AbstractSequentialWithArguments.java:192)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java: 
>>>>> 332)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.events.EventBus.send(EventBus.java: 
>>>>> 125)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:176)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:296)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow 
>>>>> .nodes.functions.AbstractFunction.post(AbstractFunction.java:46)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java: 
>>>>> 51)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.nodes.Sequential.executeChildren(Sequential.java:27)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow 
>>>>> .nodes 
>>>>> .functions 
>>>>> .AbstractFunction.executeChildren(AbstractFunction.java:40)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java: 
>>>>> 63)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:233)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java: 
>>>>> 278)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java: 
>>>>> 391)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java: 
>>>>> 329)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog 
>>>>> .karajan 
>>>>> .workflow.FlowElementWrapper.event(FlowElementWrapper.java:227)
>>>>>   at  
>>>>> org 
>>>>> .globus.cog.karajan.workflow.events.EventBus.send(EventBus.java: 
>>>>> 125)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
>>>>>   at  
>>>>> org 
>>>>> .globus 
>>>>> .cog.karajan.workflow.events.EventWorker.run(EventWorker.java:69)
>>>>> SwiftScript trace: T1af7, Round, 0, Sim, 7
>>>>> _______________________________________________
>>>>> Swift-devel mailing list
>>>>> Swift-devel at ci.uchicago.edu
>>>>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>>>> _______________________________________________
>>>> Swift-devel mailing list
>>>> Swift-devel at ci.uchicago.edu
>>>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>>> _______________________________________________
>>> Swift-devel mailing list
>>> Swift-devel at ci.uchicago.edu
>>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel

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