[Swift-devel] null pointer exception from nested loops

Tue Mar 17 16:26:25 CDT 2009

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
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>>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
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