[Swift-devel] null pointer exception from nested loops

Tue Mar 17 16:25:32 CDT 2009

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