[Swift-devel] null pointer exception from nested loops
Michael Wilde
wilde at mcs.anl.gov
Tue Mar 17 16:46:21 CDT 2009
I got the error narrowed down to this example:
type file;
app (file editedParams) setTemps ( file inParams )
{
echo @inParams stdout=@editedParams;
}
file inParams<single_file_mapper; file="params.tloop" >;
string config [] = readData( setTemps(inParams ) );
trace(0,config[0]);
trace(1,config[1]);
trace(2,config[2]);
--
params.tloops contains:
DEFAULT_INIT_TEMP_=_ at DTI@
TEMP_UPDATE_INTERVAL_=_ at TUI@
KILL_TIME_=_3
MAX_NUMBER_OF_ANNEALING_STEPS_=_0
--
In other code, readData() seemed happy to take a file *or* a filename
string as input, but I wonder if it was not as happy as it seemed.
I'd been taking advantage of the flexibility with good results (luck?)
so far, though.
On 3/17/09 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
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