[Swift-devel] null pointer exception from nested loops
Mihael Hategan
hategan at mcs.anl.gov
Tue Mar 17 17:10:02 CDT 2009
Looks like it might be the nested procedure call interacting badly with
readData.
On Tue, 2009-03-17 at 17:02 -0500, Michael Wilde wrote:
> OK, I think this is it:
>
> The following script *works* with the commented out code and fails with
> the currently enabled alternative statement:
>
> --
>
> type file;
>
> app (file editedParams) setTemps ( file inParams )
> {
> sed "-e" "s/@DTI@/123/" @inParams stdout=@editedParams;
> }
>
> file inParams<single_file_mapper; file="params.tloop" >;
>
> /* works:
> file o<"pout">;
> o = setTemps(inParams);
> string config [] = readData(o);
> */
>
> /* Fails: */
> string config [] = readData( setTemps(inParams ) );
>
> trace(0,config[0]);
> trace(1,config[1]);
> trace(2,config[2]);
>
> --
>
> So readData is indeed happy to take a file-value var as an arg but not a
> file-valued expression (procedure return in this case).
>
>
>
> On 3/17/09 4:46 PM, Michael Wilde wrote:
> > 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
> >>>> _______________________________________________
> >>>> 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
> > _______________________________________________
> > Swift-devel mailing list
> > Swift-devel at ci.uchicago.edu
> > http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
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