[Fwd: Re: [Swift-devel] Problems with Swift trunk on abe]
Michael Wilde
wilde at mcs.anl.gov
Tue Nov 3 11:23:54 CST 2009
Indeed, taking 0024-compound, and just copying it to a local test
directory, gives very similar *and random, various* errors.
See below (abe: ~wilde/swiftbug for logs)
Still digging.
- Mike
honest4$ which swift
~/swift/src/cog/modules/swift/dist/swift-svn/bin/swift
honest4$ cat >t.swift
type messagefile {}
(messagefile t) greeting(string m) {
app {
echo m stdout=@filename(t);
}
}
(messagefile first, messagefile second) compound() {
first = greeting("f");
second = greeting("s");
}
messagefile a <"0024-compound.Q.out">;
messagefile b <"0024-compound.R.out">;
(a,b) = compound();
honest4$
honest4$ pwd
/u/ac/wilde/swiftbug
honest4$
honest4$ which swift
~/swift/src/cog/modules/swift/dist/swift-svn/bin/swift
honest4$ swift t.swift
Swift svn swift-r3186 cog-r2572
RunID: 20091103-1120-xnfyl1i5
Progress:
Failed to transfer wrapper log from t-20091103-1120-xnfyl1i5/info/k on
localhost
Progress: Stage in:1 Finished successfully:1
Final status: Finished successfully:2
honest4$ swift t.swift
Swift svn swift-r3186 cog-r2572
RunID: 20091103-1121-2pgjnht8
Progress:
Execution failed:
First argument must be an identifier or a list of identifiers
honest4$ swift t.swift
Swift svn swift-r3186 cog-r2572
RunID: 20091103-1121-m64zk3p8
Progress:
Execution failed:
Variable not found: r
Failed to transfer wrapper log from t-20091103-1121-m64zk3p8/info/p on
localhost
honest4$ swift t.swift
Swift svn swift-r3186 cog-r2572
RunID: 20091103-1121-effamg5e
Progress:
Ex098
org.globus.cog.karajan.workflow.KarajanRuntimeException: Invalid
identifier: [$, org.griphyn.vdl.mapping.RootDataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20091103-1121-5rjnv1z5:720000000004
type messagefile with no value at dataset=b (not closed)]
at org.globus.cog.karajan.util.TypeUtil.toIdentifier(TypeUtil.java:286)
at
org.globus.cog.karajan.workflow.nodes.ChannelTo.partialArgumentsEvaluated(ChannelTo.java:32)
at
org.globus.cog.karajan.workflow.nodes.PartialArgumentsContainer.childCompleted(PartialArgumentsContainer.java:81)
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:134)
at
org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
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.AbstractSequentialIterator.iterationCompleted(AbstractSequentialIterator.java:90)
at
org.globus.cog.karajan.workflow.nodes.AbstractSequentialIterator.nonArgChildCompleted(AbstractSequentialIterator.java:75)
at
org.globus.cog.karajan.workflow.nodes.PartialArgumentsContainer.childCompleted(PartialArgumentsContainer.java:85)
at
org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
at
org.globus.cog.karajan.workflow.nodes.AbstractSequentialIterator.notificationEvent(AbstractSequentialIterator.java:132)
at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:332)
at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:134)
at
org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
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.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:134)
at
org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
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:229)
at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:134)
at
org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
at
org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:43)
at
edu.emory.mathcs.backport.java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:431)
at
edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166)
at
edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:643)
at
edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:668)
at java.lang.Thread.run(Thread.java:595)
Execution failed:
Invalid identifier: [$, org.griphyn.vdl.mapping.RootDataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20091103-1121-5rjnv1z5:720000000004
type messagefile with no value at dataset=b (not closed)]
honest4$
On 11/3/09 11:15 AM, Michael Wilde wrote:
> Im running the Swift test battery on Ranger and Abe.
>
> Tests on Abe just got this, which is similar to what I was seeing:
>
> ...
> Running test 0024-compound at Tue Nov 3 11:11:33 CST 2009
> Swift svn swift-r3186 cog-r2572
>
> RunID: 20091103-1111-as1yb7s3
> Progress:
> Execution failed:
> First argument must be an identifier or a list of identifiers
> SWIFT RETURN CODE NON-ZERO - test 0024-compound.swift
> ...
>
> ---
>
> Ranger passed all syntax tests but is hanging on 001-echo. Not sure why yet.
>
> I'll keep trying to zero in on something small thats reproducble.
> 0024-compound might be a good starting point.
>
> Let me know if you need something specific from me, or have suggestions
> on what to try, where.
>
> Thanks,
>
> Mike
>
>
>
>
>
> On 11/3/09 11:05 AM, Mihael Hategan wrote:
>> Thanks. I'm looking into it.
>>
>> On Tue, 2009-11-03 at 10:19 -0600, Michael Wilde wrote:
>>> Similar problems happen on Ranger. I used an older Swift build
>>> initially, and it ran.
>>>
>>> Then I updated to the latest, and I get the following similar failure:
>>>
>>> RunID: 20091103-1016-khfn59yf
>>> Progress:
>>> Ex098
>>> java.lang.NullPointerException
>>> at
>>> org.globus.cog.karajan.workflow.nodes.functions.Variable.function(Variable.java:38)
>>> at
>>> org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:45)
>>> at
>>> org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)
>>> ...
>>> edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:643)
>>> at
>>> edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:668)
>>> at java.lang.Thread.run(Thread.java:619)
>>> Execution failed:
>>> Argument size mismatch. Got 1 names and 2 values
>>> login3$
>>>
>>> Im going try the bgp next. If it works there, we can leave this issue
>>> for after SC. Else, I'll need to resolve it.
>>>
>>> - Mike
>>>
>>> -------- Original Message --------
>>> Subject: Re: [Swift-devel] Problems with Swift trunk on abe
>>> Date: Tue, 03 Nov 2009 08:18:55 -0600
>>> From: Michael Wilde <wilde at mcs.anl.gov>
>>> To: swift-devel <swift-devel at ci.uchicago.edu>
>>> References: <4AF03842.70300 at mcs.anl.gov>
>>>
>>> Using the Swift build (and swift.properties) that works on communicado,
>>> I still get the same failures on Abe.
>>>
>>> I'm going to try a few other systems to see if the problem is widespread
>>> or local to Abe.
>>>
>>> - Mike
>>>
>>>
>>> On 11/3/09 8:03 AM, Michael Wilde wrote:
>>>> What seems like the a build of the same Swift & CoG svn revision is
>>>> working on communicado but giving strange and transient results on Abe.
>>>>
>>>> A series of 5 runs of the same code (with .xml and .kml files left in
>>>> place) give the set of errors below.
>>>>
>>>> I will try to use the release build on communicado, to see if this is
>>>> being caused by some Java compiler difference on Abe.
>>>>
>>>> Suggestions welcome. Mihael, I can get you the logs - they are on abe in
>>>> ~wilde/run.58, along with the source: psim.basicex1.swift
>>>>
>>>> - Mike
>>>>
>>>> Output with a few progress and blank lines removed:
>>>>
>>>> (full output is in: http://www.ci.uchicago.edu/~wilde/abe.swiftproblem.txt )
>>>>
>>>> honest4$ ls
>>>>
>>>> Protein.map* Protein.map~* etc input@ logs/ psim.basicex1.swift*
>>>> sites.xml t.swift* t.swift~* tc tc~
>>>>
>>>> honest4$ swift -tc.file tc -sites.file sites.xml psim.basicex1.swift
>>>>
>>>> Swift svn swift-r3186 cog-r2572
>>>> RunID: 20091103-0750-p7z85z61
>>>> Execution failed:
>>>> Argument size mismatch. Got 5 names and 0 values
>>>>
>>>> honest4$ swift -tc.file tc -sites.file sites.xml psim.basicex1.swift
>>>>
>>>> Swift svn swift-r3186 cog-r2572
>>>> RunID: 20091103-0751-sfxthnne
>>>> Execution failed:
>>>> Argument size mismatch. Got 5 names and 0 values
>>>>
>>>> honest4$ swift -tc.file tc -sites.file sites.xml psim.basicex1.swift
>>>>
>>>> Swift svn swift-r3186 cog-r2572
>>>> RunID: 20091103-0751-oxnhztrc
>>>> Progress:
>>>> Execution failed:
>>>> Argument size mismatch. Got 5 names and 0 values
>>>>
>>>> honest4$ swift -tc.file tc -sites.file sites.xml psim.basicex1.swift
>>>>
>>>> Swift svn swift-r3186 cog-r2572
>>>> RunID: 20091103-0751-amtfuvq9
>>>> Execution failed:
>>>> Variable not found: path
>>>>
>>>> honest4$ swift -tc.file tc -sites.file sites.xml psim.basicex1.swift
>>>>
>>>> Swift svn swift-r3186 cog-r2572
>>>> RunID: 20091103-0751-b4sr44x2
>>>> Execution failed:
>>>> Ex098
>>>> org.globus.cog.karajan.workflow.KarajanRuntimeException: Invalid
>>>> identifier: [$, org.griphyn.vdl.mapping.DataNode identifier tag:benc at ci.uch\
>>>> icago.edu,2008:swift:dataset:20091103-0751-b65c863d:720000000020 type
>>>> ProtGeo with no value at dataset=structure path=[1] (not closed)]
>>>> at
>>>> org.globus.cog.karajan.util.TypeUtil.toIdentifier(TypeUtil.java:286)
>>>> ...
>>>> at java.lang.Thread.run(Thread.java:595)
>>>> Variable not found: path
>>>> honest4$
>>>>
>>>>
>>>> _______________________________________________
>>>> Swift-devel mailing list
>>>> Swift-devel at ci.uchicago.edu
>>>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>>> _______________________________________________
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