[Fwd: Re: [Swift-devel] Problems with Swift trunk on abe]

[Mihael Hategan]

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: [$, org.griphyn.vdl.mapping.DataNode identifier tag:benc at ci.uch\
> > icago.edu,2008:swift:dataset:20091103-0751-b65c863d:720000000020 type 
> > ProtGeo with no value at dataset=structure path=[1] (not closed)]
> >          at 
> > org.globus.cog.karajan.util.TypeUtil.toIdentifier(TypeUtil.java:286)
> > ...
> >          at java.lang.Thread.run(Thread.java:595)
> > Variable not found: path
> > honest4$
> > 
> > 
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