[Swift-devel] Trunk failing with provenance.log=true

[Mihael Hategan]

Should now be fixed in r7042.

Mihael

On Tue, 2013-09-03 at 23:57 -0300, Luiz Gadelha wrote:
> That's indeed what happens, I get the warning about the sites file and 
> the scripts execute correctly with provenance.log disabled.
> 
> Thanks,
> 
> Luiz
> 
> On 09/03/2013 12:08 PM, Mihael Hategan wrote:
> > While that is true, schema checking of the sites file is optional.
> > You'll get the warning seen below and swift should continue.
> >
> > I believe that the other error is due to the run-time. I'll take a look
> > when I can.
> >
> > Mihael
> >
> > On Tue, 2013-09-03 at 07:43 -0500, Michael Wilde wrote:
> >> Luiz, in trunk, stricter XML parsing is used now.  You need to start sites.xml with these two lines:
> >>
> >> <?xml version="1.0" encoding="UTF-8"?>
> >> <config xmlns="http://swift-lang.org/sites">
> >>
> >> We need to start using the README and Download pages to make people aware of changes like this.
> >>
> >> - Mike
> >>
> >>
> >> ----- Original Message -----
> >>> From: "Luiz Gadelha" <lgadelha at lncc.br>
> >>> To: swift-devel at ci.uchicago.edu
> >>> Sent: Tuesday, September 3, 2013 6:33:09 AM
> >>> Subject: [Swift-devel] Trunk failing with provenance.log=true
> >>>
> >>> Hi,
> >>>
> >>> I'm getting the error message below when setting the provenance.log
> >>> parameter to true in the latest trunk version. Both scripts I tested
> >>> work with provenance.log disabled.
> >>>
> >>> Regards,
> >>>
> >>> Luiz
> >>>
> >>> $ swift -sites.file sites-vortex.xml -tc.file tc-vortex.data
> >>> blast.swift
> >>> -d=genes.pep -i=seq3.seq -n=64
> >>> Swift trunk swift-r7023 cog-r3768
> >>> RunID: 20130903-0731-gg3aup4d
> >>> Warning: The @ syntax for function invocation is deprecated
> >>> [Error] sites-vortex.xml, line 1, col 9: cvc-elt.1: Cannot find the
> >>> declaration of element 'config'.
> >>>
> >>> Execution failed:
> >>> java.lang.UnsupportedOperationException
> >>> 	k:concat @ swift.k, line: 29
> >>> Caused by: java.lang.UnsupportedOperationException
> >>> 	at k.rt.Sink.getAll(Sink.java:45)
> >>> 	at org.globus.cog.karajan.util.TypeUtil.toString(TypeUtil.java:201)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.functions.Misc$Concat.function(Misc.java:448)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.functions.AbstractFunction.runBody(AbstractFunction.java:38)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:154)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:147)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> >>> 	at
> >>> 	org.globus.cog.karajan.compiled.nodes.Sequential.run(Sequential.java:22)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> >>> 	at
> >>> 	org.globus.cog.karajan.compiled.nodes.Sequential.run(Sequential.java:22)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.user.Function.runBody(Function.java:99)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.runBody(InvocationWrapper.java:245)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.run(InvocationWrapper.java:69)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.FramedInternalFunction.run(FramedInternalFunction.java:63)
> >>> 	at org.globus.cog.karajan.compiled.nodes.Main.run(Main.java:79)
> >>> 	at k.thr.LWThread.run(LWThread.java:228)
> >>> 	at
> >>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
> >>> 	at
> >>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> >>> 	at java.lang.Thread.run(Thread.java:679)
> >>>
> >>>
> >>> $ swift foreach.swift
> >>> Swift trunk swift-r7023 cog-r3768
> >>> RunID: 20130903-0755-r4lxbb67
> >>> Warning: The @ syntax for function invocation is deprecated
> >>> [Error] sites.xml, line 1, col 9: cvc-elt.1: Cannot find the
> >>> declaration
> >>> of element 'config'.
> >>>
> >>> Execution failed:
> >>> java.lang.UnsupportedOperationException
> >>> 	k:concat @ swift.k, line: 29
> >>> Caused by: java.lang.UnsupportedOperationException
> >>> 	at k.rt.Sink.getAll(Sink.java:45)
> >>> 	at org.globus.cog.karajan.util.TypeUtil.toString(TypeUtil.java:201)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.functions.Misc$Concat.function(Misc.java:448)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.functions.AbstractFunction.runBody(AbstractFunction.java:38)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:154)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:147)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> >>> 	at
> >>> 	org.globus.cog.karajan.compiled.nodes.Sequential.run(Sequential.java:22)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> >>> 	at
> >>> 	org.globus.cog.karajan.compiled.nodes.Sequential.run(Sequential.java:22)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.user.Function.runBody(Function.java:99)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.runBody(InvocationWrapper.java:245)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.run(InvocationWrapper.java:69)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> >>> 	at
> >>> org.globus.cog.karajan.compiled.nodes.FramedInternalFunction.run(FramedInternalFunction.java:63)
> >>> 	at org.globus.cog.karajan.compiled.nodes.Main.run(Main.java:79)
> >>> 	at k.thr.LWThread.run(LWThread.java:228)
> >>> 	at
> >>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
> >>> 	at
> >>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> >>> 	at java.lang.Thread.run(Thread.java:679)
> >>>
> >>> --
> >>> Luiz Gadelha
> >>> http://www.lncc.br/~lgadelha
> >>> _______________________________________________
> >>> Swift-devel mailing list
> >>> Swift-devel at ci.uchicago.edu
> >>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
> >>>
> >> _______________________________________________
> >> Swift-devel mailing list
> >> Swift-devel at ci.uchicago.edu
> >> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
> >
> >
> 
>