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

[Michael Wilde]

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
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>