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

[Luiz Gadelha]

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
>>>
>> _______________________________________________
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>
>


-- 
Luiz Gadelha
http://www.lncc.br/~lgadelha