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

Ketan Maheshwari ketancmaheshwari at gmail.com
Sun Sep 8 10:49:36 CDT 2013 

Hi,

I add this line to sites.xml suggested by Mike:

<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://swift-lang.org/sites">

I still get this message at runtime:
[Error] sites.blues.xml, line 2, col 45: cvc-elt.1: Cannot find the
declaration of element 'config'.

The run however proceeds fine.

Swift is trunk: r7042

Thanks,
Ketan


On Sun, Sep 8, 2013 at 2:51 AM, Mihael Hategan <hategan at mcs.anl.gov> wrote:

> 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
> > >
> > >
> >
> >
>
>
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
>



-- 
Ketan
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