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

Sun Sep 8 20:12:50 CDT 2013

Mihael,

I've just tested the same scripts and they're now working with 
provenance.log=true.

Thanks,

Luiz

On 09/08/2013 04:51 AM, Mihael Hategan 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
>>>
>>>
>>
>>
>
>

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