[Swift-devel] Swift compile issues on IBI cluster

[Mihael Hategan]

I don't think I have access to said cluster, but it may be worth getting
some recent version of xerces, sticking it into some directory,
specifying java.endorsed.dirs and seeing if that fixes the problem with
1.6.0_07-b06.

Mihael

On Sat, 2011-01-22 at 12:08 -0600, Tim Armstrong wrote:
> Thanks, that appears to fix it.  It is a very strange issue.  It
> almost looks like the output from the .swift -> .xml stage isn't
> written to the .xml file before the next stage tries to read.  Either
> that or there is a silent failure somewhere in that stage
> 
> On Sat, Jan 22, 2011 at 7:09 AM, Michael Wilde <wilde at mcs.anl.gov>
> wrote:
>         Mihael commented on this problem in this post Nov 3:
>         http://mail.ci.uchicago.edu/mailman/private/swift-devel/2010-November/006990.html
>         (likely SAX incompatibility problem with that particular Java
>         version)
>         
>         
>         ______________________________________________________________
>         
>                 Tim, I forgot to mention: on IBI you need to use the
>                 Java in my home dir (or any recent Java).  The
>                 particular SUn java thats the default there has some
>                 weird issue in xml parsing that causes this failure.
>                 
>                 
>                 - Mike
>                 
>                 
>                 ______________________________________________________
>                         Hi,
>                           I'm trying to get a Swift script running on
>                         the IBI cluster but have been running into
>                         some issues.  I'm using a recent development
>                         version 3029.  Running the script fails at the
>                         compile stage.  
>                         
>                         Strangely, this script compiles without issue
>                         using exactly the same swift on other
>                         machines.  
>                         Even more strangely, it looks like the swift
>                         ->  intermediate xml step completes without
>                         any exceptions being thrown, but when I look
>                         at the xml file it contains precisely zero
>                         bytes.  It appears that this is what actually
>                         causes the karajan parser to crash.
>                         What would cause the first compile step to
>                         complete without causing an exception but not
>                         produce any output?  Do we maybe have a
>                         buffering issue?  Any suggestions for how I
>                         might solve this?
>                         
>                         The log contents are:
>                         
>                         2011-01-21 16:43:13,448-0600 DEBUG Loader Max
>                         heap: 238616576
>                         2011-01-21 16:43:13,449-0600 INFO  Loader
>                         rserver.swift: source file is new.
>                         Recompiling.
>                         2011-01-21 16:43:13,919-0600 DEBUG Loader
>                         Detailed exception:
>                         org.griphyn.vdl.karajan.CompilationException:
>                         Unable to parse intermediate XML
>                                 at
>                         org.griphyn.vdl.engine.Karajan.compile(Karajan.java:98)
>                                 at
>                         org.griphyn.vdl.karajan.Loader.compile(Loader.java:300)
>                                 at
>                         org.griphyn.vdl.karajan.Loader.main(Loader.java:145)
>                         Caused by:
>                         org.apache.xmlbeans.XmlException: /tmp/tga/SwiftR/swift.local.2306/rserver.xml:2:1: error: Unexpected end of file after null
>                                 at
>                         org.apache.xmlbeans.impl.store.Locale
>                         $SaxLoader.load(Locale.java:3467)
>                                 at
>                         org.apache.xmlbeans.impl.store.Locale.parseToXmlObject(Locale.java:1270)
>                                 at
>                         org.apache.xmlbeans.impl.store.Locale.parseToXmlObject(Locale.java:1257)
>                                 at
>                         org.apache.xmlbeans.impl.schema.SchemaTypeLoaderBase.parse(SchemaTypeLoaderBase.java:345)
>                                 at
>                         org.apache.xmlbeans.impl.schema.SchemaTypeLoaderBase.parse(SchemaTypeLoaderBase.java:252)
>                                 at
>                         org.globus.swift.language.ProgramDocument
>                         $Factory.parse(ProgramDocument.java:499)
>                                 at
>                         org.griphyn.vdl.engine.Karajan.parseProgramXML(Karajan.java:122)
>                                 at
>                         org.griphyn.vdl.engine.Karajan.compile(Karajan.java:96)
>                                 ... 2 more
>                         Caused by: org.xml.sax.SAXParseException:
>                         Unexpected end of file after null
>                                 at
>                         org.apache.xmlbeans.impl.piccolo.xml.Piccolo.reportFatalError(Piccolo.java:1038)
>                                 at
>                         org.apache.xmlbeans.impl.piccolo.xml.Piccolo.parse(Piccolo.java:723)
>                                 at
>                         org.apache.xmlbeans.impl.store.Locale
>                         $SaxLoader.load(Locale.java:3435)
>                                 ... 9 more
>                         
>                         
>                         
>                         
>                         _______________________________________________
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>                         Swift-devel at ci.uchicago.edu
>                         http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>                 
>                 
>                 
>                 -- 
>                 Michael Wilde
>                 Computation Institute, University of Chicago
>                 Mathematics and Computer Science Division
>                 Argonne National Laboratory
>                 
>                 
>         
>         
>         
>         -- 
>         Michael Wilde
>         Computation Institute, University of Chicago
>         Mathematics and Computer Science Division
>         Argonne National Laboratory
>         
>         
> 
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