[Swift-devel] Swift compile issues on IBI cluster
Tim Armstrong
tim.g.armstrong at gmail.com
Mon Jan 24 08:37:20 CST 2011
It doesn't appear that changing the version of xerces helps. I'm not that
familiar with the java.endorsed.dirs mechanism, but I believe I'm using it
correctly: adding the xerces jars to the class path and then adding the
containing directory as an endorsed dir.
I still get exactly the same failure.
eval java -Xmx256M
-Djavax.xml.parsers.SAXParserFactory=org.apache.xerces.jaxp.SAXParserFactoryImpl
-Djava.endorsed.dirs=/cchome/tga/xerces-2_11_0 -DUID=667327
-DGLOBUS_HOSTNAME=ibicluster.uchicago.cc-DCOG_INSTALL_PATH=/userhom3/1/tga/R/library/Swift/exec/../swift/bin/..
-Dswift.home=/userhom3/1/tga/R/library/Swift/exec/../swift/bin/..
-Djava.security.egd=file:///dev/urandom -classpath
/cchome/tga/xerces-2_11_0/xercesImpl.jar:/cchome/tga/xerces-2_11_0/xercesSamples.jar:/cchome/tga/xerces-2_11_0/xml-apis.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../etc:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../libexec:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/addressing-1.0.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/ant.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/antlr-2.7.5.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/axis.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/axis-url.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/backport-util-concurrent.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/castor-0.9.6.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/coaster-bootstrap.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-abstraction-common-2.4.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-axis.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-grapheditor-0.47.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-jglobus-1.7.0.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-karajan-0.36-dev.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-provider-clref-gt4_0_0.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-provider-coaster-0.3.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-provider-dcache-0.1.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-provider-gt2-2.4.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-provider-gt4_0_0-2.5.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-provider-local-2.2.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-provider-localscheduler-0.4.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-provider-ssh-2.4.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-provider-webdav-2.1.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-resources-1.0.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-swift-svn.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-trap-1.0.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-url.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cog-util-0.92.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/commonj.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/commons-beanutils.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/commons-collections-3.0.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/commons-digester.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/commons-discovery.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/commons-httpclient.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/commons-logging-1.1.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/concurrent.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cryptix32.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cryptix-asn1.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/cryptix.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/globus_delegation_service.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/globus_delegation_stubs.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/globus_wsrf_mds_aggregator_stubs.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/globus_wsrf_rendezvous_service.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/globus_wsrf_rendezvous_stubs.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/globus_wsrf_rft_stubs.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/gram-client.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/gram-stubs.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/gram-utils.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/j2ssh-common-0.2.2.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/j2ssh-core-0.2.2-patch-b.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/jakarta-regexp-1.2.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/jakarta-slide-webdavlib-2.0.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/jaxrpc.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/jce-jdk13-131.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/jgss.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/jline-0.9.94.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/jsr173_1.0_api.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/jug-lgpl-2.0.0.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/junit.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/log4j-1.2.8.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/naming-common.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/naming-factory.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/naming-java.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/naming-resources.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/opensaml.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/puretls.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/resolver.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/saaj.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/stringtemplate.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/vdldefinitions.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/wsdl4j.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/wsrf_core.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/wsrf_core_stubs.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/wsrf_mds_index_stubs.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/wsrf_mds_usefulrp_schema_stubs.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/wsrf_provider_jce.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/wsrf_tools.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/wss4j.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/xalan.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/xbean.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/xbean_xpath.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/xercesImpl.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/xml-apis.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/xmlsec.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/xpp3-1.1.3.4d_b4_min.jar:/userhom3/1/tga/R/library/Swift/exec/../swift/bin/../lib/xstream-1.1.1-patched.jar:
org.griphyn.vdl.karajan.Loader '-config' 'cf' '-tc.file' 'tc' '-sites.file'
'sites.xml' 'rserver.swift' '-pipedir=/tmp/tga/SwiftR/swift.local'
2011-01-24 08:19:37,519-0600 DEBUG Loader Max heap: 238616576
2011-01-24 08:19:37,540-0600 INFO Loader rserver.swift: source file is new.
Recompiling.
2011-01-24 08:19:39,454-0600 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.4111/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
On Sat, Jan 22, 2011 at 2:29 PM, Mihael Hategan <hategan at mcs.anl.gov> wrote:
> 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
> >
> >
> >
> >
> > _______________________________________________
> > Swift-devel mailing list
> > 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
> >
> >
> >
> > _______________________________________________
> > Swift-devel mailing list
> > Swift-devel at ci.uchicago.edu
> > http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/swift-devel/attachments/20110124/21331866/attachment.html>
More information about the Swift-devel
mailing list