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.<br>
<br>I still get exactly the same failure.<br><br><br>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=<a href="http://ibicluster.uchicago.cc">ibicluster.uchicago.cc</a> -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'<br>
<br><br><br>2011-01-24 08:19:37,519-0600 DEBUG Loader Max heap: 238616576<br>2011-01-24 08:19:37,540-0600 INFO Loader rserver.swift: source file is new. Recompiling.<br>2011-01-24 08:19:39,454-0600 DEBUG Loader Detailed exception:<br>
org.griphyn.vdl.karajan.CompilationException: Unable to parse intermediate XML<br> at org.griphyn.vdl.engine.Karajan.compile(Karajan.java:98)<br> at org.griphyn.vdl.karajan.Loader.compile(Loader.java:300)<br>
at org.griphyn.vdl.karajan.Loader.main(Loader.java:145)<br>Caused by: org.apache.xmlbeans.XmlException: /tmp/tga/SwiftR/swift.local.4111/rserver.xml:2:1: error: Unexpected end of file after null<br> at org.apache.xmlbeans.impl.store.Locale$SaxLoader.load(Locale.java:3467)<br>
at org.apache.xmlbeans.impl.store.Locale.parseToXmlObject(Locale.java:1270)<br> at org.apache.xmlbeans.impl.store.Locale.parseToXmlObject(Locale.java:1257)<br> at org.apache.xmlbeans.impl.schema.SchemaTypeLoaderBase.parse(SchemaTypeLoaderBase.java:345)<br>
at org.apache.xmlbeans.impl.schema.SchemaTypeLoaderBase.parse(SchemaTypeLoaderBase.java:252)<br> at org.globus.swift.language.ProgramDocument$Factory.parse(ProgramDocument.java:499)<br> at org.griphyn.vdl.engine.Karajan.parseProgramXML(Karajan.java:122)<br>
at org.griphyn.vdl.engine.Karajan.compile(Karajan.java:96)<br> ... 2 more<br>Caused by: org.xml.sax.SAXParseException: Unexpected end of file after null<br> at org.apache.xmlbeans.impl.piccolo.xml.Piccolo.reportFatalError(Piccolo.java:1038)<br>
at org.apache.xmlbeans.impl.piccolo.xml.Piccolo.parse(Piccolo.java:723)<br> at org.apache.xmlbeans.impl.store.Locale$SaxLoader.load(Locale.java:3435)<br> ... 9 more<br><br><br><div class="gmail_quote">
On Sat, Jan 22, 2011 at 2:29 PM, Mihael Hategan <span dir="ltr"><<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I don't think I have access to said cluster, but it may be worth getting<br>
some recent version of xerces, sticking it into some directory,<br>
specifying java.endorsed.dirs and seeing if that fixes the problem with<br>
1.6.0_07-b06.<br>
<font color="#888888"><br>
Mihael<br>
</font><div><div></div><div class="h5"><br>
On Sat, 2011-01-22 at 12:08 -0600, Tim Armstrong wrote:<br>
> Thanks, that appears to fix it. It is a very strange issue. It<br>
> almost looks like the output from the .swift -> .xml stage isn't<br>
> written to the .xml file before the next stage tries to read. Either<br>
> that or there is a silent failure somewhere in that stage<br>
><br>
> On Sat, Jan 22, 2011 at 7:09 AM, Michael Wilde <<a href="mailto:wilde@mcs.anl.gov">wilde@mcs.anl.gov</a>><br>
> wrote:<br>
> Mihael commented on this problem in this post Nov 3:<br>
> <a href="http://mail.ci.uchicago.edu/mailman/private/swift-devel/2010-November/006990.html" target="_blank">http://mail.ci.uchicago.edu/mailman/private/swift-devel/2010-November/006990.html</a><br>
> (likely SAX incompatibility problem with that particular Java<br>
> version)<br>
><br>
><br>
> ______________________________________________________________<br>
><br>
> Tim, I forgot to mention: on IBI you need to use the<br>
> Java in my home dir (or any recent Java). The<br>
> particular SUn java thats the default there has some<br>
> weird issue in xml parsing that causes this failure.<br>
><br>
><br>
> - Mike<br>
><br>
><br>
> ______________________________________________________<br>
> Hi,<br>
> I'm trying to get a Swift script running on<br>
> the IBI cluster but have been running into<br>
> some issues. I'm using a recent development<br>
> version 3029. Running the script fails at the<br>
> compile stage.<br>
><br>
> Strangely, this script compiles without issue<br>
> using exactly the same swift on other<br>
> machines.<br>
> Even more strangely, it looks like the swift<br>
> -> intermediate xml step completes without<br>
> any exceptions being thrown, but when I look<br>
> at the xml file it contains precisely zero<br>
> bytes. It appears that this is what actually<br>
> causes the karajan parser to crash.<br>
> What would cause the first compile step to<br>
> complete without causing an exception but not<br>
> produce any output? Do we maybe have a<br>
> buffering issue? Any suggestions for how I<br>
> might solve this?<br>
><br>
> The log contents are:<br>
><br>
> 2011-01-21 16:43:13,448-0600 DEBUG Loader Max<br>
> heap: 238616576<br>
> 2011-01-21 16:43:13,449-0600 INFO Loader<br>
> rserver.swift: source file is new.<br>
> Recompiling.<br>
> 2011-01-21 16:43:13,919-0600 DEBUG Loader<br>
> Detailed exception:<br>
> org.griphyn.vdl.karajan.CompilationException:<br>
> Unable to parse intermediate XML<br>
> at<br>
> org.griphyn.vdl.engine.Karajan.compile(Karajan.java:98)<br>
> at<br>
> org.griphyn.vdl.karajan.Loader.compile(Loader.java:300)<br>
> at<br>
> org.griphyn.vdl.karajan.Loader.main(Loader.java:145)<br>
> Caused by:<br>
> org.apache.xmlbeans.XmlException: /tmp/tga/SwiftR/swift.local.2306/rserver.xml:2:1: error: Unexpected end of file after null<br>
> at<br>
> org.apache.xmlbeans.impl.store.Locale<br>
> $SaxLoader.load(Locale.java:3467)<br>
> at<br>
> org.apache.xmlbeans.impl.store.Locale.parseToXmlObject(Locale.java:1270)<br>
> at<br>
> org.apache.xmlbeans.impl.store.Locale.parseToXmlObject(Locale.java:1257)<br>
> at<br>
> org.apache.xmlbeans.impl.schema.SchemaTypeLoaderBase.parse(SchemaTypeLoaderBase.java:345)<br>
> at<br>
> org.apache.xmlbeans.impl.schema.SchemaTypeLoaderBase.parse(SchemaTypeLoaderBase.java:252)<br>
> at<br>
> org.globus.swift.language.ProgramDocument<br>
> $Factory.parse(ProgramDocument.java:499)<br>
> at<br>
> org.griphyn.vdl.engine.Karajan.parseProgramXML(Karajan.java:122)<br>
> at<br>
> org.griphyn.vdl.engine.Karajan.compile(Karajan.java:96)<br>
> ... 2 more<br>
> Caused by: org.xml.sax.SAXParseException:<br>
> Unexpected end of file after null<br>
> at<br>
> org.apache.xmlbeans.impl.piccolo.xml.Piccolo.reportFatalError(Piccolo.java:1038)<br>
> at<br>
> org.apache.xmlbeans.impl.piccolo.xml.Piccolo.parse(Piccolo.java:723)<br>
> at<br>
> org.apache.xmlbeans.impl.store.Locale<br>
> $SaxLoader.load(Locale.java:3435)<br>
> ... 9 more<br>
><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Swift-devel mailing list<br>
> <a href="mailto:Swift-devel@ci.uchicago.edu">Swift-devel@ci.uchicago.edu</a><br>
> <a href="http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel" target="_blank">http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel</a><br>
><br>
><br>
><br>
> --<br>
> Michael Wilde<br>
> Computation Institute, University of Chicago<br>
> Mathematics and Computer Science Division<br>
> Argonne National Laboratory<br>
><br>
><br>
><br>
><br>
><br>
> --<br>
> Michael Wilde<br>
> Computation Institute, University of Chicago<br>
> Mathematics and Computer Science Division<br>
> Argonne National Laboratory<br>
><br>
><br>
><br>
> _______________________________________________<br>
> Swift-devel mailing list<br>
> <a href="mailto:Swift-devel@ci.uchicago.edu">Swift-devel@ci.uchicago.edu</a><br>
> <a href="http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel" target="_blank">http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel</a><br>
<br>
<br>
</div></div></blockquote></div><br>