[Swift-user] Re: [Swift-devel] errors from HNL machines/swift

[Mihael Hategan]

Can't help you much there. It seems to be a bug in the JVM. Again, I'd
try other versions of java.

On Thu, 2009-07-23 at 15:23 -0500, Michael Andric wrote:
> there are a couple here:  andrew.bsd.uchicago.edu:/tmp/hs*.log
> 
> On Thu, Jul 23, 2009 at 1:20 PM, Mihael Hategan <hategan at mcs.anl.gov>
> wrote:
>         There's a JVM dump, namely hs_err_pid32310.log. I'd like to
>         see that.
>         
>         Otherwise it seems related to this:
>         http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6390352
>         
>         You could try a newer JVM and see if the problem persists.
>         
>         
>         On Thu, 2009-07-23 at 13:13 -0500, Michael Andric wrote:
>         > HI Support, Swift dev, anyone else reading,
>         >
>         > I keep getting this crash on swift jobs submitted from HNL
>         machines
>         > (both andrew.bsd.uchicago.edu and gwynn.bsd.uchicago.edu).
>          These
>         > happen for different workflows, involving different
>         processes.  I am
>         > totally in the dark as to what this error is referring to as
>         well as
>         > to what may be causing it.  This crash has occurred on
>         workflows that
>         > have just gone 'Active' as well as on workflows that were
>         running for
>         > hours before crashing.
>         >
>         >
>         > Below is the error message.  The log file is too big to
>         attach but can
>         > be found here:
>         > /gpfs/pads/fmri/cnari/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/tpChiSqTests-20090723-1113-na2cuboc.log
>         > from one of the HNL machines (e.g., gwynn.bsd.uchicago.edu)
>         >
>         >
>         > Any insight is hugely appreciated - like i said, i don't
>         even know
>         > what to debug b/c i don't know what the error is referring
>         to.
>         > Michael
>         >
>         >
>         >
>         >
>         >
>         >
>         >
>         > Progress:  Submitted:11 Active:1
>         > Progress:  Active:10 Stage out:2
>         > #
>         > # An unexpected error has been detected by HotSpot Virtual
>         Machine:
>         > #
>         > #  SIGBUS (0x7) at pc=0xb75b9a62, pid=32310, tid=2949090208
>         > #
>         > # Java VM: Java HotSpot(TM) Client VM (1.5.0_06-b05 mixed
>         mode,
>         > sharing)
>         > # Problematic frame:
>         > # C  [libzip.so+0xfa62]
>         > #
>         > # An error report file with more information is saved as
>         > hs_err_pid32310.log
>         > #
>         > # If you would like to submit a bug report, please visit:
>         > #   http://java.sun.com/webapps/bugreport/crash.jsp
>         > #
>         > /gpfs/pads/fmri/apps/swift/bin/swift: line 100: 32310
>         Aborted
>         > java -Xmx2048M
>         >
>         -Djava.endorsed.dirs=/gpfs/pads/fmri/apps/swift/bin/../lib/endorsed
>         > -DUID=1309 -DGLOBUS_TCP_PORT_RANGE=50000,51000
>         > -DGLOBUS_HOSTNAME=andrew.bsd.uchicago.edu
>         -DCOG_INSTALL_PATH=/gpfs/pads/fmri/apps/swift/bin/..
>         -Dvds.home=/gpfs/pads/fmri/apps/swift/bin/..
>         -Dswift.home=/gpfs/pads/fmri/apps/swift/bin/..
>         -Djava.security.egd=file:///dev/urandom -Xmx1024m
>         -classpath /gpfs/pads/fmri/apps/swift/bin/../etc:/gpfs/pads/fmri/apps/swift/bin/../libexec:/gpfs/pads/fmri/apps/swift/bin/../lib/addressing-1.0.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/ant.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/antlr-2.7.5.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/axis.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/axis-url.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/backport-util-concurrent.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/castor-0.9.6.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/coaster-bootstrap.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-abstraction-common-2.3.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-axis.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-grapheditor-0.47.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-jglobus-dev-080222.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-karajan-0.36-dev.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-provider-clref-gt4_0_0.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-provider-coaster-0.2.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-provider-dcache-0.1.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-provider-gt2-2.4.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-provider-gt4_0_0-2.5.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-provider-local-2.2.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-provider-localscheduler-0.4.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-provider-ssh-2.4.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-provider-webdav-2.1.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-resources-1.0.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-swift-svn.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-trap-1.0.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-url.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cog-util-0.92.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/commonj.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/commons-beanutils.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/commons-collections-3.0.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/commons-digester.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/commons-discovery.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/commons-httpclient.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/commons-logging-1.1.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/concurrent.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cryptix32.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cryptix-asn1.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/cryptix.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/globus_delegation_service.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/globus_delegation_stubs.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/globus_wsrf_mds_aggregator_stubs.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/globus_wsrf_rendezvous_service.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/globus_wsrf_rendezvous_stubs.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/globus_wsrf_rft_stubs.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/gram-client.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/gram-stubs.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/gram-utils.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/gvds.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/j2ssh-common-0.2.2.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/j2ssh-core-0.2.2-patched.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/jakarta-regexp-1.2.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/jakarta-slide-webdavlib-2.0.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/jaxrpc.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/jce-jdk13-131.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/jgss.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/jsr173_1.0_api.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/jug-lgpl-2.0.0.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/junit.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/log4j-1.2.8.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/naming-common.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/naming-factory.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/naming-java.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/naming-resources.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/opensaml.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/puretls.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/resolver.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/saaj.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/stringtemplate.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/vdldefinitions.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/wsdl4j.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/wsrf_core.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/wsrf_core_stubs.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/wsrf_mds_index_stubs.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/wsrf_mds_usefulrp_schema_stubs.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/wsrf_provider_jce.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/wsrf_tools.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/wss4j.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/xalan.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/xbean.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/xbean_xpath.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/xercesImpl.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/xml-apis.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/xmlsec.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/xpp3-1.1.3.4d_b4_min.jar:/gpfs/pads/fmri/apps/swift/bin/../lib/xstream-1.1.1-patched.jar: org.griphyn.vdl.karajan.Loader 'tpChiSqTests.swift' '-sites.file' '/gpfs/pads/fmri/cnari_svn/config/coaster_ranger.xml' '-user=andric'
>         
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