[Swift-user] [CI Ticketing System #1372] errors from HNL machines/swift
Ti Leggett
support at ci.uchicago.edu
Fri Jul 24 08:50:21 CDT 2009
Try adding +java-1.6.0_03-sun-r1 above any other lines in your ~/.soft
and run resoft. See if that helps your issues.
On Thu Jul 23 15:33:34 2009, hategan at mcs.anl.gov wrote:
> 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:/gpf
s/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'
> >
> > > _______________________________________________
> > > Swift-devel mailing list
> > > Swift-devel at ci.uchicago.edu
> > > http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> >
> >
>
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