[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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