[Swift-user] errors from HNL machines/swift

[Michael Andric]

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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