Uncaught Exception while loading ontology - Segmentation error

[GoogleCodeExporter]

What steps will reproduce the problem?
1. runme_HIGH.sh
2. load from bookmark:  http://bioinfo.icapture.ubc.ca/subversion/BuildOWL/
Ontologies/MOBY_Objects.owl
3. during the load it dies

Note:  This is an IBM P570 with four processors and 12Gig memory on a 
logical partition.

What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?
SWOOP 2.2.2 from Google Code

Please provide any additional information below.
I have no (conspicuous) problems with other ontologies.  I know there's a 
problem in that ontology because I can't get Pellet to reason over it, but 
I'm trying to debug it.

full error message below:




/SW/SWOOP_2.2.2# ./runme_HIGH.sh 
Loaded ontologies: []
Loaded SWOOP Preferences from disk..
Try creating renderer 
org.mindswap.swoop.renderer.ontology.SwoopOntologyInfo
Try creating renderer 
org.mindswap.swoop.renderer.ontology.SwoopSpeciesValidationRenderer
Try creating reasoner org.mindswap.swoop.reasoner.PelletReasoner
Try creating reasoner org.mindswap.swoop.reasoner.SwoopRDFSReasoner
Try creating reasoner org.mindswap.swoop.reasoner.SwoopToldReasoner
loading ontology: start time-- 11:11:0:322
parsing ontology in RDF: start time-- 11:11:0:760
RDFParser: Importing: http://biomoby.org/RESOURCES/MOBY-S/Namespaces
RDFParser: No Logical URI can be determined. Using physical URI: http://
biomoby.org/RESOURCES/MOBY-S/Namespaces
parsing ontology in RDF: end time-- 11:11:3:926
Model changed 3
Unhandled exception
Type=Segmentation error vmState=0x00000000
Target=2_30_20060220_05389_BHdSMr (Linux 2.6.5-7.244-pseries64)
CPU=ppc64 (4 logical CPUs) (0x2f24e5000 RAM)
J9Generic_Signal_Number=00000004 Signal_Number=0000000b 
Error_Value=00000000 Signal_Code=00000001
Handler1=00000080005A1238 Handler2=0000008000653F80
R0=0000000000000000 R1=000000802543DC40 R2=00000080010DEE88 
R3=0000800913414800
R4=0000000000000D90 R5=00000000103E92C4 R6=00000080253051E1 
R7=00000000103E92B4
R8=0000008025305609 R9=000000001061FAD8 R10=000000802543F340 
R11=0000008025301030
R12=FFFFFFFFFFFFFF78 R13=0000008025446920 R14=00000080253051F0 
R15=00000080252FAA00
R16=0000000000000003 R17=0000000000000000 R18=00000080005AA1E8 
R19=00000000000000E6
R20=0000008022D0D778 R21=0000008025305220 R22=000000800B331528 
R23=0000000000000000
R24=0000000000000000 R25=0000008005CD0768 R26=0000008005C09F48 
R27=000000800ABCEA78
R28=0000008025305609 R29=00000080062B8B98 R30=0000008009133E58 
R31=0000000000000000
NIP=000000800104ECF8 MSR=800000000000D032 ORIG_GPR3=000000802543D578 
CTR=000000800104ECB0
LINK=0000008000BFDE68 XER=0000000000000000 CCR=0000000044002484 
SOFTE=0000000000000000
TRAP=0000000000000380 DAR=0000800913414810 dsisr=0000000000200000 
RESULT=0000000000000000
FPR0 3fe8000000000000 (f: 0.000000, d: 7.500000e-01)
FPR1 4028000000000000 (f: 0.000000, d: 1.200000e+01)
FPR2 c1e0000000000000 (f: 0.000000, d: -2.147484e+09)
FPR3 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR4 c3e0000000000000 (f: 0.000000, d: -9.223372e+18)
FPR5 c330000000000000 (f: 0.000000, d: -4.503600e+15)
FPR6 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR7 00000080236f5038 (f: 594497600.000000, d: 2.719092e-312)
FPR8 00000080236f5218 (f: 594498048.000000, d: 2.719092e-312)
FPR9 00000080236f5200 (f: 594498048.000000, d: 2.719092e-312)
FPR10 00000080236f51d0 (f: 594497984.000000, d: 2.719092e-312)
FPR11 4070000000000000 (f: 0.000000, d: 2.560000e+02)
FPR12 3fe8000000000000 (f: 0.000000, d: 7.500000e-01)
FPR13 4068000000000000 (f: 0.000000, d: 1.920000e+02)
FPR14 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR15 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR16 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR17 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR18 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR19 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR20 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR21 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR22 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR23 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR24 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR25 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR26 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR27 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR28 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR29 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR30 0000000000000000 (f: 0.000000, d: 0.000000e+00)
FPR31 0000000000000000 (f: 0.000000, d: 0.000000e+00)
Module=/opt/ibm/java2-ppc64-50/jre/bin/libjclscar_23.so
Module_base_address=000000800101A000
JVMDUMP006I Processing Dump Event "gpf", detail "" - Please Wait.
JVMDUMP007I JVM Requesting System Dump using '/root/SW/SWOOP_2.2.2/
core.20070221.111103.20404.dmp'
JVMDUMP010I System Dump written to /root/SW/SWOOP_2.2.2/
core.20070221.111103.20404.dmp
JVMDUMP007I JVM Requesting Snap Dump using '/root/SW/SWOOP_2.2.2/
Snap0001.20070221.111103.20404.trc'
JVMDUMP010I Snap Dump written to /root/SW/SWOOP_2.2.2/
Snap0001.20070221.111103.20404.trc
JVMDUMP007I JVM Requesting Java Dump using '/root/SW/SWOOP_2.2.2/
javacore.20070221.111103.20404.txt'
JVMDUMP012E Error in Java Dump: /root/SW/SWOOP_2.2.2/
javacore.20070221.111103.20404.txt
JVMDUMP013I Processed Dump Event "gpf", detail "".

Original issue reported on code.google.com by [email protected] on 21 Feb 2007 at 7:21