JAXB 2.1 w/JDK 6 Error. bootstrap classloader issue.

When I run one of my JUnit tests, I get this error:
JAXB 2.0 API is being loaded from the bootstrap classloader, but this RI (from jar:file:/usr/local/netbeans-6.0/java1/modules/ext/jaxws21/jaxb-impl.jar!/com/sun/xml/bind/v2/model/impl/ModelBuilder.class) needs 2.1 API. Use the endorsed directory mechanism to place jaxb-api.jar in the bootstrap classloader.
So, I copy jaxb-api.jar into /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/endorsed/jaxb-impl.jar
Then I get this error:
JAXB 2.0 API is being loaded from the bootstrap classloader, but this RI (from jar:file:/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/endorsed/jaxb-impl.jar!/com/sun/xml/bind/v2/model/impl/ModelBuilder.class) needs 2.1 API
OS: Ubuntu 7.10
JVM: Sun 1.6.0.03
IDE: NetBeans 6.0
How do I resolve?

This seems to be the answer: https://jaxb.dev.java.net/guide/Migrating_JAXB_2_0_applications_to_JavaSE_6.html#Using_JAXB_2_1_with_JavaSE_6
Place the 2.1 jaxb-api.jar into $JRE_HOME/lib/endorsed. This essentially makes your JRE to "JRE 6 + JAXB 2.1". This won't affect any other applications that use this JRE, and it's easy. On the other hand, in various scenarios you may not be able to alter the JRE.

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    In the /home/username/WebNMS/apache/tomcat/webapps/WebServices/WEB-INF/lib directory is where all the jar files from JAX-WS 2.2.6 are, including jaxb-api.jar.
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    This seems to be the answer: https://jaxb.dev.java.net/guide/Migrating_JAXB_2_0_applications_to_JavaSE_6.html#Using_JAXB_2_1_with_JavaSE_6
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    Please find below is C:\usr\sap\J2E\JC00\work\dev_server0 content
    trc file: "C:\usr\sap\J2E\JC00\work\dev_server0", trc level: 1, release: "640"
    node name   : ID4467550
    pid         : 5648
    system name : J2E
    system nr.  : 00
    started at  : Tue Sep 04 10:03:42 2007
    arguments   :
        arg[00] : C:\usr\sap\J2E\JC00/j2ee/os_libs/jlaunch.exe
        arg[01] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
        arg[02] : -DSAPINFO=J2E_00_server
        arg[03] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
    [Thr 4672] Tue Sep 04 10:03:42 2007
    [Thr 4672] *** ERROR => Invalid property value [box.number/J2EJC00senthil] [jstartxx.c   789]
    [Thr 4672] *** ERROR => Invalid property value [en.host/PWDF3013] [jstartxx.c   789]
    [Thr 4672] *** ERROR => Invalid property value [en.port/3201] [jstartxx.c   789]
    [Thr 4672] *** ERROR => Invalid property value [system.id/0] [jstartxx.c   789]
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    -> ms host    : senthil
    -> ms port    : 3601
    -> OS libs    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> Admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Used property files
    -> files [00] : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    Instance properties
    -> ms host    : senthil
    -> ms port    : 3601
    -> os libs    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Bootstrap nodes
    -> [00] bootstrap            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [01] bootstrap_ID4467500  : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [02] bootstrap_ID4467550  : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    Worker nodes
    -> [00] ID4467500            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [01] ID4467550            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    [Thr 4672] JLaunchRequestQueueInit: create named pipe for ipc
    [Thr 4672] JLaunchRequestQueueInit: create pipe listener thread
    [Thr 2992] WaitSyncSemThread: Thread 2992 started as semaphore monitor thread.
    [Thr 3280] JLaunchRequestFunc: Thread 3280 started as listener thread for np messages.
    [Thr 4672] Tue Sep 04 10:03:43 2007
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    [Thr 4672] [Node: server0] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_08
    JStartupIReadSection: read node properties [ID4467550]
    -> node name       : server0
    -> node type       : server
    -> java path       : C:\j2sdk1.4.2_08
    -> java parameters : -Djava.security.policy=./java.policy -Djava.security.egd=file:/dev/urandom -Dorg.omg.CORBA.ORBClass=com.sap.engine.system.ORBProxy -Dorg.omg.CORBA.ORBSingletonClass=com.sap.engine.system.ORBSingletonProxy -Djavax.rmi.CORBA.PortableRemoteObjectClass=com.sap.engine.system.PortableRemoteObjectProxy -Djco.jarm=1 -Dsun.io.useCanonCaches=false -verbose:gc -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar -Dsys.global.dir=C:/usr/sap/J2E/SYS/global -Djava.awt.headless=true -XX:NewSize=85m -XX:MaxNewSize=85m -XX:MaxPermSize=192m -XX:PermSize=192m -XX:DisableExplicitGC -XX:UseParNewGC -XX:PrintGCDetails -XX:PrintGCTimeStamps -XX:SurvivorRatio=2 -XX:TargetSurvivorRatio=90 -XX:SoftRefLRUPolicyMSPerMB=1 -verbose:gc
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    -> java vm vendor  : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type    : server
    -> java vm cpu     : x86
    -> heap size       : 512M
    -> init heap size  : 512M
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    -> registr. class  : com.sap.bc.proj.jstartup.JStartupNatives
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    -> debuggable      : yes
    -> debug mode      : no
    -> debug port      : 50021
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    [Thr 4932] JLaunchIStartFunc: Thread 4932 started as Java VM thread.
    JHVM_LoadJavaVM: VM Arguments of node [server0]
    -> stack   : 262144 Bytes
    -> arg[  0]: exit
    -> arg[  1]: abort
    -> arg[  2]: -Djava.security.policy=./java.policy
    -> arg[  3]: -Djava.security.egd=file:/dev/urandom
    -> arg[  4]: -Dorg.omg.CORBA.ORBClass=com.sap.engine.system.ORBProxy
    -> arg[  5]: -Dorg.omg.CORBA.ORBSingletonClass=com.sap.engine.system.ORBSingletonProxy
    -> arg[  6]: -Djavax.rmi.CORBA.PortableRemoteObjectClass=com.sap.engine.system.PortableRemoteObjectProxy
    -> arg[  7]: -Djco.jarm=1
    -> arg[  8]: -Dsun.io.useCanonCaches=false
    -> arg[  9]: -verbose:gc
    -> arg[ 10]: -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar
    -> arg[ 11]: -Dsys.global.dir=C:/usr/sap/J2E/SYS/global
    -> arg[ 12]: -Djava.awt.headless=true
    -> arg[ 13]: -XX:NewSize=85m
    -> arg[ 14]: -XX:MaxNewSize=85m
    -> arg[ 15]: -XX:MaxPermSize=192m
    -> arg[ 16]: -XX:PermSize=192m
    -> arg[ 17]: -XX:+DisableExplicitGC
    -> arg[ 18]: -XX:+UseParNewGC
    -> arg[ 19]: -XX:+PrintGCDetails
    -> arg[ 20]: -XX:+PrintGCTimeStamps
    -> arg[ 21]: -XX:SurvivorRatio=2
    -> arg[ 22]: -XX:TargetSurvivorRatio=90
    -> arg[ 23]: -XX:SoftRefLRUPolicyMSPerMB=1
    -> arg[ 24]: -verbose:gc
    -> arg[ 25]: -Dsys.global.dir=C:\usr\sap\J2E\SYS\global
    -> arg[ 26]: -Dapplication.home=C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> arg[ 27]: -Djava.class.path=C:\usr\sap\J2E\JC00\j2ee\os_libs\jstartup.jar;.\bin\boot\boot.jar;.\bin\boot\jaas.jar;.\bin\system\bytecode.jar;.
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    -> arg[ 29]: -Dmemory.manager=512M
    -> arg[ 30]: -Xmx512M
    -> arg[ 31]: -Xms512M
    -> arg[ 32]: -DLoadBalanceRestricted=no
    -> arg[ 33]: -Djstartup.mode=JCONTROL
    -> arg[ 34]: -Djstartup.ownProcessId=5648
    -> arg[ 35]: -Djstartup.ownHardwareId=Z2123283434
    -> arg[ 36]: -Djstartup.whoami=server
    -> arg[ 37]: -Djstartup.debuggable=yes
    -> arg[ 38]: -DSAPINFO=J2E_00_server
    -> arg[ 39]: -DSAPSTARTUP=1
    -> arg[ 40]: -DSAPSYSTEM=00
    -> arg[ 41]: -DSAPSYSTEMNAME=J2E
    -> arg[ 42]: -DSAPMYNAME=senthil_J2E_00
    -> arg[ 43]: -DSAPDBHOST=
    -> arg[ 44]: -Dj2ee.dbhost=senthil
    [Thr 4932] JHVM_LoadJavaVM: Java VM created OK.
    JHVM_BuildArgumentList: main method arguments of node [server0]
    [Thr 5412] Tue Sep 04 10:03:50 2007
    [Thr 5412] JHVM_RegisterNatives: registering methods in com.sap.bc.proj.jstartup.JStartupFramework
    [Thr 5412] JLaunchISetClusterId: set cluster id 4467550
    [Thr 5412] JLaunchISetState: change state from [Initial (0)] to [Waiting for start (1)]
    [Thr 5412] JLaunchISetState: change state from [Waiting for start (1)] to [Starting (2)]
    [Thr 5184] Tue Sep 04 10:04:23 2007
    [Thr 5184] JHVM_RegisterNatives: registering methods in com.sap.security.core.server.vsi.service.jni.VirusScanInterface
    [Thr 5184] *** ERROR => JHVM_RegisterNatives: registration for class com.sap.security.core.server.vsi.service.jni.VirusScanInterface failed. [jhvmxx.c     338]
    [Thr 5412] Tue Sep 04 10:04:49 2007
    [Thr 5412] JLaunchISetState: change state from [Starting (2)] to [Starting applications (10)]
    [Thr 3120] Tue Sep 04 10:04:50 2007
    [Thr 3120] JHVM_RegisterNatives: registering methods in com.sap.mw.rfc.driver.CpicDriver
    [Thr 336] Tue Sep 04 10:09:06 2007
    [Thr 336] JLaunchISetState: change state from [Starting applications (10)] to [Running (3)]
    [Thr 2592] Tue Sep 04 12:34:36 2007
    [Thr 2592] JLaunchIExitJava: exit hook is called (rc=-337)
    [Thr 2592] JLaunchCloseProgram: good bye (exitcode=-337)
    trc file: "C:\usr\sap\J2E\JC00\work\dev_server0", trc level: 1, release: "640"
    node name   : ID4467550
    pid         : 1432
    system name : J2E
    system nr.  : 00
    started at  : Tue Sep 04 12:34:40 2007
    arguments   :
        arg[00] : C:\usr\sap\J2E\JC00/j2ee/os_libs/jlaunch.exe
        arg[01] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
        arg[02] : -DSAPINFO=J2E_00_server
        arg[03] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
    [Thr 5984] Tue Sep 04 12:34:40 2007
    [Thr 5984] *** ERROR => Invalid property value [box.number/J2EJC00senthil] [jstartxx.c   789]
    [Thr 5984] *** ERROR => Invalid property value [en.host/PWDF3013] [jstartxx.c   789]
    [Thr 5984] *** ERROR => Invalid property value [en.port/3201] [jstartxx.c   789]
    [Thr 5984] *** ERROR => Invalid property value [system.id/0] [jstartxx.c   789]
    JStartupReadInstanceProperties: read instance properties [C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties]
    -> ms host    : senthil
    -> ms port    : 3601
    -> OS libs    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> Admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Used property files
    -> files [00] : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    Instance properties
    -> ms host    : senthil
    -> ms port    : 3601
    -> os libs    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Bootstrap nodes
    -> [00] bootstrap            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [01] bootstrap_ID4467500  : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [02] bootstrap_ID4467550  : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    Worker nodes
    -> [00] ID4467500            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [01] ID4467550            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    [Thr 5984] JLaunchRequestQueueInit: create named pipe for ipc
    [Thr 5984] JLaunchRequestQueueInit: create pipe listener thread
    [Thr 5096] JLaunchRequestFunc: Thread 5096 started as listener thread for np messages.
    [Thr 1600] WaitSyncSemThread: Thread 1600 started as semaphore monitor thread.
    [Thr 5984] Tue Sep 04 12:34:41 2007
    [Thr 5984] INFO: Invalid property value [JLaunchParameters/]
    [Thr 5984] [Node: server0] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_08
    JStartupIReadSection: read node properties [ID4467550]
    -> node name       : server0
    -> node type       : server
    -> java path       : C:\j2sdk1.4.2_08
    -> java parameters : -Djava.security.policy=./java.policy -Djava.security.egd=file:/dev/urandom -Dorg.omg.CORBA.ORBClass=com.sap.engine.system.ORBProxy -Dorg.omg.CORBA.ORBSingletonClass=com.sap.engine.system.ORBSingletonProxy -Djavax.rmi.CORBA.PortableRemoteObjectClass=com.sap.engine.system.PortableRemoteObjectProxy -Djco.jarm=1 -Dsun.io.useCanonCaches=false -verbose:gc -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar -Dsys.global.dir=C:/usr/sap/J2E/SYS/global -Djava.awt.headless=true -XX:NewSize=85m -XX:MaxNewSize=85m -XX:MaxPermSize=192m -XX:PermSize=192m -XX:DisableExplicitGC -XX:UseParNewGC -XX:PrintGCDetails -XX:PrintGCTimeStamps -XX:SurvivorRatio=2 -XX:TargetSurvivorRatio=90 -XX:SoftRefLRUPolicyMSPerMB=1 -verbose:gc
    -> java vm version : 1.4.2_08-b03
    -> java vm vendor  : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type    : server
    -> java vm cpu     : x86
    -> heap size       : 512M
    -> init heap size  : 512M
    -> root path       : C:\usr\sap\J2E\JC00\j2ee\cluster\server0
    -> class path      : .\bin\boot\boot.jar;.\bin\boot\jaas.jar;.\bin\system\bytecode.jar;.
    -> OS libs path    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> main class      : com.sap.engine.boot.Start
    -> framework class : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class  : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path  : C:\usr\sap\J2E\JC00\j2ee\os_libs\jstartup.jar
    -> shutdown class  : com.sap.engine.boot.Start
    -> parameters      :
    -> debuggable      : yes
    -> debug mode      : no
    -> debug port      : 50021
    -> shutdown timeout: 120000
    [Thr 5984] JLaunchISetDebugMode: set debug mode [no]
    [Thr 4812] JLaunchIStartFunc: Thread 4812 started as Java VM thread.
    JHVM_LoadJavaVM: VM Arguments of node [server0]
    -> stack   : 262144 Bytes
    -> arg[  0]: exit
    -> arg[  1]: abort
    -> arg[  2]: -Djava.security.policy=./java.policy
    -> arg[  3]: -Djava.security.egd=file:/dev/urandom
    -> arg[  4]: -Dorg.omg.CORBA.ORBClass=com.sap.engine.system.ORBProxy
    -> arg[  5]: -Dorg.omg.CORBA.ORBSingletonClass=com.sap.engine.system.ORBSingletonProxy
    -> arg[  6]: -Djavax.rmi.CORBA.PortableRemoteObjectClass=com.sap.engine.system.PortableRemoteObjectProxy
    -> arg[  7]: -Djco.jarm=1
    -> arg[  8]: -Dsun.io.useCanonCaches=false
    -> arg[  9]: -verbose:gc
    -> arg[ 10]: -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar
    -> arg[ 11]: -Dsys.global.dir=C:/usr/sap/J2E/SYS/global
    -> arg[ 12]: -Djava.awt.headless=true
    -> arg[ 13]: -XX:NewSize=85m
    -> arg[ 14]: -XX:MaxNewSize=85m
    -> arg[ 15]: -XX:MaxPermSize=192m
    -> arg[ 16]: -XX:PermSize=192m
    -> arg[ 17]: -XX:+DisableExplicitGC
    -> arg[ 18]: -XX:+UseParNewGC
    -> arg[ 19]: -XX:+PrintGCDetails
    -> arg[ 20]: -XX:+PrintGCTimeStamps
    -> arg[ 21]: -XX:SurvivorRatio=2
    -> arg[ 22]: -XX:TargetSurvivorRatio=90
    -> arg[ 23]: -XX:SoftRefLRUPolicyMSPerMB=1
    -> arg[ 24]: -verbose:gc
    -> arg[ 25]: -Dsys.global.dir=C:\usr\sap\J2E\SYS\global
    -> arg[ 26]: -Dapplication.home=C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> arg[ 27]: -Djava.class.path=C:\usr\sap\J2E\JC00\j2ee\os_libs\jstartup.jar;.\bin\boot\boot.jar;.\bin\boot\jaas.jar;.\bin\system\bytecode.jar;.
    -> arg[ 28]: -Djava.library.path=C:\j2sdk1.4.2_08\jre\bin\server;C:\j2sdk1.4.2_08\jre\bin;C:\j2sdk1.4.2_08\bin;C:\usr\sap\J2E\JC00\j2ee\os_libs;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI.ACE\;C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727;C:\usr\sap\J2E\SCS01\exe;C:\usr\sap\J2E\JC00\exe;C:\usr\sap\J2E\SYS\exe\run
    -> arg[ 29]: -Dmemory.manager=512M
    -> arg[ 30]: -Xmx512M
    -> arg[ 31]: -Xms512M
    -> arg[ 32]: -DLoadBalanceRestricted=no
    -> arg[ 33]: -Djstartup.mode=JCONTROL
    -> arg[ 34]: -Djstartup.ownProcessId=1432
    -> arg[ 35]: -Djstartup.ownHardwareId=Z2123283434
    -> arg[ 36]: -Djstartup.whoami=server
    -> arg[ 37]: -Djstartup.debuggable=yes
    -> arg[ 38]: -DSAPINFO=J2E_00_server
    -> arg[ 39]: -DSAPSTARTUP=1
    -> arg[ 40]: -DSAPSYSTEM=00
    -> arg[ 41]: -DSAPSYSTEMNAME=J2E
    -> arg[ 42]: -DSAPMYNAME=senthil_J2E_00
    -> arg[ 43]: -DSAPDBHOST=
    -> arg[ 44]: -Dj2ee.dbhost=senthil
    [Thr 4812] Tue Sep 04 12:34:42 2007
    [Thr 4812] JHVM_LoadJavaVM: Java VM created OK.
    JHVM_BuildArgumentList: main method arguments of node [server0]
    [Thr 4216] Tue Sep 04 12:35:05 2007
    [Thr 4216] JHVM_RegisterNatives: registering methods in com.sap.bc.proj.jstartup.JStartupFramework
    [Thr 4216] JLaunchISetClusterId: set cluster id 4467550
    [Thr 4216] JLaunchISetState: change state from [Initial (0)] to [Waiting for start (1)]
    [Thr 4216] JLaunchISetState: change state from [Waiting for start (1)] to [Starting (2)]
    [Thr 5892] Tue Sep 04 12:35:49 2007
    [Thr 5892] JHVM_RegisterNatives: registering methods in com.sap.security.core.server.vsi.service.jni.VirusScanInterface
    [Thr 5892] *** ERROR => JHVM_RegisterNatives: registration for class com.sap.security.core.server.vsi.service.jni.VirusScanInterface failed. [jhvmxx.c     338]
    [Thr 4216] Tue Sep 04 12:36:14 2007
    [Thr 4216] JLaunchISetState: change state from [Starting (2)] to [Starting applications (10)]
    [Thr 516] Tue Sep 04 12:36:16 2007
    [Thr 516] JHVM_RegisterNatives: registering methods in com.sap.mw.rfc.driver.CpicDriver
    [Thr 332] Tue Sep 04 12:41:00 2007
    [Thr 332] JLaunchISetState: change state from [Starting applications (10)] to [Running (3)]
    [Thr 5096] Tue Sep 04 20:53:33 2007
    [Thr 5096] JLaunchRequestFunc: receive command:17, argument:0 from pid:1152
    [Thr 5096] JLaunchIShutdownInvoke: set shutdown interval (stop:1188910413/end:1188910533/TO:120)
    [Thr 5096] JLaunchProcessCommand: Invoke VM Shutdown
    [Thr 5096] JHVM_FrameworkShutdownDirect: invoke direct shutdown
    [Thr 4196] JLaunchISetState: change state from [Running (3)] to [Waiting for stop (4)]
    [Thr 4196] JLaunchISetState: change state from [Waiting for stop (4)] to [Stopping (5)]
    [Thr 4196] Tue Sep 04 20:53:58 2007
    [Thr 4196] JLaunchISetState: change state from [Stopping (5)] to [Stopped (6)]
    [Thr 4988] Tue Sep 04 20:53:59 2007
    [Thr 4988] JLaunchIExitJava: exit hook is called (rc=0)
    [Thr 4988] JLaunchCloseProgram: good bye (exitcode=0)
    trc file: "C:\usr\sap\J2E\JC00\work\dev_server0", trc level: 1, release: "640"
    node name   : ID4467550
    pid         : 272
    system name : J2E
    system nr.  : 00
    started at  : Tue Sep 04 20:54:04 2007
    arguments   :
        arg[00] : C:\usr\sap\J2E\JC00/j2ee/os_libs/jlaunch.exe
        arg[01] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
        arg[02] : -DSAPINFO=J2E_00_server
        arg[03] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
    [Thr 4792] Tue Sep 04 20:54:04 2007
    [Thr 4792] *** ERROR => Invalid property value [box.number/J2EJC00senthil] [jstartxx.c   789]
    [Thr 4792] *** ERROR => Invalid property value [en.host/PWDF3013] [jstartxx.c   789]
    [Thr 4792] *** ERROR => Invalid property value [en.port/3201] [jstartxx.c   789]
    [Thr 4792] *** ERROR => Invalid property value [system.id/0] [jstartxx.c   789]
    JStartupReadInstanceProperties: read instance properties [C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties]
    -> ms host    : senthil
    -> ms port    : 3601
    -> OS libs    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> Admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Used property files
    -> files [00] : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    Instance properties
    -> ms host    : senthil
    -> ms port    : 3601
    -> os libs    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Bootstrap nodes
    -> [00] bootstrap            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [01] bootstrap_ID4467500  : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [02] bootstrap_ID4467550  : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    Worker nodes
    -> [00] ID4467500            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [01] ID4467550            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    [Thr 4792] JLaunchRequestQueueInit: create named pipe for ipc
    [Thr 4792] JLaunchRequestQueueInit: create pipe listener thread
    [Thr 1072] JLaunchRequestFunc: Thread 1072 started as listener thread for np messages.
    [Thr 3240] WaitSyncSemThread: Thread 3240 started as semaphore monitor thread.
    [Thr 4792] Tue Sep 04 20:54:05 2007
    [Thr 4792] INFO: Invalid property value [JLaunchParameters/]
    [Thr 4792] JStartupIReadSection: debug mode is specified by program arguments
    [Thr 4792] [Node: server0] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_08
    JStartupIReadSection: read node properties [ID4467550]
    -> node name       : server0
    -> node type       : server
    -> java path       : C:\j2sdk1.4.2_08
    -> java parameters : -Djava.security.policy=./java.policy -Djava.security.egd=file:/dev/urandom -Dorg.omg.CORBA.ORBClass=com.sap.engine.system.ORBProxy -Dorg.omg.CORBA.ORBSingletonClass=com.sap.engine.system.ORBSingletonProxy -Djavax.rmi.CORBA.PortableRemoteObjectClass=com.sap.engine.system.PortableRemoteObjectProxy -Djco.jarm=1 -Dsun.io.useCanonCaches=false -verbose:gc -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar -Dsys.global.dir=C:/usr/sap/J2E/SYS/global -Djava.awt.headless=true -XX:NewSize=85m -XX:MaxNewSize=85m -XX:MaxPermSize=192m -XX:PermSize=192m -XX:DisableExplicitGC -XX:UseParNewGC -XX:PrintGCDetails -XX:PrintGCTimeStamps -XX:SurvivorRatio=2 -XX:TargetSurvivorRatio=90 -XX:SoftRefLRUPolicyMSPerMB=1 -verbose:gc
    -> java vm version : 1.4.2_08-b03
    -> java vm vendor  : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type    : server
    -> java vm cpu     : x86
    -> heap size       : 512M
    -> init heap size  : 512M
    -> root path       : C:\usr\sap\J2E\JC00\j2ee\cluster\server0
    -> class path      : .\bin\boot\boot.jar;.\bin\boot\jaas.jar;.\bin\system\bytecode.jar;.
    -> OS libs path    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> main class      : com.sap.engine.boot.Start
    -> framework class : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class  : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path  : C:\usr\sap\J2E\JC00\j2ee\os_libs\jstartup.jar
    -> shutdown class  : com.sap.engine.boot.Start
    -> parameters      :
    -> debuggable      : yes
    -> debug mode      : yes
    -> debug port      : 50021
    -> shutdown timeout: 120000
    [Thr 4792] JLaunchISetDebugMode: set debug mode [yes]
    [Thr 2100] JLaunchIStartFunc: Thread 2100 started as Java VM thread.
    JHVM_LoadJavaVM: VM Arguments of node [server0]
    -> stack   : 262144 Bytes
    -> arg[  0]: exit
    -> arg[  1]: abort
    -> arg[  2]: -Djava.security.policy=./java.policy
    -> arg[  3]: -Djava.security.egd=file:/dev/urandom
    -> arg[  4]: -Dorg.omg.CORBA.ORBClass=com.sap.engine.system.ORBProxy
    -> arg[  5]: -Dorg.omg.CORBA.ORBSingletonClass=com.sap.engine.system.ORBSingletonProxy
    -> arg[  6]: -Djavax.rmi.CORBA.PortableRemoteObjectClass=com.sap.engine.system.PortableRemoteObjectProxy
    -> arg[  7]: -Djco.jarm=1
    -> arg[  8]: -Dsun.io.useCanonCaches=false
    -> arg[  9]: -verbose:gc
    -> arg[ 10]: -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar
    -> arg[ 11]: -Dsys.global.dir=C:/usr/sap/J2E/SYS/global
    -> arg[ 12]: -Djava.awt.headless=true
    -> arg[ 13]: -XX:NewSize=85m
    -> arg[ 14]: -XX:MaxNewSize=85m
    -> arg[ 15]: -XX:MaxPermSize=192m
    -> arg[ 16]: -XX:PermSize=192m
    -> arg[ 17]: -XX:+DisableExplicitGC
    -> arg[ 18]: -XX:+UseParNewGC
    -> arg[ 19]: -XX:+PrintGCDetails
    -> arg[ 20]: -XX:+PrintGCTimeStamps
    -> arg[ 21]: -XX:SurvivorRatio=2
    -> arg[ 22]: -XX:TargetSurvivorRatio=90
    -> arg[ 23]: -XX:SoftRefLRUPolicyMSPerMB=1
    -> arg[ 24]: -verbose:gc
    -> arg[ 25]: -Dsys.global.dir=C:\usr\sap\J2E\SYS\global
    -> arg[ 26]: -Dapplication.home=C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> arg[ 27]: -Djava.class.path=C:\usr\sap\J2E\JC00\j2ee\os_libs\jstartup.jar;.\bin\boot\boot.jar;.\bin\boot\jaas.jar;.\bin\system\bytecode.jar;.
    -> arg[ 28]: -Djava.library.path=C:\j2sdk1.4.2_08\jre\bin\server;C:\j2sdk1.4.2_08\jre\bin;C:\j2sdk1.4.2_08\bin;C:\usr\sap\J2E\JC00\j2ee\os_libs;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI.ACE\;C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727;C:\usr\sap\J2E\SCS01\exe;C:\usr\sap\J2E\JC00\exe;C:\usr\sap\J2E\SYS\exe\run
    -> arg[ 29]: -Xdebug
    -> arg[ 30]: -Xnoagent
    -> arg[ 31]: -Djava.compiler=NONE
    -> arg[ 32]: -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=50021
    -> arg[ 33]: -Dmemory.manager=512M
    -> arg[ 34]: -Xmx512M
    -> arg[ 35]: -Xms512M
    -> arg[ 36]: -DLoadBalanceRestricted=no
    -> arg[ 37]: -Djstartup.mode=JCONTROL
    -> arg[ 38]: -Djstartup.ownProcessId=272
    -> arg[ 39]: -Djstartup.ownHardwareId=Z2123283434
    -> arg[ 40]: -Djstartup.whoami=server
    -> arg[ 41]: -Djstartup.debuggable=yes
    -> arg[ 42]: -DSAPINFO=J2E_00_server
    -> arg[ 43]: -DSAPSTARTUP=1
    -> arg[ 44]: -DSAPSYSTEM=00
    -> arg[ 45]: -DSAPSYSTEMNAME=J2E
    -> arg[ 46]: -DSAPMYNAME=senthil_J2E_00
    -> arg[ 47]: -DSAPDBHOST=
    -> arg[ 48]: -Dj2ee.dbhost=senthil
    [Thr 2100] JHVM_LoadJavaVM: Java VM created OK.
    JHVM_BuildArgumentList: main method arguments of node [server0]
    [Thr 2588] Tue Sep 04 20:54:11 2007
    [Thr 2588] JHVM_RegisterNatives: registering methods in com.sap.bc.proj.jstartup.JStartupFramework
    [Thr 2588] JLaunchISetClusterId: set cluster id 4467550
    [Thr 2588] JLaunchISetState: change state from [Initial (0)] to [Waiting for start (1)]
    [Thr 2588] JLaunchISetState: change state from [Waiting for start (1)] to [Starting (2)]
    [Thr 3600] Tue Sep 04 20:54:52 2007
    [Thr 3600] JHVM_RegisterNatives: registering methods in com.sap.security.core.server.vsi.service.jni.VirusScanInterface
    [Thr 3600] *** ERROR => JHVM_RegisterNatives: registration for class com.sap.security.core.server.vsi.service.jni.VirusScanInterface failed. [jhvmxx.c     338]
    [Thr 2588] Tue Sep 04 20:55:21 2007
    [Thr 2588] JLaunchISetState: change state from [Starting (2)] to [Starting applications (10)]
    [Thr 4848] JHVM_RegisterNatives: registering methods in com.sap.mw.rfc.driver.CpicDriver
    [Thr 5320] Tue Sep 04 21:01:07 2007
    [Thr 5320] JLaunchISetState: change state from [Starting applications (10)] to [Running (3)]
    trc file: "C:\usr\sap\J2E\JC00\work\dev_server0", trc level: 1, release: "640"
    node name   : ID4467550
    pid         : 5276
    system name : J2E
    system nr.  : 00
    started at  : Tue Sep 04 22:04:45 2007
    arguments   :
        arg[00] : C:\usr\sap\J2E\JC00/j2ee/os_libs/jlaunch.exe
        arg[01] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
        arg[02] : -DSAPINFO=J2E_00_server
        arg[03] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
    [Thr 1532] Tue Sep 04 22:04:45 2007
    [Thr 1532] *** ERROR => Invalid property value [box.number/J2EJC00senthil] [jstartxx.c   789]
    [Thr 1532] *** ERROR => Invalid property value [en.host/PWDF3013] [jstartxx.c   789]
    [Thr 1532] *** ERROR => Invalid property value [en.port/3201] [jstartxx.c   789]
    [Thr 1532] *** ERROR => Invalid property value [system.id/0] [jstartxx.c   789]
    JStartupReadInstanceProperties: read instance properties [C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties]
    -> ms host    : senthil
    -> ms port    : 3601
    -> OS libs    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> Admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Used property files
    -> files [00] : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    Instance properties
    -> ms host    : senthil
    -> ms port    : 3601
    -> os libs    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Bootstrap nodes
    -> [00] bootstrap            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [01] bootstrap_ID4467500  : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [02] bootstrap_ID4467550  : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    Worker nodes
    -> [00] ID4467500            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    -> [01] ID4467550            : C:\usr\sap\J2E\JC00\j2ee\cluster\instance.properties
    [Thr 1532] JLaunchRequestQueueInit: create named pipe for ipc
    [Thr 1532] JLaunchRequestQueueInit: create pipe listener thread
    [Thr 1636] JLaunchRequestFunc: Thread 1636 started as listener thread for np messages.
    [Thr 644] WaitSyncSemThread: Thread 644 started as semaphore monitor thread.
    [Thr 1532] Tue Sep 04 22:04:46 2007
    [Thr 1532] INFO: Invalid property value [JLaunchParameters/]
    [Thr 1532] JStartupIReadSection: debug mode is specified by program arguments
    [Thr 1532] [Node: server0] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_08
    JStartupIReadSection: read node properties [ID4467550]
    -> node name       : server0
    -> node type       : server
    -> java path       : C:\j2sdk1.4.2_08
    -> java parameters : -Djava.security.policy=./java.policy -Djava.security.egd=file:/dev/urandom -Dorg.omg.CORBA.ORBClass=com.sap.engine.system.ORBProxy -Dorg.omg.CORBA.ORBSingletonClass=com.sap.engine.system.ORBSingletonProxy -Djavax.rmi.CORBA.PortableRemoteObjectClass=com.sap.engine.system.PortableRemoteObjectProxy -Djco.jarm=1 -Dsun.io.useCanonCaches=false -verbose:gc -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar -Dsys.global.dir=C:/usr/sap/J2E/SYS/global -Djava.awt.headless=true -XX:NewSize=85m -XX:MaxNewSize=85m -XX:MaxPermSize=192m -XX:PermSize=192m -XX:DisableExplicitGC -XX:UseParNewGC -XX:PrintGCDetails -XX:PrintGCTimeStamps -XX:SurvivorRatio=2 -XX:TargetSurvivorRatio=90 -XX:SoftRefLRUPolicyMSPerMB=1 -verbose:gc
    -> java vm version : 1.4.2_08-b03
    -> java vm vendor  : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type    : server
    -> java vm cpu     : x86
    -> heap size       : 512M
    -> init heap size  : 512M
    -> root path       : C:\usr\sap\J2E\JC00\j2ee\cluster\server0
    -> class path      : .\bin\boot\boot.jar;.\bin\boot\jaas.jar;.\bin\system\bytecode.jar;.
    -> OS libs path    : C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> main class      : com.sap.engine.boot.Start
    -> framework class : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class  : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path  : C:\usr\sap\J2E\JC00\j2ee\os_libs\jstartup.jar
    -> shutdown class  : com.sap.engine.boot.Start
    -> parameters      :
    -> debuggable      : yes
    -> debug mode      : yes
    -> debug port      : 50021
    -> shutdown timeout: 120000
    [Thr 1532] JLaunchISetDebugMode: set debug mode [yes]
    [Thr 5300] JLaunchIStartFunc: Thread 5300 started as Java VM thread.
    JHVM_LoadJavaVM: VM Arguments of node [server0]
    -> stack   : 262144 Bytes
    -> arg[  0]: exit
    -> arg[  1]: abort
    -> arg[  2]: -Djava.security.policy=./java.policy
    -> arg[  3]: -Djava.security.egd=file:/dev/urandom
    -> arg[  4]: -Dorg.omg.CORBA.ORBClass=com.sap.engine.system.ORBProxy
    -> arg[  5]: -Dorg.omg.CORBA.ORBSingletonClass=com.sap.engine.system.ORBSingletonProxy
    -> arg[  6]: -Djavax.rmi.CORBA.PortableRemoteObjectClass=com.sap.engine.system.PortableRemoteObjectProxy
    -> arg[  7]: -Djco.jarm=1
    -> arg[  8]: -Dsun.io.useCanonCaches=false
    -> arg[  9]: -verbose:gc
    -> arg[ 10]: -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar
    -> arg[ 11]: -Dsys.global.dir=C:/usr/sap/J2E/SYS/global
    -> arg[ 12]: -Djava.awt.headless=true
    -> arg[ 13]: -XX:NewSize=85m
    -> arg[ 14]: -XX:MaxNewSize=85m
    -> arg[ 15]: -XX:MaxPermSize=192m
    -> arg[ 16]: -XX:PermSize=192m
    -> arg[ 17]: -XX:+DisableExplicitGC
    -> arg[ 18]: -XX:+UseParNewGC
    -> arg[ 19]: -XX:+PrintGCDetails
    -> arg[ 20]: -XX:+PrintGCTimeStamps
    -> arg[ 21]: -XX:SurvivorRatio=2
    -> arg[ 22]: -XX:TargetSurvivorRatio=90
    -> arg[ 23]: -XX:SoftRefLRUPolicyMSPerMB=1
    -> arg[ 24]: -verbose:gc
    -> arg[ 25]: -Dsys.global.dir=C:\usr\sap\J2E\SYS\global
    -> arg[ 26]: -Dapplication.home=C:\usr\sap\J2E\JC00\j2ee\os_libs
    -> arg[ 27]: -Djava.class.path=C:\usr\sap\J2E\JC00\j2ee\os_libs\jstartup.jar;.\bin\boot\boot.jar;.\bin\boot\jaas.jar;.\bin\system\bytecode.jar;.
    -> arg[ 28]: -Djava.library.path=C:\j2sdk1.4.2_08\jre\bin\server;C:\j2sdk1.4.2_08\jre\bin;C:\j2sdk1.4.2_08\bin;C:\usr\sap\J2E\JC00\j2ee\os_libs;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI.ACE\;C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727;C:\usr\sap\J2E\SCS01\exe;C:\usr\sap\J2E\JC00\exe;C:\usr\sap\J2E\SYS\exe\run
    -> arg[ 29]: -Xdebug
    -> arg[ 30]: -Xnoagent
    -> arg[ 31]: -Djava.compiler=NONE
    -> arg[ 32]: -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=50021
    -> arg[ 33]: -Dmemory.manager=512M
    -> arg[ 34]: -Xmx512M
    -> arg[ 35]: -Xms512M
    -> arg[ 36]: -DLoadBalanceRestricted=no
    -> arg[ 37]: -Djstartup.mode=JCONTROL
    -> arg[ 38]: -Djstartup.ownProcessId=5276
    -> arg[ 39]: -Djstartup.ownHardwareId=Z2123283434
    -> arg[ 40]: -Djstartup.whoami=server
    -> arg[ 41]: -Djstartup.debuggable=yes
    -> arg[ 42]: -DSAPINFO=J2E_00_server
    -> arg[ 43]: -DSAPSTARTUP=1
    -> arg[ 44]: -DSAPSYSTEM=00
    -> arg[ 45]: -DSAPSYSTEMNAME=J2E
    -> arg[ 46]: -DSAPMYNAME=senthil_J2E_00
    -> arg[ 47]: -DSAPDBHOST=
    -> arg[ 48]: -Dj2ee.dbhost=senthil
    [Thr 5300] JHVM_LoadJavaVM: Java VM created OK.
    JHVM_BuildArgumentList: main method arguments of node [server0]
    [Thr 2320] Tue Sep 04 22:04:55 2007
    [Thr 2320] JHVM_RegisterNatives: registering methods in com.sap.bc.proj.jstartup.JStartupFramework
    [Thr 2320] JLaunchISetClusterId: set cluster id 4467550
    [Thr 2320] JLaunchISetState: change state from [Initial (0)] to [Waiting for start (1)]
    [Thr 2320] JLaunchISetState: change state from [Waiting for start (1)] to [Starting (2)]
    [Thr 4712] Tue Sep 04 22:05:41 2007
    [Thr 4712] JHVM_RegisterNatives: registering methods in com.sap.security.core.server.vsi.service.jni.VirusScanInterface
    [Thr 4712] *** ERROR => JHVM_RegisterNatives: registration for class com.sap.security.core.server.vsi.service.jni.VirusScanInterface failed. [jhvmxx.c     338]
    [Thr 2320] Tue Sep 04 22:06:47 2007
    [Thr 2320] JLaunchISetState: change state from [Starting (2)] to [Starting applications (10)]
    [Thr 6132] Tue Sep 04 22:06:48 2007
    [Thr 6132] JHVM_RegisterNatives: registering methods in com.sap.mw.rfc.driver.CpicDriver
    [Thr 2128] Tue Sep 04 22:13:14 2007
    [Thr 2128] JLaunchISetState: change state from [Starting applications (10)] to [Running (3)]
    [Thr 5860] Wed Sep 05 21:49:01 2007
    [Thr 5860] JLaunchIExitJava: exit hook is called (rc=-335)
    [Thr 5860] JLaunchCloseProgram: good bye (exitcode=-335)
    trc file: "C:\usr\sap\J2E\JC00\work\dev_server0", trc level: 1, release: "640"
    node name   : ID4467550
    pid         : 5224
    system name : J2E
    system nr.  : 00
    started at  : Wed Sep 05 21:49:06 2007
    arguments   :
        arg[00] : C:\usr\sap\J2E\JC00/j2ee/os_libs/jlaunch.exe
        arg[01] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
        arg[02] : -DSAPINFO=J2E_00_server
        arg[03] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC00_senthil
    [Thr 5568] Wed Sep 05 21:49:06 2007
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    -> arg[ 12]: -Djava.awt.headless=true
    -> arg[ 13]: -XX:NewSize=85m
    -> arg[ 14]: -XX:MaxNewSize=85m
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    -> arg[ 16]: -XX:PermSize=192m
    -> arg[ 17]: -XX:+DisableExplicitGC
    -> arg[ 18]: -XX:+UseParNewGC
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                                                                jarfile3.toURL(),
                                                                jarfile4.toURL(),
                                                                jarfile5.toURL(),
                                                                jarfile6.toURL(),
                                                                jarfile7.toURL(),
                                                                jarfile8.toURL(),
                                                                jarfile9.toURL(),
                                                                jarfile10.toURL(),
                                                                jarfile11.toURL(),
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                  System.exit(0);
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                   System.exit(1);
         public app1()
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                System.out.println("Successfully loaded JAXB Context");          
            catch (JAXBException jbe)
                jbe.printStackTrace();

    I'm doing something very similar. In fact my launcher is also stored in launcher.jar. It will start any application on the classpath and load dependencies jars located in the specified directory.
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    After this I was still raning into the "jaxb.properties not found" exception in some situations. Basically if the class using the jaxb files is located in the same jar as jaxb.properties everything worked fine. However if the class using the jaxb objects was located in a different jar it did not work.
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    As far as I can tell JAXB using the Context class loader to find the jaxb.properties file.
    I'm using JAXB 1.1
    I hope this helps!

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