Classpath Problem in WebSphere 6.0 (WAS 6.0)

We were trying to configure WAS 6 for the last 10 days to work for an existing application.
The problem was pointing to some jar files (log4j, j2sh and jdom etc). Although we added it to the class path of the EJB project but still RAD was not picking it up at run time. Following 2 steps helped us solve it
1. For referring to any jar file that RAD is not picking up, add that jar directly to your EAR project (copy it rt in the EAR Project) and make your EJB and WAR projects point to it though JAVA JAR DEPENDENCIES tab from the project properties. Since this was the first time we were working with RAD, we wasted a lot of time trying to figure this workaround.
2. If there is any jar file (like jdom) that is already present in the lib directory of your Server, then the CLASSLOADER will refer to that version, not the version that we configure using CLASSPATH of our EJB Project. Thus, replace the older version of all the jar files in the lib directory of server with the latest version that you want it to work with.
All this might be pretty much obvious to experts but being a novice and having spent a lot of time, I thought that this may help someone out there.

We were trying to configure WAS 6 for the last 10 days to work for an existing application.
The problem was pointing to some jar files (log4j, j2sh and jdom etc). Although we added it to the class path of the EJB project but still RAD was not picking it up at run time. Following 2 steps helped us solve it
1. For referring to any jar file that RAD is not picking up, add that jar directly to your EAR project (copy it rt in the EAR Project) and make your EJB and WAR projects point to it though JAVA JAR DEPENDENCIES tab from the project properties. Since this was the first time we were working with RAD, we wasted a lot of time trying to figure this workaround.
2. If there is any jar file (like jdom) that is already present in the lib directory of your Server, then the CLASSLOADER will refer to that version, not the version that we configure using CLASSPATH of our EJB Project. Thus, replace the older version of all the jar files in the lib directory of server with the latest version that you want it to work with.
All this might be pretty much obvious to experts but being a novice and having spent a lot of time, I thought that this may help someone out there.

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    Hi Frndz,
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    I would really appreciate any help on this.
    Thanks in advance.
    ************ Start Display Current Environment ************
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    Current trace specification = *=info
    ************* End Display Current Environment *************
    [4/3/08 17:01:59:093 GMT+05:30] 0000000a ManagerAdmin I TRAS0017I: The startup trace state is *=info.
    [4/3/08 17:01:59:203 GMT+05:30] 0000000a MBeanDescript W ADMN0001W: The service is unable to parse the MBean descriptor file com/ibm/ws/management/descriptor/xml/mbeans.xml.
    [4/3/08 17:01:59:265 GMT+05:30] 0000000a AdminInitiali A ADMN0015I: The administration service is initialized.
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R java.lang.NullPointerException
         at javax.management.MBeanNotificationInfo.equals(MBeanNotificationInfo.java:146)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.addFeatures(MBeanDescriptorLoader.java:461)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.loadParentTypes(MBeanDescriptorLoader.java:434)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.endDocument(MBeanDescriptorLoader.java:217)
         at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endDocument(AbstractSAXParser.java:769)
         at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endDocument(XMLDTDValidator.java:981)
         at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.endEntity(XMLDocumentScannerImpl.java:560)
         at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.endEntity(XMLEntityManager.java:1779)
         at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1758)
         at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.skipSpaces(XMLEntityScanner.java:1274)
         at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(XMLDocumentScannerImpl.java:1247)
         at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:368)
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         at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:764)
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         at com.ibm.ws.management.descriptor.MBeanDescriptorManager.loadDescriptorFile(MBeanDescriptorManager.java:319)
         at com.ibm.ws.management.descriptor.MBeanDescriptorManager.getDescriptor(MBeanDescriptorManager.java:133)
         at com.ibm.ws.management.MBeanFactoryImpl.activateMBean(MBeanFactoryImpl.java:375)
         at com.ibm.ws.management.MBeanFactoryImpl.activateMBean(MBeanFactoryImpl.java:348)
         at com.ibm.ws.management.component.AdminImpl.initialize(AdminImpl.java:350)
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         at com.ibm.ws.runtime.component.ContainerImpl.initializeComponents(ContainerImpl.java:1015)
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         at com.ibm.ws.runtime.WsServerImpl.start(WsServerImpl.java:120)
         at com.ibm.ws.runtime.WsServerImpl.main(WsServerImpl.java:378)
         at com.ibm.ws.runtime.WsServer.main(WsServer.java:50)
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         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
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         at java.lang.reflect.Method.invoke(Method.java:585)
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    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.loadParentTypes(MBeanDescriptorLoader.java:434)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.endDocument(MBeanDescriptorLoader.java:217)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endDocument(AbstractSAXParser.java:769)
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    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.endEntity(XMLDocumentScannerImpl.java:560)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.endEntity(XMLEntityManager.java:1779)
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    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(XMLDocumentScannerImpl.java:1247)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:368)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:834)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:764)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:148)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1242)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.loadDescriptor(MBeanDescriptorLoader.java:155)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.management.descriptor.MBeanDescriptorManager.loadDescriptorFile(MBeanDescriptorManager.java:319)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.management.descriptor.MBeanDescriptorManager.getDescriptor(MBeanDescriptorManager.java:133)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.management.MBeanFactoryImpl.activateMBean(MBeanFactoryImpl.java:375)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.management.MBeanFactoryImpl.activateMBean(MBeanFactoryImpl.java:348)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.management.component.AdminImpl.initialize(AdminImpl.java:350)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.component.ContainerImpl.initializeComponent(ContainerImpl.java:1161)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.component.ContainerImpl.initializeComponents(ContainerImpl.java:1015)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.component.ServerImpl.initialize(ServerImpl.java:245)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.WsServerImpl.bootServerContainer(WsServerImpl.java:157)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.WsServerImpl.start(WsServerImpl.java:120)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.WsServerImpl.main(WsServerImpl.java:378)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.WsServer.main(WsServer.java:50)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at java.lang.reflect.Method.invoke(Method.java:585)
    [4/3/08 17:01:59:312 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.bootstrap.WSLauncher.main(WSLauncher.java:190)
    [4/3/08 17:01:59:328 GMT+05:30] 0000000a MBeanDescript W ADMN0001W: The service is unable to parse the MBean descriptor file com.ibm.websphere.management.exception.DescriptorParseException: ADMN0001W: The service is unable to parse the MBean descriptor file com/ibm/ws/management/descriptor/xml/JVM.xml.
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         at com.ibm.ws.management.descriptor.MBeanDescriptorManager.loadDescriptorFile(MBeanDescriptorManager.java:319)
         at com.ibm.ws.management.descriptor.MBeanDescriptorManager.getDescriptor(MBeanDescriptorManager.java:133)
         at com.ibm.ws.management.MBeanFactoryImpl.activateMBean(MBeanFactoryImpl.java:375)
         at com.ibm.ws.management.MBeanFactoryImpl.activateMBean(MBeanFactoryImpl.java:348)
         at com.ibm.ws.management.component.AdminImpl.initialize(AdminImpl.java:350)
         at com.ibm.ws.runtime.component.ContainerImpl.initializeComponent(ContainerImpl.java:1161)
         at com.ibm.ws.runtime.component.ContainerImpl.initializeComponents(ContainerImpl.java:1015)
         at com.ibm.ws.runtime.component.ServerImpl.initialize(ServerImpl.java:245)
         at com.ibm.ws.runtime.WsServerImpl.bootServerContainer(WsServerImpl.java:157)
         at com.ibm.ws.runtime.WsServerImpl.start(WsServerImpl.java:120)
         at com.ibm.ws.runtime.WsServerImpl.main(WsServerImpl.java:378)
         at com.ibm.ws.runtime.WsServer.main(WsServer.java:50)
         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:585)
         at com.ibm.ws.bootstrap.WSLauncher.main(WSLauncher.java:190)
    Caused by: java.lang.NullPointerException
         at javax.management.MBeanNotificationInfo.equals(MBeanNotificationInfo.java:146)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.addFeatures(MBeanDescriptorLoader.java:461)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.loadParentTypes(MBeanDescriptorLoader.java:434)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.endDocument(MBeanDescriptorLoader.java:217)
         at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endDocument(AbstractSAXParser.java:769)
         at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endDocument(XMLDTDValidator.java:981)
         at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.endEntity(XMLDocumentScannerImpl.java:560)
         at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.endEntity(XMLEntityManager.java:1779)
         at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1758)
         at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.skipSpaces(XMLEntityScanner.java:1274)
         at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(XMLDocumentScannerImpl.java:1247)
         at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:368)
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         at com.ibm.ws.runtime.WsServerImpl.bootServerContainer(WsServerImpl.java:157)
         at com.ibm.ws.runtime.WsServerImpl.start(WsServerImpl.java:120)
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         at com.ibm.ws.runtime.WsServer.main(WsServer.java:50)
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         ... 12 more
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         at com.ibm.ws.management.MBeanFactoryImpl.activateMBean(MBeanFactoryImpl.java:600)
         at com.ibm.ws.management.MBeanFactoryImpl.activateMBean(MBeanFactoryImpl.java:348)
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         ... 12 more
    Caused by: com.ibm.websphere.management.exception.DescriptorParseException: ADMN0001W: The service is unable to parse the MBean descriptor file com/ibm/ws/management/descriptor/xml/JVM.xml.
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.loadDescriptor(MBeanDescriptorLoader.java:164)
         at com.ibm.ws.management.descriptor.MBeanDescriptorManager.loadDescriptorFile(MBeanDescriptorManager.java:319)
         at com.ibm.ws.management.descriptor.MBeanDescriptorManager.getDescriptor(MBeanDescriptorManager.java:133)
         at com.ibm.ws.management.MBeanFactoryImpl.activateMBean(MBeanFactoryImpl.java:375)
         ... 14 more
    Caused by: java.lang.NullPointerException
         at javax.management.MBeanNotificationInfo.equals(MBeanNotificationInfo.java:146)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.addFeatures(MBeanDescriptorLoader.java:461)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.loadParentTypes(MBeanDescriptorLoader.java:434)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.endDocument(MBeanDescriptorLoader.java:217)
         at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endDocument(AbstractSAXParser.java:769)
         at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.endDocument(XMLDTDValidator.java:981)
         at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.endEntity(XMLDocumentScannerImpl.java:560)
         at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.endEntity(XMLEntityManager.java:1779)
         at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1758)
         at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.skipSpaces(XMLEntityScanner.java:1274)
         at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(XMLDocumentScannerImpl.java:1247)
         at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:368)
         at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:834)
         at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:764)
         at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:148)
         at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1242)
         at com.ibm.ws.management.descriptor.MBeanDescriptorLoader.loadDescriptor(MBeanDescriptorLoader.java:155)
         ... 17 more
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.management.component.AdminImpl.initialize(AdminImpl.java:697)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.component.ContainerImpl.initializeComponent(ContainerImpl.java:1161)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.component.ContainerImpl.initializeComponents(ContainerImpl.java:1015)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.component.ServerImpl.initialize(ServerImpl.java:245)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.WsServerImpl.bootServerContainer(WsServerImpl.java:157)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.WsServerImpl.start(WsServerImpl.java:120)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.WsServerImpl.main(WsServerImpl.java:378)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.runtime.WsServer.main(WsServer.java:50)
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    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at java.lang.reflect.Method.invoke(Method.java:585)
    [4/3/08 17:01:59:343 GMT+05:30] 0000000a SystemErr R      at com.ibm.ws.bootstrap.WSLauncher.main(WSLauncher.java:190)
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