war file extraction issues in tomcat
===

i am finding many issues in it but still not able to resolve this. Is there any expert opinion on this... I have this setup in Cpanel.

I have added export JAVA_OPTS="-XX:PermSize=128M -XX:MaxPermSize=524M" in catlina.sh but n

**Log file info in catalina.err**

        Jul 10, 2012 3:23:16 AM org.apache.catalina.core.AprLifecycleListener init
        INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/local/jdk/jre/lib/i386/client:/usr/local/jdk/jre/lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib
        Jul 10, 2012 3:23:17 AM org.apache.coyote.http11.Http11BaseProtocol init
        INFO: Initializing Coyote HTTP/1.1 on http-8080
        Jul 10, 2012 3:23:17 AM org.apache.catalina.startup.Catalina load
        INFO: Initialization processed in 434 ms
        Jul 10, 2012 3:23:17 AM org.apache.catalina.core.StandardService start
        INFO: Starting service Catalina
        Jul 10, 2012 3:23:17 AM org.apache.catalina.core.StandardEngine start
        INFO: Starting Servlet Engine: Apache Tomcat/5.5.35
        Jul 10, 2012 3:23:17 AM org.apache.catalina.core.StandardHost start
        INFO: XML validation disabled
        Jul 10, 2012 3:23:17 AM org.apache.catalina.startup.HostConfig deployWAR
        INFO: Deploying web application archive sample.war
        Jul 10, 2012 3:23:17 AM org.apache.catalina.startup.ContextConfig init
        SEVERE: Exception fixing docBase: {0}
        java.io.FileNotFoundException: /home/surgnet/public_html/sample/META-INF/MANIFEST.MF (No such file or directory)
                at java.io.FileOutputStream.open(Native Method)
                at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
                at java.io.FileOutputStream.<init>(FileOutputStream.java:145)
                at org.apache.catalina.startup.ExpandWar.expand(ExpandWar.java:457)
                at org.apache.catalina.startup.ExpandWar.expand(ExpandWar.java:173)
                at org.apache.catalina.startup.ContextConfig.fixDocBase(ContextConfig.java:864)
                at org.apache.catalina.startup.ContextConfig.init(ContextConfig.java:999)
                at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:279)
                at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
                at org.apache.catalina.core.StandardContext.init(StandardContext.java:5095)
                at org.apache.catalina.core.StandardContext.start(StandardContext.java:4024)
                at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
                at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740)
                at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544)
                at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:884)
                at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:737)
                at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:498)
                at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1203)
                at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:319)
                at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
                at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022)
                at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
                at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014)
                at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
                at org.apache.catalina.core.StandardService.start(StandardService.java:448)
                at org.apache.catalina.core.StandardServer.start(StandardServer.java:700)
                at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
                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:597)
                at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
                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:597)
                at org.apache.commons.daemon.support.DaemonLoader.start(DaemonLoader.java:243)
        Jul 10, 2012 3:23:17 AM org.apache.catalina.startup.HostConfig deployWAR
        INFO: Deploying web application archive surgeryplanet.war
        Jul 10, 2012 3:23:17 AM org.apache.catalina.startup.ContextConfig init
        SEVERE: Exception fixing docBase: {0}
        java.io.FileNotFoundException: /home/surgnet/public_html/surgeryplanet/META-INF/MANIFEST.MF (No such file or directory)
                at java.io.FileOutputStream.open(Native Method)
                at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
                at java.io.FileOutputStream.<init>(FileOutputStream.java:145)
                at org.apache.catalina.startup.ExpandWar.expand(ExpandWar.java:457)
                at org.apache.catalina.startup.ExpandWar.expand(ExpandWar.java:173)
                at org.apache.catalina.startup.ContextConfig.fixDocBase(ContextConfig.java:864)
                at org.apache.catalina.startup.ContextConfig.init(ContextConfig.java:999)
                at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:279)
                at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
                at org.apache.catalina.core.StandardContext.init(StandardContext.java:5095)
                at org.apache.catalina.core.StandardContext.start(StandardContext.java:4024)
                at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
                at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740)
                at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544)
                at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:884)
                at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:737)
                at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:498)
                at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1203)
                at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:319)
                at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
                at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022)
                at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
                at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014)
                at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
                at org.apache.catalina.core.StandardService.start(StandardService.java:448)
                at org.apache.catalina.core.StandardServer.start(StandardServer.java:700)
                at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
                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:597)
                at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
                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:597)
                at org.apache.commons.daemon.support.DaemonLoader.start(DaemonLoader.java:243)
        Jul 10, 2012 3:23:18 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
        INFO: validateJarFile(/usr/local/jakarta/apache-tomcat-5.5.35/work/Catalina/surgeryplanet.net/surgeryplanet/WEB-INF/lib/javaee.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
        Jul 10, 2012 3:23:18 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
        INFO: validateJarFile(/usr/local/jakarta/apache-tomcat-5.5.35/work/Catalina/surgeryplanet.net/surgeryplanet/WEB-INF/lib/jsp-api.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/jsp/JspPage.class
        Jul 10, 2012 3:23:34 AM org.apache.catalina.core.StandardContext start
        SEVERE: Error listenerStart
        Jul 10, 2012 3:23:34 AM org.apache.catalina.core.StandardContext start
        SEVERE: Context [/surgeryplanet] startup failed due to previous errors
        Jul 10, 2012 3:23:35 AM org.apache.catalina.core.StandardHost start
        INFO: XML validation disabled
        Jul 10, 2012 3:23:35 AM org.apache.catalina.core.ApplicationContext log
        INFO: ContextListener: contextInitialized()
        Jul 10, 2012 3:23:35 AM org.apache.catalina.core.ApplicationContext log
        INFO: SessionListener: contextInitialized()
        Jul 10, 2012 3:23:35 AM org.apache.catalina.core.ApplicationContext log
        INFO: ContextListener: contextInitialized()
        Jul 10, 2012 3:23:35 AM org.apache.catalina.core.ApplicationContext log
        INFO: SessionListener: contextInitialized()
        Jul 10, 2012 3:23:35 AM org.apache.catalina.core.ApplicationContext log
        INFO: org.apache.webapp.balancer.BalancerFilter: init(): ruleChain: [org.apache.webapp.balancer.RuleChain: [org.apache.webapp.balancer.rules.URLStringMatchRule: Target string: News / Redirect URL: http://www.cnn.com], [org.apache.webapp.balancer.rules.RequestParameterRule: Target param name: paramName / Target param value: paramValue / Redirect URL: http://www.yahoo.com], [org.apache.webapp.balancer.rules.AcceptEverythingRule: Redirect URL: http://jakarta.apache.org]]
        Jul 10, 2012 3:23:35 AM org.apache.coyote.http11.Http11BaseProtocol start
        INFO: Starting Coyote HTTP/1.1 on http-8080
        Jul 10, 2012 3:23:35 AM org.apache.jk.common.ChannelSocket init
        INFO: JK: ajp13 listening on /0.0.0.0:8009
        Jul 10, 2012 3:23:35 AM org.apache.jk.server.JkMain start
        INFO: Jk running ID=0 time=0/14  config=null
        Jul 10, 2012 3:23:35 AM org.apache.catalina.storeconfig.StoreLoader load
        INFO: Find registry server-registry.xml at classpath resource
        Jul 10, 2012 3:23:36 AM org.apache.catalina.startup.Catalina start
        INFO: Server startup in 19200 ms
        Jul 10, 2012 3:25:29 AM org.apache.catalina.core.ApplicationContext log
        INFO: HTMLManager: init: Associated with Deployer 'Catalina:type=Deployer,host=surgeryplanet.net'
        Jul 10, 2012 3:25:29 AM org.apache.catalina.core.ApplicationContext log
        INFO: HTMLManager: init: Global resources are available
        Jul 10, 2012 3:25:29 AM org.apache.catalina.core.ApplicationContext log
        INFO: HTMLManager: list: Listing contexts for virtual host 'surgeryplanet.net'
        Jul 10, 2012 3:25:34 AM org.apache.catalina.core.ApplicationContext log
        INFO: HTMLManager: start: Starting web application at '/surgeryplanet'
        Jul 10, 2012 3:25:35 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
        INFO: validateJarFile(/usr/local/jakarta/apache-tomcat-5.5.35/work/Catalina/surgeryplanet.net/surgeryplanet/WEB-INF/lib/javaee.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
        Jul 10, 2012 3:25:35 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
        INFO: validateJarFile(/usr/local/jakarta/apache-tomcat-5.5.35/work/Catalina/surgeryplanet.net/surgeryplanet/WEB-INF/lib/jsp-api.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/jsp/JspPage.class
        Jul 10, 2012 3:25:51 AM org.apache.catalina.core.StandardContext start
        SEVERE: Error listenerStart
        Jul 10, 2012 3:25:51 AM org.apache.catalina.core.StandardContext start
        SEVERE: Context [/surgeryplanet] startup failed due to previous errors
        Jul 10, 2012 3:25:52 AM org.apache.catalina.core.ApplicationContext log
        INFO: HTMLManager: list: Listing contexts for virtual host 'surgeryplanet.net'

