Tomcat deployment failing - java-8

Question

I have 2 environments. The first one is a mac where I have installed Tomcat 8 by extracting the .zip file downloaded from Apache's homepage. The second one is a virtual machine on this mac which runs Ubuntu 15.04.
I have my web application as a war-file and can deploy that on my mac's Tomcat without any problem. Now, I want to do exactly the same deployment on the Ubuntu. So I copy the Tomcat-folder over to my Ubuntu along with my war-file and try to do the same deployment there. Before I do this I check so that JRE_HOME and JAVA_HOME is set the Java 8 installation I installed via PPA. I then start Tomcat and it seems to work so far. I go to localhost:8080 and Tomcat is running. I look at the JVM version at the status page and it reads 1.8.0_91_b14, seems good right? But then I try the deployment and I get this error:
FAIL - Application at context path /app could not be started
FAIL - Encountered exception org.apache.catalina.LifecycleException: Failed to start component ...
I tried with a very simple web app as well, one that only contained a index.html file. That is working. But this one, with compiled java classes and jsp and stuff does not. Here is more from the tomcat log files:
28-Jun-2016 03:02:00.557 SEVERE [localhost-startStop-1] org.apache.catalina.core.ContainerBase.addChildInternal ContainerBase.addChild: start:
org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/app]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:153)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:725)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:701)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:717)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:940)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1816)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NoSuchMethodError: org.apache.jasper.xmlparser.ParserUtils.<init>(Z)V
at org.apache.jasper.runtime.TldScanner.scanTld(TldScanner.java:603)
at org.apache.jasper.runtime.TldScanner.scanJar(TldScanner.java:460)
at org.apache.jasper.runtime.TldScanner.scanJars(TldScanner.java:697)
at org.apache.jasper.runtime.TldScanner.scanTlds(TldScanner.java:353)
at org.apache.jasper.runtime.TldScanner.onStartup(TldScanner.java:242)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5292)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
... 10 more
28-Jun-2016 03:02:00.561 SEVERE [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Error deploying web application archive /home/ubuntu/Java/apache-tomcat-8.0.36/webapps/app.war
java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/app]]
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:729)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:701)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:717)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:940)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1816)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
What is different from my mac that causes this?
UPDATE:
I can run a simple war with a jsp file, a servlet class. I think it's very strange and confusing.
UPDATE:
Ok, now I have tested with Glassfish on the virtual machine and the application is running there, but instead I get sql exception that no connection to database could be created.
I went back to my mac and noticed that I get no exceptions, but no items from my database are shown in my page. The only time they are shown is when started with Eclipse. So I let eclipse build the war file and do manual deployment, but same thing, no items loaded.
My hypothesis is that the database (driver, config, ect) are not enough/corrupted when I manually deploy to the server. ANYONE KNOWING A BIT MORE ABOUT HOW SERVERS WORK?? And still, why does deployment work on mac but not Ubuntu?
UPDATE:
Apparently the logging with log4j doesn't work either when I deploy manually. Somehow all my external resources and communication gets fucked up when I deploy manually. Why doesn't the log files tell me what is the problem??
UPDATE:
I changed eclipse tomcat server installation location to the same location as my tomcat home. Now I can se how Eclipse changed the Tomcat folder. I copied over that tomcat installation to Ubuntu and tried, but same failure..
UPDATE:
Now, I recognized the log-files for the virtual host called localhost, and it gives me a much more precise cause of the problem:
30-Jun-2016 06:36:08.586 SEVERE [http-nio-8080-exec-10] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class com.app.AppContextListener
javax.persistence.PersistenceException: Unable to build entity manager factory
at org.hibernate.jpa.HibernatePersistenceProvider.createEntityManagerFactory(HibernatePersistenceProvider.java:66)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:55)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:39)
at com.app.AppContextListener.createEntityManagerFactory(AppContextListener.java:67)
at com.app.AppContextListener.contextInitialized(AppContextListener.java:63)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4842)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5303)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.manager.ManagerServlet.start(ManagerServlet.java:1284)
at org.apache.catalina.manager.HTMLManagerServlet.start(HTMLManagerServlet.java:666)
at org.apache.catalina.manager.HTMLManagerServlet.doPost(HTMLManagerServlet.java:217)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:648)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.apache.catalina.filters.CsrfPreventionFilter.doFilter(CsrfPreventionFilter.java:136)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:108)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:614)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:528)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1099)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:670)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1520)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1476)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.hibernate.boot.archive.spi.ArchiveException: Could not build ClassFile
at org.hibernate.boot.archive.scan.spi.ClassFileArchiveEntryHandler.toClassFile(ClassFileArchiveEntryHandler.java:64)
at org.hibernate.boot.archive.scan.spi.ClassFileArchiveEntryHandler.handleEntry(ClassFileArchiveEntryHandler.java:47)
at org.hibernate.boot.archive.internal.ExplodedArchiveDescriptor.processDirectory(ExplodedArchiveDescriptor.java:143)
at org.hibernate.boot.archive.internal.ExplodedArchiveDescriptor.visitArchive(ExplodedArchiveDescriptor.java:54)
at org.hibernate.boot.archive.scan.spi.AbstractScannerImpl.scan(AbstractScannerImpl.java:46)
at org.hibernate.boot.model.process.internal.ScanningCoordinator.coordinateScan(ScanningCoordinator.java:75)
at org.hibernate.boot.model.process.spi.MetadataBuildingProcess.prepare(MetadataBuildingProcess.java:98)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.<init>(EntityManagerFactoryBuilderImpl.java:199)
at org.hibernate.jpa.boot.spi.Bootstrap.getEntityManagerFactoryBuilder(Bootstrap.java:34)
at org.hibernate.jpa.HibernatePersistenceProvider.getEntityManagerFactoryBuilder(HibernatePersistenceProvider.java:165)
at org.hibernate.jpa.HibernatePersistenceProvider.getEntityManagerFactoryBuilderOrNull(HibernatePersistenceProvider.java:114)
at org.hibernate.jpa.HibernatePersistenceProvider.getEntityManagerFactoryBuilderOrNull(HibernatePersistenceProvider.java:71)
at org.hibernate.jpa.HibernatePersistenceProvider.createEntityManagerFactory(HibernatePersistenceProvider.java:52)
... 39 more
UPDATE:
There was another post on this new error and it turned out that I had duplicate jar files of type javassist-xyz.jar of different versions. I removed one of them and now I get this instead:
com.mchange.v2.resourcepool.CannotAcquireResourceException: A ResourcePool could not acquire a resource from its primary factory or source
Another with the exact same problem now: com.mchange.v2.resourcepool.CannotAcquireResourceException: A ResourcePool could not acquire a resource from its primary factory or source
SOLVED:
I finally solved it! Apperently the port on which my tcp database server runs on was not closed when Tomcat started, so it could not start a new one from the old state. The situation evolved when the application context couldn't be destroyed properly on all my attempts to get it working. I added some more logging to my AppContextListener class and that did spot this problem. The only real severe problem I had in the end, was a duplicate of two jar files!