Hi Theirry,

Can you send us the full catalina and labkey log files? The error you provided doesn't give us much detail to work with.

Also, can you provide us with more specifics on the versions of Java, Tomcat, and LabKey you're using and the version of Postgres or MS SQL you're running as well? This will give us a better idea of what you're working with.

Regards,

Jon

Dear Jon,
Thank you very much for your quick reply.
I'm using Postgres 9.6.4, java version "1.8.0_144", tomcat 8.5.20

Here is the catalina log file:
**************************************
22-Aug-2017 15:00:18.074 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.20
22-Aug-2017 15:00:18.076 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Aug 2 2017 21:35:49 UTC
22-Aug-2017 15:00:18.076 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.20.0
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.2.0-1-amd64
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-8-oracle/jre
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_144-b01
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/apache-tomcat-8.5.20//conf/logging.properties
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
22-Aug-2017 15:00:18.077 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
22-Aug-2017 15:00:18.078 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
22-Aug-2017 15:00:18.078 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 15:00:18.078 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 15:00:18.078 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/apache-tomcat-8.5.20//temp
22-Aug-2017 15:00:18.078 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/home/thierry/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86/:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
22-Aug-2017 15:00:18.180 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 15:00:18.194 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
22-Aug-2017 15:00:18.196 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 15:00:18.198 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
22-Aug-2017 15:00:18.198 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 428 ms
22-Aug-2017 15:00:18.216 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
22-Aug-2017 15:00:18.216 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.20
22-Aug-2017 15:00:18.227 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
22-Aug-2017 15:00:18.271 WARNING [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase [/usr/local/apache-tomcat-8.5.20/webapps/@@/usr/local/labkey/labkeywebapp/@@] inside the host appBase has been specified, and will be ignored
22-Aug-2017 15:00:18.299 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[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@a6ccaa2]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4860)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4992)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 10 more
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/usr/local/apache-tomcat-8.5.20/webapps/labkey] is not valid
    at org.apache.catalina.webresources.StandardRoot.createMainResourceSet(StandardRoot.java:745)
    at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:703)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 13 more

22-Aug-2017 15:00:18.300 SEVERE [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
 java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:756)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

22-Aug-2017 15:00:18.302 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml] has finished in [74] ms
22-Aug-2017 15:00:18.303 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs]
22-Aug-2017 15:00:18.704 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:00:18.733 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs] has finished in [429] ms
22-Aug-2017 15:00:18.733 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager]
22-Aug-2017 15:00:18.900 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:00:18.905 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager] has finished in [172] ms
22-Aug-2017 15:00:18.906 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager]
22-Aug-2017 15:00:19.028 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:00:19.030 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager] has finished in [124] ms
22-Aug-2017 15:00:19.030 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT]
22-Aug-2017 15:00:19.133 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:00:19.135 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT] has finished in [105] ms
22-Aug-2017 15:00:19.135 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples]
22-Aug-2017 15:00:19.368 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:00:19.380 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples] has finished in [244] ms
22-Aug-2017 15:00:19.383 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
22-Aug-2017 15:00:19.392 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 15:00:19.394 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 1195 ms
22-Aug-2017 15:19:42.771 INFO [main] org.apache.catalina.core.StandardServer.await A valid shutdown command was received via the shutdown port. Stopping the Server instance.
22-Aug-2017 15:19:42.772 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 15:19:42.826 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 15:19:42.877 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
22-Aug-2017 15:19:42.911 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
22-Aug-2017 15:19:42.913 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 15:19:42.914 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
22-Aug-2017 15:19:42.915 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 15:19:42.917 WARNING [main] org.apache.catalina.deploy.NamingResourcesImpl.cleanUp Failed to retrieve JNDI naming context for container [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]] so no cleanup was performed for that container
 javax.naming.NamingException: No naming context bound to this class loader
    at org.apache.naming.ContextBindings.getClassLoader(ContextBindings.java:268)
    at org.apache.catalina.deploy.NamingResourcesImpl.cleanUp(NamingResourcesImpl.java:993)
    at org.apache.catalina.deploy.NamingResourcesImpl.stopInternal(NamingResourcesImpl.java:976)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5443)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:264)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardService.destroyInternal(StandardService.java:585)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardServer.destroyInternal(StandardServer.java:883)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.startup.Catalina.stop(Catalina.java:730)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:691)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 15:19:46.697 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.20
22-Aug-2017 15:19:46.699 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Aug 2 2017 21:35:49 UTC
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.20.0
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.2.0-1-amd64
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-8-oracle/jre
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_144-b01
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 15:19:46.700 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/apache-tomcat-8.5.20//conf/logging.properties
22-Aug-2017 15:19:46.701 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
22-Aug-2017 15:19:46.701 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
22-Aug-2017 15:19:46.701 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
22-Aug-2017 15:19:46.701 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 15:19:46.701 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 15:19:46.701 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/apache-tomcat-8.5.20//temp
22-Aug-2017 15:19:46.701 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/home/thierry/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86/:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
22-Aug-2017 15:19:46.816 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 15:19:46.832 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
22-Aug-2017 15:19:46.834 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 15:19:46.835 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
22-Aug-2017 15:19:46.836 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 450 ms
22-Aug-2017 15:19:46.857 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
22-Aug-2017 15:19:46.857 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.20
22-Aug-2017 15:19:46.869 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
22-Aug-2017 15:19:46.903 WARNING [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase [/usr/local/apache-tomcat-8.5.20/webapps/@@/usr/local/labkey/labkeywebapp/@@] inside the host appBase has been specified, and will be ignored
22-Aug-2017 15:19:46.926 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[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@1902143e]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4860)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4992)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 10 more
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/usr/local/apache-tomcat-8.5.20/webapps/labkey] is not valid
    at org.apache.catalina.webresources.StandardRoot.createMainResourceSet(StandardRoot.java:745)
    at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:703)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 13 more

22-Aug-2017 15:19:46.928 SEVERE [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
 java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:756)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

22-Aug-2017 15:19:46.929 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml] has finished in [59] ms
22-Aug-2017 15:19:46.930 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs]
22-Aug-2017 15:19:47.295 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:19:47.325 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs] has finished in [394] ms
22-Aug-2017 15:19:47.325 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager]
22-Aug-2017 15:19:47.495 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:19:47.499 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager] has finished in [174] ms
22-Aug-2017 15:19:47.500 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager]
22-Aug-2017 15:19:47.618 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:19:47.619 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager] has finished in [120] ms
22-Aug-2017 15:19:47.619 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT]
22-Aug-2017 15:19:47.727 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:19:47.728 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT] has finished in [109] ms
22-Aug-2017 15:19:47.729 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples]
22-Aug-2017 15:19:47.965 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 15:19:47.976 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples] has finished in [247] ms
22-Aug-2017 15:19:48.007 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
22-Aug-2017 15:19:48.017 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 15:19:48.019 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 1183 ms
22-Aug-2017 15:20:04.743 INFO [http-nio-8080-exec-7] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 15:20:05.701 INFO [http-nio-8080-exec-5] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 15:20:06.518 INFO [http-nio-8080-exec-12] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 15:20:07.279 INFO [http-nio-8080-exec-10] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 15:35:01.141 INFO [http-nio-8080-exec-17] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 15:35:06.482 INFO [http-nio-8080-exec-18] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 15:35:07.338 INFO [http-nio-8080-exec-21] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 15:35:08.640 INFO [http-nio-8080-exec-20] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 15:35:09.460 INFO [http-nio-8080-exec-22] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 15:49:59.646 INFO [http-nio-8080-exec-29] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:35:01.879 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.20
22-Aug-2017 16:35:01.881 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Aug 2 2017 21:35:49 UTC
22-Aug-2017 16:35:01.881 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.20.0
22-Aug-2017 16:35:01.881 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
22-Aug-2017 16:35:01.881 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.2.0-1-amd64
22-Aug-2017 16:35:01.881 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
22-Aug-2017 16:35:01.881 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-8-oracle/jre
22-Aug-2017 16:35:01.882 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_144-b01
22-Aug-2017 16:35:01.882 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
22-Aug-2017 16:35:01.882 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 16:35:01.882 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 16:35:01.882 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/apache-tomcat-8.5.20//conf/logging.properties
22-Aug-2017 16:35:01.882 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
22-Aug-2017 16:35:01.882 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
22-Aug-2017 16:35:01.882 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
22-Aug-2017 16:35:01.883 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 16:35:01.883 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 16:35:01.883 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/apache-tomcat-8.5.20//temp
22-Aug-2017 16:35:01.883 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/home/thierry/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86/:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
22-Aug-2017 16:35:01.992 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:35:02.005 SEVERE [main] org.apache.coyote.AbstractProtocol.init Failed to initialize end point associated with ProtocolHandler ["http-nio-8080"]
 java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:66)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)

22-Aug-2017 16:35:02.006 SEVERE [main] org.apache.catalina.core.StandardService.initInternal Failed to initialize connector [Connector[HTTP/1.1-8080]]
 org.apache.catalina.LifecycleException: Failed to initialize component [Connector[HTTP/1.1-8080]]
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:112)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:999)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    ... 12 more
Caused by: java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:66)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    ... 13 more

22-Aug-2017 16:35:02.007 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:35:02.008 SEVERE [main] org.apache.coyote.AbstractProtocol.init Failed to initialize end point associated with ProtocolHandler ["ajp-nio-8009"]
 java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)

22-Aug-2017 16:35:02.009 SEVERE [main] org.apache.catalina.core.StandardService.initInternal Failed to initialize connector [Connector[AJP/1.3-8009]]
 org.apache.catalina.LifecycleException: Failed to initialize component [Connector[AJP/1.3-8009]]
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:112)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:999)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    ... 12 more
Caused by: java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    ... 13 more

22-Aug-2017 16:35:02.009 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 480 ms
22-Aug-2017 16:35:02.031 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
22-Aug-2017 16:35:02.031 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.20
22-Aug-2017 16:35:02.038 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
22-Aug-2017 16:35:02.078 WARNING [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase [/usr/local/apache-tomcat-8.5.20/webapps/@@/usr/local/labkey/labkeywebapp/@@] inside the host appBase has been specified, and will be ignored
22-Aug-2017 16:35:02.103 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[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@fc9645e]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4860)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4992)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 10 more
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/usr/local/apache-tomcat-8.5.20/webapps/labkey] is not valid
    at org.apache.catalina.webresources.StandardRoot.createMainResourceSet(StandardRoot.java:745)
    at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:703)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 13 more

22-Aug-2017 16:35:02.103 SEVERE [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
 java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:756)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

22-Aug-2017 16:35:02.104 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml] has finished in [66] ms
22-Aug-2017 16:35:02.106 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs]
22-Aug-2017 16:35:02.509 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:35:02.537 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs] has finished in [432] ms
22-Aug-2017 16:35:02.537 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager]
22-Aug-2017 16:35:02.704 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:35:02.712 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager] has finished in [175] ms
22-Aug-2017 16:35:02.713 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager]
22-Aug-2017 16:35:02.834 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:35:02.836 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager] has finished in [124] ms
22-Aug-2017 16:35:02.836 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT]
22-Aug-2017 16:35:02.939 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:35:02.941 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT] has finished in [105] ms
22-Aug-2017 16:35:02.941 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples]
22-Aug-2017 16:35:03.214 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:35:03.229 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples] has finished in [288] ms
22-Aug-2017 16:35:03.232 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 1223 ms
22-Aug-2017 16:35:03.234 SEVERE [main] org.apache.catalina.core.StandardServer.await StandardServer.await: create[localhost:8005]:
 java.net.BindException: Address already in use (Bind failed)
    at java.net.PlainSocketImpl.socketBind(Native Method)
    at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
    at java.net.ServerSocket.bind(ServerSocket.java:375)
    at java.net.ServerSocket.<init>(ServerSocket.java:237)
    at org.apache.catalina.core.StandardServer.await(StandardServer.java:440)
    at org.apache.catalina.startup.Catalina.await(Catalina.java:744)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:690)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 16:35:03.235 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:35:03.235 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:35:03.235 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
22-Aug-2017 16:35:03.280 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:35:03.280 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:35:03.280 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:35:03.280 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:35:03.282 WARNING [main] org.apache.catalina.deploy.NamingResourcesImpl.cleanUp Failed to retrieve JNDI naming context for container [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]] so no cleanup was performed for that container
 javax.naming.NamingException: No naming context bound to this class loader
    at org.apache.naming.ContextBindings.getClassLoader(ContextBindings.java:268)
    at org.apache.catalina.deploy.NamingResourcesImpl.cleanUp(NamingResourcesImpl.java:993)
    at org.apache.catalina.deploy.NamingResourcesImpl.stopInternal(NamingResourcesImpl.java:976)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5443)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:264)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardService.destroyInternal(StandardService.java:585)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardServer.destroyInternal(StandardServer.java:883)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.startup.Catalina.stop(Catalina.java:730)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:691)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 16:35:09.654 INFO [http-nio-8080-exec-39] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:37:06.288 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.20
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Aug 2 2017 21:35:49 UTC
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.20.0
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.2.0-1-amd64
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-8-oracle/jre
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_144-b01
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 16:37:06.290 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 16:37:06.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/apache-tomcat-8.5.20//conf/logging.properties
22-Aug-2017 16:37:06.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
22-Aug-2017 16:37:06.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
22-Aug-2017 16:37:06.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
22-Aug-2017 16:37:06.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 16:37:06.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 16:37:06.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/apache-tomcat-8.5.20//temp
22-Aug-2017 16:37:06.291 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/home/thierry/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86/:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
22-Aug-2017 16:37:06.391 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:37:06.404 SEVERE [main] org.apache.coyote.AbstractProtocol.init Failed to initialize end point associated with ProtocolHandler ["http-nio-8080"]
 java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:66)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)

22-Aug-2017 16:37:06.405 SEVERE [main] org.apache.catalina.core.StandardService.initInternal Failed to initialize connector [Connector[HTTP/1.1-8080]]
 org.apache.catalina.LifecycleException: Failed to initialize component [Connector[HTTP/1.1-8080]]
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:112)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:999)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    ... 12 more
Caused by: java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:66)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    ... 13 more

22-Aug-2017 16:37:06.405 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:37:06.407 SEVERE [main] org.apache.coyote.AbstractProtocol.init Failed to initialize end point associated with ProtocolHandler ["ajp-nio-8009"]
 java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)

22-Aug-2017 16:37:06.407 SEVERE [main] org.apache.catalina.core.StandardService.initInternal Failed to initialize connector [Connector[AJP/1.3-8009]]
 org.apache.catalina.LifecycleException: Failed to initialize component [Connector[AJP/1.3-8009]]
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:112)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:999)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    ... 12 more
Caused by: java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    ... 13 more

22-Aug-2017 16:37:06.407 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 416 ms
22-Aug-2017 16:37:06.427 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
22-Aug-2017 16:37:06.427 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.20
22-Aug-2017 16:37:06.436 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
22-Aug-2017 16:37:06.458 WARNING [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase [/usr/local/apache-tomcat-8.5.20/webapps/@@/usr/local/labkey/labkeywebapp/@@] inside the host appBase has been specified, and will be ignored
22-Aug-2017 16:37:06.475 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[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@fc9645e]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4860)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4992)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 10 more
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/usr/local/apache-tomcat-8.5.20/webapps/labkey] is not valid
    at org.apache.catalina.webresources.StandardRoot.createMainResourceSet(StandardRoot.java:745)
    at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:703)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 13 more

22-Aug-2017 16:37:06.475 SEVERE [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
 java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:756)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

22-Aug-2017 16:37:06.477 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml] has finished in [40] ms
22-Aug-2017 16:37:06.477 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs]
22-Aug-2017 16:37:06.794 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:06.818 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs] has finished in [341] ms
22-Aug-2017 16:37:06.818 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager]
22-Aug-2017 16:37:06.968 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:06.973 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager] has finished in [155] ms
22-Aug-2017 16:37:06.973 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager]
22-Aug-2017 16:37:07.075 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:07.076 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager] has finished in [103] ms
22-Aug-2017 16:37:07.076 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT]
22-Aug-2017 16:37:07.166 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:07.167 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT] has finished in [91] ms
22-Aug-2017 16:37:07.167 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples]
22-Aug-2017 16:37:07.362 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:07.374 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples] has finished in [207] ms
22-Aug-2017 16:37:07.376 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 969 ms
22-Aug-2017 16:37:07.378 SEVERE [main] org.apache.catalina.core.StandardServer.await StandardServer.await: create[localhost:8005]:
 java.net.BindException: Address already in use (Bind failed)
    at java.net.PlainSocketImpl.socketBind(Native Method)
    at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
    at java.net.ServerSocket.bind(ServerSocket.java:375)
    at java.net.ServerSocket.<init>(ServerSocket.java:237)
    at org.apache.catalina.core.StandardServer.await(StandardServer.java:440)
    at org.apache.catalina.startup.Catalina.await(Catalina.java:744)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:690)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 16:37:07.378 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:37:07.378 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:37:07.378 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
22-Aug-2017 16:37:07.429 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:37:07.430 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:37:07.430 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:37:07.430 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:37:07.431 WARNING [main] org.apache.catalina.deploy.NamingResourcesImpl.cleanUp Failed to retrieve JNDI naming context for container [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]] so no cleanup was performed for that container
 javax.naming.NamingException: No naming context bound to this class loader
    at org.apache.naming.ContextBindings.getClassLoader(ContextBindings.java:268)
    at org.apache.catalina.deploy.NamingResourcesImpl.cleanUp(NamingResourcesImpl.java:993)
    at org.apache.catalina.deploy.NamingResourcesImpl.stopInternal(NamingResourcesImpl.java:976)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5443)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:264)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardService.destroyInternal(StandardService.java:585)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardServer.destroyInternal(StandardServer.java:883)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.startup.Catalina.stop(Catalina.java:730)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:691)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 16:37:21.093 INFO [http-nio-8080-exec-49] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:37:24.446 INFO [http-nio-8080-exec-53] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:37:24.949 INFO [http-nio-8080-exec-53] org.apache.catalina.startup.HostConfig.undeploy Undeploying context [/labkey]
22-Aug-2017 16:37:32.056 INFO [main] org.apache.catalina.core.StandardServer.await A valid shutdown command was received via the shutdown port. Stopping the Server instance.
22-Aug-2017 16:37:32.057 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:37:32.111 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:37:32.161 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
22-Aug-2017 16:37:32.207 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:37:32.209 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:37:32.210 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:37:32.211 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:37:34.491 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.20
22-Aug-2017 16:37:34.493 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Aug 2 2017 21:35:49 UTC
22-Aug-2017 16:37:34.493 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.20.0
22-Aug-2017 16:37:34.493 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.2.0-1-amd64
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-8-oracle/jre
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_144-b01
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/apache-tomcat-8.5.20//conf/logging.properties
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
22-Aug-2017 16:37:34.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
22-Aug-2017 16:37:34.495 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
22-Aug-2017 16:37:34.495 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 16:37:34.495 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 16:37:34.495 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/apache-tomcat-8.5.20//temp
22-Aug-2017 16:37:34.495 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/home/thierry/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86/:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
22-Aug-2017 16:37:34.602 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:37:34.617 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
22-Aug-2017 16:37:34.619 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:37:34.621 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
22-Aug-2017 16:37:34.621 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 439 ms
22-Aug-2017 16:37:34.643 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
22-Aug-2017 16:37:34.644 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.20
22-Aug-2017 16:37:34.654 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs]
22-Aug-2017 16:37:35.066 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:35.094 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs] has finished in [440] ms
22-Aug-2017 16:37:35.094 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager]
22-Aug-2017 16:37:35.278 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:35.290 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager] has finished in [195] ms
22-Aug-2017 16:37:35.290 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager]
22-Aug-2017 16:37:35.449 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:35.554 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager] has finished in [264] ms
22-Aug-2017 16:37:35.554 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT]
22-Aug-2017 16:37:35.729 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:35.731 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT] has finished in [177] ms
22-Aug-2017 16:37:35.731 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples]
22-Aug-2017 16:37:35.980 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 16:37:35.992 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples] has finished in [261] ms
22-Aug-2017 16:37:36.026 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
22-Aug-2017 16:37:36.033 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 16:37:36.035 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 1413 ms
22-Aug-2017 16:38:16.034 INFO [localhost-startStop-2] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
22-Aug-2017 16:38:16.036 WARNING [localhost-startStop-2] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase [/usr/local/apache-tomcat-8.5.20/webapps/@@/usr/local/labkey/labkeywebapp/@@] inside the host appBase has been specified, and will be ignored
22-Aug-2017 16:38:16.044 SEVERE [localhost-startStop-2] org.apache.catalina.core.ContainerBase.addChildInternal ContainerBase.addChild: start:
 org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@53ffd086]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4860)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4992)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 10 more
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/usr/local/apache-tomcat-8.5.20/webapps/labkey] is not valid
    at org.apache.catalina.webresources.StandardRoot.createMainResourceSet(StandardRoot.java:745)
    at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:703)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 13 more

22-Aug-2017 16:38:16.047 SEVERE [localhost-startStop-2] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
 java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:756)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

22-Aug-2017 16:38:16.048 INFO [localhost-startStop-2] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml] has finished in [15] ms
22-Aug-2017 16:38:46.055 INFO [ContainerBackgroundProcessor[StandardEngine[Catalina]]] org.apache.catalina.startup.HostConfig.undeploy Undeploying context [/labkey]
22-Aug-2017 16:38:46.057 WARNING [ContainerBackgroundProcessor[StandardEngine[Catalina]]] org.apache.catalina.deploy.NamingResourcesImpl.cleanUp Failed to retrieve JNDI naming context for container [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]] so no cleanup was performed for that container
 javax.naming.NameNotFoundException: Name [comp/env] is not bound in this Context. Unable to find [comp].
    at org.apache.naming.NamingContext.lookup(NamingContext.java:816)
    at org.apache.naming.NamingContext.lookup(NamingContext.java:173)
    at org.apache.catalina.deploy.NamingResourcesImpl.cleanUp(NamingResourcesImpl.java:994)
    at org.apache.catalina.deploy.NamingResourcesImpl.stopInternal(NamingResourcesImpl.java:976)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5443)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:264)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.startup.HostConfig.undeploy(HostConfig.java:1437)
    at org.apache.catalina.startup.HostConfig.checkResources(HostConfig.java:1345)
    at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1623)
    at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:314)
    at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:94)
    at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1164)
    at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1388)
    at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1392)
    at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1360)
    at java.lang.Thread.run(Thread.java:748)

22-Aug-2017 16:38:46.061 INFO [localhost-startStop-3] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
22-Aug-2017 16:38:46.063 WARNING [localhost-startStop-3] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase [/usr/local/apache-tomcat-8.5.20/webapps/@@/usr/local/labkey/labkeywebapp/@@] inside the host appBase has been specified, and will be ignored
22-Aug-2017 16:38:46.069 SEVERE [localhost-startStop-3] org.apache.catalina.core.ContainerBase.addChildInternal ContainerBase.addChild: start:
 org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@2a544c]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4860)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4992)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 10 more
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/usr/local/apache-tomcat-8.5.20/webapps/labkey] is not valid
    at org.apache.catalina.webresources.StandardRoot.createMainResourceSet(StandardRoot.java:745)
    at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:703)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 13 more

22-Aug-2017 16:38:46.070 SEVERE [localhost-startStop-3] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
 java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:756)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

22-Aug-2017 16:38:46.071 INFO [localhost-startStop-3] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml] has finished in [10] ms
22-Aug-2017 16:42:37.319 INFO [http-nio-8080-exec-7] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:38.016 INFO [http-nio-8080-exec-2] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:38.361 INFO [http-nio-8080-exec-8] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:38.540 INFO [http-nio-8080-exec-11] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:38.712 INFO [http-nio-8080-exec-16] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:39.112 INFO [http-nio-8080-exec-11] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:39.298 INFO [http-nio-8080-exec-13] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:39.501 INFO [http-nio-8080-exec-10] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:39.671 INFO [http-nio-8080-exec-4] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:39.848 INFO [http-nio-8080-exec-16] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:42:40.015 INFO [http-nio-8080-exec-2] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:51:10.071 INFO [http-nio-8080-exec-18] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 16:56:03.266 INFO [http-nio-8080-exec-30] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.
22-Aug-2017 17:36:05.905 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.20
22-Aug-2017 17:36:05.907 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Aug 2 2017 21:35:49 UTC
22-Aug-2017 17:36:05.907 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.20.0
22-Aug-2017 17:36:05.907 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
22-Aug-2017 17:36:05.907 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.2.0-1-amd64
22-Aug-2017 17:36:05.908 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
22-Aug-2017 17:36:05.908 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-8-oracle/jre
22-Aug-2017 17:36:05.908 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_144-b01
22-Aug-2017 17:36:05.908 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
22-Aug-2017 17:36:05.908 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 17:36:05.908 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 17:36:05.908 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/apache-tomcat-8.5.20//conf/logging.properties
22-Aug-2017 17:36:05.908 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
22-Aug-2017 17:36:05.909 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
22-Aug-2017 17:36:05.909 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
22-Aug-2017 17:36:05.909 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 17:36:05.909 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 17:36:05.909 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/apache-tomcat-8.5.20//temp
22-Aug-2017 17:36:05.909 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/home/thierry/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86/:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
22-Aug-2017 17:36:06.017 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:06.031 SEVERE [main] org.apache.coyote.AbstractProtocol.init Failed to initialize end point associated with ProtocolHandler ["http-nio-8080"]
 java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:66)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)

22-Aug-2017 17:36:06.032 SEVERE [main] org.apache.catalina.core.StandardService.initInternal Failed to initialize connector [Connector[HTTP/1.1-8080]]
 org.apache.catalina.LifecycleException: Failed to initialize component [Connector[HTTP/1.1-8080]]
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:112)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:999)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    ... 12 more
Caused by: java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:66)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    ... 13 more

22-Aug-2017 17:36:06.033 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:06.034 SEVERE [main] org.apache.coyote.AbstractProtocol.init Failed to initialize end point associated with ProtocolHandler ["ajp-nio-8009"]
 java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)

22-Aug-2017 17:36:06.035 SEVERE [main] org.apache.catalina.core.StandardService.initInternal Failed to initialize connector [Connector[AJP/1.3-8009]]
 org.apache.catalina.LifecycleException: Failed to initialize component [Connector[AJP/1.3-8009]]
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:112)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:999)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    ... 12 more
Caused by: java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    ... 13 more

22-Aug-2017 17:36:06.035 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 418 ms
22-Aug-2017 17:36:06.058 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
22-Aug-2017 17:36:06.058 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.20
22-Aug-2017 17:36:06.069 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
22-Aug-2017 17:36:06.109 WARNING [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase [/usr/local/apache-tomcat-8.5.20/webapps/@@/usr/local/labkey/labkeywebapp/@@] inside the host appBase has been specified, and will be ignored
22-Aug-2017 17:36:06.135 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[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@fc9645e]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4860)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4992)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 10 more
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/usr/local/apache-tomcat-8.5.20/webapps/labkey] is not valid
    at org.apache.catalina.webresources.StandardRoot.createMainResourceSet(StandardRoot.java:745)
    at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:703)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 13 more

22-Aug-2017 17:36:06.135 SEVERE [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
 java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:756)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

22-Aug-2017 17:36:06.137 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml] has finished in [67] ms
22-Aug-2017 17:36:06.138 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs]
22-Aug-2017 17:36:06.507 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:06.534 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs] has finished in [396] ms
22-Aug-2017 17:36:06.534 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager]
22-Aug-2017 17:36:06.705 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:06.711 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager] has finished in [177] ms
22-Aug-2017 17:36:06.712 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager]
22-Aug-2017 17:36:06.838 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:06.840 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager] has finished in [129] ms
22-Aug-2017 17:36:06.840 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT]
22-Aug-2017 17:36:06.944 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:06.945 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT] has finished in [105] ms
22-Aug-2017 17:36:06.945 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples]
22-Aug-2017 17:36:07.193 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:07.207 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples] has finished in [262] ms
22-Aug-2017 17:36:07.246 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 1210 ms
22-Aug-2017 17:36:07.249 SEVERE [main] org.apache.catalina.core.StandardServer.await StandardServer.await: create[localhost:8005]:
 java.net.BindException: Address already in use (Bind failed)
    at java.net.PlainSocketImpl.socketBind(Native Method)
    at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
    at java.net.ServerSocket.bind(ServerSocket.java:375)
    at java.net.ServerSocket.<init>(ServerSocket.java:237)
    at org.apache.catalina.core.StandardServer.await(StandardServer.java:440)
    at org.apache.catalina.startup.Catalina.await(Catalina.java:744)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:690)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 17:36:07.250 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:07.250 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:07.250 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
22-Aug-2017 17:36:07.267 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:07.267 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:07.267 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:07.268 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:07.268 WARNING [main] org.apache.catalina.deploy.NamingResourcesImpl.cleanUp Failed to retrieve JNDI naming context for container [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]] so no cleanup was performed for that container
 javax.naming.NamingException: No naming context bound to this class loader
    at org.apache.naming.ContextBindings.getClassLoader(ContextBindings.java:268)
    at org.apache.catalina.deploy.NamingResourcesImpl.cleanUp(NamingResourcesImpl.java:993)
    at org.apache.catalina.deploy.NamingResourcesImpl.stopInternal(NamingResourcesImpl.java:976)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5443)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:264)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardService.destroyInternal(StandardService.java:585)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardServer.destroyInternal(StandardServer.java:883)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.startup.Catalina.stop(Catalina.java:730)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:691)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 17:36:13.211 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.20
22-Aug-2017 17:36:13.213 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Aug 2 2017 21:35:49 UTC
22-Aug-2017 17:36:13.213 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.20.0
22-Aug-2017 17:36:13.213 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
22-Aug-2017 17:36:13.213 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.2.0-1-amd64
22-Aug-2017 17:36:13.213 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
22-Aug-2017 17:36:13.214 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-8-oracle/jre
22-Aug-2017 17:36:13.214 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_144-b01
22-Aug-2017 17:36:13.214 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
22-Aug-2017 17:36:13.214 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 17:36:13.214 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/apache-tomcat-8.5.20
22-Aug-2017 17:36:13.214 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/apache-tomcat-8.5.20//conf/logging.properties
22-Aug-2017 17:36:13.214 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
22-Aug-2017 17:36:13.214 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
22-Aug-2017 17:36:13.214 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
22-Aug-2017 17:36:13.215 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 17:36:13.215 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/apache-tomcat-8.5.20/
22-Aug-2017 17:36:13.215 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/apache-tomcat-8.5.20//temp
22-Aug-2017 17:36:13.215 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/home/thierry/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86_64/:/home/thierry/AMD/AMDAPPSDK-3.0/lib/x86/:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
22-Aug-2017 17:36:13.327 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:13.341 SEVERE [main] org.apache.coyote.AbstractProtocol.init Failed to initialize end point associated with ProtocolHandler ["http-nio-8080"]
 java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:66)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)

22-Aug-2017 17:36:13.342 SEVERE [main] org.apache.catalina.core.StandardService.initInternal Failed to initialize connector [Connector[HTTP/1.1-8080]]
 org.apache.catalina.LifecycleException: Failed to initialize component [Connector[HTTP/1.1-8080]]
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:112)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:999)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    ... 12 more
Caused by: java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:66)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    ... 13 more

22-Aug-2017 17:36:13.343 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:13.344 SEVERE [main] org.apache.coyote.AbstractProtocol.init Failed to initialize end point associated with ProtocolHandler ["ajp-nio-8009"]
 java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)

22-Aug-2017 17:36:13.344 SEVERE [main] org.apache.catalina.core.StandardService.initInternal Failed to initialize connector [Connector[AJP/1.3-8009]]
 org.apache.catalina.LifecycleException: Failed to initialize component [Connector[AJP/1.3-8009]]
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:112)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:549)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:875)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:607)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:630)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:311)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:494)
Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:999)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:107)
    ... 12 more
Caused by: java.net.BindException: Address already in use
    at sun.nio.ch.Net.bind0(Native Method)
    at sun.nio.ch.Net.bind(Net.java:433)
    at sun.nio.ch.Net.bind(Net.java:425)
    at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
    at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
    at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:210)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:982)
    at org.apache.tomcat.util.net.AbstractJsseEndpoint.init(AbstractJsseEndpoint.java:244)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:620)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:997)
    ... 13 more

22-Aug-2017 17:36:13.344 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 431 ms
22-Aug-2017 17:36:13.366 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
22-Aug-2017 17:36:13.366 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.20
22-Aug-2017 17:36:13.374 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
22-Aug-2017 17:36:13.408 WARNING [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase [/usr/local/apache-tomcat-8.5.20/webapps/@@/usr/local/labkey/labkeywebapp/@@] inside the host appBase has been specified, and will be ignored
22-Aug-2017 17:36:13.434 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[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@fc9645e]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
    at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4860)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4992)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 10 more
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/usr/local/apache-tomcat-8.5.20/webapps/labkey] is not valid
    at org.apache.catalina.webresources.StandardRoot.createMainResourceSet(StandardRoot.java:745)
    at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:703)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 13 more

22-Aug-2017 17:36:13.434 SEVERE [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml]
 java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:756)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

22-Aug-2017 17:36:13.436 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of configuration descriptor [/usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost/labkey.xml] has finished in [61] ms
22-Aug-2017 17:36:13.437 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs]
22-Aug-2017 17:36:13.808 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:13.836 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/docs] has finished in [399] ms
22-Aug-2017 17:36:13.837 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager]
22-Aug-2017 17:36:14.005 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:14.011 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/host-manager] has finished in [174] ms
22-Aug-2017 17:36:14.011 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager]
22-Aug-2017 17:36:14.159 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:14.162 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/manager] has finished in [150] ms
22-Aug-2017 17:36:14.162 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT]
22-Aug-2017 17:36:14.309 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:14.310 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/ROOT] has finished in [148] ms
22-Aug-2017 17:36:14.310 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples]
22-Aug-2017 17:36:14.522 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
22-Aug-2017 17:36:14.531 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/apache-tomcat-8.5.20/webapps/examples] has finished in [221] ms
22-Aug-2017 17:36:14.535 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 1190 ms
22-Aug-2017 17:36:14.537 SEVERE [main] org.apache.catalina.core.StandardServer.await StandardServer.await: create[localhost:8005]:
 java.net.BindException: Address already in use (Bind failed)
    at java.net.PlainSocketImpl.socketBind(Native Method)
    at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
    at java.net.ServerSocket.bind(ServerSocket.java:375)
    at java.net.ServerSocket.<init>(ServerSocket.java:237)
    at org.apache.catalina.core.StandardServer.await(StandardServer.java:440)
    at org.apache.catalina.startup.Catalina.await(Catalina.java:744)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:690)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 17:36:14.538 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:14.538 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:14.538 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
22-Aug-2017 17:36:14.562 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:14.562 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:14.562 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:14.562 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:14.564 WARNING [main] org.apache.catalina.deploy.NamingResourcesImpl.cleanUp Failed to retrieve JNDI naming context for container [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]] so no cleanup was performed for that container
 javax.naming.NamingException: No naming context bound to this class loader
    at org.apache.naming.ContextBindings.getClassLoader(ContextBindings.java:268)
    at org.apache.catalina.deploy.NamingResourcesImpl.cleanUp(NamingResourcesImpl.java:993)
    at org.apache.catalina.deploy.NamingResourcesImpl.stopInternal(NamingResourcesImpl.java:976)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5443)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:264)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardService.destroyInternal(StandardService.java:585)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardServer.destroyInternal(StandardServer.java:883)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.startup.Catalina.stop(Catalina.java:730)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:691)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 17:36:24.016 INFO [main] org.apache.catalina.core.StandardServer.await A valid shutdown command was received via the shutdown port. Stopping the Server instance.
22-Aug-2017 17:36:24.017 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:24.072 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:24.123 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
22-Aug-2017 17:36:24.158 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:24.162 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:24.165 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
22-Aug-2017 17:36:24.166 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]
22-Aug-2017 17:36:24.168 WARNING [main] org.apache.catalina.deploy.NamingResourcesImpl.cleanUp Failed to retrieve JNDI naming context for container [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]] so no cleanup was performed for that container
 javax.naming.NamingException: No naming context bound to this class loader
    at org.apache.naming.ContextBindings.getClassLoader(ContextBindings.java:268)
    at org.apache.catalina.deploy.NamingResourcesImpl.cleanUp(NamingResourcesImpl.java:993)
    at org.apache.catalina.deploy.NamingResourcesImpl.stopInternal(NamingResourcesImpl.java:976)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5443)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:226)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:264)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:854)
    at org.apache.catalina.core.ContainerBase.destroyInternal(ContainerBase.java:1036)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardService.destroyInternal(StandardService.java:585)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.core.StandardServer.destroyInternal(StandardServer.java:883)
    at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
    at org.apache.catalina.startup.Catalina.stop(Catalina.java:730)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:691)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

22-Aug-2017 17:36:24.168 INFO [main] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [WebappLoader[/labkey]] after stop() had already been called. The second call will be ignored.

In my labkey path i have no log files.

Thanks for the log output.

The error message here provides info on what's happening:

22-Aug-2017 15:00:18.271 WARNING [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase [/usr/local/apache-tomcat-8.5.20/webapps/@@/usr/local/labkey/labkeywebapp/@@] inside the host appBase has been specified, and will be ignored

It looks like you're using a labkey.xml file that has placeholder values. It should be in /usr/local/apache-tomcat-8.5.20/conf/Catalina/localhost. At a minimum, you'll need to edit a line that looks like this:

<Context docBase="@@appDocBase@@" reloadable="true" crossContext="true">

to replace the @@appDocBase@@ to point at the directory where you have installed the labkeywebapp directory. There may be other @@value@@ tokens that need to be updated as well, especially around information about connecting to your database. The correct values are described here:

https://www.labkey.org/Documentation/wiki-page.view?name=cpasxml

Thanks,
Josh

Dear Josh,
Thank you very much for your help.
I indeed replaced the @@value@@ fields but kept the double @@.
sorry ..!
It's now running!

Thanks,
Best regards,

Thierry