Trouble Starting LabKey Server Community Edition: /home/Support/LabKey Support Forum

Trouble Starting LabKey Server Community Edition

LabKey Support Forum

View Message

Trouble Starting LabKey Server Community Edition etr 2021-05-07 15:27

Status: Active

Hello,
I am trying to install the Labkey server but I am experiencing some difficulties.
Please keep in mind I am not a usual user of either windows or tomcat for that matter.
Running on Windows Server 2012 R2, openjdk 16, tomcat 9.0

Catalina- log says something like this:

07-May-2021 22:05:40.736 SEVERE [Catalina-utility-2] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying deployment descriptor [C:\labkey\apps\tomcat\conf\Catalina\localhost\labkey.xml]
	java.lang.IllegalStateException: Error starting child
		at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:720)
		at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
		at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:706)
		at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:689)
		at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1881)
		at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
		at java.util.concurrent.FutureTask.run(Unknown Source)
		at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
		at java.util.concurrent.AbstractExecutorService.submit(Unknown Source)
		at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:582)
		at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:472)
		at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1660)
		at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:315)
		at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
		at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1151)
		at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1353)
		at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1357)
		at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1335)
		at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
		at java.util.concurrent.FutureTask.runAndReset(Unknown Source)
		at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
		at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
		at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
		at java.lang.Thread.run(Unknown Source)
	Caused by: org.apache.catalina.LifecycleException: Error starting the loader
		at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:432)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
		at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5028)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
		at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
		... 25 more
	Caused by: java.lang.UnsupportedClassVersionError: org/labkey/bootstrap/LabKeyBootstrapClassLoader has been compiled by a more recent version of the Java Runtime (class file version 58.0), this version of the Java Runtime only recognizes class file versions up to 52.0
		at java.lang.ClassLoader.defineClass1(Native Method)
		at java.lang.ClassLoader.defineClass(Unknown Source)
		at java.security.SecureClassLoader.defineClass(Unknown Source)
		at java.net.URLClassLoader.defineClass(Unknown Source)
		at java.net.URLClassLoader.access$100(Unknown Source)
		at java.net.URLClassLoader$1.run(Unknown Source)
		at java.net.URLClassLoader$1.run(Unknown Source)
		at java.security.AccessController.doPrivileged(Native Method)
		at java.net.URLClassLoader.findClass(Unknown Source)
		at java.lang.ClassLoader.loadClass(Unknown Source)
		at java.lang.ClassLoader.loadClass(Unknown Source)
		at java.lang.Class.forName0(Native Method)
		at java.lang.Class.forName(Unknown Source)
		at org.apache.catalina.loader.WebappLoader.createClassLoader(WebappLoader.java:536)
		at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:408)
		... 29 more
07-May-2021 22:05:40.738 INFO [Catalina-utility-2] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of deployment descriptor [C:\labkey\apps\tomcat\conf\Catalina\localhost\labkey.xml] has finished in [10] ms

If anyone can provide some info please.

Thanks,
ET

adam responded:	2021-05-07 15:39
The root exception ("...this version of the Java Runtime only recognizes class file versions up to 52.0") indicates that Tomcat is running under JDK 8, not JDK 16. Recent releases of LabKey Server require JDK 14, 15, or 16. See our Supported Technologies page. Adam

etr responded:	2021-05-07 16:31
Did manage to find out that the windows installer of tomcat was automatically pointing to another folder of the Java Installation indeed. Changed but still continues to get errors: 07-May-2021 23:26:40.492 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/9.0.45 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Mar 30 2021 10:29:04 UTC 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.45.0 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Windows Server 2012 R2 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 6.3 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: C:\OpenJDK-16 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 16+36-2231 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: C:\labkey\apps\tomcat 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: C:\labkey\apps\tomcat 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=C:\labkey\apps\tomcat 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=C:\labkey\apps\tomcat 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=C:\labkey\apps\tomcat\temp 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=C:\labkey\apps\tomcat\conf\logging.properties 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang=ALL-UNNAMED 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.io=ALL-UNNAMED 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: exit 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: abort 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms128m 07-May-2021 23:26:40.523 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx256m 07-May-2021 23:26:40.539 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded Apache Tomcat Native library [1.2.27] using APR version [1.7.0]. 07-May-2021 23:26:40.539 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true]. 07-May-2021 23:26:40.539 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR/OpenSSL configuration: useAprConnector [false], useOpenSSL [true] 07-May-2021 23:26:40.539 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 1.1.1k 25 Mar 2021] 07-May-2021 23:26:41.695 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"] 07-May-2021 23:26:42.023 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [2102] milliseconds 07-May-2021 23:26:42.117 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina] 07-May-2021 23:26:42.117 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.45] 07-May-2021 23:26:42.117 INFO [main] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying deployment descriptor [C:\labkey\apps\tomcat\conf\Catalina\localhost\labkey.xml] 07-May-2021 23:26:42.382 SEVERE [main] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying deployment descriptor [C:\labkey\apps\tomcat\conf\Catalina\localhost\labkey.xml] java.lang.IllegalStateException: Error starting child at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:720) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:706) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:689) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1881) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75) at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:123) at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:582) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:472) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1611) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:319) at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123) at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:423) at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:366) at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:936) at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:843) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1384) at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1374) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75) at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:145) at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:909) at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:262) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) at org.apache.catalina.core.StandardService.startInternal(StandardService.java:433) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:930) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) at org.apache.catalina.startup.Catalina.start(Catalina.java:772) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:78) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:567) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:342) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:473) Caused by: org.apache.catalina.LifecycleException: Error starting the loader at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:432) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5028) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717) ... 37 more Caused by: java.lang.ClassNotFoundException: org.labkey.bootstrap.LabKeyBootstrapClassLoader at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:433) at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:586) at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:519) at java.base/java.lang.Class.forName0(Native Method) at java.base/java.lang.Class.forName(Class.java:375) at org.apache.catalina.loader.WebappLoader.createClassLoader(WebappLoader.java:536) at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:408) ... 41 more 07-May-2021 23:26:42.382 INFO [main] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of deployment descriptor [C:\labkey\apps\tomcat\conf\Catalina\localhost\labkey.xml] has finished in [265] ms 07-May-2021 23:26:42.398 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [C:\labkey\apps\tomcat\webapps\docs] 07-May-2021 23:26:43.183 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [C:\labkey\apps\tomcat\webapps\docs] has finished in [785] ms 07-May-2021 23:26:43.183 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [C:\labkey\apps\tomcat\webapps\examples] 07-May-2021 23:26:44.324 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [C:\labkey\apps\tomcat\webapps\examples] has finished in [1,141] ms 07-May-2021 23:26:44.324 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [C:\labkey\apps\tomcat\webapps\host-manager] 07-May-2021 23:26:44.402 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [C:\labkey\apps\tomcat\webapps\host-manager] has finished in [78] ms 07-May-2021 23:26:44.402 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [C:\labkey\apps\tomcat\webapps\manager] 07-May-2021 23:26:44.636 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [C:\labkey\apps\tomcat\webapps\manager] has finished in [234] ms 07-May-2021 23:26:44.636 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [C:\labkey\apps\tomcat\webapps\ROOT] 07-May-2021 23:26:44.683 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [C:\labkey\apps\tomcat\webapps\ROOT] has finished in [47] ms 07-May-2021 23:26:44.683 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"] 07-May-2021 23:26:44.699 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [2668] milliseconds the labkey.xml looks like this: `<?xml version='1.0' encoding='utf-8'?> <Context docBase="C:\labkey\labkey\labkeyWebapp" reloadable="true" crossContext="true"> <Resource name="jdbc/labkeyDataSource" auth="Container" type="javax.sql.DataSource" username="labkey" password="XXXXX" driverClassName="org.postgresql.Driver" url="jdbc:postgresql://localhost/labkey" maxTotal="20" maxIdle="10" maxWaitMillis="120000" accessToUnderlyingConnectionAllowed="true" validationQuery="SELECT 1" /> [...]` is this the correct way to write paths in windows? `<Context docBase="C:\labkey\labkey\labkeyWebapp" reloadable="true" crossContext="true">`

adam responded:	2021-05-07 17:17
Are you following the installation instructions here? https://www.labkey.org/Documentation/wiki-page.view?name=manualInstallWindows Did you copy the "Tomcat Libraries" into CATALINA_HOME\lib? Tomcat is apparently not able to find labkeyBootstrap.jar. LabKey offers a free 30-day cloud-hosted trial of LabKey Server. I strongly recommend this over attempting a manual installation, especially if you're not familiar with Windows or Tomcat. See https://www.labkey.com/trial-sign-up/ Adam

etr responded:	2021-05-07 17:57
Status: Closed
Adam, Indeed, it was my fault. After reinstalling tomcat I forgot to recopy the files. Thanks for the help. Will definitely use the 30 day free version also since i see tutorials work better there.