Installing XNAT 1.8.2, web app does not start

[James Bartolotti]

I am a new xnat admin trying to setup XNAT 1.8.2 on RHEL 7.9, but I cannot get the web app to start. I have Tomcat 9, PostgreSQL 12.6, and Java 1.8.0 installed. 

I created a PostgreSQL user xnat, assigned a password, and created the database xnat owned by user xnat. PostgreSQL and XNAT are located on the same server. I configured pg_hba.conf by adding

host xnat xnat 127.0.0.1/32 md5

host xnat xnat ::1/128 md5

For testing I configured postgresql.conf by adding

listen_addresses = '*' but plan to revert it to listen_addresses = 'localhost'

My xnat-conf.properties file contains the appropriate username and password.

datasource.driver=org.postgresql.Driver

datasource.url=jdbc:postgresql://localhost/xnat

datasource.username=xnat

datasource.password=**REDACTED**

hibernate.dialect=org.hibernate.dialect.PostgreSQL9Dialect

hibernate.hbm2ddl.auto=update

hibernate.show_sql=false

hibernate.cache.use_second_level_cache=true

hibernate.cache.use_query_cache=true

Tomcat9 was installed from a zip file into /usr/local/tomcat9. I moved the xnat .war into /usr/local/tomcat9/webapps/ROOT.war and exploded it. I created the file /usr/local/tomcat9/bin/setenv.sh which contains

CATALINA_OPTS="${CATALINA_OPTS} -Dxnat.home=/xnatdata/home2"

The xnat.home location is on an NFS mounted drive. I created an xnat user, set its home directory to /xnatdata/home2, and gave the user ownership of everything in /usr/local/tomcat9 and in /xnatdata/home2. I edited tomcat9.service to run as user xnat by adding

[Service]

User=xnat

Group=xnat

When I start tomcat, either with /usr/local/tomcat9/bin/startup.sh or with systemctl start tomcat9, tomcat and the web application manager start up fine. I can access the tomcat landing page from http://localhost:8080/tomcat or externally at http://myaddress:8080/tomcat. No matter what I've tried, I can't get the XNAT webpage to start. The error indicates that "one or more listeners failed to start" but I can't figure out how to fix it.

from catalina.out:

23-Jul-2021 14:00:17.400 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name:   Apache Tomcat/9.0.50

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built:          Jun 28 2021 08:46:44 UTC

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.50.0

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name:               Linux

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version:            3.10.0-1160.31.1.el7.x86_64

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture:          amd64

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home:             /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/jre

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version:           1.8.0_292-b10

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor:            Red Hat, Inc.

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE:         /usr/local/tomcat9

23-Jul-2021 14:00:17.403 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME:         /usr/local/tomcat9

23-Jul-2021 14:00:17.405 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat9/conf/logging.properties

23-Jul-2021 14:00:17.405 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager

23-Jul-2021 14:00:17.405 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048

23-Jul-2021 14:00:17.406 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources

23-Jul-2021 14:00:17.406 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027

23-Jul-2021 14:00:17.406 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dxnat.home=/xnatdata/home2

23-Jul-2021 14:00:17.406 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=

23-Jul-2021 14:00:17.406 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/tomcat9

23-Jul-2021 14:00:17.406 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/tomcat9

23-Jul-2021 14:00:17.406 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/tomcat9/temp

23-Jul-2021 14:00:17.407 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The Apache Tomcat Native library which allows using OpenSSL was not found on the java.library.path: [/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]

23-Jul-2021 14:00:17.742 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]

23-Jul-2021 14:00:17.780 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [569] milliseconds

23-Jul-2021 14:00:17.823 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]

23-Jul-2021 14:00:17.823 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.50]

23-Jul-2021 14:00:17.848 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [/usr/local/tomcat9/webapps/ROOT.war]

23-Jul-2021 14:00:27.094 INFO [main] 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.

23-Jul-2021 14:00:33.397 SEVERE [main] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file

23-Jul-2021 14:00:33.401 SEVERE [main] org.apache.catalina.core.StandardContext.startInternal Context [] startup failed due to previous errors

23-Jul-2021 14:00:33.444 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [hbmCacheManager] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

 java.lang.Object.wait(Native Method)

 java.util.TimerThread.mainLoop(Timer.java:552)

 java.util.TimerThread.run(Timer.java:505)

23-Jul-2021 14:00:33.454 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/usr/local/tomcat9/webapps/ROOT.war] has finished in [15,605] ms

23-Jul-2021 14:00:33.455 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat9/webapps/docs]

23-Jul-2021 14:00:33.476 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat9/webapps/docs] has finished in [21] ms

23-Jul-2021 14:00:33.477 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat9/webapps/examples]

23-Jul-2021 14:00:33.594 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat9/webapps/examples] has finished in [117] ms

23-Jul-2021 14:00:33.594 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat9/webapps/host-manager]

23-Jul-2021 14:00:33.608 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat9/webapps/host-manager] has finished in [14] ms

23-Jul-2021 14:00:33.608 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat9/webapps/manager]

From /xnatdata/home2/logs/spring.log:

2021-07-23 14:08:43,927 [main] ERROR org.springframework.web.context.ContextLoader - Context initialization failed

org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'updateSecurityFilterHandlerMethod' defined in file [/usr/local/tomcat9/webapps/ROOT/WEB-INF/classes/org/nrg/xnat/event/listeners/methods/UpdateSecurityFilterHandlerMethod.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.nrg.xnat.configuration.ApplicationConfig': Unsatisfied dependency expressed through method 'setAsyncOperationsPreferences' parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'asyncOperationsPreferences' defined in file [/usr/local/tomcat9/webapps/ROOT/WEB-INF/classes/org/nrg/xnat/preferences/AsyncOperationsPreferences.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'defaultNrgPreferenceService' defined in URL [jar:file:/usr/local/tomcat9/webapps/ROOT/WEB-INF/lib/prefs-1.8.2.jar!/org/nrg/prefs/services/impl/DefaultNrgPreferenceService.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'hibernateToolService': Unsatisfied dependency expressed through method 'setDao' parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'toolRepository': Unsatisfied dependency expressed through method 'setSessionFactory' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [org/nrg/xnat/configuration/OrmConfig.class]: Invocation of init method failed; nested exception is org.hibernate.service.spi.ServiceException: Unable to create requested service [org.hibernate.engine.spi.CacheImplementor]

        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)

        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)

        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1196)

        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1098)

        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)

        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)

        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)

        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)

        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)

        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)

        at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:237)

        at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:703)

        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:527)

        at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)

        at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)

        at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)

        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4766)

        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5230)

        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)

        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:728)

        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:700)

        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:696)

        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1024)

        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1911)

        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

        at java.util.concurrent.FutureTask.run(FutureTask.java:266)

        at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)

        at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)

        at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:825)

        at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:475)

        at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1618)

        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:948)

        at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:835)

        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1398)

        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1388)

        at java.util.concurrent.FutureTask.run(FutureTask.java:266)

        at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)

        at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)

        at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:921)

        at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:263)

        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)

        at org.apache.catalina.core.StandardService.startInternal(StandardService.java:437)

        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)

        at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:934)

        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)

        at org.apache.catalina.startup.Catalina.start(Catalina.java:772)

        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:345)

        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:476)

[Herrick, Rick]

You’re missing a property in xnat-conf.properties:

 

hibernate.cache.region.factory_class=org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory

 

If you have hibernate.cache.use_second_level_cache set to true, you have to provide an implementation for the cache region factory class.

 

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Phone: +1 (314) 273-1645

 

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of James Bartolotti <jamesba...@gmail.com>
Date: Monday, July 26, 2021 at 9:03 AM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] Installing XNAT 1.8.2, web app does not start

* External Email - Caution *

--
You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to xnat_discussi...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/3c23cfbf-acc3-4483-a045-8a3572cf0291n%40googlegroups.com.

 

---

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

[James Bartolotti]

I'm getting the same error, regardless of whether xnat-conf.properties contains: 
hibernate.cache.use_second_level_cache=true
hibernate.cache.region.factory_class=org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory

hibernate.cache.use_second_level_cache=false

hibernate.cache.use_second_level_cache=true

I still get the same errors. In catalina.out it says

26-Jul-2021 11:25:43.704 SEVERE [main] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file

26-Jul-2021 11:25:43.707 SEVERE [main] org.apache.catalina.core.StandardContext.startInternal Context [] startup failed due to previous errors

Does the listener start issue mean there's a problem with xnat connecting to postgres?

[Thibaut Woog]

Hello, 

It seems I have the same problem. Do you have fixed your problem ?

I'm using XNAT 1.8.6 on ubuntu server 22.04, tomcat9, openjdk11 and postgresql 12. Connection to postgres with xnat user works.

Here an extract of spring.log :  

2022-11-15 14:12:11,538 [main] ERROR org.springframework.web.context.ContextLoader - Context initialization failed
org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'updateSecurityFilterHandlerMethod' defined in file [/var/lib/tomcat9/webapps/ROOT/WEB-INF/classes/org/nrg/xnat/event/listeners/methods/UpdateSecurityFilterHandlerMethod.class]: Unsatisfied dependency expressed through constructor parameter 2; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.nrg.xnat.initialization.SecurityConfig': Unsatisfied dependency expressed through method 'setContentNegotationStrategy' parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.springframework.web.servlet.config.annotation.DelegatingWebMvcConfiguration': Unsatisfied dependency expressed through method 'setConfigurers' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'webConfig' defined in file [/var/lib/tomcat9/webapps/ROOT/WEB-INF/classes/org/nrg/xnat/configuration/WebConfig.class]: Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.nrg.xnat.configuration.WebConfig$$EnhancerBySpringCGLIB$$ed1a0b5b]: Constructor threw exception; nested exception is java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException

    at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1196)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1098)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
    at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:237)
    at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:703)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:527)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)

    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4683)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5146)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:705)
    at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1132)
    at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1866)
    at java.base/java.util.concurrent.Executors$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:118)
    at org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:1044)
    at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:429)
    at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1575)
    at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:309)

    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:841)
    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:140)
    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:421)
    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:633)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:343)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:478)

Thank's in advance, 

Best,
 

[Kate Alpert]

Try with openjdk8, see https://wiki.xnat.org/documentation/getting-started-with-xnat/xnat-installation-guide/prerequisites-for-installing-xnat#PrerequisitesforInstallingXNAT-java-8.