XNAT 1.7.4 installation problems

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Robin Kämpe

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Feb 1, 2018, 4:57:15 AM2/1/18
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Hey XNAT experts.

I have problems very similar to this post:
https://groups.google.com/forum/#!topic/xnat_discussion/Latg4EOf83s

i.e. issues like these: WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]. I had a similar problem once before and I solved it by changing the permissions but this time it has not helped.

Background: I'm preparing to upgrade our 1.6.5 to 1.7.4, later I will try to move the database to a new server so I'm practising and preparing by preforming a clean from scratch install of 1.7.4 on a clean ubuntu server. I have followed all the steps but run into issues. So here the logs follow and some key information on what I have done so far. So there will be a lot of info below but I will try to strucure it. Can something be wrong with my JAVA and CATALINA paths? Is tomcat actually using xnat as user?
E.g. this error in the log:WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]. xnat has full rights as you see below. But still can't create common or classes. Also potential problem with postgresql? Both v10 and 9.3 seem to be installed. It seems like it is using v10.

xnat@Vader:/var/log/tomcat7$ psql --version
psql (PostgreSQL) 10.1
xnat@Vader:/var/log/tomcat7$

Is this a problem? It seems to use 10 but there is only 9 under /var/lib/postgresql/:
xnat@Vader:/var/log/tomcat7$ ls -l /var/lib/postgresql/
total 8
drwxr-xr-x 3 postgres postgres 4096 jan 31 11:48 9.3
drwxrwxr-x 2 postgres postgres 4096 jan 31 11:53 matlab

But both are under /usr/lib/postgresql:
xnat@Vader:/var/log/tomcat7$ ls -la /usr/lib/postgresql/
total 24
drwxr-xr-x   4 root root  4096 jan 31 11:48 .
drwxr-xr-x 151 root root 12288 jan 31 11:48 ..
drwxr-xr-x   3 root root  4096 jan 31 11:48 10
drwxr-xr-x   4 root root  4096 jan 31 11:48 9.3

I did install just version 9 by:  sudo apt-get install postgresql-9.3 pgadmin3 (not as the xnat user)



All of this is structured below!


Catalina.out:
Listening for transport dt_socket at address: 8000
Feb 01, 2018 9:10:13 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Feb 01, 2018 9:10:13 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Feb 01, 2018 9:10:13 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Feb 01, 2018 9:10:13 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Feb 01, 2018 9:10:13 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Feb 01, 2018 9:10:13 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/7.0.68 (Ubuntu)
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Jun 27 2016 18:13:17 UTC
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.68.0
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.10.0-42-generic
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-7-openjdk-amd64/jre
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.7.0_95-b00
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat7
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat7
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.awt.headless=true
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx2g
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseConcMarkSweepGC
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:-OmitStackTraceInFastThrow
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=512m
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSIncrementalMode
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xdebug
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dxnat.home=/data/xnat/home
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat7
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat7
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp
Feb 01, 2018 9:10:14 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Feb 01, 2018 9:10:14 AM org.apache.coyote.AbstractProtocol init
SEVERE: Failed to initialize end point associated with ProtocolHandler ["http-bio-8080"]
java.net.BindException: Address already in use <null>:8080
    at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:413)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:650)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:434)
    at org.apache.coyote.http11.AbstractHttp11JsseProtocol.init(AbstractHttp11JsseProtocol.java:119)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:978)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:560)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:820)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:642)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:667)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:253)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:427)
Caused by: java.net.BindException: Address already in use
    at java.net.PlainSocketImpl.socketBind(Native Method)
    at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:376)
    at java.net.ServerSocket.bind(ServerSocket.java:376)
    at java.net.ServerSocket.<init>(ServerSocket.java:237)
    at java.net.ServerSocket.<init>(ServerSocket.java:181)
    at org.apache.tomcat.util.net.DefaultServerSocketFactory.createSocket(DefaultServerSocketFactory.java:49)
    at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:400)
    ... 17 more

Feb 01, 2018 9:10:14 AM org.apache.catalina.core.StandardService initInternal
SEVERE: 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:107)
    at org.apache.catalina.core.StandardService.initInternal(StandardService.java:560)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:820)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:642)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:667)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:253)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:427)
Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:982)
    at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    ... 12 more
Caused by: java.net.BindException: Address already in use <null>:8080
    at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:413)
    at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:650)
    at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:434)
    at org.apache.coyote.http11.AbstractHttp11JsseProtocol.init(AbstractHttp11JsseProtocol.java:119)
    at org.apache.catalina.connector.Connector.initInternal(Connector.java:978)
    ... 13 more
Caused by: java.net.BindException: Address already in use
    at java.net.PlainSocketImpl.socketBind(Native Method)
    at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:376)
    at java.net.ServerSocket.bind(ServerSocket.java:376)
    at java.net.ServerSocket.<init>(ServerSocket.java:237)
    at java.net.ServerSocket.<init>(ServerSocket.java:181)
    at org.apache.tomcat.util.net.DefaultServerSocketFactory.createSocket(DefaultServerSocketFactory.java:49)
    at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:400)
    ... 17 more

Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 536 ms
Feb 01, 2018 9:10:14 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Feb 01, 2018 9:10:14 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.68 (Ubuntu)
Feb 01, 2018 9:10:14 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/ROOT.war
Feb 01, 2018 9:10:23 AM org.apache.catalina.startup.TldConfig execute
INFO: 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.
Feb 01, 2018 9:10:24 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Feb 01, 2018 9:10:24 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [] startup failed due to previous errors
Feb 01, 2018 9:10:24 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat7/webapps/ROOT.war has finished in 9,744 ms
Feb 01, 2018 9:10:24 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT_old
Feb 01, 2018 9:10:24 AM org.apache.catalina.core.StandardContext setPath
WARNING: A context path must either be an empty string or start with a '/' and do not end with a '/'. The path [/] does not meet these criteria and has been changed to []
Feb 01, 2018 9:10:24 AM org.apache.catalina.startup.TldConfig execute
INFO: 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.
Feb 01, 2018 9:10:24 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat7/webapps/ROOT_old has finished in 256 ms
Feb 01, 2018 9:10:24 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 10056 ms
Feb 01, 2018 9:10:24 AM org.apache.catalina.core.StandardServer await
SEVERE: StandardServer.await: create[localhost:8005]:
java.net.BindException: Address already in use
    at java.net.PlainSocketImpl.socketBind(Native Method)
    at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:376)
    at java.net.ServerSocket.bind(ServerSocket.java:376)
    at java.net.ServerSocket.<init>(ServerSocket.java:237)
    at org.apache.catalina.core.StandardServer.await(StandardServer.java:427)
    at org.apache.catalina.startup.Catalina.await(Catalina.java:781)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:727)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:294)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:428)

Feb 01, 2018 9:10:24 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Feb 01, 2018 9:10:24 AM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Feb 01, 2018 9:10:24 AM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Feb 01, 2018 9:10:24 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]

Localhost.log
Feb 01, 2018 9:10:23 AM org.apache.catalina.core.ApplicationContext log
INFO: 1 Spring WebApplicationInitializers detected on classpath
Feb 01, 2018 9:10:24 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Feb 01, 2018 9:10:24 AM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
java.lang.NoSuchMethodError: java.util.concurrent.ConcurrentHashMap.keySet()Ljava/util/concurrent/ConcurrentHashMap$KeySetView;
    at org.apache.catalina.core.ApplicationContext.getInitParameterNames(ApplicationContext.java:368)
    at org.apache.catalina.core.ApplicationContextFacade.getInitParameterNames(ApplicationContextFacade.java:367)
    at org.apache.catalina.core.StandardContext$NoPluggabilityServletContext.getInitParameterNames(StandardContext.java:6994)
    at org.springframework.web.context.support.WebApplicationContextUtils.registerEnvironmentBeans(WebApplicationContextUtils.java:229)
    at org.springframework.web.context.support.AbstractRefreshableWebApplicationContext.postProcessBeanFactory(AbstractRefreshableWebApplicationContext.java:165)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:522)
    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:5066)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)

Feb 01, 2018 9:10:24 AM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext

/data/xnat/home/logs/spring.log
2018-02-01 09:10:24,216 [localhost-startStop-1] ERROR org.springframework.web.context.ContextLoader - Context initialization failed
java.lang.NoSuchMethodError: java.util.concurrent.ConcurrentHashMap.keySet()Ljava/util/concurrent/ConcurrentHashMap$KeySetView;
    at org.apache.catalina.core.ApplicationContext.getInitParameterNames(ApplicationContext.java:368)
    at org.apache.catalina.core.ApplicationContextFacade.getInitParameterNames(ApplicationContextFacade.java:367)
    at org.apache.catalina.core.StandardContext$NoPluggabilityServletContext.getInitParameterNames(StandardContext.java:6994)
    at org.springframework.web.context.support.WebApplicationContextUtils.registerEnvironmentBeans(WebApplicationContextUtils.java:229)
    at org.springframework.web.context.support.AbstractRefreshableWebApplicationContext.postProcessBeanFactory(AbstractRefreshableWebApplicationContext.java:165)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:522)
    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:5066)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
2018-02-01 09:10:24,260 [localhost-startStop-1] WARN  org.springframework.web.context.support.AnnotationConfigWebApplicationContext - Exception thrown from LifecycleProcessor on context close
java.lang.IllegalStateException: LifecycleProcessor not initialized - call 'refresh' before invoking lifecycle methods via the context: Root WebApplicationContext: startup date [Thu Feb 01 09:10:24 GMT+01:00 2018]; root of context hierarchy
    at org.springframework.context.support.AbstractApplicationContext.getLifecycleProcessor(AbstractApplicationContext.java:427)
    at org.springframework.context.support.AbstractApplicationContext.doClose(AbstractApplicationContext.java:999)
    at org.springframework.context.support.AbstractApplicationContext.close(AbstractApplicationContext.java:958)
    at org.springframework.web.context.ContextLoader.closeWebApplicationContext(ContextLoader.java:583)
    at org.springframework.web.context.ContextLoaderListener.contextDestroyed(ContextLoaderListener.java:116)
    at org.apache.catalina.core.StandardContext.listenerStop(StandardContext.java:5113)
    at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5779)
    at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:224)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:159)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)


Key setup stuff:

Folder structure:
xnat@Vader:/var/log/tomcat7$ tree /data/
/data/
└── xnat
    ├── archive
    ├── build
    ├── cache
    ├── ftp
    ├── home
    │   ├── config
    │   │   └── xnat-conf.properties
    │   ├── logs
    │   │   ├── access.log
    │   │   ├── anon.log
    │   │   ├── application.log
    │   │   ├── automation.log
    │   │   ├── avalon.log
    │   │   ├── axis.log
    │   │   ├── configuration.log
    │   │   ├── dicom.log
    │   │   ├── identifiers.log
    │   │   ├── jms.log
    │   │   ├── launch.log
    │   │   ├── orm.log
    │   │   ├── pipeline.log
    │   │   ├── prearchive.log
    │   │   ├── received.log
    │   │   ├── remote.log
    │   │   ├── restlet.log
    │   │   ├── scheduler.log
    │   │   ├── security.log
    │   │   ├── spring.log
    │   │   ├── sql.log
    │   │   ├── tasks.log
    │   │   ├── turbine.log
    │   │   ├── velocity.log
    │   │   ├── xapi.log
    │   │   ├── xdat.log
    │   │   └── xnatfs.log
    │   ├── plugins
    │   └── work
    ├── pipeline
    └── prearchive

12 directories, 28 files
xnat@Vader:/var/log/tomcat7$


/etc/tomca7/server.xml
xnat@Vader:/var/log/tomcat7$ cat /etc/tomcat7/server.xml
<?xml version='1.0' encoding='utf-8'?>
<!--
  Licensed to the Apache Software Foundation (ASF) under one or more
  contributor license agreements.  See the NOTICE file distributed with
  this work for additional information regarding copyright ownership.
  The ASF licenses this file to You under the Apache License, Version 2.0
  (the "License"); you may not use this file except in compliance with
  the License.  You may obtain a copy of the License at

      http://www.apache.org/licenses/LICENSE-2.0

  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
-->
<!-- Note:  A "Server" is not itself a "Container", so you may not
     define subcomponents such as "Valves" at this level.
     Documentation at /docs/config/server.html
 -->
<Server port="8005" shutdown="SHUTDOWN">
  <Listener className="org.apache.catalina.startup.VersionLoggerListener" />
  <!-- Security listener. Documentation at /docs/config/listeners.html
  <Listener className="org.apache.catalina.security.SecurityListener" />
  -->
  <!--APR library loader. Documentation at /docs/apr.html -->
  <!--
  <Listener className="org.apache.catalina.core.AprLifecycleListener" SSLEngine="on" />
  -->
  <!--Initialize Jasper prior to webapps are loaded. Documentation at /docs/jasper-howto.html -->
  <Listener className="org.apache.catalina.core.JasperListener" />
  <!-- Prevent memory leaks due to use of particular java/javax APIs-->
  <Listener className="org.apache.catalina.core.JreMemoryLeakPreventionListener" />
  <Listener className="org.apache.catalina.mbeans.GlobalResourcesLifecycleListener" />
  <Listener className="org.apache.catalina.core.ThreadLocalLeakPreventionListener" />

  <!-- Global JNDI resources
       Documentation at /docs/jndi-resources-howto.html
  -->
  <GlobalNamingResources>
    <!-- Editable user database that can also be used by
         UserDatabaseRealm to authenticate users
    -->
    <Resource name="UserDatabase" auth="Container"
              type="org.apache.catalina.UserDatabase"
              description="User database that can be updated and saved"
              factory="org.apache.catalina.users.MemoryUserDatabaseFactory"
              pathname="conf/tomcat-users.xml" />
  </GlobalNamingResources>

  <!-- A "Service" is a collection of one or more "Connectors" that share
       a single "Container" Note:  A "Service" is not itself a "Container",
       so you may not define subcomponents such as "Valves" at this level.
       Documentation at /docs/config/service.html
   -->
  <Service name="Catalina">

    <!--The connectors can use a shared executor, you can define one or more named thread pools-->
    <!--
    <Executor name="tomcatThreadPool" namePrefix="catalina-exec-"
        maxThreads="150" minSpareThreads="4"/>
    -->


    <!-- A "Connector" represents an endpoint by which requests are received
         and responses are returned. Documentation at :
         Java HTTP Connector: /docs/config/http.html (blocking & non-blocking)
         Java AJP  Connector: /docs/config/ajp.html
         APR (HTTP/AJP) Connector: /docs/apr.html
         Define a non-SSL HTTP/1.1 Connector on port 8080
    -->
    <Connector port="8080" protocol="HTTP/1.1"
               connectionTimeout="20000"
               URIEncoding="UTF-8"
               redirectPort="8443" />
    <!-- A "Connector" using the shared thread pool-->
    <!--
    <Connector executor="tomcatThreadPool"
               port="8080" protocol="HTTP/1.1"
               connectionTimeout="20000"
               redirectPort="8443" />
    -->
    <!-- Define a SSL HTTP/1.1 Connector on port 8443
         This connector uses the BIO implementation that requires the JSSE
         style configuration. When using the APR/native implementation, the
         OpenSSL style configuration is required as described in the APR/native
         documentation -->
    <!--
    <Connector port="8443" protocol="org.apache.coyote.http11.Http11Protocol"
               maxThreads="150" SSLEnabled="true" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" />
    -->

    <!-- Define an AJP 1.3 Connector on port 8009 -->
    <!--
    <Connector port="8009" protocol="AJP/1.3" redirectPort="8443" />
    -->


    <!-- An Engine represents the entry point (within Catalina) that processes
         every request.  The Engine implementation for Tomcat stand alone
         analyzes the HTTP headers included with the request, and passes them
         on to the appropriate Host (virtual host).
         Documentation at /docs/config/engine.html -->

    <!-- You should set jvmRoute to support load-balancing via AJP ie :
    <Engine name="Catalina" defaultHost="localhost" jvmRoute="jvm1">
    -->
    <Engine name="Catalina" defaultHost="localhost">

      <!--For clustering, please take a look at documentation at:
          /docs/cluster-howto.html  (simple how to)
          /docs/config/cluster.html (reference documentation) -->
      <!--
      <Cluster className="org.apache.catalina.ha.tcp.SimpleTcpCluster"/>
      -->

      <!-- Use the LockOutRealm to prevent attempts to guess user passwords
           via a brute-force attack -->
      <Realm className="org.apache.catalina.realm.LockOutRealm">
        <!-- This Realm uses the UserDatabase configured in the global JNDI
             resources under the key "UserDatabase".  Any edits
             that are performed against this UserDatabase are immediately
             available for use by the Realm.  -->
        <Realm className="org.apache.catalina.realm.UserDatabaseRealm"
               resourceName="UserDatabase"/>
      </Realm>

      <Host name="localhost"  appBase="webapps"
            unpackWARs="true" autoDeploy="true">

        <!-- SingleSignOn valve, share authentication between web applications
             Documentation at: /docs/config/valve.html -->
        <!--
        <Valve className="org.apache.catalina.authenticator.SingleSignOn" />
        -->

        <!-- Access log processes all example.
             Documentation at: /docs/config/valve.html
             Note: The pattern used is equivalent to using pattern="common" -->
        <Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
               prefix="localhost_access_log." suffix=".txt"
               pattern="%h %l %u %t &quot;%r&quot; %s %b" />

      </Host>
    </Engine>
  </Service>
</Server>

/data/xnat/home/conf/xnat-conf.properties
xnat@Vader:/var/log/tomcat7$ cat /data/xnat/home/config/xnat-conf.properties
datasource.driver=org.postgresql.Driver
datasource.url=jdbc:postgresql://localhost/xnat
datasource.username=xnat
datasource.password=xnat
 
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
xnat@Vader:/var/log/tomcat7$

/etc/default/tomcat7
xnat@Vader:/var/log/tomcat7$ cat /etc/default/tomcat7
# Run Tomcat as this user ID. Not setting this or leaving it blank will use the
# default of tomcat7.
TOMCAT7_USER=xnat

# Run Tomcat as this group ID. Not setting this or leaving it blank will use
# the default of tomcat7.
TOMCAT7_GROUP=xnat

# The home directory of the Java development kit (JDK). You need at least
# JDK version 6. If JAVA_HOME is not set, some common directories for
# OpenJDK, the Oracle JDK, and various Java SE 6+ versions are tried.
#JAVA_HOME=/usr/lib/jvm/openjdk-6-jdk
#JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64

# You may pass JVM startup parameters to Java here. If unset, the default
# options will be: -Djava.awt.headless=true -Xmx128m -XX:+UseConcMarkSweepGC
#
# Use "-XX:+UseConcMarkSweepGC" to enable the CMS garbage collector (improved
# response time). If you use that option and you run Tomcat on a machine with
# exactly one CPU chip that contains one or two cores, you should also add
# the "-XX:+CMSIncrementalMode" option.
#JAVA_OPTS="-Djava.awt.headless=true -Xmx128m -XX:+UseConcMarkSweepGC"
JAVA_OPTS="-Djava.awt.headless=true -Xms512m -Xmx2g -XX:+UseConcMarkSweepGC -XX:-OmitStackTraceInFastThrow"
JAVA_OPTS="${JAVA_OPTS} -XX:MaxPermSize=512m -XX:+CMSIncrementalMode -XX:+CMSClassUnloadingEnabled"



# To enable remote debugging uncomment the following line.
# You will then be able to use a java debugger on port 8000.
JAVA_OPTS="${JAVA_OPTS} -Xdebug -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n"
JAVA_OPTS="${JAVA_OPTS} -Dxnat.home=/data/xnat/home"

# Java compiler to use for translating JavaServer Pages (JSPs). You can use all
# compilers that are accepted by Ant's build.compiler property.
#JSP_COMPILER=javac

# Use the Java security manager? (yes/no, default: no)
#TOMCAT7_SECURITY=no

# Number of days to keep logfiles in /var/log/tomcat7. Default is 14 days.
#LOGFILE_DAYS=14
# Whether to compress logfiles older than today's
#LOGFILE_COMPRESS=1

# Location of the JVM temporary directory
# WARNING: This directory will be destroyed and recreated at every startup !
#JVM_TMP=/tmp/tomcat7-temp

# If you run Tomcat on port numbers that are all higher than 1023, then you
# do not need authbind.  It is used for binding Tomcat to lower port numbers.
# (yes/no, default: no)
#AUTHBIND=no
xnat@Vader:/var/log/tomcat7$

Not  used to Java but I set up this in the /etc/profile:
export JAVA_HOME="/usr/lib/jvm/java-7-openjdk-amd64"
export PATH=$JAVA_HOME/bin:$PATH
export CATALINA_HOME="/usr/share/tomcat7"
export CATALINA_BASE="/var/lib/tomcat7"

Java -version
xnat@Vader:/var/log/tomcat7$ java -version
java version "1.7.0_95"
OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-3)
OpenJDK 64-Bit Server VM (build 24.95-b01, mixed mode)
xnat@Vader:/var/log/tomcat7$

Java Path
xnat@Vader:/var/log/tomcat7$ ls -l /usr/lib/jvm/
total 4
lrwxrwxrwx 1 root root   20 mar 27  2016 java-1.7.0-openjdk-amd64 -> java-7-openjdk-amd64
drwxr-xr-x 7 root root 4096 jan 31 11:18 java-7-openjdk-amd64
xnat@Vader:/var/log/tomcat7$

Catalina Home path
xnat@Vader:/var/log/tomcat7$ ls -la /usr/share/tomcat7
total 40
drwxr-xr-x   4 xnat xnat  4096 jan 31 17:54 .
drwxr-xr-x 324 root root 12288 jan 31 11:48 ..
drwxr-xr-x   2 xnat xnat  4096 jan 31 11:23 bin
-rw-r--r--   1 xnat xnat    39 feb 18  2016 defaults.md5sum
-rw-r--r--   1 xnat xnat  1958 feb 18  2016 defaults.template
drwxr-xr-x   2 xnat xnat  4096 jan 31 11:23 lib
-rw-r--r--   1 xnat xnat    53 feb 18  2016 logrotate.md5sum
-rw-r--r--   1 xnat xnat   118 feb 18  2016 logrotate.template
xnat@Vader:/var/log/tomcat7$

Catalina Base path
xnat@Vader:/var/log/tomcat7$ ls -la /var/lib/tomcat7
total 24
drwxr-xr-x  6 xnat xnat 4096 jan 31 11:23 .
drwxr-xr-x 73 root root 4096 jan 31 11:48 ..
drwxr-xr-x  3 xnat xnat 4096 jan 31 11:23 common
lrwxrwxrwx  1 xnat xnat   12 jun 27  2016 conf -> /etc/tomcat7
lrwxrwxrwx  1 xnat xnat   17 jun 27  2016 logs -> ../../log/tomcat7
drwxr-xr-x  3 xnat xnat 4096 jan 31 11:23 server
drwxr-xr-x  3 xnat xnat 4096 jan 31 11:23 shared
drwxrwxr-x  4 xnat xnat 4096 feb  1 09:10 webapps
lrwxrwxrwx  1 xnat xnat   19 jun 27  2016 work -> ../../cache/tomcat7
xnat@Vader:/var/log/tomcat7$

Postgresql version
xnat@Vader:/var/log/tomcat7$ psql
psql (10.1, server 9.3.20)
Type "help" for help.

xnat=>

and

xnat@Vader:/var/log/tomcat7$ psql --version
psql (PostgreSQL) 10.1
xnat@Vader:/var/log/tomcat7$


Postgresql /usr/lib/postgressql:
xnat@Vader:/var/log/tomcat7$ ls -la /usr/lib/postgresql/
total 24
drwxr-xr-x   4 root root  4096 jan 31 11:48 .
drwxr-xr-x 151 root root 12288 jan 31 11:48 ..
drwxr-xr-x   3 root root  4096 jan 31 11:48 10
drwxr-xr-x   4 root root  4096 jan 31 11:48 9.3
xnat@Vader:/var/log/tomcat7$

Postgresql /var/lib/postgressql:
xnat@Vader:/var/log/tomcat7$ ls -la /var/lib/postgresql/
total 24
drwxr-xr-x  4 postgres postgres 4096 jan 31 11:54 .
drwxr-xr-x 73 root     root     4096 jan 31 11:48 ..
drwxr-xr-x  3 postgres postgres 4096 jan 31 11:48 9.3
-rw-------  1 postgres postgres   53 jan 31 11:54 .bash_history
drwxrwxr-x  2 postgres postgres 4096 jan 31 11:53 matlab
-rw-------  1 postgres postgres   18 jan 31 11:54 .psql_history
xnat@Vader:/var/log/tomcat7$


Postgresql /var/lib/postgressq/9.3
xnat@Vader:/var/log/tomcat7$ ls -la /var/lib/postgresql/9.3/
total 12
drwxr-xr-x  3 postgres postgres 4096 jan 31 11:48 .
drwxr-xr-x  4 postgres postgres 4096 jan 31 11:54 ..
drwx------ 15 postgres postgres 4096 jan 31 11:55 main
xnat@Vader:/var/log/tomcat7$



Permissions1:
xnat@Vader:/var/log/tomcat7$ ls -la /var/lib/tomcat7
total 24
drwxr-xr-x  6 xnat xnat 4096 jan 31 11:23 .
drwxr-xr-x 73 root root 4096 jan 31 11:48 ..
drwxr-xr-x  3 xnat xnat 4096 jan 31 11:23 common
lrwxrwxrwx  1 xnat xnat   12 jun 27  2016 conf -> /etc/tomcat7
lrwxrwxrwx  1 xnat xnat   17 jun 27  2016 logs -> ../../log/tomcat7
drwxr-xr-x  3 xnat xnat 4096 jan 31 11:23 server
drwxr-xr-x  3 xnat xnat 4096 jan 31 11:23 shared
drwxrwxr-x  4 xnat xnat 4096 feb  1 09:10 webapps
lrwxrwxrwx  1 xnat xnat   19 jun 27  2016 work -> ../../cache/tomcat7
xnat@Vader:/var/log/tomcat7$

Permissions2:
xnat@Vader:/var/log/tomcat7$ ls -l /usr/share/tomcat7
total 24
drwxr-xr-x 2 xnat xnat 4096 jan 31 11:23 bin
-rw-r--r-- 1 xnat xnat   39 feb 18  2016 defaults.md5sum
-rw-r--r-- 1 xnat xnat 1958 feb 18  2016 defaults.template
drwxr-xr-x 2 xnat xnat 4096 jan 31 11:23 lib
-rw-r--r-- 1 xnat xnat   53 feb 18  2016 logrotate.md5sum
-rw-r--r-- 1 xnat xnat  118 feb 18  2016 logrotate.template
xnat@Vader:/var/log/tomcat7$

Permissions3:
xnat@Vader:/var/log/tomcat7$ ls -l /etc/tomcat7/
total 204
drwxrwxr-x 3 xnat xnat   4096 feb  1 09:01 Catalina
-rw-r--r-- 1 xnat xnat   6506 jun 27  2016 catalina.properties
-rw-r--r-- 1 xnat xnat   1394 jan 25  2014 context.xml
-rw-r--r-- 1 xnat xnat   2370 feb 18  2016 logging.properties
drwxr-xr-x 2 xnat xnat   4096 feb  1 09:00 policy.d
-rw-r--r-- 1 xnat xnat   6678 jun 27  2016 server.xml
-rw-r----- 1 xnat xnat   1530 jan 25  2014 tomcat-users.xml
-rw-r--r-- 1 xnat xnat 168099 nov 25  2015 web.xml
xnat@Vader:/var/log/tomcat7$

Permissions4:
xnat@Vader:/var/log/tomcat7$ ls -l /etc/default/tomcat7
-rw-r--r-- 1 xnat xnat 2260 jan 31 15:07 /etc/default/tomcat7
xnat@Vader:/var/log/tomcat7$

Permissions5:
xnat@Vader:/var/log/tomcat7$ ls -la /var/log/tomcat7/
total 44
drwxr-x---  2 xnat xnat    4096 feb  1 09:10 .
drwxrwxr-x 15 root syslog  4096 feb  1 07:35 ..
-rw-r--r--  1 xnat xnat   13524 feb  1 09:10 catalina.2018-02-01.log
-rw-r--r--  1 xnat root   13575 feb  1 09:10 catalina.out
-rw-r--r--  1 xnat xnat    2766 feb  1 09:10 localhost.2018-02-01.log
-rw-r--r--  1 xnat xnat       0 feb  1 09:10 localhost_access_log.2018-02-01.txt
xnat@Vader:/var/log/tomcat7$

Webapp
The ROOT.war is generating a /var/lib/tomcat7/webapps/ROOT dir:
xnat@Vader:/var/log/tomcat7$ ls -la /var/lib/tomcat7/webapps/
total 187544
drwxrwxr-x  4 xnat xnat      4096 feb  1 09:10 .
drwxr-xr-x  6 xnat xnat      4096 jan 31 11:23 ..
drwxr-xr-x 17 xnat xnat      4096 feb  1 09:10 ROOT
drwxr-xr-x  3 xnat xnat      4096 jan 31 11:23 ROOT_old
-rwxr-xr-x  1 xnat xnat 192027012 jan 31 13:57 ROOT.war
xnat@Vader:/var/log/tomcat7$

And:
xnat@Vader:/var/log/tomcat7$ ls -la /var/lib/tomcat7/webapps/ROOT
total 72
drwxr-xr-x 17 xnat xnat 4096 feb  1 09:10 .
drwxrwxr-x  4 xnat xnat 4096 feb  1 09:10 ..
drwxr-xr-x  2 xnat xnat 4096 feb  1 09:10 axis
drwxr-xr-x  3 xnat xnat 4096 feb  1 09:10 base-templates
-rw-r--r--  1 xnat xnat 1150 jul  6  2017 favicon.ico
drwxr-xr-x  2 xnat xnat 4096 feb  1 09:10 images
drwxr-xr-x  2 xnat xnat 4096 feb  1 09:10 META-INF
drwxr-xr-x  5 xnat xnat 4096 feb  1 09:10 page
drwxr-xr-x  2 xnat xnat 4096 feb  1 09:10 pdf
drwxr-xr-x  4 xnat xnat 4096 feb  1 09:10 resources
drwxr-xr-x 31 xnat xnat 4096 feb  1 09:10 scripts
drwxr-xr-x  2 xnat xnat 4096 feb  1 09:10 setup
drwxr-xr-x  5 xnat xnat 4096 feb  1 09:10 style
drwxr-xr-x  3 xnat xnat 4096 feb  1 09:10 templates
drwxr-xr-x  4 xnat xnat 4096 feb  1 09:10 themes
drwxr-xr-x  7 xnat xnat 4096 feb  1 09:10 WEB-INF
drwxr-xr-x  6 xnat xnat 4096 feb  1 09:10 xdat-templates
drwxr-xr-x  5 xnat xnat 4096 feb  1 09:10 xnat-templates
xnat@Vader:/var/log/tomcat7$


Thanks a bunch!







Robin Kämpe

unread,
Feb 1, 2018, 5:13:08 AM2/1/18
to xnat_discussion
Also adding this:
sudo service tomcat7 status
 Active: active (running) since tor 2018-02-01 09:10:18 CET; 1h 50min ago
     Docs: man:systemd-sysv-generator(8)
  Process: 45083 ExecStop=/etc/init.d/tomcat7 stop (code=exited, status=0/SUCCESS)
  Process: 45107 ExecStart=/etc/init.d/tomcat7 start (code=exited, status=0/SUCCESS)
   CGroup: /system.slice/tomcat7.service
           └─13365 /usr/lib/jvm/java-7-openjdk-amd64/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.awt.headless=true -Xmx128m -XX:+UseConcMarkSweepGC -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start

feb 01 09:10:13 Vader systemd[1]: Starting LSB: Start Tomcat....
feb 01 09:10:13 Vader tomcat7[45107]:  * Starting Tomcat servlet engine tomcat7
feb 01 09:10:18 Vader tomcat7[45107]:    ...done.
feb 01 09:10:18 Vader systemd[1]: Started LSB: Start Tomcat..

The xnat home path is not mentioned here. Should it?


Herrick, Rick

unread,
Feb 1, 2018, 10:49:43 AM2/1/18
to xnat_di...@googlegroups.com

There are a few things going on here…

 

Re: PostgreSQL, it’s possible you have different versions of the client and server. Try something like this:

 

postgres@Gumby:~$ psql --version

psql (PostgreSQL) 9.6.6

postgres@Gumby:~$ psql

psql (9.6.6, server 9.5.10)

Type "help" for help.

 

postgres=# SELECT version();

                                                     version

------------------------------------------------------------------------------------------------------------------

PostgreSQL 9.5.10 on x86_64-pc-linux-gnu, compiled by gcc (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609, 64-bit

(1 row)

 

You can see here I have v9.6.6 of the client and 9.5.10 of the server. This generally isn’t an issue. We haven’t done any testing with PostgreSQL 10 so I’m not sure if there would be any problems with that on the server side, but the client version would have no effect on XNAT itself.

 

Re: the Tomcat messages, that’s really a configuration issue caused by a bug in the Tomcat installation. Check out this Stack Overflow post for more information. The tl;dr is that you can change a few properties in the Tomcat catalina.properties file or you can create symlinks to folders in /var/lib/tomcat7 in the /usr/share/tomcat7 folder, e.g.:

 

$ sudo ln -s /var/lib/tomcat7/common /usr/share/tomcat7/common

$ sudo ln -s /var/lib/tomcat7/server /usr/share/tomcat7/server

$ sudo ln -s /var/lib/tomcat7/shared /usr/share/tomcat7/shared

 

I usually do the latter, which eliminates those warning messages.

 

The thing that’s really causing you trouble is this:

 

SEVERE: Failed to initialize end point associated with ProtocolHandler ["http-bio-8080"]
java.net.BindException: Address already in use <null>:8080

That means that another process is running and is listening on 8080, so Tomcat is cut off and can’t receive requests. You need to figure out what’s blocking that port:

 

$ lsof -i TCP:8080

COMMAND   PID USER   FD   TYPE  DEVICE SIZE/OFF NODE NAME

java    30179 xnat   58u  IPv6 2089852      0t0  TCP *:http-alt (LISTEN)

 

In this case, I have Tomcat running happily on 8080. You may see something different though, in which case you’d need to change the Tomcat port or shut down the other service. In most cases though this ends up being a hung Tomcat process that just won’t go away. You can check that process like this:

 

$ ps u -q 30179

USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND

xnat     30179 18.5 14.6 6676060 893496 ?      Sl   15:36   1:24 /usr/lib/jvm/java-8-openjdk-amd64/bin/java -Djava.util.logging.config.file=…

 

One other thing I noted is that you’re getting this warning:

 

INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT_old

 

If that’s your old XNAT application, you definitely want to remove that! Two XNATs competing on a single Tomcat is not a good thing. Or if it’s the default Tomcat ROOT app, go ahead and remove that as well. You can zip it up and put it elsewhere for archive purposes or in case you want to roll back for whatever reason, but I’d really advise having only the XNAT application deployed to your Tomcat.

 

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Phone: +1 (314) 273-1645

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Herrick, Rick

unread,
Feb 1, 2018, 11:07:12 AM2/1/18
to xnat_di...@googlegroups.com

Re: xnat.home, yes it should probably appear in the application parameters. If XNAT can’t find a value for xnat.home, it tries to fall back on other settings, e.g. the value set for the Tomcat user’s XNAT_HOME environment variable and finally the HOME variable for the Tomcat user, which is always set (HOME is a standard *nix variable that indicates the user’s home folder, i.e. ~). If Tomcat is running with the xnat user and the user’s home folder is where you have your config, logs, etc., folders, this may work fine, but it’s probably better to have it explicitly configured.

 

Where that should be configured depends on your OS and Tomcat installation: there are differences between Ubuntu 14.04 and 16.04, CentOS 6 and 7, and so forth. On Ubuntu 16.04, the proper place to set this is in /etc/default/tomcat7, while on CentOS 7 it’s in /etc/sysconfig/tomcat7 or /etc/sysconfig/tomcat.

 

Another difference is that some Tomcat configurations use both CATALINA_OPTS and JAVA_OPTS (Tomcat 7 on Ubuntu 16.04 for example) while others only use JAVA_OPTS (Tomcat 7 on CentOS 7). This is a relatively minor issue, especially when just setting an environment variable (here’s an explainer for this), but can be confusing.

 

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Phone: +1 (314) 273-1645

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Robin Kämpe

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Feb 2, 2018, 4:55:49 AM2/2/18
to xnat_discussion
Thanks!

So I fixed the symbolic links and removed all the folders from tomcat7/webapps and killed the "java PID tomcat7" process that I found and seemed to be stuck like you said. Now it looks better:

COMMAND   PID USER   FD   TYPE    DEVICE SIZE/OFF NODE NAME
java    36182 xnat   49u  IPv6 986505384      0t0  TCP *:http-alt (LISTEN)
xnat@Vader:/var/lib/tomcat7/webapps$ sudo service tomcat7 status
● tomcat7.service - LSB: Start Tomcat.
   Loaded: loaded (/etc/init.d/tomcat7; bad; vendor preset: enabled)
   Active: active (running) since fre 2018-02-02 10:43:36 CET; 4min 32s ago
     Docs: man:systemd-sysv-generator(8)
  Process: 28245 ExecStop=/etc/init.d/tomcat7 stop (code=exited, status=0/SUCCESS)
  Process: 36124 ExecStart=/etc/init.d/tomcat7 start (code=exited, status=0/SUCCESS)
   CGroup: /system.slice/tomcat7.service
           └─36182 /usr/lib/jvm/java-7-openjdk-amd64/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava
feb 02 10:43:31 Vader systemd[1]: Starting LSB: Start Tomcat....
feb 02 10:43:31 Vader tomcat7[36124]:  * Starting Tomcat servlet engine tomcat7
feb 02 10:43:36 Vader tomcat7[36124]:    ...done.
feb 02 10:43:36 Vader systemd[1]: Started LSB: Start Tomcat..
lines 1-13/13 (END)


ReXnatHome. I do give it the xnat home dir via JAVA _OPTS in /etc/default/tomcat7. And since there are logs in /data/xnat/home/logs that must mean that is finds the path? :).

JAVA_OPTS="-Djava.awt.headless=true -Xms512m -Xmx2g -XX:+UseConcMarkSweepGC -XX:-OmitStackTraceInFastThrow"
JAVA_OPTS="${JAVA_OPTS} -XX:MaxPermSize=512m -XX:+CMSIncrementalMode -XX:+CMSClassUnloadingEnabled"
JAVA_OPTS="${JAVA_OPTS} -Xdebug -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n"
JAVA_OPTS="${JAVA_OPTS} -Dxnat.home=/data/xnat/home"

Now the xnat structure has something in the work dir as well but it is empty...

    │       └── xnat_24153850255277891790757726923948614
    ├── pipeline
    └── prearchive


Logs:
catalina.out:
Listening for transport dt_socket at address: 8000
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Server version:        Apache Tomcat/7.0.68 (Ubuntu)
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Server built:          Jun 27 2016 18:13:17 UTC
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.68.0
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.10.0-42-generic
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-7-openjdk-amd64/jre
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.7.0_95-b00
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: JVM Vendor:            Oracle Corporation
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat7
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat7
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.awt.headless=true
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Xms512m
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Xmx2g
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:+UseConcMarkSweepGC
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:-OmitStackTraceInFastThrow
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:MaxPermSize=512m
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:+CMSIncrementalMode
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Xdebug
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dxnat.home=/data/xnat/home
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat7
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat7
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp
Feb 02, 2018 10:43:32 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 525 ms
Feb 02, 2018 10:43:32 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Feb 02, 2018 10:43:32 AM org.apache.catalina.core.StandardEngine startInternal

INFO: Starting Servlet Engine: Apache Tomcat/7.0.68 (Ubuntu)
Feb 02, 2018 10:43:32 AM org.apache.catalina.startup.HostConfig deployWAR

INFO: Deploying web application archive /var/lib/tomcat7/webapps/ROOT.war
Feb 02, 2018 10:43:42 AM org.apache.catalina.startup.TldConfig execute

INFO: 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.
Feb 02, 2018 10:43:42 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Feb 02, 2018 10:43:42 AM org.apache.catalina.core.StandardContext startInternal

SEVERE: Context [] startup failed due to previous errors

Feb 02, 2018 10:43:42 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat7/webapps/ROOT.war has finished in 9,972 ms
Feb 02, 2018 10:43:42 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 02, 2018 10:43:42 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 10037 ms

Only logfile under /data/xnat/home/logs with content is the spring.log file:

xnat@Vader:/data/xnat/home/work$ cat /data/xnat/home/logs/spring.log
2018-02-02 10:43:42,524 [localhost-startStop-1] ERROR org.springframework.web.context.ContextLoader - Context initialization failed

java.lang.NoSuchMethodError: java.util.concurrent.ConcurrentHashMap.keySet()Ljava/util/concurrent/ConcurrentHashMap$KeySetView;
        at org.apache.catalina.core.ApplicationContext.getInitParameterNames(ApplicationContext.java:368)
        at org.apache.catalina.core.ApplicationContextFacade.getInitParameterNames(ApplicationContextFacade.java:367)
        at org.apache.catalina.core.StandardContext$NoPluggabilityServletContext.getInitParameterNames(StandardContext.java:6994)
        at org.springframework.web.context.support.WebApplicationContextUtils.registerEnvironmentBeans(WebApplicationContextUtils.java:229)
        at org.springframework.web.context.support.AbstractRefreshableWebApplicationContext.postProcessBeanFactory(AbstractRefreshableWebApplicationContext.java:165)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:522)
        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:5066)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
        at java.util.concurrent.FutureTask.run(FutureTask.java:262)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)
2018-02-02 10:43:42,566 [localhost-startStop-1] WARN  org.springframework.web.context.support.AnnotationConfigWebApplicationContext - Exception thrown from LifecycleProcessor on context close
java.lang.IllegalStateException: LifecycleProcessor not initialized - call 'refresh' before invoking lifecycle methods via the context: Root WebApplicationContext: startup date [Fri Feb 02 10:43:42 GMT+01:00 2018]; root of context hierarchy

        at org.springframework.context.support.AbstractApplicationContext.getLifecycleProcessor(AbstractApplicationContext.java:427)
        at org.springframework.context.support.AbstractApplicationContext.doClose(AbstractApplicationContext.java:999)
        at org.springframework.context.support.AbstractApplicationContext.close(AbstractApplicationContext.java:958)
        at org.springframework.web.context.ContextLoader.closeWebApplicationContext(ContextLoader.java:583)
        at org.springframework.web.context.ContextLoaderListener.contextDestroyed(ContextLoaderListener.java:116)
        at org.apache.catalina.core.StandardContext.listenerStop(StandardContext.java:5113)
        at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5779)
        at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:224)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:159)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
        at java.util.concurrent.FutureTask.run(FutureTask.java:262)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)

I feel we are getting somewhere but not all the way. Thanks!

Robin Kämpe

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Feb 2, 2018, 7:06:34 AM2/2/18
to xnat_discussion
Also adding the log from /var/lib/tomcat7/logs/localhost*


xnat@Vader:~$ cat /var/lib/tomcat7/logs/localhost.2018-02-02.log
Feb 02, 2018 10:43:42 AM org.apache.catalina.core.ApplicationContext log

INFO: 1 Spring WebApplicationInitializers detected on classpath
Feb 02, 2018 10:43:42 AM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring root WebApplicationContext
Feb 02, 2018 10:43:42 AM org.apache.catalina.core.StandardContext listenerStart

SEVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
java.lang.NoSuchMethodError: java.util.concurrent.ConcurrentHashMap.keySet()Ljava/util/concurrent/ConcurrentHashMap$KeySetView;
    at org.apache.catalina.core.ApplicationContext.getInitParameterNames(ApplicationContext.java:368)
    at org.apache.catalina.core.ApplicationContextFacade.getInitParameterNames(ApplicationContextFacade.java:367)
    at org.apache.catalina.core.StandardContext$NoPluggabilityServletContext.getInitParameterNames(StandardContext.java:6994)
    at org.springframework.web.context.support.WebApplicationContextUtils.registerEnvironmentBeans(WebApplicationContextUtils.java:229)
    at org.springframework.web.context.support.AbstractRefreshableWebApplicationContext.postProcessBeanFactory(AbstractRefreshableWebApplicationContext.java:165)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:522)
    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:5066)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)

Feb 02, 2018 10:43:42 AM org.apache.catalina.core.ApplicationContext log

INFO: Closing Spring root WebApplicationContext
xnat@Vader:~$ cat /var/lib/tomcat7/logs/localhost_access_log.2018-02-02.txt

Herrick, Rick

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Feb 2, 2018, 1:35:01 PM2/2/18
to xnat_di...@googlegroups.com

This is actually a Tomcat bug: https://stackoverflow.com/questions/42474281/tomcat-7-nosuchmethoderror-java-util-concurrent-concurrenthashmap-keyset

 

The problem is that the code is calling a method on the ConcurrentHashMap that had a signature change in Java 8. The Tomcat code was compiled using Java 8 to Java 6-compatible byte code. This is the header of the ApplicationContext class that’s throwing the error:

 

0000000 feca beba 0000 3200 8204 000a 0254 0782

 

For more info on what this means, check out the Java class file article on Wikipedia, but basically that “3200” in there means that the byte code is Java 6. It therefore runs on your Java 7 installation which supports byte code compiled for Java 6 and earlier, but it was compiled using the Java 8 run-time libraries, so that’s what it thinks it should be calling. We actually have a configuration in the XNAT build configuration so that we can specify a Java 7 run-time library to prevent exactly this problem.

 

There are two possible fixes to this:

 

  • Try to upgrade your Tomcat 7 installation to see if you get an updated version that was compiled properly (the standard repo for Ubuntu 16.04 is still on 7.0.68, but CentOS 7.4 is up to 7.0.76)
  • Install Java 8 instead of Java 7 and set your JAVA_HOME variable to point to the new Java 8 installation (unless you’re using alternatives and can just change the configuration for java there)

 

I’d definitely recommend doing the second fix regardless, as there are some performance and memory management improvements between 7 and 8. You may get a warning that some command-line options for Java are obsolete or invalid, especially with “-XX:MaxPermSize=512m”. You can remove those options from your configuration to get rid of the messages, but they’re harmless.

 

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Phone: +1 (314) 273-1645

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Robin Kämpe

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Feb 2, 2018, 1:44:45 PM2/2/18
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Thanks, I'll try on Monday. I chose java 7 since our other sever runs xnat without problem using java7 and since the installation guide hinted that java 7 was more extensively tested:

XNAT 1.7 was developed and tested extensively with Java 7. We have also successfully run it using Java 8, although the degree of validation is not as thorough as with Java 7

Why would it give me problems now but not on the other older virtual machine (over 3y old)? Perhaps my current Ubuntu uses an even more ancient repo.


My knowledge of Java is very limited so I'll just install Java 8 and change the to:

export $JAVA_HOME="path to java8"

In /etc/profile where I currently point to java7.

Thanks!

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Herrick, Rick

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Feb 2, 2018, 1:52:16 PM2/2/18
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The older VM probably had an earlier version of Tomcat 7 that was properly compiled against a Java 6 run-time library. This pops up from time to time. An earlier release, I believe 7.0.48, had the same issue which was fixed in the next release.

Thanks!

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Robin Kämpe

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Feb 2, 2018, 1:53:41 PM2/2/18
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Then I'll go for 8 and hope for the best. I'll check back in on Monday. Thanks for a quick reply.

Have a nice weekend!

Robin Kämpe

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Feb 5, 2018, 6:04:53 AM2/5/18
to xnat_discussion
Hi again,

Again the old errors are gone but new have arrived (one of which I think I have seen in a recent thread regarding relation "xdat_user" does not exist).

Catalina.out
xnat@Vader:~$ cat /var/lib/tomcat7/logs/catalina.out
Feb 05, 2018 11:13:13 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Feb 05, 2018 11:13:13 AM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Feb 05, 2018 11:13:13 AM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Feb 05, 2018 11:13:13 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=512m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release

Listening for transport dt_socket at address: 8000
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Server version:        Apache Tomcat/7.0.68 (Ubuntu)
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Server built:          Jun 27 2016 18:13:17 UTC
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.68.0
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.10.0-42-generic
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-8-openjdk-amd64/jre
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: JVM Vendor:            Oracle Corporation
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat7
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat7
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.awt.headless=true
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Xms512m
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Xmx2g
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:+UseConcMarkSweepGC
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:-OmitStackTraceInFastThrow
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:MaxPermSize=512m
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:+CMSIncrementalMode
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Xdebug
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dxnat.home=/data/xnat/home
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat7
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat7
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp
Feb 05, 2018 11:17:15 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 358 ms
Feb 05, 2018 11:17:15 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Feb 05, 2018 11:17:15 AM org.apache.catalina.core.StandardEngine startInternal

INFO: Starting Servlet Engine: Apache Tomcat/7.0.68 (Ubuntu)
Feb 05, 2018 11:17:15 AM org.apache.catalina.startup.HostConfig deployWAR

INFO: Deploying web application archive /var/lib/tomcat7/webapps/ROOT.war
Feb 05, 2018 11:17:23 AM org.apache.catalina.startup.TldConfig execute

INFO: 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.
SOURCE: /var/lib/tomcat7/webapps/ROOT/
===========================
New Database -- BEGINNING Initialization
===========================
===========================
Database initialization complete.
===========================
Feb 05, 2018 11:17:56 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat7/webapps/ROOT.war has finished in 41,063 ms
Feb 05, 2018 11:17:56 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 05, 2018 11:17:56 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 41123 ms
xnat@Vader:~$

Localhost.out
xnat@Vader:~$ cat /var/lib/tomcat7/logs/localhost.2018-02-05.log
Feb 05, 2018 11:17:24 AM org.apache.catalina.core.ApplicationContext log

INFO: 1 Spring WebApplicationInitializers detected on classpath
Feb 05, 2018 11:17:24 AM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring root WebApplicationContext
Feb 05, 2018 11:17:55 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring FrameworkServlet 'dispatcher'
xnat@Vader:~$

Logs in /data/xnat/home/logs

Axis.log
xnat@Vader:~$ cat /data/xnat/home/logs/axis.log
9966 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet  - Unable to find config file.  Creating new servlet engine config file: /WEB-INF/server-config.wsdd
10104 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet  - Unable to find config file.  Creating new servlet engine config file: /WEB-INF/server-config.wsdd
xnat@Vader:~$

Sql.log
xnat@Vader:~$ cat /data/xnat/home/logs/sql.log
2018-02-05 11:17:46,454 - An error occurred trying to execute the user null query: SELECT COUNT(*) FROM xdat_user
org.postgresql.util.PSQLException: ERROR: relation "xdat_user" does not exist
  Position: 22
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2310)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2023)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:217)
    at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:421)
    at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:318)
    at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:281)
    at org.apache.commons.dbcp2.DelegatingStatement.executeQuery(DelegatingStatement.java:207)
    at org.apache.commons.dbcp2.DelegatingStatement.executeQuery(DelegatingStatement.java:207)
    at org.nrg.xft.db.PoolDBUtils.executeQuery(PoolDBUtils.java:885)
    at org.nrg.xft.db.PoolDBUtils.returnStatisticQuery(PoolDBUtils.java:375)
    at org.nrg.xft.db.PoolDBUtils.ReturnStatisticQuery(PoolDBUtils.java:398)
    at org.nrg.xdat.servlet.XDATServlet.updateDatabase(XDATServlet.java:108)
    at org.nrg.xdat.servlet.XDATServlet.init(XDATServlet.java:82)
    at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1282)
    at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1195)
    at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1085)
    at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5318)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5610)

    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
    at java.util.concurrent.Executors$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)
2018-02-05 11:17:46,456 - SELECT COUNT(*) FROM xdat_user
2018-02-05 11:17:50,065 - An error occurred trying to execute the user null query: SELECT xdat_element_security.element_name AS xdat_element_security0 FROM xdat_element_security xdat_element_security;
org.postgresql.util.PSQLException: ERROR: relation "xdat_element_security" does not exist
  Position: 74
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2310)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2023)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:217)
    at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:421)
    at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:318)
    at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:281)
    at org.apache.commons.dbcp2.DelegatingStatement.executeQuery(DelegatingStatement.java:207)
    at org.apache.commons.dbcp2.DelegatingStatement.executeQuery(DelegatingStatement.java:207)
    at org.nrg.xft.db.PoolDBUtils.executeQuery(PoolDBUtils.java:885)
    at org.nrg.xft.db.PoolDBUtils.executeSelectQuery(PoolDBUtils.java:421)
    at org.nrg.xft.search.TableSearch.Execute(TableSearch.java:104)
    at org.nrg.xft.search.ItemSearch.getIdentifierResults(ItemSearch.java:312)
    at org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:424)
    at org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:110)
    at org.nrg.xdat.search.DisplaySearch.SearchForItems(DisplaySearch.java:1214)
    at org.nrg.xdat.security.ElementSecurity.GetElementSecurities(ElementSecurity.java:96)
    at org.nrg.xdat.security.ElementSecurity.GetSecureElements(ElementSecurity.java:320)
    at org.nrg.xdat.security.ElementSecurity.GetSecurityElements(ElementSecurity.java:334)
    at org.nrg.xdat.security.SecurityManager.getSecurityElements(SecurityManager.java:58)
    at org.nrg.xdat.security.SecurityManager.isSecurityElement(SecurityManager.java:68)
    at org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperUtils.GetUpdateFunctions(GenericWrapperUtils.java:2188)
    at org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperUtils.GetFunctionStatements(GenericWrapperUtils.java:2268)
    at org.nrg.xdat.servlet.XDATServlet$DatabaseUpdater.run(XDATServlet.java:233)
    at org.nrg.xdat.servlet.XDATServlet.updateDatabase(XDATServlet.java:172)
    at org.nrg.xdat.servlet.XDATServlet.init(XDATServlet.java:82)
    at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1282)
    at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1195)
    at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1085)
    at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5318)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5610)

    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
    at java.util.concurrent.Executors$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$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
2018-02-05 11:17:50,066 - SELECT xdat_element_security.element_name AS xdat_element_security0 FROM xdat_element_security xdat_element_security;
xnat@Vader:~$

Xdat.log
xnat@Vader:~$ cat /data/xnat/home/logs/xdat.log
2018-02-05 11:17:54,684 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_launch_request_event to use sequence for default value.
2018-02-05 11:17:54,684 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-02-05 11:17:54,684 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction -  *** CREATE SEQUENCE xhbm_script_launch_request_event_id_seq
2018-02-05 11:17:54,684 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction -  *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET DEFAULT nextval('xhbm_script_launch_request_event_id_seq')
2018-02-05 11:17:54,684 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction -  *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET NOT NULL
2018-02-05 11:17:54,684 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction -  *** ALTER SEQUENCE xhbm_script_launch_request_event_id_seq OWNED BY xhbm_script_launch_request_event.id
2018-02-05 11:17:54,710 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_launch_request_event and got the value 1
2018-02-05 11:17:54,710 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_launch_request_event_id_seq', 1) AS value
2018-02-05 11:17:54,711 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_aud to use sequence for default value.
2018-02-05 11:17:54,711 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-02-05 11:17:54,711 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction -  *** CREATE SEQUENCE xhbm_script_aud_id_seq
2018-02-05 11:17:54,711 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction -  *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET DEFAULT nextval('xhbm_script_aud_id_seq')
2018-02-05 11:17:54,711 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction -  *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET NOT NULL
2018-02-05 11:17:54,711 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction -  *** ALTER SEQUENCE xhbm_script_aud_id_seq OWNED BY xhbm_script_aud.id
2018-02-05 11:17:54,712 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_aud and got the value 1
2018-02-05 11:17:54,712 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_aud_id_seq', 1) AS value
xnat@Vader:~$

Folder tree:
xnat@Vader:~$ tree /data/
    │       ├── cache
    │       │   ├── %0044efault%0043atalog%0053ervice%0043ache.data
    │       │   ├── nrg.data
    │       │   ├── org%002ehibernate%002ecache%002einternal%002e%0053tandard%0051uery%0043ache.data
    │       │   └── org%002ehibernate%002ecache%002espi%002e%0055pdate%0054imestamps%0043ache.data
    │       └── xnat_26766068074987982369479930426820323
    ├── pipeline
    └── prearchive

14 directories, 32 files
xnat@Vader:~$

lsof -i TCP:8080
xnat@Vader:~$ sudo lsof -i TCP:8080
[sudo] password for xnat:
COMMAND  PID USER   FD   TYPE     DEVICE SIZE/OFF NODE NAME
java    1142 xnat   55u  IPv6 1160569293      0t0  TCP *:http-alt (LISTEN)
xnat@Vader:~$

sudo service tomcat7 status
xnat@Vader:~$ sudo service tomcat7 status
● tomcat7.service - LSB: Start Tomcat.
   Loaded: loaded (/etc/init.d/tomcat7; bad; vendor preset: enabled)
   Active: active (running) since mån 2018-02-05 11:17:19 CET; 47min ago
     Docs: man:systemd-sysv-generator(8)
  Process: 22707 ExecStop=/etc/init.d/tomcat7 stop (code=exited, status=0/SUCCESS)
  Process: 1085 ExecStart=/etc/init.d/tomcat7 start (code=exited, status=0/SUCCESS)
   CGroup: /system.slice/tomcat7.service
           └─1142 /usr/lib/jvm/java-8-openjdk-amd64/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.awt.headless=true -Xms512m -Xmx2g -XX:+UseConcMarkSweepGC -XX:-OmitStackT

feb 05 11:17:14 Vader systemd[1]: Starting LSB: Start Tomcat....
feb 05 11:17:14 Vader tomcat7[1085]:  * Starting Tomcat servlet engine tomcat7
feb 05 11:17:19 Vader tomcat7[1085]:    ...done.
feb 05 11:17:19 Vader systemd[1]: Started LSB: Start Tomcat..
lines 1-13/13 (END)









Robin Kämpe

unread,
Feb 5, 2018, 6:48:38 AM2/5/18
to xnat_discussion
Update: I disabled the browser proxy and XNAT seems to be up and running if I from the server itself (via thinklink) go to http://localhost:8080.

Still: There are the errors in the xnat logs pasted aboive
and
I cannot access it via its IP address on the server or any other sever on the network.

Robin Kämpe

unread,
Feb 5, 2018, 9:58:10 AM2/5/18
to xnat_di...@googlegroups.com
Ok, it is reachable via:
http://ip:8080 from other machines.

I guess I have to install nginx and try to configure it so I don't have to put 8080 at the end. I guess  just: 
sudo apt-get install nginx
and then try this:


Still the errors in the loggfile worries me. Should they?

Thanks


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Herrick, Rick

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Feb 6, 2018, 10:17:33 AM2/6/18
to xnat_di...@googlegroups.com

Don’t worry about the error that was in xdat.log on initialization. That error happens because the code runs before the XNAT database schema (including xdat_user) have been generated. I’d like to get rid of that error, but it’s being trapped and recorded pretty deep in the XFT code. Changing it so that it can be caught and disregarded at the appropriate point farther up the call stack would have effects on other code that calls into that, so we haven’t messed with it. I’ll add a note to the exception that says to disregard it on new system deployments.

 

-- 

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 Robin Kämpe <robin....@gmail.com>
Reply-To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Date: Monday, February 5, 2018 at 8:58 AM
To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] Re: XNAT 1.7.4 installation problems

 

http://ip:8080 from other machines.

 

I guess I have to install nginx and try to configure it so I don't have to put 8080 at the end. I guess  just: 

sudo apt-get install nginx

and then try this:

 


Still the errors in the loggfile worries me. Should they?

 

Thanks

 

 

On Mon, Feb 5, 2018 at 12:48 PM, Robin Kämpe <robin....@gmail.com> wrote:

Update: I disabled the browser proxy and XNAT seems to be up and running if I from the server itself (via thinklink) go to http://localhost:8080.

Still: There are the errors in the xnat logs pasted aboive
and
I cannot access it via its IP address on the server or any other sever on the network.

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You received this message because you are subscribed to a topic in the Google Groups "xnat_discussion" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/xnat_discussion/7AwtxVYYoDQ/unsubscribe

.
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To post to this group, send email to xnat_di...@googlegroups.com.
Visit this group at https://groups.google.com/group/xnat_discussion.
For more options, visit https://groups.google.com/d/optout.

 

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Robin Kämpe

unread,
Feb 6, 2018, 10:58:12 AM2/6/18
to xnat_di...@googlegroups.com
OK! So I guess I can assume I have managed to install XNAT 1.7 from scratch? :) Thanks!

1. I also installed the pipeline, is there a way to confirm that it was installed successfully?

2. My end goal is to transfer our current XNAT 1.6.5, that runs on a Virtual Machine (a WM on this very host where I  just installed a blank XNAT). My next step is to upgrade the WM 1.6.5 to 1.7. Then I plan to move my xnat from the WM to the, on the host server, directly installed xnat.
I plan to use pg_dump to create a database "backup" from the WM that I then pg_restore to the new  local installation of xnat. Then I'll move (copy) the /data/archive + prearchive to the server. Do you see any problems with this? Will all users/accounts follow?

Thanks!

On Tue, Feb 6, 2018 at 4:17 PM, Herrick, Rick <jrhe...@wustl.edu> wrote:

Don’t worry about the error that was in xdat.log on initialization. That error happens because the code runs before the XNAT database schema (including xdat_user) have been generated. I’d like to get rid of that error, but it’s being trapped and recorded pretty deep in the XFT code. Changing it so that it can be caught and disregarded at the appropriate point farther up the call stack would have effects on other code that calls into that, so we haven’t messed with it. I’ll add a note to the exception that says to disregard it on new system deployments.

 

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Phone: +1 (314) 273-1645

From: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com> on behalf of Robin Kämpe <robin....@gmail.com>
Reply-To: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com>
Date: Monday, February 5, 2018 at 8:58 AM
To: "xnat_discussion@googlegroups.com" <xnat_discussion@googlegroups.com>
Subject: Re: [XNAT Discussion] Re: XNAT 1.7.4 installation problems

 

 

I guess I have to install nginx and try to configure it so I don't have to put 8080 at the end. I guess  just: 

sudo apt-get install nginx

and then try this:

 


Still the errors in the loggfile worries me. Should they?

 

Thanks

 

On Mon, Feb 5, 2018 at 12:48 PM, Robin Kämpe <robin....@gmail.com> wrote:

Update: I disabled the browser proxy and XNAT seems to be up and running if I from the server itself (via thinklink) go to http://localhost:8080.

Still: There are the errors in the xnat logs pasted aboive
and
I cannot access it via its IP address on the server or any other sever on the network.

--
You received this message because you are subscribed to a topic in the Google Groups "xnat_discussion" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/xnat_discussion/7AwtxVYYoDQ/unsubscribe

.
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To post to this group, send email to xnat_discussion@googlegroups.com.
Visit this group at https://groups.google.com/group/xnat_discussion.
For more options, visit https://groups.google.com/d/optout.

 

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