Test installing XNAT 1.7.1: Tomcat 7 restard failed

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Robin Kämpe

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Dec 20, 2016, 1:20:57 PM12/20/16

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Hi!

I am trying to make a fresh xnat 1.7.1 install on a new virtual Ubuntu machine as practice . I have followed the Comprehensive installation guide and I thought I was done. Something is wrong. I see some people have had similar problems but perhaps not identical.

This is the status of tomcat7 after I tried a restard:

tomcat7.service - LSB: Start Tomcat.
   Loaded: loaded (/etc/init.d/tomcat7; generated; vendor preset: enabled)
   Active: failed (Result: exit-code) since Tue 2016-12-20 17:53:24 GMT; 19min ago
     Docs: man:systemd-sysv-generator(8)
Process: 14877 ExecStop=/etc/init.d/tomcat7 stop (code=exited, status=0/SUCCESS)
Process: 14886 ExecStart=/etc/init.d/tomcat7 start (code=exited, status=1/FAILURE)
    Tasks: 16 (limit: 4915)
   CGroup: /system.slice/tomcat7.service
           └─8133 /usr/lib/jvm/java-7-oracle/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassL

Dec 20 17:53:19 osboxes systemd[1]: Stopped LSB: Start Tomcat..
Dec 20 17:53:19 osboxes systemd[1]: Starting LSB: Start Tomcat....
Dec 20 17:53:19 osboxes tomcat7[14886]: * Starting Tomcat servlet engine tomcat7
Dec 20 17:53:24 osboxes tomcat7[14886]:    ...fail!
Dec 20 17:53:24 osboxes systemd[1]: tomcat7.service: Control process exited, code=exited status=1
Dec 20 17:53:24 osboxes systemd[1]: Failed to start LSB: Start Tomcat..
Dec 20 17:53:24 osboxes systemd[1]: tomcat7.service: Unit entered failed state.
Dec 20 17:53:24 osboxes systemd[1]: tomcat7.service: Failed with result 'exit-code'.
lines 1-18/18 (END)

When looking in the catalina logs I get overwhelmed but I do find one thing (highlighted):
xnat@osboxes:~/Downloads$ cat /var/log/tomcat7/catalina.2016-12-20.log
Dec 20, 2016 5:07:39 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Dec 20, 2016 5:07:39 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Dec 20, 2016 5:07:39 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Dec 20, 2016 5:07:39 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Dec 20, 2016 5:07:39 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Dec 20, 2016 5:07:39 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/7.0.72 (Ubuntu)
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Sep 20 2016 11:28:54 UTC
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.72.0
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.8.0-22-generic
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-7-oracle/jre
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.7.0_80-b15
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat7
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat7
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.awt.headless=true
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx128m
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseConcMarkSweepGC
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat7
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat7
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp
Dec 20, 2016 5:07:40 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 1289 ms
Dec 20, 2016 5:07:40 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 20, 2016 5:07:40 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.72 (Ubuntu)
Dec 20, 2016 5:07:40 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Dec 20, 2016 5:07:40 PM 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 []
Dec 20, 2016 5:07:42 PM 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.
Dec 20, 2016 5:07:42 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat7/webapps/ROOT has finished in 1,726 ms
Dec 20, 2016 5:07:42 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 20, 2016 5:07:42 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 1850 ms
Dec 20, 2016 5:52:02 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/xnat-web-1.7.1.war
Dec 20, 2016 5:52:02 PM org.apache.catalina.startup.ContextConfig beforeStart
SEVERE: Exception fixing docBase for context [/xnat-web-1.7.1]
java.io.IOException: Unable to create the directory [/var/lib/tomcat7/webapps/xnat-web-1.7.1]
    at org.apache.catalina.startup.ExpandWar.expand(ExpandWar.java:98)
    at org.apache.catalina.startup.ContextConfig.fixDocBase(ContextConfig.java:737)
    at org.apache.catalina.startup.ContextConfig.beforeStart(ContextConfig.java:862)
    at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:390)
    at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
    at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
    at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:388)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:144)
    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:1092)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
    at java.util.concurrent.Executors$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)

Dec 20, 2016 5:52:03 PM org.apache.catalina.core.StandardContext postWorkDirectory
WARNING: Failed to create work directory [/var/lib/tomcat7/work/Catalina/localhost/xnat-web-1.7.1] for context [/xnat-web-1.7.1]
Dec 20, 2016 5:52:03 PM org.apache.catalina.loader.WebappLoader startInternal
SEVERE: LifecycleException
java.io.IOException: Failed to create destination directory to copy resources
    at org.apache.catalina.loader.WebappLoader.setRepositories(WebappLoader.java:895)
    at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:606)
    at org.apache.catalina.loader.VirtualWebappLoader.startInternal(VirtualWebappLoader.java:191)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5499)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    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:1092)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
    at java.util.concurrent.Executors$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)

Dec 20, 2016 5:52:03 PM org.apache.catalina.core.ContainerBase addChildInternal
SEVERE: ContainerBase.addChild: start:
org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/xnat-web-1.7.1]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:162)
    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:1092)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
    at java.util.concurrent.Executors$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)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [WebappLoader[/xnat-web-1.7.1]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:162)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5499)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    ... 10 more
Caused by: org.apache.catalina.LifecycleException: start:
    at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:632)
    at org.apache.catalina.loader.VirtualWebappLoader.startInternal(VirtualWebappLoader.java:191)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    ... 12 more
Caused by: java.io.IOException: Failed to create destination directory to copy resources
    at org.apache.catalina.loader.WebappLoader.setRepositories(WebappLoader.java:895)
    at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:606)
    ... 14 more

Dec 20, 2016 5:52:03 PM org.apache.catalina.startup.HostConfig deployWAR
SEVERE: Error deploying web application archive /var/lib/tomcat7/webapps/xnat-web-1.7.1.war
java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/xnat-web-1.7.1]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:903)
    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:1092)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
    at java.util.concurrent.Executors$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)

Dec 20, 2016 5:52:03 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat7/webapps/xnat-web-1.7.1.war has finished in 718 ms
xnat@osboxes:~/Downloads$

I have set the permissions so that tomcat7 is owned by xnat and I succeeded with the test:
xnat@osboxes:~/Downloads$ ^C
xnat@osboxes:~/Downloads$ ls -ld /var/lib/tomcat7 /var/lib/tomcat7/* /etc/tomcat7 /var/log/tomcat7 /var/cache/tomcat7
drwxr-xr-x 4 xnat xnat 4096 Dec 20 17:07 /etc/tomcat7
drwxr-x--- 3 xnat xnat 4096 Dec 20 17:07 /var/cache/tomcat7
drwxr-xr-x 6 xnat xnat 4096 Dec 20 17:07 /var/lib/tomcat7
drwxr-xr-x 3 xnat xnat 4096 Dec 20 17:07 /var/lib/tomcat7/common
lrwxrwxrwx 1 xnat xnat   12 Sep 20 12:28 /var/lib/tomcat7/conf -> /etc/tomcat7
lrwxrwxrwx 1 xnat xnat   17 Sep 20 12:28 /var/lib/tomcat7/logs -> ../../log/tomcat7
drwxr-xr-x 3 xnat xnat 4096 Dec 20 17:07 /var/lib/tomcat7/server
drwxr-xr-x 3 xnat xnat 4096 Dec 20 17:07 /var/lib/tomcat7/shared
drwxrwxr-x 3 xnat xnat 4096 Dec 20 17:51 /var/lib/tomcat7/webapps
lrwxrwxrwx 1 xnat xnat   19 Sep 20 12:28 /var/lib/tomcat7/work -> ../../cache/tomcat7
drwxr-x--- 2 xnat xnat 4096 Dec 20 17:07 /var/log/tomcat7
xnat@osboxes:~/Downloads$

But I did find that /var/lib/tomcat7/work/ is owned by tomcatt7 and not xnat. Should I try to change this to xnat as well?
xnat@osboxes:~/Downloads$ ls -ld /var/lib/tomcat7/work/*
drwxr-xr-x 3 tomcat7 tomcat7 4096 Dec 20 17:07 /var/lib/tomcat7/work/Catalina
-rw-r--r-- 1 root    root    9281 Dec 20 17:53 /var/lib/tomcat7/work/catalina.policy
xnat@osboxes:~/Downloads$

Could this be it? Prior to trying a fresh install I tried to upgrade an old xnat verson. This is actually the same error I ran into there and that was the reason I tried a fresh install.. Thansk!
Best
Robin

Herrick, Rick

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Dec 20, 2016, 5:02:29 PM12/20/16

to xnat_di...@googlegroups.com

I suspect you have something configured in the Tomcat server.xml file, something along the lines of:

</Context>

Because there’s this warning:

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 []

Tomcat won’t do that on its own, I don’t think. Have a look at your server.xml and, if there’s anything in there like this, you can comment it out or remove it.

Now the error you highlighted is definitely due to permissions and ownership issues. If tomcat owns the folder, it’s highly likely that xnat can’t write there. You need to make sure that all of the folders in your Tomcat installation are owned by the user specified by TOMCAT_USER. This includes following the symlinks under /var/lib/tomcat7! You can do something like this:

# chown -Rh xnat.xnat /var/lib/tomcat7

# chown -RH xnat.xnat /var/lib/tomcat7

I think that’s correct. The -h and -H options tell chown to work through the links or to affect the links directly, so the two executions change everything under the specified folder including all of the subfolders in symlinked locations AND the symlinks themselves.

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Voice: (314) 273-1645

Web: http://www.xnat.org

Twitter: @NrgXnat

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Robin Kämpe

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Dec 21, 2016, 6:16:46 AM12/21/16

to xnat_discussion

Thanks Rick!

1. There were nothing like that in the server.xml file. The problem was probably due to permissions. Your command did not fix permissions to the links. I had to manually add xnat.xnat as owner of /etc/tomcat7 as well. No there was now error.

I'm not completely there yet though. I don't know if xnat is successfully running because I cannot reach the web server. I have not set up a front end proxy but I feel that could be a last step. Without one, how would I access the page? I have tried:
http://xnat
http://xnat:8080
http://xnat:8080:xnat
http://localhost
http://localhost:8080
http://localhost:8080:xnat

So either Im putting the wrong stuff in the address bar or xnat is not successfully installed.

2. In xnat_1.7 where do I put the stuff I used to put in build.properties?
3. In xnat_1.7 where do I put the stuff I used to put in services.properties (e.g. ldap1)?

How to see if xnat is installed:

Tomcat managed to restart:

xnat@osboxes:/data/xnat$ sudo service tomcat7 status
[sudo] password for xnat:
● tomcat7.service - LSB: Start Tomcat.

Loaded: loaded (/etc/init.d/tomcat7; generated; vendor preset: enabled)

   Active: active (running) since Wed 2016-12-21 10:46:32 GMT; 15min ago
     Docs: man:systemd-sysv-generator(8)
Process: 21378 ExecStart=/etc/init.d/tomcat7 start (code=exited, status=0/SUCCESS)
    Tasks: 19 (limit: 4915)
   CGroup: /system.slice/tomcat7.service
           └─21403 /usr/lib/jvm/java-7-oracle/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djav

Dec 21 10:46:27 osboxes systemd[1]: Starting LSB: Start Tomcat....
Dec 21 10:46:27 osboxes tomcat7[21378]: * Starting Tomcat servlet engine tomcat7
Dec 21 10:46:32 osboxes tomcat7[21378]:    ...done.
Dec 21 10:46:32 osboxes systemd[1]: Started LSB: Start Tomcat..

The war file was used:

xnat@osboxes:/var/log/tomcat7$ ls -ld /var/lib/tomcat7/webapps/*
drwxr-xr-x 3 xnat xnat      4096 Dec 20 17:07 /var/lib/tomcat7/webapps/ROOT
drwxr-xr-x 18 xnat xnat      4096 Dec 21 11:07 /var/lib/tomcat7/webapps/xnat-web-1.7.1
-rw-r--r-- 1 xnat xnat 207252960 Dec 20 17:51 /var/lib/tomcat7/webapps/xnat-web-1.7.1.war
xnat@osboxes:/var/log/tomcat7$

Catalina logfiles says something is still wrong. But thee is no folder called common under /usr/share/tomcat7/...:

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Server version: Apache Tomcat/7.0.72 (Ubuntu)

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Server built: Sep 20 2016 11:28:54 UTC

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         7.0.72.0
Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.8.0-22-generic
Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-7-oracle/jre
Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.7.0_80-b15
Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: JVM Vendor: Oracle Corporation

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE: /var/lib/tomcat7
Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME: /usr/share/tomcat7
Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties

Dec 21, 2016 11:06:58 AM org.apache.catalina.startup.VersionLoggerListener log
:

Stuff is happening under /data/xnat. There are new logs. But nothing under build. Does this look right?

xnat@osboxes:/data/xnat$ tree .
.
├── 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
│   │   ├── 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
│       └── xnat_8085373303954567252911952388602
├── pipeline
└── prearchive

Thats all the relative info I could muster. Perhaps the answer is somewhere else. But Since I solved all permission issues and it still complains about a non existing folder I dont know what the next step is.

Robin Kämpe

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Dec 22, 2016, 7:59:33 AM12/22/16

to xnat_discussion

Adding some info:

I might have installed the "wrong" java version. I installed:
I did:
sudo apt-get install oracle-java7-installer
Which gave me:
xnat@osboxes:/var/log/tomcat7$ java -version
java version "1.7.0_80"
Java(TM) SE Runtime Environment (build 1.7.0_80-b15)
Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)
xnat@osboxes:/var/log/tomcat7$

My xnat.conf file:
#
# xnat-conf.properties
# XNAT http://www.xnat.org
# Copyright (c) 2016, Washington University School of Medicine
# All Rights Reserved
#
# Released under the Simplified BSD.
#
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
/data/xnat/home/config/xnat-conf.properties (END)

My /etctomcat7 file:

# OpenJDK, the Oracle JDK, and various Java SE 6+ versions are tried.
#JAVA_HOME=/usr/lib/jvm/openjdk-6-jdk

# 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"

# 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 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
~
~
(END)

SHOULD this file have some extra variables defined? I found on some forum some fix to a problem similar to mine. Add to /etc/tomcat7:

export JAVA_HOME=/usr/lib/jvm/java-7-oracle/ CATALINA_HOME=/usr/share/tomcat7 CATALINA_BASE=/var/lib/tomcat7 CATALINA_PID=/var/run/tomcat7.pid CATALINA_TMPDIR=/tmp
/usr/share/tomcat7/bin/catalina.sh run

Not sure were the error is. Probably something with java variables?

Should echo $JAVA_HOME give something? Because I get nothing out of it.

Should I re-install the whole WM just to get the java JDK 7? :/

Thanks!

Robin Kämpe

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Dec 22, 2016, 8:01:32 AM12/22/16

to xnat_discussion

Also:

xnat@osboxes:/data$ cat xnat/home/logs/*
2016-12-22 11:17:49,178 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource class, using the default value of org.apache.commons.dbcp2.BasicDataSource
2016-12-22 11:17:49,179 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource initial connection pool size, using the default value of 20
2016-12-22 11:17:49,179 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource maximum connection pool size, using the default value of 40
2016-12-22 11:17:49,179 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource connection pool idle size, using the default value of 10
2016-12-22 11:28:54,699 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource class, using the default value of org.apache.commons.dbcp2.BasicDataSource
2016-12-22 11:28:54,700 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource initial connection pool size, using the default value of 20
2016-12-22 11:28:54,700 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource maximum connection pool size, using the default value of 40
2016-12-22 11:28:54,700 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource connection pool idle size, using the default value of 10
2016-12-22 11:31:03,996 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource class, using the default value of org.apache.commons.dbcp2.BasicDataSource
2016-12-22 11:31:03,997 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource initial connection pool size, using the default value of 20
2016-12-22 11:31:03,997 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource maximum connection pool size, using the default value of 40
2016-12-22 11:31:03,997 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource connection pool idle size, using the default value of 10
2016-12-22 12:50:54,276 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource class, using the default value of org.apache.commons.dbcp2.BasicDataSource
2016-12-22 12:50:54,276 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource initial connection pool size, using the default value of 20
2016-12-22 12:50:54,276 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource maximum connection pool size, using the default value of 40
2016-12-22 12:50:54,276 [localhost-startStop-1] WARN org.nrg.xnat.initialization.DatabaseConfig - No value set for the XNAT datasource connection pool idle size, using the default value of 10
2016-12-22 11:18:17,896 [localhost-startStop-1] WARN org.springframework.web.context.support.AnnotationConfigWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'requestMappingHandlerAdapter' defined in class path resource [org/springframework/web/servlet/config/annotation/DelegatingWebMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter]: Factory method 'requestMappingHandlerAdapter' threw exception; nested exception is java.lang.OutOfMemoryError: PermGen space
2016-12-22 11:29:24,084 [localhost-startStop-1] WARN org.springframework.web.context.support.AnnotationConfigWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'requestMappingHandlerAdapter' defined in class path resource [org/springframework/web/servlet/config/annotation/DelegatingWebMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter]: Factory method 'requestMappingHandlerAdapter' threw exception; nested exception is java.lang.OutOfMemoryError: PermGen space
2016-12-22 11:31:35,203 [localhost-startStop-1] WARN org.springframework.web.context.support.AnnotationConfigWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'requestMappingHandlerAdapter' defined in class path resource [org/springframework/web/servlet/config/annotation/DelegatingWebMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter]: Factory method 'requestMappingHandlerAdapter' threw exception; nested exception is java.lang.OutOfMemoryError: PermGen space
2016-12-22 12:51:32,301 [localhost-startStop-1] WARN org.springframework.web.context.support.AnnotationConfigWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'requestMappingHandlerAdapter' defined in class path resource [org/springframework/web/servlet/config/annotation/DelegatingWebMvcConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter]: Factory method 'requestMappingHandlerAdapter' threw exception; nested exception is java.lang.OutOfMemoryError: PermGen space
xnat@osboxes:/data$

Not sure if this is the wrong end to trouble shoot from

Robin Kämpe

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Dec 22, 2016, 10:31:08 AM12/22/16

to xnat_discussion

Current Catalina.out: Warnings in beginning and something about xnat and memory in the end:

Dec 22, 2016 3:13:55 PM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]

Dec 22, 2016 3:13:55 PM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]

Dec 22, 2016 3:13:55 PM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]

Dec 22, 2016 3:13:55 PM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]

Dec 22, 2016 3:13:55 PM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]

Dec 22, 2016 3:13:55 PM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]