Fwd: Problem during upgrade to Apollo 2.0.5

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Fwd: Problem during upgrade to Apollo 2.0.5

nathandunn

Just wanted to forward this to the list as it may help other users with installations that might be wonky when upgrading.  

If your system does not come up and you see an error like this in your tomcat logs, 

Caused by: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)

Even if you upgrade from Java 7 to Java 8 (required for 2.0.5), you have to make sure that tomcat is using the correct version of java even if you updated it correctly.  

This can be done by setting JAVA_HOME to the appropriate directory on your system (usually above the bin directory of your java and javac binaries)


or just removing the older version of Java. 

Nathan
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
[hidden email]


Begin forwarded message:

From: "Robin A. Ohm" <[hidden email]>
Subject: Re: Problem during upgrade to Apollo 2.0.5
Date: January 16, 2017 at 4:39:51 AM PST
To: Nathan Dunn <[hidden email]>

Hi Nathan,

Your second suggestion led me to the solution: tomcat7 indeed still used the old java version. I fixed this by setting 'JAVA_HOME' in the setting file '/etc/default/tomcat7' to the same path as in the environment variable $JAVA_HOME (in my case '/usr/lib/jvm/java-8-openjdk-amd64'). I would have thought that tomcat would pick up this environmental variable, but I guess it didn't...

Thanks a lot for your quick help! I'm fine with you forwarding it to the mailing list, of course. I guess I should have done that in the first place.

Best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]

On 14-01-17 17:28, Nathan Dunn wrote:
So, some other things to try (that is the right version).    I’ve gotten this error before:

UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0
And its a JDK version incompatibility error typically.

A couple of things to try:

1 - make sure that your apollo directory is removed before you drop the war file into it
2 - make sure that the tomcat java is also 8, e.ig.  "ps -ef | grep java” is the same as "which java”

Do you mind if I forward this to the Apollo list in case other people run into this?

Nathan

On Jan 14, 2017, at 3:31 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

Thanks for the suggestion, but I had already upgraded to JDK8 before trying 2.0.5, so I don't think that was the problem. Does this look correct?

root@science-vs62:~# java -version
openjdk version "1.8.0_111"
OpenJDK Runtime Environment (build 1.8.0_111-8u111-b14-3~14.04.1-b14)
OpenJDK 64-Bit Server VM (build 25.111-b14, mixed mode)

I tried your suggestion to run './apollo clean' first, but this didn't change anything. Deploying apollo finishes without errors, but the errors appear in catalina.out after tomcat7 is restarted.

Best regards, Robin


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016

________________________________________
From: Nathan Dunn [[hidden email]]
Sent: Saturday, January 14, 2017 2:36
To: Ohm, R.A. (Robin)
Subject: Re: Problem during upgrade to Apollo 2.0.5

Sorry for the delay.

What version of Java are you using?

You should be using the Java + JDK 8 instead of 7 now.   You’ll need to do an “./apollo clean” following by an “./apollo deploy”.  You can test it by doing “./apollo run-local” to make sure its working before you deploy onto tomcat, however.

Let me know if that works.

Nathan

On Jan 13, 2017, at 6:20 AM, Robin A. Ohm <[hidden email]> wrote:

Hi Nathan,

I've run into a problem while upgrading Apollo to from version 2.0.4 to 2.0.5. After restarting tomcat7 Apollo never becomes available in the webbrowser. There are some error messages in catalina.out (see below), but I don't really understand what they mean.

In the meantime I've rolled back to 2.0.4 and that still works fine. Hopefully you can point me to a solution.

Thanks in advance! Best regards,

Robin Ohm


Jan 13, 2017 3:05:59 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Jan 13, 2017 3:05:59 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Jan 13, 2017 3:05:59 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Jan 13, 2017 3:05:59 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
Jan 13, 2017 3:06:00 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Jan 13, 2017 3:06:00 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
Jan 13, 2017 3:06:00 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Jan 13, 2017 3:06:00 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
Jan 13, 2017 3:06:00 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Jan 13, 2017 3:06:00 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Jan 13, 2017 3:06:01 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Jan 13, 2017 3:06:01 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 1249 ms
Jan 13, 2017 3:06:01 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Jan 13, 2017 3:06:01 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Jan 13, 2017 3:06:01 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
Jan 13, 2017 3:06:22 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Jan 13, 2017 3:06:22 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
2017-01-13 15:06:34,681 [localhost-startStop-1] ERROR context.ContextLoader  - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
    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: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
    at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
    at java.lang.Class.getDeclaredFields(Class.java:1819)
    ... 5 more
2017-01-13 15:06:34,696 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
    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: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
    at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
    at java.lang.Class.getDeclaredFields(Class.java:1819)
    ... 5 more
2017-01-13 15:06:34,698 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginManager' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
    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: java.lang.UnsupportedClassVersionError: org/grails/plugin/config/AbstractConfigHelper : Unsupported major.minor version 52.0 (unable to load class org.grails.plugin.config.AbstractConfigHelper) (unable to load class org.grails.plugin.config.DefaultConfigHelper)
    at java.lang.Class.privateGetDeclaredFields(Class.java:2509)
    at java.lang.Class.getDeclaredFields(Class.java:1819)
    ... 5 more
Jan 13, 2017 3:06:34 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Jan 13, 2017 3:06:34 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Jan 13, 2017 3:06:34 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Jan 13, 2017 3:06:36 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jan 13, 2017 3:06:36 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 34874 ms




--
Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]







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