[ome-users] OMERO installation

Urs Utzinger uutzinger at azcc.arizona.edu
Mon Mar 24 20:07:16 GMT 2008 

What is a recommended operating system and java installation to get OMERO
working?

 

 

 

 

I have been trying to install OMERO on both an Ubuntu as well as Fedora 8 on
VMware virtual machine. So far with both installations I am unable to get
the OMERO to boot. 

 

Below are the results of the latest attempt using Fedora 8 on VMware server
1.0.4. I used default java and postgresql using package installer.

Following the OMERO installation guidelines I received the following output:

 

java -version

java version "1.7.0"

IcedTea Runtime Environment (build 1.7.0-b21)

IcedTea Client VM (build 1.7.0-b21, mixed mode)

 

javac -version

javac 1.7.0-internal

 

psql -h localhost -U omero -l

Password for user omero: 

        List of databases

   Name    |  Owner   | Encoding 

-----------+----------+----------

 omero3    | omero    | UTF8

 postgres  | postgres | UTF8

 template0 | postgres | UTF8

 template1 | postgres | UTF8

(4 rows)

 

java omero update setup-db deploy

No Errors

 

$JBOSS_HOME/bin/run.sh

[omero at omero omero]$ $JBOSS_HOME/bin/run.sh

=========================================================================

 

  JBoss Bootstrap Environment

 

  JBOSS_HOME: /home/omero/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA

 

  JAVA: java

 

  JAVA_OPTS: -Dprogram.name=run.sh -Xms128m -Xmx512m
-Dsun.rmi.dgc.client.gcInterval=3600000
-Dsun.rmi.dgc.server.gcInterval=3600000 -Djava.net.preferIPv4Stack=true
-XX:MaxPermSize=128M -Djava.awt.headless=true

 

  CLASSPATH:
/home/omero/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA/bin/run.jar

 

=========================================================================

 

12:34:42,060 INFO  [Server] Starting JBoss (MX MicroKernel)...

12:34:42,061 INFO  [Server] Release ID: JBoss [Trinity] 4.2.1.GA (build:
SVNTag=JBoss_4_2_1_GA date=200707131605)

12:34:42,063 INFO  [Server] Home Dir:
/home/omero/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA

12:34:42,063 INFO  [Server] Home URL:
file:/home/omero/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA/

12:34:42,063 INFO  [Server] Patch URL: null

12:34:42,064 INFO  [Server] Server Name: default

12:34:42,064 INFO  [Server] Server Home Dir:
/home/omero/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA/server/default

12:34:42,065 INFO  [Server] Server Home URL:
file:/home/omero/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA/server/default/

12:34:42,065 INFO  [Server] Server Log Dir:
/home/omero/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA/server/default/log

12:34:42,066 INFO  [Server] Server Temp Dir:
/home/omero/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA/server/default/tmp

12:34:42,066 INFO  [Server] Root Deployment Filename: jboss-service.xml

12:34:42,335 INFO  [ServerInfo] Java version: 1.7.0,Sun Microsystems Inc.

12:34:42,336 INFO  [ServerInfo] Java VM: IcedTea Client VM 1.7.0-b21,Sun
Microsystems Inc.

12:34:42,336 INFO  [ServerInfo] OS-System: Linux 2.6.24.3-34.fc8,i386

12:34:42,630 INFO  [Server] Core system initialized

12:34:43,891 WARN  [BasicMBeanRegistry]
javax.management.MBeanRegistrationException: preRegister() failed:
[ObjectName='jboss.remoting:service=NetworkRegistry',
Class=org.jboss.remoting.network.NetworkRegistry
(org.jboss.remoting.network.NetworkRegistry at 716cb7)]

12:34:43,905 ERROR [MainDeployer] Could not create deployment:
file:/home/omero/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA/server/default/con
f/jboss-service.xml

org.jboss.deployment.DeploymentException: - nested throwable:
(java.lang.reflect.InvocationTargetException)

        at
org.jboss.system.ServiceConfigurator.install(ServiceConfigurator.java:196)

        at
org.jboss.system.ServiceController.install(ServiceController.java:226)

        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:623)

        at
org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java
:155)

        at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)

        at
org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:26
4)

        at
org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

        at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)

        at $Proxy4.install(Unknown Source)

        at org.jboss.deployment.SARDeployer.create(SARDeployer.java:249)

        at org.jboss.deployment.MainDeployer.create(MainDeployer.java:969)

        at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:818)

        at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:782)

        at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:766)

        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:623)

        at
org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java
:155)

        at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

        at
org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java
:133)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

        at
org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOpe
rationInterceptor.java:142)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

        at
org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:26
4)

        at
org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

        at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)

        at $Proxy5.deploy(Unknown Source)

        at org.jboss.system.server.ServerImpl.doStart(ServerImpl.java:482)

        at org.jboss.system.server.ServerImpl.start(ServerImpl.java:362)

        at org.jboss.Main.boot(Main.java:200)

        at org.jboss.Main$1.run(Main.java:508)

        at java.lang.Thread.run(Thread.java:675)

Caused by: java.lang.reflect.InvocationTargetException

        at
org.jboss.mx.server.MBeanServerImpl.registerMBean(MBeanServerImpl.java:1451)

        at
org.jboss.mx.server.MBeanServerImpl.registerMBean(MBeanServerImpl.java:1350)

        at
org.jboss.mx.server.MBeanServerImpl.createMBean(MBeanServerImpl.java:345)

        at org.jboss.system.ServiceCreator.install(ServiceCreator.java:157)

        at
org.jboss.system.ServiceConfigurator.internalInstall(ServiceConfigurator.jav
a:449)

        at
org.jboss.system.ServiceConfigurator.install(ServiceConfigurator.java:171)

        ... 36 more

Caused by: javax.management.MBeanException

        at
org.jboss.mx.interceptor.ReflectedDispatcher.handleInvocationExceptions(Refl
ectedDispatcher.java:180)

        at
org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java
:163)

        at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

        at
org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java
:133)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

        at
org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOpe
rationInterceptor.java:142)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

        at
org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:26
4)

        at
org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

        at
org.jboss.mx.server.MBeanServerImpl$3.run(MBeanServerImpl.java:1422)

        at java.security.AccessController.doPrivileged(Native Method)

        at
org.jboss.mx.server.MBeanServerImpl.registerMBean(MBeanServerImpl.java:1417)

        ... 41 more

Caused by: javax.management.MBeanRegistrationException: preRegister()
failed: [ObjectName='jboss.remoting:service=NetworkRegistry',
Class=org.jboss.remoting.network.NetworkRegistry
(org.jboss.remoting.network.NetworkRegistry at 716cb7)]

        at
org.jboss.mx.server.registry.BasicMBeanRegistry.invokePreRegister(BasicMBean
Registry.java:713)

        at
org.jboss.mx.server.registry.BasicMBeanRegistry.registerMBean(BasicMBeanRegi
stry.java:211)

        at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)

        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
.java:43)

        at java.lang.reflect.Method.invoke(Method.java:623)

        at
org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java
:155)

        ... 51 more

Caused by: java.lang.RuntimeException: Exception creating identity:
omero.spx.arizona.edu: omero.spx.arizona.edu

        at org.jboss.remoting.ident.Identity.get(Identity.java:211)

        at
org.jboss.remoting.network.NetworkRegistry.preRegister(NetworkRegistry.java:
268)

        at
org.jboss.mx.server.AbstractMBeanInvoker.invokePreRegister(AbstractMBeanInvo
ker.java:966)

        at
org.jboss.mx.modelmbean.ModelMBeanInvoker.invokePreRegister(ModelMBeanInvoke
r.java:489)

        at
org.jboss.mx.server.AbstractMBeanInvoker.preRegister(AbstractMBeanInvoker.ja
va:654)

        at
org.jboss.mx.server.registry.BasicMBeanRegistry.invokePreRegister(BasicMBean
Registry.java:697)

        ... 56 more

Failed to boot JBoss:

org.jboss.deployment.DeploymentException: - nested throwable:
(java.lang.reflect.InvocationTargetException)

        at
org.jboss.system.ServiceConfigurator.install(ServiceConfigurator.java:196)

        at
org.jboss.system.ServiceController.install(ServiceController.java:226)

        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:623)

        at
org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java
:155)

        at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)

        at
org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:26
4)

        at
org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

        at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)

        at $Proxy4.install(Unknown Source)

        at org.jboss.deployment.SARDeployer.create(SARDeployer.java:249)

        at org.jboss.deployment.MainDeployer.create(MainDeployer.java:969)

        at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:818)

        at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:782)

        at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:766)

        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:623)

        at
org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java
:155)

        at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

        at
org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java
:133)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

        at
org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOpe
rationInterceptor.java:142)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

        at
org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:26
4)

        at
org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

        at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)

        at $Proxy5.deploy(Unknown Source)

        at org.jboss.system.server.ServerImpl.doStart(ServerImpl.java:482)

        at org.jboss.system.server.ServerImpl.start(ServerImpl.java:362)

        at org.jboss.Main.boot(Main.java:200)

        at org.jboss.Main$1.run(Main.java:508)

        at java.lang.Thread.run(Thread.java:675)

Caused by: java.lang.reflect.InvocationTargetException

        at
org.jboss.mx.server.MBeanServerImpl.registerMBean(MBeanServerImpl.java:1451)

        at
org.jboss.mx.server.MBeanServerImpl.registerMBean(MBeanServerImpl.java:1350)

        at
org.jboss.mx.server.MBeanServerImpl.createMBean(MBeanServerImpl.java:345)

        at org.jboss.system.ServiceCreator.install(ServiceCreator.java:157)

        at
org.jboss.system.ServiceConfigurator.internalInstall(ServiceConfigurator.jav
a:449)

        at
org.jboss.system.ServiceConfigurator.install(ServiceConfigurator.java:171)

        ... 36 more

Caused by: javax.management.MBeanException

        at
org.jboss.mx.interceptor.ReflectedDispatcher.handleInvocationExceptions(Refl
ectedDispatcher.java:180)

        at
org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java
:163)

        at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

        at
org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java
:133)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

        at
org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOpe
rationInterceptor.java:142)

        at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

        at
org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:26
4)

        at
org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

        at
org.jboss.mx.server.MBeanServerImpl$3.run(MBeanServerImpl.java:1422)

        at java.security.AccessController.doPrivileged(Native Method)

        at
org.jboss.mx.server.MBeanServerImpl.registerMBean(MBeanServerImpl.java:1417)

        ... 41 more

Caused by: javax.management.MBeanRegistrationException: preRegister()
failed: [ObjectName='jboss.remoting:service=NetworkRegistry',
Class=org.jboss.remoting.network.NetworkRegistry
(org.jboss.remoting.network.NetworkRegistry at 716cb7)]

        at
org.jboss.mx.server.registry.BasicMBeanRegistry.invokePreRegister(BasicMBean
Registry.java:713)

        at
org.jboss.mx.server.registry.BasicMBeanRegistry.registerMBean(BasicMBeanRegi
stry.java:211)

        at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)

        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
.java:43)

        at java.lang.reflect.Method.invoke(Method.java:623)

        at
org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java
:155)

        ... 51 more

Caused by: java.lang.RuntimeException: Exception creating identity:
omero.spx.arizona.edu: omero.spx.arizona.edu

        at org.jboss.remoting.ident.Identity.get(Identity.java:211)

        at
org.jboss.remoting.network.NetworkRegistry.preRegister(NetworkRegistry.java:
268)

        at
org.jboss.mx.server.AbstractMBeanInvoker.invokePreRegister(AbstractMBeanInvo
ker.java:966)

        at
org.jboss.mx.modelmbean.ModelMBeanInvoker.invokePreRegister(ModelMBeanInvoke
r.java:489)

        at
org.jboss.mx.server.AbstractMBeanInvoker.preRegister(AbstractMBeanInvoker.ja
va:654)

        at
org.jboss.mx.server.registry.BasicMBeanRegistry.invokePreRegister(BasicMBean
Registry.java:697)

        ... 56 more

12:34:43,918 INFO  [Server] Runtime shutdown hook called, forceHalt: true

12:34:43,918 INFO  [Server] JBoss SHUTDOWN: Undeploying all packages

12:34:43,929 INFO  [Server] Shutdown complete

Shutdown complete

Halting VM

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