Open Microscopy Environment

Hi everyone,
first sorry for my bad english ...

i have problems with omero and Ubuntu Linux 9.10.

I have installed the following packages:
- Ubuntu 9.10 Server i386 minimal installation with openssh-server
- ICE -> zeroc-ice, python-zero-ice, ice33-services
- JAVA -> sun-java6-bin, sun-java6-jre
- Python 2.6.4 from the baseinstallation
- Postgresql 8.4
- Matplot python-matplotlib

I setup the Postgresql and "omero config set ..." without errors.

i cant start the omero Server

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omero@omero-server:~/omero_dist$ bin/omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................Failed to startup after 5 minutes


master.err

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Traceback (most recent call last):
  File "lib/python/runTables.py", line 13, in <module>
    __import__("tables")
ImportError: No module named tables
21.02.2010 12:40:07 java.util.prefs.FileSystemPreferences$7 run
WARNUNG: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
21.02.2010 12:40:08 java.util.prefs.FileSystemPreferences$7 run
WARNUNG: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
02/21/10 12:40:23.109 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
02/21/10 12:40:23.112 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Unhandled exception in thread started by
Error in sys.excepthook:

Original exception was:


This is from the Processor-0.log

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2010-02-21 12:54:51,390 INFO  [                       omero.util.Server] (MainThread) Starting
2010-02-21 12:54:51,394 INFO  [                    omero.util.Resources] (Thread-2  ) Starting
2010-02-21 12:54:51,400 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 1
2010-02-21 12:55:01,411 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 2
2010-02-21 12:55:11,426 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 3
2010-02-21 12:55:21,438 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 4
2010-02-21 12:55:31,449 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 5
2010-02-21 12:55:41,461 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 6
2010-02-21 12:55:51,468 WARNI [                             omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t @ BlitzAdapters
}
2010-02-21 12:55:51,470 ERROR [                       omero.util.Server] (MainThread) Failed initialization
Traceback (most recent call last):
  File "/opt/omero/omero_dist/lib/python/omero/util/__init__.py", line 350, in run
    self.impl = self.impl_class(ctx)
  File "/opt/omero/omero_dist/lib/python/omero/processor.py", line 546, in __init__
    omero.util.Servant.__init__(self, ctx, needs_session = True)
  File "/opt/omero/omero_dist/lib/python/omero/util/__init__.py", line 417, in __init__
    self.ctx.newSession()
  File "/opt/omero/omero_dist/lib/python/omero/util/__init__.py", line 231, in newSession
    self.session = internal_service_factory(self.communicator, stop_event = self.stop_event)
  File "/opt/omero/omero_dist/lib/python/omero/util/__init__.py", line 150, in internal_service_factory
    raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t @ BlitzAdapters
}
2010-02-21 12:55:51,477 INFO  [                       omero.util.Server] (MainThread) Cleanup
2010-02-21 12:55:51,479 INFO  [                       omero.util.Server] (MainThread) Stopped
2010-02-21 12:55:51,492 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2010-02-21 12:55:51,494 INFO  [              omero.processor.ProcessorI] (MainThread) Cleaning up
2010-02-21 12:55:51,496 INFO  [                    omero.util.Resources] (MainThread) Cleanup done
2010-02-21 12:55:51,497 INFO  [              omero.processor.ProcessorI] (MainThread) Done
2010-02-21 12:55:51,499 WARNI [                                  stderr] (MainThread) Traceback (most recent call last):
2010-02-21 12:55:51,501 WARNI [                                  stderr] (MainThread) File "/usr/lib/pymodules/python2.6/Ice.py", line 766, in main
2010-02-21 12:55:51,517 WARNI [                                  stderr] (MainThread) status = self.run(args)
2010-02-21 12:55:51,519 WARNI [                                  stderr] (MainThread) File "/opt/omero/omero_dist/lib/python/omero/util/__init__.py", line 354, in run
2010-02-21 12:55:51,521 WARNI [                                  stderr] (MainThread) sys.exit(100)
2010-02-21 12:55:51,523 WARNI [                                  stderr] (MainThread) SystemExit: 100
2010-02-21 12:55:51,539 INFO  [                    omero.util.Resources] (Thread-2  ) Halted
2010-02-21 12:55:53,439 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2010-02-21 12:55:53,440 INFO  [                       omero.util.Server] (MainThread) Starting
2010-02-21 12:55:53,444 INFO  [                    omero.util.Resources] (Thread-2  ) Starting


At this Point i nead help ...


I change the Topic to "- solved -"

Could you let us know what is in Blitz-0.log?

Hi "Cxallan",

this is a part from Blitz-0.log.
These messages can be seen after the start of

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omero admin start

as System User omero.

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2010-02-22 19:05:23,691 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2010-02-22 19:05:29,130 WARN  [                         java.util.prefs] (      main) Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
2010-02-22 19:05:29,465 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2010-02-22 19:05:45,579 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2010-02-22 19:05:45,632 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Shutting down EHCache CacheManager
2010-02-22 19:05:45,664 ERROR [                ome.services.blitz.Entry] (      main) Error on startup.
org.springframework.beans.factory.access.BootstrapException: Unable to return specified BeanFactory instance: factory key [OMERO.blitz], from group with resource name [classpath*:beanRe                       fContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/opt/omero/omero_dist/li                       b/server/blitz.jar!/beanRefContext.xml]: Cannot resolve reference to bean 'ome.server' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCrea                       tionException: Error creating bean with name 'ome.server' defined in URL [jar:file:/opt/omero/omero_dist/lib/server/server.jar!/beanRefContext.xml]: Instantiation of bean failed; nested                        exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.spri                       ngframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/services/sec-primitives.xml]: Cannot resolve referenc                       e to bean 'executor' while setting bean property 'executor'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'executor' define                       d in class path resource [ome/services/services.xml]: Cannot resolve reference to bean 'sessionFactory' while setting constructor argument; nested exception is org.springframework.beans                       .factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [ome/services/hibernate.xml]: Invocation of init method failed; nested exce                       ption is org.hibernate.HibernateException: Unable to initialize: FullText
        at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:410)
        at ome.system.OmeroContext.getInstance(OmeroContext.java:203)
        at ome.services.blitz.Entry.start(Entry.java:203)
        at ome.services.blitz.Entry.main(Entry.java:121)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/opt/omero/omero_dist/lib/server/blitz.jar!/bean                       RefContext.xml]: Cannot resolve reference to bean 'ome.server' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error cre                       ating bean with name 'ome.server' defined in URL [jar:file:/opt/omero/omero_dist/lib/server/server.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.spring                       framework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factor                       y.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/services/sec-primitives.xml]: Cannot resolve reference to bean 'executor' whi                       le setting bean property 'executor'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'executor' defined in class path resource                        [ome/services/services.xml]: Cannot resolve reference to bean 'sessionFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationExc                       eption: Error creating bean with name 'sessionFactory' defined in class path resource [ome/services/hibernate.xml]: Invocation of init method failed; nested exception is org.hibernate.H                       ibernateException: Unable to initialize: FullText
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:275)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:479)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:162)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:925)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:835)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:440)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:168)
        at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:885)
        at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397)
        ... 3 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.server' defined in URL [jar:file:/opt/omero/omero_dist/lib/server/server.jar!/bean                       RefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Cons                       tructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/                       services/sec-primitives.xml]: Cannot resolve reference to bean 'executor' while setting bean property 'executor'; nested exception is org.springframework.beans.factory.BeanCreationExcep                       tion: Error creating bean with name 'executor' defined in class path resource [ome/services/services.xml]: Cannot resolve reference to bean 'sessionFactory' while setting constructor ar                       gument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [ome/services/hibernat                       e.xml]: Invocation of init method failed; nested exception is org.hibernate.HibernateException: Unable to initialize: FullText
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:254)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:925)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:835)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:440)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269)
        ... 19 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springf                       ramework.beans.factory.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/services/sec-primitives.xml]: Cannot resolve reference t                       o bean 'executor' while setting bean property 'executor'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'executor' defined i                       n class path resource [ome/services/services.xml]: Cannot resolve reference to bean 'sessionFactory' while setting constructor argument; nested exception is org.springframework.beans.fa                       ctory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [ome/services/hibernate.xml]: Invocation of init method failed; nested excepti                       on is org.hibernate.HibernateException: Unable to initialize: FullText
        at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:115)
        at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:248)
        ... 31 more


Have you created the data directory? It's /OMERO by default.

omero and the Data Repository are installed to a separate Partition

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/opt/omero

root@omero-server:~# cd /opt/omero/
root@omero-server:/opt/omero# ll
insgesamt 99140
drwx------ 2 omero omero     16384 2010-02-20 22:10 lost+found
drwx------ 3 omero omero      4096 2010-02-21 11:37 omero
drwxr-xr-x 2 omero omero      4096 2010-02-21 11:07 OMERO
-rw-r--r-- 1 omero omero 101383003 2009-12-02 13:05 omero-Beta4.1.1.tar.bz2
drwxr-xr-x 9 omero omero      4096 2010-02-21 11:37 omero_dist



The Path "/opt/omero/OMERO" is in "/opt/omero/omero_dist/etc/omero.properties"

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omero.data.dir=/opt/omero/OMERO/


You must use bin/omero config set for those properties. Modifying the properties file will not have the desired effect:

http://www.openmicroscopy.org/site/supp ... repository

ok, with

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omero@omero-server:~/omero_dist$ bin/omero config set omero.data.dir /opt/omero/OMERO


the Server start.

Many Thanks ...