Open Microscopy Environment

I just did a fresh install of OMERO following the linux walkthrough but it won't start. I seem to get getting errors in both Blitz and the indexer. Could someone help me understand the log files?

Blitz-0.log

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2011-08-12 22:20:57,304 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2011-08-12 22:21:16,637 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2011-08-12 22:22:18,938 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2011-08-12 22:22:21,960 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Shutting down EHCache CacheManager
2011-08-12 22:22:21,963 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*:beanRefContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/home/jose/opt/OMERO/OMERO.server-Beta-4.3.1/lib/server/blitz.jar!/beanRefContext.xml]: Cannot resolve reference to bean 'ome.server' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.server' defined in URL [jar:file:/home/jose/opt/OMERO/OMERO.server-Beta-4.3.1/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.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.BeanCreationException: Error creating bean with name 'executor' defined in class path resource [ome/services/services.xml]: Cannot resolve reference to bean 'omeroSessionFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'omeroSessionFactory' defined in class path resource [ome/services/hibernate.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 exception is org.hibernate.HibernateException: could not init listeners


Is there anything else in the log? If so, could you attach it here as a zip file?

Thanks,
~Josh.

Here are the three logs with errors in them, although it looks like the main error in the blitz log

Hi José,

the main error in the log files is :

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Caused by: java.io.FileNotFoundException: /home/jose/opt/OMERO/OMERO.data/FullText/segments_3 (No such file or directory)
        at java.io.RandomAccessFile.open(Native Method)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:233)


which may be caused by http://trac.openmicroscopy.org.uk/ome/ticket/5526. Does the directory "/home/jose/opt/OMERO/OMERO.data/FullText" exist? Is it on an NFS mount? Have you tried shutting down all the services and restarting? (bin/omero admin restart)? Which version are you using? (Sorry for the barrage of questions)

Cheers,
~Josh.

The directory does exist, and it contains two files, segments.gen and segments_1. I have tried to restart the service without issues and the folder is located on a normal drive.

Anything else I should be looking at?
Jose

Sorry I forgot to mention that I am using Omero server-Beta-4.3.1, and I am trying to install this on ubuntu 10.10

Thanks for the help

Jose

Hi Josh

I have this installed on a VM for testing, so I thought the best thing might be to try and rebuild it from scratch just to make sure I didn't do something stupid. so I am rebuilding the VM and will try doing a fresh install again. I'll let you know if I run into the same issues. In the mean time if you think of anything else please let me know

Jose

It looks like its working now! This time after I built the VM and installed all the required packages, I used galternatives to manually make sure that anything related to java was using sun-java and not openjdk.

Thanks for the help
Jose

Jose,

thanks for the update. I've added a note to #5526 that this may be related to OpenJDK. Let us know if you have any more problems.

Cheers,
~Josh.