Fresh install Blitz Error

[jxpasto]

OS: I dug out Ubuntu 10.04.4 LTS (64bit Server Edition)
OMERO: OMERO.server-Beta-4.3.4

I followed these instructions: http://www.openmicroscopy.org/site/supp ... alkthrough

All seemed to go well until I try to start the server:

Code: Select all

omero@ubuntu:~/apps/OMERO$ omero admin start
Creating /home/omero/apps/OMERO/OMERO.server/var/master
Creating /home/omero/apps/OMERO/OMERO.server/var/registry
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................
Failed to startup some components after 5 minutes
Calling "stop" on remaining components
Waiting on shutdown. Use CTRL-C to exit

I just used default values from the tutorial as this was just a test. I have verified that these are correct.

Code: Select all

omero.data.dir=/home/omero/apps/OMERO/OMERO.data
omero.db.name=omerodb
omero.db.pass=omeropass
omero.db.user=omerouser

master.err suggests it's a Blitz error:

Code: Select all

05/02/12 15:33:07.939 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
05/02/12 15:33:07.943 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'

Blitz-0.log:

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2012-05-02 15:32:39,351 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2012-05-02 15:32:46,822 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2012-05-02 15:33:06,590 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2012-05-02 15:33:07,208 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Shutting down EHCache CacheManager
2012-05-02 15:33:07,209 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/omero/apps/OMERO/OMERO.server-Beta-4.3.4/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/omero/apps/OMERO/OMERO.server-Beta-4.3.4/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
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:409)
   at ome.system.OmeroContext.getInstance(OmeroContext.java:203)
   at ome.services.blitz.Entry.start(Entry.java:196)
   at ome.services.blitz.Entry.main(Entry.java:114)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/home/omero/apps/OMERO/OMERO.server-Beta-4.3.4/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/omero/apps/OMERO/OMERO.server-Beta-4.3.4/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
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
   at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:586)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
   at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048)
   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:/home/omero/apps/OMERO/OMERO.server-Beta-4.3.4/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
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:281)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
   ... 16 more
Caused by: 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
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:141)
   at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:107)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:273)
   ... 25 more
Caused by: 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
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1308)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1067)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:562)
   at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:871)
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:423)
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:105)
   at ome.system.OmeroContext.<init>(OmeroContext.java:98)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126)
   ... 27 more
Caused by: 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
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
   at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:600)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
   ... 47 more
Caused by: 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
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
   at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:600)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
   ... 59 more
Caused by: 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
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1403)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
   ... 71 more
Caused by: org.hibernate.HibernateException: could not init listeners
   at org.hibernate.event.EventListeners.initializeListeners(EventListeners.java:205)
   at org.hibernate.cfg.Configuration.getInitializedEventListeners(Configuration.java:1396)
   at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1385)
   at org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:954)
   at org.springframework.orm.hibernate3.LocalSessionFactoryBean.newSessionFactory(LocalSessionFactoryBean.java:855)
   at org.springframework.orm.hibernate3.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:774)
   at org.springframework.orm.hibernate3.AbstractSessionFactoryBean.afterPropertiesSet(AbstractSessionFactoryBean.java:211)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1460)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400)
   ... 78 more
Caused by: org.hibernate.search.SearchException: Unable to initialize: FullText
   at org.hibernate.search.store.DirectoryProviderFactory.createDirectoryProvider(DirectoryProviderFactory.java:132)
   at org.hibernate.search.store.DirectoryProviderFactory.createDirectoryProviders(DirectoryProviderFactory.java:63)
   at org.hibernate.search.impl.SearchFactoryImpl.initDocumentBuilders(SearchFactoryImpl.java:404)
   at org.hibernate.search.impl.SearchFactoryImpl.<init>(SearchFactoryImpl.java:119)
   at org.hibernate.search.event.ContextHolder.getOrBuildSearchFactory(ContextHolder.java:30)
   at org.hibernate.search.event.FullTextIndexEventListener.initialize(FullTextIndexEventListener.java:79)
   at org.hibernate.event.EventListeners$1.processListener(EventListeners.java:198)
   at org.hibernate.event.EventListeners.processListeners(EventListeners.java:181)
   at org.hibernate.event.EventListeners.initializeListeners(EventListeners.java:194)
   ... 86 more
Caused by: org.hibernate.search.SearchException: Unable to initialize index: FullText
   at org.hibernate.search.store.FSDirectoryProvider.initialize(FSDirectoryProvider.java:47)
   at org.hibernate.search.store.DirectoryProviderFactory.createDirectoryProvider(DirectoryProviderFactory.java:129)
   ... 94 more
Caused by: org.apache.lucene.index.CorruptIndexException: failed to locate current segments_N file
   at org.apache.lucene.index.IndexFileDeleter.<init>(IndexFileDeleter.java:214)
   at org.apache.lucene.index.IndexWriter.init(IndexWriter.java:1109)
   at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:686)
   at org.hibernate.search.store.DirectoryProviderHelper.createFSIndex(DirectoryProviderHelper.java:81)
   at org.hibernate.search.store.FSDirectoryProvider.initialize(FSDirectoryProvider.java:44)
   ... 95 more


I'd say I'd made a mistake, but I actually initially tried this on an old ubuntu installation I had lying around and got exactly the same problem which is what made me restart from scratch with 10.0.4LTS. So this is the second time with the same result.

I did some googling but didn't find any of the exact same problems, but just for the record: I'm not using NFS to mount the data directory, or at all. This is actually a Virtual Machine running in VMWare. The only installed java on the machine is sun-java6-jdk.

I attach an archive of the logs from the failed startup.

Thanks.

EDIT: This is similar: https://gist.github.com/1036306. Sadly I can't find any context or discussion about that gist.

[jmoore]

Have you tried stopping and restarting the server? The issue is that Lucene has attempted from multiple processes to grab control of the /OMERO/FullText directory. This is an issue that appears periodically during first starts based on the speed of the FS. If after a restart it occurs again, we will need to look more closely.

Sorry for the inconvenience.
~Josh

[jxpasto]

Yeah, I read thought it might be that as I read it wasn't threadsafe.

I've tried doing "omero admin start" again, and you're right, I didn't get the same error, however, the end result is the same, looks like it can't initialise the Ice component. I removed the log files and ran "omero admin start" so I attach data for the latest startup. It's less clear to me this time what is causing the problem.

Attached in Logs2.tar.gz

[jmoore]

The Blitz.log looks like the server is still starting. Could you look at the latest, and possibly attach the output from bin/omero admin diagnostics?

Thanks,
~Josh

[jxpasto]

The Blitz.log looks like the server is still starting. Could you look at the latest, and possibly attach the output from bin/omero admin diagnostics?

Thanks,
~Josh

Sorry, look at the latest what?

Code: Select all

omero@ubuntu:~/apps/OMERO/OMERO.server/var/log$ omero admin diagnostics

================================================================================
OMERO Diagnostics 4.3.4-dbcbce5a-b4
================================================================================
       
Commands:   java -version                  1.6.0     (/usr/bin/java)
Commands:   python -V                      2.6.5     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 8.4.11    (/usr/bin/psql -- 2 others)

Server:     icegridnode                    not started

Log dir:    /home/omero/apps/OMERO/OMERO.server/var/log exists

Log files:  Blitz-0.log                    2.0 KB       
Log files:  DropBox.log                    2.0 KB        errors=4    warnings=2   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  7.0 KB        errors=6    warnings=4   
Log files:  MonitorServer.log              0.0 KB       
Log files:  OMEROweb.log                   0.0 KB       
Log files:  PixelData-0.log                1.0 KB       
Log files:  Processor-0.log                22.0 KB       errors=6    warnings=42 
Log files:  Tables-0.log                   23.0 KB       errors=6    warnings=42 
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.06 MB


Environment:OMERO_HOME=/home/omero/apps/OMERO/OMERO.server
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/lib/jvm/java-6-sun/bin:/usr/share/Ice-3.3.1:/usr/lib/postgresql/8.4/bin:/home/omero/apps/OMERO/OMERO.server/bin
Environment:ICE_HOME=/usr/share/Ice-3.3.1 
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=(unset)     

OMERO data dir: '/home/omero/apps/OMERO/OMERO.data'   Exists? True   Is writable? True
OMERO.web status... [NOT STARTED]

[jxpasto]

Ok, I've done some more experimentation. The server is starting up fine now and all I did was restart the virtual machine. However, it was running like an absolute dog so I upped it's RAM allocation from 512MB to 2GB and it seems much happier. Perhaps having to use swap was causing it some major problems with timing somehow.

I still have some errors in my logs and I'd like to make sure that these aren't going to cause major problems down the line.

Code: Select all

05/03/12 03:37:02.860 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
05/03/12 03:37:02.862 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'

and

Code: Select all

2012-05-03 03:36:07,946 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2012-05-03 03:36:07,947 INFO  [                       omero.util.Server] (MainThread) Starting
2012-05-03 03:36:07,954 INFO  [                    omero.util.Resources] (Thread-2  ) Starting
2012-05-03 03:37:02,859 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 1
2012-05-03 03:37:12,865 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 2
2012-05-03 03:37:23,039 INFO  [              omero.processor.ProcessorI] (MainThread) Registering processor Processor -t @ Processor-0.ProcessorAdapter
2012-05-03 03:37:23,080 INFO  [                       omero.util.Server] (MainThread) Entering main loop

This second one looks simply like some components expected another to be ready when it wasn't yet, merely causing a retry and no harm done. Correct?

Thanks for the help so far!

[jmoore]

...
This second one looks simply like some components expected another to be ready when it wasn't yet, merely causing a retry and no harm done. Correct?

That's exactly what happened. You should be ready to go now.

Thanks for the help so far!

Gladly. ~J.