Open Microscopy Environment

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.

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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:

Code: Select all

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.

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

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

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

jmoore wrote: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]

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!

jxpasto wrote:...
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.