Open Microscopy Environment

Solved !!!!
It was a bad mail-senders.xml file !!!!

Sorry


Hi,
Again ...

After reboot of the sever (due to electrical maintenance) the omero server fail to start. After a long time to try to start I get this message :

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omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................
Failed to startup some components after 300 seconds
Calling "stop" on remaining components
Waiting on shutdown. Use CTRL-C to exit


omero confug get :

Code: Select all

omero.data.dir=/OMERO
omero.db.name=omero_database
omero.db.pass=******************
omero.db.user=db_omero
omero.jvmcfg.percent.blitz=20
omero.jvmcfg.system_memory=32000
omero.mail.config=true
omero.mail.host=smtp.college-de-france.fr
omero.mail.password=*******************
omero.mail.port=25
omero.mail.username=philippe.mailly@college-de-france.fr
omero.web.admins=[["Philippe Mailly", "philippe.mailly@college-de-france.fr"]]
omero.web.apps=["figure", "figure"]
omero.web.debug=False
omero.web.login_logo=/omero/static/webclient/image/logo_CIRB.jpg
omero.web.prefix=/omero
omero.web.public.enabled=False
omero.web.static_url=/omero/static/
omero.web.ui.top_links=[["Data", "webindex", {"title": "Browse Data via Projects, Tags etc"}], ["History", "history", {"title": "History"}], ["Help", "http://help.openmicroscopy.org/", {"target": "new", "title": "Open OMERO user guide in a new tab"}], ["Figure", "figure_index", {"title": "Fast figures from your OMERO images"}]]



omero admin diagnostics :

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================================================================================
OMERO Diagnostics 5.1.0-ice35-b40
================================================================================
       
Commands:   java -version                  1.7.0     (/usr/bin/java)
Commands:   python -V                      2.6.6     (/usr/bin/python)
Commands:   icegridnode --version          3.5.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.3.6     (/usr/pgsql-9.3/bin/psql -- 2 others)

Server:     icegridnode                    not started

Log dir:    /opt/OMERO.server/var/log      exists

Log files:  Blitz-0.log                    27.0 MB       errors=41   warnings=743
Log files:  DropBox.log                    22.0 KB       errors=8    warnings=10 
Log files:  FileServer.log                 3.0 KB       
Log files:  Indexer-0.log                  229.0 KB      errors=37   warnings=0   
Log files:  MonitorServer.log              10.0 KB     
Log files:  OMEROweb.log                   63.0 KB       errors=4    warnings=0   
Log files:  OMEROweb_request.log           0.0 KB       
Log files:  PixelData-0.log                120.0 KB      errors=33   warnings=0   
Log files:  Processor-0.log                71.0 KB       errors=32   warnings=20 
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     10.0 KB       errors=11   warnings=10 
Log files:  master.out                     0.0 KB       
Log files:  Total size                     28.37 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_TEMPDIR=/tmp             
Environment:PATH=/usr/pgsql-9.3/bin/:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/dell/srvadmin/bin:/opt/OMERO.server/bin:/opt/dell/srvadmin/sbin:/usr/java/latest/bin
Environment:PYTHONPATH=(unset)             
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)     

Cannot list deployed applications.
OMERO data dir:'/OMERO'                       Exists? True   Is writable? True
OMERO temp dir:'/tmp/omero/tmp'               Exists? True   Is writable? True   (Size: 0)

JVM settings: Blitz                         -Xmx6400m -XX:MaxPermSize=1g # Settings({'system_memory': '32000', 'percent': '20'})
JVM settings: Indexer                       -Xmx3200m -XX:MaxPermSize=1g # Settings({'system_memory': '32000'})
JVM settings: Pixeldata                     -Xmx4800m -XX:MaxPermSize=1g # Settings({'system_memory': '32000'})
JVM settings: Repository                    -Xmx3200m -XX:MaxPermSize=1g # Settings({'system_memory': '32000'})

OMERO.web status... [RUNNING] (PID 7724)



And Blitz.log :

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at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.parsers.DOMParser.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.springframework.beans.factory.xml.DefaultDocumentLoader.loadDocument(DefaultDocumentLoader.java:75) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:388) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 46 common frames omitted
[omero@omero ~]$ tail -n 50 /opt/OMERO.server/var/log/Blitz-0.log
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 16 common frames omitted
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 56 in XML document from file [/opt/OMERO.server-5.1.0-ice35-b40/etc/blitz/mail-senders.xml] is invalid; nested exception is org.xml.sax.SAXParseException; lineNumber: 56; columnNumber: 11; The string "--" is not permitted within comments.
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:141) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:107) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:273) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 25 common frames omitted
Caused by: org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 56 in XML document from file [/opt/OMERO.server-5.1.0-ice35-b40/etc/blitz/mail-senders.xml] is invalid; nested exception is org.xml.sax.SAXParseException; lineNumber: 56; columnNumber: 11; The string "--" is not permitted within comments.
   at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:396) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:334) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:302) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:143) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:178) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:149) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:212) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractXmlApplicationContext.loadBeanDefinitions(AbstractXmlApplicationContext.java:126) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractXmlApplicationContext.loadBeanDefinitions(AbstractXmlApplicationContext.java:92) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:130) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.obtainFreshBeanFactory(AbstractApplicationContext.java:465) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:395) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:105) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at ome.system.OmeroContext.<init>(OmeroContext.java:98) ~[common.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_67]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_67]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_67]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:526) ~[na:1.7.0_67]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 27 common frames omitted
Caused by: org.xml.sax.SAXParseException: The string "--" is not permitted within comments.
   at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.impl.XMLScanner.scanComment(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanComment(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.parsers.DOMParser.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source) ~[xercesImpl.jar:na]
   at org.springframework.beans.factory.xml.DefaultDocumentLoader.loadDocument(DefaultDocumentLoader.java:75) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:388) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 46 common frames omitted


Master.err :

Code: Select all

from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory
-! 04/21/15 09:34:46.782 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
   Reference.cpp:1663: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters'
-! 04/21/15 09:34:46.782 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
   Reference.cpp:1663: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters'
Traceback (most recent call last):
  File "lib/python/runTables.py", line 15, in <module>
    import omero.tables
  File "/opt/OMERO.server-5.1.0-ice35-b40/lib/python/omero/tables.py", line 32, in <module>
    tables = __import__("tables")  # Pytables
  File "/usr/lib64/python2.6/site-packages/tables/__init__.py", line 30, in <module>
    from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory
-! 04/21/15 09:39:54.634 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
   Reference.cpp:1663: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters'
-! 04/21/15 09:39:54.634 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
   Reference.cpp:1663: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters'
Traceback (most recent call last):
  File "lib/python/runTables.py", line 15, in <module>
    import omero.tables
  File "/opt/OMERO.server-5.1.0-ice35-b40/lib/python/omero/tables.py", line 32, in <module>
    tables = __import__("tables")  # Pytables
  File "/usr/lib64/python2.6/site-packages/tables/__init__.py", line 30, in <module>
    from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory
-! 04/21/15 09:51:53.711 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
   Reference.cpp:1663: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters'
-! 04/21/15 09:51:53.712 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
   Reference.cpp:1663: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters'
Traceback (most recent call last):
  File "lib/python/runTables.py", line 15, in <module>
    import omero.tables
  File "/opt/OMERO.server-5.1.0-ice35-b40/lib/python/omero/tables.py", line 32, in <module>
    tables = __import__("tables")  # Pytables
  File "/usr/lib64/python2.6/site-packages/tables/__init__.py", line 30, in <module>
    from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory
-! 04/21/15 10:01:57.410 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
   Reference.cpp:1663: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters'
-! 04/21/15 10:01:57.411 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
   Reference.cpp:1663: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters'



Philippe

Thanks for the update, Philippe. Do let us know if there's anything you would change/improve in the new mail config.

~Josh.

jmoore wrote:Thanks for the update, Philippe. Do let us know if there's anything you would change/improve in the new mail config.

~Josh.

Hi Josh,

For the email config no, but as I said in the previous topic something to known if a user is connected or transfer files. For example, in the Web admin interface something like "Who is online" and on the statistics tab is some active transfers.

Cheers,


Philippe