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OMERO server don't restart (Solved)

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The OMERO.server installation documentation begins here and you can find OMERO.web deployment documentation here.

OMERO server don't restart (Solved)

Postby phm » Tue Apr 21, 2015 8:16 am

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 :

Code: Select all
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 :
Code: Select all

================================================================================
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 :
Code: Select all
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
phm
 
Posts: 185
Joined: Tue Mar 19, 2013 3:39 pm

Re: OMERO server don't restart (Solved)

Postby jmoore » Tue Apr 21, 2015 10:17 am

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

~Josh.
User avatar
jmoore
Site Admin
 
Posts: 1591
Joined: Fri May 22, 2009 1:29 pm
Location: Germany

Re: OMERO server don't restart (Solved)

Postby phm » Tue Apr 21, 2015 12:19 pm

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
phm
 
Posts: 185
Joined: Tue Mar 19, 2013 3:39 pm


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