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 :
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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 :
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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
