- Code: Select all
...
Server: Tables-0 inactive (disabled)
...
We'd need to see the contents of var/log/Tables-0.log to know what's up.
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Server: Tables-0 inactive (disabled)
...
Traceback (most recent call last):
File "lib/python/runTables.py", line 15, in ?
import omero.tables
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 11, in ?
import numpy
ImportError: No module named numpy
03/21/12 15:56:35.428 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
03/21/12 15:56:35.429 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 15, in ?
import omero.tables
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 11, in ?
import numpy
ImportError: No module named numpy
03/21/12 16:02:23.121 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
03/21/12 16:02:23.123 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 15, in ?
import omero.tables
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 11, in ?
import numpy
ImportError: No module named numpy
03/22/12 16:41:33.071 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
03/22/12 16:41:33.078 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 15, in ?
import omero.tables
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 11, in ?
import numpy
ImportError: No module named numpy
3/22/12 17:05:26:627 warning: Blitz-0-Ice.ThreadPool.Server-3: dispatch exception:
identity: session-952364e2-fe7f-42c1-bb4a-6b8b94ef6caf/063660a7-2e31-4994-9ff0-96a0ab043e97
facet:
operation: destroy
Ice.ObjectAdapterDeactivatedException
name = "BlitzAdapter"
at Ice.ObjectAdapterI.checkForDeactivation(ObjectAdapterI.java:1028)
at Ice.ObjectAdapterI.findFacet(ObjectAdapterI.java:459)
at Ice.ObjectAdapterI.find(ObjectAdapterI.java:453)
at ome.services.blitz.impl.ServiceFactoryI.unregisterServant(ServiceFactoryI.java:1005)
at ome.services.blitz.impl.ServiceFactoryI.doDestroy(ServiceFactoryI.java:801)
at ome.services.blitz.impl.ServiceFactoryI.destroy(ServiceFactoryI.java:703)
at Glacier2._SessionDisp.___destroy(_SessionDisp.java:82)
at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1263)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
Traceback (most recent call last):
File "lib/python/runTables.py", line 15, in ?
import omero.tables
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 11, in ?
import numpy
ImportError: No module named numpy
Traceback (most recent call last):
File "lib/python/runTables.py", line 15, in ?
import omero.tables
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 35, in ?
tables = __import__("tables") # Pytables
File "/usr/lib64/python2.4/site-packages/tables/__init__.py", line 59, in ?
from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.7: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "lib/python/runTables.py", line 15, in ?
import omero.tables
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 11, in ?
import numpy
ImportError: No module named numpy
Traceback (most recent call last):
File "lib/python/runTables.py", line 15, in ?
import omero.tables
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/tables.py", line 35, in ?
tables = __import__("tables") # Pytables
File "/usr/lib64/python2.4/site-packages/tables/__init__.py", line 59, in ?
from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.7: cannot open shared object file: No such file or directory
>>> import tables
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib64/python2.4/site-packages/tables/__init__.py", line 59, in ?
from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.7: cannot open shared object file: No such file or directory
>>> import tables
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib64/python2.4/site-packages/tables/__init__.py", line 59, in ?
from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.7: cannot open shared object file: No such file or directory
python tables.py
No handlers could be found for logger "blitz_gateway"
True
Traceback (most recent call last):
File "tables.py", line 55, in ?
table.initialize(columns)
AttributeError: 'NoneType' object has no attribute 'initialize'
python tables.py
No handlers could be found for logger "blitz_gateway"
True
WARNING:blitz_gateway:ValidationException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <d1d99b2f-2541-4eef-9977-40fabef4a998omero.api.IUpdate> saveAndReturnObject((object #0 (::omero::model::DatasetAnnotationLink)
{
_id = <nil>
_details = object #1 (::omero::model::Details)
{
_owner = <nil>
_group = <nil>
_creationEvent = <nil>
_updateEvent = <nil>
_permissions = <nil>
_externalInfo = <nil>
}
_loaded = True
_version = <nil>
_parent = object #2 (::omero::model::Dataset)
{
_id = object #3 (::omero::RLong)
{
_val = 33
}
_details = <nil>
_loaded = False
_version = <nil>
_projectLinksSeq = {}
_projectLinksLoaded = False
_projectLinksCountPerOwner = {}
_imageLinksSeq = {}
_imageLinksLoaded = False
_imageLinksCountPerOwner = {}
_annotationLinksSeq = {}
_annotationLinksLoaded = False
_annotationLinksCountPerOwner = {}
_name = <nil>
_description = <nil>
}
_child = object #4 (::omero::model::FileAnnotation)
{
_id = object #5 (::omero::RLong)
{
_val = 51
}
_details = <nil>
_loaded = False
_version = <nil>
_ns = <nil>
_description = <nil>
_annotationLinksSeq = {}
_annotationLinksLoaded = False
_annotationLinksCountPerOwner = {}
_file = <nil>
}
},), {})
Traceback (most recent call last):
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/gateway/__init__.py", line 2956, in __call__
return self.f(*args, **kwargs)
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero_api_IUpdate_ice.py", line 97, in saveAndReturnObject
return _M_omero.api.IUpdate._op_saveAndReturnObject.invoke(self, ((obj, ), _ctx))
ValidationException: exception ::omero::ValidationException
{
serverStackTrace = ome.conditions.ValidationException: No row with the given identifier exists: [ome.model.containers.Dataset#33]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#33]
at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:663)
at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy77.saveAndReturnObject(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy77.saveAndReturnObject(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:136)
at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:64)
at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92)
at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:185)
at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:365)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
serverExceptionClass = ome.conditions.ValidationException
message = No row with the given identifier exists: [ome.model.containers.Dataset#33]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#33]
}
Traceback (most recent call last):
File "tables.py", line 82, in ?
conn.getUpdateService().saveAndReturnObject(link)
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/gateway/__init__.py", line 2959, in __call__
return self.handle_exception(e, *args, **kwargs)
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero/gateway/__init__.py", line 2956, in __call__
return self.f(*args, **kwargs)
File "/data/applications/OMERO.server-Beta-4.3.4/lib/python/omero_api_IUpdate_ice.py", line 97, in saveAndReturnObject
return _M_omero.api.IUpdate._op_saveAndReturnObject.invoke(self, ((obj, ), _ctx))
omero.ValidationException: exception ::omero::ValidationException
{
serverStackTrace = ome.conditions.ValidationException: No row with the given identifier exists: [ome.model.containers.Dataset#33]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#33]
at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:663)
at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy77.saveAndReturnObject(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy77.saveAndReturnObject(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:136)
at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:64)
at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92)
at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:185)
at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:365)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
serverExceptionClass = ome.conditions.ValidationException
message = No row with the given identifier exists: [ome.model.containers.Dataset#33]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#33]
}
bin/omero admin restart
/omero admin diagnostics
================================================================================
OMERO Diagnostics 4.3.4-dbcbce5a-b4
================================================================================
Commands: java -version 1.6.0 (/data/applications/jdk1.6.0_31/bin/java -- 2 others)
Commands: python -V 2.4.3 (/usr/bin/python)
Commands: icegridnode --version 3.3.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.3.1 (/usr/bin/icegridadmin)
Commands: psql --version 9.1.3 (/usr/bin/psql)
Server: icegridnode running
Server: Blitz-0 active (pid = 13382, enabled)
Server: DropBox active (pid = 13408, enabled)
Server: FileServer active (pid = 13410, enabled)
Server: Indexer-0 active (pid = 13415, enabled)
Server: MonitorServer active (pid = 13432, enabled)
Server: OMERO.Glacier2 active (pid = 13417, enabled)
Server: OMERO.IceStorm active (pid = 13419, enabled)
Server: PixelData-0 active (pid = 13424, enabled)
Server: Processor-0 active (pid = 13420, enabled)
Server: Tables-0 active (pid = 13446, enabled)
Server: TestDropBox inactive (enabled)
Log dir: /data/applications/OMERO.server-Beta-4.3.4/var/log exists
Log files: Blitz-0.log 241.0 MB errors=30 warnings=25
Log files: DropBox.log 15.0 KB errors=8 warnings=6
Log files: FileServer.log 2.0 KB
Log files: Indexer-0.log 230.0 KB errors=6 warnings=9
Log files: MonitorServer.log 9.0 KB errors=5 warnings=1
Log files: OMEROweb.log 176.0 KB errors=348 warnings=0
Log files: PixelData-0.log 154.0 KB errors=6 warnings=9
Log files: Processor-0.log 1.0 MB errors=0 warnings=3
Log files: Processor-0.log.1 4.0 MB
Log files: Processor-0.log.2 4.0 MB
Log files: Processor-0.log.3 4.0 MB
Log files: Processor-0.log.4 4.0 MB
Log files: Processor-0.log.5 4.0 MB
Log files: Processor-0.log.6 4.0 MB
Log files: Processor-0.log.7 4.0 MB
Log files: Processor-0.log.8 4.0 MB errors=1467 warnings=8805
Log files: Tables-0.log 3.0 KB
Log files: TestDropBox.log n/a
Log files: master.err 7.0 KB
Log files: master.out 0.0 KB
Log files: Total size 283.62 MB
Parsing Blitz-0.log:[line:863] => Server restarted <=
Parsing Blitz-0.log:[line:2047] => Server restarted <=
Parsing Blitz-0.log:[line:1534950] => Server restarted <=
Parsing Blitz-0.log:[line:1568218] => Server restarted <=
Parsing Blitz-0.log:[line:1569073] => Server restarted <=
Parsing Blitz-0.log:[line:1571086] => Server restarted <=
Environment:OMERO_HOME=/data/applications/OMERO.server-Beta-4.3.4
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/data/applications/jdk1.6.0_31/bin:/usr/share/Ice-3.3.1/bin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/data/applications/jdk1.6.0_31/bin:/usr/share/Ice-3.3.1/bin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/data/applications/jdk1.6.0_31/bin:/usr/share/Ice-3.3.1/bin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/data/applications/jdk1.6.0_31/bin:/usr/share/Ice-3.3.1/bin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/data/applications/jdk1.6.0_31/bin:/usr/share/Ice-3.3.1/bin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/data/applications/jdk1.6.0_31/bin:/usr/share/Ice-3.3.1/bin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/data/oracle/product/11g/db_1/bin:/usr/sbin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/data/applications/apache-ant-1.8.3/bin:/data/applications/jdk1.6.0_31/bin:/root/bin:/data/applications/hdf5-1.8.8/bin:/data/applications/hdf5-1.8.8/bin:/data/applications/hdf5-1.8.8/bin:/data/applications/hdf5-1.8.8/bin:/data/applications/hdf5-1.8.8/bin:/data/applications/hdf5-1.8.8/bin
Environment:ICE_HOME=/usr/share/Ice-3.3.1
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:/usr/local/lib:/usr/local/hdf5/lib/
Environment:DYLD_LIBRARY_PATH=/usr/share/java:/usr/lib/:/usr/share/java:/usr/lib/:/usr/share/java:/usr/lib/:/usr/share/java:/usr/lib/:/usr/share/java:/usr/lib/:
OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO.web status... [RUNNING] (PID 27118)
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