[ome-users] Omero 4.4.9 to 5.0.0 RC1 upgrade - Error connecting to database table dbpatch
Paulo Almeida
palmeida at igc.gulbenkian.pt
Thu Jan 9 15:58:48 GMT 2014
Hi,
I just upgraded to Omero 5.0.0 and apparently it went well, but the
server failed to restart, with exceptions in Blitz-0.log and the
following message:
Error connecting to database table dbpatch. You may need to bootstrap.
I did run the database script and the dbpatch table exists, with this as
the second and last entry (result of "SELECT * from db_patch"):
2 | 0 | OMERO5.0 | -52 | 2014-01-09
13:51:28.813421 | Database updated. | 0 | OMERO4.4 |
I was using Java 6, but I saw an old Omero bug report mentioning a
similar message with this version of Java, so I tried upgrading to 7.
Nothing changed though. This is the bug report:
http://trac.openmicroscopy.org.uk/ome/ticket/1269
It's very old and the only thing in common is the message about not
being able to connect to dbpatch, so I don't know if it's relevant.
I'm attaching the output of bin/omero admin diagnostics, as well as
Blitz-0.log and master.err , in case it helps diagnosing.
Thanks,
Paulo Almeida
Instituto Gulbenkian de Ciência
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Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/opt/omero/OMERO.server-5.0.0-rc1-ice34-b10/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 01/09/14 13:55:06.634 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 01/09/14 13:55:06.646 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/opt/omero/OMERO.server-5.0.0-rc1-ice34-b10/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 01/09/14 14:08:46.296 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 01/09/14 14:08:46.300 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/opt/omero/OMERO.server-5.0.0-rc1-ice34-b10/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 01/09/14 14:17:02.979 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 01/09/14 14:17:02.986 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/opt/omero/OMERO.server-5.0.0-rc1-ice34-b10/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 01/09/14 14:25:49.498 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 01/09/14 14:25:49.503 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/opt/omero/OMERO.server-5.0.0-rc1-ice34-b10/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 01/09/14 14:49:44.380 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 01/09/14 14:49:44.386 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/opt/omero/OMERO.server-5.0.0-rc1-ice34-b10/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 01/09/14 15:14:06.986 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 01/09/14 15:14:06.992 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/opt/omero/OMERO.server-5.0.0-rc1-ice34-b10/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 01/09/14 15:29:49.517 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 01/09/14 15:29:49.528 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/opt/omero/OMERO.server-5.0.0-rc1-ice34-b10/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 01/09/14 15:34:16.424 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 01/09/14 15:34:16.432 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1566: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
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================================================================================
OMERO Diagnostics 5.0.0-rc1-ice34-b10
================================================================================
Commands: java -version 1.7.0 (/usr/bin/java -- 2 others)
Commands: python -V 2.7.3 (/usr/bin/python)
Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin)
Commands: psql --version 9.1.11 (/usr/bin/psql -- 2 others)
Server: icegridnode running
Server: Blitz-0 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 7311, enabled)
Server: Indexer-0 inactive (disabled)
Server: MonitorServer active (pid = 7297, enabled)
Server: OMERO.Glacier2 active (pid = 7305, enabled)
Server: OMERO.IceStorm active (pid = 7307, enabled)
Server: PixelData-0 inactive (disabled)
Server: Processor-0 activating (enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
OMERO: SSL port 4064
OMERO: TCP port 4063
Log dir: /opt/omero/OMERO.server/var/log exists
Log files: Blitz-0.log 434.0 KB errors=208 warnings=0
Log files: DropBox.log 11.0 KB errors=16 warnings=8
Log files: FileServer.log 2.0 KB
Log files: Indexer-0.log 428.0 KB errors=280 warnings=0
Log files: MonitorServer.log 3.0 KB
Log files: OMEROweb.log n/a
Log files: PixelData-0.log 428.0 KB errors=280 warnings=0
Log files: Processor-0.log 225.0 KB errors=126 warnings=63
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 6.0 KB errors=8 warnings=16
Log files: master.out 0.0 KB
Log files: Total size 1.54 MB
Environment:OMERO_HOME=/opt/omero/OMERO.server
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/java-6-sun/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.1/bin:/opt/omero/OMERO.server/bin
Environment:ICE_HOME=/usr/share/Ice-3.4.2
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=/usr/share/java:/usr/lib:
OMERO data dir: '/afs/igc.gulbenkian.pt/folders/UBI/SERVICES/OMERO/binary-repository' Exists? True Is writable? True
OMERO temp dir: '/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
OMERO.web status... [NOT STARTED]
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