[ome-users] OMERO 4.4.9 won't start after upgrade from 4.4.5
Rainer Poehlmann
rainer.poehlmann at unibas.ch
Tue Nov 5 09:11:13 GMT 2013
To whom it may concern,
I upgraded OMERO as described on the Server Upgrade page.
OLD Version: OMERO.server-4.4.5-ice34-b20
NEW version: OMERO.server-4.4.9-ice35-b98
Consequently, ice was also upgraded to "3.5.1-1" using RHEL6 RPM
packages as available at "http://www.zeroc.com/download/Ice/3.5"
When trying to start up the new 4.4.9 version the following error is
seen in the various log files:
DropBox.log:
NoEndpointException: exception ::Ice::NoEndpointException
Processor-0.log:
2013-11-05 09:29:43,668 INFO [ omero.utils]
(MainThread) Failed to get session on attempt 6
2013-11-05 09:29:53,669 WARNI [ omero.utils]
(MainThread) Reason: exception ::Ice::NoEndpointException
Tables-0.log:
File
"/home/omeronas/OMERO.server-4.4.9-ice35-b98/lib/python/omero/util/__init__.py",
line 193, in internal_service_factory
raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
master.err:
-! 11/05/13 09:25:19.666 OMERO.Glacier2: warning: unable to contact
session manager `BlitzManager at BlitzAdapters'
Reference.cpp:1663: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @
BlitzAdapters'
bin/omero admin diagnostics output:
================================================================================
OMERO Diagnostics 4.4.9-ice35-b98
================================================================================
Commands: java -version 1.7.0
(/usr/java/latest/bin/java -- 3 others)
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 9.2.4 (/usr/pgsql-9.2/bin/psql)
Server: icegridnode not started
Cannot list deployed applications.
Log dir: /home/omeronas/OMERO.server/var/log exists
Log files: Blitz-0.log 125.0 MB errors=68
warnings=262
Log files: Blitz-0.log.1 512.0 MB errors=170
warnings=2641
Log files: Blitz-0.log.2 512.0 MB errors=144
warnings=155
Log files: Blitz-0.log.3 512.0 MB errors=155
warnings=428
Log files: Blitz-0.log.4 512.0 MB errors=224
warnings=681
Log files: Blitz-0.log.5 512.0 MB errors=90
warnings=247
Log files: Blitz-0.log.6 512.0 MB errors=66
warnings=449
Log files: Blitz-0.log.7 512.0 MB errors=68
warnings=51
Log files: Blitz-0.log.8 512.0 MB errors=129
warnings=91
Log files: Blitz-0.log.9 512.0 MB errors=133
warnings=972
Log files: DropBox.log 69.0 KB errors=6
warnings=28
Log files: FileServer.log 9.0 KB
Log files: Indexer-0.log 241.0 MB errors=35839
warnings=8715
Log files: MonitorServer.log 35.0 KB
Log files: OMEROweb.log 1.0 MB errors=5
warnings=10
Log files: OMEROweb.log.1 0.0 KB
Log files: OMEROweb.log.2 0.0 KB
Log files: OMEROweb.log.3 0.0 KB
Log files: OMEROweb.log.4 0.0 KB
Log files: OMEROweb.log.5 0.0 KB
Log files: OMEROweb_request.log 43.0 KB errors=13
warnings=230
Log files: PixelData-0.log 198.0 KB errors=41
warnings=79
Log files: Processor-0.log 934.0 KB errors=196
warnings=1315
Log files: Processor-0.log.1 4.0 MB errors=170
warnings=1370
Log files: Processor-0.log.2 4.0 MB errors=3 warnings=0
Log files: Processor-0.log.3 4.0 MB errors=1 warnings=0
Log files: Processor-0.log.4 4.0 MB errors=10
warnings=2
Log files: Processor-0.log.5 4.0 MB
Log files: Processor-0.log.6 4.0 MB errors=1 warnings=0
Log files: Processor-0.log.7 4.0 MB
Log files: Processor-0.log.8 4.0 MB errors=1 warnings=0
Log files: Processor-0.log.9 4.0 MB errors=4 warnings=0
Log files: Tables-0.log 93.0 KB errors=26
warnings=31
Log files: TestDropBox.log n/a
Log files: master.err 486.0 KB errors=1819
warnings=37
Log files: master.out 0.0 KB
Log files: Total size 5023.22 MB
Parsing Blitz-0.log:[line:853012] => Server restarted <=
Parsing Blitz-0.log:[line:853269] => Server restarted <=
Parsing Blitz-0.log:[line:853526] => Server restarted <=
Environment:OMERO_HOME=/home/omeronas/OMERO.server
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=/export02/omeronas/tmp
Environment:PATH=/usr/java/latest/bin:/usr/java/jdk1.7.0_09/bin:/usr/java/jre1.7.0_09/bin:/usr/bin/bin:/usr/pgsql-9.2/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/omeronas/bin
Environment:ICE_HOME=/usr/bin
Environment:LD_LIBRARY_PATH=/usr/java/jdk1.7.0_09/lib:/usr/lib64:/usr/pgsql-9.2/lib:
Environment:DYLD_LIBRARY_PATH=/usr/javajdk1.7.0_09/lib:/usr/lib64:/usr/pgsql-9.2/lib:
OMERO data dir: '/export/omero/OMERO/' Exists? True Is writable? True
OMERO temp dir: '/export02/omeronas/tmp/omero/tmp' Exists? True Is
writable? True (Size: 0)
OMERO.web status... [NOT STARTED]
OS: CentOS release 6.4 (Final)
Python 2.6.6
java version "1.7.0_09"
Java(TM) SE Runtime Environment (build 1.7.0_09-b05)
Java HotSpot(TM) 64-Bit Server VM (build 23.5-b02, mixed mode)
Any help would be appreciated.
Best,
-Rainer
P.S.: I now reverted to the previously installed 4.4.5 version using
Ice-3.4.2-1 which worked out-of-the-box.
--
Rainer Pöhlmann
Research IT
Biozentrum Universität Basel &
Swiss Institute of Bioinformatics (SIB)
Klingelbergstr. 50-70, CH-4056 Basel, Switzerland
phone: +41-61-267 20 76 | fax: +41-61-267 15 85
web: http://www.biozentrum.unibas.ch/researchit
http://www.isb-sib.ch | http://www.bc2.ch
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