Hi Simon,
I repeated the relevant steps for the install procedure according to the manual you send me.
Since everything was already in place and running with OMERO 5.0.2/Ice-3.4.1, in fact I only
switched the OMERO version from
OMERO.server-5.0.2-ice34-b26 to
OMERO.server-5.0.2-ice35-b26.
For the required Ice-3.4 to Ice-3.5 switch, I this time used the ICE repo as discribed in
https://www.openmicroscopy.org/site/sup ... centos6.shIn previous attempts, I've downloaded the "http://www.zeroc.com/download/Ice/3.5/Ice-3.5.1-el6-x86_64-rpm.tar.gz" bundled RPM's and installed them manually.
So, the complete Ice upgrade procedure I performed looks as follows:
1) Remove Ice-3.4 and db48 packages
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rpm -qa | grep ice- | grep "3.4.2-1"
yum remove ice-python-3.4.2-1.rhel6.x86_64 ice-libs-3.4.2-1.rhel6.x86_64 ice-c++-devel-3.4.2-1.rhel6.x86_64 ice-utils-3.4.2-1.rhel6.x86_64 ice-java-devel-3.4.2-1.rhel6.x86_64 ice-servers-3.4.2-1.rhel6.x86_64 ice-python-devel-3.4.2-1.rhel6.x86_64 ice-3.4.2-1.rhel6.noarch ice-sqldb-3.4.2-1.rhel6.x86_64 ice-java-3.4.2-1.rhel6.noarch
rpm -qa | grep db48
yum remove db48-4.8.30-1ice.rhel6.x86_64 db48-utils-4.8.30-1ice.rhel6.x86_64 db48-java-4.8.30-1ice.rhel6.x86_64
2) Install Ice-3.5 using the Ice repo
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curl -o /etc/yum.repos.d/zeroc-ice-el6.repo http://download.zeroc.com/Ice/3.5/el6/zeroc-ice-el6.repo
yum install ice ice-python ice-servers
3) all other dependencies as described there (java-1.70ioenjdk) including the python/hdf5/etc stuff already existed from my previous OMERO Ice-3.4 install.
Output of
omero admin diagnostics:
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[omeronas@bc2-omerodev01 bin]$ ./omero admin diagnostics
================================================================================
OMERO Diagnostics 5.0.2-ice35-b26
================================================================================
Commands: java -version 1.7.0 (/usr/java/latest/bin/java -- 2 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 9.2.8 (/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 103.0 MB errors=85 warnings=2096
Log files: DropBox.log 21.0 KB errors=10 warnings=9
Log files: FileServer.log 3.0 KB
Log files: Indexer-0.log 8.0 MB errors=811 warnings=15810
Log files: MonitorServer.log 11.0 KB
Log files: OMEROweb.log 606.0 KB errors=1 warnings=66
Log files: OMEROweb_request.log 0.0 KB
Log files: PixelData-0.log 217.0 KB errors=89 warnings=25
Log files: Processor-0.log 107.0 KB errors=40 warnings=21
Log files: RP_Blitz-0.log 43.0 KB errors=8 warnings=0
Log files: RP_Processor-0.log 18.0 KB errors=10 warnings=5
Log files: Tables-0.log 82.0 KB errors=38 warnings=22
Log files: TestDropBox.log n/a
Log files: master.err 4.0 KB errors=21 warnings=11
Log files: master.out 0.0 KB
Log files: Total size 113.26 MB
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/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:PYTHONPATH=(unset)
Environment:ICE_HOME=/usr/share/Ice-3.4.2
Environment:LD_LIBRARY_PATH=/usr/java/jdk1.7.0_09/lib:/usr/lib64:/usr/pgsql-9.2/lib:
Environment:DYLD_LIBRARY_PATH=(unset)
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]
Output from
omero config get:
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[omeronas@bc2-omerodev01 bin]$ ./omero config get
omero.data.dir=/export/omero/OMERO/
omero.db.gist=localhost
omero.db.name=omerodb_dev
omero.db.pass=***************
omero.db.poolsize=80
omero.db.user=omerouser
omero.ldap.base=OU=BIOPZ,OU=Institutes,DC=unibasel,DC=ads,DC=unibas,DC=ch
omero.ldap.config=true
omero.ldap.password=************
omero.ldap.urls=ldap://unibasel.ads.unibas.ch:389
omero.ldap.user_mapping=omeName=sAMAccountName,firstName=givenName,lastName=sn,email=mail
omero.ldap.username=podldap@unibasel.ads.unibas.ch
omero.web.admins=[["Rainer Poehlmann", "rainer.poehlmann@unibas.ch"], ["Niko Ehrenfeuchter", "nikolaus.ehrenfeuchter@unibas.ch"]]
omero.web.application_server=fastcgi
omero.web.email_host=bc2-linux00.bc2.unibas.ch
omero.web.email_subject_prefix=OMERODEV@Biozentrum Notification:
omero.web.server_email=omerodev-biozentrum@unibas.ch
omero.web.server_list=[["omerodev.biozentrum.unibas.ch", 4064, "OMERODEV@BZ"]]
omero.web.webstart_host=[omerodev.biozentrum.unibas.ch]
Dropbox.log
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[omeronas@bc2-omerodev01 log]$ tail -60 DropBox.log
Traceback (most recent call last):
File "lib/python/fsDropBox.py", line 87, in run
retries=self.maxRetries, interval=self.retryInterval)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 194, in internal_service_factory
raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-16 11:50:55,090 ERROR [ fsclient.DropBox] (MainThread) Quitting
2014-06-16 11:50:55,093 INFO [ fsclient.DropBox] (MainThread) Exiting with exit code: -1
2014-06-16 12:07:40,275 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2014-06-16 12:07:43,453 INFO [ fsclient.DropBox] (MainThread) Monitor parameters = {'default': {'ignoreSysFiles': True, 'importArgs': '', 'watchDir': '', 'readers': '', 'blockSize': 0, 'whitelist': [], 'throttleImport': 10, 'ignoreDirEvents': True, 'blacklist': [], 'fileWait': 15.0, 'dirImportWait': 60, 'timeout': 0.0, 'pathMode': Follow, 'eventTypes': [Creation, Modification], 'timeToLive': 0L, 'timeToIdle': 600000L, 'fileBatch': 10}}
2014-06-16 12:07:43,510 INFO [ fsclient.DropBox] (MainThread) Creating client for user: default
2014-06-16 12:07:43,511 INFO [ omero.util.Resources] (Thread-2 ) Starting
2014-06-16 12:07:43,512 INFO [ fsclient.fsDropBoxMonitorClient] (MainThread) EVENT_RECORD::Cookie::1402913263.51::Directory::/export/omero/OMERO/DropBox
2014-06-16 12:07:43,516 INFO [ fsclient.DropBox] (MainThread) Created monitor with id = 0eba84ee-f53e-11e3-a9a9-00215ec60f34
2014-06-16 12:07:43,519 INFO [ fsclient.DropBox] (MainThread) Started OMERO.fs DropBox client
2014-06-17 14:32:27,354 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2014-06-17 14:32:30,357 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2
2014-06-17 14:32:33,359 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3
2014-06-17 14:32:36,362 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4
2014-06-17 14:32:39,364 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5
2014-06-17 14:32:42,365 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException
{
proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-17 14:32:42,365 ERROR [ fsclient.DropBox] (MainThread) Failed to get Session:
Traceback (most recent call last):
File "lib/python/fsDropBox.py", line 87, in run
retries=self.maxRetries, interval=self.retryInterval)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 194, in internal_service_factory
raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-17 14:32:42,374 ERROR [ fsclient.DropBox] (MainThread) Quitting
2014-06-17 14:32:42,377 INFO [ fsclient.DropBox] (MainThread) Exiting with exit code: -1
2014-06-17 14:53:13,578 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2014-06-17 14:53:16,581 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2
2014-06-17 14:53:19,583 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3
2014-06-17 14:53:22,587 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4
2014-06-17 14:53:25,589 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5
2014-06-17 14:53:28,590 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException
{
proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-17 14:53:28,590 ERROR [ fsclient.DropBox] (MainThread) Failed to get Session:
Traceback (most recent call last):
File "lib/python/fsDropBox.py", line 87, in run
retries=self.maxRetries, interval=self.retryInterval)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 194, in internal_service_factory
raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-17 14:53:28,591 ERROR [ fsclient.DropBox] (MainThread) Quitting
2014-06-17 14:53:28,593 INFO [ fsclient.DropBox] (MainThread) Exiting with exit code: -1
Tables-0.log:
- Code: Select all
[omeronas@bc2-omerodev01 log]$ tail -70 Tables-0.log
2014-06-17 14:33:27,382 INFO [ omero.util.Server] (MainThread) ********************************************************************************
2014-06-17 14:33:27,382 INFO [ omero.tables.TablesI] (MainThread) Cleaning up
2014-06-17 14:33:27,382 INFO [ omero.tables.TablesI] (MainThread) Done
2014-06-17 14:33:27,383 WARNI [ stderr] (MainThread) 2014-06-17 14:33:27.383571 Tables-0: error: Traceback (most recent call last):
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 1127, in main
status = self.doMain(args, initData)
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 1174, in doMain
return self.run(args)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 461, in run
sys.exit(100)
SystemExit: 100
2014-06-17 14:33:27,410 INFO [ omero.util.Resources] (Thread-2 ) Halted
2014-06-17 14:53:02,620 INFO [ omero.util.Server] (MainThread) ********************************************************************************
2014-06-17 14:53:02,621 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup
2014-06-17 14:53:12,621 INFO [ omero.util.Server] (MainThread) Starting
2014-06-17 14:53:12,621 INFO [ omero.util.Server] (MainThread) Loaded dependency numpy (1.6.2)
2014-06-17 14:53:12,621 INFO [ omero.util.Server] (MainThread) Loaded dependency tables (2.4.0, hdf=1.8.9)
2014-06-17 14:53:12,624 INFO [ omero.util.Resources] (Thread-2 ) Starting
2014-06-17 14:53:13,578 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2014-06-17 14:53:23,581 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2
2014-06-17 14:53:33,584 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3
2014-06-17 14:53:43,586 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4
2014-06-17 14:53:53,589 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5
2014-06-17 14:54:03,591 INFO [ omero.utils] (MainThread) Failed to get session on attempt 6
2014-06-17 14:54:13,592 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException
{
proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-17 14:54:13,592 ERROR [ omero.util.Server] (MainThread) Failed initialization
Traceback (most recent call last):
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 457, in run
self.impl = self.impl_class(ctx)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/tables.py", line 825, in __init__
omero.util.Servant.__init__(self, ctx, needs_session = True)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 534, in __init__
self.ctx.newSession()
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 311, in newSession
self.session = internal_service_factory(self.communicator, stop_event = self.stop_event)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 194, in internal_service_factory
raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-17 14:54:13,593 INFO [ omero.util.Server] (MainThread) Cleanup
2014-06-17 14:54:13,593 INFO [ omero.util.Server] (MainThread) Stopped
2014-06-17 14:54:13,593 INFO [ omero.util.Server] (MainThread) ********************************************************************************
2014-06-17 14:54:13,594 INFO [ omero.tables.TablesI] (MainThread) Cleaning up
2014-06-17 14:54:13,594 INFO [ omero.tables.TablesI] (MainThread) Done
2014-06-17 14:54:13,595 WARNI [ stderr] (MainThread) 2014-06-17 14:54:13.595251 Tables-0: error: Traceback (most recent call last):
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 1127, in main
status = self.doMain(args, initData)
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 1174, in doMain
return self.run(args)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 461, in run
sys.exit(100)
SystemExit: 100
2014-06-17 14:54:13,642 INFO [ omero.util.Resources] (Thread-2 ) Halted
2014-06-17 14:54:14,975 INFO [ omero.util.Server] (MainThread) ********************************************************************************
2014-06-17 14:54:14,976 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup
2014-06-17 14:54:24,976 INFO [ omero.util.Server] (MainThread) Starting
2014-06-17 14:54:24,976 INFO [ omero.util.Server] (MainThread) Loaded dependency numpy (1.6.2)
2014-06-17 14:54:24,976 INFO [ omero.util.Server] (MainThread) Loaded dependency tables (2.4.0, hdf=1.8.9)
2014-06-17 14:54:24,980 INFO [ omero.util.Resources] (Thread-2 ) Starting
2014-06-17 14:54:24,984 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2014-06-17 14:54:34,986 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2
2014-06-17 14:54:44,989 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3
2014-06-17 14:54:54,992 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4
2014-06-17 14:55:04,994 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5
2014-06-17 14:55:14,997 INFO [ omero.utils] (MainThread) Failed to get session on attempt 6
Processor-0.log
- Code: Select all
[omeronas@bc2-omerodev01 log]$ tail -60 Processor-0.log
2014-06-17 14:54:13,595 WARNI [ stderr] (MainThread) 2014-06-17 14:54:13.595076 Processor-0: error: Traceback (most recent call last):
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 1127, in main
status = self.doMain(args, initData)
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 1174, in doMain
return self.run(args)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 461, in run
sys.exit(100)
SystemExit: 100
2014-06-17 14:54:13,610 INFO [ omero.util.Resources] (Thread-2 ) Halted
2014-06-17 14:54:14,936 INFO [ omero.util.Server] (MainThread) ********************************************************************************
2014-06-17 14:54:14,937 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup
2014-06-17 14:54:24,937 INFO [ omero.util.Server] (MainThread) Starting
2014-06-17 14:54:24,940 INFO [ omero.util.Resources] (Thread-2 ) Starting
2014-06-17 14:54:24,945 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2014-06-17 14:54:34,948 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2
2014-06-17 14:54:44,951 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3
2014-06-17 14:54:54,954 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4
2014-06-17 14:55:04,956 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5
2014-06-17 14:55:14,959 INFO [ omero.utils] (MainThread) Failed to get session on attempt 6
2014-06-17 14:55:24,960 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException
{
proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-17 14:55:24,960 ERROR [ omero.util.Server] (MainThread) Failed initialization
Traceback (most recent call last):
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 457, in run
self.impl = self.impl_class(ctx)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/processor.py", line 732, in __init__
omero.util.Servant.__init__(self, ctx, needs_session = needs_session)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 534, in __init__
self.ctx.newSession()
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 311, in newSession
self.session = internal_service_factory(self.communicator, stop_event = self.stop_event)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 194, in internal_service_factory
raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-17 14:55:24,961 INFO [ omero.util.Server] (MainThread) Cleanup
2014-06-17 14:55:24,961 INFO [ omero.util.Server] (MainThread) Stopped
2014-06-17 14:55:24,962 INFO [ omero.util.Server] (MainThread) ********************************************************************************
2014-06-17 14:55:24,962 INFO [ omero.processor.ProcessorI] (MainThread) Cleaning up
2014-06-17 14:55:24,962 INFO [ omero.processor.ProcessorI] (MainThread) Done
2014-06-17 14:55:24,963 WARNI [ stderr] (MainThread) 2014-06-17 14:55:24.963327 Processor-0: error: Traceback (most recent call last):
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 1127, in main
status = self.doMain(args, initData)
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 1174, in doMain
return self.run(args)
File "/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/__init__.py", line 461, in run
sys.exit(100)
SystemExit: 100
2014-06-17 14:55:24,973 INFO [ omero.util.Resources] (Thread-2 ) Halted
2014-06-17 14:55:26,305 INFO [ omero.util.Server] (MainThread) ********************************************************************************
2014-06-17 14:55:26,305 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup
2014-06-17 14:55:36,305 INFO [ omero.util.Server] (MainThread) Starting
2014-06-17 14:55:36,309 INFO [ omero.util.Resources] (Thread-2 ) Starting
2014-06-17 14:55:36,314 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2014-06-17 14:55:46,316 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2
2014-06-17 14:55:56,319 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3
PixelData-0.log
- Code: Select all
[omeronas@bc2-omerodev01 log]$ tail -60 PixelData-0.log
at ome.services.blitz.Entry.main(Entry.java:150) [blitz.jar:na]
Caused by: java.net.SocketException: Protocol family unavailable
at sun.nio.ch.Net.bind0(Native Method) ~[na:1.7.0_09]
at sun.nio.ch.Net.bind(Net.java:344) ~[na:1.7.0_09]
at sun.nio.ch.Net.bind(Net.java:336) ~[na:1.7.0_09]
at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:199) ~[na:1.7.0_09]
at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74) ~[na:1.7.0_09]
at IceInternal.Network.doBind(Network.java:245) ~[ice.jar:na]
... 8 common frames omitted
2014-06-17 13:32:30,540 INFO [ ome.services.blitz.Entry] ( main) Calling close on context ome.pixeldata
2014-06-17 13:32:30,545 INFO [ ome.services.fulltext.FullTextThread] ( main) Shutting down Full-Text Indexer
2014-06-17 13:32:30,547 INFO [ o.s.scheduler.SchedulerFactoryBean] ( main) Shutting down Quartz Scheduler
2014-06-17 13:32:30,548 INFO [ ome.services.pixeldata.PixelDataThread] ( main) Shutting down PixelDataThread
2014-06-17 13:32:30,564 INFO [.s.ShutdownSafeEhcacheManagerFactoryBean] ( main) Shutting down EHCache CacheManager
2014-06-17 13:32:30,565 INFO [ ome.services.blitz.Entry] ( main) Finished shutdown.
2014-06-17 13:53:02,426 INFO [ ome.services.blitz.Entry] ( main) Waiting 10000 ms on startup
2014-06-17 13:53:12,432 INFO [ ome.services.blitz.Entry] ( main) Creating ome.pixeldata. Please wait...
2014-06-17 13:53:13,996 INFO [ ome.services.util.DBUserCheck] ( main) User root.id = 0
2014-06-17 13:53:13,997 INFO [ ome.services.util.DBUserCheck] ( main) User guest.id = 1
2014-06-17 13:53:13,997 INFO [ ome.services.util.DBUserCheck] ( main) Group system.id = 0
2014-06-17 13:53:13,997 INFO [ ome.services.util.DBUserCheck] ( main) Group user.id = 1
2014-06-17 13:53:13,997 INFO [ ome.services.util.DBUserCheck] ( main) Group guest.id = 2
2014-06-17 13:53:13,999 INFO [ ome.services.util.JvmSettingsCheck] ( main) Java version: 1.7.0_09; Linux; amd64; 2.6.32-431.17.1.el6.x86_64
2014-06-17 13:53:14,000 INFO [ ome.services.util.JvmSettingsCheck] ( main) Max Memory (MB): = 910
2014-06-17 13:53:14,000 INFO [ ome.services.util.JvmSettingsCheck] ( main) OS Memory (MB): = 48257
2014-06-17 13:53:14,001 INFO [ ome.services.util.JvmSettingsCheck] ( main) Processors: = 16
2014-06-17 13:53:14,027 INFO [.s.ShutdownSafeEhcacheManagerFactoryBean] ( main) Initializing EHCache CacheManager
2014-06-17 13:53:16,294 INFO [ ome.services.fulltext.FullTextAnalyzer] ( main) Initialized FullTextAnalyzer
2014-06-17 13:53:22,381 INFO [ ome.io.nio.PixelsService] ( main) Using Bio-Formats Cache: /export/omero/OMERO/BioFormatsCache
2014-06-17 13:53:22,382 INFO [ ome.io.nio.PixelsService] ( main) PixelsService(path=/export/omero/OMERO/, resolver=ome.services.OmeroFilePathResolver@3c2e1b2f, backoff=ome.io.nio.SimpleBackOff(factor=42.7), sizes=ome.io.nio.ConfiguredTileSizes(w=256,h=256,W=3192,H=3192))
2014-06-17 13:53:22,388 INFO [ ome.services.pixeldata.PixelDataThread] ( main) Initializing PixelDataThread (threads=2)
2014-06-17 13:53:22,653 INFO [ ome.services.db.DatabaseIdentity] ( main) Using LSID format: urn:lsid:export.openmicroscopy.org:%s:1d19f2e5-1db1-419c-8841-1b16c5e66b55_%s%s
2014-06-17 13:53:22,821 INFO [ ome.services.fulltext.FullTextThread] ( main) Initializing Full-Text Indexer
2014-06-17 13:53:22,833 INFO [ ome.tools.hibernate.ExtendedMetadata] ( main) Calculating ExtendedMetadata...
2014-06-17 13:53:22,995 INFO [ o.s.scheduler.SchedulerFactoryBean] ( main) Starting Quartz Scheduler now
2014-06-17 13:53:23,087 ERROR [ ome.services.blitz.Entry] ( main) Error on startup.
Ice.SocketException: java.net.SocketException: Protocol family unavailable
at IceInternal.Network.doBind(Network.java:251) ~[ice.jar:na]
at IceInternal.TcpAcceptor.<init>(TcpAcceptor.java:119) ~[ice.jar:na]
at IceInternal.TcpEndpointI.acceptor(TcpEndpointI.java:414) ~[ice.jar:na]
at IceInternal.IncomingConnectionFactory.<init>(IncomingConnectionFactory.java:376) ~[ice.jar:na]
at Ice.ObjectAdapterI.<init>(ObjectAdapterI.java:1028) ~[ice.jar:na]
at IceInternal.ObjectAdapterFactory.createObjectAdapter(ObjectAdapterFactory.java:160) ~[ice.jar:na]
at Ice.CommunicatorI.createObjectAdapter(CommunicatorI.java:77) ~[ice.jar:na]
at ome.services.blitz.Entry.start(Entry.java:202) [blitz.jar:na]
at ome.services.blitz.Entry.main(Entry.java:150) [blitz.jar:na]
Caused by: java.net.SocketException: Protocol family unavailable
at sun.nio.ch.Net.bind0(Native Method) ~[na:1.7.0_09]
at sun.nio.ch.Net.bind(Net.java:344) ~[na:1.7.0_09]
at sun.nio.ch.Net.bind(Net.java:336) ~[na:1.7.0_09]
at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:199) ~[na:1.7.0_09]
at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74) ~[na:1.7.0_09]
at IceInternal.Network.doBind(Network.java:245) ~[ice.jar:na]
... 8 common frames omitted
2014-06-17 13:53:23,088 INFO [ ome.services.blitz.Entry] ( main) Calling close on context ome.pixeldata
2014-06-17 13:53:23,094 INFO [ ome.services.fulltext.FullTextThread] ( main) Shutting down Full-Text Indexer
2014-06-17 13:53:23,095 INFO [ o.s.scheduler.SchedulerFactoryBean] ( main) Shutting down Quartz Scheduler
2014-06-17 13:53:23,096 INFO [ ome.services.pixeldata.PixelDataThread] ( main) Shutting down PixelDataThread
2014-06-17 13:53:23,112 INFO [.s.ShutdownSafeEhcacheManagerFactoryBean] ( main) Shutting down EHCache CacheManager
2014-06-17 13:53:23,113 INFO [ ome.services.blitz.Entry] ( main) Finished shutdown.
Indexer-0.log
- Code: Select all
[omeronas@bc2-omerodev01 log]$ tail -60 Indexer-0.log
at IceInternal.ObjectAdapterFactory.createObjectAdapter(ObjectAdapterFactory.java:160) ~[ice.jar:na]
at Ice.CommunicatorI.createObjectAdapter(CommunicatorI.java:77) ~[ice.jar:na]
at ome.services.blitz.Entry.start(Entry.java:202) [blitz.jar:na]
at ome.services.blitz.Entry.main(Entry.java:150) [blitz.jar:na]
Caused by: java.net.SocketException: Protocol family unavailable
at sun.nio.ch.Net.bind0(Native Method) ~[na:1.7.0_09]
at sun.nio.ch.Net.bind(Net.java:344) ~[na:1.7.0_09]
at sun.nio.ch.Net.bind(Net.java:336) ~[na:1.7.0_09]
at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:199) ~[na:1.7.0_09]
at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74) ~[na:1.7.0_09]
at IceInternal.Network.doBind(Network.java:245) ~[ice.jar:na]
... 8 common frames omitted
2014-06-17 13:32:28,198 INFO [ ome.services.blitz.Entry] ( main) Calling close on context ome.fulltext
2014-06-17 13:32:28,215 INFO [ o.s.scheduler.SchedulerFactoryBean] ( main) Shutting down Quartz Scheduler
2014-06-17 13:32:28,216 INFO [ ome.services.fulltext.FullTextThread] ( main) Shutting down Full-Text Indexer
2014-06-17 13:32:28,233 INFO [.s.ShutdownSafeEhcacheManagerFactoryBean] ( main) Shutting down EHCache CacheManager
2014-06-17 13:32:28,234 INFO [ ome.services.blitz.Entry] ( main) Finished shutdown.
2014-06-17 13:53:02,412 INFO [ ome.services.blitz.Entry] ( main) Waiting 10000 ms on startup
2014-06-17 13:53:12,420 INFO [ ome.services.blitz.Entry] ( main) Creating ome.fulltext. Please wait...
2014-06-17 13:53:13,957 INFO [ ome.services.util.DBUserCheck] ( main) User root.id = 0
2014-06-17 13:53:13,959 INFO [ ome.services.util.DBUserCheck] ( main) User guest.id = 1
2014-06-17 13:53:13,959 INFO [ ome.services.util.DBUserCheck] ( main) Group system.id = 0
2014-06-17 13:53:13,959 INFO [ ome.services.util.DBUserCheck] ( main) Group user.id = 1
2014-06-17 13:53:13,959 INFO [ ome.services.util.DBUserCheck] ( main) Group guest.id = 2
2014-06-17 13:53:13,961 INFO [ ome.services.util.JvmSettingsCheck] ( main) Java version: 1.7.0_09; Linux; amd64; 2.6.32-431.17.1.el6.x86_64
2014-06-17 13:53:13,961 INFO [ ome.services.util.JvmSettingsCheck] ( main) Max Memory (MB): = 245
2014-06-17 13:53:13,962 INFO [ ome.services.util.JvmSettingsCheck] ( main) OS Memory (MB): = 48257
2014-06-17 13:53:13,962 INFO [ ome.services.util.JvmSettingsCheck] ( main) Processors: = 16
2014-06-17 13:53:13,989 INFO [.s.ShutdownSafeEhcacheManagerFactoryBean] ( main) Initializing EHCache CacheManager
2014-06-17 13:53:16,251 INFO [ ome.services.fulltext.FullTextAnalyzer] ( main) Initialized FullTextAnalyzer
2014-06-17 13:53:19,987 WARN [ ome.services.fulltext.FileParser] ( main) Indexer maximum file size is set to more than half of total heap size. Excessively large text files may cause search index corruption. Consider decreasing the maximum file size or increasing the Indexer heap size.
2014-06-17 13:53:19,991 WARN [ ome.services.fulltext.FileParser] ( main) Indexer maximum file size is set to more than half of total heap size. Excessively large text files may cause search index corruption. Consider decreasing the maximum file size or increasing the Indexer heap size.
2014-06-17 13:53:20,012 INFO [ ome.services.fulltext.FullTextThread] ( main) Initializing Full-Text Indexer
2014-06-17 13:53:20,311 INFO [ ome.services.db.DatabaseIdentity] ( main) Using LSID format: urn:lsid:export.openmicroscopy.org:%s:1d19f2e5-1db1-419c-8841-1b16c5e66b55_%s%s
2014-06-17 13:53:20,493 INFO [ ome.tools.hibernate.ExtendedMetadata] ( main) Calculating ExtendedMetadata...
2014-06-17 13:53:20,673 INFO [ o.s.scheduler.SchedulerFactoryBean] ( main) Starting Quartz Scheduler now
2014-06-17 13:53:20,769 ERROR [ ome.services.blitz.Entry] ( main) Error on startup.
Ice.SocketException: java.net.SocketException: Protocol family unavailable
at IceInternal.Network.doBind(Network.java:251) ~[ice.jar:na]
at IceInternal.TcpAcceptor.<init>(TcpAcceptor.java:119) ~[ice.jar:na]
at IceInternal.TcpEndpointI.acceptor(TcpEndpointI.java:414) ~[ice.jar:na]
at IceInternal.IncomingConnectionFactory.<init>(IncomingConnectionFactory.java:376) ~[ice.jar:na]
at Ice.ObjectAdapterI.<init>(ObjectAdapterI.java:1028) ~[ice.jar:na]
at IceInternal.ObjectAdapterFactory.createObjectAdapter(ObjectAdapterFactory.java:160) ~[ice.jar:na]
at Ice.CommunicatorI.createObjectAdapter(CommunicatorI.java:77) ~[ice.jar:na]
at ome.services.blitz.Entry.start(Entry.java:202) [blitz.jar:na]
at ome.services.blitz.Entry.main(Entry.java:150) [blitz.jar:na]
Caused by: java.net.SocketException: Protocol family unavailable
at sun.nio.ch.Net.bind0(Native Method) ~[na:1.7.0_09]
at sun.nio.ch.Net.bind(Net.java:344) ~[na:1.7.0_09]
at sun.nio.ch.Net.bind(Net.java:336) ~[na:1.7.0_09]
at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:199) ~[na:1.7.0_09]
at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74) ~[na:1.7.0_09]
at IceInternal.Network.doBind(Network.java:245) ~[ice.jar:na]
... 8 common frames omitted
2014-06-17 13:53:20,770 INFO [ ome.services.blitz.Entry] ( main) Calling close on context ome.fulltext
2014-06-17 13:53:20,776 INFO [ o.s.scheduler.SchedulerFactoryBean] ( main) Shutting down Quartz Scheduler
2014-06-17 13:53:20,777 INFO [ ome.services.fulltext.FullTextThread] ( main) Shutting down Full-Text Indexer
2014-06-17 13:53:20,793 INFO [.s.ShutdownSafeEhcacheManagerFactoryBean] ( main) Shutting down EHCache CacheManager
2014-06-17 13:53:20,794 INFO [ ome.services.blitz.Entry] ( main) Finished shutdown.
master.err
- Code: Select all
-! 06/17/14 14:32:27.354 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'
-! 06/17/14 14:32:27.355 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'
-! 06/17/14 14:53:13.578 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'
-! 06/17/14 14:53:13.580 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'
Thanks a lot for your help, best,
-Rainer