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omero.server-5.0.0-ice35-b19 would not start on CentOS 6.2

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Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby manics » Tue Jun 17, 2014 8:17 am

Hi Rainer

Could you post the output of
Code: Select all
omero admin diagnostics
, and
Code: Select all
omero config get
(blank out any passwords for the latter).

Thanks, Simon
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manics
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Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby rpoehlmann » Tue Jun 17, 2014 1:07 pm

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.sh

In 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
Code: Select all
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
Code: Select all
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:
Code: Select all
[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:
Code: Select all
[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
Code: Select all
[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
User avatar
rpoehlmann
 
Posts: 42
Joined: Thu Feb 09, 2012 2:04 pm

Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby rpoehlmann » Tue Jun 17, 2014 1:26 pm

Maybe the Blitz-0.log would be of interest as well. Here it is:

Code: Select all
2014-06-17 14:15:40,490 INFO  [o.services.blitz.util.BlitzConfiguration] (      main) Shutting down Ice.Communicator
2014-06-17 14:15:40,497 ERROR [                ome.services.blitz.Entry] (      main) Error on startup.
org.springframework.beans.factory.access.BootstrapException: Unable to return specified BeanFactory instance: factory key [OMERO.blitz], from group with resource name [classpath*:beanRefContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'omero.rtypes.RTypeObjectFactoryRegistry#0' defined in class path resource [ome/services/objectfactories.xml]: Cannot resolve reference to bean 'Ice.Communicator' while setting bean property 'iceCommunicator'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:409) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at ome.system.OmeroContext.getInstance(OmeroContext.java:203) ~[common.jar:na]
   at ome.services.blitz.Entry.start(Entry.java:193) [blitz.jar:na]
   at ome.services.blitz.Entry.main(Entry.java:150) [blitz.jar:na]
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'omero.rtypes.RTypeObjectFactoryRegistry#0' defined in class path resource [ome/services/objectfactories.xml]: Cannot resolve reference to bean 'Ice.Communicator' while setting bean property 'iceCommunicator'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:281) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   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:193) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 3 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.BeanCreationException: Error creating bean with name 'omero.rtypes.RTypeObjectFactoryRegistry#0' defined in class path resource [ome/services/objectfactories.xml]: Cannot resolve reference to bean 'Ice.Communicator' while setting bean property 'iceCommunicator'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   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]
   ... 13 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'omero.rtypes.RTypeObjectFactoryRegistry#0' defined in class path resource [ome/services/objectfactories.xml]: Cannot resolve reference to bean 'Ice.Communicator' while setting bean property 'iceCommunicator'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1308) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1067) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   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.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:562) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:871) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:423) ~[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 ome.system.OmeroContext.<init>(OmeroContext.java:103) ~[common.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_09]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_09]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_09]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:525) ~[na:1.7.0_09]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 15 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:281) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   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.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:344) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:964) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:870) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   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]
   ... 34 common frames omitted
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   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]
   ... 52 common frames omitted
Caused by: org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at ome.services.blitz.util.BlitzConfiguration.createAdapter(BlitzConfiguration.java:246) ~[blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:120) ~[blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:82) ~[blitz.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_09]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_09]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_09]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:525) ~[na:1.7.0_09]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 54 common frames omitted
2014-06-17 14:19:24,031 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2014-06-17 14:19:25,408 INFO  [.s.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2014-06-17 14:19:25,758 INFO  [          ome.services.util.DBPatchCheck] (      main) Verified database patch: OMERO5.0__0
2014-06-17 14:19:25,795 INFO  [           ome.services.util.DBUserCheck] (      main) User root.id = 0
2014-06-17 14:19:25,797 INFO  [           ome.services.util.DBUserCheck] (      main) User guest.id = 1
2014-06-17 14:19:25,797 INFO  [           ome.services.util.DBUserCheck] (      main) Group system.id = 0
2014-06-17 14:19:25,797 INFO  [           ome.services.util.DBUserCheck] (      main) Group user.id = 1
2014-06-17 14:19:25,798 INFO  [           ome.services.util.DBUserCheck] (      main) Group guest.id = 2
2014-06-17 14:19:28,072 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2014-06-17 14:19:31,103 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 14:19:32,037 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011171158] time[878] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,188 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172038] time[150] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,366 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172188] time[177] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,416 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172366] time[49] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,577 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172418] time[158] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,624 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172577] time[46] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,671 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172624] time[46] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,716 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172671] time[45] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,762 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172716] time[46] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,809 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172763] time[46] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,853 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172810] time[43] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,897 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172853] time[43] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,941 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172897] time[44] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:32,984 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172941] time[43] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:33,029 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011172985] time[44] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:33,077 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011173029] time[48] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:33,125 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011173077] time[47] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:33,171 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011173125] time[45] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:33,216 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011173171] time[45] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:33,260 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011173217] time[43] tag[ome.io.nio.SimpleBackOff.256X256]
2014-06-17 14:19:33,274 INFO  [                ome.io.nio.PixelsService] (      main) Using Bio-Formats Cache: /export/omero/OMERO/BioFormatsCache
2014-06-17 14:19:33,274 INFO  [                ome.io.nio.PixelsService] (      main) PixelsService(path=/export/omero/OMERO/, resolver=ome.services.OmeroFilePathResolver@4a5f9cf1, backoff=ome.io.nio.SimpleBackOff(factor=44.5), sizes=ome.io.nio.ConfiguredTileSizes(w=256,h=256,W=3192,H=3192))
2014-06-17 14:19:33,475 INFO  [    ome.services.fulltext.FullTextThread] (      main) Initializing Full-Text Indexer
2014-06-17 14:19:33,487 INFO  [  ome.services.pixeldata.PixelDataThread] (      main) Initializing PixelDataThread (create events only)
2014-06-17 14:19:33,490 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 14:19:33,490 INFO  [      ome.services.util.JvmSettingsCheck] (      main) Max Memory (MB):   =   1820
2014-06-17 14:19:33,491 INFO  [      ome.services.util.JvmSettingsCheck] (      main) OS Memory (MB):    =  48257
2014-06-17 14:19:33,491 INFO  [      ome.services.util.JvmSettingsCheck] (      main) Processors:        =     16
2014-06-17 14:19:33,657 INFO  [    ome.services.util.ServerVersionCheck] (      main) -------------------------------------------------
2014-06-17 14:19:33,657 INFO  [    ome.services.util.ServerVersionCheck] (      main) OMERO Version: 5.0.2-ice35-b26 Ready.
2014-06-17 14:19:33,657 INFO  [    ome.services.util.ServerVersionCheck] (      main) -------------------------------------------------
2014-06-17 14:19:35,192 INFO  [                 ome.system.UpgradeCheck] (      main) no update needed
2014-06-17 14:19:35,198 INFO  [    ome.tools.hibernate.ExtendedMetadata] (      main) Calculating ExtendedMetadata...
2014-06-17 14:19:35,337 INFO  [      o.s.scheduler.SchedulerFactoryBean] (      main) Starting Quartz Scheduler now
2014-06-17 14:19:35,343 INFO  [        ome.services.util.ServiceHandler] (      main)  Executor.doWork -- ome.services.util.NamespaceCheck.namespaceCheck
2014-06-17 14:19:35,344 INFO  [        ome.services.util.ServiceHandler] (      main)  Args:   [null, InternalSF@2125597018]
2014-06-17 14:19:35,515 INFO  [         ome.security.basic.EventHandler] (      main)  Auth:   user=0,group=0,event=1336051(Internal),sess=83a7560c-607e-4ef7-ba0e-0565a2dfb561
2014-06-17 14:19:35,558 INFO  [                 org.perf4j.TimingLogger] (      main) start[1403011175344] time[214] tag[omero.call.success.ome.services.util.NamespaceCheck$1.doWork]
2014-06-17 14:19:35,558 INFO  [        ome.services.util.ServiceHandler] (      main)  Rslt:   null
2014-06-17 14:19:35,775 INFO  [o.services.blitz.util.BlitzConfiguration] (      main) Initializing Ice.Communicator
2014-06-17 14:19:35,875 ERROR [            ome.services.blitz.fire.Ring] (      main) Error stopping ring ome.services.blitz.fire.Ring@67bd0dbb
java.lang.NullPointerException: null
   at ome.services.blitz.fire.Ring.destroy(Ring.java:201) ~[blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.destroy(BlitzConfiguration.java:283) [blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:135) [blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:82) [blitz.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.7.0_09]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) [na:1.7.0_09]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [na:1.7.0_09]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:525) [na:1.7.0_09]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) [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]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   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.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:344) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:964) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:870) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   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]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1308) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1067) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   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.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:562) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:871) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:423) [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 ome.system.OmeroContext.<init>(OmeroContext.java:103) [common.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.7.0_09]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) [na:1.7.0_09]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [na:1.7.0_09]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:525) [na:1.7.0_09]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) [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]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   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:193) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at ome.system.OmeroContext.getInstance(OmeroContext.java:203) [common.jar:na]
   at ome.services.blitz.Entry.start(Entry.java:193) [blitz.jar:na]
   at ome.services.blitz.Entry.main(Entry.java:150) [blitz.jar:na]
2014-06-17 14:19:35,877 ERROR [            ome.services.blitz.fire.Ring] (      main) Error signaling down to: null
java.lang.NullPointerException: null
   at ome.services.blitz.fire.Ring.destroy(Ring.java:214) ~[blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.destroy(BlitzConfiguration.java:283) [blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:135) [blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:82) [blitz.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.7.0_09]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) [na:1.7.0_09]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [na:1.7.0_09]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:525) [na:1.7.0_09]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) [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]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   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.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:344) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:964) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:870) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   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]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1308) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1067) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   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.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:562) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:871) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:423) [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 ome.system.OmeroContext.<init>(OmeroContext.java:103) [common.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.7.0_09]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) [na:1.7.0_09]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [na:1.7.0_09]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:525) [na:1.7.0_09]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) [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]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   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:193) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at ome.system.OmeroContext.getInstance(OmeroContext.java:203) [common.jar:na]
   at ome.services.blitz.Entry.start(Entry.java:193) [blitz.jar:na]
   at ome.services.blitz.Entry.main(Entry.java:150) [blitz.jar:na]
2014-06-17 14:19:35,877 INFO  [o.services.blitz.util.BlitzConfiguration] (      main) Shutting down Ice.Communicator
2014-06-17 14:19:35,884 ERROR [                ome.services.blitz.Entry] (      main) Error on startup.
org.springframework.beans.factory.access.BootstrapException: Unable to return specified BeanFactory instance: factory key [OMERO.blitz], from group with resource name [classpath*:beanRefContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'omero.rtypes.RTypeObjectFactoryRegistry#0' defined in class path resource [ome/services/objectfactories.xml]: Cannot resolve reference to bean 'Ice.Communicator' while setting bean property 'iceCommunicator'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:409) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at ome.system.OmeroContext.getInstance(OmeroContext.java:203) ~[common.jar:na]
   at ome.services.blitz.Entry.start(Entry.java:193) [blitz.jar:na]
   at ome.services.blitz.Entry.main(Entry.java:150) [blitz.jar:na]
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'omero.rtypes.RTypeObjectFactoryRegistry#0' defined in class path resource [ome/services/objectfactories.xml]: Cannot resolve reference to bean 'Ice.Communicator' while setting bean property 'iceCommunicator'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:281) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   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:193) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 3 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.BeanCreationException: Error creating bean with name 'omero.rtypes.RTypeObjectFactoryRegistry#0' defined in class path resource [ome/services/objectfactories.xml]: Cannot resolve reference to bean 'Ice.Communicator' while setting bean property 'iceCommunicator'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   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]
   ... 13 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'omero.rtypes.RTypeObjectFactoryRegistry#0' defined in class path resource [ome/services/objectfactories.xml]: Cannot resolve reference to bean 'Ice.Communicator' while setting bean property 'iceCommunicator'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1308) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1067) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   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.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:562) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:871) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:423) ~[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 ome.system.OmeroContext.<init>(OmeroContext.java:103) ~[common.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_09]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_09]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_09]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:525) ~[na:1.7.0_09]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 15 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configuration' defined in URL [jar:file:/home/omeronas/OMERO.server-5.0.2-ice35-b26/lib/server/blitz.jar!/ome/services/blitz-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:281) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   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.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:344) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:964) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:870) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   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]
   ... 34 common frames omitted
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.util.BlitzConfiguration]: Constructor threw exception; nested exception is org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   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]
   ... 52 common frames omitted
Caused by: org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at ome.services.blitz.util.BlitzConfiguration.createAdapter(BlitzConfiguration.java:246) ~[blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:120) ~[blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:82) ~[blitz.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_09]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_09]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_09]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:525) ~[na:1.7.0_09]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 54 common frames omitted
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Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby manics » Tue Jun 17, 2014 3:54 pm

Hi Rainer

Looking at omero admin diagnostics there's a couple of potential issues:
Code: Select all
Environment:OMERO_HOME=/home/omeronas/OMERO.server
...
Environment:ICE_HOME=/usr/share/Ice-3.4.2 


Setting OMERO_HOME can often cause problems, since it's used internally by the server, see:
http://www.openmicroscopy.org/site/supp ... refix.html

ICE_HOME is still referring to your previous installation. In theory this shouldn't matter unless you're building your server from source, though it'd be best to fix it- either unset it since OMERO will normally run without it, or change it to the current Ice version.

Could you see if your server works after making these changes?

Cheers, Simon
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Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby rpoehlmann » Thu Jun 19, 2014 2:10 pm

Hi Simon,

I corrected/removed those 2 entries as suggested:
Code: Select all
Environment:OMERO_HOME=(unset)             
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-3.5.1 
Environment:LD_LIBRARY_PATH=/usr/java/jdk1.7.0_09/lib:/usr/lib64:/usr/pgsql-9.2/lib:
Environment:DYLD_LIBRARY_PATH=(unset)


Unfortunately, still the same. I am kind of running out of ideas.
The Processor-0-log always complains the same way:
Code: Select all
2014-06-19 15:54:24,014 WARNI [                             omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}
2014-06-19 15:54:24,014 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


During the omero admin start process, several attempts are made to get a successful Ice session. And, during this time I can even connect to an Ice console and can see that the master node is running:
Code: Select all
>>> server list
Blitz-0
DropBox
FileServer
Indexer-0
MonitorServer
OMERO.Glacier2
OMERO.IceStorm
PixelData-0
Processor-0
Tables-0
TestDropBox
>>> node list
master
>>> server state Processor-0
activating (enabled)
>>> server state OMERO.IceStorm
active (pid = 19052, enabled)
>>> server state OMERO.Glacier2
active (pid = 19051, enabled)


I gathered some additional output from the ICE console of the master node:
Code: Select all
node `master' stderr:
-! 05/07/14 12:45:11.952 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
   Reference.cpp:1566: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 05/07/14 12:45:11.953 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
   Reference.cpp:1566: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
-! 05/07/14 13:31:27.927 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
   Reference.cpp:1566: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 05/07/14 13:31:27.928 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
   Reference.cpp:1566: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Exception in thread "bitronix-task-scheduler" java.lang.OutOfMemoryError: Java heap space
Exception in thread "OMERO.scheduler_QuartzSchedulerThread" java.lang.OutOfMemoryError: Java heap space
Exception in thread "bitronix-task-scheduler" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Indexer-0-Ice.Timer" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Ice.Timer" java.lang.OutOfMemoryError: Java heap space

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "OMERO.scheduler_QuartzSchedulerThread"
Exception in thread "bitronix-task-scheduler" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Ice.Timer" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "Indexer-0-Ice.Timer" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "perf4j-async-stats-appender-sink-CoalescingStatistics" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "OMERO.scheduler_QuartzSchedulerThread" java.lang.OutOfMemoryError: Java heap space
-! 05/21/14 16:53:29.050 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
   Reference.cpp:1566: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
-! 05/21/14 16:53:29.061 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
   Reference.cpp:1566: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
Exception in thread "bitronix-task-scheduler" java.lang.OutOfMemoryError: Java heap space

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "Ice.Timer"
Exception in thread "Indexer-0-Ice.Timer" java.lang.OutOfMemoryError: Java heap space
Exception in thread "OMERO.scheduler_QuartzSchedulerThread" java.lang.OutOfMemoryError: Java heap space

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "perf4j-async-stats-appender-sink-CoalescingStatistics"
-! 06/10/14 10:50:31.765 icegridnode: warning: failed to deploy application `/home/omeronas/OMERO.server/etc/grid/default.xml':
   DescriptorParser.cpp:727: IceXML::ParserException
   error in </home/omeronas/OMERO.server/etc/grid/templates.xml> descriptor, line 282, column 10:
   not well-formed (invalid token)
Exception in thread "bitronix-task-scheduler" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Ice.Timer" java.lang.OutOfMemoryError: Java heap space
Exception in thread "OMERO.scheduler_QuartzSchedulerThread" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Indexer-0-Ice.Timer" java.lang.OutOfMemoryError: Java heap space
-! 06/16/14 11:50:40.078 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'
-! 06/16/14 11:50:40.079 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 14:32:27.354 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'
-! 06/17/14 15:15:40.826 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 15:15:40.827 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 15:19:36.213 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 15:19:36.214 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 16:01:56.831 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 16:01:56.832 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 16:55:59.582 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 16:55:59.583 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'
-! 06/19/14 15:04:34.456 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'
-! 06/19/14 15:04:34.457 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'
-! 06/19/14 15:52:12.586 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'
-! 06/19/14 15:52:12.587 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'
-! 06/19/14 16:00:32.472 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'
-! 06/19/14 16:00:32.473 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'


I can see those OutOfMemory errors:
Code: Select all
Exception in thread "bitronix-task-scheduler" java.lang.OutOfMemoryError: Java heap space
Exception in thread "OMERO.scheduler_QuartzSchedulerThread" java.lang.OutOfMemoryError: Java heap space
Exception in thread "bitronix-task-scheduler" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Indexer-0-Ice.Timer" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Ice.Timer" java.lang.OutOfMemoryError: Java heap space

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "OMERO.scheduler_QuartzSchedulerThread"
Exception in thread "bitronix-task-scheduler" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Ice.Timer" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "Indexer-0-Ice.Timer" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "perf4j-async-stats-appender-sink-CoalescingStatistics" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "OMERO.scheduler_QuartzSchedulerThread" java.lang.OutOfMemoryError: Java heap space


Might this eventually be the culprit?

Cheers,
-Rainer
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Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby manics » Thu Jun 19, 2014 2:43 pm

It could be a problem, though if I'm reading your logs correctly it last occurred on 06/10/14, and you must've restarted your server several times since then. I also noticed one of your older logs:
Code: Select all
-! 06/10/14 10:50:31.765 icegridnode: warning: failed to deploy application `/home/omeronas/OMERO.server/etc/grid/default.xml':
   DescriptorParser.cpp:727: IceXML::ParserException
   error in </home/omeronas/OMERO.server/etc/grid/templates.xml> descriptor, line 282, column 10:
   not well-formed (invalid token)


I'm guessing you modified the templates.xml file? Can you remember what broke it, and what you changed to get it working? If you've modified it from the default would you mind pasting it here?

Thanks, Simon
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Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby rpoehlmann » Thu Jun 19, 2014 2:55 pm

Yes, you're right, my bad.

The ICE console apparently concatenates stderr output including errors from very old sessions. I did not realize this when looking at the output, sorry!
Those "OutOfMemory" errors then reflect the fact that I once increased the standard PermSize from 128M to 256M and the PixelData Xmx value to 1024M since the had problems with the upload of larger datasets. This was done when upgrading from OMERO 4.4 -> 5.0.2

So, the only actual error then reads
Code: Select all
-! 06/19/14 16:35:24.743 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'


And that's unfortunately not very helpful, is it :?

Cheers,
-Rainer
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Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby jmoore » Fri Jun 20, 2014 4:23 pm

Hi Rainer,

sorry, I'm coming to this thread a bit late, so hopefully you want mind my starting from scratch. The error you posted works out to roughly "the server's not reachable" which as you say, isn't very helpful.

Would you mind turning off your server (bin/omero admin stop) and then move the var/log files out of the way via "mv var/logs var/logs_old". (If you want to keep them then you can put them back into place after this experiment; otherwise, they can be deleted, backed up, etc.)

Then start the server. Now there should be clean logs of exactly what's wrong. Zip up all of var/log and send that. The output of bin/omero admin diagnostics again at that point would be really appreciated.

Thanks for your patience!
~Josh.
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Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby rpoehlmann » Wed Jun 25, 2014 1:38 pm

Hi Josh,

thanks for joining. And, sorry, I've been quite busy the past days with other stuff, please excuse my delayed reply.
I'm currently testing this OMERO5.0.2/ice35/CentOS 6.5 combination on our DEV server, so no worries about trying out things or moving log files around. The PROD server is still happy elsewhere with OMERO5.0.2/ice34/CentOS 6.5

Diagnostics output:
Code: Select all
[omeronas@bc2-omerodev01 OMERO.server]$ ./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-5.0.2-ice35-b26/var/log exists

Log files:  Blitz-0.log                    43.0 KB       errors=8    warnings=0   
Log files:  DropBox.log                    1.0 KB        errors=2    warnings=1   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  4.0 KB        errors=1    warnings=2   
Log files:  MonitorServer.log              0.0 KB       
Log files:  OMEROweb.log                   n/a
Log files:  PixelData-0.log                4.0 KB        errors=1    warnings=0   
Log files:  Processor-0.log                18.0 KB       errors=10   warnings=5   
Log files:  Tables-0.log                   19.0 KB       errors=10   warnings=5   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB        errors=0    warnings=2   
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.09 MB


Environment:OMERO_HOME=(unset)             
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-3.5.1 
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]


Hope this helps & thanks for your help,
-Rainer
Attachments
log.zip
Fresh Log dir with all logs generated during failing OMERO service start
(11.33 KiB) Downloaded 125 times
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rpoehlmann
 
Posts: 42
Joined: Thu Feb 09, 2012 2:04 pm

Re: omero.server-5.0.0-ice35-b19 would not start on CentOS 6

Postby jmoore » Wed Jun 25, 2014 6:52 pm

Hi Rainer,

the error at the bottom of your Blitz-0.log is pretty catastrophic:
Code: Select all
Caused by: org.springframework.beans.FatalBeanException: Could not find Ice config for object adapter [ BlitzAdapter ]
   at ome.services.blitz.util.BlitzConfiguration.createAdapter(BlitzConfiguration.java:246) ~[blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:120) ~[blitz.jar:na]
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:82) ~[blitz.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_09]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_09]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_09]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:525) ~[na:1.7.0_09]

but is unfortunately hiding another error that can be seen in your Indexer-0.log, for example:
Code: Select all
2014-06-25 14:17:59,175 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

which points us to this other thread https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7527.

Would you mind trying, the solution suggested there, namely adding:
Code: Select all
<property name="Ice.IPv6" value="0"/>


I'll keep my fingers crossed!
~Josh.
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jmoore
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