Ice::NoEndpointException: (SOLVED)

[SteveO]

I'm trying to install omero 4.1 server on ubuntu (jaunty).

I think I successfully fulfilled all the perquisites, but the server fails on startup:

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/usr/local/omero_dist$ bin/omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................Failed to startup after 5 minutes

python -V is 2.6.2
sun-java6-jdk installed with apt-get and selected via update-java-alternatives, javac -version indicates correct version (by sun) is selected.
ice installed with apt-get install zeroc-ice, so I haven't had to set any environment variables
postgres is 8.3.8, again installed via apt-get which also starts the RDBM
initialising the omero user, db, adding pglpql worked fine (as far as I could tell) output of:
psql -h localhost -U omero -l indicates the omero database exists.

binary directory is in the standard spot /OMERO and is owned by the user trying to start omero (after failed startup there is even a new directory here, "FullText"



I've looked through both the master.err and the Blitz logs and to me they are not so illuminating

master.err

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Traceback (most recent call last):
  File "lib/python/runTables.py", line 12, in <module>
    __import__("numpy")
ImportError: No module named numpy
Oct 24, 2009 1:25:00 PM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
Oct 24, 2009 1:25:00 PM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
10/24/09 13:25:59.298 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
10/24/09 13:25:59.422 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'

Blitz log

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2009-10-24 13:24:58,143 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2009-10-24 13:25:01,051 WARN  [                         java.util.prefs] (      main) Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
2009-10-24 13:25:01,235 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2009-10-24 13:25:11,823 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer

the Processor-log at least has more stuff in it to wade through, here's a snippet:

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2009-10-24 14:21:58,325 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2009-10-24 14:21:58,333 INFO  [                       omero.util.Server] (MainThread) Starting
2009-10-24 14:21:58,337 INFO  [                    omero.util.Resources] (Thread-2  ) Starting
2009-10-24 14:23:00,669 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 1
2009-10-24 14:23:13,614 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 2
2009-10-24 14:23:23,698 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 3
2009-10-24 14:23:33,731 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 4
2009-10-24 14:23:43,759 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 5
2009-10-24 14:23:53,884 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 6
2009-10-24 14:24:04,153 WARNI [                             omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t @ BlitzAdapters
}
2009-10-24 14:24:04,441 ERROR [                       omero.util.Server] (MainThread) Failed initialization
Traceback (most recent call last):
  File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 349, in run
    self.impl = self.impl_class(ctx)
  File "/usr/local/omero_dist/lib/python/omero/processor.py", line 546, in __init__
    omero.util.Servant.__init__(self, ctx, needs_session = True)
  File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 416, in __init__
    self.ctx.newSession()
  File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 231, in newSession
    self.session = internal_service_factory(self.communicator, stop_event = self.stop_event)
  File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 150, in internal_service_factory
    raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t @ BlitzAdapters
}
2009-10-24 14:24:05,949 INFO  [                       omero.util.Server] (MainThread) Cleanup
2009-10-24 14:24:05,953 INFO  [                       omero.util.Server] (MainThread) Stopped
2009-10-24 14:24:05,953 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2009-10-24 14:24:06,309 INFO  [              omero.processor.ProcessorI] (MainThread) Cleaning up
2009-10-24 14:24:06,309 INFO  [                    omero.util.Resources] (MainThread) Cleanup done
2009-10-24 14:24:06,313 INFO  [              omero.processor.ProcessorI] (MainThread) Done
2009-10-24 14:24:06,409 WARNI [                                  stderr] (MainThread) Traceback (most recent call last):
2009-10-24 14:24:06,429 INFO  [                    omero.util.Resources] (Thread-2  ) Halted
2009-10-24 14:24:06,485 WARNI [                                  stderr] (MainThread) File "/var/lib/python-support/python2.6/Ice.py", line 790, in main
2009-10-24 14:24:07,465 WARNI [                                  stderr] (MainThread) status = self.run(args)
2009-10-24 14:24:07,465 WARNI [                                  stderr] (MainThread) File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 353, in run
2009-10-24 14:24:07,465 WARNI [                                  stderr] (MainThread) sys.exit(100)
2009-10-24 14:24:07,465 WARNI [                                  stderr] (MainThread) SystemExit: 100
2009-10-24 14:24:41,399 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2009-10-24 14:24:41,747 INFO  [                       omero.util.Server] (MainThread) Starting
2009-10-24 14:24:41,751 INFO  [                    omero.util.Resources] (Thread-2  ) Starting
2009-10-24 14:24:43,223 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 1
2009-10-24 14:24:53,223 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 2
2009-10-24 14:25:03,240 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 3
2009-10-24 14:25:13,241 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 4
2009-10-24 14:25:23,249 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 5
2009-10-24 14:25:33,250 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 6
2009-10-24 14:25:43,546 WARNI [                             omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t @ BlitzAdapters
}
2009-10-24 14:25:43,554 ERROR [                       omero.util.Server] (MainThread) Failed initialization
Traceback (most recent call last):
  File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 349, in run
    self.impl = self.impl_class(ctx)
  File "/usr/local/omero_dist/lib/python/omero/processor.py", line 546, in __init__
    omero.util.Servant.__init__(self, ctx, needs_session = True)
  File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 416, in __init__
    self.ctx.newSession()
  File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 231, in newSession
    self.session = internal_service_factory(self.communicator, stop_event = self.stop_event)
  File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 150, in internal_service_factory
    raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t @ BlitzAdapters
}
2009-10-24 14:25:44,518 INFO  [                       omero.util.Server] (MainThread) Cleanup
2009-10-24 14:25:44,526 INFO  [                       omero.util.Server] (MainThread) Stopped
2009-10-24 14:25:44,526 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2009-10-24 14:25:44,534 INFO  [              omero.processor.ProcessorI] (MainThread) Cleaning up
2009-10-24 14:25:44,534 INFO  [                    omero.util.Resources] (MainThread) Cleanup done
2009-10-24 14:25:44,538 INFO  [              omero.processor.ProcessorI] (MainThread) Done
2009-10-24 14:25:44,538 WARNI [                                  stderr] (MainThread) Traceback (most recent call last):
2009-10-24 14:25:44,538 WARNI [                                  stderr] (MainThread) File "/var/lib/python-support/python2.6/Ice.py", line 790, in main
2009-10-24 14:25:44,538 INFO  [                    omero.util.Resources] (Thread-2  ) Halted
2009-10-24 14:25:44,642 WARNI [                                  stderr] (MainThread) status = self.run(args)
2009-10-24 14:25:44,646 WARNI [                                  stderr] (MainThread) File "/usr/local/omero_dist/lib/python/omero/util/__init__.py", line 353, in run
2009-10-24 14:25:44,650 WARNI [                                  stderr] (MainThread) sys.exit(100)
2009-10-24 14:25:44,650 WARNI [                                  stderr] (MainThread) SystemExit: 100
2009-10-24 14:26:06,624 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2009-10-24 14:26:06,716 INFO  [                       omero.util.Server] (MainThread) Starting
2009-10-24 14:26:06,720 INFO  [                    omero.util.Resources] (Thread-2  ) Starting
2009-10-24 14:26:06,808 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 1
2009-10-24 14:26:16,808 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 2
2009-10-24 14:26:26,809 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 3

Do I need to define the environment variables as I do if I install Ice in /opt/ice?
Any help appreciated. I've tried this configuration twice now and got the same error both times.
I'm guessing (hoping) it's something silly that I've done?

Thanks
Steve

[jmoore]

The various NoEndpointExceptions (in master.err and Processor-0.log) all point to the fact that the Blitz server (Blitz-0.log) didn't start up correctly. One typical cause is that the database was not configured correctly, but this doesn't appear in the short log section you showed. Is there anything else in the blitz log file?

[SteveO]

Here's the entire Blitz-0.log:

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2009-10-26 06:58:24,580 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2009-10-26 06:58:29,584 WARN  [                         java.util.prefs] (      main) Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
2009-10-26 06:58:29,840 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2009-10-26 06:58:40,541 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2009-10-26 06:59:57,545 INFO  [           ome.system.PermissionsContext] (      main) Setting omero.security.default_permissions to rw----
2009-10-26 07:00:32,719 INFO  [    ome.services.fulltext.FullTextThread] (      main) Initializing Full-Text Indexer
2009-10-26 07:00:36,524 INFO  [          ome.services.util.DBPatchCheck] (      main) Verified database patch: OMERO4.1__0
2009-10-26 07:00:36,528 INFO  [    ome.services.util.ServerVersionCheck] (      main) -------------------------------------------------
2009-10-26 07:00:36,528 INFO  [    ome.services.util.ServerVersionCheck] (      main) OMERO Version: Beta-4.1.0-r5585-b12 Ready.
2009-10-26 07:00:36,528 INFO  [    ome.services.util.ServerVersionCheck] (      main) -------------------------------------------------
2009-10-26 07:00:39,768 WARN  [                 ome.system.UpgradeCheck] (      main) UPGRADE AVAILABLE:Please upgrade to Beta-4.1.0 See http://trac.openmicroscopy.org.uk/omero for t
he latest version
2009-10-26 07:00:39,888 INFO  [    ome.tools.hibernate.ExtendedMetadata] (      main) Calculating ExtendedMetadata...
2009-10-26 07:01:37,235 INFO  [e.services.blitz.util.BlitzConfiguration] (      main) Initializing Ice.Communicator

I tried again from a fresh install of jaunty. I used cxallan's excellent instructions (from the CentOS 5.3 topic)
and modified these instructions for ubuntu. essentially, as root I used apt-get to install:
sun-java6-jdk
zeroc-ice
postresql
and all their dependencies, then switched to non-privileged user to wget and install omero.

Everything seemed fine until the bin/omero admin command failed on startup.

[jmoore]

Hi Steve,

sorry, I'm a bit at a loss. Could you do me a favor? Run:

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bin/omero admin stop
Waiting on shutdown. Use CTRL-C to exit


and make sure that there are no icegridnode processes running. For example,

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josh@mac:~/code/omero.git/dist$ ps auxw | grep icegridnode
josh      9870   0.0 -0.0    27368    448  p7  S+    4:59PM   0:00.00 grep icegridnode
josh@mac:~/code/omero.git/dist$


Then, delete the var directory:

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rm -rf var


and startup:

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bin/omero admin start


When you see Blitz-0.log hang again, stop:

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bin/omero admin stop


and tar up all of the log files:

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tar cjf logs.tar.bz2 var/log


Either attach those here or send them to me off-list/forum. I'll see if I can piece things together.

Thanks for your patience,
~Josh.

P.S. just in case, you might also attach the output of:

Code: Select all

bin/omero admin diagnostics


[SteveO]

Hi Josh-
here is the diagnostics ouptut after I get the failed to start after 5 minutes error, and issuing the bin/omero admin stop command.

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steve@slice102174:~/omero_dist$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics Beta-4.1.0-r5585-b12
================================================================================
       
Commands:   java -version                  1.6.0     (/usr/bin/java)
Commands:   python -V                      2.6       (/usr/bin/python)
Commands:   icegridnode --version          3.3       (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.3       (/usr/bin/icegridadmin)
Commands:   psql --version                 8.3.8     (/usr/bin/psql)

Server:     icegridnode                    not started

Log dir:    /home/steve/omero_dist/var/log exists

Log files:  Blitz-0.log                    0.0 KB        errors=0    warnings=3   
Log files:  DropBox.log                    1.0 KB        errors=2    warnings=0   
Log files:  FSServer.log                   0.0 KB        errors=1    warnings=0   
Log files:  Indexer-0.log                  0.0 KB        errors=0    warnings=1   
Log files:  OMEROweb.log                   n/a
Log files:  Processor-0.log                52.0 KB       errors=14   warnings=98 
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     1.0 KB        errors=0    warnings=4   
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.06 MB

and the log files are all attached as "logs.tar.bz2"

[jmoore]

Hi Steve,

sorry but we're still at a loss on this side. The only thing discernible from the logs is that your Java installation might not be happy. So two questions:

* What OS are you running on?

* After bin/omero admin start, could you run:

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bin/omero admin ice server signal Blitz-0 SIGQUIT


That will print a long message to var/log/master.out which I'd be grateful if you'd send us.

Thanks for all the help,
~Josh.

[SteveO]

Hi Josh -
Here is the master.out output for you. I tried to attach, but was told that the extension "out" is not allowed. After changing the name of the file to "master", and trying to attach it, I was told that the extension "txt" is not allowed. Easier just to include it inline.
I'm running linux ubuntu 9.04 (jaunty)

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2009-11-03 01:37:16
Full thread dump Java HotSpot(TM) 64-Bit Server VM (11.3-b02 mixed mode):

"Blitz-0-Ice.Timer" prio=10 tid=0x000000004079b000 nid=0x1ea0 in Object.wait() [0x00007f1a4d75a000..0x00007f1a4d75ad70]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00007f1a61528c60> (a IceInternal.Timer)
   at IceInternal.Timer.run(Timer.java:211)
   - locked <0x00007f1a61528c60> (a IceInternal.Timer)

"OMERO.scheduler_QuartzSchedulerThread" prio=10 tid=0x00007f1a40047000 nid=0x1e56 runnable [0x00007f1a4de7b000..0x00007f1a4de7ba70]
   java.lang.Thread.State: RUNNABLE
   at java.lang.AbstractStringBuilder.<init>(AbstractStringBuilder.java:45)
   at java.lang.StringBuffer.<init>(StringBuffer.java:79)
   at org.quartz.simpl.TriggerWrapper.getTriggerNameKey(RAMJobStore.java:1501)
   at org.quartz.simpl.RAMJobStore.triggerFired(RAMJobStore.java:1198)
   - locked <0x00007f1a61252bd0> (a java.lang.Object)
   at org.quartz.core.QuartzSchedulerThread.run(QuartzSchedulerThread.java:308)

"OMERO.scheduler_Worker-9" prio=10 tid=0x00007f1a40042c00 nid=0x1e55 in Object.wait() [0x00007f1a4df7c000..0x00007f1a4df7c9f0]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.getNextRunnable(SimpleThreadPool.java:428)
   - locked <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.access$000(SimpleThreadPool.java:47)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:518)

"OMERO.scheduler_Worker-8" prio=10 tid=0x00007f1a411cc000 nid=0x1e54 runnable [0x00007f1a4e07d000..0x00007f1a4e07db70]
   java.lang.Thread.State: RUNNABLE
   at java.lang.Thread.setPriority0(Native Method)
   at java.lang.Thread.setPriority(Thread.java:1021)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:541)

"OMERO.scheduler_Worker-7" prio=10 tid=0x00007f1a40666800 nid=0x1e53 runnable [0x00007f1a4e17e000..0x00007f1a4e17eaf0]
   java.lang.Thread.State: RUNNABLE
   at java.lang.Thread.setPriority0(Native Method)
   at java.lang.Thread.setPriority(Thread.java:1021)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:541)

"OMERO.scheduler_Worker-6" prio=10 tid=0x00007f1a40052000 nid=0x1e52 in Object.wait() [0x00007f1a4e27f000..0x00007f1a4e27fc70]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.getNextRunnable(SimpleThreadPool.java:428)
   - locked <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.access$000(SimpleThreadPool.java:47)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:518)

"OMERO.scheduler_Worker-5" prio=10 tid=0x00007f1a40050c00 nid=0x1e51 in Object.wait() [0x00007f1a4e380000..0x00007f1a4e380bf0]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.getNextRunnable(SimpleThreadPool.java:428)
   - locked <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.access$000(SimpleThreadPool.java:47)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:518)

"OMERO.scheduler_Worker-4" prio=10 tid=0x00007f1a40096000 nid=0x1e50 runnable [0x00007f1a4e481000..0x00007f1a4e481d70]
   java.lang.Thread.State: RUNNABLE
   at java.lang.Thread.setPriority0(Native Method)
   at java.lang.Thread.setPriority(Thread.java:1021)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:541)

"OMERO.scheduler_Worker-3" prio=10 tid=0x00007f1a404fac00 nid=0x1e4f in Object.wait() [0x00007f1a4e582000..0x00007f1a4e582cf0]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.getNextRunnable(SimpleThreadPool.java:428)
   - locked <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.access$000(SimpleThreadPool.java:47)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:518)

"OMERO.scheduler_Worker-2" prio=10 tid=0x00007f1a40091000 nid=0x1e4e in Object.wait() [0x00007f1a4e683000..0x00007f1a4e683a70]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.getNextRunnable(SimpleThreadPool.java:428)
   - locked <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.access$000(SimpleThreadPool.java:47)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:518)

"OMERO.scheduler_Worker-1" prio=10 tid=0x00007f1a40086c00 nid=0x1e4d in Object.wait() [0x00007f1a4e784000..0x00007f1a4e7849f0]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.getNextRunnable(SimpleThreadPool.java:428)
   - locked <0x00007f1a61246fd8> (a java.lang.Object)
   at org.quartz.simpl.SimpleThreadPool.access$000(SimpleThreadPool.java:47)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:518)

"OMERO.scheduler_Worker-0" prio=10 tid=0x00007f1a40086400 nid=0x1e4c runnable [0x00007f1a4e885000..0x00007f1a4e885b70]
   java.lang.Thread.State: RUNNABLE
   at java.lang.Thread.setPriority0(Native Method)
   at java.lang.Thread.setPriority(Thread.java:1021)
   at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:541)

"Ice.Timer" prio=10 tid=0x00000000407a5000 nid=0x1cd2 in Object.wait() [0x00007f1a4e986000..0x00007f1a4e986af0]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00007f1a5abe5ca8> (a IceInternal.Timer)
   at IceInternal.Timer.run(Timer.java:211)
   - locked <0x00007f1a5abe5ca8> (a IceInternal.Timer)

"bitronix-scheduler" daemon prio=10 tid=0x00000000402ec800 nid=0x1ccf runnable [0x00007f1a4ea87000..0x00007f1a4ea87c70]
   java.lang.Thread.State: RUNNABLE
   at bitronix.tm.timer.TaskScheduler.run(TaskScheduler.java:179)

"Timer-0" daemon prio=10 tid=0x0000000040410c00 nid=0x1ccd runnable [0x00007f1a4ec9f000..0x00007f1a4ec9fbf0]
   java.lang.Thread.State: RUNNABLE
   at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:444)
   at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:33)
   at java.util.prefs.FileSystemPreferences$4.run(FileSystemPreferences.java:419)
   at java.util.TimerThread.mainLoop(Timer.java:512)
   at java.util.TimerThread.run(Timer.java:462)

"Thread-1" daemon prio=10 tid=0x00000000405d9400 nid=0x1ccb runnable [0x00007f1a4eda0000..0x00007f1a4eda0d70]
   java.lang.Thread.State: RUNNABLE
   at java.io.UnixFileSystem.getBooleanAttributes0(Native Method)
   at java.io.UnixFileSystem.getBooleanAttributes(UnixFileSystem.java:228)
   at java.io.File.exists(File.java:733)
   at org.apache.log4j.helpers.FileWatchdog.checkAndConfigure(FileWatchdog.java:76)
   at org.apache.log4j.helpers.FileWatchdog.run(FileWatchdog.java:107)

"perf4j-async-stats-appender-sink-CoalescingStatistics" daemon prio=10 tid=0x000000004058a800 nid=0x1cc9 waiting on condition [0x00007f1a4eea1000..0x00007f1a4eea1cf0]
   java.lang.Thread.State: WAITING (parking)
   at sun.misc.Unsafe.park(Native Method)
   - parking to wait for  <0x00007f1a5a9b8fd0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
   at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
   at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
   at java.util.concurrent.ArrayBlockingQueue.take(ArrayBlockingQueue.java:317)
   at org.perf4j.log4j.AsyncCoalescingStatisticsAppender$StopWatchesFromQueueIterator.getNext(AsyncCoalescingStatisticsAppender.java:404)
   at org.perf4j.log4j.AsyncCoalescingStatisticsAppender$StopWatchesFromQueueIterator.hasNext(AsyncCoalescingStatisticsAppender.java:368)
   at org.perf4j.helpers.GroupingStatisticsIterator.getNext(GroupingStatisticsIterator.java:144)
   at org.perf4j.helpers.GroupingStatisticsIterator.hasNext(GroupingStatisticsIterator.java:97)
   at org.perf4j.log4j.AsyncCoalescingStatisticsAppender$Dispatcher.run(AsyncCoalescingStatisticsAppender.java:323)
   at java.lang.Thread.run(Thread.java:619)

"Low Memory Detector" daemon prio=10 tid=0x00000000401c7c00 nid=0x1c5a runnable [0x0000000000000000..0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"CompilerThread1" daemon prio=10 tid=0x00000000401c5c00 nid=0x1c59 waiting on condition [0x0000000000000000..0x00007f1a4f5d23b0]
   java.lang.Thread.State: RUNNABLE

"CompilerThread0" daemon prio=10 tid=0x00000000401c1c00 nid=0x1c58 waiting on condition [0x0000000000000000..0x00007f1a4f6d3380]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=10 tid=0x00000000401c0000 nid=0x1c57 waiting on condition [0x0000000000000000..0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=10 tid=0x000000004019dc00 nid=0x1c56 in Object.wait() [0x00007f1a4f8d6000..0x00007f1a4f8d6bf0]
   java.lang.Thread.State: WAITING (on object monitor)
   at java.lang.Object.wait(Native Method)
   - waiting on <0x00007f1a5a94dfc8> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:116)
   - locked <0x00007f1a5a94dfc8> (a java.lang.ref.ReferenceQueue$Lock)
   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:132)
   at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=10 tid=0x000000004019c000 nid=0x1c55 runnable [0x00007f1a4f9d7000..0x00007f1a4f9d7d70]
   java.lang.Thread.State: RUNNABLE
   at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:109)
   - locked <0x00007f1a5a94e0a8> (a java.lang.ref.Reference$Lock)

"main" prio=10 tid=0x0000000040112000 nid=0x1c53 runnable [0x00007f1a79241000..0x00007f1a79245eb0]
   java.lang.Thread.State: RUNNABLE
   at sun.nio.ch.ServerSocketChannelImpl.socket(ServerSocketChannelImpl.java:92)
   - locked <0x00007f1a6152aaf0> (a java.lang.Object)
   at IceInternal.Network.setReuseAddress(Network.java:239)
   at IceInternal.TcpAcceptor.<init>(TcpAcceptor.java:101)
   at IceInternal.TcpEndpointI.acceptor(TcpEndpointI.java:381)
   at IceInternal.IncomingConnectionFactory.<init>(IncomingConnectionFactory.java:449)
   at Ice.ObjectAdapterI.<init>(ObjectAdapterI.java:906)
   at IceInternal.ObjectAdapterFactory.createObjectAdapter(ObjectAdapterFactory.java:183)
   - locked <0x00007f1a61528110> (a IceInternal.ObjectAdapterFactory)
   at IceInternal.Instance.getAdmin(Instance.java:391)
   - locked <0x00007f1a61527400> (a IceInternal.Instance)
   at IceInternal.Instance.finishSetup(Instance.java:858)
   at Ice.CommunicatorI.finishSetup(CommunicatorI.java:225)
   at Ice.Util.initialize(Util.java:97)
   at ome.services.blitz.util.BlitzConfiguration.createCommunicator(BlitzConfiguration.java:197)
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:134)
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:100)
   at ome.services.blitz.util.BlitzConfiguration.<init>(BlitzConfiguration.java:81)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:100)
   at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:248)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:925)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:835)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:440)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
   at java.security.AccessController.doPrivileged(Native Method)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
   - locked <0x00007f1a614cb0c0> (a java.util.concurrent.ConcurrentHashMap)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
   at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeansOfType(DefaultListableBeanFactory.java:308)
   at org.springframework.context.support.AbstractApplicationContext.getBeansOfType(AbstractApplicationContext.java:948)
   at org.springframework.context.support.AbstractApplicationContext.registerListeners(AbstractApplicationContext.java:702)
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:378)
   - locked <0x00007f1a614ca388> (a java.lang.Object)
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
   at ome.system.OmeroContext.<init>(OmeroContext.java:103)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:100)
   at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:248)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:925)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:835)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:440)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
   at java.security.AccessController.doPrivileged(Native Method)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
   - locked <0x00007f1a5aa22830> (a java.util.concurrent.ConcurrentHashMap)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:168)
   at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:885)
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397)
   - locked <0x00007f1a5aa22938> (a java.util.HashMap)
   at ome.system.OmeroContext.getInstance(OmeroContext.java:203)
   at ome.services.blitz.Entry.start(Entry.java:203)
   at ome.services.blitz.Entry.main(Entry.java:121)

"VM Thread" prio=10 tid=0x0000000040196800 nid=0x1c54 runnable

"VM Periodic Task Thread" prio=10 tid=0x00000000401ca000 nid=0x1c5b waiting on condition

JNI global references: 633

Heap
def new generation   total 87424K, used 699K [0x00007f1a4fea0000, 0x00007f1a55d70000, 0x00007f1a5a940000)
  eden space 77760K,   0% used [0x00007f1a4fea0000, 0x00007f1a4ff4ecb0, 0x00007f1a54a90000)
  from space 9664K,   0% used [0x00007f1a54a90000, 0x00007f1a54a90000, 0x00007f1a55400000)
  to   space 9664K,   0% used [0x00007f1a55400000, 0x00007f1a55400000, 0x00007f1a55d70000)
tenured generation   total 193964K, used 116376K [0x00007f1a5a940000, 0x00007f1a666ab000, 0x00007f1a6fea0000)
   the space 193964K,  59% used [0x00007f1a5a940000, 0x00007f1a61ae6080, 0x00007f1a61ae6200, 0x00007f1a666ab000)
compacting perm gen  total 40960K, used 40729K [0x00007f1a6fea0000, 0x00007f1a726a0000, 0x00007f1a752a0000)
   the space 40960K,  99% used [0x00007f1a6fea0000, 0x00007f1a72666578, 0x00007f1a72666600, 0x00007f1a726a0000)
No shared spaces configured.

Thanks for your help
Steve

[jmoore]

In an private message from Steve:

... I tried with the new release of Ubuntu (9.10) and followed exactly (I think) the same set of procedures for installing the different components required by OMERO. Installation took 15 minutes at most, and OMERO started flawlessly....

We're still unsure of the cause. If anyone has any information, let us know.

~Josh