Open Microscopy Environment

by **fuho** » Wed Sep 12, 2012 4:57 am

Hi,
I have installed OMERO on Ubuntu 10.04 LTS server following the Ubuntu tutorial in the sticky on this forum.
When I tried to login to OMERO.web as root (the only user created during install) I am getting "Error: Server is not responding, please contact administrator."

I tried to figure out what is going on, looked online, then went to terminal and tried to restart OMERO from console:

Code: Select all: omero> admin restart Waiting on shutdown. Use CTRL-C to exit ......No descriptor given. Using etc/grid/default.xml Waiting on startup. Use CTRL-C to exit ............................. Failed to startup some components after 5 minutes Calling "stop" on remaining components Waiting on shutdown. Use CTRL-C to exit ......omero> admin diagnostics =================================================================== OMERO Diagnostics 4.4.3-ice34-b5 =================================================================== Commands: java -version 1.6.0 (/usr/bin/java Commands: python -V 2.6.5 (/usr/bin/pyth Commands: icegridnode --version 3.4.2 (/usr/bin/iceg Commands: icegridadmin --version 3.4.2 (/usr/bin/iceg Commands: psql --version 8.4.13 (/usr/bin/psql Server: icegridnode not started Log dir: /home/omero/OMERO.server-4.4.3-ice34-b5/var/log exists Log files: Blitz-0.log 0.0 KB Log files: DropBox.log 5.0 KB errors=8 Log files: FileServer.log 0.0 KB Log files: Indexer-0.log 54.0 KB errors=1 Log files: MonitorServer.log 0.0 KB Log files: OMEROweb.log 23.0 KB errors=24 Log files: OMEROweb_request.log 0.0 KB Log files: PixelData-0.log 0.0 KB Log files: Processor-0.log 63.0 KB errors=18 Log files: Tables-0.log 132.0 KB errors=35 Log files: TestDropBox.log n/a Log files: master.err 2.0 KB Log files: master.out 0.0 KB Log files: Total size 0.29 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin: Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO.web status... [RUNNING] (PID 17782) omero> quit omero@urpad:~/OMERO.server-4.4.3-ice34-b5$ mc

As you can see after 5 minutes it gives up and tries (and succeeds) to stop all other OMERO services which means nothing is running (checked using #top). I spent hours trying to make some sense from log files but this being my first day I failed at understanding them :oops:

Can someone please have a look and possibly help me out? It would really help me a lot.

Here are excerpts from log files:
Processor-0.log

Code: Select all: 2012-09-12 07:50:12,756 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:50:12,756 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup 2012-09-12 07:50:22,756 INFO [ omero.util.Server] (MainThread) Starting 2012-09-12 07:50:22,759 INFO [ omero.util.Resources] (Thread-2 ) Starting 2012-09-12 07:51:08,859 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1 2012-09-12 07:51:18,860 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2 2012-09-12 07:51:28,862 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3 2012-09-12 07:51:38,863 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4 2012-09-12 07:51:48,865 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5 2012-09-12 07:51:58,867 INFO [ omero.utils] (MainThread) Failed to get session on attempt 6 2012-09-12 07:52:08,867 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:52:08,868 ERROR [ omero.util.Server] (MainThread) Failed initialization Traceback (most recent call last): File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 436, in run self.impl = self.impl_class(ctx) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/processor.py", line 662, in __init__ omero.util.Servant.__init__(self, ctx, needs_session = needs_session) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 513, in __init__ self.ctx.newSession() File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 290, in newSession self.session = internal_service_factory(self.communicator, stop_event = self.stop_event) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 193, in internal_service_factory raise excpt NoEndpointException: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:52:08,950 INFO [ omero.util.Server] (MainThread) Cleanup 2012-09-12 07:52:08,950 INFO [ omero.util.Server] (MainThread) Stopped 2012-09-12 07:52:08,951 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:52:08,951 INFO [ omero.processor.ProcessorI] (MainThread) Cleaning up 2012-09-12 07:52:08,951 INFO [ omero.processor.ProcessorI] (MainThread) Done 2012-09-12 07:52:08,952 WARNI [ stderr] (MainThread) 2012-09-12 07:52:08.952122 Processor-0: error: Traceback (most recent call last): File "/usr/lib/pymodules/python2.6/Ice.py", line 984, in main status = self.doMain(args, initData) File "/usr/lib/pymodules/python2.6/Ice.py", line 1031, in doMain return self.run(args) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 440, in run sys.exit(100) SystemExit: 100 2012-09-12 07:52:08,952 INFO [ omero.util.Resources] (Thread-2 ) Halted 2012-09-12 07:52:11,652 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:52:11,652 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup 2012-09-12 07:52:21,652 INFO [ omero.util.Server] (MainThread) Starting 2012-09-12 07:52:21,655 INFO [ omero.util.Resources] (Thread-2 ) Starting 2012-09-12 07:52:21,657 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1 2012-09-12 07:52:31,658 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2 2012-09-12 07:52:41,660 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3 2012-09-12 07:52:51,661 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4 2012-09-12 07:53:01,663 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5 2012-09-12 07:53:11,664 INFO [ omero.utils] (MainThread) Failed to get session on attempt 6 2012-09-12 07:53:21,665 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:53:21,665 ERROR [ omero.util.Server] (MainThread) Failed initialization Traceback (most recent call last): File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 436, in run self.impl = self.impl_class(ctx) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/processor.py", line 662, in __init__ omero.util.Servant.__init__(self, ctx, needs_session = needs_session) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 513, in __init__ self.ctx.newSession() File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 290, in newSession self.session = internal_service_factory(self.communicator, stop_event = self.stop_event) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 193, in internal_service_factory raise excpt NoEndpointException: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:53:21,666 INFO [ omero.util.Server] (MainThread) Cleanup 2012-09-12 07:53:21,666 INFO [ omero.util.Server] (MainThread) Stopped 2012-09-12 07:53:21,666 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:53:21,666 INFO [ omero.processor.ProcessorI] (MainThread) Cleaning up 2012-09-12 07:53:21,666 INFO [ omero.processor.ProcessorI] (MainThread) Done 2012-09-12 07:53:21,666 WARNI [ stderr] (MainThread) 2012-09-12 07:53:21.666938 Processor-0: error: Traceback (most recent call last): File "/usr/lib/pymodules/python2.6/Ice.py", line 984, in main status = self.doMain(args, initData) File "/usr/lib/pymodules/python2.6/Ice.py", line 1031, in doMain return self.run(args) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 440, in run sys.exit(100) SystemExit: 100 2012-09-12 07:53:21,750 INFO [ omero.util.Resources] (Thread-2 ) Halted 2012-09-12 07:53:24,359 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:53:24,359 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup 2012-09-12 07:53:34,359 INFO [ omero.util.Server] (MainThread) Starting 2012-09-12 07:53:34,362 INFO [ omero.util.Resources] (Thread-2 ) Starting 2012-09-12 07:53:34,364 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1 2012-09-12 07:53:44,365 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2 2012-09-12 07:53:54,450 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3 2012-09-12 07:54:04,452 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4 2012-09-12 07:54:14,453 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5 2012-09-12 07:54:24,455 INFO [ omero.utils] (MainThread) Failed to get session on attempt 6 2012-09-12 07:54:34,455 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:54:34,456 ERROR [ omero.util.Server] (MainThread) Failed initialization Traceback (most recent call last): File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 436, in run self.impl = self.impl_class(ctx) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/processor.py", line 662, in __init__ omero.util.Servant.__init__(self, ctx, needs_session = needs_session) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 513, in __init__ self.ctx.newSession() File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 290, in newSession self.session = internal_service_factory(self.communicator, stop_event = self.stop_event) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 193, in internal_service_factory raise excpt NoEndpointException: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:54:34,456 INFO [ omero.util.Server] (MainThread) Cleanup 2012-09-12 07:54:34,457 INFO [ omero.util.Server] (MainThread) Stopped 2012-09-12 07:54:34,457 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:54:34,457 INFO [ omero.processor.ProcessorI] (MainThread) Cleaning up 2012-09-12 07:54:34,457 INFO [ omero.processor.ProcessorI] (MainThread) Done 2012-09-12 07:54:34,458 INFO [ omero.util.Resources] (Thread-2 ) Halted 2012-09-12 07:54:34,458 WARNI [ stderr] (MainThread) 2012-09-12 07:54:34.458696 Processor-0: error: Traceback (most recent call last): File "/usr/lib/pymodules/python2.6/Ice.py", line 984, in main status = self.doMain(args, initData) File "/usr/lib/pymodules/python2.6/Ice.py", line 1031, in doMain return self.run(args) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 440, in run sys.exit(100) SystemExit: 100 2012-09-12 07:54:37,162 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:54:37,163 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup 2012-09-12 07:54:47,163 INFO [ omero.util.Server] (MainThread) Starting 2012-09-12 07:54:47,166 INFO [ omero.util.Resources] (Thread-2 ) Starting 2012-09-12 07:54:47,251 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1 2012-09-12 07:54:57,252 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2 2012-09-12 07:55:07,254 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3 2012-09-12 07:55:17,255 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4 2012-09-12 07:55:27,257 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5 2012-09-12 07:55:37,258 INFO [ omero.utils] (MainThread) Failed to get session on attempt 6 2012-09-12 07:55:47,259 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:55:47,259 ERROR [ omero.util.Server] (MainThread) Failed initialization Traceback (most recent call last): File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 436, in run self.impl = self.impl_class(ctx) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/processor.py", line 662, in __init__ omero.util.Servant.__init__(self, ctx, needs_session = needs_session) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 513, in __init__ self.ctx.newSession() File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 290, in newSession self.session = internal_service_factory(self.communicator, stop_event = self.stop_event) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 193, in internal_service_factory raise excpt NoEndpointException: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:55:47,259 INFO [ omero.util.Server] (MainThread) Cleanup 2012-09-12 07:55:47,259 INFO [ omero.util.Server] (MainThread) Stopped 2012-09-12 07:55:47,259 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:55:47,260 INFO [ omero.processor.ProcessorI] (MainThread) Cleaning up 2012-09-12 07:55:47,260 INFO [ omero.processor.ProcessorI] (MainThread) Done 2012-09-12 07:55:47,260 WARNI [ stderr] (MainThread) 2012-09-12 07:55:47.260787 Processor-0: error: Traceback (most recent call last): File "/usr/lib/pymodules/python2.6/Ice.py", line 984, in main status = self.doMain(args, initData) File "/usr/lib/pymodules/python2.6/Ice.py", line 1031, in doMain return self.run(args) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 440, in run sys.exit(100) SystemExit: 100 2012-09-12 07:55:47,350 INFO [ omero.util.Resources] (Thread-2 ) Halted 2012-09-12 07:55:50,052 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:55:50,052 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup 2012-09-12 07:56:00,052 INFO [ omero.util.Server] (MainThread) Starting 2012-09-12 07:56:00,055 INFO [ omero.util.Resources] (Thread-2 ) Starting 2012-09-12 07:56:00,057 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1 2012-09-12 07:56:10,059 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2 2012-09-12 07:56:20,060 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3 2012-09-12 07:56:30,061 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4 2012-09-12 07:56:40,063 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5 2012-09-12 07:56:50,064 INFO [ omero.utils] (MainThread) Failed to get session on attempt 6 2012-09-12 07:57:00,064 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:57:00,065 ERROR [ omero.util.Server] (MainThread) Failed initialization Traceback (most recent call last): File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 436, in run self.impl = self.impl_class(ctx) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/processor.py", line 662, in __init__ omero.util.Servant.__init__(self, ctx, needs_session = needs_session) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 513, in __init__ self.ctx.newSession() File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 290, in newSession self.session = internal_service_factory(self.communicator, stop_event = self.stop_event) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 193, in internal_service_factory raise excpt NoEndpointException: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:57:00,065 INFO [ omero.util.Server] (MainThread) Cleanup 2012-09-12 07:57:00,065 INFO [ omero.util.Server] (MainThread) Stopped 2012-09-12 07:57:00,065 INFO [ omero.util.Server] (MainThread) ******************************************************************************** 2012-09-12 07:57:00,065 INFO [ omero.processor.ProcessorI] (MainThread) Cleaning up 2012-09-12 07:57:00,066 INFO [ omero.processor.ProcessorI] (MainThread) Done 2012-09-12 07:57:00,066 WARNI [ stderr] (MainThread) 2012-09-12 07:57:00.066359 Processor-0: error: Traceback (most recent call last): File "/usr/lib/pymodules/python2.6/Ice.py", line 984, in main status = self.doMain(args, initData) File "/usr/lib/pymodules/python2.6/Ice.py", line 1031, in doMain return self.run(args) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 440, in run sys.exit(100) SystemExit: 100 2012-09-12 07:57:00,070 INFO [ omero.util.Resources] (Thread-2 ) Halted

master.err

Code: Select all: -! 09/12/12 07:50:08.733 icegridnode: warning: couldn't reach the IceGrid registry (this is expected if it's down, otherwise please check the value of the Ice.Default.Locator property): Outgoing.cpp:226: Ice::TimeoutException: timeout while sending or receiving data -! 09/12/12 07:51:08.859 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters' Reference.cpp:1566: Ice::NoEndpointException: no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters' -! 09/12/12 07:51:08.860 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters' Reference.cpp:1566: Ice::NoEndpointException: no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'

DropBox.log

Code: Select all: 2012-09-12 07:51:08,860 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1 2012-09-12 07:51:11,861 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2 2012-09-12 07:51:14,863 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3 2012-09-12 07:51:17,864 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4 2012-09-12 07:51:20,951 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5 2012-09-12 07:51:23,951 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:51:23,951 ERROR [ fsclient.DropBox] (MainThread) Failed to get Session: Traceback (most recent call last): File "lib/python/fsDropBox.py", line 85, in run retries=self.maxRetries, interval=self.retryInterval) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 193, in internal_service_factory raise excpt NoEndpointException: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:51:23,952 ERROR [ fsclient.DropBox] (MainThread) Quitting 2012-09-12 07:51:23,953 INFO [ fsclient.DropBox] (MainThread) Exiting with exit code: -1 2012-09-12 07:51:26,360 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1 2012-09-12 07:51:29,361 INFO [ omero.utils] (MainThread) Failed to get session on attempt 2 2012-09-12 07:51:32,363 INFO [ omero.utils] (MainThread) Failed to get session on attempt 3 2012-09-12 07:51:35,364 INFO [ omero.utils] (MainThread) Failed to get session on attempt 4 2012-09-12 07:51:38,365 INFO [ omero.utils] (MainThread) Failed to get session on attempt 5 2012-09-12 07:51:41,366 WARNI [ omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:51:41,366 ERROR [ fsclient.DropBox] (MainThread) Failed to get Session: Traceback (most recent call last): File "lib/python/fsDropBox.py", line 85, in run retries=self.maxRetries, interval=self.retryInterval) File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/util/__init__.py", line 193, in internal_service_factory raise excpt NoEndpointException: exception ::Ice::NoEndpointException { proxy = BlitzManager -t @ BlitzAdapters } 2012-09-12 07:51:41,367 ERROR [ fsclient.DropBox] (MainThread) Quitting 2012-09-12 07:51:41,451 INFO [ fsclient.DropBox] (MainThread) Exiting with exit code: -1

OMEROweb.log

Code: Select all: 2012-09-12 04:29:59,364 INFO [ omero.gateway] (proc.17787) connect:1714 Failed to create session. 2012-09-12 04:29:59,366 INFO [ omeroweb.webadmin.webadmin_utils] (proc.17787) getGuestConnection:18 Have connection as Guest 2012-09-12 04:29:59,366 ERROR [ omeroweb.webadmin.webadmin_utils] (proc.17787) _checkVersion:42 Traceback (most recent call last): File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omeroweb/webadmin/webadmin_utils.py", line 30, in _checkVersion agent = conn.getServerVersion() File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omeroweb/webclient/webclient_gateway.py", line 310, in getServerVersion conf = self.getConfigService() File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/gateway/__init__.py", line 2057, in getConfigService return self._proxies['config'] File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/gateway/__init__.py", line 1215, in __getitem__ raise Ice.ConnectionLostException ConnectionLostException: Ice.ConnectionLostException: recv() returned zero 2012-09-12 04:29:59,462 INFO [ omero.gateway] (proc.17787) connect:1714 Failed to create session. 2012-09-12 04:29:59,463 INFO [ omeroweb.webadmin.webadmin_utils] (proc.17787) getGuestConnection:18 Have connection as Guest 2012-09-12 04:29:59,463 ERROR [ omeroweb.webadmin.webadmin_utils] (proc.17787) _isServerOn:52 Traceback (most recent call last): File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omeroweb/webadmin/webadmin_utils.py", line 49, in _isServerOn conn.getServerVersion() File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omeroweb/webclient/webclient_gateway.py", line 310, in getServerVersion conf = self.getConfigService() File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/gateway/__init__.py", line 2057, in getConfigService return self._proxies['config'] File "/home/omero/OMERO.server-4.4.3-ice34-b5/lib/python/omero/gateway/__init__.py", line 1215, in __getitem__ raise Ice.ConnectionLostException ConnectionLostException: Ice.ConnectionLostException: recv() returned zero

Could anyone point me in the right direction as to what am I doing wrong? This is my first time with OMERO and I would really like to get it running so I can start fiddling with it and start understanding it much more. Thanks in advance for any help.

by **jmoore** » Wed Sep 12, 2012 7:12 am

Hi,

what's odd is that there's nothing in var/log/Blitz-0.log. That's the main process which needs to be started for you to be able to login. Can you try starting via:

Code: Select all: bin/omero admin startasync

which will exit immediately and not wait for start. Then send us the output of:

Code: Select all: bin/omero admin diagnostics

Thanks,
~Josh

by **fuho** » Wed Sep 12, 2012 2:38 pm

Hi Josh,
here is the output of

bin/omero admin diagnostics

in different times:

Code: Select all: omero@urpad:~/OMERO.server-4.4.3-ice34-b5$ ./bin/omero admin startasync;for i in {0,'1s','10s','30s','1m','2m','5m',};do sleep $i;date;echo $i;./bin/omero admin diagnostics;done;echo DONE; No descriptor given. Using etc/grid/default.xml Wed Sep 12 18:26:41 MSK 2012 0 ================================================================================ OMERO Diagnostics 4.4.3-ice34-b5 ================================================================================ Commands: java -version 1.6.0 (/usr/bin/java) Commands: python -V 2.6.5 (/usr/bin/python) Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode) Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin) Commands: psql --version 8.4.13 (/usr/bin/psql) Server: icegridnode running Server: Blitz-0 activating (enabled) Server: DropBox activating (enabled) Server: FileServer active (pid = 9960, enabled) Server: Indexer-0 activating (enabled) Server: MonitorServer active (pid = 9945, enabled) Server: OMERO.Glacier2 active (pid = 9948, enabled) Server: OMERO.IceStorm active (pid = 9958, enabled) Server: PixelData-0 activating (enabled) Server: Processor-0 activating (enabled) Server: Tables-0 activating (enabled) Server: TestDropBox inactive (enabled) Log dir: /home/omero/OMERO.server-4.4.3-ice34-b5/var/log exists Log files: Blitz-0.log 1.0 KB Log files: DropBox.log 16.0 KB errors=22 warnings=11 Log files: FileServer.log 2.0 KB Log files: Indexer-0.log 56.0 KB errors=1 warnings=6 Log files: MonitorServer.log 3.0 KB Log files: OMEROweb.log 29.0 KB errors=32 warnings=6 Log files: OMEROweb_request.log 0.0 KB Log files: PixelData-0.log 1.0 KB Log files: Processor-0.log 111.0 KB errors=31 warnings=62 Log files: Tables-0.log 255.0 KB errors=67 warnings=134 Log files: TestDropBox.log n/a Log files: master.err 5.0 KB Log files: master.out 2.0 KB Log files: Total size 0.49 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO.web status... [RUNNING] (PID 17782) Wed Sep 12 18:26:54 MSK 2012 1s ================================================================================ OMERO Diagnostics 4.4.3-ice34-b5 ================================================================================ Commands: java -version 1.6.0 (/usr/bin/java) Commands: python -V 2.6.5 (/usr/bin/python) Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode) Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin) Commands: psql --version 8.4.13 (/usr/bin/psql) Server: icegridnode running Server: Blitz-0 activating (enabled) Server: DropBox activating (enabled) Server: FileServer active (pid = 9960, enabled) Server: Indexer-0 activating (enabled) Server: MonitorServer active (pid = 9945, enabled) Server: OMERO.Glacier2 active (pid = 9948, enabled) Server: OMERO.IceStorm active (pid = 9958, enabled) Server: PixelData-0 activating (enabled) Server: Processor-0 activating (enabled) Server: Tables-0 activating (enabled) Server: TestDropBox inactive (enabled) Log dir: /home/omero/OMERO.server-4.4.3-ice34-b5/var/log exists Log files: Blitz-0.log 1.0 KB Log files: DropBox.log 16.0 KB errors=22 warnings=11 Log files: FileServer.log 2.0 KB Log files: Indexer-0.log 56.0 KB errors=1 warnings=6 Log files: MonitorServer.log 3.0 KB Log files: OMEROweb.log 29.0 KB errors=32 warnings=6 Log files: OMEROweb_request.log 0.0 KB Log files: PixelData-0.log 1.0 KB Log files: Processor-0.log 111.0 KB errors=31 warnings=62 Log files: Tables-0.log 255.0 KB errors=67 warnings=134 Log files: TestDropBox.log n/a Log files: master.err 5.0 KB Log files: master.out 2.0 KB Log files: Total size 0.49 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO.web status... [RUNNING] (PID 17782) Wed Sep 12 18:27:13 MSK 2012 10s ================================================================================ OMERO Diagnostics 4.4.3-ice34-b5 ================================================================================ Commands: java -version 1.6.0 (/usr/bin/java) Commands: python -V 2.6.5 (/usr/bin/python) Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode) Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin) Commands: psql --version 8.4.13 (/usr/bin/psql) Server: icegridnode running Server: Blitz-0 inactive (disabled) Server: DropBox activating (enabled) Server: FileServer active (pid = 9960, enabled) Server: Indexer-0 activating (enabled) Server: MonitorServer active (pid = 9945, enabled) Server: OMERO.Glacier2 active (pid = 9948, enabled) Server: OMERO.IceStorm active (pid = 9958, enabled) Server: PixelData-0 inactive (disabled) Server: Processor-0 activating (enabled) Server: Tables-0 activating (enabled) Server: TestDropBox inactive (enabled) Log dir: /home/omero/OMERO.server-4.4.3-ice34-b5/var/log exists Log files: Blitz-0.log 1.0 KB Log files: DropBox.log 16.0 KB errors=22 warnings=11 Log files: FileServer.log 2.0 KB Log files: Indexer-0.log 57.0 KB errors=1 warnings=6 Log files: MonitorServer.log 3.0 KB Log files: OMEROweb.log 29.0 KB errors=32 warnings=6 Log files: OMEROweb_request.log 0.0 KB Log files: PixelData-0.log 1.0 KB Log files: Processor-0.log 111.0 KB errors=31 warnings=62 Log files: Tables-0.log 256.0 KB errors=67 warnings=134 Log files: TestDropBox.log n/a Log files: master.err 6.0 KB Log files: master.out 3.0 KB Log files: Total size 0.49 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO.web status... [RUNNING] (PID 17782) Wed Sep 12 18:27:50 MSK 2012 30s ================================================================================ OMERO Diagnostics 4.4.3-ice34-b5 ================================================================================ Commands: java -version 1.6.0 (/usr/bin/java) Commands: python -V 2.6.5 (/usr/bin/python) Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode) Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin) Commands: psql --version 8.4.13 (/usr/bin/psql) Server: icegridnode running Server: Blitz-0 inactive (disabled) Server: DropBox inactive (disabled) Server: FileServer active (pid = 9960, enabled) Server: Indexer-0 inactive (disabled) Server: MonitorServer active (pid = 9945, enabled) Server: OMERO.Glacier2 active (pid = 9948, enabled) Server: OMERO.IceStorm active (pid = 9958, enabled) Server: PixelData-0 inactive (disabled) Server: Processor-0 activation timed out (pid = 9937, enabled) Server: Tables-0 activation timed out (pid = 9985, enabled) Server: TestDropBox inactive (enabled) Log dir: /home/omero/OMERO.server-4.4.3-ice34-b5/var/log exists Log files: Blitz-0.log 1.0 KB Log files: DropBox.log 17.0 KB errors=24 warnings=12 Log files: FileServer.log 2.0 KB Log files: Indexer-0.log 57.0 KB errors=1 warnings=6 Log files: MonitorServer.log 3.0 KB Log files: OMEROweb.log 29.0 KB errors=32 warnings=6 Log files: OMEROweb_request.log 0.0 KB Log files: PixelData-0.log 1.0 KB Log files: Processor-0.log 112.0 KB errors=31 warnings=62 Log files: Tables-0.log 256.0 KB errors=67 warnings=134 Log files: TestDropBox.log n/a Log files: master.err 6.0 KB Log files: master.out 3.0 KB Log files: Total size 0.49 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO.web status... [RUNNING] (PID 17782) Wed Sep 12 18:28:58 MSK 2012 1m ================================================================================ OMERO Diagnostics 4.4.3-ice34-b5 ================================================================================ Commands: java -version 1.6.0 (/usr/bin/java) Commands: python -V 2.6.5 (/usr/bin/python) Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode) Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin) Commands: psql --version 8.4.13 (/usr/bin/psql) Server: icegridnode running Server: Blitz-0 inactive (disabled) Server: DropBox inactive (disabled) Server: FileServer active (pid = 9960, enabled) Server: Indexer-0 inactive (disabled) Server: MonitorServer active (pid = 9945, enabled) Server: OMERO.Glacier2 active (pid = 9948, enabled) Server: OMERO.IceStorm active (pid = 9958, enabled) Server: PixelData-0 inactive (disabled) Server: Processor-0 inactive (disabled) Server: Tables-0 activating (enabled) Server: TestDropBox inactive (enabled) Log dir: /home/omero/OMERO.server-4.4.3-ice34-b5/var/log exists Log files: Blitz-0.log 1.0 KB Log files: DropBox.log 17.0 KB errors=24 warnings=12 Log files: FileServer.log 2.0 KB Log files: Indexer-0.log 57.0 KB errors=1 warnings=6 Log files: MonitorServer.log 3.0 KB Log files: OMEROweb.log 29.0 KB errors=32 warnings=6 Log files: OMEROweb_request.log 0.0 KB Log files: PixelData-0.log 1.0 KB Log files: Processor-0.log 114.0 KB errors=32 warnings=64 Log files: Tables-0.log 260.0 KB errors=68 warnings=136 Log files: TestDropBox.log n/a Log files: master.err 6.0 KB Log files: master.out 3.0 KB Log files: Total size 0.50 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO.web status... [RUNNING] (PID 17782) Wed Sep 12 18:31:06 MSK 2012 2m ================================================================================ OMERO Diagnostics 4.4.3-ice34-b5 ================================================================================ Commands: java -version 1.6.0 (/usr/bin/java) Commands: python -V 2.6.5 (/usr/bin/python) Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode) Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin) Commands: psql --version 8.4.13 (/usr/bin/psql) Server: icegridnode running Server: Blitz-0 inactive (disabled) Server: DropBox inactive (disabled) Server: FileServer active (pid = 9960, enabled) Server: Indexer-0 inactive (disabled) Server: MonitorServer active (pid = 9945, enabled) Server: OMERO.Glacier2 active (pid = 9948, enabled) Server: OMERO.IceStorm active (pid = 9958, enabled) Server: PixelData-0 inactive (disabled) Server: Processor-0 inactive (disabled) Server: Tables-0 activating (enabled) Server: TestDropBox inactive (enabled) Log dir: /home/omero/OMERO.server-4.4.3-ice34-b5/var/log exists Log files: Blitz-0.log 1.0 KB Log files: DropBox.log 17.0 KB errors=24 warnings=12 Log files: FileServer.log 2.0 KB Log files: Indexer-0.log 57.0 KB errors=1 warnings=6 Log files: MonitorServer.log 3.0 KB Log files: OMEROweb.log 29.0 KB errors=32 warnings=6 Log files: OMEROweb_request.log 0.0 KB Log files: PixelData-0.log 1.0 KB Log files: Processor-0.log 114.0 KB errors=32 warnings=64 Log files: Tables-0.log 267.0 KB errors=70 warnings=140 Log files: TestDropBox.log n/a Log files: master.err 6.0 KB Log files: master.out 3.0 KB Log files: Total size 0.51 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO.web status... [RUNNING] (PID 17782) Wed Sep 12 18:36:13 MSK 2012 5m ================================================================================ OMERO Diagnostics 4.4.3-ice34-b5 ================================================================================ Commands: java -version 1.6.0 (/usr/bin/java) Commands: python -V 2.6.5 (/usr/bin/python) Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode) Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin) Commands: psql --version 8.4.13 (/usr/bin/psql) Server: icegridnode running Server: Blitz-0 inactive (disabled) Server: DropBox inactive (disabled) Server: FileServer active (pid = 9960, enabled) Server: Indexer-0 inactive (disabled) Server: MonitorServer active (pid = 9945, enabled) Server: OMERO.Glacier2 active (pid = 9948, enabled) Server: OMERO.IceStorm active (pid = 9958, enabled) Server: PixelData-0 inactive (disabled) Server: Processor-0 inactive (disabled) Server: Tables-0 activating (enabled) Server: TestDropBox inactive (enabled) Log dir: /home/omero/OMERO.server-4.4.3-ice34-b5/var/log exists Log files: Blitz-0.log 1.0 KB Log files: DropBox.log 17.0 KB errors=24 warnings=12 Log files: FileServer.log 2.0 KB Log files: Indexer-0.log 57.0 KB errors=1 warnings=6 Log files: MonitorServer.log 3.0 KB Log files: OMEROweb.log 29.0 KB errors=32 warnings=6 Log files: OMEROweb_request.log 0.0 KB Log files: PixelData-0.log 1.0 KB Log files: Processor-0.log 114.0 KB errors=32 warnings=64 Log files: Tables-0.log 282.0 KB errors=74 warnings=148 Log files: TestDropBox.log n/a Log files: master.err 6.0 KB Log files: master.out 3.0 KB Log files: Total size 0.52 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO.web status... [RUNNING] (PID 17782) DONE omero@urpad:~/OMERO.server-4.4.3-ice34-b5$

Does it help at all?

Just in case, here is the COMPLETE Blitz-0.log

Code: Select all: 2012-09-12 06:26:21,751 INFO [ ome.services.blitz.Entry] ( main) Creating OMERO.blitz. Please wait... 2012-09-12 06:26:42,161 INFO [ng.ShutdownSafeEhcacheManagerFactoryBean] ( main) Initializing EHCache CacheManager 2012-09-12 06:26:44,754 INFO [ ome.services.util.ServerDirectoryCheck] ( main) Creating /OMERO/FullText 2012-09-12 06:27:30,165 INFO [ ome.services.fulltext.FullTextAnalyzer] ( main) Initialized FullTextAnalyzer 2012-09-12 07:16:38,060 INFO [ ome.services.blitz.Entry] ( main) Creating OMERO.blitz. Please wait... 2012-09-12 07:50:19,256 INFO [ ome.services.blitz.Entry] ( main) Creating OMERO.blitz. Please wait... 2012-09-12 18:22:08,561 INFO [ ome.services.blitz.Entry] ( main) Creating OMERO.blitz. Please wait... 2012-09-12 18:22:29,856 INFO [ng.ShutdownSafeEhcacheManagerFactoryBean] ( main) Initializing EHCache CacheManager 2012-09-12 18:23:07,261 INFO [ ome.services.fulltext.FullTextAnalyzer] ( main) Initialized FullTextAnalyzer 2012-09-12 18:26:54,551 INFO [ ome.services.blitz.Entry] ( main) Creating OMERO.blitz. Please wait...

by **fuho** » Wed Sep 12, 2012 2:44 pm

I just edited my message and added the log,probably just as you were typing the response

EDIT: This is now a response to nonexistent message, but I will keep it here just in case.

by **jmoore** » Wed Sep 12, 2012 2:51 pm

(missing messages: no problem!

)

There's not really anything help in Blitz-0.log which is very odd. Is there anything new in master.out or master.err? Additionally, could you possibly get a stack dump from the Blitz process while it's starting up?

If you list processes with:

Code: Select all: $ ps auxw -H | grep log4j.xml ... omero 4936 0.1 2.9 957348 487272 ? Sl Aug21 48:07 java -Xmx512M -XX:MaxPermSize=128m -Djava.awt.headless=true -Dlog4j.configuration=etc/log4j.xml -Domero.logfile=var/log/${omero.name}.log -Domero.name=Blitz-0 -jar lib/server/blitz.jar --Ice.Config=/home/omero/ome.git/dist/var/master/servers/Blitz-0/config/config

Then you can get the stack trace with:

Code: Select all: jstack 4936

Cheers,
~Josh

by **fuho** » Wed Sep 12, 2012 3:19 pm

This is master.out

Code: Select all: # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007f6f962f3592, pid=21588, tid=140117158713088 # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # Problematic frame: # V [libjvm.so+0x386592] CodeCache::free(CodeBlob*)+0x12 # # An error report file with more information is saved as: # /home/omero/OMERO.server-4.4.3-ice34-b5/hs_err_pid21588.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # # # A fatal error has been detected by the Java Runtime Environment: # # Internal Error (relocInfo_x86.cpp:77), pid=24667, tid=140361197065984 # Error: ShouldNotReachHere() # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # An error report file with more information is saved as: # /home/omero/OMERO.server-4.4.3-ice34-b5/hs_err_pid24667.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # # # A fatal error has been detected by the Java Runtime Environment: # # Internal Error (assembler_x86.cpp:678), pid=802, tid=140090013214464 # Error: ShouldNotReachHere() # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # An error report file with more information is saved as: # /home/omero/OMERO.server-4.4.3-ice34-b5/hs_err_pid802.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # # # A fatal error has been detected by the Java Runtime Environment: # # Internal Error (synchronizer.cpp:1286), pid=8781, tid=140460782647040 # guarantee(object->mark() == markOopDesc::INFLATING()) failed: invariant # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # An error report file with more information is saved as: # /home/omero/OMERO.server-4.4.3-ice34-b5/hs_err_pid8781.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007fcc2f804592, pid=9991, tid=140514866878208 # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # Problematic frame: # V [libjvm.so+0x386592] CodeCache::free(CodeBlob*)+0x12 # # An error report file with more information is saved as: # /home/omero/OMERO.server-4.4.3-ice34-b5/hs_err_pid9991.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x0000000000000000, pid=9920, tid=140372714419968 # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # Problematic frame: # C 0x0000000000000000 float+0xe9aa6000 # # An error report file with more information is saved as: # /home/omero/OMERO.server-4.4.3-ice34-b5/hs_err_pid9920.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007f10e24f8592, pid=9947, tid=139710414006016 # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # Problematic frame: # V [libjvm.so+0x386592] CodeCache::free(CodeBlob*)+0x12 # # An error report file with more information is saved as: # /home/omero/OMERO.server-4.4.3-ice34-b5/hs_err_pid9947.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp #

master.err

Code: Select all: -! 09/12/12 18:21:51.669 icegridnode: warning: couldn't reach the IceGrid registry (this is expected if it's down, otherwise please check the value of the Ice.Default.Locator property): Outgoing.cpp:226: Ice::TimeoutException: timeout while sending or receiving data -! 09/12/12 18:22:52.251 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters' Reference.cpp:1566: Ice::NoEndpointException: no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters' -! 09/12/12 18:22:52.253 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters' Reference.cpp:1566: Ice::NoEndpointException: no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters' -! 09/12/12 18:26:40.961 icegridnode: warning: couldn't reach the IceGrid registry (this is expected if it's down, otherwise please check the value of the Ice.Default.Locator property): Outgoing.cpp:226: Ice::TimeoutException: timeout while sending or receiving data -! 09/12/12 18:27:10.168 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters' Reference.cpp:1566: Ice::NoEndpointException: no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters' -! 09/12/12 18:27:10.169 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters' Reference.cpp:1566: Ice::NoEndpointException: no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'

While trying to get the stack I always get that the process doesn't exist error. I guess it dies too quickly? I can try to put together a script which will get the pid asap and then get the output, but wanted to make sure it will be necessary before investing time in it.

by **jmoore** » Wed Sep 12, 2012 3:26 pm

Ok. The contents of master.err help to explain somewhat. Your Java installation seems to be quite unhappy. How did you install it? Has it worked in the past? (if so, did anything change recently like environment variables, etc.)

by **fuho** » Wed Sep 12, 2012 3:33 pm

The server is freshly installed yesterday, haven't used the Java for anything else yet. You can't get Oracle Java from official repos anymore so added couple unofficial repos and installed from there.

Here are the 3 error logs generated by Java when i run OMERO.

hs_err_pid17712.log

Code: Select all: # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007f1903110592, pid=17712, tid=139745186965248 # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # Problematic frame: # V [libjvm.so+0x386592] CodeCache::free(CodeBlob*)+0x12 # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # --------------- T H R E A D --------------- Current thread (0x0000000040911000): JavaThread "C2 CompilerThread1" daemon [_thread_in_vm, id=17804, stack(0x00007f18f62a6000,0x00007f18f63a7000)] siginfo:si_signo=SIGSEGV: si_errno=0, si_code=128 (), si_addr=0x0000000000000000 Registers: RAX=0x00007f18fed358c0, RBX=0x00007f18fed2b890, RCX=0x0000000000000000, RDX=0x0000000000000001 RSP=0x00007f18f63a4270, RBP=0x00007f18f63a4280, RSI=0x0000000000000000, RDI=0x00007f18fed2b890 R8 =0x0000000000000001, R9 =0x00007f1903824000, R10=0x00007f1903827e58, R11=0x00007f19038209d0 R12=0x00007f18fed2b890, R13=0x0000000000000006, R14=0x00007f1903827f70, R15=0x00007f18f63a4fb0 RIP=0x00007f1903110592, EFLAGS=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000000 TRAPNO=0x000000000000000d Top of Stack: (sp=0x00007f18f63a4270) 0x00007f18f63a4270: 0000000040911000 0000000040911000 0x00007f18f63a4280: 00007f18f63a42c0 00007f190310cae3 0x00007f18f63a4290: 000000004082fc60 0000000000000008 0x00007f18f63a42a0: 0000000040911000 0000000000000005 0x00007f18f63a42b0: 00007f18f63a4f40 00000000408e4c60 0x00007f18f63a42c0: 00007f18f63a42e0 00007f19031261c3 0x00007f18f63a42d0: 00007f18f63a5634 00007f18f63a5800 0x00007f18f63a42e0: 00007f18f63a4f80 00007f1903127f3b 0x00007f18f63a42f0: 0000000000000006 0000000040e7daa0 0x00007f18f63a4300: 00007f18f63a5800 00007f18f63a5818 0x00007f18f63a4310: 00000000408e4c60 0000000000000004 0x00007f18f63a4320: 0000000000000001 0000000000000000 0x00007f18f63a4330: 0000000000000000 0000000040a055b8 0x00007f18f63a4340: 00007f18f63a44f0 00007f18f63a4ef0 0x00007f18f63a4350: 00007f18f63a4f40 00007f18f63a5818 0x00007f18f63a4360: 00007f18f63a5800 00007f18f63a5698 0x00007f18f63a4370: 00007f18f63a55f0 00000000408e4c60 0x00007f18f63a4380: 0000000040911880 00000000413ac4e0 0x00007f18f63a4390: 00000000413b0450 00000000413b44c8 0x00007f18f63a43a0: 0000000000000002 00007f18f63a4fb0 0x00007f18f63a43b0: 0000000040911880 0000000000000100 0x00007f18f63a43c0: 00000000413b0480 0000000000000043 0x00007f18f63a43d0: 00007f1903827f70 0000000040911880 0x00007f18f63a43e0: 0000000000000008 00000000413b0c80 0x00007f18f63a43f0: 0000000000000000 0000000000000000 0x00007f18f63a4400: 0000000000000000 0000000000000000 0x00007f18f63a4410: 0000000000000000 0000000000000000 0x00007f18f63a4420: 0000000000000000 0000000000000000 0x00007f18f63a4430: 0000000000000000 0000000000000000 0x00007f18f63a4440: 0000000000000000 0000000000000000 0x00007f18f63a4450: 0000000000000000 0000000000000000 0x00007f18f63a4460: 0000000000000000 0000000000000000 Instructions: (pc=0x00007f1903110592) 0x00007f1903110572: 00 eb 8c 90 66 66 66 90 66 66 90 66 66 90 55 48 0x00007f1903110582: 89 e5 48 83 ec 10 48 89 5d f8 48 8b 07 48 89 fb 0x00007f1903110592: ff 50 08 84 c0 74 21 48 8b 15 10 85 84 00 ff 0a 0x00007f19031105a2: 48 63 93 c0 00 00 00 39 93 bc 00 00 00 74 09 48 Register to memory mapping: RAX=0x00007f18fed358c0 is an unknown value RBX=0x00007f18fed2b890 is an unknown value RCX=0x0000000000000000 is an unknown value RDX=0x0000000000000001 is an unknown value RSP=0x00007f18f63a4270 is pointing into the stack for thread: 0x0000000040911000 RBP=0x00007f18f63a4280 is pointing into the stack for thread: 0x0000000040911000 RSI=0x0000000000000000 is an unknown value RDI=0x00007f18fed2b890 is an unknown value R8 =0x0000000000000001 is an unknown value R9 =0x00007f1903824000: <offset 0xa9a000> in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f1902d8a000 R10=0x00007f1903827e58: <offset 0xa9de58> in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f1902d8a000 R11=0x00007f19038209d0: _ZTV12CodeHeapPool+0x10 in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f1902d8a000 R12=0x00007f18fed2b890 is an unknown value R13=0x0000000000000006 is an unknown value R14=0x00007f1903827f70: _ZTV3Set+0x10 in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f1902d8a000 R15=0x00007f18f63a4fb0 is pointing into the stack for thread: 0x0000000040911000 Stack: [0x00007f18f62a6000,0x00007f18f63a7000], sp=0x00007f18f63a4270, free space=1016k Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) V [libjvm.so+0x386592] CodeCache::free(CodeBlob*)+0x12 V [libjvm.so+0x382ae3] BufferBlob::free(BufferBlob*)+0x63 V [libjvm.so+0x39c1c3] CompileWrapper::~CompileWrapper()+0x23 V [libjvm.so+0x39df3b] Compile::Compile(ciEnv*, C2Compiler*, ciMethod*, int, bool, bool)+0x9db V [libjvm.so+0x320d2e] C2Compiler::compile_method(ciEnv*, ciMethod*, int)+0x9e V [libjvm.so+0x3a862a] CompileBroker::invoke_compiler_on_method(CompileTask*)+0x2ca V [libjvm.so+0x3a7f15] CompileBroker::compiler_thread_loop()+0x355 V [libjvm.so+0x81fbe9] compiler_thread_entry(JavaThread*, Thread*)+0x9 V [libjvm.so+0x8190f1] JavaThread::run()+0x121 V [libjvm.so+0x710adf] java_start(Thread*)+0x13f Current CompileTask: C2: 11912 182 java.util.HashMap.entrySet0()Ljava/util/Set; (28 bytes) --------------- P R O C E S S --------------- Java Threads: ( => current thread ) 0x00007f18f837d000 JavaThread "Thread-1" daemon [_thread_blocked, id=17987, stack(0x00007f18fd99d000,0x00007f18fda9e000)] 0x00007f18f83e1000 JavaThread "perf4j-async-stats-appender-sink-CoalescingStatistics" daemon [_thread_blocked, id=17982, stack(0x00007f18fda9e000,0x00007f18fdb9f000)] 0x0000000040916800 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=17813, stack(0x00007f18fe2a6000,0x00007f18fe3a7000)] =>0x0000000040911000 JavaThread "C2 CompilerThread1" daemon [_thread_in_vm, id=17804, stack(0x00007f18f62a6000,0x00007f18f63a7000)] 0x000000004090f000 JavaThread "C2 CompilerThread0" daemon [_thread_in_vm, id=17802, stack(0x00007f18fe3a7000,0x00007f18fe4a8000)] 0x000000004090d000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=17798, stack(0x00007f18fe4a8000,0x00007f18fe5a9000)] 0x00000000408ec000 JavaThread "Finalizer" daemon [_thread_blocked, id=17796, stack(0x00007f18fe5a9000,0x00007f18fe6aa000)] 0x00000000408ea000 JavaThread "Reference Handler" daemon [_thread_blocked, id=17795, stack(0x00007f18fe6aa000,0x00007f18fe7ab000)] 0x0000000040833800 JavaThread "main" [_thread_in_native, id=17775, stack(0x00007f1902a06000,0x00007f1902b07000)] Other Threads: 0x00000000408e3000 VMThread [stack: 0x00007f18fe7ab000,0x00007f18fe8ac000] [id=17793] 0x0000000040921800 WatcherThread [stack: 0x00007f18fe1a5000,0x00007f18fe2a6000] [id=17814] VM state:not at safepoint (normal execution) VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event]) [0x000000004082fc60] CodeCache_lock - owner thread: 0x0000000040911000 Heap def new generation total 18304K, used 6903K [0x00000000d8000000, 0x00000000d93d0000, 0x00000000e2aa0000) eden space 16320K, 30% used [0x00000000d8000000, 0x00000000d84cdf60, 0x00000000d8ff0000) from space 1984K, 100% used [0x00000000d8ff0000, 0x00000000d91e0000, 0x00000000d91e0000) to space 1984K, 0% used [0x00000000d91e0000, 0x00000000d91e0000, 0x00000000d93d0000) tenured generation total 40532K, used 34199K [0x00000000e2aa0000, 0x00000000e5235000, 0x00000000f8000000) the space 40532K, 84% used [0x00000000e2aa0000, 0x00000000e4c05c70, 0x00000000e4c05e00, 0x00000000e5235000) compacting perm gen total 21248K, used 10609K [0x00000000f8000000, 0x00000000f94c0000, 0x0000000100000000) the space 21248K, 49% used [0x00000000f8000000, 0x00000000f8a5c758, 0x00000000f8a5c800, 0x00000000f94c0000) No shared spaces configured. Code Cache [0x00007f18fec71000, 0x00007f18feee1000, 0x00007f1901c71000) total_blobs=427 nmethods=181 adapters=200 free_code_cache=49519360 largest_free_block=12352 Dynamic libraries: 40000000-40009000 r-xp 00000000 09:7f 37620687 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/bin/java 40108000-4010a000 rwxp 00008000 09:7f 37620687 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/bin/java 4082b000-41704000 rwxp 00000000 00:00 0 [heap] d8000000-d93d0000 rwxp 00000000 00:00 0 d93d0000-e2aa0000 rwxp 00000000 00:00 0 e2aa0000-e5235000 rwxp 00000000 00:00 0 e5235000-f8000000 rwxp 00000000 00:00 0 f8000000-f94c0000 rwxp 00000000 00:00 0 f94c0000-100000000 rwxp 00000000 00:00 0 7f18f62a6000-7f18f62a9000 ---p 00000000 00:00 0 7f18f62a9000-7f18f63a7000 rwxp 00000000 00:00 0 7f18f8000000-7f18f889d000 rwxp 00000000 00:00 0 7f18f889d000-7f18fc000000 ---p 00000000 00:00 0 7f18fd99d000-7f18fd9a0000 ---p 00000000 00:00 0 7f18fd9a0000-7f18fda9e000 rwxp 00000000 00:00 0 7f18fda9e000-7f18fdaa1000 ---p 00000000 00:00 0 7f18fdaa1000-7f18fdb9f000 rwxp 00000000 00:00 0 7f18fdb9f000-7f18fdba5000 r-xp 00000000 09:7f 37620592 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libmanagement.so 7f18fdba5000-7f18fdca4000 ---p 00006000 09:7f 37620592 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libmanagement.so 7f18fdca4000-7f18fdca6000 rwxp 00005000 09:7f 37620592 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libmanagement.so 7f18fdca6000-7f18fdcab000 r-xs 00010000 09:7f 39071633 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xml-apis-ext.jar 7f18fdcab000-7f18fdcae000 r-xs 00012000 09:7f 39071630 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-security-ldap.jar 7f18fdcae000-7f18fdcb8000 r-xs 00041000 09:7f 39071629 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-security-core.jar 7f18fdcb8000-7f18fdcbb000 r-xs 00025000 09:7f 39071628 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-security-config.jar 7f18fdcbb000-7f18fdcc3000 r-xs 00034000 09:7f 39071627 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-ldap.jar 7f18fdcc3000-7f18fdcd0000 r-xs 000d0000 09:7f 39071622 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/server.jar 7f18fdcd0000-7f18fdce4000 r-xs 000e3000 09:7f 39071632 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xercesImpl.jar 7f18fdce4000-7f18fdcf6000 r-xs 0019c000 09:7f 39071631 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xalan.jar 7f18fdcf6000-7f18fdcfa000 r-xs 0006c000 09:7f 39071626 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/specification.jar 7f18fdcfa000-7f18fdd02000 r-xs 00028000 09:7f 39071634 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xml-apis.jar 7f18fdd02000-7f18fdd05000 r-xs 00041000 09:7f 39071621 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/serializer.jar 7f18fdd05000-7f18fdd07000 r-xs 00011000 09:7f 39071619 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/romio.jar 7f18fdd07000-7f18fdd09000 r-xs 00012000 09:7f 39071618 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/rendering.jar 7f18fdd09000-7f18fdd0d000 r-xs 0005b000 09:7f 39071617 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/quartz.jar 7f18fdd0d000-7f18fdd10000 r-xs 00016000 09:7f 39071608 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.context.support.jar 7f18fdd10000-7f18fdd13000 r-xs 0000e000 09:7f 39071603 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/omero-shares.jar 7f18fdd13000-7f18fdd1c000 r-xs 0005f000 09:7f 39071601 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ome-java.jar 7f18fdd1c000-7f18fdd1d000 r-xs 00016000 09:7f 39071600 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ome-io.jar 7f18fdd1d000-7f18fdd38000 r-xs 00255000 09:7f 39071599 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/netcdf.jar 7f18fdd38000-7f18fdd3e000 r-xs 00055000 09:7f 39071595 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/mail.jar 7f18fdd3e000-7f18fdd4b000 r-xs 00086000 09:7f 39071587 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/jts.jar 7f18fdd4b000-7f18fdd4d000 r-xs 00001000 09:7f 39071586 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/jsr107cache.jar 7f18fdd4d000-7f18fdd4f000 r-xs 00009000 09:7f 39071584 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/java-image-scaling.jar 7f18fdd4f000-7f18fdd50000 r-xs 0000d000 09:7f 39071583 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/java-getopt.jar 7f18fdd50000-7f18fdd52000 r-xs 00007000 09:7f 39071580 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ini4j.jar 7f18fdd52000-7f18fdd89000 r-xs 0029c000 09:7f 39071579 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ice.jar 7f18fdd89000-7f18fdd8e000 r-xs 0003f000 09:7f 39071578 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ice-freeze.jar 7f18fdd8e000-7f18fdd98000 r-xs 0007e000 09:7f 39071577 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ice-db.jar 7f18fdd98000-7f18fdd9c000 r-xs 00049000 09:7f 39071572 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/grib.jar 7f18fdd9c000-7f18fdd9e000 r-xs 00002000 09:7f 39071571 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/geronimo-spec-jta.jar 7f18fdd9e000-7f18fdda3000 r-xs 0003c000 09:7f 39071570 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ehcache.jar 7f18fdda3000-7f18fdda5000 r-xs 00009000 09:7f 39071567 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-pool.jar 7f18fdda5000-7f18fddaa000 r-xs 00040000 09:7f 39071565 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-lang.jar 7f18fddaa000-7f18fddad000 r-xs 00018000 09:7f 39071564 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-io.jar 7f18fddad000-7f18fddb3000 r-xs 00045000 09:7f 39071563 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-httpclient.jar 7f18fddb3000-7f18fddb5000 r-xs 0000a000 09:7f 39071561 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-codec.jar 7f18fddb5000-7f18fddbb000 r-xs 00077000 09:7f 39071616 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/postgresql.jar 7f18fddbb000-7f18fddc2000 r-xs 00031000 09:7f 39071613 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.transaction.jar 7f18fddc2000-7f18fddca000 r-xs 00049000 09:7f 39071612 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.orm.jar 7f18fddca000-7f18fddd4000 r-xs 00053000 09:7f 39071611 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.jdbc.jar 7f18fddd4000-7f18fddd8000 r-xs 00023000 09:7f 39071610 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.expression.jar 7f18fddd8000-7f18fdde9000 r-xs 00090000 09:7f 39071607 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.context.jar 7f18fdde9000-7f18fddf4000 r-xs 0007b000 09:7f 39071606 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.beans.jar 7f18fddf4000-7f18fddf5000 r-xs 0000c000 09:7f 39071605 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.asm.jar 7f18fddf5000-7f18fddfe000 r-xs 00101000 09:7f 39071598 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/model-psql.jar 7f18fddfe000-7f18fddff000 r-xs 00004000 09:7f 39071594 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/lucene-spellchecker.jar 7f18fddff000-7f18fde00000 r-xs 0000c000 09:7f 39071593 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/lucene-misc.jar 7f18fde00000-7f18fde03000 r-xs 00014000 09:7f 39071592 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/lucene-highlighter.jar 7f18fde03000-7f18fde11000 r-xs 000bb000 09:7f 39071591 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/lucene-core.jar 7f18fde11000-7f18fde19000 r-xs 0008a000 09:7f 39071585 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/javassist.jar 7f18fde19000-7f18fde5a000 r-xs 00376000 09:7f 39071576 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/hibernate.jar 7f18fde5a000-7f18fde5d000 r-xs 0000d000 09:7f 39071575 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/hibernate-validator.jar 7f18fde5d000-7f18fde64000 r-xs 00046000 09:7f 39071574 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/hibernate-search.jar 7f18fde64000-7f18fde69000 r-xs 00014000 09:7f 39071573 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/hibernate-jpa-2.0-api.jar 7f18fde69000-7f18fde6e000 r-xs 0006a000 09:7f 39071623 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/services.jar 7f18fde6e000-7f18fde6f000 r-xs 00002000 09:7f 39071625 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/slf4j-log4j12.jar 7f18fde6f000-7f18fde70000 r-xs 00005000 09:7f 39071624 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/slf4j-api.jar 7f18fde70000-7f18fde73000 r-xs 00015000 09:7f 39071614 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/perf4j.jar 7f18fde73000-7f18fde7b000 r-xs 0004f000 09:7f 39071609 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.core.jar 7f18fde7b000-7f18fde84000 r-xs 00046000 09:7f 39071604 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.aop.jar 7f18fde84000-7f18fde8b000 r-xs 0004f000 09:7f 39071590 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/log4j.jar 7f18fde8b000-7f18fde8d000 r-xs 00000000 09:7f 39071588 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/jul-to-slf4j.jar 7f18fde8d000-7f18fde90000 r-xs 00022000 09:7f 39071582 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/jamon.jar 7f18fde90000-7f18fde91000 r-xs 0000f000 09:7f 39071569 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/dsl.jar 7f18fde91000-7f18fde96000 r-xs 00048000 09:7f 39071568 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/dom4j.jar 7f18fde96000-7f18fdea3000 r-xs 0007f000 09:7f 39071562 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-collections.jar 7f18fdea3000-7f18fdea8000 r-xs 00034000 09:7f 39071560 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-beanutils.jar 7f18fdea8000-7f18fdeaa000 r-xs 00015000 09:7f 39071559 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/common.jar 7f18fdeaa000-7f18fdeac000 r-xs 00000000 09:7f 39071558 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/com.springsource.org.aopalliance.jar 7f18fdeac000-7f18fdeb2000 r-xs 00049000 09:7f 39071557 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/cglib-nodep.jar 7f18fdeb2000-7f18fdeb5000 r-xs 00071000 09:7f 39071556 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/bufr.jar 7f18fdeb5000-7f18fdeba000 r-xs 00041000 09:7f 39071555 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/btm.jar 7f18fdeba000-7f18fdecb000 r-xs 00101000 09:7f 39071581 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/jai_imageio.jar 7f18fdecb000-7f18fded1000 r-xs 000d7000 09:7f 39071620 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/scifio.jar 7f18fded1000-7f18fded3000 r-xs 0000d000 09:7f 39071566 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-logging.jar 7f18fded3000-7f18fdee0000 r-xs 000d2000 09:7f 39071615 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/poi-loci.jar 7f18fdee0000-7f18fdee6000 r-xs 0005f000 09:7f 39071602 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ome-xml.jar 7f18fdee6000-7f18fdee7000 r-xs 00002000 09:7f 39071597 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/metakit.jar 7f18fdee7000-7f18fdeea000 r-xs 00012000 09:7f 39071596 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/mdbtools-java.jar 7f18fdeea000-7f18fdeec000 r-xs 00016000 09:7f 39071589 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/loci-common.jar 7f18fdeec000-7f18fdef1000 r-xs 000ed000 09:7f 39071553 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/bio-formats.jar 7f18fdef1000-7f18fdf3d000 r-xs 002dd000 09:7f 39071552 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/batik-all.jar 7f18fdf3d000-7f18fe071000 r-xs 010f1000 09:7f 39071554 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/blitz.jar 7f18fe071000-7f18fe1a5000 r-xs 010f1000 09:7f 39071554 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/blitz.jar 7f18fe1a5000-7f18fe1a6000 ---p 00000000 00:00 0 7f18fe1a6000-7f18fe2a6000 rwxp 00000000 00:00 0 7f18fe2a6000-7f18fe2a9000 ---p 00000000 00:00 0 7f18fe2a9000-7f18fe3a7000 rwxp 00000000 00:00 0 7f18fe3a7000-7f18fe3aa000 ---p 00000000 00:00 0 7f18fe3aa000-7f18fe4a8000 rwxp 00000000 00:00 0 7f18fe4a8000-7f18fe4ab000 ---p 00000000 00:00 0 7f18fe4ab000-7f18fe5a9000 rwxp 00000000 00:00 0 7f18fe5a9000-7f18fe5ac000 ---p 00000000 00:00 0 7f18fe5ac000-7f18fe6aa000 rwxp 00000000 00:00 0 7f18fe6aa000-7f18fe6ad000 ---p 00000000 00:00 0 7f18fe6ad000-7f18fe7ab000 rwxp 00000000 00:00 0 7f18fe7ab000-7f18fe7ac000 ---p 00000000 00:00 0 7f18fe7ac000-7f18fe8ac000 rwxp 00000000 00:00 0 7f18fe8ac000-7f18fea44000 r-xs 03029000 09:7f 37508868 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/rt.jar 7f18fea44000-7f18fea4f000 rwxp 00000000 00:00 0 7f18fea4f000-7f18fea85000 rwxp 00000000 00:00 0 7f18fea85000-7f18fea99000 rwxp 00000000 00:00 0 7f18fea99000-7f18feb30000 rwxp 00000000 00:00 0 7f18feb30000-7f18feb3a000 rwxp 00000000 00:00 0 7f18feb3a000-7f18feb85000 rwxp 00000000 00:00 0 7f18feb85000-7f18feb9a000 rwxp 00000000 00:00 0 7f18feb9a000-7f18fec30000 rwxp 00000000 00:00 0 7f18fec30000-7f18fec3b000 rwxp 00000000 00:00 0 7f18fec3b000-7f18fec70000 rwxp 00000000 00:00 0 7f18fec70000-7f18feee1000 rwxp 00000000 00:00 0 7f18feee1000-7f1901c71000 rwxp 00000000 00:00 0 7f1901c71000-7f1901c7f000 r-xp 00000000 09:7f 37620611 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libzip.so 7f1901c7f000-7f1901d81000 ---p 0000e000 09:7f 37620611 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libzip.so 7f1901d81000-7f1901d84000 rwxp 00010000 09:7f 37620611 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libzip.so 7f1901d84000-7f1901d85000 rwxp 00000000 00:00 0 7f1901d85000-7f1901d91000 r-xp 00000000 09:7f 36840231 /lib/libnss_files-2.11.1.so 7f1901d91000-7f1901f90000 ---p 0000c000 09:7f 36840231 /lib/libnss_files-2.11.1.so 7f1901f90000-7f1901f91000 r-xp 0000b000 09:7f 36840231 /lib/libnss_files-2.11.1.so 7f1901f91000-7f1901f92000 rwxp 0000c000 09:7f 36840231 /lib/libnss_files-2.11.1.so 7f1901f92000-7f1901f9c000 r-xp 00000000 09:7f 36836991 /lib/libnss_nis-2.11.1.so 7f1901f9c000-7f190219b000 ---p 0000a000 09:7f 36836991 /lib/libnss_nis-2.11.1.so 7f190219b000-7f190219c000 r-xp 00009000 09:7f 36836991 /lib/libnss_nis-2.11.1.so 7f190219c000-7f190219d000 rwxp 0000a000 09:7f 36836991 /lib/libnss_nis-2.11.1.so 7f190219d000-7f19021a5000 r-xp 00000000 09:7f 36834332 /lib/libnss_compat-2.11.1.so 7f19021a5000-7f19023a4000 ---p 00008000 09:7f 36834332 /lib/libnss_compat-2.11.1.so 7f19023a4000-7f19023a5000 r-xp 00007000 09:7f 36834332 /lib/libnss_compat-2.11.1.so 7f19023a5000-7f19023a6000 rwxp 00008000 09:7f 36834332 /lib/libnss_compat-2.11.1.so 7f19023a6000-7f19023bd000 r-xp 00000000 09:7f 36831758 /lib/libnsl-2.11.1.so 7f19023bd000-7f19025bc000 ---p 00017000 09:7f 36831758 /lib/libnsl-2.11.1.so 7f19025bc000-7f19025bd000 r-xp 00016000 09:7f 36831758 /lib/libnsl-2.11.1.so 7f19025bd000-7f19025be000 rwxp 00017000 09:7f 36831758 /lib/libnsl-2.11.1.so 7f19025be000-7f19025c0000 rwxp 00000000 00:00 0 7f19025c0000-7f19025e9000 r-xp 00000000 09:7f 37620609 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libjava.so 7f19025e9000-7f19026e8000 ---p 00029000 09:7f 37620609 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libjava.so 7f19026e8000-7f19026ef000 rwxp 00028000 09:7f 37620609 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libjava.so 7f19026ef000-7f19026fc000 r-xp 00000000 09:7f 37620600 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libverify.so 7f19026fc000-7f19027fb000 ---p 0000d000 09:7f 37620600 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libverify.so 7f19027fb000-7f19027fe000 rwxp 0000c000 09:7f 37620600 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libverify.so 7f19027fe000-7f1902805000 r-xp 00000000 09:7f 36832348 /lib/librt-2.11.1.so 7f1902805000-7f1902a04000 ---p 00007000 09:7f 36832348 /lib/librt-2.11.1.so 7f1902a04000-7f1902a05000 r-xp 00006000 09:7f 36832348 /lib/librt-2.11.1.so 7f1902a05000-7f1902a06000 rwxp 00007000 09:7f 36832348 /lib/librt-2.11.1.so 7f1902a06000-7f1902a09000 ---p 00000000 00:00 0 7f1902a09000-7f1902b07000 rwxp 00000000 00:00 0 7f1902b07000-7f1902b89000 r-xp 00000000 09:7f 36831754 /lib/libm-2.11.1.so 7f1902b89000-7f1902d88000 ---p 00082000 09:7f 36831754 /lib/libm-2.11.1.so 7f1902d88000-7f1902d89000 r-xp 00081000 09:7f 36831754 /lib/libm-2.11.1.so 7f1902d89000-7f1902d8a000 rwxp 00082000 09:7f 36831754 /lib/libm-2.11.1.so 7f1902d8a000-7f19036a4000 r-xp 00000000 09:7f 37620616 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so 7f19036a4000-7f19037a6000 ---p 0091a000 09:7f 37620616 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so 7f19037a6000-7f190395b000 rwxp 0091c000 09:7f 37620616 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so 7f190395b000-7f1903995000 rwxp 00000000 00:00 0 7f1903995000-7f1903b0f000 r-xp 00000000 09:7f 36840227 /lib/libc-2.11.1.so 7f1903b0f000-7f1903d0e000 ---p 0017a000 09:7f 36840227 /lib/libc-2.11.1.so 7f1903d0e000-7f1903d12000 r-xp 00179000 09:7f 36840227 /lib/libc-2.11.1.so 7f1903d12000-7f1903d13000 rwxp 0017d000 09:7f 36840227 /lib/libc-2.11.1.so 7f1903d13000-7f1903d18000 rwxp 00000000 00:00 0 7f1903d18000-7f1903d1a000 r-xp 00000000 09:7f 36840232 /lib/libdl-2.11.1.so 7f1903d1a000-7f1903f1a000 ---p 00002000 09:7f 36840232 /lib/libdl-2.11.1.so 7f1903f1a000-7f1903f1b000 r-xp 00002000 09:7f 36840232 /lib/libdl-2.11.1.so 7f1903f1b000-7f1903f1c000 rwxp 00003000 09:7f 36840232 /lib/libdl-2.11.1.so 7f1903f1c000-7f1903f34000 r-xp 00000000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f1903f34000-7f1904133000 ---p 00018000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f1904133000-7f1904134000 r-xp 00017000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f1904134000-7f1904135000 rwxp 00018000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f1904135000-7f1904139000 rwxp 00000000 00:00 0 7f1904139000-7f1904159000 r-xp 00000000 09:7f 36831821 /lib/ld-2.11.1.so 7f190415b000-7f1904163000 r-xs 00047000 09:7f 39071551 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/backport-util-concurrent.jar 7f1904163000-7f1904165000 r-xs 00003000 09:7f 39071549 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/asm-attrs.jar 7f1904165000-7f190416b000 r-xs 00067000 09:7f 39071548 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/antlr.jar 7f190416b000-7f1904179000 r-xs 0031d000 09:7f 39071546 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/PDFBox.jar 7f1904179000-7f1904183000 rwxp 00000000 00:00 0 7f1904183000-7f1904239000 rwxp 00000000 00:00 0 7f1904239000-7f1904241000 rwxs 00000000 09:7f 37627621 /tmp/hsperfdata_omero/17712 7f1904241000-7f1904244000 rwxp 00000000 00:00 0 7f1904244000-7f190424b000 r-xp 00000000 09:7f 37620607 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/jli/libjli.so 7f190424b000-7f190434c000 ---p 00007000 09:7f 37620607 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/jli/libjli.so 7f190434c000-7f190434e000 rwxp 00008000 09:7f 37620607 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/jli/libjli.so 7f190434e000-7f190434f000 rwxp 00000000 00:00 0 7f190434f000-7f1904350000 r-xs 00006000 09:7f 39071550 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/asm.jar 7f1904350000-7f1904352000 r-xs 0000c000 09:7f 39071547 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/activation.jar 7f1904352000-7f1904354000 r-xs 0000e000 09:7f 39071545 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/FontBox.jar 7f1904354000-7f1904355000 rwxp 00000000 00:00 0 7f1904355000-7f1904356000 r-xp 00000000 00:00 0 7f1904356000-7f1904358000 rwxp 00000000 00:00 0 7f1904358000-7f1904359000 r-xp 0001f000 09:7f 36831821 /lib/ld-2.11.1.so 7f1904359000-7f190435a000 rwxp 00020000 09:7f 36831821 /lib/ld-2.11.1.so 7f190435a000-7f190435b000 rwxp 00000000 00:00 0 7fff851d5000-7fff851ea000 rwxp 00000000 00:00 0 [stack] 7fff851fe000-7fff85200000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] VM Arguments: jvm_args: -Xmx512M -XX:MaxPermSize=128m -Djava.awt.headless=true -Dlog4j.configuration=etc/log4j.xml -Domero.logfile=var/log/${omero.name}.log -Domero.name=Blitz-0 java_command: lib/server/blitz.jar --Ice.Config=/home/omero/OMERO.server-4.4.3-ice34-b5/var/master/servers/Blitz-0/config/config Launcher Type: SUN_STANDARD Environment Variables: PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games USERNAME=omero LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server:/usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64:/usr/lib/jvm/java-6-sun-1.6.0.26/jre/../lib/amd64 SHELL=/bin/bash Signal Handlers: SIGSEGV: [libjvm.so+0x85f800], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGBUS: [libjvm.so+0x85f800], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGFPE: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGPIPE: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGXFSZ: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGILL: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGUSR2: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGHUP: SIG_IGN, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGINT: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGTERM: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGQUIT: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 --------------- S Y S T E M --------------- OS:squeeze/sid uname:Linux 2.6.32-042stab059.7 #1 SMP Tue Jul 24 19:12:01 MSK 2012 x86_64 libc:glibc 2.11.1 NPTL 2.11.1 rlimit: STACK 8192k, CORE 0k, NPROC infinity, NOFILE 1024, AS infinity load average:5.70 10.34 12.45 /proc/meminfo: MemTotal: 1048576 kB MemFree: 397884 kB Cached: 104216 kB Active: 590680 kB Inactive: 33364 kB Active(anon): 503688 kB Inactive(anon): 16140 kB Active(file): 86992 kB Inactive(file): 17224 kB Unevictable: 0 kB Mlocked: 0 kB SwapTotal: 0 kB SwapFree: 0 kB Dirty: 140 kB Writeback: 0 kB AnonPages: 519828 kB Shmem: 31224 kB Slab: 26608 kB SReclaimable: 10752 kB SUnreclaim: 15856 kB CPU:total 1 (4 cores per cpu, 2 threads per core) family 6 model 58 stepping 9, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, ht /proc/cpuinfo: processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 58 model name : Intel(R) Xeon(R) CPU E3-1230 V2 @ 3.30GHz stepping : 9 cpu MHz : 3292.547 cache size : 8192 KB physical id : 0 siblings : 8 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 x2apic popcnt aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms bogomips : 6585.09 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: Memory: 4k page, physical 1048576k(397884k free), swap 0k(0k free) vm_info: Java HotSpot(TM) 64-Bit Server VM (20.1-b02) for linux-amd64 JRE (1.6.0_26-b03), built on May 4 2011 01:13:47 by "java_re" with gcc 3.2.2 (SuSE Linux) time: Wed Sep 12 19:13:25 2012 elapsed time: 11 seconds

..other two in next message for exceeding max length.

by **fuho** » Wed Sep 12, 2012 3:33 pm

hs_err_pid17733.log

Code: Select all: # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007f48bb564592, pid=17733, tid=139950278305536 # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # Problematic frame: # V [libjvm.so+0x386592] CodeCache::free(CodeBlob*)+0x12 # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # --------------- T H R E A D --------------- Current thread (0x000000004170a000): JavaThread "C2 CompilerThread0" daemon [_thread_in_vm, id=17811, stack(0x00007f48b68fe000,0x00007f48b69ff000)] siginfo:si_signo=SIGSEGV: si_errno=0, si_code=128 (), si_addr=0x0000000000000000 Registers: RAX=0x00007f48b7156980, RBX=0x00007f48b714f090, RCX=0x0000000000000000, RDX=0x0000000000000001 RSP=0x00007f48b69fc470, RBP=0x00007f48b69fc480, RSI=0x0000000000000000, RDI=0x00007f48b714f090 R8 =0x0000000000000001, R9 =0x00007f48bbc78000, R10=0x00007f48bbc7be58, R11=0x0000000000000202 R12=0x00007f48b714f090, R13=0x0000000000000006, R14=0x00007f48bbc7bf70, R15=0x00007f48b69fd1b0 RIP=0x00007f48bb564592, EFLAGS=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000000 TRAPNO=0x000000000000000d Top of Stack: (sp=0x00007f48b69fc470) 0x00007f48b69fc470: 000000004170a000 000000004170a000 0x00007f48b69fc480: 00007f48b69fc4c0 00007f48bb560ae3 0x00007f48b69fc490: 000000004162ac70 0000000000000008 0x00007f48b69fc4a0: 000000004170a000 0000000000000007 0x00007f48b69fc4b0: 00007f48b69fd140 00000000416dfca0 0x00007f48b69fc4c0: 00007f48b69fc4e0 00007f48bb57a1c3 0x00007f48b69fc4d0: 00007f48b69fd834 00007f48b69fda00 0x00007f48b69fc4e0: 00007f48b69fd180 00007f48bb57bf3b 0x00007f48b69fc4f0: 0000000000000006 00007f48b0474880 0x00007f48b69fc500: 00007f48b69fda00 00007f48b69fda18 0x00007f48b69fc510: 00000000416dfca0 00007f4800000004 0x00007f48b69fc520: 00007f48b69f6501 0000000000000000 0x00007f48b69fc530: 0000000200000000 00007f48b048f948 0x00007f48b69fc540: 00007f48b69fc6f0 00007f48b69fd0f0 0x00007f48b69fc550: 00007f48b69fd140 00007f48b69fda18 0x00007f48b69fc560: 00007f48b69fda00 00007f48b69fd898 0x00007f48b69fc570: 00007f48b69fd7f0 00000000416dfca0 0x00007f48b69fc580: 000000004170a5c0 00007f48b02029c0 0x00007f48b69fc590: 00007f48b0206a40 00007f48b020a9a8 0x00007f48b69fc5a0: ffffffff00000002 00007f48b69fd1b0 0x00007f48b69fc5b0: 000000004170a5c0 0000000000000200 0x00007f48b69fc5c0: 00007f48b0206a70 00000000000000b3 0x00007f48b69fc5d0: 00007f48bbc7bf70 000000004170a5c0 0x00007f48b69fc5e0: 00007f4800000010 00007f48b0207a70 0x00007f48b69fc5f0: 00007f4800000000 00007f48b7123c10 0x00007f48b69fc600: 0000000041776a80 0000000041776a80 0x00007f48b69fc610: 0000000041776a88 00007f48b7122c00 0x00007f48b69fc620: 0000000000000001 00007f48b69fc5d8 0x00007f48b69fc630: 00007f48b7122520 0000000000000000 0x00007f48b69fc640: 00007f48b7122571 00007f48b7122b40 0x00007f48b69fc650: 0000000041776a00 0000000041776a00 0x00007f48b69fc660: 0000000041776a7c 00007f48b7122520 Instructions: (pc=0x00007f48bb564592) 0x00007f48bb564572: 00 eb 8c 90 66 66 66 90 66 66 90 66 66 90 55 48 0x00007f48bb564582: 89 e5 48 83 ec 10 48 89 5d f8 48 8b 07 48 89 fb 0x00007f48bb564592: ff 50 08 84 c0 74 21 48 8b 15 10 85 84 00 ff 0a 0x00007f48bb5645a2: 48 63 93 c0 00 00 00 39 93 bc 00 00 00 74 09 48 Register to memory mapping: RAX=0x00007f48b7156980 is an unknown value RBX=0x00007f48b714f090 is an unknown value RCX=0x0000000000000000 is an unknown value RDX=0x0000000000000001 is an unknown value RSP=0x00007f48b69fc470 is pointing into the stack for thread: 0x000000004170a000 RBP=0x00007f48b69fc480 is pointing into the stack for thread: 0x000000004170a000 RSI=0x0000000000000000 is an unknown value RDI=0x00007f48b714f090 is an unknown value R8 =0x0000000000000001 is an unknown value R9 =0x00007f48bbc78000: <offset 0xa9a000> in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f48bb1de000 R10=0x00007f48bbc7be58: <offset 0xa9de58> in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f48bb1de000 R11=0x0000000000000202 is an unknown value R12=0x00007f48b714f090 is an unknown value R13=0x0000000000000006 is an unknown value R14=0x00007f48bbc7bf70: _ZTV3Set+0x10 in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f48bb1de000 R15=0x00007f48b69fd1b0 is pointing into the stack for thread: 0x000000004170a000 Stack: [0x00007f48b68fe000,0x00007f48b69ff000], sp=0x00007f48b69fc470, free space=1017k Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) V [libjvm.so+0x386592] CodeCache::free(CodeBlob*)+0x12 V [libjvm.so+0x382ae3] BufferBlob::free(BufferBlob*)+0x63 V [libjvm.so+0x39c1c3] CompileWrapper::~CompileWrapper()+0x23 V [libjvm.so+0x39df3b] Compile::Compile(ciEnv*, C2Compiler*, ciMethod*, int, bool, bool)+0x9db V [libjvm.so+0x320d2e] C2Compiler::compile_method(ciEnv*, ciMethod*, int)+0x9e V [libjvm.so+0x3a862a] CompileBroker::invoke_compiler_on_method(CompileTask*)+0x2ca V [libjvm.so+0x3a7f15] CompileBroker::compiler_thread_loop()+0x355 V [libjvm.so+0x81fbe9] compiler_thread_entry(JavaThread*, Thread*)+0x9 V [libjvm.so+0x8190f1] JavaThread::run()+0x121 V [libjvm.so+0x710adf] java_start(Thread*)+0x13f Current CompileTask: C2: 10108 108 java.util.HashMap$EntryIterator.next()Ljava/lang/Object; (5 bytes) --------------- P R O C E S S --------------- Java Threads: ( => current thread ) 0x0000000041711000 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=17822, stack(0x00007f48b66fc000,0x00007f48b67fd000)] 0x000000004170f000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=17818, stack(0x00007f48b67fd000,0x00007f48b68fe000)] =>0x000000004170a000 JavaThread "C2 CompilerThread0" daemon [_thread_in_vm, id=17811, stack(0x00007f48b68fe000,0x00007f48b69ff000)] 0x0000000041708000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=17809, stack(0x00007f48b69ff000,0x00007f48b6b00000)] 0x00000000416e7000 JavaThread "Finalizer" daemon [_thread_blocked, id=17792, stack(0x00007f48b6b00000,0x00007f48b6c01000)] 0x00000000416e5000 JavaThread "Reference Handler" daemon [_thread_blocked, id=17791, stack(0x00007f48b6c01000,0x00007f48b6d02000)] 0x000000004162e800 JavaThread "main" [_thread_in_vm, id=17772, stack(0x00007f48bae5a000,0x00007f48baf5b000)] Other Threads: 0x00000000416de000 VMThread [stack: 0x00007f48b6d02000,0x00007f48b6e03000] [id=17778] 0x000000004171c800 WatcherThread [stack: 0x00007f48b65fb000,0x00007f48b66fc000] [id=17823] VM state:not at safepoint (normal execution) VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event]) [0x000000004162ac70] CodeCache_lock - owner thread: 0x000000004170a000 Heap def new generation total 18304K, used 3590K [0x00000000eae00000, 0x00000000ec1d0000, 0x00000000f0350000) eden space 16320K, 22% used [0x00000000eae00000, 0x00000000eb181be0, 0x00000000ebdf0000) from space 1984K, 0% used [0x00000000ebdf0000, 0x00000000ebdf0000, 0x00000000ebfe0000) to space 1984K, 0% used [0x00000000ebfe0000, 0x00000000ebfe0000, 0x00000000ec1d0000) tenured generation total 40532K, used 24317K [0x00000000f0350000, 0x00000000f2ae5000, 0x00000000fae00000) the space 40532K, 59% used [0x00000000f0350000, 0x00000000f1b0f5e0, 0x00000000f1b0f600, 0x00000000f2ae5000) compacting perm gen total 21248K, used 4203K [0x00000000fae00000, 0x00000000fc2c0000, 0x0000000100000000) the space 21248K, 19% used [0x00000000fae00000, 0x00000000fb21ad38, 0x00000000fb21ae00, 0x00000000fc2c0000) No shared spaces configured. Code Cache [0x00007f48b70c5000, 0x00007f48b7335000, 0x00007f48ba0c5000) total_blobs=302 nmethods=112 adapters=144 free_code_cache=49712192 largest_free_block=12416 Dynamic libraries: 40000000-40009000 r-xp 00000000 09:7f 37620687 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/bin/java 40108000-4010a000 rwxp 00008000 09:7f 37620687 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/bin/java 41626000-41c97000 rwxp 00000000 00:00 0 [heap] eae00000-ec1d0000 rwxp 00000000 00:00 0 ec1d0000-f0350000 rwxp 00000000 00:00 0 f0350000-f2ae5000 rwxp 00000000 00:00 0 f2ae5000-fae00000 rwxp 00000000 00:00 0 fae00000-fc2c0000 rwxp 00000000 00:00 0 fc2c0000-100000000 rwxp 00000000 00:00 0 7f48b0000000-7f48b0a87000 rwxp 00000000 00:00 0 7f48b0a87000-7f48b4000000 ---p 00000000 00:00 0 7f48b6393000-7f48b64c7000 r-xs 010f1000 09:7f 39071554 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/blitz.jar 7f48b64c7000-7f48b65fb000 r-xs 010f1000 09:7f 39071554 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/blitz.jar 7f48b65fb000-7f48b65fc000 ---p 00000000 00:00 0 7f48b65fc000-7f48b66fc000 rwxp 00000000 00:00 0 7f48b66fc000-7f48b66ff000 ---p 00000000 00:00 0 7f48b66ff000-7f48b67fd000 rwxp 00000000 00:00 0 7f48b67fd000-7f48b6800000 ---p 00000000 00:00 0 7f48b6800000-7f48b68fe000 rwxp 00000000 00:00 0 7f48b68fe000-7f48b6901000 ---p 00000000 00:00 0 7f48b6901000-7f48b69ff000 rwxp 00000000 00:00 0 7f48b69ff000-7f48b6a02000 ---p 00000000 00:00 0 7f48b6a02000-7f48b6b00000 rwxp 00000000 00:00 0 7f48b6b00000-7f48b6b03000 ---p 00000000 00:00 0 7f48b6b03000-7f48b6c01000 rwxp 00000000 00:00 0 7f48b6c01000-7f48b6c04000 ---p 00000000 00:00 0 7f48b6c04000-7f48b6d02000 rwxp 00000000 00:00 0 7f48b6d02000-7f48b6d03000 ---p 00000000 00:00 0 7f48b6d03000-7f48b6e03000 rwxp 00000000 00:00 0 7f48b6e03000-7f48b6f9b000 r-xs 03029000 09:7f 37508868 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/rt.jar 7f48b6f9b000-7f48b6fa6000 rwxp 00000000 00:00 0 7f48b6fa6000-7f48b6fc5000 rwxp 00000000 00:00 0 7f48b6fc5000-7f48b6fd9000 rwxp 00000000 00:00 0 7f48b6fd9000-7f48b701b000 rwxp 00000000 00:00 0 7f48b701b000-7f48b7025000 rwxp 00000000 00:00 0 7f48b7025000-7f48b7045000 rwxp 00000000 00:00 0 7f48b7045000-7f48b705a000 rwxp 00000000 00:00 0 7f48b705a000-7f48b709b000 rwxp 00000000 00:00 0 7f48b709b000-7f48b70a6000 rwxp 00000000 00:00 0 7f48b70a6000-7f48b70c4000 rwxp 00000000 00:00 0 7f48b70c4000-7f48b7335000 rwxp 00000000 00:00 0 7f48b7335000-7f48ba0c5000 rwxp 00000000 00:00 0 7f48ba0c5000-7f48ba0d3000 r-xp 00000000 09:7f 37620611 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libzip.so 7f48ba0d3000-7f48ba1d5000 ---p 0000e000 09:7f 37620611 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libzip.so 7f48ba1d5000-7f48ba1d8000 rwxp 00010000 09:7f 37620611 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libzip.so 7f48ba1d8000-7f48ba1d9000 rwxp 00000000 00:00 0 7f48ba1d9000-7f48ba1e5000 r-xp 00000000 09:7f 36840231 /lib/libnss_files-2.11.1.so 7f48ba1e5000-7f48ba3e4000 ---p 0000c000 09:7f 36840231 /lib/libnss_files-2.11.1.so 7f48ba3e4000-7f48ba3e5000 r-xp 0000b000 09:7f 36840231 /lib/libnss_files-2.11.1.so 7f48ba3e5000-7f48ba3e6000 rwxp 0000c000 09:7f 36840231 /lib/libnss_files-2.11.1.so 7f48ba3e6000-7f48ba3f0000 r-xp 00000000 09:7f 36836991 /lib/libnss_nis-2.11.1.so 7f48ba3f0000-7f48ba5ef000 ---p 0000a000 09:7f 36836991 /lib/libnss_nis-2.11.1.so 7f48ba5ef000-7f48ba5f0000 r-xp 00009000 09:7f 36836991 /lib/libnss_nis-2.11.1.so 7f48ba5f0000-7f48ba5f1000 rwxp 0000a000 09:7f 36836991 /lib/libnss_nis-2.11.1.so 7f48ba5f1000-7f48ba5f9000 r-xp 00000000 09:7f 36834332 /lib/libnss_compat-2.11.1.so 7f48ba5f9000-7f48ba7f8000 ---p 00008000 09:7f 36834332 /lib/libnss_compat-2.11.1.so 7f48ba7f8000-7f48ba7f9000 r-xp 00007000 09:7f 36834332 /lib/libnss_compat-2.11.1.so 7f48ba7f9000-7f48ba7fa000 rwxp 00008000 09:7f 36834332 /lib/libnss_compat-2.11.1.so 7f48ba7fa000-7f48ba811000 r-xp 00000000 09:7f 36831758 /lib/libnsl-2.11.1.so 7f48ba811000-7f48baa10000 ---p 00017000 09:7f 36831758 /lib/libnsl-2.11.1.so 7f48baa10000-7f48baa11000 r-xp 00016000 09:7f 36831758 /lib/libnsl-2.11.1.so 7f48baa11000-7f48baa12000 rwxp 00017000 09:7f 36831758 /lib/libnsl-2.11.1.so 7f48baa12000-7f48baa14000 rwxp 00000000 00:00 0 7f48baa14000-7f48baa3d000 r-xp 00000000 09:7f 37620609 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libjava.so 7f48baa3d000-7f48bab3c000 ---p 00029000 09:7f 37620609 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libjava.so 7f48bab3c000-7f48bab43000 rwxp 00028000 09:7f 37620609 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libjava.so 7f48bab43000-7f48bab50000 r-xp 00000000 09:7f 37620600 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libverify.so 7f48bab50000-7f48bac4f000 ---p 0000d000 09:7f 37620600 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libverify.so 7f48bac4f000-7f48bac52000 rwxp 0000c000 09:7f 37620600 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libverify.so 7f48bac52000-7f48bac59000 r-xp 00000000 09:7f 36832348 /lib/librt-2.11.1.so 7f48bac59000-7f48bae58000 ---p 00007000 09:7f 36832348 /lib/librt-2.11.1.so 7f48bae58000-7f48bae59000 r-xp 00006000 09:7f 36832348 /lib/librt-2.11.1.so 7f48bae59000-7f48bae5a000 rwxp 00007000 09:7f 36832348 /lib/librt-2.11.1.so 7f48bae5a000-7f48bae5d000 ---p 00000000 00:00 0 7f48bae5d000-7f48baf5b000 rwxp 00000000 00:00 0 7f48baf5b000-7f48bafdd000 r-xp 00000000 09:7f 36831754 /lib/libm-2.11.1.so 7f48bafdd000-7f48bb1dc000 ---p 00082000 09:7f 36831754 /lib/libm-2.11.1.so 7f48bb1dc000-7f48bb1dd000 r-xp 00081000 09:7f 36831754 /lib/libm-2.11.1.so 7f48bb1dd000-7f48bb1de000 rwxp 00082000 09:7f 36831754 /lib/libm-2.11.1.so 7f48bb1de000-7f48bbaf8000 r-xp 00000000 09:7f 37620616 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so 7f48bbaf8000-7f48bbbfa000 ---p 0091a000 09:7f 37620616 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so 7f48bbbfa000-7f48bbdaf000 rwxp 0091c000 09:7f 37620616 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so 7f48bbdaf000-7f48bbde9000 rwxp 00000000 00:00 0 7f48bbde9000-7f48bbf63000 r-xp 00000000 09:7f 36840227 /lib/libc-2.11.1.so 7f48bbf63000-7f48bc162000 ---p 0017a000 09:7f 36840227 /lib/libc-2.11.1.so 7f48bc162000-7f48bc166000 r-xp 00179000 09:7f 36840227 /lib/libc-2.11.1.so 7f48bc166000-7f48bc167000 rwxp 0017d000 09:7f 36840227 /lib/libc-2.11.1.so 7f48bc167000-7f48bc16c000 rwxp 00000000 00:00 0 7f48bc16c000-7f48bc16e000 r-xp 00000000 09:7f 36840232 /lib/libdl-2.11.1.so 7f48bc16e000-7f48bc36e000 ---p 00002000 09:7f 36840232 /lib/libdl-2.11.1.so 7f48bc36e000-7f48bc36f000 r-xp 00002000 09:7f 36840232 /lib/libdl-2.11.1.so 7f48bc36f000-7f48bc370000 rwxp 00003000 09:7f 36840232 /lib/libdl-2.11.1.so 7f48bc370000-7f48bc388000 r-xp 00000000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f48bc388000-7f48bc587000 ---p 00018000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f48bc587000-7f48bc588000 r-xp 00017000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f48bc588000-7f48bc589000 rwxp 00018000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f48bc589000-7f48bc58d000 rwxp 00000000 00:00 0 7f48bc58d000-7f48bc5ad000 r-xp 00000000 09:7f 36831821 /lib/ld-2.11.1.so 7f48bc5cd000-7f48bc5d7000 rwxp 00000000 00:00 0 7f48bc5d7000-7f48bc68d000 rwxp 00000000 00:00 0 7f48bc68d000-7f48bc695000 rwxs 00000000 09:7f 37618457 /tmp/hsperfdata_omero/17733 7f48bc695000-7f48bc698000 rwxp 00000000 00:00 0 7f48bc698000-7f48bc69f000 r-xp 00000000 09:7f 37620607 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/jli/libjli.so 7f48bc69f000-7f48bc7a0000 ---p 00007000 09:7f 37620607 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/jli/libjli.so 7f48bc7a0000-7f48bc7a2000 rwxp 00008000 09:7f 37620607 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/jli/libjli.so 7f48bc7a2000-7f48bc7a3000 rwxp 00000000 00:00 0 7f48bc7a8000-7f48bc7a9000 rwxp 00000000 00:00 0 7f48bc7a9000-7f48bc7aa000 r-xp 00000000 00:00 0 7f48bc7aa000-7f48bc7ac000 rwxp 00000000 00:00 0 7f48bc7ac000-7f48bc7ad000 r-xp 0001f000 09:7f 36831821 /lib/ld-2.11.1.so 7f48bc7ad000-7f48bc7ae000 rwxp 00020000 09:7f 36831821 /lib/ld-2.11.1.so 7f48bc7ae000-7f48bc7af000 rwxp 00000000 00:00 0 7ffff0280000-7ffff0295000 rwxp 00000000 00:00 0 [stack] 7ffff03fe000-7ffff0400000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] VM Arguments: jvm_args: -Xmx256M -Djava.awt.headless=true -Dlog4j.configuration=etc/log4j-indexing.xml -Domero.logfile=var/log/${omero.name}.log -Domero.name=Indexer-0 java_command: lib/server/blitz.jar ome.fulltext --Ice.Config=/home/omero/OMERO.server-4.4.3-ice34-b5/var/master/servers/Indexer-0/config/config Launcher Type: SUN_STANDARD Environment Variables: PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games USERNAME=omero LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server:/usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64:/usr/lib/jvm/java-6-sun-1.6.0.26/jre/../lib/amd64 SHELL=/bin/bash Signal Handlers: SIGSEGV: [libjvm.so+0x85f800], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGBUS: [libjvm.so+0x85f800], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGFPE: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGPIPE: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGXFSZ: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGILL: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGUSR2: [libjvm.so+0x711110], sa_mask[0]=0x00000000, sa_flags=0x10000004 SIGHUP: SIG_IGN, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGINT: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGTERM: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGQUIT: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 --------------- S Y S T E M --------------- OS:squeeze/sid uname:Linux 2.6.32-042stab059.7 #1 SMP Tue Jul 24 19:12:01 MSK 2012 x86_64 libc:glibc 2.11.1 NPTL 2.11.1 rlimit: STACK 8192k, CORE 0k, NPROC infinity, NOFILE 1024, AS infinity load average:5.70 10.34 12.45 /proc/meminfo: MemTotal: 1048576 kB MemFree: 371624 kB Cached: 104220 kB Active: 616468 kB Inactive: 33416 kB Active(anon): 529524 kB Inactive(anon): 16140 kB Active(file): 86944 kB Inactive(file): 17276 kB Unevictable: 0 kB Mlocked: 0 kB SwapTotal: 0 kB SwapFree: 0 kB Dirty: 132 kB Writeback: 0 kB AnonPages: 545664 kB Shmem: 31224 kB Slab: 26964 kB SReclaimable: 10756 kB SUnreclaim: 16208 kB CPU:total 1 (4 cores per cpu, 2 threads per core) family 6 model 58 stepping 9, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, ht /proc/cpuinfo: processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 58 model name : Intel(R) Xeon(R) CPU E3-1230 V2 @ 3.30GHz stepping : 9 cpu MHz : 3292.547 cache size : 8192 KB physical id : 0 siblings : 8 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 x2apic popcnt aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms bogomips : 6585.09 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: Memory: 4k page, physical 1048576k(371596k free), swap 0k(0k free) vm_info: Java HotSpot(TM) 64-Bit Server VM (20.1-b02) for linux-amd64 JRE (1.6.0_26-b03), built on May 4 2011 01:13:47 by "java_re" with gcc 3.2.2 (SuSE Linux) time: Wed Sep 12 19:13:23 2012 elapsed time: 10 seconds

hs_err_pid17779.log

Code: Select all: # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007f9cbc23b592, pid=17779, tid=140311069021952 # # JRE version: 6.0_26-b03 # Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops) # Problematic frame: # V [libjvm.so+0x386592] CodeCache::free(CodeBlob*)+0x12 # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # --------------- T H R E A D --------------- Current thread (0x00007f9cb001e800): JavaThread "C2 CompilerThread0" daemon [_thread_in_vm, id=17825, stack(0x00007f9cb75d5000,0x00007f9cb76d6000)] siginfo:si_signo=SIGSEGV: si_errno=0, si_code=128 (), si_addr=0x0000000000000000 Registers: RAX=0x00007f9cb7e42900, RBX=0x00007f9cb7e3f290, RCX=0x0000000000000000, RDX=0x0000000000000001 RSP=0x00007f9cb76d3170, RBP=0x00007f9cb76d3180, RSI=0x0000000000000000, RDI=0x00007f9cb7e3f290 R8 =0x0000000000000001, R9 =0x00007f9cbc94f000, R10=0x00007f9cbc952e58, R11=0x00007f9cbc94b9d0 R12=0x00007f9cb7e3f290, R13=0x0000000000000006, R14=0x00007f9cbc952f70, R15=0x00007f9cb76d3eb0 RIP=0x00007f9cbc23b592, EFLAGS=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000000 TRAPNO=0x000000000000000d Top of Stack: (sp=0x00007f9cb76d3170) 0x00007f9cb76d3170: 00007f9cb001e800 00007f9cb001e800 0x00007f9cb76d3180: 00007f9cb76d31c0 00007f9cbc237ae3 0x00007f9cb76d3190: 000000004154ac80 0000000000000008 0x00007f9cb76d31a0: 00007f9cb001e800 0000000000000007 0x00007f9cb76d31b0: 00007f9cb76d3e40 00007f9cb001bd50 0x00007f9cb76d31c0: 00007f9cb76d31e0 00007f9cbc2511c3 0x00007f9cb76d31d0: 00007f9cb76d4534 00007f9cb76d4700 0x00007f9cb76d31e0: 00007f9cb76d3e80 00007f9cbc252f3b 0x00007f9cb76d31f0: 0000000000000006 0000000041913eb0 0x00007f9cb76d3200: 00007f9cb76d4700 00007f9cb76d4718 0x00007f9cb76d3210: 00007f9cb001bd50 0000000000000004 0x00007f9cb76d3220: 0000000000000001 0000000000000000 0x00007f9cb76d3230: 0000000000000000 00000000418e7848 0x00007f9cb76d3240: 00007f9cb76d33f0 00007f9cb76d3df0 0x00007f9cb76d3250: 00007f9cb76d3e40 00007f9cb76d4718 0x00007f9cb76d3260: 00007f9cb76d4700 00007f9cb76d4598 0x00007f9cb76d3270: 00007f9cb76d44f0 00007f9cb001bd50 0x00007f9cb76d3280: 00007f9cb001ef10 00007f9cb05e0370 0x00007f9cb76d3290: 00007f9cb05e4320 00007f9cb05e8358 0x00007f9cb76d32a0: 0000000000000002 00007f9cb76d3eb0 0x00007f9cb76d32b0: 00007f9cb001ef10 0000000000000200 0x00007f9cb76d32c0: 00007f9cb05e4350 00000000000000b3 0x00007f9cb76d32d0: 00007f9cbc952f70 00007f9cb001ef10 0x00007f9cb76d32e0: 0000000000000010 00007f9cb05e5350 0x00007f9cb76d32f0: 0000000000000000 0000000000000000 0x00007f9cb76d3300: 0000000000000000 0000000000000000 0x00007f9cb76d3310: 0000000000000000 0000000000000000 0x00007f9cb76d3320: 0000000000000000 0000000000000000 0x00007f9cb76d3330: 0000000000000000 0000000000000000 0x00007f9cb76d3340: 0000000000000000 0000000000000000 0x00007f9cb76d3350: 0000000000000000 0000000000000000 0x00007f9cb76d3360: 0000000000000000 0000000000000000 Instructions: (pc=0x00007f9cbc23b592) 0x00007f9cbc23b572: 00 eb 8c 90 66 66 66 90 66 66 90 66 66 90 55 48 0x00007f9cbc23b582: 89 e5 48 83 ec 10 48 89 5d f8 48 8b 07 48 89 fb 0x00007f9cbc23b592: ff 50 08 84 c0 74 21 48 8b 15 10 85 84 00 ff 0a 0x00007f9cbc23b5a2: 48 63 93 c0 00 00 00 39 93 bc 00 00 00 74 09 48 Register to memory mapping: RAX=0x00007f9cb7e42900 is an unknown value RBX=0x00007f9cb7e3f290 is an unknown value RCX=0x0000000000000000 is an unknown value RDX=0x0000000000000001 is an unknown value RSP=0x00007f9cb76d3170 is pointing into the stack for thread: 0x00007f9cb001e800 RBP=0x00007f9cb76d3180 is pointing into the stack for thread: 0x00007f9cb001e800 RSI=0x0000000000000000 is an unknown value RDI=0x00007f9cb7e3f290 is an unknown value R8 =0x0000000000000001 is an unknown value R9 =0x00007f9cbc94f000: <offset 0xa9a000> in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f9cbbeb5000 R10=0x00007f9cbc952e58: <offset 0xa9de58> in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f9cbbeb5000 R11=0x00007f9cbc94b9d0: _ZTV12CodeHeapPool+0x10 in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f9cbbeb5000 R12=0x00007f9cb7e3f290 is an unknown value R13=0x0000000000000006 is an unknown value R14=0x00007f9cbc952f70: _ZTV3Set+0x10 in /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server/libjvm.so at 0x00007f9cbbeb5000 R15=0x00007f9cb76d3eb0 is pointing into the stack for thread: 0x00007f9cb001e800 Stack: [0x00007f9cb75d5000,0x00007f9cb76d6000], sp=0x00007f9cb76d3170, free space=1016k Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) V [libjvm.so+0x386592] CodeCache::free(CodeBlob*)+0x12 V [libjvm.so+0x382ae3] BufferBlob::free(BufferBlob*)+0x63 V [libjvm.so+0x39c1c3] CompileWrapper::~CompileWrapper()+0x23 V [libjvm.so+0x39df3b] Compile::Compile(ciEnv*, C2Compiler*, ciMethod*, int, bool, bool)+0x9db V [libjvm.so+0x320d2e] C2Compiler::compile_method(ciEnv*, ciMethod*, int)+0x9e V [libjvm.so+0x3a862a] CompileBroker::invoke_compiler_on_method(CompileTask*)+0x2ca V [libjvm.so+0x3a7f15] CompileBroker::compiler_thread_loop()+0x355 V [libjvm.so+0x81fbe9] compiler_thread_entry(JavaThread*, Thread*)+0x9 V [libjvm.so+0x8190f1] JavaThread::run()+0x121 V [libjvm.so+0x710adf] java_start(Thread*)+0x13f Current CompileTask: C2: 23921 158 java.util.HashMap$EntryIterator.next()Ljava/util/Map$Entry; (5 bytes) --------------- P R O C E S S --------------- Java Threads: ( => current thread ) 0x00007f9cb0552000 JavaThread "Thread-1" daemon [_thread_blocked, id=18008, stack(0x00007f9cb6aca000,0x00007f9cb6bcb000)] 0x00007f9cb0551000 JavaThread "perf4j-async-stats-appender-sink-CoalescingStatistics" daemon [_thread_blocked, id=18007, stack(0x00007f9cb6bcb000,0x00007f9cb6ccc000)] 0x00007f9cb0023000 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=17828, stack(0x00007f9cb73d3000,0x00007f9cb74d4000)] 0x00007f9cb0020800 JavaThread "C2 CompilerThread1" daemon [_thread_in_native, id=17827, stack(0x00007f9cb74d4000,0x00007f9cb75d5000)] =>0x00007f9cb001e800 JavaThread "C2 CompilerThread0" daemon [_thread_in_vm, id=17825, stack(0x00007f9cb75d5000,0x00007f9cb76d6000)] 0x00007f9cb001c800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=17824, stack(0x00007f9cb76d6000,0x00007f9cb77d7000)] 0x00007f9cb0001000 JavaThread "Finalizer" daemon [_thread_blocked, id=17801, stack(0x00007f9cb77d7000,0x00007f9cb78d8000)] 0x0000000041605000 JavaThread "Reference Handler" daemon [_thread_blocked, id=17799, stack(0x00007f9cb78d8000,0x00007f9cb79d9000)] 0x000000004154e800 JavaThread "main" [_thread_in_Java, id=17794, stack(0x00007f9cbbb31000,0x00007f9cbbc32000)] Other Threads: 0x00000000415fe000 VMThread [stack: 0x00007f9cb79d9000,0x00007f9cb7ada000] [id=17797] 0x00007f9cb002e800 WatcherThread [stack: 0x00007f9cb72d2000,0x00007f9cb73d3000] [id=17829] VM state:not at safepoint (normal execution) VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event]) [0x000000004154ac80] CodeCache_lock - owner thread: 0x00007f9cb001e800 Heap def new generation total 18304K, used 3717K [0x00000000eae00000, 0x00000000ec1d0000, 0x00000000f0350000) eden space 16320K, 10% used [0x00000000eae00000, 0x00000000eafb17d8, 0x00000000ebdf0000) from space 1984K, 100% used [0x00000000ebdf0000, 0x00000000ebfe0000, 0x00000000ebfe0000) to space 1984K, 0% used [0x00000000ebfe0000, 0x00000000ebfe0000, 0x00000000ec1d0000) tenured generation total 40532K, used 34214K [0x00000000f0350000, 0x00000000f2ae5000, 0x00000000fae00000) the space 40532K, 84% used [0x00000000f0350000, 0x00000000f24b9a70, 0x00000000f24b9c00, 0x00000000f2ae5000) compacting perm gen total 21248K, used 10723K [0x00000000fae00000, 0x00000000fc2c0000, 0x0000000100000000) the space 21248K, 50% used [0x00000000fae00000, 0x00000000fb878d20, 0x00000000fb878e00, 0x00000000fc2c0000) No shared spaces configured. Code Cache [0x00007f9cb7d9c000, 0x00007f9cb800c000, 0x00007f9cbad9c000) total_blobs=404 nmethods=153 adapters=205 free_code_cache=49545920 largest_free_block=10176 Dynamic libraries: 40000000-40009000 r-xp 00000000 09:7f 37620687 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/bin/java 40108000-4010a000 rwxp 00008000 09:7f 37620687 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/bin/java 41546000-41f45000 rwxp 00000000 00:00 0 [heap] eae00000-ec1d0000 rwxp 00000000 00:00 0 ec1d0000-f0350000 rwxp 00000000 00:00 0 f0350000-f2ae5000 rwxp 00000000 00:00 0 f2ae5000-fae00000 rwxp 00000000 00:00 0 fae00000-fc2c0000 rwxp 00000000 00:00 0 fc2c0000-100000000 rwxp 00000000 00:00 0 7f9cb0000000-7f9cb08e6000 rwxp 00000000 00:00 0 7f9cb08e6000-7f9cb4000000 ---p 00000000 00:00 0 7f9cb6aca000-7f9cb6acd000 ---p 00000000 00:00 0 7f9cb6acd000-7f9cb6bcb000 rwxp 00000000 00:00 0 7f9cb6bcb000-7f9cb6bce000 ---p 00000000 00:00 0 7f9cb6bce000-7f9cb6ccc000 rwxp 00000000 00:00 0 7f9cb6ccc000-7f9cb6cd2000 r-xp 00000000 09:7f 37620592 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libmanagement.so 7f9cb6cd2000-7f9cb6dd1000 ---p 00006000 09:7f 37620592 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libmanagement.so 7f9cb6dd1000-7f9cb6dd3000 rwxp 00005000 09:7f 37620592 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/libmanagement.so 7f9cb6dd3000-7f9cb6dd8000 r-xs 00010000 09:7f 39071633 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xml-apis-ext.jar 7f9cb6dd8000-7f9cb6ddb000 r-xs 00012000 09:7f 39071630 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-security-ldap.jar 7f9cb6ddb000-7f9cb6de5000 r-xs 00041000 09:7f 39071629 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-security-core.jar 7f9cb6de5000-7f9cb6de8000 r-xs 00025000 09:7f 39071628 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-security-config.jar 7f9cb6de8000-7f9cb6df0000 r-xs 00034000 09:7f 39071627 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/spring-ldap.jar 7f9cb6df0000-7f9cb6dfd000 r-xs 000d0000 09:7f 39071622 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/server.jar 7f9cb6dfd000-7f9cb6e11000 r-xs 000e3000 09:7f 39071632 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xercesImpl.jar 7f9cb6e11000-7f9cb6e23000 r-xs 0019c000 09:7f 39071631 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xalan.jar 7f9cb6e23000-7f9cb6e27000 r-xs 0006c000 09:7f 39071626 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/specification.jar 7f9cb6e27000-7f9cb6e2f000 r-xs 00028000 09:7f 39071634 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/xml-apis.jar 7f9cb6e2f000-7f9cb6e32000 r-xs 00041000 09:7f 39071621 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/serializer.jar 7f9cb6e32000-7f9cb6e34000 r-xs 00011000 09:7f 39071619 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/romio.jar 7f9cb6e34000-7f9cb6e36000 r-xs 00012000 09:7f 39071618 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/rendering.jar 7f9cb6e36000-7f9cb6e3a000 r-xs 0005b000 09:7f 39071617 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/quartz.jar 7f9cb6e3a000-7f9cb6e3d000 r-xs 00016000 09:7f 39071608 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/org.springframework.context.support.jar 7f9cb6e3d000-7f9cb6e40000 r-xs 0000e000 09:7f 39071603 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/omero-shares.jar 7f9cb6e40000-7f9cb6e49000 r-xs 0005f000 09:7f 39071601 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ome-java.jar 7f9cb6e49000-7f9cb6e4a000 r-xs 00016000 09:7f 39071600 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ome-io.jar 7f9cb6e4a000-7f9cb6e65000 r-xs 00255000 09:7f 39071599 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/netcdf.jar 7f9cb6e65000-7f9cb6e6b000 r-xs 00055000 09:7f 39071595 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/mail.jar 7f9cb6e6b000-7f9cb6e78000 r-xs 00086000 09:7f 39071587 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/jts.jar 7f9cb6e78000-7f9cb6e7a000 r-xs 00001000 09:7f 39071586 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/jsr107cache.jar 7f9cb6e7a000-7f9cb6e7c000 r-xs 00009000 09:7f 39071584 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/java-image-scaling.jar 7f9cb6e7c000-7f9cb6e7d000 r-xs 0000d000 09:7f 39071583 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/java-getopt.jar 7f9cb6e7d000-7f9cb6e7f000 r-xs 00007000 09:7f 39071580 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ini4j.jar 7f9cb6e7f000-7f9cb6eb6000 r-xs 0029c000 09:7f 39071579 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ice.jar 7f9cb6eb6000-7f9cb6ebb000 r-xs 0003f000 09:7f 39071578 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ice-freeze.jar 7f9cb6ebb000-7f9cb6ec5000 r-xs 0007e000 09:7f 39071577 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ice-db.jar 7f9cb6ec5000-7f9cb6ec9000 r-xs 00049000 09:7f 39071572 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/grib.jar 7f9cb6ec9000-7f9cb6ecb000 r-xs 00002000 09:7f 39071571 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/geronimo-spec-jta.jar 7f9cb6ecb000-7f9cb6ed0000 r-xs 0003c000 09:7f 39071570 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/ehcache.jar 7f9cb6ed0000-7f9cb6ed2000 r-xs 00009000 09:7f 39071567 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-pool.jar 7f9cb6ed2000-7f9cb6ed7000 r-xs 00040000 09:7f 39071565 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-lang.jar 7f9cb6ed7000-7f9cb6eda000 r-xs 00018000 09:7f 39071564 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-io.jar 7f9cb6eda000-7f9cb6ee0000 r-xs 00045000 09:7f 39071563 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-httpclient.jar 7f9cb6ee0000-7f9cb6ee2000 r-xs 0000a000 09:7f 39071561 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/commons-codec.jar 7f9cb6ee2000-7f9cb6ee8000 r-xs 00077000 09:7f 39071616 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/postgresql.jar 7f9cb6ee8000-7f9cb6eef000 r-xs 00031000 09:7f 39071613 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---p 0017a000 09:7f 36840227 /lib/libc-2.11.1.so 7f9cbce39000-7f9cbce3d000 r-xp 00179000 09:7f 36840227 /lib/libc-2.11.1.so 7f9cbce3d000-7f9cbce3e000 rwxp 0017d000 09:7f 36840227 /lib/libc-2.11.1.so 7f9cbce3e000-7f9cbce43000 rwxp 00000000 00:00 0 7f9cbce43000-7f9cbce45000 r-xp 00000000 09:7f 36840232 /lib/libdl-2.11.1.so 7f9cbce45000-7f9cbd045000 ---p 00002000 09:7f 36840232 /lib/libdl-2.11.1.so 7f9cbd045000-7f9cbd046000 r-xp 00002000 09:7f 36840232 /lib/libdl-2.11.1.so 7f9cbd046000-7f9cbd047000 rwxp 00003000 09:7f 36840232 /lib/libdl-2.11.1.so 7f9cbd047000-7f9cbd05f000 r-xp 00000000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f9cbd05f000-7f9cbd25e000 ---p 00018000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f9cbd25e000-7f9cbd25f000 r-xp 00017000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f9cbd25f000-7f9cbd260000 rwxp 00018000 09:7f 36837289 /lib/libpthread-2.11.1.so 7f9cbd260000-7f9cbd264000 rwxp 00000000 00:00 0 7f9cbd264000-7f9cbd284000 r-xp 00000000 09:7f 36831821 /lib/ld-2.11.1.so 7f9cbd286000-7f9cbd28e000 r-xs 00047000 09:7f 39071551 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/backport-util-concurrent.jar 7f9cbd28e000-7f9cbd290000 r-xs 00003000 09:7f 39071549 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/asm-attrs.jar 7f9cbd290000-7f9cbd296000 r-xs 00067000 09:7f 39071548 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/antlr.jar 7f9cbd296000-7f9cbd2a4000 r-xs 0031d000 09:7f 39071546 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/PDFBox.jar 7f9cbd2a4000-7f9cbd2ae000 rwxp 00000000 00:00 0 7f9cbd2ae000-7f9cbd364000 rwxp 00000000 00:00 0 7f9cbd364000-7f9cbd36c000 rwxs 00000000 09:7f 37627622 /tmp/hsperfdata_omero/17779 7f9cbd36c000-7f9cbd36f000 rwxp 00000000 00:00 0 7f9cbd36f000-7f9cbd376000 r-xp 00000000 09:7f 37620607 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/jli/libjli.so 7f9cbd376000-7f9cbd477000 ---p 00007000 09:7f 37620607 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/jli/libjli.so 7f9cbd477000-7f9cbd479000 rwxp 00008000 09:7f 37620607 /usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/jli/libjli.so 7f9cbd479000-7f9cbd47a000 rwxp 00000000 00:00 0 7f9cbd47a000-7f9cbd47b000 r-xs 00006000 09:7f 39071550 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/asm.jar 7f9cbd47b000-7f9cbd47d000 r-xs 0000c000 09:7f 39071547 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/activation.jar 7f9cbd47d000-7f9cbd47f000 r-xs 0000e000 09:7f 39071545 /home/omero/OMERO.server-4.4.3-ice34-b5/lib/server/FontBox.jar 7f9cbd47f000-7f9cbd480000 rwxp 00000000 00:00 0 7f9cbd480000-7f9cbd481000 r-xp 00000000 00:00 0 7f9cbd481000-7f9cbd483000 rwxp 00000000 00:00 0 7f9cbd483000-7f9cbd484000 r-xp 0001f000 09:7f 36831821 /lib/ld-2.11.1.so 7f9cbd484000-7f9cbd485000 rwxp 00020000 09:7f 36831821 /lib/ld-2.11.1.so 7f9cbd485000-7f9cbd486000 rwxp 00000000 00:00 0 7fffdc82e000-7fffdc843000 rwxp 00000000 00:00 0 [stack] 7fffdc95d000-7fffdc95f000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] VM Arguments: jvm_args: -Xmx256M -Djava.awt.headless=true -Dlog4j.configuration=etc/log4j-indexing.xml -Domero.logfile=var/log/${omero.name}.log -Domero.name=PixelData-0 java_command: lib/server/blitz.jar ome.pixeldata --Ice.Config=/home/omero/OMERO.server-4.4.3-ice34-b5/var/master/servers/PixelData-0/config/config Launcher Type: SUN_STANDARD Environment Variables: PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games USERNAME=omero LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/server:/usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64:/usr/lib/jvm/java-6-sun-1.6.0.26/jre/../lib/amd64 SHELL=/bin/bash Signal Handlers: SIGSEGV: [libjvm.so+0x85f800], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGBUS: [libjvm.so+0x85f800], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGFPE: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGPIPE: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGXFSZ: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGILL: [libjvm.so+0x70e300], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGUSR2: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGHUP: SIG_IGN, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGINT: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGTERM: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGQUIT: [libjvm.so+0x710d10], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 --------------- S Y S T E M --------------- OS:squeeze/sid uname:Linux 2.6.32-042stab059.7 #1 SMP Tue Jul 24 19:12:01 MSK 2012 x86_64 libc:glibc 2.11.1 NPTL 2.11.1 rlimit: STACK 8192k, CORE 0k, NPROC infinity, NOFILE 1024, AS infinity load average:8.52 10.74 12.55 /proc/meminfo: MemTotal: 1048576 kB MemFree: 460844 kB Cached: 104260 kB Active: 528280 kB Inactive: 33240 kB Active(anon): 441120 kB Inactive(anon): 16140 kB Active(file): 87160 kB Inactive(file): 17100 kB Unevictable: 0 kB Mlocked: 0 kB SwapTotal: 0 kB SwapFree: 0 kB Dirty: 136 kB Writeback: 0 kB AnonPages: 457260 kB Shmem: 31224 kB Slab: 26180 kB SReclaimable: 10748 kB SUnreclaim: 15432 kB CPU:total 1 (4 cores per cpu, 2 threads per core) family 6 model 58 stepping 9, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, ht /proc/cpuinfo: processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 58 model name : Intel(R) Xeon(R) CPU E3-1230 V2 @ 3.30GHz stepping : 9 cpu MHz : 3292.547 cache size : 8192 KB physical id : 0 siblings : 8 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 x2apic popcnt aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms bogomips : 6585.09 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: Memory: 4k page, physical 1048576k(460844k free), swap 0k(0k free) vm_info: Java HotSpot(TM) 64-Bit Server VM (20.1-b02) for linux-amd64 JRE (1.6.0_26-b03), built on May 4 2011 01:13:47 by "java_re" with gcc 3.2.2 (SuSE Linux) time: Wed Sep 12 19:13:37 2012 elapsed time: 24 seconds

by **jmoore** » Wed Sep 12, 2012 3:48 pm

What instructions did you follow to install the Sun Java packages? Have you seen https://www.openmicroscopy.org/site/support/omero4-staging/sysadmins/unix/server-install-linux.html

Cheers,
~Josh

Open Microscopy Environment

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