I updated to omero 5.3.2 and to do so upgrade my debian server to stretch anticipating a bit the stable release. This was the only way to get ice3.6.
Any attempt to log in omero fails. On the CLI running on the server, I obtain the following message
- Code: Select all
root@cedre-5a:/usr/local/OMERO# sudo -u cedre-agent OMERO.server-Current/bin/omero search "Image" "zyg-9"
Previously logged in to localhost:4064 as root
Server: [localhost:4064]
Username: [root]jacques
Password:
InternalException: Failed to connect: exception ::Ice::ProtocolException
{
reason = SSL error occurred for new outgoing connection:
remote address = 127.0.0.1:4064
sslv3 alert handshake failure
}
Below is the diagnostics for your information about versions.
There is no erroneous entry in master.err, master.out or Blitz-0.log at the time of the issue.
Googleing a bit my issue, I found that IceSSL and java 8 may not interact correctly and tried to change params after the recommendation I found
sudo -u cedre-agent OMERO.server-Current/bin/omero config set IceSSL.Ciphers "NONE (DH_anon.*AES)”
sudo -u cedre-agent OMERO.server-Current/bin/omero config set IceSSL.VerifyPeer 0
But it did not help. I have no knowledge about Ice and its implementation in omero. So it was maybe a naive approach.
I also tried the patch (find in the omero forum)
http://blog.openmicroscopy.org/tech-iss ... ava-issue/
but it no longer apply
- Code: Select all
patching file etc/grid/templates.xml
Hunk #1 FAILED at 469.
1 out of 1 hunk FAILED -- saving rejects to file etc/grid/templates.xml.rej
At other times and repeated several times (see below), I found (I don’t know if it is related). For the sake of completeness, there is also an issue at omero stop reproduced below (129.20.159.125 is the IP of the server, named cedre-5a).
Thank you very much for your help.
Best
Jacques
Diagnostics
================================================================================
OMERO Diagnostics 5.3.2-ice36-b62
================================================================================
Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.13 (/usr/bin/python)
Commands: icegridnode --version 3.6.3 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.3 (/usr/bin/icegridadmin)
Commands: psql --version 9.6.3 (/usr/bin/psql)
Server: icegridnode running
Server: Blitz-0 active (pid = 11737, enabled)
Server: DropBox active (pid = 11770, enabled)
Server: FileServer active (pid = 11772, enabled)
Server: Indexer-0 active (pid = 11775, enabled)
Server: MonitorServer active (pid = 11776, enabled)
Server: OMERO.Glacier2 active (pid = 11778, enabled)
Server: OMERO.IceStorm active (pid = 11781, enabled)
Server: PixelData-0 active (pid = 11782, enabled)
Server: Processor-0 active (pid = 11798, enabled)
Server: Tables-0 active (pid = 11796, enabled)
Server: TestDropBox inactive (enabled)
Log dir: /usr2/local/OMERO/OMERO.server-Current/var/log exists
Log files: Blitz-0.log 8.0 MB errors=301 warnings=31
Log files: DropBox.log 41.0 KB errors=6 warnings=17
Log files: FileServer.log 5.0 KB
Log files: Indexer-0.log 3.0 MB errors=613 warnings=224
Log files: MonitorServer.log 20.0 KB
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 0.0 KB
Log files: PixelData-0.log 1.0 MB errors=304 warnings=109
Log files: Processor-0.log 354.0 KB errors=12 warnings=298
Log files: Tables-0.log 72.0 KB errors=12 warnings=25
Log files: TestDropBox.log n/a
Log files: master.err 36.0 KB errors=23 warnings=20
Log files: master.out 0.0 KB
Log files: Total size 14.27 MB
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/OMERO' Exists? True Is writable? True
OMERO temp dir:'/home/cedre-agent/omero/tmp' Exists? True Is writable? True (Size: 4622106653)
JVM settings: Blitz-${index} -Xmx19200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
OMERO.web status... [NOT STARTED]
Django version: 1.8.18
Errors found several times in Blitz-0.log
2017-06-05 07:28:33,081 INFO [ ome.services.util.ServiceHandler] (l.Server-1) Executor.doWork -- ome.services.sessions.SessionManagerImpl.update[]
2017-06-05 07:28:33,081 INFO [ ome.services.util.ServiceHandler] (l.Server-1) Args: [null, InternalSF@1397795607]
2017-06-05 07:28:33,092 INFO [ ome.security.basic.EventHandler] (l.Server-1) Auth: user=0,group=0,event=193541526(Sessions),sess=0551402d-286b-456e-a143-fa9e8f2febbc
2017-06-05 07:28:33,097 INFO [ ome.security.basic.CurrentDetails] (l.Server-1) Adding log:UPDATE,class ome.model.meta.Session,345620
2017-06-05 07:28:33,121 INFO [ org.perf4j.TimingLogger] (l.Server-1) start[1496640513081] time[39] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$4.doWork]
2017-06-05 07:28:33,121 INFO [ ome.services.util.ServiceHandler] (l.Server-1) Rslt: ome.model.meta.Session:Id_345620
2017-06-05 07:28:33,135 ERROR [ ome.services.blitz.util.ParamsCache] (2-thread-5) Failed to load params for 1254620
omero.InternalException: null
at sun.reflect.GeneratedConstructorAccessor179.newInstance(Unknown Source) ~[na:na]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_131]
at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[na:1.8.0_131]
at java.lang.Class.newInstance(Class.java:442) ~[na:1.8.0_131]
at IceInternal.BasicStream.createUserException(BasicStream.java:2779) ~[ice.jar:na]
at IceInternal.BasicStream.access$300(BasicStream.java:14) ~[ice.jar:na]
at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3614) ~[ice.jar:na]
at IceInternal.BasicStream.throwException(BasicStream.java:2291) ~[ice.jar:na]
at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) ~[ice.jar:na]
at omero.grid.InteractiveProcessorPrxHelper.end_params(InteractiveProcessorPrxHelper.java:874) ~[blitz.jar:na]
at omero.grid.InteractiveProcessorPrxHelper.params(InteractiveProcessorPrxHelper.java:761) ~[blitz.jar:na]
at omero.grid.InteractiveProcessorPrxHelper.params(InteractiveProcessorPrxHelper.java:754) ~[blitz.jar:na]
at omero.grid.ParamsHelper.generateScriptParams(ParamsHelper.java:153) ~[blitz.jar:na]
at ome.services.blitz.util.ParamsCache$Loader.createParams(ParamsCache.java:304) ~[blitz.jar:na]
at ome.services.blitz.util.ParamsCache._load(ParamsCache.java:217) [blitz.jar:na]
at ome.services.blitz.util.ParamsCache.lookupAll(ParamsCache.java:181) [blitz.jar:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_131]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_131]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_131]
at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_131]
at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:273) [spring-core.jar:3.0.1.RELEASE]
at org.springframework.scheduling.quartz.MethodInvokingJobDetailFactoryBean$MethodInvokingJob.executeInternal(MethodInvokingJobDetailFactoryBean.java:264) [spring-context-support.jar:3.0.1.RELEASE]
at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86) [spring-context-support.jar:3.0.1.RELEASE]
at org.quartz.core.JobRunShell.run(JobRunShell.java:203) [quartz.jar:1.5.2]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_131]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_131]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_131]
2017-06-05 07:28:33,135 INFO [ ome.services.blitz.util.ParamsCache] (2-thread-5) New size of scripts cache: 0 (5160 ms.)
2017-06-05 07:28:33,135 INFO [ org.perf4j.TimingLogger] (2-thread-5) start[1496640507975] time[5160] tag[omero.scripts.cache.all]
2017-06-05 07:28:33,135 INFO [o.services.sessions.SessionContext$Count] (2-thread-5) -Reference count: 3da73cc1-20e6-48b5-bedf-64bf674ec495=0
2017-06-05 07:28:33,135 INFO [ omero.cmd.SessionI] (2-thread-5) doDestroy(ServiceFactoryI(session-dc7c6d34-6e30-46a8-88bf-88f66065b632/3da73cc1-20e6-48b5-bedf-64bf674ec495))
Error at stopping omero
! 6/5/17 07:22:56:531 warning: Blitz-0-Ice.ThreadPool.Server-457: dispatch exception:
identity: session-85f0946d-d622-4287-8bab-e0f53f2fba85/f42b9e96-4f7f-4ca8-ae6d-4253381e422e
facet:
operation: destroy
remote host: 129.20.159.125 remote port: 49532
Ice.ObjectAdapterDeactivatedException
name = "BlitzAdapter"
at Ice.ObjectAdapterI.checkForDeactivation(ObjectAdapterI.java:1170)
at Ice.ObjectAdapterI.findFacet(ObjectAdapterI.java:498)
at Ice.ObjectAdapterI.find(ObjectAdapterI.java:491)
at omero.cmd.SessionI.unregisterServant(SessionI.java:633)
at omero.cmd.SessionI.cleanServants(SessionI.java:449)
at omero.cmd.SessionI.cleanServants(SessionI.java:379)
at omero.cmd.SessionI.doDestroy(SessionI.java:369)
at omero.cmd.SessionI.destroy(SessionI.java:297)
at omero.api._ServiceFactoryTie.destroy(_ServiceFactoryTie.java:65)
at Glacier2._SessionDisp.___destroy(_SessionDisp.java:94)
at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1263)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:745)
!! 06/05/17 07:22:56.621 error: communicator not destroyed during global destruction.
