Open Microscopy Environment

Hi,

When I try to use the "Create Movie" button in OmeroInsight 4.11, a error dialog is returned that tells me it can't create a movie. I built the Insight in eclipse and ran with the debugger and received the following error trace:

Code: Select all

org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot create a movie for image: 412
   at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:545)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.createMovie(OMEROGateway.java:4626)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.createMovie(OmeroImageServiceImpl.java:688)
   at org.openmicroscopy.shoola.env.data.views.calls.MovieCreator$1.doCall(MovieCreator.java:76)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:145)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Thread.java:613)
Caused by: Ice.UnknownLocalException
    unknown = "Ice::NoEndpointException
               Ice.NoEndpointException
                   proxy = "Processor-0 -t @ Processor-0.ProcessorAdapter"
                  at IceInternal.RoutableReference$2.setEndpoints(RoutableReference.java:524)
                  at IceInternal.LocatorInfo$RequestCallback.response(LocatorInfo.java:51)
                  at IceInternal.LocatorInfo$Request.response(LocatorInfo.java:188)
                  at IceInternal.LocatorInfo$AdapterRequest$1.ice_response(LocatorInfo.java:298)
                  at Ice.AMI_Locator_findAdapterById.__response(AMI_Locator_findAdapterById.java:85)
                  at IceInternal.OutgoingAsync.__finished(OutgoingAsync.java:201)
                  at Ice.ConnectionI.message(ConnectionI.java:964)
                  at IceInternal.ThreadPool.run(ThreadPool.java:577)
                  at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                  at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
               "
   at IceInternal.Outgoing.invoke(Outgoing.java:147)
   at omero.api._IScriptDelM.runScript(_IScriptDelM.java:341)
   at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:457)
   at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:429)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.createMovie(OMEROGateway.java:4619)
   ... 9 more
org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot create a movie for image: 412
   at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:545)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.createMovie(OMEROGateway.java:4626)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.createMovie(OmeroImageServiceImpl.java:688)
   at org.openmicroscopy.shoola.env.data.views.calls.MovieCreator$1.doCall(MovieCreator.java:76)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:145)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Thread.java:613)
Caused by: Ice.UnknownLocalException
    unknown = "Ice::NoEndpointException
               Ice.NoEndpointException
                   proxy = "Processor-0 -t @ Processor-0.ProcessorAdapter"
                  at IceInternal.RoutableReference$2.setEndpoints(RoutableReference.java:524)
                  at IceInternal.LocatorInfo$RequestCallback.response(LocatorInfo.java:51)
                  at IceInternal.LocatorInfo$Request.response(LocatorInfo.java:188)
                  at IceInternal.LocatorInfo$AdapterRequest$1.ice_response(LocatorInfo.java:298)
                  at Ice.AMI_Locator_findAdapterById.__response(AMI_Locator_findAdapterById.java:85)
                  at IceInternal.OutgoingAsync.__finished(OutgoingAsync.java:201)
                  at Ice.ConnectionI.message(ConnectionI.java:964)
                  at IceInternal.ThreadPool.run(ThreadPool.java:577)
                  at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                  at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
               "
   at IceInternal.Outgoing.invoke(Outgoing.java:147)
   at omero.api._IScriptDelM.runScript(_IScriptDelM.java:341)
   at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:457)
   at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:429)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.createMovie(OMEROGateway.java:4619)
   ... 9 more

Any ideas?

Hi Chris,

This looks like a problem is occurring with ICE, I wonder if you could send me a copy of the log files: Processor-0.log, master.err and master.out in /dist/var/log?

Regards

D.

Hi,

I will get together the log files, but I noticed that when I run omero admin diagnostics that Processor-0 is inactive and disabled. How do I activate Processor-0?

Thanks

Code: Select all

================================================================================
OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================
       
Commands:   java -version                  1.6.0     (/usr/local/jdk1.6.0_18/bin/java)
Commands:   python -V                      2.4.3     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 8.1.18    (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 20821, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FSServer                       inactive (disabled)
Server:     Indexer-0                      active (pid = 20836, enabled)
Server:     OMERO.Glacier2                 active (pid = 20839, enabled)
Server:     OMERO.IceStorm                 active (pid = 20840, enabled)
Server:     Processor-0                    inactive (disabled)
Server:     Tables-0                       active (pid = 20875, enabled)
Server:     TestDropBox                    inactive (enabled)
Server:     Web                            inactive (enabled)

Log dir:    /OMERO/omero_dist/var/log      exists

Log files:  Blitz-0.log                    226.0 MB      errors=831  warnings=552685
Log files:  DropBox.log                    n/a
Log files:  FSServer.log                   8.0 KB        errors=10   warnings=0   
Log files:  Indexer-0.log                  95.0 MB       errors=5    warnings=549693
Log files:  OMEROweb.log                   n/a
Log files:  Processor-0.log                n/a


The details for the how and why will be in master.err, master.out and Processor-0.log (if it exists). The processor is configured to be running by default, unless you've gone out of your way to disable it the service should be running.

I looked in the logs and found that omero (running under user apache) is trying to write to my /home directory that is nfs mounted (so the apache user is local to my omero system, while writing to my home directory is managed by our domain). I changed the rw permissions on the directory, so now creating movies works.

I am using CentOS 5:
The system is trying to write to ~/omero/tmp/omero_apache, but the omero distribution is on a local drive at /OMERO/omero_dist. I really don't want OMERO to be writing tmp files onto a network mounted drive.
It looks like this is the tmp directory for rendering movies, so moving all of this over the network is inefficient.

I have looked at the install docs and config files but I can't find anything about how to change this. Do you have any suggestions?

Thanks for your help.

Chris

Hi Chris,

to change the temp directory used, set the OMERO_TEMPDIR environment variable before starting your server:

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josh@mac:~/code/git/components/tools/OmeroPy/src $ PYTHONPATH=. python omero/util/temp_files.py
Usage: omero/util/temp_files.py clean
   or: omero/util/temp_files.py dir 
josh@mac:~/code/git/components/tools/OmeroPy/src $ PYTHONPATH=. python omero/util/temp_files.py dir
/Users/josh/omero/tmp/omero_josh/11688
josh@mac:~/code/git/components/tools/OmeroPy/src $ OMERO_TEMPDIR=/tmp PYTHONPATH=. python omero/util/temp_files.py dir
/tmp/omero/tmp/omero_josh/11689
josh@mac:~/code/git/components/tools/OmeroPy/src $


Documentation for the temp file manager is on the wiki: https://trac.openmicroscopy.org.uk/omero/wiki/TempFileManager, but we're probably missing a link from the install documentation, which we'll fix. Sorry.

One question, though, where is the apache user's home directory?
~Josh.

Hi Josh,

Thanks for help, that is working now.

My apache home directory is /var/www (from /etc/passwd).

One other thing about creating movies: It doesn't seem to work for Zeiss zvi files, but works great for all other file types. ZVI files are imported fine and displayed correctly in Insight, but movies fail.

Thanks again
Chris

Any information in Processor-0.log for the ZVI failures?

Here is the output from the log file for a ZVI file (a zstack with 108 planes)

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2010-04-12 09:16:59,283 INFO  [                            omero.remote] (Dummy-4   )  Meth: ProcessorI.parseJob
2010-04-12 09:16:59,294 INFO  [              omero.processor.ProcessorI] (Dummy-4   ) parseJob: Session = 0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4, JobId = 302
2010-04-12 09:16:59,400 INFO  [              omero.processor.ProcessorI] (Dummy-4   ) processJob: Session = 0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4, JobId = 302
2010-04-12 09:16:59,401 INFO  [                omero.processor.ProcessI] (Dummy-4   ) Created 0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4 in /tmp/omero/tmp/omero_apache/32739/process0-o50O.dir
2010-04-12 09:16:59,401 INFO  [                    omero.util.Resources] (Dummy-4   ) Adding object <proc:None,rc=None,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4>
2010-04-12 09:16:59,432 INFO  [              omero.processor.ProcessorI] (Dummy-4   ) Downloaded file: 2
2010-04-12 09:16:59,440 INFO  [                omero.processor.ProcessI] (Dummy-4   ) <proc:6431,rc=None,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Activated
2010-04-12 09:16:59,443 INFO  [                            omero.remote] (Dummy-9   )  Meth: ProcessI.wait
2010-04-12 09:16:59,444 INFO  [                omero.processor.ProcessI] (Dummy-9   ) <proc:6431,rc=None,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Waiting
2010-04-12 09:17:00,069 INFO  [                omero.processor.ProcessI] (Dummy-9   ) <proc:6431,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Deactivating
2010-04-12 09:17:00,070 INFO  [                            omero.remote] (Dummy-9   )  Meth: ProcessI.shutdown
2010-04-12 09:17:00,071 INFO  [                            omero.remote] (Dummy-9   )  Rslt:                 None in 6.69956207275e-05s
2010-04-12 09:17:00,094 INFO  [                omero.processor.ProcessI] (Dummy-9   ) <proc:6431,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Lived 0s. Deactivation took 0s.
2010-04-12 09:17:00,095 INFO  [                omero.processor.ProcessI] (Dummy-9   ) <proc:6431,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Callback processFinished
2010-04-12 09:17:00,095 INFO  [                            omero.remote] (Dummy-9   )  Rslt:                    1 in 0.651309013367s
2010-04-12 09:17:00,111 INFO  [                            omero.remote] (Dummy-4   )  Rslt: object #0 (::omero:: in 0.828050851822s
2010-04-12 09:17:00,124 INFO  [                            omero.remote] (Dummy-10  )  Meth: ProcessorI.processJob
2010-04-12 09:17:00,139 INFO  [              omero.processor.ProcessorI] (Dummy-10  ) parseJob: Session = 0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4, JobId = 302
2010-04-12 09:17:00,239 INFO  [              omero.processor.ProcessorI] (Dummy-10  ) processJob: Session = 0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4, JobId = 302
2010-04-12 09:17:00,240 INFO  [                omero.processor.ProcessI] (Dummy-10  ) Created 0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4 in /tmp/omero/tmp/omero_apache/32739/processHBtp5R.dir
2010-04-12 09:17:00,241 INFO  [                    omero.util.Resources] (Dummy-10  ) Adding object <proc:None,rc=None,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4>
2010-04-12 09:17:00,289 INFO  [              omero.processor.ProcessorI] (Dummy-10  ) Downloaded file: 2
2010-04-12 09:17:00,343 INFO  [                omero.processor.ProcessI] (Dummy-10  ) <proc:6455,rc=None,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Activated
2010-04-12 09:17:00,351 INFO  [                            omero.remote] (Dummy-11  )  Meth: ProcessI.wait
2010-04-12 09:17:00,352 INFO  [                omero.processor.ProcessI] (Dummy-11  ) <proc:6455,rc=None,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Waiting
2010-04-12 09:17:00,913 INFO  [                omero.processor.ProcessI] (Dummy-11  ) <proc:6455,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Deactivating
2010-04-12 09:17:00,913 INFO  [                            omero.remote] (Dummy-11  )  Meth: ProcessI.shutdown
2010-04-12 09:17:00,913 INFO  [                            omero.remote] (Dummy-11  )  Rslt:                 None in 4.60147857666e-05s2010-04-12 09:17:00,927 INFO  [                omero.processor.ProcessI] (Dummy-11  ) <proc:6455,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Lived 0s. Deactivation took 0s.
2010-04-12 09:17:00,928 INFO  [                omero.processor.ProcessI] (Dummy-11  ) <proc:6455,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Callback processFinished2010-04-12 09:17:00,928 INFO  [                            omero.remote] (Dummy-11  )  Rslt:                    1 in 0.575919866562s
2010-04-12 09:17:01,005 INFO  [              omero.processor.ProcessorI] (Dummy-10  ) processJob: Session = 0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4, JobId = 302
2010-04-12 09:17:01,006 INFO  [                omero.processor.ProcessI] (Dummy-10  ) Created 0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4 in /tmp/omero/tmp/omero_apache/32739/processpVMB7f.dir
2010-04-12 09:17:01,007 INFO  [                    omero.util.Resources] (Dummy-10  ) Adding object <proc:None,rc=None,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4>
2010-04-12 09:17:01,038 INFO  [              omero.processor.ProcessorI] (Dummy-10  ) Downloaded file: 2
2010-04-12 09:17:01,046 INFO  [                omero.processor.ProcessI] (Dummy-10  ) <proc:6474,rc=None,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Activated
2010-04-12 09:17:01,050 INFO  [                            omero.remote] (Dummy-10  )  Rslt: AE120534-E53C-490F-A in 0.924717903137s
2010-04-12 09:17:01,053 INFO  [                            omero.remote] (Dummy-7   )  Meth: ProcessI.wait
2010-04-12 09:17:01,053 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6474,rc=None,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Waiting
2010-04-12 09:17:02,327 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Deactivating
2010-04-12 09:17:02,327 INFO  [                            omero.remote] (Dummy-7   )  Meth: ProcessI.shutdown
2010-04-12 09:17:02,328 INFO  [                            omero.remote] (Dummy-7   )  Rslt:                 None in 6.22272491455e-05s
2010-04-12 09:17:02,537 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Uploaded 971 bytes of /tmp/omero/tmp/omero_apache/32739/process
pVMB7f.dir/out to 654
2010-04-12 09:17:02,662 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Uploaded 378 bytes of /tmp/omero/tmp/omero_apache/32739/process
pVMB7f.dir/err to 655
2010-04-12 09:17:02,666 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Lived 1s. Deactivation took 0s.
2010-04-12 09:17:02,666 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Callback processFinished
2010-04-12 09:17:02,666 INFO  [                            omero.remote] (Dummy-7   )  Rslt:                    1 in 1.61336302757s
2010-04-12 09:17:02,668 INFO  [                            omero.remote] (Dummy-8   )  Meth: ProcessI.poll
2010-04-12 09:17:02,668 INFO  [                            omero.remote] (Dummy-8   )  Rslt: object #0 (::omero:: in 0.000104904174805s
2010-04-12 09:17:30,118 INFO  [                            omero.remote] (Thread-2  )  Meth: ProcessI.poll
2010-04-12 09:17:30,119 INFO  [                            omero.remote] (Thread-2  )  Rslt: object #0 (::omero:: in 8.10623168945e-05s
2010-04-12 09:17:30,123 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Keep alive failed
2010-04-12 09:17:30,124 INFO  [                            omero.remote] (Thread-2  )  Meth: ProcessI.poll
2010-04-12 09:17:30,124 INFO  [                            omero.remote] (Thread-2  )  Rslt: object #0 (::omero:: in 0.000102043151855s
2010-04-12 09:17:30,128 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6455,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Keep alive failed
2010-04-12 09:17:30,128 INFO  [                            omero.remote] (Thread-2  )  Meth: ProcessI.poll
2010-04-12 09:17:30,129 INFO  [                            omero.remote] (Thread-2  )  Rslt: object #0 (::omero:: in 7.70092010498e-05s
2010-04-12 09:17:30,132 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6431,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Keep alive failed
2010-04-12 09:17:30,134 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Cleaning
2010-04-12 09:17:30,135 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Killing session
2010-04-12 09:17:30,138 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6455,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Cleaning
2010-04-12 09:17:30,140 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6431,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Cleaning


Here is the output for the same image exported as ome.tif and imported

Code: Select all

2010-04-12 09:26:19,974 INFO  [                            omero.remote] (Dummy-5   )  Meth: ProcessorI.parseJob
2010-04-12 09:26:19,984 INFO  [              omero.processor.ProcessorI] (Dummy-5   ) parseJob: Session = b227af53-fabc-4dbd-93bf-0b01c34732e5, JobId = 303
2010-04-12 09:26:20,073 INFO  [              omero.processor.ProcessorI] (Dummy-5   ) processJob: Session = b227af53-fabc-4dbd-93bf-0b01c34732e5, JobId = 303
2010-04-12 09:26:20,074 INFO  [                omero.processor.ProcessI] (Dummy-5   ) Created b227af53-fabc-4dbd-93bf-0b01c34732e5 in /tmp/omero/tmp/omero_apache/32739/processO0Hi3q.dir
2010-04-12 09:26:20,075 INFO  [                    omero.util.Resources] (Dummy-5   ) Adding object <proc:None,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5>
2010-04-12 09:26:20,139 INFO  [              omero.processor.ProcessorI] (Dummy-5   ) Downloaded file: 2
2010-04-12 09:26:20,157 INFO  [                omero.processor.ProcessI] (Dummy-5   ) <proc:6533,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Activated
2010-04-12 09:26:20,160 INFO  [                            omero.remote] (Dummy-11  )  Meth: ProcessI.wait
2010-04-12 09:26:20,160 INFO  [                omero.processor.ProcessI] (Dummy-11  ) <proc:6533,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Waiting
2010-04-12 09:26:20,793 INFO  [                omero.processor.ProcessI] (Dummy-11  ) <proc:6533,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Deactivating
2010-04-12 09:26:20,793 INFO  [                            omero.remote] (Dummy-11  )  Meth: ProcessI.shutdown
2010-04-12 09:26:20,793 INFO  [                            omero.remote] (Dummy-11  )  Rslt:                 None in 3.981590271e-05s
2010-04-12 09:26:20,807 INFO  [                omero.processor.ProcessI] (Dummy-11  ) <proc:6533,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Lived 0s. Deactivation took 0s.
2010-04-12 09:26:20,808 INFO  [                omero.processor.ProcessI] (Dummy-11  ) <proc:6533,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Callback processFinished
2010-04-12 09:26:20,808 INFO  [                            omero.remote] (Dummy-11  )  Rslt:                    1 in 0.647959947586s
2010-04-12 09:26:20,819 INFO  [                            omero.remote] (Dummy-5   )  Rslt: object #0 (::omero:: in 0.844326019287s
2010-04-12 09:26:20,827 INFO  [                            omero.remote] (Dummy-7   )  Meth: ProcessorI.processJob
2010-04-12 09:26:20,837 INFO  [              omero.processor.ProcessorI] (Dummy-7   ) parseJob: Session = b227af53-fabc-4dbd-93bf-0b01c34732e5, JobId = 303
2010-04-12 09:26:20,897 INFO  [              omero.processor.ProcessorI] (Dummy-7   ) processJob: Session = b227af53-fabc-4dbd-93bf-0b01c34732e5, JobId = 303
2010-04-12 09:26:20,898 INFO  [                omero.processor.ProcessI] (Dummy-7   ) Created b227af53-fabc-4dbd-93bf-0b01c34732e5 in /tmp/omero/tmp/omero_apache/32739/process_US9Fi.dir
2010-04-12 09:26:20,898 INFO  [                    omero.util.Resources] (Dummy-7   ) Adding object <proc:None,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5>
2010-04-12 09:26:20,933 INFO  [              omero.processor.ProcessorI] (Dummy-7   ) Downloaded file: 2
2010-04-12 09:26:20,972 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6557,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Activated
2010-04-12 09:26:20,974 INFO  [                            omero.remote] (Dummy-8   )  Meth: ProcessI.wait
2010-04-12 09:26:20,975 INFO  [                omero.processor.ProcessI] (Dummy-8   ) <proc:6557,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Waiting
2010-04-12 09:26:21,526 INFO  [                omero.processor.ProcessI] (Dummy-8   ) <proc:6557,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Deactivating
2010-04-12 09:26:21,526 INFO  [                            omero.remote] (Dummy-8   )  Meth: ProcessI.shutdown
2010-04-12 09:26:21,526 INFO  [                            omero.remote] (Dummy-8   )  Rslt:                 None in 4.00543212891e-05s
2010-04-12 09:26:21,540 INFO  [                omero.processor.ProcessI] (Dummy-8   ) <proc:6557,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Lived 0s. Deactivation took 0s.
2010-04-12 09:26:21,541 INFO  [                omero.processor.ProcessI] (Dummy-8   ) <proc:6557,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Callback processFinished
2010-04-12 09:26:21,541 INFO  [                            omero.remote] (Dummy-8   )  Rslt:                    1 in 0.566602945328s
2010-04-12 09:26:21,607 INFO  [              omero.processor.ProcessorI] (Dummy-7   ) processJob: Session = b227af53-fabc-4dbd-93bf-0b01c34732e5, JobId = 303
2010-04-12 09:26:21,608 INFO  [                omero.processor.ProcessI] (Dummy-7   ) Created b227af53-fabc-4dbd-93bf-0b01c34732e5 in /tmp/omero/tmp/omero_apache/32739/processiID-69.dir
2010-04-12 09:26:21,608 INFO  [                    omero.util.Resources] (Dummy-7   ) Adding object <proc:None,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5>
2010-04-12 09:26:21,637 INFO  [              omero.processor.ProcessorI] (Dummy-7   ) Downloaded file: 2
2010-04-12 09:26:21,645 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6576,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Activated
2010-04-12 09:26:21,649 INFO  [                            omero.remote] (Dummy-7   )  Rslt: 8A7660A3-7E20-4276-B in 0.821001052856s
2010-04-12 09:26:21,653 INFO  [                            omero.remote] (Dummy-3   )  Meth: ProcessI.wait
2010-04-12 09:26:21,654 INFO  [                omero.processor.ProcessI] (Dummy-3   ) <proc:6576,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Waiting
2010-04-12 09:26:33,163 INFO  [                            omero.remote] (Thread-2  )  Meth: ProcessI.poll
2010-04-12 09:26:33,163 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6576,rc=None,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Polling
2010-04-12 09:26:33,164 INFO  [                            omero.remote] (Thread-2  )  Rslt:                 None in 0.000774145126343s
2010-04-12 09:26:33,191 INFO  [                            omero.remote] (Thread-2  )  Meth: ProcessI.poll
2010-04-12 09:26:33,192 INFO  [                            omero.remote] (Thread-2  )  Rslt: object #0 (::omero:: in 9.89437103271e-05s
2010-04-12 09:26:33,219 INFO  [                            omero.remote] (Thread-2  )  Meth: ProcessI.poll
2010-04-12 09:26:33,219 INFO  [                            omero.remote] (Thread-2  )  Rslt: object #0 (::omero:: in 8.89301300049e-05s
2010-04-12 09:27:07,016 INFO  [                omero.processor.ProcessI] (Dummy-3   ) <proc:6576,rc=0,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Deactivating
2010-04-12 09:27:07,017 INFO  [                            omero.remote] (Dummy-3   )  Meth: ProcessI.shutdown
2010-04-12 09:27:07,017 INFO  [                            omero.remote] (Dummy-3   )  Rslt:                 None in 3.91006469727e-05s
2010-04-12 09:27:07,193 INFO  [                omero.processor.ProcessI] (Dummy-3   ) <proc:6576,rc=0,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Uploaded 11278 bytes of /tmp/omero/tmp/omero_apache/32739/processiID-69.dir/out to 657
2010-04-12 09:27:07,313 INFO  [                omero.processor.ProcessI] (Dummy-3   ) <proc:6576,rc=0,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Uploaded 510 bytes of /tmp/omero/tmp/omero_apache/32739/processiID-69.dir/err to 658
2010-04-12 09:27:07,341 INFO  [                omero.processor.ProcessI] (Dummy-3   ) <proc:6576,rc=0,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Lived 45s. Deactivation took 0s.
2010-04-12 09:27:07,341 INFO  [                omero.processor.ProcessI] (Dummy-3   ) <proc:6576,rc=0,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Callback processFinished
2010-04-12 09:27:07,342 INFO  [                            omero.remote] (Dummy-3   )  Rslt:                    0 in 45.6880891323s
2010-04-12 09:27:07,343 INFO  [                            omero.remote] (Dummy-6   )  Meth: ProcessI.poll
2010-04-12 09:27:07,343 INFO  [                            omero.remote] (Dummy-6   )  Rslt: object #0 (::omero:: in 5.79357147217e-05s
2010-04-12 09:27:33,248 INFO  [                            omero.remote] (Thread-2  )  Meth: ProcessI.poll
2010-04-12 09:27:33,249 INFO  [                            omero.remote] (Thread-2  )  Rslt: object #0 (::omero:: in 4.88758087158e-05s
2010-04-12 09:27:33,252 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6576,rc=0,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Keep alive failed
2010-04-12 09:27:33,253 INFO  [                            omero.remote] (Thread-2  )  Meth: ProcessI.poll
2010-04-12 09:27:33,253 INFO  [                            omero.remote] (Thread-2  )  Rslt: object #0 (::omero:: in 7.79628753662e-05s
2010-04-12 09:27:33,257 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6557,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Keep alive failed
2010-04-12 09:27:33,257 INFO  [                            omero.remote] (Thread-2  )  Meth: ProcessI.poll
2010-04-12 09:27:33,258 INFO  [                            omero.remote] (Thread-2  )  Rslt: object #0 (::omero:: in 7.70092010498e-05s
2010-04-12 09:27:33,261 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6533,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Keep alive failed
2010-04-12 09:27:33,263 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6576,rc=0,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Cleaning
2010-04-12 09:27:33,264 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6576,rc=0,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Killing session
2010-04-12 09:27:33,267 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6557,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Cleaning
2010-04-12 09:27:33,268 INFO  [                omero.processor.ProcessI] (Thread-2  ) <proc:6533,rc=1,uuid=b227af53-fabc-4dbd-93bf-0b01c34732e5> : Cleaning


The details will be in the STDERR and STDOUT of the actual script run. If you look at Proccessor-0.log closely you'll see the following lines:

Code: Select all

2010-04-12 09:17:02,537 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Uploaded 971 bytes of /tmp/omero/tmp/omero_apache/32739/process
pVMB7f.dir/out to 654
2010-04-12 09:17:02,662 INFO  [                omero.processor.ProcessI] (Dummy-7   ) <proc:6474,rc=1,uuid=0e3e32da-1f02-40cd-ae98-afdbe9d1dcb4> : Uploaded 378 bytes of /tmp/omero/tmp/omero_apache/32739/process
pVMB7f.dir/err to 655


This tells you where STDOUT and STDERR are within the binary repository. Assuming /OMERO this will be /OMERO/Files/654 and /OMERO/Files/655. We'll need to look at those files to find out what's going wrong. You can attach them here if you like.