[ome-users] Unable to import image files
José Salavert Torres
josator at ebi.ac.uk
Tue Mar 24 17:08:05 GMT 2015
I attached new logs from a clean startup after checking.
> On 24 Mar 2015, at 14:01, Sebastien Besson (Staff) <s.besson at dundee.ac.uk> wrote:
>
> Hi José,
>
> have you tried following the suggestion from the troubleshooting section of the
> documentation
> http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/troubleshooting.html#server-fails-to-start <http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/troubleshooting.html#server-fails-to-start>
> If not, can you try and let us know if that clears the problem in master.err?
>
> Best regards,
> Sebastien
>
>> On 24 Mar 2015, at 13:50, José Salavert Torres <josator at ebi.ac.uk <mailto:josator at ebi.ac.uk>> wrote:
>>
>> I did that already with:
>>
>> omero admin stop
>> omero admin start
>>
>> and the problem persists.
>>
>> How can this lock be released?
>>
>>> On 24 Mar 2015, at 13:43, Josh Moore <josh at glencoesoftware.com <mailto:josh at glencoesoftware.com>> wrote:
>>>
>>> On Tue, Mar 24, 2015 at 1:36 PM, José Salavert Torres <josator at ebi.ac.uk <mailto:josator at ebi.ac.uk>> wrote:
>>>> I have extracted with grep the error messages:
>>>
>>> Thanks, José. The most related error message I see is from master.err:
>>>
>>> !! 03/23/15 11:23:45.482 OMERO.IceStorm: error: ServiceManager:
>>> exception while starting service OMERO.IceStorm:
>>> FileUtil.cpp:385: IceUtil::FileLockedException:
>>> could not lock file:
>>> `/net/isilonP/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/var/master/servers/OMERO.IceStorm/dbs/OMERO.IceStorm/__Freeze/lock'
>>> syscall exception: Resource temporarily unavailable
>>>
>>> When was the last time the server was restarted? If before that time,
>>> can it be restarted and then master.err checked for the same problem?
>>>
>>> Cheers,
>>> ~Josh.
>>>
>>>
>>>
>>>> On 24 Mar 2015, at 11:24, Josh Moore <josh at glencoesoftware.com <mailto:josh at glencoesoftware.com>> wrote:
>>>>
>>>> Hi José,
>>>>
>>>>
>>>> On Tue, Mar 24, 2015 at 10:59 AM, José Salavert Torres
>>>> <josator at ebi.ac.uk <mailto:josator at ebi.ac.uk>> wrote:
>>>>
>>>> Sorry, I can not execute the second command, I do not have root permissions
>>>> on the OMERO machine.
>>>>
>>>>
>>>> Hmmm....do you have access to the server logs? Can you put us in
>>>> contact with your server administrator?
>>>>
>>>> Thanks,
>>>> ~Josh
>>>>
>>>> (I had to build and manually install every dependency).
>>>>
>>>> omero admin diagnostics
>>>>
>>>> ================================================================================
>>>> OMERO Diagnostics 5.1.0-m2-ice35-SNAPSHOT
>>>> ================================================================================
>>>>
>>>> Commands: java -version 1.6.0 (/usr/bin/java)
>>>> Commands: python -V 2.6.6
>>>> (/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin/python -- 2
>>>> others)
>>>> Commands: icegridnode --version 3.5.1
>>>> (/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridnode)
>>>> Commands: icegridadmin --version 3.5.1
>>>> (/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridadmin)
>>>> Commands: psql --version 8.4.20 (/usr/bin/psql)
>>>>
>>>> Server: icegridnode running
>>>> Server: Blitz-0 active (pid = 4104, enabled)
>>>> Server: DropBox active (pid = 4116, enabled)
>>>> Server: FileServer active (pid = 4123, enabled)
>>>> Server: Indexer-0 active (pid = 4125, enabled)
>>>> Server: MonitorServer active (pid = 4124, enabled)
>>>> Server: OMERO.Glacier2 active (pid = 4126, enabled)
>>>> Server: OMERO.IceStorm inactive (disabled)
>>>> Server: PixelData-0 active (pid = 4129, enabled)
>>>> Server: Processor-0 active (pid = 4127, enabled)
>>>> Server: Tables-0 inactive (disabled)
>>>> Server: TestDropBox inactive (enabled)
>>>>
>>>> Log dir:
>>>> /nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/var/log
>>>> exists
>>>>
>>>> Log files: Blitz-0.log 17.0 MB errors=1
>>>> warnings=912
>>>> Log files: Blitz-0.log.1 524.0 MB errors=65
>>>> warnings=9855
>>>> Log files: Blitz-0.log.2 524.0 MB errors=3900
>>>> warnings=6595
>>>> Log files: DropBox.log 41.0 KB errors=20
>>>> warnings=19
>>>> Log files: FileServer.log 7.0 KB errors=2
>>>> warnings=0
>>>> Log files: Indexer-0.log 2.0 MB errors=162
>>>> warnings=590
>>>> Log files: MonitorServer.log 20.0 KB errors=3
>>>> warnings=0
>>>> Log files: OMEROweb.log 1.0 MB errors=316
>>>> warnings=294
>>>> Log files: OMEROweb_request.log 176.0 KB errors=205
>>>> warnings=290
>>>> Log files: PixelData-0.log 419.0 KB errors=23
>>>> warnings=290
>>>> Log files: Processor-0.log 109.0 KB errors=46
>>>> warnings=30
>>>> Log files: Tables-0.log n/a
>>>> Log files: TestDropBox.log n/a
>>>> Log files: master.err 78.0 KB errors=53
>>>> warnings=53
>>>> Log files: master.out 0.0 KB errors=1
>>>> warnings=0
>>>> Log files: Total size 1070.65 MB
>>>>
>>>>
>>>> Environment:OMERO_HOME=(unset)
>>>> Environment:OMERO_NODE=(unset)
>>>> Environment:OMERO_MASTER=(unset)
>>>> Environment:OMERO_TEMPDIR=(unset)
>>>> Environment:PATH=/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin:/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/bin:/nfs/public/rw/pdbe/mol2cell/software/bin:/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/bin:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/bin:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin:/usr/lib64/ccache:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/net/isilonP/public/rw/homes/pdb_em/bin
>>>> Environment:PYTHONPATH=/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/lib/python:/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/lib/python2.6:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/python::/net/isilonP/public/rw/homes/pdb_em/python-2.6-libraries
>>>> Environment:ICE_HOME=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1
>>>> Environment:LD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/lib:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib64:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/lib:
>>>> Environment:DYLD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib:
>>>>
>>>> OMERO SSL port:4064
>>>> OMERO TCP port:4063
>>>> OMERO data
>>>> dir:'/nfs/public/rw/pdbe/mol2cell/omero/development/var/OMERO.data' Exists?
>>>> True Is writable? True
>>>> OMERO temp dir:'/net/isilonP/public/rw/homes/pdb_em/omero/tmp' Exists? True
>>>> Is writable? True (Size: 0)
>>>>
>>>> JVM settings: Blitz -Xmx602m -XX:MaxPermSize=512m
>>>> JVM settings: Indexer -Xmx401m -XX:MaxPermSize=512m
>>>> JVM settings: Pixeldata -Xmx602m -XX:MaxPermSize=512m
>>>> JVM settings: Repository -Xmx401m -XX:MaxPermSize=512m
>>>>
>>>> OMERO.web status... [RUNNING] (PID 4375)
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 23 Mar 2015, at 18:54, Josh Moore <josh at glencoesoftware.com <mailto:josh at glencoesoftware.com>> wrote:
>>>>
>>>> Hi José,
>>>>
>>>> On Mon, Mar 23, 2015 at 2:11 PM, José Salavert Torres <josator at ebi.ac.uk <mailto:josator at ebi.ac.uk>>
>>>> wrote:
>>>>
>>>> Dear OMERO users:
>>>>
>>>> I was able to do the import before but now without changing configuration or
>>>> anything it fails from any machine (even localhost). However Romero insight
>>>> is working properly. Can you help me?:
>>>>
>>>> ...
>>>>
>>>> 2015-03-23 10:40:43,444 2219 [ main] ERROR
>>>> ome.formats.importer.ImportLibrary - Error on import
>>>> java.lang.RuntimeException: Cannot exclusively use the managed repository.
>>>> at
>>>> ome.formats.importer.ImportLibrary.checkManagedRepo(ImportLibrary.java:709)
>>>> ~[blitz.jar:na]
>>>> at
>>>> ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:316)
>>>> ~[blitz.jar:na]
>>>> at
>>>> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:465)
>>>> ~[blitz.jar:na]
>>>> at
>>>> ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271)
>>>> ~[blitz.jar:na]
>>>> at
>>>> ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216)
>>>> [blitz.jar:na]
>>>> at
>>>> ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:752)
>>>> [blitz.jar:na]
>>>> 2015-03-23 10:40:43,444 2219 [ main] INFO
>>>> ome.formats.importer.ImportLibrary - Exiting on error
>>>>
>>>>
>>>> This looks like there is some server error. Could you provide use the output
>>>> of:
>>>>
>>>> $ bin/omero admin diagnostics
>>>>
>>>> as well as:
>>>>
>>>>
>>>> $ bin/omero -s root at localhost fs repos
>>>>
>>>> e.g.
>>>>
>>>> # | Id | UUID | Type | Path
>>>> ---+-------+--------------------------------------+---------+-------------------------------------------------------------------
>>>> 0 | 17 | ce1e2766-089f-4555-a52a-f75746fd44da | Public |
>>>> /repositories/OMERO-5.0-latest-deploy
>>>> 1 | 18 | ScriptRepo | Script |
>>>> /opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/scripts
>>>> 2 | 10901 | a5a2b4b3-d146-4ccc-98fa-7353a1ba023b | Managed |
>>>> /repositories/OMERO-5.1-merge-deploy/ManagedRepository
>>>> 3 | 18651 | 34b38044-0ff6-4019-8f97-4e0093f5a3c3 | Public |
>>>> /repositories/OMERO-5.0-latest-deploy
>>>> 4 | 18701 | 640d985e-0ba5-47a6-bacb-42b7cf60354b | Public |
>>>> /repositories/OMERO-5.1-merge-deploy
>>>> (5 rows)
>>>>
>>>> Cheers,
>>>> ~Josh
>>>> _______________________________________________
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>>>>
>>>>
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>
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