[ome-users] Unable to import image files
José Salavert Torres
josator at ebi.ac.uk
Tue Mar 24 17:19:13 GMT 2015
I checked netstat -a for port 4064 and it is not there.
Also I did:
omero config set Ice.Default.Host 0.0.0.0
But did not solved it.
> On 24 Mar 2015, at 17:08, José Salavert Torres <josator at ebi.ac.uk> wrote:
>
> I attached new logs from a clean startup after checking.
>
> <omero-logs.tgz>
>
>
>> On 24 Mar 2015, at 14:01, Sebastien Besson (Staff) <s.besson at dundee.ac.uk <mailto: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
>>>>> _______________________________________________
>>>>> ome-users mailing list
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>>>>>
>>>>>
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>>>>>
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>>>>>
>>>>>
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>>
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