[ome-users] Unable to import image files
José Salavert Torres
josator at ebi.ac.uk
Tue Mar 24 13:50:47 GMT 2015
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> 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> wrote:
>>
>> Hi José,
>>
>>
>> On Tue, Mar 24, 2015 at 10:59 AM, José Salavert Torres
>> <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> wrote:
>>
>> Hi José,
>>
>> On Mon, Mar 23, 2015 at 2:11 PM, José Salavert Torres <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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