[ome-users] Unable to import image files
Josh Moore
josh at glencoesoftware.com
Tue Mar 24 13:43:33 GMT 2015
On Tue, Mar 24, 2015 at 1:36 PM, José Salavert Torres <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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