[ome-users] Unable to import image files
Simon Li
spli at dundee.ac.uk
Tue Mar 24 17:21:39 GMT 2015
Hi José
It looks like you're building your OMERO server from source, is this correct? Did you obtain it from GitHub or a source.zip? Have you previously been able to run an official released server on this system?
Thanks, Simon
On 24 March 2015 at 17:08, José Salavert Torres <josator at ebi.ac.uk<mailto:josator at ebi.ac.uk>> wrote:
I attached new logs from a clean startup after checking.
The University of Dundee is a registered Scottish Charity, No: SC015096
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
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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