[ome-users] Repository on share?
Chris Allan
callan at lifesci.dundee.ac.uk
Fri Nov 13 15:20:55 GMT 2009
On 6 Nov 2009, at 16:22, McCaughey, Michael J wrote:
> Okay, here goes:
> Chris-
>
Thanks Mike.
Sorry for the delay in getting back to you, we've been trying to
squash a few tricky 4.1.0 bugs.
> Here's the output from diagnostics:
>
> mrmike at cisrome omero_dist]$ bin/omero admin diagnostics
>
> =
> =
> =
> =
> =
> =
> =
> =
> =
> =
> ======================================================================
> OMERO Diagnostics Beta-4.1.0-r5585-b12
> =
> =
> =
> =
> =
> =
> =
> =
> =
> =
> ======================================================================
>
> Commands: java -version 1.6.0 (/usr/bin/java)
> Commands: python -V error:'NoneType' object
> has no attribute 'group'
> Commands: icegridnode --version 3.3 (/usr/bin/
> icegridnode)
> Commands: icegridadmin --version 3.3 (/usr/bin/
> icegridadmin)
> Commands: psql --version 8.3.8 (/usr/bin/psql)
>
> Server: icegridnode running
> Server: Blitz-0 active (pid = 8144,
> enabled)
> Server: DropBox inactive (disabled)
> Server: FSServer inactive (disabled)
> Server: Indexer-0 active (pid = 8161,
> enabled)
> Server: OMERO.Glacier2 active (pid = 8174,
> enabled)
> Server: OMERO.IceStorm active (pid = 8184,
> enabled)
> Server: Processor-0 active (pid = 8185,
> enabled)
> Server: Tables-0 inactive (disabled)
> Server: TestDropBox inactive (enabled)
> Server: Web inactive (enabled)
>
> Log dir: /home/mrmike/Documents/omero_dist/var/log exists
>
> Log files: Blitz-0.log 21.0 MB errors=37
> warnings=39229
> Log files: DropBox.log 10.0 KB errors=10
> warnings=0
> Log files: FSServer.log 4.0 KB errors=5
> warnings=0
> Log files: Indexer-0.log 6.0 MB errors=0
> warnings=39212
> Log files: OMEROweb.log 0.0 KB
> Log files: OMEROweb.log.2009-10-30 32.0 KB errors=26
> warnings=2
> Log files: OMEROweb.log.2009-10-31 0.0 KB errors=2
> warnings=0
> Log files: OMEROweb.log.2009-11-02 1.0 KB errors=2
> warnings=2
> Log files: OMEROweb.log.2009-11-03 0.0 KB
> Log files: Processor-0.log 12.0 KB errors=0
> warnings=12
> Log files: Tables-0.log n/a
> Log files: TestDropBox.log n/a
> Log files: master.err 12.0 MB errors=0
> warnings=78406
> Log files: master.out 0.0 KB
> Log files: Total size 40.01 MB
>
> From the Blitz log, I start the server, then login as root on the
> Web.admin and try checking disk space, then wait around for
> something to happen:
>
> 2009-11-06 10:04:19,723 INFO
> [ ome.services.blitz.Entry] (
> main) Creating OMERO.blitz. Please wait...
> 2009-11-06 10:04:21,900 WARN
> [ java.util.prefs] (
> main) Could not create system preferences directory. System
> preferences are unus
> able.
> 2009-11-06 10:04:21,947 WARN
> [ java.util.prefs] (
> main) Prefs file removed in background /usr/lib/jvm/java-1.6.0-
> openjdk-1.6.0.0.x
> 86_64/jre/.systemPrefs/prefs.xml
> 2009-11-06 10:04:22,034 INFO
> [ng.ShutdownSafeEhcacheManagerFactoryBean] (
> main) Initializing EHCache CacheManager
> 2009-11-06 10:04:26,113 INFO
> [ ome.services.fulltext.FullTextAnalyzer] (
> main) Initialized FullTextAnalyzer
> 2009-11-06 10:04:51,046 INFO
> [ ome.system.PermissionsContext] (
> main) Setting omero.security.default_permissions to rw----
> 2009-11-06 10:04:51,326 INFO
> [ ome.services.fulltext.FullTextThread] (
> main) Initializing Full-Text Indexer
> 2009-11-06 10:04:51,351 INFO
> [ ome.services.util.DBPatchCheck] (
> main) Verified database patch: OMERO4.1__0
> 2009-11-06 10:04:51,351 INFO
> [ ome.services.util.ServerVersionCheck] (
> main) -------------------------------------------------
> 2009-11-06 10:04:51,352 INFO
> [ ome.services.util.ServerVersionCheck] (
> main) OMERO Version: Beta-4.1.0-r5585-b12 Ready.
> 2009-11-06 10:04:51,352 INFO
> [ ome.services.util.ServerVersionCheck] (
> main) -------------------------------------------------
> 2009-11-06 10:04:53,188 WARN
> [ ome.system.UpgradeCheck] (
> main) UPGRADE AVAILABLE:Please upgrade to Beta-4.1.0 See http://trac.openmicrosc
> opy.org.uk/omero for the latest version
> 2009-11-06 10:04:53,189 INFO
> [ ome.tools.hibernate.ExtendedMetadata] (
> main) Calculating ExtendedMetadata...
> 2009-11-06 10:04:53,402 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:04:53,402 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:04:53,516 INFO
> [e.services.blitz.util.BlitzConfiguration] (
> main) Initializing Ice.Communicator
> 2009-11-06 10:04:53,883 INFO
> [ ome.services.blitz.fire.Ring] (
> main) Checking cluster
> 2009-11-06 10:04:53,927 INFO
> [ ome.services.blitz.fire.Registry] (
> main) Found 0 cluster node(s) : []
> 2009-11-06 10:04:53,927 INFO
> [ ome.services.blitz.fire.Ring] (
> main) Got 0 cluster uuids : []
> 2009-11-06 10:04:53,938 INFO
> [ ome.services.util.ServiceHandler] (
> main) Executor.doWork -- ome.services.blitz.fire.Ring.getManagerList
> 2009-11-06 10:04:53,938 INFO
> [ ome.services.util.ServiceHandler] (
> main) Args: [null,
> ome.tools.spring.InternalServiceFactory at 2d04cf67]
> 2009-11-06 10:04:53,984 INFO
> [ ome.security.basic.EventHandler] (
> main) Auth:
> user=0,group=0,event=null(Internal),sess=3900f5cc-44f3-4bf3-9bb7
> -ea0b70fc84f7
> 2009-11-06 10:04:54,042 INFO
> [ org.perf4j.TimingLogger] (
> main) start[1257523493938] time[104] tag[omero.call.success]
> 2009-11-06 10:04:54,042 INFO
> [ ome.services.util.ServiceHandler] (
> main) Rslt: (3c28ff1f-49f0-4c8c-8a9d-74a7df31fe42)
> 2009-11-06 10:04:54,043 INFO
> [ ome.services.blitz.fire.Ring] (
> main) Purging node: 3c28ff1f-49f0-4c8c-8a9d-74a7df31fe42
> 2009-11-06 10:04:54,082 INFO
> [ ome.services.util.ServiceHandler] (
> main) Executor.doWork -- ome.services.blitz.fire.Ring.executeUpdate
> - set close
> d = now()
> 2009-11-06 10:04:54,082 INFO
> [ ome.services.util.ServiceHandler] (
> main) Args: [null,
> ome.tools.spring.InternalServiceFactory at 23bdb02e]
> 2009-11-06 10:04:54,217 INFO
> [ ome.security.basic.EventHandler] (
> main) Auth:
> user=0,group=0,event=146601(Internal),sess=3900f5cc-44f3-4bf3-9b
> b7-ea0b70fc84f7
> 2009-11-06 10:04:54,256 INFO
> [ org.perf4j.TimingLogger] (
> main) start[1257523494082] time[173] tag[omero.call.success]
> 2009-11-06 10:04:54,256 INFO
> [ ome.services.util.ServiceHandler] (
> main) Rslt: 0
> 2009-11-06 10:04:54,256 INFO
> [ ome.services.blitz.fire.Ring] (
> main) Removed 0 entries with value
> 3c28ff1f-49f0-4c8c-8a9d-74a7df31fe42
> 2009-11-06 10:04:54,257 INFO
> [ ome.services.util.ServiceHandler] (
> main) Executor.doWork -- ome.services.blitz.fire.Ring.setManagerDown
> 2009-11-06 10:04:54,257 INFO
> [ ome.services.util.ServiceHandler] (
> main) Args: [null,
> ome.tools.spring.InternalServiceFactory at 483457f1]
> 2009-11-06 10:04:54,286 INFO
> [ ome.security.basic.EventHandler] (
> main) Auth:
> user=0,group=0,event=146602(Internal),sess=3900f5cc-44f3-4bf3-9b
> b7-ea0b70fc84f7
> 2009-11-06 10:04:54,299 INFO
> [ org.perf4j.TimingLogger] (
> main) start[1257523494257] time[42] tag[omero.call.success]
> 2009-11-06 10:04:54,299 INFO
> [ ome.services.util.ServiceHandler] (
> main) Rslt: 1
> 2009-11-06 10:04:54,300 INFO
> [ ome.services.blitz.fire.Ring] (
> main) Removed manager: 3c28ff1f-49f0-4c8c-8a9d-74a7df31fe42
> 2009-11-06 10:04:54,300 INFO
> [ ome.services.blitz.fire.Ring] (
> main) handleRingShutdown: 3c28ff1f-49f0-4c8c-8a9d-74a7df31fe42
> 2009-11-06 10:04:54,301 INFO
> [ ome.services.util.ServiceHandler] (
> main) Executor.doWork -- ome.services.blitz.fire.Ring.addManager
> 2009-11-06 10:04:54,301 INFO
> [ ome.services.util.ServiceHandler] (
> main) Args: [null,
> ome.tools.spring.InternalServiceFactory at 7730661d]
> 2009-11-06 10:04:54,319 INFO
> [ ome.security.basic.EventHandler] (
> main) Auth:
> user=0,group=0,event=146603(Internal),sess=3900f5cc-44f3-4bf3-9b
> b7-ea0b70fc84f7
> 2009-11-06 10:04:54,326 INFO
> [ ome.security.basic.CurrentDetails] (
> main) Adding log:INSERT,class ome.model.meta.Node,201
> 2009-11-06 10:04:54,341 INFO
> [ org.perf4j.TimingLogger] (
> main) start[1257523494301] time[40] tag[omero.call.success]
> 2009-11-06 10:04:54,341 INFO
> [ ome.services.util.ServiceHandler] (
> main) Rslt: ome.model.meta.Node:Id_201
> 2009-11-06 10:04:54,364 INFO
> [ ome.services.blitz.fire.Registry] (
> main) Added ClusterNode/3900f5cc-44f3-4bf3-9bb7-ea0b70fc84f7 to
> registry
> 2009-11-06 10:04:54,371 INFO
> [ ome.system.PermissionsContext] (
> main) Setting omero.security.default_permissions to rw----
> 2009-11-06 10:04:54,379 INFO
> [me.services.blitz.repo.LegacyRepositoryI] (
> main) Initializing repository in /OMERODIR
> 2009-11-06 10:04:54,447 INFO
> [ ome.services.roi.PopulateRoiJob] (
> main) Script found: 63a410e344cc22b2fcae09951137a5b59fb8baae
> 2009-11-06 10:04:54,448 INFO
> [ ome.services.util.ServiceHandler] (
> main) Executor.doWork --
> ome.services.roi.PopulateRoiJob.populateroi.py
> 2009-11-06 10:04:54,448 INFO
> [ ome.services.util.ServiceHandler] (
> main) Args: [null,
> ome.tools.spring.InternalServiceFactory at 1664978b]
> 2009-11-06 10:04:54,486 INFO
> [ ome.security.basic.EventHandler] (
> main) Auth:
> user=0,group=0,event=146604(Internal),sess=3900f5cc-44f3-4bf3-9b
> b7-ea0b70fc84f7
> 2009-11-06 10:04:54,641 INFO
> [ org.perf4j.TimingLogger] (
> main) start[1257523494448] time[193] tag[omero.call.success]
> 2009-11-06 10:04:54,641 INFO
> [ ome.services.util.ServiceHandler] (
> main) Rslt: ome.model.core.OriginalFile:Id_1
> 2009-11-06 10:04:54,646 INFO
> [ ome.services.scripts.MakeMovieJob] (
> main) Script found: 5f408441299c22320dc56b8d12829d9e9fa814a2
> 2009-11-06 10:04:54,646 INFO
> [ ome.services.util.ServiceHandler] (
> main) Executor.doWork --
> ome.services.scripts.MakeMovieJob.makemovie.py
> 2009-11-06 10:04:54,646 INFO
> [ ome.services.util.ServiceHandler] (
> main) Args: [null,
> ome.tools.spring.InternalServiceFactory at 73abdb5e]
> 2009-11-06 10:04:54,662 INFO
> [ ome.security.basic.EventHandler] (
> main) Auth:
> user=0,group=0,event=146605(Internal),sess=3900f5cc-44f3-4bf3-9b
> b7-ea0b70fc84f7
> 2009-11-06 10:04:54,674 INFO
> [ org.perf4j.TimingLogger] (
> main) start[1257523494646] time[28] tag[omero.call.success]
> 2009-11-06 10:04:54,674 INFO
> [ ome.services.util.ServiceHandler] (
> main) Rslt: ome.model.core.OriginalFile:Id_2
> 2009-11-06 10:04:54,680 INFO
> [ ome.services.blitz.Entry] (
> main) OMERO.blitz now accepting connections.
> 2009-11-06 10:04:54,686 INFO
> [ ome.services.util.ServiceHandler] (r_Work
> er-0) Executor.doWork --
> ome.services.blitz.repo.LegacyRepositoryI.takeover
> 2009-11-06 10:04:54,686 INFO
> [ ome.services.util.ServiceHandler] (r_Work
> er-0) Args: [null,
> ome.tools.spring.InternalServiceFactory at 64b25680]
> 2009-11-06 10:04:54,686 INFO
> [ ome.services.util.ServiceHandler] (r_Work
> er-9) Executor.doWork --
> ome.services.roi.GeomTool.backgroundSynchronization
> 2009-11-06 10:04:54,687 INFO
> [ ome.services.util.ServiceHandler] (r_Work
> er-9) Args: [null,
> ome.tools.spring.InternalServiceFactory at fbb41d7]
> 2009-11-06 10:04:54,717 INFO
> [ ome.security.basic.EventHandler] (r_Work
> er-0) Auth:
> user=0,group=0,event=146606(Internal),sess=3900f5cc-44f3-4bf3-9b
> b7-ea0b70fc84f7
> 2009-11-06 10:04:54,732 INFO
> [ ome.security.basic.EventHandler] (r_Work
> er-9) Auth:
> user=0,group=0,event=146607(Internal),sess=3900f5cc-44f3-4bf3-9b
> b7-ea0b70fc84f7
> 2009-11-06 10:04:54,739 INFO
> [ org.perf4j.TimingLogger] (r_Work
> er-9) start[1257523494687] time[52] tag[omero.call.success]
> 2009-11-06 10:04:54,739 INFO
> [ ome.services.util.ServiceHandler] (r_Work
> er-9) Rslt: 0
> 2009-11-06 10:04:54,864 INFO
> [me.services.blitz.repo.LegacyRepositoryI] (r_Work
> er-0) Opened repository: f8624fa3-f646-4ea9-8b0c-c5c837888ae2
> 2009-11-06 10:04:54,874 INFO
> [ ome.services.blitz.fire.Registry] (r_Work
> er-0) Updated InternalRepository-f8624fa3-f646-4ea9-8b0c-
> c5c837888ae2 in registr
> y
> 2009-11-06 10:04:54,881 INFO
> [ ome.services.blitz.fire.Registry] (r_Work
> er-0) Updated PublicRepository-f8624fa3-f646-4ea9-8b0c-c5c837888ae2
> in registry
> 2009-11-06 10:04:54,886 INFO
> [me.services.blitz.repo.LegacyRepositoryI] (r_Work
> er-0) Repository now active
> 2009-11-06 10:04:54,891 INFO
> [ org.perf4j.TimingLogger] (r_Work
> er-0) start[1257523494686] time[205] tag[omero.call.success]
> 2009-11-06 10:04:54,891 INFO
> [ ome.services.util.ServiceHandler] (r_Work
> er-0) Rslt: null
> 2009-11-06 10:05:03,916 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-2) Executor.doWork --
> ome.services.sessions.SessionManagerImpl.createSession
> 2009-11-06 10:05:03,917 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-2) Args: [null,
> ome.tools.spring.InternalServiceFactory at 548ea21d]
> 2009-11-06 10:05:03,944 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-2) Auth:
> user=0,group=0,event=146608(Sessions),sess=3900f5cc-44f3-4bf3-9b
> b7-ea0b70fc84f7
> 2009-11-06 10:05:03,994 INFO
> [ ome.security.basic.CurrentDetails] (l.Serv
> er-2) Adding log:INSERT,class ome.model.meta.Session,462
> 2009-11-06 10:05:04,049 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-2) start[1257523503917] time[132] tag[omero.call.success]
> 2009-11-06 10:05:04,049 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-2) Rslt: (ome.model.meta.Experimenter:Id_0,
> ome.model.meta.ExperimenterGr
> oup:Id_0, [0, 1], ... 4 more)
> 2009-11-06 10:05:04,051 INFO
> [ ome.services.licenses.Store] (l.Serv
> er-2) Acquired license from example license store.
> 2009-11-06 10:05:04,053 INFO
> [ ome.services.blitz.fire.SessionManagerI] (l.Serv
> er-2) Created session 302fda6d-3ef5-4fcb-b0d2-c6979a1852a8 for user
> root
> 2009-11-06 10:05:20,113 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-8) Keep alive: 302fda6d-3ef5-4fcb-b0d2-c6979a1852a8
> 2009-11-06 10:05:23,402 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:05:23,402 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:05:53,401 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:05:53,401 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:06:00,011 INFO
> [ ome.services.blitz.fire.SessionManagerI] (r_Work
> er-6) Performing requestHeartbeats
> 2009-11-06 10:06:20,114 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-1) Keep alive: 302fda6d-3ef5-4fcb-b0d2-c6979a1852a8
> 2009-11-06 10:06:23,402 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:06:23,402 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:06:53,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:06:53,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:07:20,115 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-1) Keep alive: 302fda6d-3ef5-4fcb-b0d2-c6979a1852a8
> 2009-11-06 10:07:23,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:07:23,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:07:53,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:07:53,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:08:20,117 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-1) Keep alive: 302fda6d-3ef5-4fcb-b0d2-c6979a1852a8
> 2009-11-06 10:08:23,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:08:23,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:08:33,620 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-4) Executor.doWork --
> ome.services.sessions.SessionManagerImpl.executeCheckP
> assword
> 2009-11-06 10:08:33,620 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-4) Args: [null,
> ome.tools.spring.InternalServiceFactory at 246fee3a]
> 2009-11-06 10:08:33,627 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-4) Auth:
> user=0,group=0,event=null(Sessions),sess=3900f5cc-44f3-4bf3-9bb7
> -ea0b70fc84f7
> 2009-11-06 10:08:33,638 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-4) start[1257523713620] time[18] tag[omero.call.success]
> 2009-11-06 10:08:33,638 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-4) Rslt: true
> 2009-11-06 10:08:33,640 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-6) Executor.doWork --
> ome.services.sessions.SessionManagerImpl.createSession
> 2009-11-06 10:08:33,640 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-6) Args: [null,
> ome.tools.spring.InternalServiceFactory at 1c344a47]
> 2009-11-06 10:08:33,661 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-6) Auth:
> user=0,group=0,event=146609(Sessions),sess=3900f5cc-44f3-4bf3-9b
> b7-ea0b70fc84f7
> 2009-11-06 10:08:33,697 INFO
> [ ome.security.basic.CurrentDetails] (l.Serv
> er-6) Adding log:INSERT,class ome.model.meta.Session,463
> 2009-11-06 10:08:33,746 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-6) start[1257523713640] time[106] tag[omero.call.success]
> 2009-11-06 10:08:33,747 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-6) Rslt: (ome.model.meta.Experimenter:Id_0,
> ome.model.meta.ExperimenterGr
> oup:Id_0, [0, 1], ... 4 more)
> 2009-11-06 10:08:33,747 INFO
> [ ome.services.licenses.Store] (l.Serv
> er-6) Acquired license from example license store.
> 2009-11-06 10:08:33,755 INFO
> [ ome.services.blitz.fire.SessionManagerI] (l.Serv
> er-6) Created session 1eb7cc94-007e-4414-ba9f-6bbb65ee49ae for user
> root
> 2009-11-06 10:08:33,758 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-2) session-5e4fe9d2-803b-4c56-
> b767-19b98f90eea8/1eb7cc94-007e-4414-ba9f-6bbb6
> 5ee49ae set callback to ClientCallback/5e4fe9d2-803b-4c56-
> b767-19b98f90eea8 -t:t
> cp -h 160.129.189.179 -p 37180:tcp -h 192.168.122.1 -p 37180
> 2009-11-06 10:08:33,787 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-7) Added servant to adapter: 1eb7cc94-007e-4414-ba9f-6bbb65ee49ae/
> omero.api.I
> Session(omero.api._ISessionTie at 7cf1cdfb)
> 2009-11-06 10:08:33,811 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-8) Meth: interface ome.api.ISession.getSession
> 2009-11-06 10:08:33,812 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-8) Args: [1eb7cc94-007e-4414-ba9f-6bbb65ee49ae]
> 2009-11-06 10:08:33,812 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-8) start[1257523713812] time[0] tag[omero.call.success]
> 2009-11-06 10:08:33,812 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-8) Rslt: ome.model.meta.Session:Id_463
> 2009-11-06 10:08:34,113 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-0) Added servant to adapter: 1eb7cc94-007e-4414-ba9f-6bbb65ee49ae/
> omero.api.I
> Admin(omero.api._IAdminTie at 26d7ad36)
> 2009-11-06 10:08:34,124 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-5) Meth: interface ome.api.IAdmin.getEventContext
> 2009-11-06 10:08:34,124 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-5) Args: ()
> 2009-11-06 10:08:34,127 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-5) Auth:
> user=0,group=0,event=null(Internal),sess=1eb7cc94-007e-4414-ba9f
> -6bbb65ee49ae
> 2009-11-06 10:08:34,128 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-5) start[1257523714124] time[4] tag[omero.call.success]
> 2009-11-06 10:08:34,128 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-5) Rslt: ome.system.SimpleEventContext at 4ec12ad8
> 2009-11-06 10:08:34,132 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-3) Meth: interface ome.api.IAdmin.getExperimenter
> 2009-11-06 10:08:34,132 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-3) Args: [0]
> 2009-11-06 10:08:34,150 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-3) Auth:
> user=0,group=0,event=146610(Internal),sess=1eb7cc94-007e-4414-ba
> 9f-6bbb65ee49ae
> 2009-11-06 10:08:34,163 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-3) start[1257523714132] time[30] tag[omero.call.success]
> 2009-11-06 10:08:34,163 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-3) Rslt: ome.model.meta.Experimenter:Id_0
> 2009-11-06 10:08:34,195 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-1) Meth: interface ome.api.IAdmin.lookupGroup
> 2009-11-06 10:08:34,195 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-1) Args: [user]
> 2009-11-06 10:08:34,210 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-1) Auth:
> user=0,group=0,event=146611(Internal),sess=1eb7cc94-007e-4414-ba
> 9f-6bbb65ee49ae
> 2009-11-06 10:08:34,239 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-1) start[1257523714195] time[44] tag[omero.call.success]
> 2009-11-06 10:08:34,240 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-1) Rslt: ome.model.meta.ExperimenterGroup:Id_1
> 2009-11-06 10:08:34,340 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-4) Keep alive: 1eb7cc94-007e-4414-ba9f-6bbb65ee49ae
> 2009-11-06 10:08:34,442 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-6) Keep alive: 1eb7cc94-007e-4414-ba9f-6bbb65ee49ae
> 2009-11-06 10:08:34,535 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-2) Keep alive: 1eb7cc94-007e-4414-ba9f-6bbb65ee49ae
> 2009-11-06 10:08:34,543 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-7) Meth: interface ome.api.IAdmin.lookupExperimenters
> 2009-11-06 10:08:34,543 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-7) Args: ()
> 2009-11-06 10:08:34,558 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-7) Auth:
> user=0,group=0,event=146612(Internal),sess=1eb7cc94-007e-4414-ba
> 9f-6bbb65ee49ae
> 2009-11-06 10:08:34,596 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-7) start[1257523714543] time[53] tag[omero.call.success]
> 2009-11-06 10:08:34,596 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-7) Rslt: (ome.model.meta.Experimenter:Id_0,
> ome.model.meta.Experimenter:I
> d_1, ome.model.meta.Experimenter:Id_2, ... 4 more)
> 2009-11-06 10:08:34,621 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-8) Meth: interface ome.api.IAdmin.lookupLdapAuthExperimenters
> 2009-11-06 10:08:34,622 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-8) Args: ()
> 2009-11-06 10:08:34,624 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-8) Auth:
> user=0,group=0,event=null(Internal),sess=1eb7cc94-007e-4414-ba9f
> -6bbb65ee49ae
> 2009-11-06 10:08:34,627 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-8) start[1257523714622] time[5] tag[omero.call.success]
> 2009-11-06 10:08:34,627 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-8) Rslt: ()
> 2009-11-06 10:08:37,131 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-9) Keep alive: 1eb7cc94-007e-4414-ba9f-6bbb65ee49ae
> 2009-11-06 10:08:37,146 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-0) Added servant to adapter: 1eb7cc94-007e-4414-ba9f-6bbb65ee49ae/
> omero.api.I
> RepositoryInfo(omero.api._IRepositoryInfoTie at 70d00109)
> 2009-11-06 10:08:37,151 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-5) Meth: interface
> ome.api.IRepositoryInfo.getFreeSpaceInKilobytes
> 2009-11-06 10:08:37,151 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-5) Args: ()
> 2009-11-06 10:08:37,167 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-5) Auth:
> user=0,group=0,event=146613(Internal),sess=1eb7cc94-007e-4414-ba
> 9f-6bbb65ee49ae
> 2009-11-06 10:08:37,303 INFO
> [ ome.logic.RepositoryInfoImpl] (l.Serv
> er-5) Total kilobytes free: 491982624
> 2009-11-06 10:08:37,307 INFO
> [ org.perf4j.TimingLogger] (l.Serv
> er-5) start[1257523717151] time[156] tag[omero.call.success]
> 2009-11-06 10:08:37,307 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-5) Rslt: 491982624
> 2009-11-06 10:08:37,310 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-3) Meth: interface
> ome.api.IRepositoryInfo.getUsedSpaceInKilobytes
> 2009-11-06 10:08:37,311 INFO
> [ ome.services.util.ServiceHandler] (l.Serv
> er-3) Args: ()
> 2009-11-06 10:08:37,333 INFO
> [ ome.security.basic.EventHandler] (l.Serv
> er-3) Auth:
> user=0,group=0,event=146614(Internal),sess=1eb7cc94-007e-4414-ba
> 9f-6bbb65ee49ae
> 2009-11-06 10:08:53,402 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:08:53,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:09:00,019 INFO
> [ ome.services.blitz.fire.SessionManagerI] (r_Work
> er-0) Performing requestHeartbeats
> 2009-11-06 10:09:20,118 INFO
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Serv
> er-1) Keep alive: 302fda6d-3ef5-4fcb-b0d2-c6979a1852a8
> 2009-11-06 10:09:23,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:09:23,403 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> 2009-11-06 10:09:53,406 WARN
> [ java.util.prefs] ( Tim
> er-0) Could not lock System prefs. Unix error code 0.
> 2009-11-06 10:09:53,407 WARN
> [ java.util.prefs] ( Tim
> er-0) Couldn't flush system prefs:
> java.util.prefs.BackingStoreException: Couldn
> 't get file lock.
> [mrmike at cisrome omero_dist]$
>
Based on the log this looks oddly fine. What is the exact error within
the importer? We've had a couple issues with home directories that are
on CIFS mounted volumes (absolutely no file locking) is it possible
you're being bitten by that?
OMERO.web not showing you a graph may also be due to a missing
matplotlib. Have you got that installed?
> Output of df-k:
>
> [mrmike at cisrome OMEROOLD]$ df -k /OMERODIR
> Filesystem 1K-blocks Used Available Use% Mounted on
> //bluearc.mc.vanderbilt.edu/cisrweb
> 6442450944 5952519104 489931840 93% /OMERODIR
>
Seems to jive with:
2009-11-06 10:08:37,151 INFO
[ ome.services.util.ServiceHandler] (l.Server-5) Meth:
interface ome.api.IRepositoryInfo.getFreeSpaceInKilobytes
2009-11-06 10:08:37,151 INFO
[ ome.services.util.ServiceHandler] (l.Server-5) Args: ()
2009-11-06 10:08:37,167 INFO
[ ome.security.basic.EventHandler] (l.Server-5) Auth:
user=0,group=0,event=146613(Internal),sess=1eb7cc94-007e-4414-ba
9f-6bbb65ee49ae2009-11-06 10:08:37,303 INFO
[ ome.logic.RepositoryInfoImpl] (l.Server-5) Total
kilobytes free: 491982624
2009-11-06 10:08:37,307 INFO
[ org.perf4j.TimingLogger] (l.Server-5)
start[1257523717151] time[156] tag[omero.call.success]
>
>
> Michael J. McCaughey, PhD
> Molecular Physiology and Biophysics
> U9203 MRBIII
> 6-6175
>
-Chris
>
>
>
> -----Original Message-----
> From: Chris Allan [mailto:callan at lifesci.dundee.ac.uk]
> Sent: Fri 11/6/2009 6:51 AM
> To: McCaughey, Michael J
> Subject: Re: [ome-users] Repository on share?
>
> Hi Mike,
>
> We regularly run repositories on shares, just not CIFS. Few things:
>
> * Can you send us the output of "bin/omero admin diagnostics"?
>
> * After attempting to view disk size, can you also have a look in var/
> log/Blitz-0.log to see if there is an exception there?
>
> * What does df -k /path/to/repository show?
>
> -Chris
>
> On 2 Nov 2009, at 18:34, McCaughey, Michael J wrote:
>
> > I'm attempting to host an Omero4.1.0 server data repository on a
> > cifs-mounted network share. The share is owned by the same user
> > that is running omero. On startup, the user runs with no logged
> > errors related to the repository. While I can create (empty)
> > projects and datasets using both Omero.insight and Omero.importer, I
> > cannot import files because the importer cannot find the available
> > disk size. Attempts to view disk size in any client (.insight or
> > WedAdmin) timeout. When the repository is on a local disk (same
> > permissions/owner) it works fine.
> >
> > Does anyone with experience running the repository on a share have
> > some insight into this?
> >
> > Thanks,
> > Mike
> >
> > VUMC
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
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