Open Microscopy Environment

Hi,

currently we are using OMERO.server-5.0.5-ice35-b47. If I freshly fire up the server with an empty log directory, everything works fine besides this one error in master.err:

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!! 10/22/14 11:10:00.822 OMERO.IceStorm: error: ServiceManager: unable to load entry point `IceStormService,34:createIceStorm': libIceStormService.so.34: cannot open shared object file: No such file or directory


This seems to aim at ICE 3.4, although the server and OMERO.server has been updated to 3.5.

Any ideas?

Thanks in advance,

Tristan

Hi Tristan

Could you paste the output of

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omero admin diagnostics

?

Maybe this could help? http://lists.openmicroscopy.org.uk/pipe ... 04401.html
(ie. might be worth checking the etc/grid configuration templates for ice-34 references)

Sorry I didn't realize that somebody already answered here. The diagnostics output is:

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================================================================================
OMERO Diagnostics 5.0.5-ice35-b47
================================================================================

Commands:   java -version                  1.7.0     (/usr/bin/java)
Commands:   python -V                      2.7.6     (/usr/bin/python)
Commands:   icegridnode --version          3.5.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.3.5     (/usr/bin/psql -- 2 others)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 2447, enabled)
Server:     DropBox                        active (pid = 2651, enabled)
Server:     FileServer                     active (pid = 2662, enabled)
Server:     Indexer-0                      active (pid = 2655, enabled)
Server:     MonitorServer                  active (pid = 2683, enabled)
Server:     OMERO.Glacier2                 active (pid = 2660, enabled)
Server:     OMERO.IceStorm                 inactive (disabled)
Server:     PixelData-0                    active (pid = 2665, enabled)
Server:     Processor-0                    active (pid = 2678, enabled)
Server:     Tables-0                       active (pid = 2681, enabled)
Server:     TestDropBox                    inactive (enabled)

OMERO:      SSL port                       4064
OMERO:      TCP port                       4063

Log dir:    /usr/local/share/omero/OMERO.server/var/log exists

Log files:  Blitz-0.log                    72.0 MB       errors=7    warnings=7786
Log files:  DropBox.log                    4.0 MB        errors=0    warnings=21
Log files:  FileServer.log                 0.0 KB
Log files:  Indexer-0.log                  213.0 KB      errors=0    warnings=1
Log files:  MonitorServer.log              162.0 KB
Log files:  MonitorServer.log.1            4.0 MB        errors=2    warnings=1
Log files:  MonitorServer.log.2            4.0 MB        errors=2    warnings=19
Log files:  MonitorServer.log.3            4.0 MB
Log files:  MonitorServer.log.4            4.0 MB
Log files:  OMEROweb.log                   351.0 KB      errors=0    warnings=5
Log files:  OMEROweb_request.log           0.0 KB
Log files:  PixelData-0.log                106.0 KB
Log files:  Processor-0.log                2.0 KB
Log files:  Tables-0.log                   2.0 KB
Log files:  TestDropBox.log                n/a
Log files:  master.err                     19.0 KB       errors=21   warnings=6
Log files:  master.out                     0.0 KB
Log files:  omero-cleanse.log              0.0 KB
Log files:  Total size                     98.15 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/default-java/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.1/bin:/usr/local/share/omero/OMERO.server/bin
Environment:PYTHONPATH=/usr/lib/pymodules/python2.7:
Environment:ICE_HOME=/usr/share/Ice-3.4.2
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/srv/omero_data'       Exists? True    Is writable? True
OMERO temp dir: '/home/omero/omero/tmp' Exists? True    Is writable? True   (Size: 0)
OMERO.web status... [RUNNING] (PID 3209)


And the current master.err looks like this:

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!! 10/22/14 11:10:00.822 OMERO.IceStorm: error: ServiceManager: unable to load entry point `IceStormService,34:createIceStorm': libIceStormService.so.34: cannot open shared object file: No such file or directory
2014-10-22 12:02:22,052 395        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-22 12:02:22,104 447        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-22 12:02:22,123 466        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-22 12:02:22,600 943        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-22 12:02:23,834 2177       [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 1228ms. (1233ms total) [0 unknowns]
2014-10-23 20:48:28,563 293        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-23 20:48:28,583 313        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-23 20:48:28,591 321        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-23 20:48:28,904 634        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-23 20:48:29,052 782        [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /srv/omero_data/DropBox/skrapp/HeLa Zellen Kontrollen 141014.lif
loci.formats.FormatException: Invalid Memory Block: found magic bytes 0, expected 112
        at loci.formats.in.LIFReader.initFile(LIFReader.java:416) ~[formats-gpl.jar:na]
        at loci.formats.FormatReader.setId(FormatReader.java:1317) ~[formats-api.jar:na]
        at loci.formats.ImageReader.setId(ImageReader.java:753) ~[formats-api.jar:na]
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) ~[formats-api.jar:na]
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:259) ~[formats-bsd.jar:na]
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) ~[formats-api.jar:na]
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) ~[formats-bsd.jar:na]
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) ~[formats-api.jar:na]
        at loci.formats.Memoizer.setId(Memoizer.java:509) ~[formats-bsd.jar:na]
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) ~[formats-api.jar:na]
        at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414) [blitz.jar:na]
        at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:596) [blitz.jar:na]
        at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371) [blitz.jar:na]
        at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229) [blitz.jar:na]
        at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180) [blitz.jar:na]
        at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:109) [blitz.jar:na]
        at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:729) [blitz.jar:na]
2014-10-23 20:48:29,054 784        [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 140ms. (150ms total) [0 unknowns]
2014-10-23 20:48:45,806 288        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-23 20:48:45,826 308        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-23 20:48:45,833 315        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-23 20:48:46,141 623        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-23 20:48:46,147 629        [      main] ERROR     ome.formats.importer.cli.ErrorHandler - UNREADABLE_FILE: /srv/omero_data/DropBox/skrapp/N.b. 231014.lif
java.io.FileNotFoundException: /srv/omero_data/DropBox/skrapp/N.b. 231014.lif
        at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:398) [blitz.jar:na]
        at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:596) [blitz.jar:na]
        at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371) [blitz.jar:na]
        at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229) [blitz.jar:na]
        at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180) [blitz.jar:na]
        at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:109) [blitz.jar:na]
        at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:729) [blitz.jar:na]
2014-10-23 20:48:46,148 630        [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 0 group(s) with 0 call(s) to setId in 0ms. (7ms total) [0 unknowns]
2014-10-23 20:50:39,004 297        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-23 20:50:39,024 317        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-23 20:50:39,032 325        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-23 20:50:39,354 647        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-23 20:51:58,313 79606      [      main] WARN   odel.enums.handlers.ImmersionEnumHandler - Unknown Immersion value 'null' will be stored as "Other"
2014-10-23 20:51:58,315 79608      [      main] WARN   del.enums.handlers.CorrectionEnumHandler - Unknown Correction value 'null' will be stored as "Other"
2014-10-23 20:51:58,353 79646      [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 78995ms. (78999ms total) [0 unknowns]
2014-10-23 20:52:15,320 291        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-23 20:52:15,340 311        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-23 20:52:15,348 319        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-23 20:52:15,665 636        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-23 20:52:17,318 2289       [      main] WARN   odel.enums.handlers.ImmersionEnumHandler - Unknown Immersion value 'null' will be stored as "Other"
2014-10-23 20:52:17,320 2291       [      main] WARN   del.enums.handlers.CorrectionEnumHandler - Unknown Correction value 'null' will be stored as "Other"
2014-10-23 20:53:44,222 89193      [      main] INFO      ome.formats.importer.ImportCandidates - 3 file(s) parsed into 3 group(s) with 3 call(s) to setId in 88550ms. (88557ms total) [0 unknowns]
2014-10-23 20:54:01,035 282        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-23 20:54:01,054 301        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-23 20:54:01,062 309        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-23 20:54:01,368 615        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-23 20:54:02,508 1755       [      main] INFO      ome.formats.importer.ImportCandidates - 2 file(s) parsed into 2 group(s) with 2 call(s) to setId in 1135ms. (1140ms total) [0 unknowns]
2014-10-23 21:32:43,508 283        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-23 21:32:43,527 302        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-23 21:32:43,535 310        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-23 21:32:43,841 616        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-23 21:32:44,658 1433       [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 813ms. (817ms total) [0 unknowns]
2014-10-23 21:33:01,492 286        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-23 21:33:01,511 305        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-23 21:33:01,519 313        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-23 21:33:01,829 623        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-23 21:33:02,655 1449       [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 822ms. (826ms total) [0 unknowns]
-! 24/10/14 01:19:21:112 warning: Blitz-0-Ice.ThreadPool.Server-1410: dispatch exception:
   identity: session-c27a0492-1367-4e97-a913-494dfdebf970/1482cc8b-a8c4-4303-bbc7-834f32eb6733
   facet:
   operation: destroy
   remote host: 131.188.231.217 remote port: 60858
   Ice.ObjectAdapterDeactivatedException
       name = "BlitzAdapter"
        at Ice.ObjectAdapterI.checkForDeactivation(ObjectAdapterI.java:1157)
        at Ice.ObjectAdapterI.findFacet(ObjectAdapterI.java:505)
        at Ice.ObjectAdapterI.find(ObjectAdapterI.java:499)
        at omero.cmd.SessionI.unregisterServant(SessionI.java:629)
        at omero.cmd.SessionI.cleanServants(SessionI.java:460)
        at omero.cmd.SessionI.cleanServants(SessionI.java:384)
        at omero.cmd.SessionI.doDestroy(SessionI.java:374)
        at omero.cmd.SessionI.destroy(SessionI.java:302)
        at omero.api._ServiceFactoryTie.destroy(_ServiceFactoryTie.java:65)
        at Glacier2._SessionDisp.___destroy(_SessionDisp.java:95)
        at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1356)
        at IceInternal.Incoming.invoke(Incoming.java:222)
        at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
        at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
        at Ice.ConnectionI.message(ConnectionI.java:1213)
        at IceInternal.ThreadPool.run(ThreadPool.java:321)
        at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
        at java.lang.Thread.run(Thread.java:745)

-! 24/10/14 01:19:21:124 warning: Blitz-0-Ice.ThreadPool.Server-1410: dispatch exception:
   identity: session-ca495b56-06f7-4332-bf62-434b48fcd958/7d966a2f-86b0-4fb6-9ad7-bf8d2524eabd
   facet:
   operation: destroy
   remote host: 131.188.231.217 remote port: 60856
   Ice.ObjectAdapterDeactivatedException
       name = "BlitzAdapter"
        at Ice.ObjectAdapterI.checkForDeactivation(ObjectAdapterI.java:1157)
        at Ice.ObjectAdapterI.findFacet(ObjectAdapterI.java:505)
        at Ice.ObjectAdapterI.find(ObjectAdapterI.java:499)
        at omero.cmd.SessionI.unregisterServant(SessionI.java:629)
        at omero.cmd.SessionI.cleanServants(SessionI.java:460)
        at omero.cmd.SessionI.cleanServants(SessionI.java:384)
        at omero.cmd.SessionI.doDestroy(SessionI.java:374)
        at omero.cmd.SessionI.destroy(SessionI.java:302)
        at omero.api._ServiceFactoryTie.destroy(_ServiceFactoryTie.java:65)
        at Glacier2._SessionDisp.___destroy(_SessionDisp.java:95)
        at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1356)
        at IceInternal.Incoming.invoke(Incoming.java:222)
        at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
        at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
        at Ice.ConnectionI.message(ConnectionI.java:1213)
        at IceInternal.ThreadPool.run(ThreadPool.java:321)
        at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
        at java.lang.Thread.run(Thread.java:745)

!! 10/24/14 01:21:23.110 OMERO.IceStorm: error: ServiceManager: unable to load entry point `IceStormService,34:createIceStorm': libIceStormService.so.34: cannot open shared object file: No such file or directory
2014-10-24 13:22:34,906 295        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-24 13:22:34,959 348        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-24 13:22:34,977 366        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-24 13:22:35,457 846        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-24 13:22:36,826 2215       [      main] INFO      ome.formats.importer.ImportCandidates - 4 file(s) parsed into 4 group(s) with 4 call(s) to setId in 1362ms. (1369ms total) [0 unknowns]
2014-10-24 13:22:53,618 285        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-24 13:22:53,638 305        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-24 13:22:53,646 313        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-24 13:22:53,958 625        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-24 13:22:54,826 1493       [      main] INFO      ome.formats.importer.ImportCandidates - 2 file(s) parsed into 2 group(s) with 2 call(s) to setId in 862ms. (868ms total) [0 unknowns]
2014-10-24 13:23:11,622 305        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-24 13:23:11,643 326        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-24 13:23:11,651 334        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-24 13:23:11,980 663        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-24 13:23:13,348 2031       [      main] INFO      ome.formats.importer.ImportCandidates - 4 file(s) parsed into 4 group(s) with 4 call(s) to setId in 1360ms. (1368ms total) [0 unknowns]
2014-10-24 14:07:30,419 294        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-24 14:07:30,439 314        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-24 14:07:30,447 322        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-24 14:07:30,776 651        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-24 14:07:33,210 3085       [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 2430ms. (2434ms total) [0 unknowns]
2014-10-24 14:07:50,022 282        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-24 14:07:50,042 302        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-24 14:07:50,050 310        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-24 14:07:50,359 619        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-24 14:07:51,528 1788       [      main] INFO      ome.formats.importer.ImportCandidates - 3 file(s) parsed into 3 group(s) with 3 call(s) to setId in 1165ms. (1169ms total) [0 unknowns]
2014-10-24 14:08:08,265 284        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-24 14:08:08,284 303        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-24 14:08:08,292 311        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-24 14:08:08,599 618        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-24 14:08:09,425 1444       [      main] INFO      ome.formats.importer.ImportCandidates - 2 file(s) parsed into 2 group(s) with 2 call(s) to setId in 820ms. (826ms total) [0 unknowns]
2014-10-30 11:49:00,879 287        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-30 11:49:00,899 307        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-30 11:49:00,906 314        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-30 11:49:01,219 627        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-30 11:49:02,035 1443       [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 813ms. (817ms total) [0 unknowns]
2014-10-30 12:10:54,908 285        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-30 12:10:54,928 305        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-30 12:10:54,936 313        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-30 12:10:55,243 620        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-30 12:10:56,282 1659       [      main] INFO      ome.formats.importer.ImportCandidates - 2 file(s) parsed into 2 group(s) with 2 call(s) to setId in 1035ms. (1039ms total) [0 unknowns]
2014-10-30 12:11:13,020 286        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.5-ice35-b47
2014-10-30 12:11:13,040 306        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.5-ice35-b47 revision: f58463b date: 23 September 2014
2014-10-30 12:11:13,047 313        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-10-30 12:11:13,359 625        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-10-30 12:11:20,420 7686       [      main] INFO      ome.formats.importer.ImportCandidates - 2 file(s) parsed into 2 group(s) with 2 call(s) to setId in 7056ms. (7061ms total) [0 unknowns]


Hi Tristan,

there are still quite a few references to an Ice 3.4 in your various environment variables (PATH and ICE_HOME in parricular). Could this leads to conflicts between Ice 3.4 and Ice 3.5? What is the output of:

Code: Select all

python -c 'import Ice; print Ice.stringVersion()'


Best,
Sebastien

Hi Sebastien,

thanks for the hints. The python output is:

Code: Select all

3.5.1

I corrected the outdated paths in my environment variables, but when I delete the master.err and restart the server, I still get:

Code: Select all

!! 10/30/14 18:42:24.160 OMERO.IceStorm: error: ServiceManager: unable to load entry point `IceStormService,34:createIceStorm': libIceStormService.so.34: cannot open shared object file: No such file or directory

Not sure what else to try.

Hi Tristan,

Mark Woodbridge had posted a very similar issue recently (see http://lists.openmicroscopy.org.uk/pipe ... 04402.html). How did you set up the configuration of your new server? More precisely, did you copy the etc/grid files from your previous Ice 3.4 server? If so there may be references to Ice 3.4 left which need to be converted.

Best,
Sebastien

Hi Sebastien,

you were correct, it was a line in etc/grid/templates.xml that still aimed to 34. Is it possible to make the config files work with every Ice version in upcoming OMERO releases? That would prevent these kind of errors when people need to update.

Cheers,

Tristan

Hi Tristan,

as described in https://www.openmicroscopy.org/site/sup ... .html#id11 the etc/grid/config.xml file which contains the server configuration should be the only one you have to copy to the new server (whether the copy is for an upgrade or an Ice version change).

Best,
Sebastien