[ome-users] Client issues

Chris Allan callan at blackcat.ca
Tue Mar 10 16:57:14 GMT 2009 

How big is this TIFF Mario? The default MemoryLimit for planes is  
64MB. :)

Ciao.

-Chris

On 10 Mar 2009, at 15:57, Mario Valle wrote:

> Tried, but the problem is in Ice.
> I have set JAVA_ARGS to the same value as the beta3.2 clients (- 
> Xms128m -Xmx512m)
> With no change. The traceback is:
>
> Ice.MemoryLimitException
>     reason = (null)
> 	at IceInternal.BasicStream.expand(BasicStream.java:2029)
> 	at IceInternal.BasicStream.writeByteSeq(BasicStream.java:688)
> 	at Ice.ByteSeqHelper.write(ByteSeqHelper.java:19)
> 	at omero.api._RawPixelsStoreDelM.setPlane(_RawPixelsStoreDelM.java: 
> 1127)
> 	at  
> omero 
> .api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java: 
> 1546)
> 	at  
> omero 
> .api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java: 
> 1518)
> 	at  
> ome 
> .formats 
> .OMEROMetadataStoreClient.setPlane(OMEROMetadataStoreClient.java:2306)
> 	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java: 
> 438)
> 	at  
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:343)
> 	at  
> ome.formats.importer.ImportHandler.importImages(ImportHandler.java: 
> 181)
> 	at ome.formats.importer.ImportHandler.access$000(ImportHandler.java: 
> 39)
> 	at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:90)
>
> BTW, in importer-gui do not put quotes around ${JAVA_ARGS} otherwise  
> you cannot put
> multiple arguments in JAVA_ARGS.
>
> Hope it helps
> 			mario
>
>
>
>
> Brian Loranger wrote:
>> Hi Mario,
>>
>> I sent you an email about your importer error right after you sent  
>> the
>> error in (not sure if you missed it).
>>
>> Just guessing based on what the error you sent me, but were you  
>> trying
>> to import something with a huge image plane (or perhaps you're  
>> running
>> the importer directly from the command line without giving the
>> application more then the default java memory allocation)?
>>
>> All the clients are also in the RC1 release cycle so you should be  
>> able
>> to use the importer and insight directly against the latest version  
>> of
>> the server.
>>
>> Cheers,
>>
>> Brian Loranger
>> Software Developer, Open Microscopy Environment
>> Division of Gene Regulation and Expression
>> University of Dundee
>> (The University of Dundee is a registered Scottish charity, No:  
>> SC015096)
>>
>>
>>
>> On 10 Mar 2009, at 15:11, Mario Valle wrote:
>>
>>> (Really I don't know if the list is the correct one, please advise)
>>>
>>> So the Beta4 adventure started.
>>>
>>> Built the server without big problems (almost...)
>>>
>>> Run .insight with a retrieval error, but anyway the db is empty.
>>>
>>> So I found a .importer zip file on Hudson and tried it. Besides  
>>> saying
>>> "version 3.1.1",
>>> it crashes importing a tif file with, seems, an out-of-memory error.
>>> Instead the messages
>>> on the console are much more pacific (see below).
>>>
>>> Maybe I should calm down and wait for a RC1 also for the clients,
>>> isn't it?
>>>
>>> Ciao!
>>>    mario
>>>
>>>
>>>
>>> pazzallo ~/Desktop/OMERO.importer-build1841 > ./importer-gui
>>> Starting OMERO.importer...
>>> Suitable java version found [java = 1.5.0_16]
>>> Configuring environment...
>>> Java exec found in PATH. Verifying...
>>> Loading OMERO.importer:
>>> java -Xmx256m -cp
>>> "./OmeroImporter.jar:./libs/FontBox.jar:./libs/PDFBox.jar:./libs/ 
>>> TableLayout.jar:./libs/activation.jar:./libs/ant.jar:./libs/asm- 
>>> attrs.jar:./libs/asm.jar:./libs/backport-util-concurrent.jar:./ 
>>> libs/bio-formats.jar:./libs/blitz.jar:./libs/btm.jar:./libs/ 
>>> bufr.jar:./libs/cglib.jar:./libs/checkstyle.jar:./libs/ 
>>> common.jar:./libs/commons-beanutils.jar:./libs/commons-codec.jar:./ 
>>> libs/commons-collections.jar:./libs/commons-httpclient.jar:./libs/ 
>>> commons-io.jar:./libs/commons-lang.jar:./libs/commons- 
>>> logging.jar:./libs/commons-pool.jar:./libs/dsl.jar:./libs/ 
>>> ehcache.jar:./libs/emma.jar:./libs/emma_ant.jar:./libs/ 
>>> freemarker.jar:./libs/geronimo-spec-jta.jar:./libs/grib.jar:./libs/ 
>>> hibernate-annotations.jar:./libs/hibernate-commons- 
>>> annotations.jar:./libs/hibernate-search.jar:./libs/hibernate- 
>>> tools.jar:./libs/hibernate-validator.jar:./libs/hsqldb.jar:./libs/ 
>>> ice-db.jar:./libs/ice.jar:./libs/ij.jar:./libs/importer- 
>>> common.jar:./libs/importer.jar:./libs/ini4j.jar:./libs/jamon.jar:./ 
>>> libs/java-ge
> top
>>>
>>> t.jar:./libs/jsr107cache.jar:./libs/jtidy.jar:./libs/loci- 
>>> common.jar:./libs/log4j.jar:./libs/lucene-core.jar:./libs/lucene- 
>>> highlighter.jar:./libs/lucene-spellchecker.jar:./libs/mail.jar:./ 
>>> libs/model-psql.jar:./libs/netcdf.jar:./libs/ome-java.jar:./libs/ 
>>> ome-xml.jar:./libs/omero-clients-util.jar:./libs/ 
>>> omero_client.jar:./libs/persistence-api.jar:./libs/poi-loci.jar:./ 
>>> libs/postgresql.jar:./libs/quaqua-filechooser-only.jar:./libs/ 
>>> quartz.jar:./libs/rendering.jar:./libs/romio.jar:./libs/ 
>>> server.jar:./libs/slf4j-api.jar:./libs/slf4j-log4j12.jar:./libs/ 
>>> spring-ldap.jar:./libs/spring.jar:./libs/swingx.jar:./libs/ 
>>> velocity-tools-generic.jar:./libs/velocity.jar:./libs/xerces.jar:./ 
>>> libs/xml-apis.jar"
>>>
>>> -Djava.library.path="/Users/mvalle/Desktop/OMERO.importer-build1841"
>>> ome.formats.importer.Main
>>> /Users/mvalle/omero/log
>>> 2009-03-10 15:36:22,186 0          [      main] INFO
>>> ome.system.UpgradeCheck  - no update needed
>>>
>>> Warning: class ch.randelshofer.quaqua.filechooser.Files couldn't  
>>> load
>>> library
>>> libquaqua.jnilib.
>>> User Name: mvalle -- Password: **********
>>> true
>>> Creating root!
>>> Tiff
>>> omero.model.Image:0 == omero.model.ImageI at 15e330,omero.model.Image:0
>>> omero.model.OriginalFile:0 ==
>>> omero.model.OriginalFileI at f69ed3,omero.model.OriginalFile:0
>>> omero.model.Pixels:0:0 == omero.model.PixelsI at 356db6,Pixels:0
>>> omero.model.Channel:0:0 ==
>>> omero.model.ChannelI at b5f36e,omero.model.Channel:0:0
>>> omero.model.LogicalChannel:0:0 ==
>>> omero.model.LogicalChannelI at 80ce9c,omero.model.LogicalChannel:0:0
>>>
>>> Starting references....
>>> Pixels:0 == omero.model.OriginalFile:0
>>>
>>> containerCache contains 5 entries.
>>> referenceCache contains 1 entries.
>>> Saving pixels id: 1
>>>
>>> -- 
>>> Ing. Mario Valle
>>> Data Analysis Group                              |
>>> http://www.cscs.ch/~mvalle
>>> Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)
>>> 610.82.60
>>> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)
>>> 610.82.82
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> Brian Loranger
>> Software Developer, Open Microscopy Environment
>> Division of Gene Regulation and Expression
>> University of Dundee
>> (The University of Dundee is a registered Scottish charity, No:  
>> SC015096)
>>
>>
>
> -- 
> Ing. Mario Valle
> Data Analysis Group                              | http://www.cscs.ch/~mvalle
> Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)  
> 610.82.60
> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)  
> 610.82.82
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

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