[ome-users] Client issues

Mario Valle mvalle at cscs.ch
Tue Mar 10 15:57:42 GMT 2009 

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

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