[ome-users] Client issues

[Brian Loranger]

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-getop
> 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)