[ome-devel] Hypercube out of memory

Mon Feb 9 16:18:17 GMT 2015

I assumed it’s in KB. So I changed it locally but it still throws the error.

I just put ice.config in my working directory and use the normal loadOmero(om_host) to load the config.

Since I still get the error, I assume I have to set it on the server?

Is my image too big?

Thanks,

Dr Christophe Trefois, Dipl.-Ing.
Technical Specialist / Post-Doc

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE
Campus Belval | House of Biomedicine
7, avenue des Hauts-Fourneaux
L-4362 Esch-sur-Alzette
T: +352 46 66 44 6124
F: +352 46 66 44 6949
http://www.uni.lu/lcsb

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On 09 Feb 2015, at 14:47, Christophe TREFOIS <christophe.trefois at uni.lu<mailto:christophe.trefois at uni.lu>> wrote:

Hi Sébastien,

What is the unit?

And, what’s the default on the server side?

Thank you for your help,

Dr Christophe Trefois, Dipl.-Ing.
Technical Specialist / Post-Doc

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE
Campus Belval | House of Biomedicine
7, avenue des Hauts-Fourneaux
L-4362 Esch-sur-Alzette
T: +352 46 66 44 6124
F: +352 46 66 44 6949
http://www.uni.lu/lcsb

[Facebook]<https://www.facebook.com/trefex> [Twitter] <https://twitter.com/Trefex>  [Google Plus] <https://plus.google.com/+ChristopheTrefois/>  [Linkedin] <https://www.linkedin.com/in/trefoischristophe>  [skype] <http://skype:Trefex?call>

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On 09 Feb 2015, at 12:31, Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>> wrote:

The University of Dundee is a registered Scottish Charity, No: SC015096

From: "Sebastien Besson (Staff)" <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>
To: OME-devel OME <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-devel] Hypercube out of memory
Date: 9 Feb 2015 12:31:46 CET

Hi Christophe,

you should be abele to set any value for MessageSizeMax via an ice.config file.

See  the corresponding line in the ice.config file included in the OMERO.matlab:
https://github.com/openmicroscopy/openmicroscopy/blob/v.5.0.7/etc/ice.config#L123

Let us know if this does not work,
Sebastien

On 9 Feb 2015, at 11:14, Christophe TREFOIS <christophe.trefois at uni.lu<mailto:christophe.trefois at uni.lu>> wrote:

Dear all,

I tried the example in the OMERO Matlab doc to load a hypercube from a 1GB tiff file

I used the following tutorial: http://www.openmicroscopy.org/site/support/omero5/developers/Matlab.html

I get the following error when trying to “getHypercube”

Java exception occurred:
Ice.UnknownLocalException
    unknown = "Ice::MemoryLimitException
               Ice.MemoryLimitException
                   reason = "requested 1424673822 bytes, maximum allowed is 67108864 bytes (see Ice.MessageSizeMax)”

Is it possible to increase the MessageSizeMax or is it not advised and if so, how could I load my hypercube into Matlab anyway?

Best,

Dr Christophe Trefois, Dipl.-Ing.
Technical Specialist / Post-Doc

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE
Campus Belval | House of Biomedicine
7, avenue des Hauts-Fourneaux
L-4362 Esch-sur-Alzette
T: +352 46 66 44 6124
F: +352 46 66 44 6949
http://www.uni.lu/lcsb

[Facebook]<https://www.facebook.com/trefex> [Twitter] <https://twitter.com/Trefex>  [Google Plus] <https://plus.google.com/+ChristopheTrefois/>  [Linkedin] <https://www.linkedin.com/in/trefoischristophe>  [skype] <http://skype:Trefex?call>

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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

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