[ome-devel] Hypercube out of memory
Sebastien Besson (Staff)
s.besson at dundee.ac.uk
Mon Feb 9 20:26:23 GMT 2015
Hi Christophe,
if you are passing the omero hostname directly to loadOmero() you are actually bypassing the
content of your ice.config file.
To pass both the hostname and custom properties, you can create a Java properties object i.e.
>> props = java.util.Properties();
>> props.setProperty('omero.host', hostname);
>> props.setProperty('Ice.MessageSizeMax', '10000000');
>> c = loadOmero(props);
then you can check that your Ice.MessageSizeMax is properly configured client-side:
>> c.getProperty('Ice.MessageSizeMax');
Sebastien
On 9 Feb 2015, at 16:18, Christophe TREFOIS <christophe.trefois at uni.lu<mailto:christophe.trefois at uni.lu>> wrote:
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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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
The University of Dundee is a registered Scottish Charity, No: SC015096
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