[ome-users] Release of OMERO & Bio-Formats 5.1.1

[Sebastien Besson]

Dear Mario,

> On 28 Apr 2015, at 19:32, Mario Emmenlauer <mario at emmenlauer.de> wrote:
> 
> 
> Dear Bio-Formats developers,
> 
> Thumbs up for the new release! However, I have a small problem using
> the new Bio-Formats 5.1.1 in Matlab R2014a. After reading a few images,
> I get the following error:
> 
> Java exception occurred:
> java.lang.OutOfMemoryError: PermGen space
>        at java.lang.ClassLoader.defineClass1(Native Method)
>        at java.lang.ClassLoader.defineClass(Unknown Source)
>        at java.security.SecureClassLoader.defineClass(Unknown Source)
>        at java.net.URLClassLoader.defineClass(Unknown Source)
>        at java.net.URLClassLoader.access$100(Unknown Source)
>        at java.net.URLClassLoader$1.run(Unknown Source)
>        at java.net.URLClassLoader$1.run(Unknown Source)
>        at java.security.AccessController.doPrivileged(Native Method)
>        at java.net.URLClassLoader.findClass(Unknown Source)
> […]

PermGen space has to do with loading the Java classes. More than the image, the
code you are running might give us some clues for this issue. In particular are you
using other Java components like MATLAB graphical interfaces? How many images
are you loading before running into this issue?

> I don't know if its related to the JPEG2000 image I'm trying to read,
> let me know if I should send in the file? I have bin/glnxa64/java.opts
> created with -Xmx512m as advised in the docs.

-Xmx512m will set the Java heap size and should address other MATLAB errors that
look like:

java.lang.OutOfMemoryError: Java heap space

For this error, something you could try as a workaround is setting the PermSize as
well in the same java.opts file, e.g. adding a line like

-XX:PermSize=512m

Let us know if this solves your problem,
Sebastien
> 
> Cheers,
> 
>    Mario
> 
> 
> 
> 
> -- 
> Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
> D-81669 München                          http://www.biodataanalysis.de/
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