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

[Curtis Rueden]

Hi Mario,

> something you could try as a workaround is setting the PermSize

In addition to Sebastien's comments, note also that Java 8 should no longer
have this issue, as it works completely differently:

    http://stackoverflow.com/a/22509753/1207769

Regards,
Curtis

On Tue, Apr 28, 2015 at 2:53 PM, Sebastien Besson <seb.besson at gmail.com>
wrote:

> 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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> > ome-users at lists.openmicroscopy.org.uk
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>
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