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

[Mario Emmenlauer]

Hi Curtis and Sebastien,

thanks for the quick response! Below more:

On 28.04.2015 22:01, Curtis Rueden wrote:
>> 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

This sounds good! But my Java is the Matlab builtin, I can not (easily)
switch. But good to know that future versions might not have this issue.
Below more:


> On Tue, Apr 28, 2015 at 2:53 PM, Sebastien Besson <seb.besson at gmail.com
> <mailto:seb.besson at gmail.com>> wrote:
>     > On 28 Apr 2015, at 19:32, Mario Emmenlauer <mario at emmenlauer.de <mailto:mario at emmenlauer.de>> wrote:
>     > 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 see! So actually I am using Matlab with -nodesktop from a terminal.
There are zero GUI components involved and I don't open any windows,
not using any graphics. In other words, I should be using as little
PermGen space as a Matlab user probably can do :-) But the error came
pretty quickly, the first time after ~8 TIFF- and JP2-images. What is
a bit annoying: the error did not come on the second try (yet) after
~1000 images. I will try to reproduce it first, then continue testing.


>     > 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.
> 
>     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

I will try it! But first I need to reproduce the issue myself :-(

Thanks for the help, and all the best,

    Mario





-- 
Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
D-81669 München                          http://www.biodataanalysis.de/