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

[Mario Emmenlauer]

Hi again,

On 29.04.2015 13:29, Mario Emmenlauer wrote:
>> 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 :-(

Ok, after a Matlab restart I could instantly produce the error
again (after exactly 8 images again). I increased the PermGen
space, first only to 265MB, and now its running fine again. I
slightly changed to spelling of the option: -XX:MaxPermSize=XXXm
(added a 'Max' in the front).

But: since the behavior is not entirely consistent, is there some
way to build up trust? Does this make sense to you, that it fails
after 8 images, works for >2000, then fails again after 8?

Cheers,

    Mario



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