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

Thu Apr 30 16:48:30 BST 2015

Hi Mario
On 29 Apr 2015, at 16:02, Mario Emmenlauer <mario at emmenlauer.de<mailto:mario at emmenlauer.de>> wrote:

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>
<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> <mailto:mario at emmenlauer.de>> wrote:
*snip*
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).

Thanks for letting us know. I opened a Pull request to make sure this
information is added to the developers documentation:
https://github.com/openmicroscopy/bioformats/pull/1776

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?

Answering this precisely needs more investigation on our side. Would it be possible
for you to upload the image you used to reproduce the error to
https://www.openmicroscopy.org/qa2/qa/upload/? Also which operating
system/version of MATLAB were you using?

Best,
Sebastien

Cheers,

   Mario

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