[ome-users] Error instantiating pixel buffer

[Mark Woodbridge]

Thanks Sebastien. That did the trick. The pyramid took a long time to 
create (~20 hours) but it was a very large image.

Mark.

On 17/03/14 09:48, Sebastien Besson wrote:
> Hi Mark,
>
> our suggestion when increasing the PixelDataTemplate is to use 1024M as of
> https://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-installation.html#jvm-memory-settings
> I would definitely start with this memory value and report if this is
> insufficient.
>
> To remove the empty pyramids files on the server, you should be able to
> use the `admin fixpyramids`
> command via CLI:
> $ bin/omero admin fixpyramids -h
>
> Then clicking on the CZI from a client should re-trigger the pyramid
> generation. Since this operation will likely
> take a while, you may want to watch the Pixel-Data0.log during
> generation to catch any error.
>
> Best,
> Sebastien
>
> On 14 Mar 2014, at 13:10, Mark Woodbridge <m.woodbridge at imperial.ac.uk
> <mailto:m.woodbridge at imperial.ac.uk>> wrote:
>
>> That makes sense. It looks like I didn't change the heap/permgen
>> settings from the defaults when doing the upgrade. Do you have any
>> suggestions for values that would enable the pyramid file to be
>> generated for an image of this size? And is there a way to trigger its
>> generation now without re-uploading the czi?
>>
>> Thanks!
>>
>> Mark.
>>
>> On 14/03/14 12:46, Josh Moore wrote:
>>>
>>> On Mar 14, 2014, at 1:20 PM, Mark Woodbridge wrote:
>>>
>>>> Hi,
>>>
>>> Hi Mark,
>>>
>>>> We've uploaded a ~30GB czi file to OMERO 5, which seemed to complete
>>>> successfully (file sizes match), but it can't be viewed in Insight.
>>>> There is a corresponding exception in the server logs which I've
>>>> attached. The 63624_pyramid file referenced is empty.
>>>>
>>>> Does anyone have any suggestions regarding the cause? We'd be really
>>>> grateful for any help.
>>>
>>> My guess would be that during generation of the pyramid file for the
>>> CZI the PixelData-0 process threw an OutOfMemoryException. You should
>>> be able to check for that in var/log/PixelData-0.log. If so, how much
>>> memory is it allocated?
>>>
>>>> Thanks,
>>>> Mark.
>>>
>>> Cheers,
>>> ~Josh.
>>>
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>
> Dr Sébastien Besson
> Open Microscopy Environment / Harvard Medical School
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096