[ome-users] getPlane memory leak

[Alexander Tournier]

Hi Sebastien,

thanks for looking into this!

to answer your questions:
- OMERO v4.3.3
- matlab 2013, OMERO.matlab.v4.3.3
- images: 1024x1024x1x30x120 uint16, the problem accords quite late, ie 
when accessing frames ~80
- I get a Java error message saying 'out of memory', I initially thought 
it might be my computer as I was often running into swap so I upgraded 
the system and now work with 32G RAM and it doesn't use it all so it's 
not a real memory problem from the hardware.
I ran visualvm which allowed me to look at java memory allocation real 
time this is how I was able to discover that all the java memory was 
going into ICE instances, in particular IceInternal.Outgoing instances, 
which are created upon call to store.setPixelsId and not being cleaned 
up by store.close().

Hope this helps!
Any ideas?
Thanks,
Alexander



On 01/05/13 11:25, Sebastien Besson wrote:
> Hi Alexander,
>
> I have not been able to reproduce your bug on our test servers using 
> the code you pasted below.
> Can you give us a little more information about:
> - the versions of the server and of OMERO.matlab you are using,
> - the size of the image you are working with,
> - how you know there is a Java memory leak. Do you get an exception 
> thrown in Matlab?
>
> Thanks
> Sebastien
>
> On 30 Apr 2013, at 18:55, Alexander Tournier wrote:
>
>> Hi there,
>>
>> I've been trolling the web for a solution to this but I just don't 
>> see it,
>> Any ideas why the following would create a memory leak in java??
>> Notice the close statement at the end!
>> And the offending object (IceInternal.Outgoing) is created during the 
>> call to setPixelsId according to visualvm and not destroyed by the 
>> close statement.
>>
>> store = session.createRawPixelsStore();
>> store.setPixelsId(imageId, false);
>>
>> Stack = zeros([sizeX,sizeY,sizeZ],'uint16');
>>
>> for z = 1:sizeZ
>>    plane = store.getPlane( z-1, channel, t);
>>    tPlane = toMatrix(plane, pixels);
>>    Stack(:,:,z) = tPlane;
>> end
>>
>> store.close();
>>
>>
>> Any ideas??
>> Thanks
>> Alexander
>>
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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
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We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. 
Cancer Research UK
Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103)
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Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
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