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<div class="moz-cite-prefix">Hi Sebastien,<br>
<br>
thanks for looking into this!<br>
<br>
to answer your questions:<br>
- OMERO v4.3.3<br>
- matlab 2013, OMERO.matlab.v4.3.3<br>
- images: 1024x1024x1x30x120 uint16, the problem accords quite
late, ie when accessing frames ~80<br>
- 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.<br>
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().<br>
<br>
Hope this helps!<br>
Any ideas?<br>
Thanks,<br>
Alexander<br>
<br>
<br>
<br>
On 01/05/13 11:25, Sebastien Besson wrote:<br>
</div>
<blockquote
cite="mid:722BCF90-2E93-4424-8F31-F1EDCF6FEA13@dundee.ac.uk"
type="cite">
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Hi Alexander,
<div><br>
</div>
<div>I have not been able to reproduce your bug on our test
servers using the code you pasted below.</div>
<div>Can you give us a little more information about:</div>
<div>- the versions of the server and of OMERO.matlab you are
using,</div>
<div>- the size of the image you are working with,</div>
<div>- how you know there is a Java memory leak. Do you get an
exception thrown in Matlab?</div>
<div><br>
</div>
<div>Thanks</div>
<div>Sebastien</div>
<div><br>
<div>
<div>On 30 Apr 2013, at 18:55, Alexander Tournier wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>Hi there,<br>
<br>
I've been trolling the web for a solution to this but I
just don't see it,<br>
Any ideas why the following would create a memory leak in
java??<br>
Notice the close statement at the end!<br>
And the offending object (IceInternal.Outgoing) is created
during the call to setPixelsId according to visualvm and
not destroyed by the close statement.<br>
<br>
store = session.createRawPixelsStore();<br>
store.setPixelsId(imageId, false);<br>
<br>
Stack = zeros([sizeX,sizeY,sizeZ],'uint16');<br>
<br>
for z = 1:sizeZ<br>
plane = store.getPlane( z-1, channel, t);<br>
tPlane = toMatrix(plane, pixels);<br>
Stack(:,:,z) = tPlane;<br>
end<br>
<br>
store.close();<br>
<br>
<br>
Any ideas??<br>
Thanks<br>
Alexander<br>
<br>
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<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical
School</div>
<div>Wellcome Trust Centre for Gene Regulation and
Expression,</div>
<div>College of Life Sciences, University of Dundee,
Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382)
386364</div>
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<span style="font-size:10pt">The University of Dundee is a
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