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Hi Alex,
<div><br>
</div>
<div>from your workaround, it looks like some objects were not properly cleanup up indeed. </div>
<div>The most recent version of the server/OMERO.matlab should have utility functions taking care of object cleanup (e.g. getStack(session, imageId, c, t))</div>
<div><br>
</div>
<div>It is hard for us to fully test the error since 4.3.3 is a legacy version. But if you want a follow up, can you send us the full script to reproduce the error with the multiple RawPixelsStore instantiations?</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>
<div>
<div>On 1 May 2013, at 17:56, Alexander Tournier wrote:</div>
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<blockquote type="cite">
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<div class="moz-cite-prefix">Hi Sebastien,<br>
<br>
the exact error msg is:<br>
<br>
Java exception occurred:<br>
java.lang.OutOfMemoryError: Java heap space<br>
at IceInternal.BasicStream.readByteSeq(BasicStream.java:786)<br>
at Ice.ByteSeqHelper.read(ByteSeqHelper.java:26)<br>
at omero.api._RawPixelsStoreDelM.getPlane(_RawPixelsStoreDelM.java:523)<br>
at omero.api.RawPixelsStorePrxHelper.getPlane(RawPixelsStorePrxHelper.java:729)<br>
at omero.api.RawPixelsStorePrxHelper.getPlane(RawPixelsStorePrxHelper.java:701)<br>
<br>
I've found a workaround,<br>
I create the RawPixelsStore only once at the beginning of the program<br>
and then reuse the same store throughout the analysis .. seems to work<br>
<br>
Best,<br>
Alex<br>
<br>
<br>
On 01/05/13 11:25, Sebastien Besson wrote:<br>
</div>
<blockquote type="cite">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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<div style="word-wrap:break-word">
<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>
</div>
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<br>
</div>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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