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Hi Christophe,
<div><br>
</div>
<div>To adjust the Ice.MessageSizeMax server-side, you may need to modify the value in templates.xml </div>
<div>and restart the server [1].</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>[1] <a href="https://www.openmicroscopy.org/site/support/omero5/sysadmins/grid.html#ice-messagesizemax">
https://www.openmicroscopy.org/site/support/omero5/sysadmins/grid.html#ice-messagesizemax</a></div>
<div><br>
<div>
<div>On 10 Feb 2015, at 15:45, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu">christophe.trefois@uni.lu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Sébastien,
<div class=""><br class="">
</div>
<div class="">Same error. I’m thinking this is a setting on the server? </div>
<div class="">Do you know how to set the Ice.MessageSizeMax on the server?</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">>> client.getProperty('Ice.MessageSizeMax')</div>
<div class=""> </div>
<div class="">ans =</div>
<div class=""> </div>
<div class="">3000000</div>
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">Java exception occurred:</div>
<div class="">Ice.UnknownLocalException</div>
<div class=""> unknown = "Ice::MemoryLimitException</div>
<div class=""> Ice.MemoryLimitException</div>
<div class=""> reason = "requested 1424673822 bytes, maximum allowed is 67108864 bytes (see Ice.MessageSizeMax)"</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at IceInternal.Ex.throwMemoryLimitException(Ex.java:34)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at IceInternal.BasicStream.expand(BasicStream.java:2515)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at IceInternal.BasicStream.writeByteSeq(BasicStream.java:841)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at Ice.ByteSeqHelper.write(ByteSeqHelper.java:28)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at omero.api._AMD_RawPixelsStore_getHypercube.ice_response(_AMD_RawPixelsStore_getHypercube.java:37)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at java.lang.reflect.Method.invoke(Method.java:606)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at ome.services.throttling.Task.response(Task.java:63)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at ome.services.throttling.Callback.run(Callback.java:57)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at ome.services.blitz.impl.RawPixelsStoreI.getHypercube_async(RawPixelsStoreI.java:109)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at java.lang.reflect.Method.invoke(Method.java:606)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at omero.cmd.CallContext.invoke(CallContext.java:78)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at com.sun.proxy.$Proxy97.getHypercube_async(Unknown Source)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at omero.api._RawPixelsStoreTie.getHypercube_async(_RawPixelsStoreTie.java:120)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at omero.api._RawPixelsStoreDisp.___getHypercube(_RawPixelsStoreDisp.java:907)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1398)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at IceInternal.Incoming.invoke(Incoming.java:222)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at Ice.ConnectionI.dispatch(ConnectionI.java:1258)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at Ice.ConnectionI.message(ConnectionI.java:1213)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at IceInternal.ThreadPool.run(ThreadPool.java:321)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at IceInternal.ThreadPool.access$300(ThreadPool.java:12)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)</div>
<div class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>at java.lang.Thread.run(Thread.java:745)</div>
<div class=""> "</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at IceInternal.Outgoing.invoke(Outgoing.java:158)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at omero.api._RawPixelsStoreDelM.getHypercube(_RawPixelsStoreDelM.java:459)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at omero.api.RawPixelsStorePrxHelper.getHypercube(RawPixelsStorePrxHelper.java:2188)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at omero.api.RawPixelsStorePrxHelper.getHypercube(RawPixelsStorePrxHelper.java:2152)</div>
<div class="">
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<span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">Dr Christophe Trefois, Dipl.-Ing.</span>
<span style="display: inline;" class=""></span><br class="">
<span style="color: rgb(61, 59, 59); display: inline; font-size:7.5pt;" class="">Technical Specialist / Post-Doc</span>
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<blockquote type="cite" class="">
<div class="">On 09 Feb 2015, at 21:26, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">Hi Christophe,</div>
<div class=""><br class="">
</div>
<div class="">if you are passing the omero hostname directly to loadOmero() you are actually bypassing the</div>
<div class="">content of your ice.config file.</div>
<div class=""><br class="">
</div>
<div class="">To pass both the hostname and custom properties, you can create a Java properties object i.e.</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-family: Menlo;" class=""><font size="2" class="">>> props = java.util.Properties();</font></div>
<div style="margin: 0px; font-family: Menlo;" class=""><font size="2" class="">>> props.setProperty('omero.host', hostname);</font></div>
<div style="margin: 0px; font-family: Menlo;" class=""><font size="2" class="">>> props.setProperty('Ice.MessageSizeMax', '10000000');</font></div>
</div>
<div style="margin: 0px; font-family: Menlo;" class=""><font size="2" class="">>> c = loadOmero(props);</font></div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
then you can check that your Ice.MessageSizeMax is properly configured client-side:
<div class="">
<div class=""><br class="">
</div>
<div class=""><font size="2" class=""><span style="font-family: Menlo;" class="">>> c.getProperty('</span><span style="font-family: Menlo;" class="">Ice.MessageSizeMax')</span><span style="font-family: Menlo;" class="">;</span></font></div>
<div class=""><br class="">
</div>
<div class="">Sebastien</div>
<div class=""><br class="">
<div class="">
<div class="">On 9 Feb 2015, at 16:18, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu" class="">christophe.trefois@uni.lu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
I assumed it’s in KB. So I changed it locally but it still throws the error.
<div class=""><br class="">
</div>
<div class="">I just put ice.config in my working directory and use the normal loadOmero(om_host) to load the config.</div>
<div class=""><br class="">
</div>
<div class="">Since I still get the error, I assume I have to set it on the server?</div>
<div class=""><br class="">
</div>
<div class="">Is my image too big?</div>
<div class=""><br class="">
</div>
<div class="">Thanks,<br class="">
<div class="">
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<span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">Dr Christophe Trefois, Dipl.-Ing.</span>
<span style="display: inline;" class=""></span><br class="">
<span style="color: rgb(61, 59, 59); display: inline; font-size:7.5pt;" class="">Technical Specialist / Post-Doc</span>
</p>
<p style="font-family: Arial, sans-serif; font-size: 7.5pt; line-height: 16px;" class="">
<span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">UNIVERSITÉ DU LUXEMBOURG</span><br class="">
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<br class="">
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L-4362 Esch-sur-Alzette </span><br class="">
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<blockquote type="cite" class="">
<div class="">On 09 Feb 2015, at 14:47, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu" class="">christophe.trefois@uni.lu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Sébastien,
<div class=""><br class="">
</div>
<div class="">What is the unit?</div>
<div class=""><br class="">
</div>
<div class="">And, what’s the default on the server side?</div>
<div class=""><br class="">
</div>
<div class="">Thank you for your help,</div>
<div class=""><br class="">
<div class="">
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<span style="display: inline;" class=""></span><br class="">
<span style="color: rgb(61, 59, 59); display: inline; font-size:7.5pt;" class="">Technical Specialist / Post-Doc</span>
</p>
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<span style="display: inline;" class=""><br class="">
</span><span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE</span><br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">Campus Belval | House of Biomedicine
<br class="">
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<blockquote type="cite" class="">
<div class="">On 09 Feb 2015, at 12:31, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><br class="">
The University of Dundee is a registered Scottish Charity, No: SC015096<br class="">
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<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"Sebastien Besson (Staff)" <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>><br class="">
</span></div>
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">To:
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Re: [ome-devel] Hypercube out of memory</b><br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">9 Feb 2015 12:31:46 CET<br class="">
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<br class="">
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Hi Christophe,
<div class=""><br class="">
</div>
<div class="">you should be abele to set any value for MessageSizeMax via an ice.config file.</div>
<div class=""><br class="">
</div>
<div class="">See the corresponding line in the ice.config file included in the OMERO.matlab:</div>
<div class=""><a href="https://github.com/openmicroscopy/openmicroscopy/blob/v.5.0.7/etc/ice.config#L123" class="">https://github.com/openmicroscopy/openmicroscopy/blob/v.5.0.7/etc/ice.config#L123</a></div>
<div class=""><br class="">
</div>
<div class="">Let us know if this does not work,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
<div class="">
<div class="">On 9 Feb 2015, at 11:14, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu" class="">christophe.trefois@uni.lu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite" class="">
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Dear all,
<div class=""><br class="">
</div>
<div class="">I tried the example in the OMERO Matlab doc to load a hypercube from a 1GB tiff file</div>
<div class=""><br class="">
</div>
<div class="">I used the following tutorial: <a href="http://www.openmicroscopy.org/site/support/omero5/developers/Matlab.html" class="">http://www.openmicroscopy.org/site/support/omero5/developers/Matlab.html</a></div>
<div class=""><br class="">
</div>
<div class="">I get the following error when trying to “getHypercube”</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">Java exception occurred:</div>
<div class="">Ice.UnknownLocalException</div>
<div class=""> unknown = "Ice::MemoryLimitException</div>
<div class=""> Ice.MemoryLimitException</div>
<div class=""> reason = "requested 1424673822 bytes, maximum allowed is 67108864 bytes (see Ice.MessageSizeMax)”</div>
<div class=""><br class="">
</div>
<div class="">Is it possible to increase the MessageSizeMax or is it not advised and if so, how could I load my hypercube into Matlab anyway?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">
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<div class="">Open Microscopy Environment / Harvard Medical School</div>
<div class="">Wellcome Trust Centre for Gene Regulation and Expression,</div>
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<div class="">Open Microscopy Environment / Harvard Medical School</div>
<div class="">Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div class="">College of Life Sciences, University of Dundee, Dow Street,</div>
<div class="">Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
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<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>
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