[ome-devel] Hypercube out of memory
Christophe TREFOIS
christophe.trefois at uni.lu
Tue Feb 10 16:24:14 GMT 2015
OK did that, now
Java exception occurred:
Ice.UnknownLocalException
unknown = "../../include/Ice/BasicStream.h:310: Ice::EncapsulationException:
protocol error: illegal encapsulation"
at IceInternal.Outgoing.invoke(Outgoing.java:158)
at omero.api._RawPixelsStoreDelM.getHypercube(_RawPixelsStoreDelM.java:459)
at omero.api.RawPixelsStorePrxHelper.getHypercube(RawPixelsStorePrxHelper.java:2188)
at omero.api.RawPixelsStorePrxHelper.getHypercube(RawPixelsStorePrxHelper.java:2152)
Dr Christophe Trefois, Dipl.-Ing.
Technical Specialist / Post-Doc
UNIVERSITÉ DU LUXEMBOURG
LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE
Campus Belval | House of Biomedicine
7, avenue des Hauts-Fourneaux
L-4362 Esch-sur-Alzette
T: +352 46 66 44 6124
F: +352 46 66 44 6949
http://www.uni.lu/lcsb <http://www.uni.lu/lcsb>
<https://www.facebook.com/trefex> <https://twitter.com/Trefex> <https://plus.google.com/+ChristopheTrefois/> <https://www.linkedin.com/in/trefoischristophe> <http://skype:Trefex?call>
----
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> On 10 Feb 2015, at 17:06, Sebastien Besson (Staff) <s.besson at dundee.ac.uk> wrote:
>
> Hi Christophe,
>
> To adjust the Ice.MessageSizeMax server-side, you may need to modify the value in templates.xml
> and restart the server [1].
>
> Best,
> Sebastien
>
> [1] https://www.openmicroscopy.org/site/support/omero5/sysadmins/grid.html#ice-messagesizemax <https://www.openmicroscopy.org/site/support/omero5/sysadmins/grid.html#ice-messagesizemax>
>
> On 10 Feb 2015, at 15:45, Christophe TREFOIS <christophe.trefois at uni.lu <mailto:christophe.trefois at uni.lu>> wrote:
>
>> Hi Sébastien,
>>
>> Same error. I’m thinking this is a setting on the server?
>> Do you know how to set the Ice.MessageSizeMax on the server?
>>
>> >> client.getProperty('Ice.MessageSizeMax')
>>
>> ans =
>>
>> 3000000
>>
>> Java exception occurred:
>> Ice.UnknownLocalException
>> unknown = "Ice::MemoryLimitException
>> Ice.MemoryLimitException
>> reason = "requested 1424673822 bytes, maximum allowed is 67108864 bytes (see Ice.MessageSizeMax)"
>>
>> at IceInternal.Ex.throwMemoryLimitException(Ex.java:34)
>>
>> at IceInternal.BasicStream.expand(BasicStream.java:2515)
>>
>> at IceInternal.BasicStream.writeByteSeq(BasicStream.java:841)
>>
>> at Ice.ByteSeqHelper.write(ByteSeqHelper.java:28)
>>
>> at omero.api._AMD_RawPixelsStore_getHypercube.ice_response(_AMD_RawPixelsStore_getHypercube.java:37)
>>
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>
>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>>
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>
>> at java.lang.reflect.Method.invoke(Method.java:606)
>>
>> at ome.services.throttling.Task.response(Task.java:63)
>>
>> at ome.services.throttling.Callback.run(Callback.java:57)
>>
>> at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
>>
>> at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149)
>>
>> at ome.services.blitz.impl.RawPixelsStoreI.getHypercube_async(RawPixelsStoreI.java:109)
>>
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>
>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>>
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>
>> at java.lang.reflect.Method.invoke(Method.java:606)
>>
>> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
>>
>> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
>>
>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
>>
>> at omero.cmd.CallContext.invoke(CallContext.java:78)
>>
>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>
>> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
>>
>> at com.sun.proxy.$Proxy97.getHypercube_async(Unknown Source)
>>
>> at omero.api._RawPixelsStoreTie.getHypercube_async(_RawPixelsStoreTie.java:120)
>>
>> at omero.api._RawPixelsStoreDisp.___getHypercube(_RawPixelsStoreDisp.java:907)
>>
>> at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1398)
>>
>> at IceInternal.Incoming.invoke(Incoming.java:222)
>>
>> at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
>>
>> at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
>>
>> at Ice.ConnectionI.message(ConnectionI.java:1213)
>>
>> at IceInternal.ThreadPool.run(ThreadPool.java:321)
>>
>> at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
>>
>> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
>>
>> at java.lang.Thread.run(Thread.java:745)
>> "
>> at IceInternal.Outgoing.invoke(Outgoing.java:158)
>> at omero.api._RawPixelsStoreDelM.getHypercube(_RawPixelsStoreDelM.java:459)
>> at omero.api.RawPixelsStorePrxHelper.getHypercube(RawPixelsStorePrxHelper.java:2188)
>> at omero.api.RawPixelsStorePrxHelper.getHypercube(RawPixelsStorePrxHelper.java:2152)
>> Dr Christophe Trefois, Dipl.-Ing.
>> Technical Specialist / Post-Doc
>>
>> UNIVERSITÉ DU LUXEMBOURG
>>
>> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE
>> Campus Belval | House of Biomedicine
>> 7, avenue des Hauts-Fourneaux
>> L-4362 Esch-sur-Alzette
>> T: +352 46 66 44 6124
>> F: +352 46 66 44 6949
>> http://www.uni.lu/lcsb <http://www.uni.lu/lcsb>
>> <https://www.facebook.com/trefex> <https://twitter.com/Trefex> <https://plus.google.com/+ChristopheTrefois/> <https://www.linkedin.com/in/trefoischristophe> <http://skype:Trefex?call>
>>
>> ----
>> This message is confidential and may contain privileged information.
>> It is intended for the named recipient only.
>> If you receive it in error please notify me and permanently delete the original message and any copies.
>> ----
>>
>>
>>> On 09 Feb 2015, at 21:26, Sebastien Besson (Staff) <s.besson at dundee.ac.uk <mailto:s.besson at dundee.ac.uk>> wrote:
>>>
>>> Hi Christophe,
>>>
>>> if you are passing the omero hostname directly to loadOmero() you are actually bypassing the
>>> content of your ice.config file.
>>>
>>> To pass both the hostname and custom properties, you can create a Java properties object i.e.
>>>
>>> >> props = java.util.Properties();
>>> >> props.setProperty('omero.host', hostname);
>>> >> props.setProperty('Ice.MessageSizeMax', '10000000');
>>> >> c = loadOmero(props);
>>>
>>>
>>> then you can check that your Ice.MessageSizeMax is properly configured client-side:
>>>
>>> >> c.getProperty('Ice.MessageSizeMax');
>>>
>>> Sebastien
>>>
>>> On 9 Feb 2015, at 16:18, Christophe TREFOIS <christophe.trefois at uni.lu <mailto:christophe.trefois at uni.lu>> wrote:
>>>
>>>> I assumed it’s in KB. So I changed it locally but it still throws the error.
>>>>
>>>> I just put ice.config in my working directory and use the normal loadOmero(om_host) to load the config.
>>>>
>>>> Since I still get the error, I assume I have to set it on the server?
>>>>
>>>> Is my image too big?
>>>>
>>>> Thanks,
>>>> Dr Christophe Trefois, Dipl.-Ing.
>>>> Technical Specialist / Post-Doc
>>>>
>>>> UNIVERSITÉ DU LUXEMBOURG
>>>>
>>>> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE
>>>> Campus Belval | House of Biomedicine
>>>> 7, avenue des Hauts-Fourneaux
>>>> L-4362 Esch-sur-Alzette
>>>> T: +352 46 66 44 6124
>>>> F: +352 46 66 44 6949
>>>> http://www.uni.lu/lcsb <http://www.uni.lu/lcsb>
>>>> <https://www.facebook.com/trefex> <https://twitter.com/Trefex> <https://plus.google.com/+ChristopheTrefois/> <https://www.linkedin.com/in/trefoischristophe> <http://skype:Trefex?call>
>>>>
>>>> ----
>>>> This message is confidential and may contain privileged information.
>>>> It is intended for the named recipient only.
>>>> If you receive it in error please notify me and permanently delete the original message and any copies.
>>>> ----
>>>>
>>>>
>>>>> On 09 Feb 2015, at 14:47, Christophe TREFOIS <christophe.trefois at uni.lu <mailto:christophe.trefois at uni.lu>> wrote:
>>>>>
>>>>> Hi Sébastien,
>>>>>
>>>>> What is the unit?
>>>>>
>>>>> And, what’s the default on the server side?
>>>>>
>>>>> Thank you for your help,
>>>>>
>>>>> Dr Christophe Trefois, Dipl.-Ing.
>>>>> Technical Specialist / Post-Doc
>>>>>
>>>>> UNIVERSITÉ DU LUXEMBOURG
>>>>>
>>>>> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE
>>>>> Campus Belval | House of Biomedicine
>>>>> 7, avenue des Hauts-Fourneaux
>>>>> L-4362 Esch-sur-Alzette
>>>>> T: +352 46 66 44 6124
>>>>> F: +352 46 66 44 6949
>>>>> http://www.uni.lu/lcsb <http://www.uni.lu/lcsb>
>>>>> <https://www.facebook.com/trefex> <https://twitter.com/Trefex> <https://plus.google.com/+ChristopheTrefois/> <https://www.linkedin.com/in/trefoischristophe> <http://skype:Trefex?call>
>>>>>
>>>>> ----
>>>>> This message is confidential and may contain privileged information.
>>>>> It is intended for the named recipient only.
>>>>> If you receive it in error please notify me and permanently delete the original message and any copies.
>>>>> ----
>>>>>
>>>>>
>>>>>> On 09 Feb 2015, at 12:31, Sebastien Besson (Staff) <s.besson at dundee.ac.uk <mailto:s.besson at dundee.ac.uk>> wrote:
>>>>>>
>>>>>>
>>>>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>>>>
>>>>>> From: "Sebastien Besson (Staff)" <s.besson at dundee.ac.uk <mailto:s.besson at dundee.ac.uk>>
>>>>>> To: OME-devel OME <ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk>>
>>>>>> Subject: Re: [ome-devel] Hypercube out of memory
>>>>>> Date: 9 Feb 2015 12:31:46 CET
>>>>>>
>>>>>>
>>>>>> Hi Christophe,
>>>>>>
>>>>>> you should be abele to set any value for MessageSizeMax via an ice.config file.
>>>>>>
>>>>>> See the corresponding line in the ice.config file included in the OMERO.matlab:
>>>>>> https://github.com/openmicroscopy/openmicroscopy/blob/v.5.0.7/etc/ice.config#L123 <https://github.com/openmicroscopy/openmicroscopy/blob/v.5.0.7/etc/ice.config#L123>
>>>>>>
>>>>>> Let us know if this does not work,
>>>>>> Sebastien
>>>>>>
>>>>>> On 9 Feb 2015, at 11:14, Christophe TREFOIS <christophe.trefois at uni.lu <mailto:christophe.trefois at uni.lu>> wrote:
>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I tried the example in the OMERO Matlab doc to load a hypercube from a 1GB tiff file
>>>>>>>
>>>>>>> I used the following tutorial: http://www.openmicroscopy.org/site/support/omero5/developers/Matlab.html <http://www.openmicroscopy.org/site/support/omero5/developers/Matlab.html>
>>>>>>>
>>>>>>> I get the following error when trying to “getHypercube”
>>>>>>>
>>>>>>> Java exception occurred:
>>>>>>> Ice.UnknownLocalException
>>>>>>> unknown = "Ice::MemoryLimitException
>>>>>>> Ice.MemoryLimitException
>>>>>>> reason = "requested 1424673822 bytes, maximum allowed is 67108864 bytes (see Ice.MessageSizeMax)”
>>>>>>>
>>>>>>> Is it possible to increase the MessageSizeMax or is it not advised and if so, how could I load my hypercube into Matlab anyway?
>>>>>>>
>>>>>>> Best,
>>>>>>> Dr Christophe Trefois, Dipl.-Ing.
>>>>>>> Technical Specialist / Post-Doc
>>>>>>>
>>>>>>> UNIVERSITÉ DU LUXEMBOURG
>>>>>>>
>>>>>>> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE
>>>>>>> Campus Belval | House of Biomedicine
>>>>>>> 7, avenue des Hauts-Fourneaux
>>>>>>> L-4362 Esch-sur-Alzette
>>>>>>> T: +352 46 66 44 6124
>>>>>>> F: +352 46 66 44 6949
>>>>>>> http://www.uni.lu/lcsb <http://www.uni.lu/lcsb>
>>>>>>> <https://www.facebook.com/trefex> <https://twitter.com/Trefex> <https://plus.google.com/+ChristopheTrefois/> <https://www.linkedin.com/in/trefoischristophe> <http://skype:Trefex?call>
>>>>>>>
>>>>>>> ----
>>>>>>> This message is confidential and may contain privileged information.
>>>>>>> It is intended for the named recipient only.
>>>>>>> If you receive it in error please notify me and permanently delete the original message and any copies.
>>>>>>> ----
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> ome-devel mailing list
>>>>>>> ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk>
>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel>
>>>>>>
>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> ome-devel mailing list
>>>>>> ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk>
>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel>
>>>>>
>>>>> _______________________________________________
>>>>> ome-devel mailing list
>>>>> ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk>
>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel>
>>>>
>>>> _______________________________________________
>>>> ome-devel mailing list
>>>> ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk>
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel>
>>>
>>>
>>>
>>> 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
>>> _______________________________________________
>>> ome-devel mailing list
>>> ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk>
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel>
>>
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk>
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
>
> 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
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
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