[ome-devel] Freezes when reading data from OMERO using the API

Will Moore will at lifesci.dundee.ac.uk
Wed Apr 13 14:07:06 BST 2011 

Hi,

  Just a suggestion:

What happens if you use the RawPixelsStore directly?
http://hudson.openmicroscopy.org.uk/job/OMERO/javadoc/slice2html/omero/api/RawPixelsStore.html#RawPixelsStore
Then you have more control over opening, closing, setting ID etc.

// pseudo Python code
rps = session.getRawPixelsStore()
rps.setPixelsId(pid)

for t in range(sizeT):
	plane = rps.getPlane(z, c, t)

rps.close()


   Will.


On 13 Apr 2011, at 13:39, Vanni Galli wrote:

> I will send to you the logs and the OMERO part of my Java code.
>
> In any case I have noticed that in the Blitz-0.log file this error  
> appear several times:
>
> 2011-04-13 14:21:32,706 ERROR  
> [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-0) Error  
> destroying servant: fe:80:0:0:0:0:0:0:58:41:db:ff:fe: 
> 2e:b9:64:271d9c5f: 
> 12f25f4ad70 
> :-7d7aomero 
> .api.RawPixelsStore=ome.services.blitz.impl.RawPixelsStoreI at 6411a446
> java.lang.RuntimeException: omero.InternalException
>
> Thanks again!
>
>
>
> -- 
> Scuola Universitaria Professionale della Svizzera Italiana
> Dipartimento Tecnologie Innovative
> Istituto Sistemi Informativi e Networking
>
> Vanni Galli
> Ricercatore
>
> Galleria 2
> CH - 6928 Manno
>
> T +41 (0)58 666 65 92
> vanni.galli at supsi.ch
> www.supsi.ch/dti
> -----Original Message----- From: Josh Moore
> Sent: Wednesday, April 13, 2011 2:31 PM
> To: Vanni Galli
> Cc: ome-devel at lists.openmicroscopy.org.uk ; Caterina Strambio De  
> Castillia
> Subject: Re: [ome-devel] Freezes when reading data from OMERO using  
> the API
>
>
> On Apr 13, 2011, at 2:21 PM, Vanni Galli wrote:
>> Hi Josh,
>>
>> I have added service.close() to the getPlane() method, but  
>> unfortunately the issue is not solved.
>
> Thanks, Vanni. Sorry that that didn't solve the whole issue. Could  
> you send the contents of the var/log directory zipped (optionally  
> off list) and perhaps more of your use of the OMERO API, like any  
> other methods from Gateway.java that you may be using?
>
>> I runned the code several times. For the first times the images  
>> were correctly loaded, then the loading started to freeze for a  
>> couple of seconds, and then more and more. The last test was  
>> completely frozen and made OMERO to stop running (this behaviour is  
>> new to me), so I had to stop and restart OMERO.
>> It seems that reading bytes from my OMERO installation makes it  
>> more and more unstable, until the complete stop of the application.
>>
>> Thanks for your help!
>
> Gladly,
> ~Josh.
>
>> Best,
>> Vanni
>>
>>
>> -----Original Message----- From: Josh Moore
>> Sent: Wednesday, April 13, 2011 1:43 PM
>> To: Vanni Galli
>> Cc: ome-devel at lists.openmicroscopy.org.uk ; Caterina Strambio De  
>> Castillia
>> Subject: Re: [ome-devel] Freezes when reading data from OMERO using  
>> the API
>>
>>
>> On Apr 13, 2011, at 12:19 PM, Vanni Galli wrote:
>>
>>> Dear All,
>>
>> Hi Vanni,
>>
>>> I have an OMERO installation on a virtual machine.
>>>
>>> For the project I’m working on (the OMEGA project), I’m reading  
>>> the images stored in OMERO using the API (in Java) and the  
>>> Gateway.class present at http://trac.openmicroscopy.org.uk/ome/browser/insight/trunk/TEST/org/openmicroscopy/shoola/examples/data/Gateway.java?rev=7855 
>>> .
>>>
>>> For a specific image I select a channel and a “Z” and I load the  
>>> bytes for each “T”:
>>>
>>> for (int i = 0; i < framesNumber; i++)
>>> {
>>> try
>>> {
>>>  byte[] pixels = gateway.getPlane(pixelsID, 1, i, 1);
>>>  // send image to my algorithm
>>> }
>>> ...
>>>
>>> My code is working and I’m able to correct read the bytes. The  
>>> problem is that the reading of the images sometimes freeze, in a  
>>> completely random way.
>>>
>>> Most of the time the loading works perfectly and in a few seconds  
>>> I’m able to load all the images, but sometimes (I would say around  
>>> the 10% of the times) the loading freeze for several seconds or  
>>> minutes and then it restart. At the end of the loading the byte  
>>> are correctly loaded, but with this freeze in the middle.
>>>
>>> I have experienced this behavior also using OMERO.insight (on the  
>>> same virtual machine): sometimes when I use the sliders (for the Z  
>>> or T) the program freeze for some seconds.
>>>
>>> Is this problem related to OMERO? Or am I using the API in a wrong  
>>> way?
>>
>> This is an issue of the test code (which is never very long  
>> running) leaking server memory:
>> http://trac.openmicroscopy.org.uk/ome/ticket/4953
>>
>> I've committed a fix here:
>> http://git.openmicroscopy.org/?p=ome.git;a=commit;h=57970aba45367b5ecf4b3a78ccef14e104e838ad
>>
>> Just fyi, any of the services which are returned by a method  
>> starting with "create" on ServiceFactoryPrx (or any instance of  
>> omero.api.StatefulServiceInterfacePrx) should have the close()  
>> method called on it when you are done.
>>
>> If you could give that a try and let us know how things go, that'd  
>> be great.
>>
>> Cheers,
>> ~Josh
>>
>>> Thank you very much for you help!
>>>
>>>
>>> These are the details about my virtual machine:
>>>
>>> Linux isin09 2.6.18-194.17.1.el5xen #1 SMP Wed Sep 29 13:30:21 EDT  
>>> 2010 x86_64 x86_64 x86_64 GNU/Linux
>>> CentOS release 5.5 (Final)
>>>
>>> memory:
>>>                              total       used       free    shared  
>>> buffers   cached
>>> Mem:                       512        475         36       0 7 59
>>> -/+ buffers/cache:                 408         103
>>> Swap:                       1192      605         586
>>>
>>> disk space:
>>> Filesystem           1K-blocks      Used Available Use% Mounted on
>>> /dev/xvda1             6940484   4174552   2407688  64% /
>>> /dev/xvda3            20641788   5621160  13971988  29% /home
>>> tmpfs                   262144         0    262144   0% /dev/shm
>>>
>>>
>>> -- 
>>> Scuola Universitaria Professionale della Svizzera Italiana
>>> Dipartimento Tecnologie Innovative
>>> Istituto Sistemi Informativi e Networking
>>>
>>> Vanni Galli
>>> Ricercatore
>>>
>>> Galleria 2
>>> CH - 6928 Manno
>>>
>>> T +41 (0)58 666 65 92
>>> vanni.galli at supsi.ch
>>> www.supsi.ch/dti_______________________________________________
>>>
>>
>
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William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
http://openmicroscopy.org

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