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

Wed Apr 13 13:39:52 BST 2011

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_______________________________________________
>>
>