[ome-users] OMERO crash: Too many open files

[Alexander Tournier]

Thanks Mark and Josh,

I've looked at my scripts and I heavily used the RawPixelStore service, 
which would seem to open a file handle on the server.
- by my calculations I did something like 20000 calls to RawPixelStore, 
with as many as 2000 opened during a single matlab session.
- my calls to RawPixelStore are within matlab routines, this would imply 
that the garbage collection doesn't apply to the handles created within 
a matlab routine and for which the handle is lost. Is that right? this 
would explain a java memory leak I noticed.
- RawPixelStore seems to be the culprit here, is there any other service 
I should be particularly aware of? (for peace of mind I've gone through 
my routines and closed all services at the end).
- I wasn't particularly 'keeping them alive' as I had to restart matlab 
often, would this indicate that these open services remained despite 
closing matlab? Is that a case where the session needs to be 
specifically closed?

Best,
Alex


On 27/01/12 12:21, Mark Henshall wrote:
> doing 'cat /proc/sys/fs/file-max' gives 596753
>
> doing 'ulimit -Hn' as omero gives 1024
>
>
>
>
>
> Quoting Josh Moore<josh at glencoesoftware.com>:
>
>> On Jan 26, 2012, at 6:41 PM, Alexander Tournier wrote:
>>
>>> Hi there,
>>>
>>> I've been using OMERO quite heavily and ... it crashed. ie I can't
>>> login to OMERO anymore although others seem to be able to.
>>> The most interesting is the error message below.
>>> I was saving quite a lot of data and I realise that I didn't close
>>> the rawPixelStore which might explain the error.
>>> The problem I have at the moment is that it doesn't seem to be
>>> rectifying itself on its own.
>>> Is there a time delay by which the open files are forcefully closed
>>> and services resumed or do we need to reboot OMERO?
>> The services won't be closed until the session is closed. If you are
>> somehow keeping that alive (e.g. by doing other activities) _and_ not
>> closing your services, then you'll run out of file handles. Do you
>> know how many are configured for your server?
>>
>> ~Josh
>>
>>> Thanks,
>>> Alexander
>>>
>>>
>>> Error using omero.client/createSession
>>> Java exception occurred:
>>> Glacier2.PermissionDeniedException
>>>     reason = "Internal error. Please contact your administrator:
>>>                Wrapped Exception:
>>>                (org.springframework.ldap.CommunicationException):
>>>               uk-lri-ldco02.crwin.crnet.org:636; nested exception is
>>>               javax.naming.CommunicationException:
>>>               uk-lri-ldco02.crwin.crnet.org:636 [Root exception is
>>>               java.net.SocketException: Too many open files]"
>>>     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>>     at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
>>>     at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown
>>>         Source)
>>>     at java.lang.reflect.Constructor.newInstance(Unknown Source)
>>>     at java.lang.Class.newInstance0(Unknown Source)
>>>     at java.lang.Class.newInstance(Unknown Source)
>>>     at
>>>
>>> IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
>>>             at IceInternal.BasicStream.throwException(BasicStream.java:1632)
>>>     at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
>>>     at Glacier2._RouterDelM.createSession(_RouterDelM.java:42)
>>>     at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:51)
>>>     at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:29)
>>>     at omero.client.createSession(client.java:628)
>>>     at omero.client.createSession(client.java:567)
>> _______________________________________________
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>> ome-users at lists.openmicroscopy.org.uk
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>>
>>
>
>
> Mark Henshall
> Unix Administrator
> Cancer Research UK London Research Institute
> Lincoln's Inn Fields Laboratories
> 44 Lincoln's Inn Fields
> London WC2A 3LY
> Registered charity number 1089464
>
> t: 0207 269 3602
> m: 07890664727
> f: 0207 061 8011
> e: Mark.Henshall at cancer.org.uk
>
>
>


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