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

[Mark Henshall]

Let me know what to change - I'm assuming it's allowing omero more file 
handles - I'm running ubuntu.

Quoting Josh Moore <josh at glencoesoftware.com>:

> On Jan 27, 2012, at 1:21 PM, Mark Henshall wrote:
>
>> doing 'cat /proc/sys/fs/file-max' gives 596753
>> doing 'ulimit -Hn' as omero gives 1024
>
> Thanks, Mark. That's definitely on the low-side for the server 
> process. We'll add specific suggestions to the regular install 
> instructions. On the flip-side, it more quickly shows programming 
> issues like not closing services. :)
>
> Cheers,
> ~Josh.
>
>
>> 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)
>
>
>



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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