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

[Josh Moore]

On Jan 27, 2012, at 2:38 PM, Mark Henshall wrote:

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

Hi Mark,

In most situations, > 8000 is a reasonable number which you can either set globally or set __before__ you call: bin/omero admin start.

cF.: http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2010-September/001682.html

Cheers,
~Josh


> 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
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> 
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> e: Mark.Henshall at cancer.org.uk
> 
> 
> 
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