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

[Mark Henshall]

OK - I'll put something large in /etc/sysctl.conf over the weekend.



Thanks.



Quoting Josh Moore <josh at glencoesoftware.com>:

>
> 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
>> 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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>
>



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




NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. 

We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. 
Cancer Research UK
Registered in England and Wales
Company Registered Number: 4325234.
Registered Charity Number: 1089464 and Scotland SC041666
Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.