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TB-SUPPORT  June 2008

TB-SUPPORT June 2008

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Subject:

Re: Unkillable processes left behind by some Atlas Jobs

From:

John Bland <[log in to unmask]>

Reply-To:

Testbed Support for GridPP member institutes <[log in to unmask]>

Date:

Wed, 18 Jun 2008 16:42:57 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (101 lines)

Hi,

There were no jobs to kill as such, the actual production jobs had been 
and gone days before on our nodes. All they had left behind was a 
single, recalcitrant 'sh' process. They were spotted because they were 
days over their wall-time limit but the node was up.

In future I'll quarantine an example but I didn't want 20+ job slots 
tied up doing nothing. The only information we could glean was that 
previous jobs had been using >1GB of RAM (using 0.5-1.0GB of swap) but 
not running out of total ram.

John

Graeme Stewart wrote:
> Hi Chris/John
> 
> Please don't kill just problematic jobs off - that way bugs never get
> fixed! (If there's a group of jobs hanging in the same way then it's
> fine to kill them all but one.)
> 
> Production shouldn't stall, but if it does then dump the process tree
> and look for open file handles and network connections to try and work
> out what the problem is.
> 
> For user jobs the parameter space is wider, but the same principle
> applies. Especially if the job is using the ganga framework then it's
> essential we get information to debug the problem. Remember that user
> analysis usually access data using rfio or dcap, so there are failure
> modes here that we're not so experienced with - and this may also be
> using the storage system in a way sites do not have experience with.
> If a particular user's jobs are really problematic then it's perfectly
> permissible to ban them from the site until we get to the bottom of
> the problem - but please raise a GGUS ticket and CC atlas operations
> or the UK operations lists.
> 
> Cheers
> 
> Graeme
> 
> On Wed, Jun 18, 2008 at 10:24 AM, John Bland <[log in to unmask]> wrote:
>> Hi,
>>
>> We have had a number of atlas production jobs failing to exit over the last
>> week or so.
>>
>> On all nodes we've seen this on a single zombie sh process belonging to a
>> production atlas pool user is left behind that can't be killed, but using no
>> cpu time. pbs_mom still claims the machine is busy so the node is out of
>> commission while it's still there.
>>
>> Killing pbs_mom allows the atlas process to die. To be on the safe side we
>> reboot the node.
>>
>> This is on SL4.4 32bit nodes.
>>
>> John
>>
>> Brew, CAJ (Chris) wrote:
>>> Hi,
>>>
>>> Over the last week or so we've had a few nodes go offline because of a
>>> steadily increasing load on them.
>>>
>>> The boxes remain responsive and you can log into them but ps -ef or ps
>>> aux just hang halfway through (indeed the load is actually caused by
>>> hanging ps processes spawned by the nagios monitoring). Shutdown then
>>> fails to restart them and we have to force a hard bounce to get the node
>>> back.
>>>
>>> Investigating on a few of them it seems the problem is probably related
>>> to so Atlas user jobs, at least on all the nodes I've looked I've found
>>> a python process running as the same pool account _even though the batch
>>> system thinks no jobs by that user are running on the node_. The python
>>> proccess is clocking up cputime according to top but is immune to kill
>>> -9.
>>>
>>> Is anyone else seeing anything like this? The WNs are running a fully up
>>> to date version of SL44.
>>>
>>> Yours,
>>> Chris.
>>
>> --
>> Dr John Bland, Systems Administrator
>> Room 210, Oliver Lodge
>> Particle Physics Group, University of Liverpool
>> Mail: [log in to unmask]
>> Tel : 0151 794 3396
>>
> 
> 
> 


-- 
Dr John Bland, Systems Administrator
Room 210, Oliver Lodge
Particle Physics Group, University of Liverpool
Mail: [log in to unmask]
Tel : 0151 794 3396

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