[Beowulf] Troubleshooting NFS stale file handles

[Neil McFadyen]

I had a similar problem and it turned out to be a disk problem.  SMART 
attributes showed high
188 Command_Timeout values for 1 of the disks in the RAID array on the 
storage server.
The server would become inaccessible, i.e., couldn't even ping it,  with 
no errors in the server's logs.  Had to reboot the server then it would 
work for a while and then happen again. After changing the disk fixed it.

Neil McFadyen
Carleton University

On 2017-04-19 1:58 PM, Prentice Bisbal wrote:
> Here's the sequence of events:
>
> 1. First job(s) run fine on the node and complete without error.
>
> 2. Eventually a job fails with a 'permission denied' error when it 
> tries to access /l/hostname.
>
> Since no jobs fail with a file I/O error, it's hard to confirm that 
> the jobs themselves are causing the problem. However, if these 
> particular jobs are the only thing running on the cluster and should 
> be the only jobs accessing these NFS shares, what else could be 
> causing them.
>
> All these systems are getting their user information from LDAP. Since 
> some jobs run before these errors appear, lack of, or inaccurate user 
> info doesn't seem to be a likely source of this problem, but I'm not 
> ruling anything out at this point.
>
> Important detail: This is NFSv3.
>
> Prentice Bisbal
> Lead Software Engineer
> Princeton Plasma Physics Laboratory
> http://www.pppl.gov
>
> On 04/19/2017 12:20 PM, Ryan Novosielski wrote:
>> Are you saying they can’t mount the filesystem, or they can’t write 
>> to a mounted filesystem? Where does this system get its user 
>> information from, if the latter?
>>
>> -- 
>> ____
>> || \\UTGERS, |---------------------------*O*---------------------------
>> ||_// the State     |         Ryan Novosielski - novosirj at rutgers.edu
>> || \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS 
>> Campus
>> ||  \\    of NJ     | Office of Advanced Research Computing - MSB 
>> C630, Newark
>>       `'
>>
>>> On Apr 19, 2017, at 12:09, Prentice Bisbal <pbisbal at pppl.gov> wrote:
>>>
>>> Beowulfers,
>>>
>>> I've been trying to troubleshoot a problem for the past two weeks 
>>> with no luck. We have a cluster here that runs only one application 
>>> (although the details of that application change significantly from 
>>> run-to-run.). Each node in the cluster has an NFS export, /local, 
>>> that can be automounted by every other node in the cluster as 
>>> /l/hostname.
>>>
>>> Starting about two weeks ago, when jobs would try to access 
>>> /l/hostname, they would get permission denied messages. I tried 
>>> analyzing this problem by turning on all NFS/RPC logging with 
>>> rpcdebug and also using tcpdump while trying to manually mount one 
>>> of the remote systems. Both approaches indicated state file handles 
>>> were prevent the share from being mounted.
>>>
>>> Since it has been 6-8 weeks since there were any seemingly relevant 
>>> system config changes, I suspect it's an application problem 
>>> (naturally). On the other hand, the application developers/users 
>>> insist that they haven't made any changes, to their code, either. To 
>>> be honest, there's no significant evidence indicating either is at 
>>> fault. Any suggestions on how to debug this and definitively find 
>>> the root cause of these stale file handles?
>>>
>>> -- 
>>> Prentice
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-- 
Neil McFadyen, M.Eng., P.Eng.
Supervisor of Computer Operations
Mechanical & Aerospace Engineering
Carleton University
Ottawa, Ontario
K1S 5B6
tel: 613-520-2600 ext 5636
fax: 613-520-5715
email: nmcfadye at mae.carleton.ca
     or NeilB.McFadyen at carleton.ca