[torqueusers] pbs_mom unable to chdir to automounted dirs --- RESOLVED

Mary Ellen Fitzpatrick mfitzpat at bu.edu
Thu Oct 23 11:32:16 MDT 2008


Good news...hard mounting the nfs dirs on the compute nodes worked.  A 
couple glitches along the way, but I got it to work.
had to turn off autofs on all nodes.

Thanks to everyone to your input/suggestions.
Mary Ellen

Mary Ellen Fitzpatrick wrote:
> Thanks.  I am testing th hard nfs mounts on the compute nodes now and 
> will, hoping post my successful results.
>
> Garrick wrote:
>   
>> You *want* the nodes to hang while nfs server is rebooting.  The 
>> alternative is to have all apps exit.
>>
>> HPCC/Linux Systems Admin
>>
>> On Oct 23, 2008, at 7:13 AM, Mary Ellen Fitzpatrick <mfitzpat at bu.edu> 
>> wrote:
>>
>>     
>>> The reason I do not want to hard mount, is that if I reboot my nfs 
>>> server then it will hang, as all of the nodes will be hard mounted to 
>>> that server. And I believe it is less load on the nfs server if 
>>> automount servers the dirs only requested instead of all nfs dirs.
>>>
>>> Greenseid, Joseph M. wrote:
>>>       
>>>> Why don't you want to hard mount NFS directories on the compute 
>>>> nodes?  What problem is this going to cause you?
>>>> --Joe
>>>>
>>>> ________________________________
>>>>
>>>> From: Mary Ellen Fitzpatrick [mailto:mfitzpat at bu.edu]
>>>> Sent: Wed 10/22/2008 3:20 PM
>>>> To: Greenseid, Joseph M.
>>>> Cc: Luke Scharf; torqueusers at supercluster.org
>>>> Subject: Re: [torqueusers] pbs_mom unable to chdir to automounted dirs
>>>>
>>>>
>>>>
>>>> Good thought... How would I slow down pbs_mom, I tried putting a sleep
>>>> command in my pbs script and as Luke suggested "ls $HOME", no 
>>>> dice.   Do
>>>> I need to edit the pbs_mom daemon?
>>>>
>>>> I guess another hack would be to mount (via: cd nfsdir) the nfs dirs on
>>>> the compute nodes, but then after the automounter timed out or 
>>>> reboot, I
>>>> would be in the same situation.  Or to hard mount the nfs dirs (do not
>>>> want to do this!!)
>>>>
>>>> Appreciate your help.
>>>>
>>>> Greenseid, Joseph M. wrote:
>>>>
>>>>         
>>>>> I don't have a real useful suggestion, but just a thought -- could 
>>>>> it simply be a timing issue in that pbs_mom is trying to stat a 
>>>>> file or the directory before it's been fully mounted?  It may take 
>>>>> a second to get the directory mounted if it wasn't already, and 
>>>>> maybe PBS is too fast for the auto-mounter, esp if the NFS server 
>>>>> is under some sort of load and could be taking a little longer to 
>>>>> respond than normal?
>>>>>
>>>>> --Joe
>>>>>
>>>>> ________________________________
>>>>>
>>>>> From: torqueusers-bounces at supercluster.org on behalf of Mary Ellen 
>>>>> Fitzpatrick
>>>>> Sent: Wed 10/22/2008 2:53 PM
>>>>> To: Luke Scharf
>>>>> Cc: torqueusers at supercluster.org
>>>>> Subject: Re: [torqueusers] pbs_mom unable to chdir to automounted dirs
>>>>>
>>>>>
>>>>>
>>>>> The node OS is CentOS5 as is the nfs server.  The pbs server is 
>>>>> running
>>>>> CentOS4.5.  I have rebooted and chanted... :-) :-(
>>>>>
>>>>> Here is my simple pbs script and it does not have absolute paths.  The
>>>>> script will run only after the nfs dirs are somehow mounted on the
>>>>> node.  I have tried it with absolute path names, and it makes no 
>>>>> difference.
>>>>>
>>>>> pbs script:
>>>>> #PBS -l nodes=node1048
>>>>> # join stderr and stdout and write the to a file
>>>>> #PBS -j oe
>>>>> #PBS -o test3.o
>>>>>      # cd into the working directory
>>>>> cd $PBS_O_WORKDIR
>>>>> # print out some diagnostic stuff
>>>>> echo Running on host `hostname`
>>>>> echo Directory is `pwd`
>>>>> echo Start time is `date`
>>>>> # run my commands
>>>>>
>>>>> ./dostuff2.pl data.txt > test3.out1
>>>>>
>>>>> # print out some diagnostic stuff
>>>>> echo Stop time is `date`
>>>>>
>>>>>
>>>>>
>>>>> Luke Scharf wrote:
>>>>>
>>>>>           
>>>>>> If it works with the shell, however, the problem almost has to be 
>>>>>> with
>>>>>> something other than the automounter.
>>>>>>
>>>>>> Are any asbolute paths in the qsub script correct?
>>>>>>
>>>>>> -Luke
>>>>>>
>>>>>>
>>>>>> Luke Scharf wrote:
>>>>>>
>>>>>>             
>>>>>>> That looks happy, too.
>>>>>>>
>>>>>>> What is the underlying OS running on the node?
>>>>>>>
>>>>>>> Have you tried just rebooting everything while muttering laments
>>>>>>> about stray alpha-particles to everyone within earshot?
>>>>>>>
>>>>>>> -Luke
>>>>>>>
>>>>>>> Mary Ellen Fitzpatrick wrote:
>>>>>>>
>>>>>>>               
>>>>>>>> Yeah, that is why I am stumped...   because I can cd to nfs dirs,
>>>>>>>> seems like autofs is working correctly.  But unless the nfs dir is
>>>>>>>> pre-mounted, pbs_mom can not find it.  Very strange...
>>>>>>>>
>>>>>>>> Yes, getent passwd give the correct home dir info
>>>>>>>> [root at node1048 mom_priv]# getent passwd
>>>>>>>> mfitzpat:!!:xxxxxx:xxx:mfitzpat:/fs/userB1/mfitzpat:/bin/bash
>>>>>>>>
>>>>>>>> Luke Scharf wrote:
>>>>>>>>
>>>>>>>>                 
>>>>>>>>> Nothing that you mention looks amiss at first glance...
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Does the "getent passwd" information for the user have a correct
>>>>>>>>> home directory on the node?
>>>>>>>>>
>>>>>>>>> -Luke
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Mary Ellen Fitzpatrick wrote:
>>>>>>>>>
>>>>>>>>>                   
>>>>>>>>>> Thanks Luke.
>>>>>>>>>> Right now, my cluster is one node, with additional 50 to be
>>>>>>>>>> brought on-line once I resolve the automount problem.  The job I
>>>>>>>>>> am running is very simple, no nfs load on server.
>>>>>>>>>>
>>>>>>>>>> my $usecp I believe is correct and works properly after the nfs
>>>>>>>>>> dir is mounted.
>>>>>>>>>> $usecp *:/fs/userB1 /fs/userB1
>>>>>>>>>>
>>>>>>>>>> My auto.home file:
>>>>>>>>>> userB1  -rw,hard,intr   userB:/userB/u1
>>>>>>>>>>
>>>>>>>>>> auto.master file:
>>>>>>>>>> #+auto.master
>>>>>>>>>> /fs     /etc/auto.home
>>>>>>>>>>
>>>>>>>>>> I believe it is an automount issue and I need to tweak a 
>>>>>>>>>> parameter
>>>>>>>>>> in a config file.  Not sure which one it is at this point.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Luke Scharf wrote:
>>>>>>>>>>
>>>>>>>>>>                     
>>>>>>>>>>> Mary Ellen Fitzpatrick wrote:
>>>>>>>>>>>
>>>>>>>>>>>                       
>>>>>>>>>>>> I have my home dirs nfs exported to all of my compute nodes.  I
>>>>>>>>>>>> can log into the nodes and cd the nfs mounted dirs, no problem.
>>>>>>>>>>>> When I submit a job to a node and the automounted nfs dirs are
>>>>>>>>>>>> not mount (timed out), I get the following error:
>>>>>>>>>>>>
>>>>>>>>>>>> Oct 21 16:08:14 node1047 pbs_mom: No such file or directory (2)
>>>>>>>>>>>> in TMomFinalizeChild, PBS: chdir to '/fs/userB1/mfitzpat'
>>>>>>>>>>>> failed: No such file or directory
>>>>>>>>>>>>
>>>>>>>>>>>> If I immediately resubmit the job to the same node, it will
>>>>>>>>>>>> run.  It appears that pbs wants the automounted nfs dirs to be
>>>>>>>>>>>> already mounted, then the job will run.  If I hard mount the 
>>>>>>>>>>>> nfs
>>>>>>>>>>>> home dirs, I have no problem running the jobs, but I do not 
>>>>>>>>>>>> want
>>>>>>>>>>>> to do that.
>>>>>>>>>>>>
>>>>>>>>>>>> Any one run into this?  Trying to figure out if it is a torque
>>>>>>>>>>>> issue or automount issue.
>>>>>>>>>>>>
>>>>>>>>>>>>                         
>>>>>>>>>>> How big is your cluster?  How capable is the NFS server?  A
>>>>>>>>>>> job-start is likely to create a mountstorm, and generate a 
>>>>>>>>>>> lot of
>>>>>>>>>>> I/O.  Some servers can handle it, some can't.
>>>>>>>>>>>
>>>>>>>>>>> Yay for scaling issues!
>>>>>>>>>>>
>>>>>>>>>>> -Luke
>>>>>>>>>>>
>>>>>>>>>>> P.S. I second the suggestion of checking the $usecp value.
>>>>>>>>>>>
>>>>>>>>>>>                       
>>>>> -- 
>>>>> Thanks
>>>>> Mary Ellen
>>>>>
>>>>> _______________________________________________
>>>>> torqueusers mailing list
>>>>> torqueusers at supercluster.org
>>>>> http://www.supercluster.org/mailman/listinfo/torqueusers
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>           
>>>> -- 
>>>> Thanks
>>>> Mary Ellen
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>         
>>> -- 
>>> Thanks
>>> Mary Ellen
>>>
>>> _______________________________________________
>>> torqueusers mailing list
>>> torqueusers at supercluster.org
>>> http://www.supercluster.org/mailman/listinfo/torqueusers
>>>       
>
>   

-- 
Thanks
Mary Ellen



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