[torqueusers] pbs_mom unable to chdir to automounted dirs
Mary Ellen Fitzpatrick
mfitzpat at bu.edu
Thu Oct 23 08:46:59 MDT 2008
I'll give these suggestions a try...
Luke Scharf wrote:
> Perhaps adding a -o intr to the fstab would help? IIRC (without
> looking at the manpage, and without checking what each platform
> actually supports), the intr flag will allow NFS errors to be passed
> to the application as I/O errors. There is also a -o soft that you
> can use, but hard,intr has worked reasonably well for me.
>
> -Luke
>
>
> Mary Ellen Fitzpatrick 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
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