[torqueusers] pbs_mom unable to chdir to automounted dirs
---RESOLVED
Stewart.Samuels at sanofi-aventis.com
Stewart.Samuels at sanofi-aventis.com
Thu Oct 23 13:02:15 MDT 2008
Interestingly, on one of our roughly 100 node clusters, we are using
autofs with soft mounts. We too use the -g option of the automount and
to date, for almost a year now, we have experienced no issues.
Cheers,
Stewart
-----Original Message-----
From: torqueusers-bounces at supercluster.org
[mailto:torqueusers-bounces at supercluster.org] On Behalf Of Mary Ellen
Fitzpatrick
Sent: Thursday, October 23, 2008 1:32 PM
To: Garrick
Cc: Greenseid, Joseph M.; torqueusers at supercluster.org
Subject: Re: [torqueusers] pbs_mom unable to chdir to automounted dirs
---RESOLVED
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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