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Subject: Re: [OMPI users] EXTERNAL: Re: How to set up state-less node /tmp for OpenMPI usage
From: TERRY DONTJE (terry.dontje_at_[hidden])
Date: 2011-11-04 10:25:29


I wasn't advocating against having the epilogue per se, but was more
curious if there was some issue going on that we did not know about. If
there isn't an issue then great.

--td

On 11/4/2011 9:59 AM, Ralph Castain wrote:
> That isn't the situation, Terry. We had problems with early OMPI
> releases, particularly the 1.2 series. In response, the labs wrote an
> epilogue to ensure that the session directories were removed.
> Executing the epilogue is now standard operating procedure, even
> though our more recent releases do a much better job of cleanup.
>
> Frankly, it's a good idea anyway. It hurts nothing, takes milliseconds
> to do, and guarantees nothing got left behind (e.g., if someone was
> using a debug version of OMPI and directed opal_output to a file).
>
> On Nov 4, 2011, at 4:43 AM, TERRY DONTJE wrote:
>
>> David, are you saying your jobs consistently leave behind session
>> files after the job exits? It really shouldn't even in the case when
>> a job aborts, I thought, mpirun took great pains to cleanup after
>> itself. Can you tell us what version of OMPI you are running
>> with? I think I could see kill -9 of mpirun and processes below
>> would cause turds to be left behind.
>>
>> --td
>>
>> On 11/4/2011 2:37 AM, David Turner wrote:
>>> % df /tmp
>>> Filesystem 1K-blocks Used Available Use% Mounted on
>>> - 12330084 822848 11507236 7% /
>>> % df /
>>> Filesystem 1K-blocks Used Available Use% Mounted on
>>> - 12330084 822848 11507236 7% /
>>>
>>> That works out to 11GB. But...
>>>
>>> The compute nodes have 24GB. Freshly booted, about 3.2GB is
>>> consumed by the kernel, various services, and the root file system.
>>> At this time, usage of /tmp is essentially nil.
>>>
>>> We set user memory limits to 20GB.
>>>
>>> I would imagine that the size of the session directories depends on a
>>> number of factors; perhaps the developers can comment on that. I have
>>> only seen total sizes in the 10s of MBs on our 8-node, 24GB nodes.
>>>
>>> As long as they're removed after each job, they don't really compete
>>> with the application for available memory.
>>>
>>> On 11/3/11 8:40 PM, Ed Blosch wrote:
>>>> Thanks very much, exactly what I wanted to hear. How big is /tmp?
>>>>
>>>> -----Original Message-----
>>>> From: users-bounces_at_[hidden]
>>>> [mailto:users-bounces_at_[hidden]] On
>>>> Behalf Of David Turner
>>>> Sent: Thursday, November 03, 2011 6:36 PM
>>>> To: users_at_[hidden]
>>>> Subject: Re: [OMPI users] EXTERNAL: Re: How to set up state-less
>>>> node /tmp
>>>> for OpenMPI usage
>>>>
>>>> I'm not a systems guy, but I'll pitch in anyway. On our cluster,
>>>> all the compute nodes are completely diskless. The root file system,
>>>> including /tmp, resides in memory (ramdisk). OpenMPI puts these
>>>> session directories therein. All our jobs run through a batch
>>>> system (torque). At the conclusion of each batch job, an epilogue
>>>> process runs that removes all files belonging to the owner of the
>>>> current batch job from /tmp (and also looks for and kills orphan
>>>> processes belonging to the user). This epilogue had to written
>>>> by our systems staff.
>>>>
>>>> I believe this is a fairly common configuration for diskless
>>>> clusters.
>>>>
>>>> On 11/3/11 4:09 PM, Blosch, Edwin L wrote:
>>>>> Thanks for the help. A couple follow-up-questions, maybe this
>>>>> starts to
>>>> go outside OpenMPI:
>>>>>
>>>>> What's wrong with using /dev/shm? I think you said earlier in
>>>>> this thread
>>>> that this was not a safe place.
>>>>>
>>>>> If the NFS-mount point is moved from /tmp to /work, would a /tmp
>>>>> magically
>>>> appear in the filesystem for a stateless node? How big would it
>>>> be, given
>>>> that there is no local disk, right? That may be something I have
>>>> to ask the
>>>> vendor, which I've tried, but they don't quite seem to get the
>>>> question.
>>>>>
>>>>> Thanks
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: users-bounces_at_[hidden]
>>>>> [mailto:users-bounces_at_[hidden]] On
>>>> Behalf Of Ralph Castain
>>>>> Sent: Thursday, November 03, 2011 5:22 PM
>>>>> To: Open MPI Users
>>>>> Subject: Re: [OMPI users] EXTERNAL: Re: How to set up state-less
>>>>> node /tmp
>>>> for OpenMPI usage
>>>>>
>>>>>
>>>>> On Nov 3, 2011, at 2:55 PM, Blosch, Edwin L wrote:
>>>>>
>>>>>> I might be missing something here. Is there a side-effect or
>>>>>> performance
>>>> loss if you don't use the sm btl? Why would it exist if there is a
>>>> wholly
>>>> equivalent alternative? What happens to traffic that is intended for
>>>> another process on the same node?
>>>>>
>>>>> There is a definite performance impact, and we wouldn't recommend
>>>>> doing
>>>> what Eugene suggested if you care about performance.
>>>>>
>>>>> The correct solution here is get your sys admin to make /tmp
>>>>> local. Making
>>>> /tmp NFS mounted across multiple nodes is a major "faux pas" in the
>>>> Linux
>>>> world - it should never be done, for the reasons stated by Jeff.
>>>>>
>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: users-bounces_at_[hidden]
>>>>>> [mailto:users-bounces_at_[hidden]] On
>>>> Behalf Of Eugene Loh
>>>>>> Sent: Thursday, November 03, 2011 1:23 PM
>>>>>> To: users_at_[hidden]
>>>>>> Subject: Re: [OMPI users] EXTERNAL: Re: How to set up state-less
>>>>>> node
>>>> /tmp for OpenMPI usage
>>>>>>
>>>>>> Right. Actually "--mca btl ^sm". (Was missing "btl".)
>>>>>>
>>>>>> On 11/3/2011 11:19 AM, Blosch, Edwin L wrote:
>>>>>>> I don't tell OpenMPI what BTLs to use. The default uses sm and
>>>>>>> puts a
>>>> session file on /tmp, which is NFS-mounted and thus not a good choice.
>>>>>>>
>>>>>>> Are you suggesting something like --mca ^sm?
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: users-bounces_at_[hidden]
>>>>>>> [mailto:users-bounces_at_[hidden]] On
>>>> Behalf Of Eugene Loh
>>>>>>> Sent: Thursday, November 03, 2011 12:54 PM
>>>>>>> To: users_at_[hidden]
>>>>>>> Subject: Re: [OMPI users] EXTERNAL: Re: How to set up state-less
>>>>>>> node
>>>> /tmp for OpenMPI usage
>>>>>>>
>>>>>>> I've not been following closely. Why must one use shared-memory
>>>>>>> communications? How about using other BTLs in a "loopback"
>>>>>>> fashion?
>>>>>>> _______________________________________________
>>>>>>> users mailing list
>>>>>>> users_at_[hidden]
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>> _______________________________________________
>>>>>>> users mailing list
>>>>>>> users_at_[hidden]
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> users mailing list
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>>>>> _______________________________________________
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>>>>
>>>>
>>>
>>>
>>
>> --
>> <Mail Attachment.gif>
>> Terry D. Dontje | Principal Software Engineer
>> Developer Tools Engineering | +1.781.442.2631
>> Oracle *- Performance Technologies*
>> 95 Network Drive, Burlington, MA 01803
>> Email terry.dontje_at_[hidden] <mailto:terry.dontje_at_[hidden]>
>>
>>
>>
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>
>
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-- 
Oracle
Terry D. Dontje | Principal Software Engineer
Developer Tools Engineering | +1.781.442.2631
Oracle *- Performance Technologies*
95 Network Drive, Burlington, MA 01803
Email terry.dontje_at_[hidden] <mailto:terry.dontje_at_[hidden]>



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