[Users] Stampede

[Yosef Zlochower]

I also tried using Roland's openmpi library.
The errors were different, but the run died during
checkpoint as before.


On 07/14/2014 04:14 PM, Yosef Zlochower wrote:
> I tried a run on stampede today and it died during checkpoint with the
> error
> " send desc error
> send desc error
> [0] Abort: Got completion with error 12, vendor code=81, dest rank=
>    at line 892 in file ../../ofa_poll.c"
>
> Have you been having success running production runs on stampede?
>
>
> On 05/02/2014 12:15 PM, Ian Hinder wrote:
>>
>> On 02 May 2014, at 16:57, Yosef Zlochower <yosef at astro.rit.edu
>> <mailto:yosef at astro.rit.edu>> wrote:
>>
>>> On 05/02/2014 10:07 AM, Ian Hinder wrote:
>>>>
>>>> On 02 May 2014, at 14:08, Yosef Zlochower <yosef at astro.rit.edu
>>>> <mailto:yosef at astro.rit.edu>
>>>> <mailto:yosef at astro.rit.edu>> wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> I have been having problems running on Stampede for a long time. I
>>>>> couldn't get the latest
>>>>> stable ET to run because during checkpointing, it would die.
>>>>
>>>> OK that's very interesting.  Has something changed in the code related
>>>> to how checkpoint files are written?
>>>>
>>>>> I had to backtrack to
>>>>> the Orsted version (unfortunately, that has a bug in the way the grid
>>>>> is set up, causing some of the
>>>>> intermediate levels to span both black holes, wasting a lot of memory).
>>>>
>>>> That bug should have been fixed in a backport; are you sure you are
>>>> checking out the branch and not the tag?  In any case, it can be worked
>>>> around by setting CarpetRegrid2::min_fraction = 1, assuming this is the
>>>> same bug I am thinking of
>>>> (http://cactuscode.org/pipermail/users/2013-January/003290.html)
>>>
>>> I was using an old executable so it wouldn't have had the backport
>>> fix.
>>>
>>>>
>>>>> Even with
>>>>> Orsted , stalling is a real issue. Currently, my "solution" is to run
>>>>> for 4 hours at a time.
>>>>> This would have been  OK on Lonestar or Ranger,
>>>>> because when I chained a bunch a runs, the next in line would start
>>>>> almost right away, but on stampede the delay is quite substantial. I
>>>>> believe Jim Healy opened
>>>>> a ticket concerning the RIT issues with running ET on stampede.
>>>>
>>>> I think this is the ticket:
>>>> https://trac.einsteintoolkit.org/ticket/1547.  I will add my information
>>>> there.  The current queue wait time on stampede is more than a day, so
>>>> splitting into 3 hour chunks is not feasible, as you say.
>>>>
>>>> I'm starting to think it might be a code problem as well.  So the
>>>> summary is:
>>>>
>>>> – Checkpointing causes jobs to die with code versions after Oersted
>>>> – All versions lead to eventual hung jobs after a few hours
>>>>
>>>> Since Stampede is the major "capability" resource in Xsede, we should
>>>> put some effort into making sure the ET can run properly there.
>>>
>>> We find issues with runs stalling on our local cluster too. The hardware
>>> setup is similar to stampede (Intel Nehalem with QDR IB and openMPI on
>>> top of a proprietary IB library). There's no guarantee that the issues
>>> are the same, but we can try to run some tests locally (note that we
>>> have no issues with runs failing to checkpoint).
>>
>> I resubmitted, and the new job hangs later on.  gdb says it is in
>> CarpetIOScalar while doing output of a maximum reduction.  I've disabled
>> this and resubmitted.
>>
>> --
>> Ian Hinder
>> http://numrel.aei.mpg.de/people/hinder
>>
>
>


-- 
Dr. Yosef Zlochower
Center for Computational Relativity and Gravitation
Associate Professor
School of Mathematical Sciences
Rochester Institute of Technology
85 Lomb Memorial Drive
Rochester, NY 14623

Office:74-2067
Phone: +1 585-475-6103

yosef at astro.rit.edu

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