[MITgcm-support] segmentation fault

Fri May 18 11:37:42 EDT 2018

Hi Andreas,

a small chance (and a bit of a guess) that one of the following might do the trick
(we have memory-related issues when running the adjoint):

In your shell script or batch job, add
ulimit -s unlimited

If compiling with ifort, you could try -mcmodel=medium

See mitgcm-support thread, e.g.
http://mailman.mitgcm.org/pipermail/mitgcm-support/2005-October/003505.html
(you'll need to scroll down to input provided by Constantinos Evangelinos).

p.

> On May 18, 2018, at 8:04 AM, Dimitris Menemenlis <menemenlis at jpl.nasa.gov> wrote:
> 
> Andreas, I have done something similar quite a few times (i.e., increase horizontal and/or vertical resolution in regional domains with obcs cut-out from a global set-up) and did not have same issue.  If helpful I can dig out and commit to contrib some examples that you can compare your set-up against.  Actually, you remind me that I already promised to do this for Gael but that it fell off the bottom of my todo list :-(
> 
> Do you have any custom routines in your "code" directory?  Have you tried compiling and linking with array-bound checks turned on?
> 
> Dimitris Menemenlis
> On 05/17/2018 11:45 PM, Andreas Klocker wrote:
>> Matt,
>> I cut all the unnecessary packages and still have the same issue.
>> I also checked 'size mitgcmuv' and compared the size to other runs which work - it asks for about half the size of other runs which work fine (same machine, same queue, same compiling options, etc).
>> The tiles are already down to 32x32 grid points, and I'm happily running configurations with a tile size almost twice as big and the same amount of vertical layers.
>> I will try some different tile sizes but I think the problem must be somewhere else..
>> Andreas
>> On 18/05/18 00:35, Matthew Mazloff wrote:
>>> Sounds like a memory issue. I think your executable has become too big for you machine. You will need to reduce tile size or do something else (e.g. reduce number of diagnostics or cut a package)
>>> 
>>> and check
>>> size mitgcmuv
>>> to get a ballpark idea of how much memory you are requesting
>>> 
>>> Matt
>>> 
>>> 
>>> 
>>>> On May 16, 2018, at 11:27 PM, Andreas Klocker <andreas.klocker at utas.edu.au<mailto:andreas.klocker at utas.edu.au>> wrote:
>>>> 
>>>> Hi guys,
>>>> 
>>>> I've taken a working 1/24 degree nested simulation (of Drake Passage)
>>>> with 42 vertical layers and tried to increase the vertical layers to 150
>>>> (without changing anything else apart from obviously my boundary files
>>>> for OBCS and recompiling with 150 vertical layers). Suddenly I get the
>>>> following error message:
>>>> 
>>>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>>>> Image              PC                Routine Line        Source
>>>> libirc.so <http://libirc.so>          00002BA1704BC2C9  Unknown Unknown  Unknown
>>>> libirc.so <http://libirc.so>          00002BA1704BAB9E  Unknown Unknown  Unknown
>>>> libifcore.so.5     00002BA1722B5F3F  Unknown Unknown  Unknown
>>>> libifcore.so.5     00002BA17221DD7F  Unknown Unknown  Unknown
>>>> libifcore.so.5     00002BA17222EF43  Unknown Unknown  Unknown
>>>> libpthread.so.0    00002BA1733B27E0  Unknown Unknown  Unknown
>>>> mitgcmuv_drake24_  00000000004E61BC  mom_calc_visc_ 3345 mom_calc_visc.f
>>>> mitgcmuv_drake24_  0000000000415127  mom_vecinv_ 3453 mom_vecinv.f
>>>> mitgcmuv_drake24_  0000000000601C33  dynamics_ 3426  dynamics.f
>>>> mitgcmuv_drake24_  0000000000613C2B  forward_step_ 2229 forward_step.f
>>>> mitgcmuv_drake24_  000000000064581E  main_do_loop_ 1886 main_do_loop.f
>>>> mitgcmuv_drake24_  000000000065E500  the_main_loop_ 1904 the_main_loop.f
>>>> mitgcmuv_drake24_  000000000065E6AE  the_model_main_ 2394 the_model_main.f
>>>> mitgcmuv_drake24_  00000000005C6439  MAIN__ 3870  main.f
>>>> mitgcmuv_drake24_  0000000000406776  Unknown Unknown  Unknown
>>>> libc.so.6          00002BA1737E2D1D  Unknown Unknown  Unknown
>>>> mitgcmuv_drake24_  0000000000406669  Unknown Unknown  Unknown
>>>> 
>>>> First this error pointed to a line in mom_calc_visc.f on which
>>>> calculations regarding the Leith viscosity are done. As a test I then
>>>> used a Smagorinsky viscosity instead and now it crashes with the same
>>>> error, but pointing to a line where Smagorinsky calculations are done. I
>>>> assume I must be chasing a way more fundamental problem than one related
>>>> to these two viscosity choices...but I'm not sure what this might be....
>>>> 
>>>> Has anyone got any idea of what could be going wrong here?
>>>> 
>>>> Thanks in advance!
>>>> 
>>>> Andreas
>>>> 
>>>> 
>>>> 
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>>>> 
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>>> 
>>> 
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>> -- 
>> ===============================================================
>> Dr. Andreas Klocker
>> Physical Oceanographer
>> ARC Centre of Excellence for Climate System Science
>> &
>> Institute for Marine and Antarctic Studies
>> University of Tasmania
>> 20 Castray Esplanade
>> Battery Point, TAS
>> 7004 Australia
>> M:     +61 437 870 182
>> W:http://www.utas.edu.au/profiles/staff/imas/andreas-klocker
>> skype: andiklocker
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