[MITgcm-devel] Re: [MITgcm-support] noise in high resolution run
Martin Losch
mlosch at awi-bremerhaven.de
Mon Apr 3 07:12:39 EDT 2006
Hi again,
I have played a little more with my configuration, turned on
useJamartWetPoints=.true., and I now have defined
USE_ISOTROPIC_SCALING and COSMETH_III in CPP_OPTIONS.h (a case of
"two-weeks-of-programming-and-testing-can-save-you-an-afternoon-in-
the-library": There were once emails about noise in the JPL 1/4
degree experiments, and this thread helped me a lot: http://
dev.mitgcm.org/pipermail/mitgcm-support/2003-December/001896.html )
With that I can increase my horizontal viscosities and diffusivities
to 3.e11 (4.e11 "bombs"). The noise pattern the same (meridional
stripes), but in different locations, e.g. near the southern boundary
just east of the antarctic peninsula, see http://mitgcm.org/~mlosch/
noise4.png (notice, that it is a much shorter run, only 20days).
changing from dst3 to 4th order advection requires that I reduce the
horizontal friction parameters to 1.e11 (3.e11 bombs), and the noise
remains, see http://mitgcm.org/~mlosch/noise5.png
Still not satified, although feeling much better already,
Martin
On Apr 1, 2006, at 6:10 PM, Martin Losch wrote:
> Hi Chris,
>
> the beers were good, the ambience even better (with Patrick in
> Hamburg's smoke stacked basement bars that are decorated like your
> grandparents living rooms in the fifties) and we tried to avoid
> talking about noise in the MITgcm (did not quite succeed).
>
> In my home directory on faulks there is a gzipped archive
> ~mlosch/dp.tgz [58MB]
> of my configuration, it unpacks into a directoy drakePassage with a
> "code" directory (please disregard btmvisc.tar: those are Matt's
> modif's for increased viscosity near the bottom, which I don't use,
> got in there by accident), "input" directory with initial
> conditions and open and surface boundary conditions etc, and a
> "run00" directory with my most recent data* files (most of them are
> just copies of the versions in the input directory. The MITgcm code
> that I ran this with was up-to-date on Thurday, Mar30, but I don't
> think that JMCs recent changes will change anything (I'll update
> and rerun on Monday anyway), so you can use up-to-date code for
> this, I guess.
> EXCEPT: I defined USE_ISOTROPIC_SCALING in GAD_OPTIONS.h, so that
> xd1-420-6::MITgcm> cvs -q diff
> Index: pkg/generic_advdiff/GAD_OPTIONS.h
> ===================================================================
> RCS file: /u/gcmpack/MITgcm/pkg/generic_advdiff/GAD_OPTIONS.h,v
> retrieving revision 1.5
> diff -r1.5 GAD_OPTIONS.h
> 31c31
> < #undef ISOTROPIC_COS_SCALING
> ---
> > #define ISOTROPIC_COS_SCALING
>
> The noise only starts to appear after few (20) days of integration,
> which take a while.
> Good luck
>
> Martin
>
>
> On Mar 31, 2006, at 8:23 PM, chris hill wrote:
>
>> Hi Martin/Patrick,
>>
>> Is it possible to transfer everything to a directory on faulks,
>> we can take a more detailed look while you all drink beer.
>>
>> Thanks,
>>
>> Chris
>> Patrick Heimbach wrote:
>>> Hi all,
>>> I am moving this to the devel list.
>>> Given that we've been seeing also somewhat strange behaviour
>>> in vertical velocity fields near topography and not so stable
>>> behaviour of the adjoint as a consequence, I am wondering
>>> (as is Martin) whether this is indicative of a bug.
>>> Haven't looked carefully recently (in particular after the adjoint
>>> bug fix for variable aliasing), will dot it soon, but don't think,
>>> the 4deg adjoint showed this behaviour in much earlier versions.
>>> The adjoint might actually tell us (if we believe it) where to
>>> look for potential sources of the problem. I'll try to have
>>> a look next week.
>>> But maybe it's all ok...
>>> OK, after making such provocative statement, I'll now
>>> be offline for a few days (and have beers with Martin instead).
>>> -p.
>>> Quoting Baylor Fox-Kemper <baylor at MIT.EDU>:
>>>> Hi Martin,
>>>>
>>>>> useJamartWetPoints is a good suggestion. I will try that next.
>>>>> Since the noise seems to be associated with the coasts it
>>>>> sounds like a good guess. What about the other flags,
>>>>
>>>>
>>>>> useJamartMomAdv
>>>>
>>>>
>>>> I was told that this one doesn't really make sense in terms of
>>>> conservation near boundaries, I believe. I'm no expert in it,
>>>> though.
>>>>
>>>>> SadournyCoriolis
>>>>
>>>>
>>>> JMC just told me that this is actually NOT the scheme that
>>>> Sadourny suggests to use, it is really one of the ones that he
>>>> suggests NOT to use in the same paper! So, I think that for
>>>> the moment this is probably not a good bet either.
>>>>
>>>>> I use
>>>>> no_slip_sides=.false.,
>>>>> the sidedrag code is a drag to debug. Each time I have a look
>>>>> at it, it looks wrong the first time around and then after 3hs
>>>>> of mind warp it turns out to be right. When I have a look at
>>>>> the plots I find it hard to believe that there is not a bug in
>>>>> the whatever- part of the code (doesn't even have to be the
>>>>> viscosity). I guess I have to start turning off terms and see
>>>>> what happens.
>>>>
>>>> sidedrag can't be the problem then...
>>>>
>>>> What I fear is what Michael suggests:
>>>>
>>>>> we had some problems like this with the NCOM (hydrostatic) at
>>>>> one time and tried all sorts of things.
>>>>> it turned out to be an indexing problem in the code.
>>>>
>>>> The question is, where?
>>>> -Baylor
>>>>
>>>>> Dimitris,
>>>>> I don't use KPP so far, although I would like to use in the
>>>>> future (maybe, I have enough problems as it is (o:). My
>>>>> experience with KPP is that it tends to amplify noise, but
>>>>> does not generate it (?). In that case the horizontal filters
>>>>> are useful. In this case, I don't think that it will help too
>>>>> much, I am afraid, because the noise is already there without
>>>>> KPP.
>>>>>
>>>>> Thanks for your suggestions.
>>>>> Martin
>>>>> On Mar 30, 2006, at 8:06 PM, Baylor Fox-Kemper wrote:
>>>>>
>>>>>> Hi Martin,
>>>>>> I've seen similar noise in W in some runs, but not so
>>>>>> obviously in U and V. Have you tried jamartwetpoints?
>>>>>> Also, are you using no-slip? We found a few bugs in the
>>>>>> sidedrag code a while back. It might be worth revisiting...I
>>>>>> suppose it is possible that there is a problem elsewhere in
>>>>>> the viscosity/viscous terms code, but I don't know why it
>>>>>> would be localized in space.
>>>>>> -Baylor
>>>>>>
>>>>>>
>>>>>> On Mar 30, 2006, at 8:30 AM, Martin Losch wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I seem to have a problem with a 1/6 by 1/6*cos(phi) run with
>>>>>>> open boundaries. The domain is the Drake Passage. A plot of
>>>>>>> bathymetry and velocities can be found in
>>>>>>> http://mitgcm.org/~mlosch/noise.png
>>>>>>>
>>>>>>> Whatever friction parameters I have tried (viscAh=1e0 to 2e1
>>>>>>> and viscA4=1e8 to 4e10, and similar for diffusivities, I
>>>>>>> also tried the Leith/Smagorinski variants), I seem to get
>>>>>>> noise in the north western part of the domain. What worries
>>>>>>> me is, that
>>>>>>> 1. The noise seems to propagate (compare day 149 to day 214
>>>>>>> in the bottom panels of the figure)
>>>>>>> 2. The noise seems to be mainly in the x-direction
>>>>>>>
>>>>>>> I use mom_fluxform. For mom_vecinv the problem is there, too.
>>>>>>> I use USE_ISOTROPIC_SCALING (for viscosities because my y-
>>>>>>> grid varies with y) and do not use COSINEMETH_III (although
>>>>>>> that probably doesn't make much of a difference). When I
>>>>>>> turn off USE_ISOTROPIC_SCALING, the noise is still there,
>>>>>>> but the x- alignment is slightly less obvious (although very
>>>>>>> much present). If the noise were deltaX in both directions,
>>>>>>> I would be concerned about my friction parameters. Here I
>>>>>>> suspect a problem in the viscosity implementation, but I
>>>>>>> cannot see how and were.
>>>>>>> There is some noise that is produced by the open boundaries,
>>>>>>> but that usually goes away. I think that the generation of
>>>>>>> the noise is connected to the topography around the tip of
>>>>>>> South America
>>>>>>>
>>>>>>> I wonder if anyone has seen something like this before. What
>>>>>>> do you think?
>>>>>>>
>>>>>>> Martin
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> MITgcm-support mailing list
>>>>>>> MITgcm-support at mitgcm.org
>>>>>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>>>>>
>>>>>>
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>>>>>
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>>> --------------------------------------------------------
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>>> FAX: +1/617/253-4464 77 Massachusetts Avenue
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