Remapped overturning into depth space, masked the mediteranean in mom5 #284

willaguiar · 2023-09-04T06:11:41Z

Closes #274

review-notebook-app · 2023-09-04T06:11:45Z

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navidcy · 2023-09-04T10:13:50Z

oftentimes people say "dask gives problems" and the respond is "give us an example that does not work".

Well, here's an example that we get a lot of struggles. When I try to run this notebook to review the PR I get a bunch of

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and more.

Do we have any suggestions for how can we this example run smoother?

Perhaps an overambitious is to be able to run the same with 0.1 degree model output... (but that's beyond imagination atm)

cc @aidanheerdegen, @angus-g, @dougiesquire, @micaeljtoliveira

dougiesquire · 2023-09-06T00:11:57Z

One issue here is that more attention needs to be paid to the chunking of some of the data being used. E.g., adding the following to the "mom5" key in psi_args means the first few cells complete more efficiently and without warnings:

"chunks": {
    "time": 1,
    "potrho": -1,
    "grid_yu_ocean": 270,
    "grid_xt_ocean": -1,
 }

This may still not be the best chunking for the subsequent calculations, but before getting to that I'm curious why the density remapping doesn't use xgcm?

navidcy · 2023-09-06T00:15:06Z

This may still not be the best chunking for the subsequent calculations, but before getting to that I'm curious why the density remapping doesn't use xgcm?

I don't think there is a particular reason we didn't use xgcm but @AndyHoggANU or @adele-morrison may have a more definite opinion?

navidcy · 2023-09-29T07:05:30Z

@willaguiar could you try @dougiesquire's suggestion here and rerun all cells?

willaguiar · 2023-10-03T02:34:48Z

One issue here is that more attention needs to be paid to the chunking of some of the data being used. E.g., adding the following to the "mom5" key in psi_args means the first few cells complete more efficiently and without warnings:
"chunks": {
    "time": 1,
    "potrho": -1,
    "grid_yu_ocean": 270,
    "grid_xt_ocean": -1,
 }

This seems to have corrected the Dask warnings ( thanks @dougiesquire ). Could you explain in a little more detail why? ( so I keep in mind for future codes).

PS:I added a new edit to the code on the mom6 remapping function. Before, I was manually setting the southernmost cutout latitude for the remapping (78S index nmin), but the index I set before would only work on panan-01. Now I changed so the cutout (78S) latitude is automatically identified in each model.

review-notebook-app · 2023-10-04T12:30:33Z

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navidcy commented on 2023-10-04T12:30:31Z
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Will could you add spaces after commas here?

Also, isn't there an xarray-way to do this?

    for ii in range(nmin,nmax):
        if model=='mom5':
            rho1 = rho2_zonal_mean.isel(yt_ocean=ii).values
            f = interp1d(rho1,z1,bounds_error=False,fill_value = (0,'NaN'))
            psi_depth[:,ii] = np.nan_to_num(f(psi_avg.potrho.values),nan=6000)
        elif model=='mom6':
            rho1 = rho2_zonal_mean.isel(yh=ii).values
            f = interp1d(rho1,z1,bounds_error=False,fill_value = (0,'NaN'))
            psi_depth[:,ii] = np.nan_to_num(f(psi_avg.rho2_l.values),nan=6000)

willaguiar commented on 2023-10-13T01:39:30Z
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I altered the code to use xarray.interp. Might be a little prolix, so any suggestions are welcome

review-notebook-app · 2023-10-04T12:30:35Z

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navidcy commented on 2023-10-04T12:30:34Z
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Will is it on purpose that only the south-most bit of the overturning shows up here?

navidcy commented on 2023-10-04T12:35:31Z
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Oh I see, it's because you used panant-01-zstar-ACCESSyr2 .

Was there any thinking behind this choice?

willaguiar commented on 2023-10-13T01:40:41Z
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Thanks for noticing! Yes - just wanted to make sure the code would work for the regional configuration. I submitted a new code where I use the global-01-v3 mom6 experiment

review-notebook-app · 2023-10-04T12:30:36Z

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navidcy commented on 2023-10-04T12:30:35Z
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how come only the southern part of the MOC is shown?

willaguiar commented on 2023-10-13T01:40:47Z
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Same as above

navidcy · 2023-10-04T12:35:32Z

Oh I see, it's because you used panant-01-zstar-ACCESSyr2 .

Was there any thinking behind this choice?

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review-notebook-app · 2023-10-04T12:35:38Z

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navidcy commented on 2023-10-04T12:35:38Z
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Let's rephrase "I recommend" to "We recommend". It reads better. We want to avoid the notion that examples are somebody's but rather that the community is talking to the users!

willaguiar commented on 2023-10-13T01:40:53Z
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done

review-notebook-app · 2023-10-04T12:35:40Z

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navidcy commented on 2023-10-04T12:35:39Z
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Line #1.    %matplotlib inline

we can delete this line as is not the default

willaguiar commented on 2023-10-13T01:41:01Z
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done in the new commit

willaguiar · 2023-10-13T01:39:31Z

Added in the new commit

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willaguiar · 2023-10-13T01:40:43Z

Thanks for noticing! Yes - just wanted to make sure the code would work for the regional configuration. I submitted a new code where I use the global-01-v3 mom6 experiment

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willaguiar · 2023-10-13T01:40:48Z

Same as above

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willaguiar · 2023-10-13T01:40:54Z

done

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willaguiar · 2023-10-13T01:41:02Z

done in the new commit

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review-notebook-app · 2023-10-13T03:19:26Z

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willaguiar commented on 2023-10-13T03:19:25Z
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Also, last time I ran the notebook was on hugemem queue, so these warnings didn't appear before. They are back on the normalbw queue. Not quite sure how to solve it

review-notebook-app · 2023-10-13T03:19:27Z

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willaguiar commented on 2023-10-13T03:19:26Z
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One thing that could be improved is the spikes on the bottom cell, below 4000m. I think at these depths small rho changes happens in large depth ranges, so the conversion of rho to z gets noisy. it would be cool if we could improve that someway?

navidcy · 2023-10-14T14:41:22Z

@dougiesquire I get a lot of similar-type warnings as in #285 here using unstable.

navidcy · 2023-10-14T14:43:26Z

@willaguiar, can you use pint to deal with the unit conversion, e.g., from m^3/s -> Sv? At the moment is done ad-hoc by dividing with the conversion factor.

Have a look at https://cosima-recipes.readthedocs.io/en/latest/DocumentedExamples/Transport_Through_Straits.html

navidcy · 2023-10-14T14:50:36Z

@willaguiar another remark: the ticks on the colorbar in the very last plot seems a bit weird... Am I right?

navidcy · 2023-10-25T16:54:58Z

Fixed the warnings and the colorbar ticks.

I'm happy for this to be merged as is; no need to deal with pint in this PR.

navidcy

lgtm

Remapped overturning into depth space, masked the mediteranean in mom5

a08f9f2

willaguiar added the 🎮 hackathon 3.0 label Sep 4, 2023

fix mom5 chuncking + corrected cutout latitude in mom6

f2003e5

navidcy added 2 commits October 4, 2023 23:22

Merge branch 'main' into Will_branch

cc8aa19

resolve conflicts

77d59c2

navidcy self-requested a review October 4, 2023 12:30

navidcy assigned willaguiar Oct 4, 2023

reviewed code

e8cd7a2

spaces after commas, use unstable, rerun all

8980061

navidcy added 2 commits October 26, 2023 03:50

use conda env 23.04

54a360b

fix colorbar tickes

c14440b

navidcy approved these changes Oct 25, 2023

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navidcy merged commit d9fc8d6 into main Oct 25, 2023
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Remapped overturning into depth space, masked the mediteranean in mom5 #284

Remapped overturning into depth space, masked the mediteranean in mom5 #284

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Remapped overturning into depth space, masked the mediteranean in mom5 #284

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