WIP: Add osnap T S climtransects #899

alicebarthel · 2022-09-23T19:49:16Z

This is to plot T,S transects at OSNAP transects, based on the obs dataset [downloaded in 2022].
I based it on woce_transects.py
A couple of questions for @milenaveneziani @xylar:
I saw that WOCE is a collection of separate transects. Currently, the obs dataset has both East and West transects in one file, is it better to split them in pre-processing to give us separate plots?
I currently only added T,S (we have no measured density).
I did not add velocities in the variables but it is in the obs dataset. I suspected the process for plotting MPAS-O velocity at transect should be separate from tracer fields. Let me know if you think otherwise.

Checklist (for @xylar) before merging:

copy OSNAP obs from /lcrc/group/e3sm/diagnostics/observations/Ocean/OSNAP to /lcrc/group/e3sm/public_html/diagnostics/observations/Ocean/OSNAP
generate README from obs.xml and copy to /lcrc/group/e3sm/public_html/diagnostics/observations/Ocean/OSNAP
sync OSNAP to Compy and Perlmutter

milenaveneziani · 2022-09-24T16:32:49Z

Currently, the obs dataset has both East and West transects in one file, is it better to split them in pre-processing to give us separate plots?

Yes, I would split them.

I suspected the process for plotting MPAS-O velocity at transect should be separate from tracer fields.

I'll let @xylar reply to this. My standalone script plots the mpas normalVelocity at the transect mask edges: so, no interpolation but unpleasant noisy visuals. I think Xylar has a more pleasant-to-the-eye alternative.

xylar · 2022-09-24T17:35:34Z

I suspected the process for plotting MPAS-O velocity at transect should be separate from tracer fields.

I'll let @xylar reply to this. My standalone script plots the mpas normalVelocity at the transect mask edges: so, no interpolation but unpleasant noisy visuals. I think Xylar has a more pleasant-to-the-eye alternative.

Hmm, I don't think we've plotted velocities at transects except for SOSE. There, we just plot zonal, meridional or magnitude. Instead, you would want velocity normal to the transect, which would require a computation based on the zonal and meridional components, and the angle of the transect edge with respect to east. I think that would be fun to do but it hasn't been done yet.

milenaveneziani · 2022-09-25T04:35:13Z

We actually don't plot velocities for the SOSE transects, only for the SOSE 2d maps.
But yes, I agree that plotting velocities is something that will take more effort and maybe should be done later.

xylar · 2022-09-25T05:27:32Z

We actually don't plot velocities for the SOSE transects, only for the SOSE 2d maps.

At least in the analysis I'm looking at, we do plot the velocities (zonal, meridional and magnitude):
https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.xylar/analysis_testing/anvil/fix_conda_mpi_on_hpc/main_py3.9/ocean/index.html#sose_transects

xylar · 2022-09-26T20:48:19Z

mpas_analysis/default.cfg

+# Horizontal bounds of the plot (in km), or an empty list for automatic bounds
+# The bounds are a 2-element list of the minimum and maximum distance along the
+# transect. Note: A21=Drake Passage; A23=South Atlantic; A12=Prime Meridian
+horizontalBounds = {'WOCE_A21': [],
+ 'WOCE_A23': [],
+ 'WOCE_A12': []}


I think you can just get rid of this. The horizontal bounds can be the whole transect unless you think you would ever want to plot part of it.

alicebarthel · 2022-12-06T19:22:05Z

An update on this:

I have been able to run the osnapTransects for all 3 combinations of grids (mpas, obs, and 5+uniform).
I am still finding some inconsistencies.

At the moment, runnning the analysis in a new directory fails with

srun: error: b577: tasks 1,10: Exited with exit code 1
Traceback (most recent call last):
  File "/gpfs/fs1/home/ac.abarthel/mpas-analysis/add_OSNAP_TSclimtransects/mpas_analysis/__main__.py", line 381, in add_task_and_subtasks
    analysisTask.setup_and_check()
  File "/gpfs/fs1/home/ac.abarthel/mpas-analysis/add_OSNAP_TSclimtransects/mpas_analysis/ocean/compute_transects_subtask.py", line 221, in setup_and_check
    super().setup_and_check()
  File "/gpfs/fs1/home/ac.abarthel/mpas-analysis/add_OSNAP_TSclimtransects/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py", line 208, in setup_and_check
    self._setup_remappers()
  File "/gpfs/fs1/home/ac.abarthel/mpas-analysis/add_OSNAP_TSclimtransects/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py", line 413, in _setup_remappers
    self.remappers[comparisonGridName] = get_remapper(
  File "/gpfs/fs1/home/ac.abarthel/mpas-analysis/add_OSNAP_TSclimtransects/mpas_analysis/shared/climatology/climatology.py", line 130, in get_remapper
    remapper.build_mapping_file(method=method, logger=logger,
  File "/lcrc/group/e3sm/ac.abarthel/mambaforge/envs/mpas_dev/lib/python3.10/site-packages/pyremap/remapper.py", line 303, in build_mapping_file
    subprocess.check_call(args, stdout=DEVNULL)
  File "/lcrc/group/e3sm/ac.abarthel/mambaforge/envs/mpas_dev/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['srun', '-n', '12', '/lcrc/group/e3sm/ac.abarthel/mambaforge/envs/mpas_dev/bin/ESMF_RegridWeightGen', '--source', '/lcrc/group/e3sm/ac.abarthel/analysis/debugl.A_WCYCL1850.ne4_oQU480.anvil/clim_3-5_ts_1-5/mapping/tmptykhhv_f/src_mesh.nc', '--destination', '/lcrc/group/e3sm/ac.abarthel/analysis/debugl.A_WCYCL1850.ne4_oQU480.anvil/clim_3-5_ts_1-5/mapping/tmptykhhv_f/dst_mesh.nc', '--weight', '/lcrc/group/e3sm/ac.abarthel/analysis/debugl.A_WCYCL1850.ne4_oQU480.anvil/clim_3-5_ts_1-5/mapping/map_oQU480_to_OSNAP_transects_5km_bilinear.nc', '--method', 'bilinear', '--netcdf4', '--no_log', '--src_loc', 'center', '--src_regional', '--dst_regional', '--ignore_unmapped']' returned non-zero exit status 1.
Warning: osnapTransects: remapTransects failed during check and will not be run
Warning: subtask of osnapTransects failed during check, so this task will not be run

but re-running it a second time (without purging) works and generates the plots. I am wondering if there is something in the order of operations that is off. After the first failure, the only logs available are:

ls /lcrc/group/e3sm/ac.abarthel/analysis/debugl.A_WCYCL1850.ne4_oQU480.anvil/clim_3-5_ts_1-5/logs
config.A_WCYCL1850.ne4_oQU480.anvil  taskProgress.log

xylar · 2022-12-06T19:28:05Z

@alicebarthel, you're getting close! Because you are using a development environment that doesn't support system MPI, you need these config options from the tutorial: https://mpas-dev.github.io/MPAS-Analysis/latest/tutorials/dev_getting_started.html#execute

That way, ESMF_RegridWeightGen won't be called with srun.

alicebarthel · 2022-12-06T19:36:00Z

Thanks @xylar ! It seems to work ok now that I added the [execute] section. Apologies for rushing through the set-up instead of reading the tutorial carefully. Just curious: Why does running it a second time solve the problem?

alicebarthel · 2022-12-06T19:41:23Z

A couple of questions/comments:

The default grid for WOCE transects is: (horiz: 5, vert: uniform_0_to_4000m_at_10m). Do we want the same for the OSNAP transects or would something else make more sense?
I plan to try to run the OSNAP analysis on a simulation with finer mesh.
Do any of you want to try to run this analysis independently to do a check on it?

xylar · 2022-12-06T20:32:41Z

Just curious: Why does running it a second time solve the problem?

I have no idea. I wouldn't expect that to be the case.

xylar · 2022-12-06T20:35:42Z

The default grid for WOCE transects is: (horiz: 5, vert: uniform_0_to_4000m_at_10m). Do we want the same for the OSNAP transects or would something else make more sense?

Maybe too deep?

Do any of you want to try to run this analysis independently to do a check on it?

Yes, I'll run a test, too, if you think it's ready.

xylar · 2022-12-06T20:37:45Z

Apologies for rushing through the set-up instead of reading the tutorial carefully.

Absolutely no worries. It's confusing and I hope we can move to the approach in compass soon, where ESMF is built with system MPI.

milenaveneziani · 2022-12-06T21:54:41Z

The default grid for WOCE transects is: (horiz: 5, vert: uniform_0_to_4000m_at_10m). Do we want the same for the OSNAP transects or would something else make more sense?

I actually think this is OK, especially for OSNAP West. Here are two sections I plotted in the past, and they go to 3500 and 4000 m, respectively:

I can also give this a try.

alicebarthel · 2022-12-07T01:13:22Z

Ok, thanks @milenaveneziani! I may need to adjust the plot options like range. I did not see observed densities. Did you recalculate these or did you have them?

alicebarthel · 2022-12-07T01:24:08Z

FYI, 2 year clim for the v2.amoc.baseline (EC30to60)
https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.abarthel/E3SMv2/analysis/v2.amoc.baseline.ne30pg2_EC30to60E2r2/clim_100-101_ts_100-101/ocean/index.html#osnap

xylar · 2022-12-07T10:56:57Z

This is really great, @alicebarthel!

xylar · 2022-12-07T10:58:11Z

mpas_analysis/__main__.py

+ analyses.append(ocean.OsnapTransects(config, oceanClimatolgyTasks['avg'],
+ controlConfig))
+


You'll need to rebase onto the current develop when you get a chance. After doing that, it will be important to fix this typo that got fixed elsewhere in this file.

Suggested change

analyses.append(ocean.OsnapTransects(config, oceanClimatolgyTasks['avg'],

controlConfig))

analyses.append(ocean.OsnapTransects(config, oceanClimatologyTasks['avg'],

controlConfig))

xylar

Things are looking great!

I ran the test suite and results are here:
https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.xasay-davis/analysis_testing/chrysalis/add_OSNAP_TSclimtransects/

In addition to a couple of very small code changes, the only thing left (other than the check-list at the top of this PR for me) are:

add the task to the API docs here: https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.xasay-davis/analysis_testing/chrysalis/add_OSNAP_TSclimtransects/
add a new file to the docs for this analysis (with an example image), similar to: https://github.com/MPAS-Dev/MPAS-Analysis/blob/develop/docs/users_guide/tasks/woceTransects.rst

xylar · 2022-12-07T11:00:17Z

mpas_analysis/ocean/osnap_transects.py

+
+from mpas_analysis.shared.io.utility import build_obs_path
+
+from collections import OrderedDict


Suggested change

from collections import OrderedDict

Let's take this out. I'm sure it was copied from elsewhere in MPAS-Analysis but it's an old concept from pyhton 2.7. In python 3, the default dict is ordered (whereas in python 2, it could end up being in random order).

It doesn't look like it's actually used anyway.

xylar · 2022-12-07T11:09:15Z

mpas_analysis/ocean/osnap_transects.py

+ The task that produced the climatology to be remapped and plotted
+ as a transect
+
+ controlconfig : mpas_tools.config.MpasConfigParser, optional


Incorrect capitalization (no doubt my fault, copied from elsewhere).

Suggested change

controlconfig : mpas_tools.config.MpasConfigParser, optional

controlConfig : mpas_tools.config.MpasConfigParser, optional

xylar · 2022-12-07T11:09:35Z

mpas_analysis/ocean/osnap_transects.py

+ """
+ # Authors
+ # -------
+ # Xylar Asay-Davis


Suggested change

# Xylar Asay-Davis

# Alice Barthel

xylar · 2022-12-07T12:32:30Z

mpas_analysis/obs/observational_datasets.xml

+ ocean
+ </component>
+ <description>
+ OSNAP,designed to provide a continuous record of the full-water column, trans-basin fluxes of heat, mass and freshwater in the subpolar North Atlantic,consists oftwo legs: one extending from southern Labrador to the southwestern tip of Greenland across the mouth of the Labrador Sea (OSNAP West), and the second from the southeastern tip of Greenland to Scotland (OSNAP East). The observing system also includes subsurface floats (OSNAP Floats) in order to trace the pathways of overflow waters in the basin and to assess the connectivity of currents crossing the OSNAP line. The location of the OSNAP East and West legs purposefully melds with a number of long-term observational efforts in the North Atlantic: the Canadian repeat AR7W program in the Labrador Sea; the German Labrador Sea western boundary array at 53°N; the global Ocean Observatories Initiative node to be placed in the southwestern Irminger Sea; the repeat A1E/AR7E hydrographic sections across the Irminger and Iceland basins; and the Ellett line in the Rockall region. Importantly, this observing system, in conjunction with the RAPID/MOCHA array at 26ºNand the EU THOR/NACLIM program, will provide a comprehensive measure of the Atlantic Meridional Overturning Circulation (AMOC) and provide a means to evaluate intergyre connectivity in the North Atlantic. OSNAP is a collaborative effort, which includes several countries including US, Canada, China, France, Germany, Netherlands and the UK.


Could you split this across several lines for simplicity? There seems to be a Nand that should be N and.

Please take a look at:
https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.xasay-davis/analysis_testing/chrysalis/add_OSNAP_TSclimtransects/docs/users_guide/obs/osnap_t_s.html#osnap-t-s
and make sure the resulting output looks like it should. It looks good to me other than the missing space I pointed out above.

xylar · 2022-12-07T12:51:29Z

I ran analysis on CRYO1950.ne30pg2_SOwISC12to60E2r4.N2Dependent.smep and it worked great:
https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.xylar/analysis/20221116.CRYO1950.ne30pg2_SOwISC12to60E2r4.N2Dependent.submeso.chrysalis/yrs121-130/ocean/index.html
It seems like we either have giant temperature biases in that run (very believable) or the bias plot has a pretty narrow range. What do you both think?

milenaveneziani · 2022-12-07T18:03:02Z

hmm, a bias of 2deg is pretty high in those regions.. We could extend the range to +-3 for the bias.

Do you understand why the range above 0 (in the vertical) is plotted?

@alicebarthel : no, I computed the sigma0's myself. They were not in the obs data set I used.

milenaveneziani · 2022-12-07T18:03:47Z

But I agree this is looking great. Thanks @alicebarthel!

xylar · 2022-12-07T19:31:39Z

Do you understand why the range above 0 (in the vertical) is plotted?

@milenaveneziani, I think that's because it plots up to the actual sea surface height, which goes at least slightly above zero. It doesn't bound the data range too tightly but instead leaves a little margin of error around it. We can manually set the vertical range in the config options if this bugs you.
https://github.com/alicebarthel/MPAS-Analysis/blob/add_OSNAP_TSclimtransects/mpas_analysis/default.cfg#L2619

milenaveneziani · 2022-12-07T20:47:16Z

yes, I would probably add vertical_bounds. Maybe 0 to -4000?
Thanks for reminding me about this option @xylar.

milenaveneziani · 2022-12-08T15:54:47Z

@alicebarthel: I think you can remove the WIP in the title and work in progress label for this one :)

alicebarthel added 2 commits September 23, 2022 14:33

mirrored woce_transects into osnap_transects

e271e20

added OSNAP ref to datasets.xml - first draft

72f9f0b

alicebarthel requested review from milenaveneziani and xylar September 23, 2022 20:32

milenaveneziani added enhancement work in progress labels Sep 24, 2022

alicebarthel added 3 commits September 26, 2022 11:46

changed file name for osnap

fe75a6a

added task in main

644ef52

added osnap section for plots in default.cfg -- FIRST DRAFT

2f70cf4

xylar reviewed Sep 26, 2022

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xylar added this to In progress in v1.8.0 via automation Oct 13, 2022

xylar self-assigned this Oct 13, 2022

xylar removed this from In progress in v1.8.0 Nov 24, 2022

updated .cfg file - DEBUGGING

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xylar reviewed Dec 7, 2022

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WIP: Add osnap T S climtransects #899

WIP: Add osnap T S climtransects #899

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milenaveneziani commented Dec 8, 2022

		analyses.append(ocean.OsnapTransects(config, oceanClimatolgyTasks['avg'],
		controlConfig))


		from mpas_analysis.shared.io.utility import build_obs_path

		from collections import OrderedDict

	controlconfig : mpas_tools.config.MpasConfigParser, optional
	controlConfig : mpas_tools.config.MpasConfigParser, optional

WIP: Add osnap T S climtransects #899

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WIP: Add osnap T S climtransects #899

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