New mesh: EC30to60kmL60E3SMv2r03 and change to gebco bathymetry by vanroekel · Pull Request #669 · MPAS-Dev/MPAS-Model

vanroekel · 2020-08-26T20:28:44Z

This PR bumps to revision 3 and uses the GEBCO bathymetry for EC6030, consistent with the 6030wISC

vanroekel · 2020-08-26T20:29:21Z

NOTE: this PR depends on #668

vanroekel · 2020-08-26T20:30:15Z

testing_and_setup/compass/ocean/global_ocean/EC60to30/init/config_E3SM_coupling_files.ini

@xylar I thought it would be good to add bathymetry to the metadata. I don't think this is the greatest phrasing though. I'd appreciate any suggestions.

I totally agree. Maybe add it in the other PR, too, if you haven't already.

vanroekel · 2020-08-26T20:31:02Z

I've decided to make local copies of config_initial_state.xml into EC6030 here so the change to GEBCO bathymetry only affects EC6030 for now.

vanroekel · 2020-08-27T18:21:56Z

@mark-petersen I just successfully ran the 6030 spinup start to finish with this PR. Test directory is here

/lustre/scratch4/turquoise/lvanroekel/EC6030v2_1900/ocean/global_ocean/EC60to30/

xylar · 2020-08-27T18:41:48Z

testing_and_setup/compass/ocean/global_ocean/EC60to30/init/config_initial_state_64_layers.xml

tabbing isn't right here.

Same with the other file but GitHub is glitching and won't let me comment on it.

testing_and_setup/compass/ocean/global_ocean/EC60to30/init/config_initial_state_64_layer.xml

xylar · 2020-09-04T12:57:42Z

GitHub is glitching and won't let me comment on the lines I want to. This refers to:
https://github.com/vanroekel/MPAS-Model/blob/ocean/updateEC6030_add_GEBCO_bathymetry/testing_and_setup/compass/ocean/global_ocean/EC60to30/init/config_initial_state.xml#L15-L17

@vanroekel, this needs to come from the bathymetry_database, not the initial_condition_database, as the path on LCRC indicates:

<get_file dest_path="bathymetry_database" file_name="BedMachineAntarctica_and_GEBCO_2019_0.05_degree.200128.nc">

xylar · 2020-09-04T13:25:56Z

@vanroekel, I'm going to push a fix to this branch. I hope that's okay.

xylar

With my last fix where the topography is from the bathymetry_database and rebasing off of #668 (and stealing the base_mesh and culled_mesh steps from my testing of that PR), I was able to run successfully through the simulation step. My results are in:

/lustre/scratch4/turquoise/xylar/test_EC30to60kmL60E3SMv2r03_link

I'm re-testing without the symlinks to base_mesh and culled_mesh here:

/lustre/scratch4/turquoise/xylar/test_EC30to60kmL60E3SMv2r03

but that will take awhile still.

The E3SM coupling step is still running but seems to be working so far:

****** Creating E3SM coupling files ******
- ice_shelf_cavities set to False
- author's name autodetected from git config: Xylar Asay-Davis
- author's name specified in config file: xylar@lanl.gov
- date string autodetected from today's date: 200904
- creation date autodetected from today's date: 09/04/2020 07:57:13
- maximum ocean depth autodetected mesh file: 5500.0
- number of vertical levels in the ocean autodetected mesh file: 60
- mesh long name specified in config file: EC30to60kmL60E3SMv2r03
- mesh short name specified in config file: EC30to60E2r03

Some example plots from the restart file at the end of the spin-up:

xylar · 2020-09-04T15:17:18Z

I think this one will need to be rebased after #668 goes in. I'm getting merge conflicts when I try to just merge it.

vanroekel · 2020-09-04T17:29:49Z

@xylar, thanks so much for the fix. I'll take care of the rebase after #668 is in.

xylar · 2020-09-04T17:45:37Z

Oh, okay, @vanroekel, can you rebase this onto ocean/develop now so the PR gives us a clean record of the changes just for this PR?

xylar · 2020-09-04T18:38:14Z

I rebased this onto ocean/develop on Cori and reran everything but base_mesh and culled_mesh. It ran fine, so I think this is good to merge as soon as @vanroekel rebases.

mark-petersen · 2020-09-04T20:49:35Z

Spun up with gnu 5.3.0 on grizzly.

/lustre/scratch3/turquoise/mpeterse/runs/200904_EC30to60kmL60E3SMv2r03_PR669_prelim_gnu5_gr/ocean/global_ocean/EC60to30

Looking more carefully at the layers here since this is a bathymetry change. Everything looks good.

mesh and IC

fields after spin-up, 20 days in

mark-petersen · 2020-09-05T03:06:50Z

@vanroekel I was testing again, so I went ahead an rebased it.

mark-petersen

Based on my testing, this all looks good.

vanroekel · 2020-09-05T03:11:13Z

thank you @mark-petersen! I was just about to get to this.

New Mesh: EC30to60kmL60E3SMv2r02 and change to 60 layers as default #668 New mesh: EC30to60kmL60E3SMv2r03 and change to gebco bathymetry #669 Fix validation for QU240 test step #660 Change block tests to partition tests for QU240 RK4 and SE #657 Update to version 0.1.11 of the compass environment #688

Update MPAS-Source: COMPASS and documentation only This PR brings in a new mpas-source submodule with changes only to the ocean core. The changes are limited to internal coupling and documentation so it should have no impact on E3SM. It includes: * new EC30to60kmL60E3SMv2r02 mesh with 60 layers as default (MPAS-Dev/MPAS-Model/pull/668) * new EC30to60kmL60E3SMv2r03 mesh with change to gebco bathymetry (MPAS-Dev/MPAS-Model/pull/669) * switch from Travis-CI to Azure Pipelines (MPAS-Dev/MPAS-Model/pull/681) * fix validation for QU240 test step (MPAS-Dev/MPAS-Model/pull/660) * change block tests to partition tests for QU240 RK4 and SE (MPAS-Dev/MPAS-Model/pull/657) * update to version 0.1.11 of the compass environment (MPAS-Dev/MPAS-Model/pull/688) [BFB]

pdate MPAS-Source: COMPASS and documentation only This PR brings in a new mpas-source submodule with changes only to the ocean core. The changes are limited to internal coupling and documentation so it should have no impact on E3SM. It includes: * new EC30to60kmL60E3SMv2r02 mesh with 60 layers as default (MPAS-Dev/MPAS-Model/pull/668) * new EC30to60kmL60E3SMv2r03 mesh with change to gebco bathymetry (MPAS-Dev/MPAS-Model/pull/669) * switch from Travis-CI to Azure Pipelines (MPAS-Dev/MPAS-Model/pull/681) * fix validation for QU240 test step (MPAS-Dev/MPAS-Model/pull/660) * change block tests to partition tests for QU240 RK4 and SE (MPAS-Dev/MPAS-Model/pull/657) * update to version 0.1.11 of the compass environment (MPAS-Dev/MPAS-Model/pull/688) [BFB]

xylar · 2020-09-14T18:03:48Z

Just a quick note that I realize in a conversation with @vanroekel that this mesh does not include a switch from the Bedmap2 to the BedMachine Antarctic coastline. This will lead to differences between the coastline in this mesh and a corresponding ECwISC30to60 mesh. I'll try to not that in the corresponding PR as well.

xylar · 2020-09-15T08:47:47Z

What I said is not correct. It turns out (for better or for worse) that I changed the coastline to BedMachine for all meshes in #433. I don't quite know how that happened without me noticing. But it means the EC30to60km and ECwISC30to60km meshes are more similar than they would otherwise be. For the current plan of making the two as similar as possible, I think this is a good thing. But I really wish this had happened on purpose in #433...

mark-petersen · 2022-06-10T17:23:16Z

Adding this here for future reference

vanroekel added Ocean COMPASS mesh labels Aug 26, 2020

vanroekel requested a review from xylar August 26, 2020 20:28

vanroekel marked this pull request as draft August 26, 2020 20:28

vanroekel commented Aug 26, 2020

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vanroekel mentioned this pull request Aug 27, 2020

New Mesh: EC30to60kmL60E3SMv2r04 and add 1900 state estimate initial condition #671

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xylar reviewed Aug 27, 2020

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vanroekel force-pushed the ocean/updateEC6030_add_GEBCO_bathymetry branch from c9ccc8c to 2409464 Compare August 27, 2020 19:30

vanroekel commented Aug 27, 2020

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testing_and_setup/compass/ocean/global_ocean/EC60to30/init/config_initial_state_64_layer.xml Outdated Show resolved Hide resolved

This was referenced Sep 1, 2020

Updating COMPASS ocean test cases based on mpas_tools reorg #577

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Update Earth radius to the CIME value #680

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vanroekel marked this pull request as ready for review September 3, 2020 21:47

xylar mentioned this pull request Sep 4, 2020

New Mesh: EC30to60kmL60E3SMv2r02 and change to 60 layers as default #668

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xylar reviewed Sep 4, 2020

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testing_and_setup/compass/ocean/global_ocean/EC60to30/init/config_initial_state_64_layer.xml Outdated Show resolved Hide resolved

xylar approved these changes Sep 4, 2020

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xylar force-pushed the ocean/updateEC6030_add_GEBCO_bathymetry branch 2 times, most recently from 58cc382 to 5a456b4 Compare September 4, 2020 16:17

mark-petersen self-assigned this Sep 4, 2020

mark-petersen self-requested a review September 4, 2020 17:08

vanroekel and others added 6 commits September 4, 2020 21:04

Updates EC6030 mesh to use GEBCO bathymetry

cdeb66b

Fixes symlink to gebco data

4ae89e6

Fixes GEBCO related namelist options

607f080

Fixes formatting

45f9450

Fix tabbing

c4ebf64

Fix bathymetry links

b4acb79

mark-petersen force-pushed the ocean/updateEC6030_add_GEBCO_bathymetry branch from 5a456b4 to b4acb79 Compare September 5, 2020 03:06

mark-petersen approved these changes Sep 5, 2020

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mark-petersen merged commit 9024df6 into MPAS-Dev:ocean/develop Sep 5, 2020

mark-petersen mentioned this pull request Sep 8, 2020

Update MPAS-Source: fix Rayleigh damping and line continuation E3SM-Project/E3SM#3817

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mark-petersen mentioned this pull request Sep 9, 2020

Update MPAS-Source: COMPASS and documentation only E3SM-Project/E3SM#3818

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xylar mentioned this pull request Sep 15, 2020

New Mesh: ECwISC30to60kmL60E3SMv2r01 and add 1900 state estimate initial condition #694

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xylar mentioned this pull request Nov 6, 2020

New Mesh: ECwISC30to60kmL60E3SMv2r01 and add 1900 state estimate initial condition MPAS-Dev/compass#15

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matthewhoffman added COMPASS mesh Ocean labels Mar 17, 2021

vanroekel mentioned this pull request Mar 10, 2023

Current EC30to60 ocean/ice initial condition should have bumped revision number E3SM-Project/E3SM#5516

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xylar mentioned this pull request Mar 12, 2023

Add metadata in files_for_e3sm for existing meshes MPAS-Dev/compass#560

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