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Fix ISOMIP+ viz scripts#642

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mark-petersen merged 1 commit intoMPAS-Dev:ocean/developfrom
xylar:update_grizzly_example
Aug 18, 2020
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Fix ISOMIP+ viz scripts#642
mark-petersen merged 1 commit intoMPAS-Dev:ocean/developfrom
xylar:update_grizzly_example

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@xylar xylar commented Jul 30, 2020 •
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This merge fixes a few complaints from xarray in the ISOMIP+ viz package.

@xylar xylar added COMPASS Documentation only Changes that impact code comments and documentation, but no executable code labels Jul 30, 2020
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xylar commented Jul 30, 2020

@cbegeman, once you join this repo, I will add you as a reviewer.

@xylar xylar requested a review from cbegeman August 1, 2020 08:37
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xylar commented Aug 7, 2020

@cbegeman pointed out and I confirmed that we're seeing the following error during the runs, seemingly related to appending to timeSeriesStatsGlobal:

PIO: ERROR: Changing the define mode for file (analysis_members/globalStats.0001-01-01_00.00.00.nc) failed. Low-level I/O library API failed. NetCDF: Operation not allowed in data mode (error num=-38), (/usr/projects/climate/SHARED_CLIMATE/software/grizzly/pio/1.10.1/intel-19.0.4/openmpi-2.1.2/scorpio/src/clib/pioc_support.c:3163)

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xylar commented Aug 7, 2020

I'm seeing warnings in the viz:

/lustre/scratch4/turquoise/.mdt1/xylar/isomip_plus_Ocean0/ocean/isomip_plus/2km/Ocean0/forward/viz/__main__.py:39: FutureWarning: In xarray version 0.15 the default behaviour of `open_mfdataset`
will change. To retain the existing behavior, pass
combine='nested'. To use future default behavior, pass
combine='by_coords'. See
http://xarray.pydata.org/en/stable/combining.html#combining-multi

  ds = xarray.open_mfdataset('{}/timeSeriesStatsMonthly*.nc'.format(folder),

This is, indeed, something that needs to be fixed. We just need to add combine='nested' to all the open_mfdataset() calls.

@xylar xylar added Ocean clean-up and removed Documentation only Changes that impact code comments and documentation, but no executable code labels Aug 7, 2020
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xylar commented Aug 12, 2020

@cbegeman, I realized that this update is silly. I already put this tutorial into the documentation, and that is where it should be updated. I'm going to make a PR for that instead.

@xylar xylar closed this Aug 12, 2020
@xylar xylar reopened this Aug 12, 2020
@xylar xylar changed the title Update ISOMIP+ readme Fix ISOMIP+ viz scripts Aug 12, 2020
@xylar xylar force-pushed the update_grizzly_example branch from b727055 to c98ef5b Compare August 12, 2020 15:42
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xylar commented Aug 12, 2020

We still want the fixes to the viz package here. The rest has been replaced with #653

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mark-petersen commented Aug 17, 2020 •
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@cbegeman can you confirm that this fixes the problem you encountered? If so, click the green approve button on the top.

@mark-petersen mark-petersen force-pushed the update_grizzly_example branch from c98ef5b to fc13e03 Compare August 18, 2020 11:58
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mark-petersen commented Aug 18, 2020

Rebased. This is so small, I'll go ahead and merge with the bunch this morning.

@mark-petersen mark-petersen requested review from mark-petersen and removed request for cbegeman August 18, 2020 11:59
@mark-petersen mark-petersen merged commit e40561b into MPAS-Dev:ocean/develop Aug 18, 2020
mark-petersen added a commit that referenced this pull request Aug 18, 2020
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Merge branch 'ocean/develop' into e3sm/develop
805bba1 
* ocean/develop:
Fix ISOMIP+ viz scripts #642
Add support for custom critical passages and land blockages #586
New Mesh: WC12to60kmL60E3SMv2r01 #555
@mark-petersen mark-petersen mentioned this pull request Aug 18, 2020
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jonbob added a commit to E3SM-Project/E3SM that referenced this pull request Aug 18, 2020
@jonbob
Merge branch 'mark-petersen/update_mpas_200817' into next (PR #3776)
72e0ed9 
Update MPAS-Source: COMPASS and Documentation files

This PRi brings in a new mpas-source submdoule with changes only to the ocean
core. It updates files unrelated to the E3SM forward model, including:
* Move load_compass_env.sh to the ocean dir  (MPAS-Dev/MPAS-Model#618);
* Update ISOMIP+ docs, including tutorial for Ocean0 on LANL IC
  (MPAS-Dev/MPAS-Model#653);
* Fix path to docs in Travis CI  (MPAS-Dev/MPAS-Model#644);
* atmosphere core init changes  (MPAS-Dev/MPAS-Model#637);
* New Mesh: WC14to60kmL60E3SMv2r03  (MPAS-Dev/MPAS-Model#628);
* Fix ISOMIP+ viz scripts  (MPAS-Dev/MPAS-Model#642);
* Add support for custom critical passages and land blockages
  (MPAS-Dev/MPAS-Model#586); and
* New Mesh: WC12to60kmL60E3SMv2r01  (MPAS-Dev/MPAS-Model#555)

[BFB]
jonbob added a commit to E3SM-Project/E3SM that referenced this pull request Aug 19, 2020
@jonbob
Merge branch 'mark-petersen/update_mpas_200817' (PR #3776)
b84ab6c 
Update MPAS-Source: COMPASS and Documentation files

This PR brings in a new mpas-source submdoule with changes only to the ocean
core. It updates files unrelated to the E3SM forward model, including:
* Move load_compass_env.sh to the ocean dir  (MPAS-Dev/MPAS-Model#618);
* Update ISOMIP+ docs, including tutorial for Ocean0 on LANL IC
  (MPAS-Dev/MPAS-Model#653);
* Fix path to docs in Travis CI  (MPAS-Dev/MPAS-Model#644);
* atmosphere core init changes  (MPAS-Dev/MPAS-Model#637);
* New Mesh: WC14to60kmL60E3SMv2r03  (MPAS-Dev/MPAS-Model#628);
* Fix ISOMIP+ viz scripts  (MPAS-Dev/MPAS-Model#642);
* Add support for custom critical passages and land blockages
  (MPAS-Dev/MPAS-Model#586); and
* New Mesh: WC12to60kmL60E3SMv2r01  (MPAS-Dev/MPAS-Model#555)

[BFB]
@xylar xylar deleted the update_grizzly_example branch August 21, 2020 11:40
caozd999 pushed a commit to caozd999/MPAS-Model that referenced this pull request Jan 14, 2021
@mark-petersen
Merge PR MPAS-Dev#642 'xylar/update_grizzly_example' into ocean/develop
f5412d4 
Fix ISOMIP+ viz scripts MPAS-Dev#642

This merge fixes a few complaints from xarray in the ISOMIP+ viz
package.
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