Merge pull request #609 from MPAS-Dev/develop

Merge develop to master
MPAS-Dev · Jul 12, 2019 · b87d99b · b87d99b
2 parents 4cc4ace + 3ffc88f
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diff --git a/README.md b/README.md
@@ -41,28 +41,31 @@ environment with the following packages:
 
  * numpy
  * scipy
- * matplotlib >= 3.2.0
+ * matplotlib >= 3.0.2
  * netCDF4
  * xarray >= 0.10.0
  * dask
  * bottleneck
  * basemap
  * lxml
- * nco >= 4.7.9
+ * nco >= 4.8.1
  * pyproj
  * pillow
  * cmocean
  * progressbar2
  * requests
  * setuptools
  * shapely
+ * cartopy
+ * geometric\_features
 
 These can be installed via the conda command:
 ``` bash
 conda config --add channels conda-forge
 conda create -n mpas-analysis numpy scipy matplotlib netCDF4 \
-    xarray dask bottleneck basemap lxml nco pyproj pillow \
-    cmocean progressbar2 requests setuptools shapely
+    xarray dask bottleneck basemap lxml nco>=4.8.1 pyproj pillow \
+    cmocean progressbar2 requests setuptools shapely cartopy \
+    geometric_features
 conda activate mpas-analysis
 ```
 
@@ -98,6 +101,40 @@ Once you have downloaded the analysis data, you will point to its location
 (your equivalent of `path/to/mpas_analysis/diagnostics` above) in the config
 option `baseDirectory` in the `[diagnostics]` section.
 
+## Download Natural Earth data for cartopy
+
+The cartopy package (used for creating inset maps) requires shapes of the land,
+ocean and coastline from [Natural Earth](https://www.naturalearthdata.com).
+Typically, these data are downloaded automatically by cartopy.  However, for
+systems with compute nodes that cannot reach the internet, you will need to
+download the data manually into your conda environment from a login node before
+launching any MPAS-Analysis jobs:
+
+```
+download_natural_earth_110m
+```
+(or if using the git repo: `./download_natural_earth_110m.py`).
+
+If the data have already been downloaded, you will see nothing.  Otherwise, you
+should see a warning that the data are being downloaded.
+
+**Note**: If you are having issues downloading the shape files (e.g., a time out error or forbidden error), follow these steps:
+
+1. Run the following in python on your local machine (i.e., one that has no trouble downloading these files):
+```python
+import cartopy.io.shapereader as shpreader
+for name in ['ocean', 'coastline', 'land']:
+    shpfilename = shpreader.natural_earth(resolution='110m',
+                                          category='physical',
+                                          name=name)
+    reader = shpreader.Reader(shpfilename)
+```
+2. On your local machine, run `python -c "import cartopy; print(cartopy.config['data_dir'])"`. This will print out the directory in which the natural earth shapefiles are being placed locally.
+3. Copy these files onto the remote machine you are working on. Include folders `shapefiles/natural_earth/physical/*` where `*` is the set of shapefiles that were downloaded.
+4. On your remote machine, run `python -c "import cartopy; print(cartopy.config['data_dir'])"`. Copy the `shapefiles` folder and all contents over to this location.
+5. `cartopy` should now be able to find these files for `MPAS-Analysis`.`
+
+
 ## List Analysis
 
 If you installed the `mpas-analysis` package, list the available analysis tasks

diff --git a/ci/requirements.yml b/ci/requirements.yml
@@ -12,10 +12,12 @@ dependencies:
   - netcdf4
   - hdf5
   - hdf4
-  - nco>=4.7.9
+  - nco>=4.8.1
   - pyproj
   - pillow
   - cmocean
   - progressbar2
   - requests
   - shapely
+  - cartopy
+  - geometric_features
diff --git a/configs/acme1/config.20180129.DECKv1b_piControl.ne30_oEC.edison b/configs/acme1/config.20180129.DECKv1b_piControl.ne30_oEC.edison
@@ -101,7 +101,8 @@ htmlSubdirectory = html
 #         all,no_ocean,all_timeSeries
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all_publicObs', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all_publicObs', 'no_landIceCavities', 'no_eke', 'no_BGC',
+            'no_icebergs', 'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/alcf/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta b/configs/alcf/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta
@@ -87,7 +87,7 @@ baseDirectory = /dir/to/analysis/output
 # option:
 #    mpas_analysis config.analysis --generate \
 #         all,no_ocean,all_timeSeries
-generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/alcf/config.20180410.A_WCYCL1950_HR.ne120_oRRS18v3_ICG.theta b/configs/alcf/config.20180410.A_WCYCL1950_HR.ne120_oRRS18v3_ICG.theta
@@ -96,7 +96,9 @@ baseDirectory = /projects/OceanClimate_2/yourUsername/path/here
 # option:
 #    mpas_analysis config.analysis --generate \
 #         all,no_ocean,all_timeSeries
-generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_timeSeriesAntarcticMelt', 'no_climatologyMapAntarcticMelt']
+generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs',
+            'no_timeSeriesAntarcticMelt', 'no_climatologyMapAntarcticMelt',
+            'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/alcf/config.20190301.GMPAS-DIB-IAF-ISMF.T62_oRRS30to10v3wLI.theta b/configs/alcf/config.20190301.GMPAS-DIB-IAF-ISMF.T62_oRRS30to10v3wLI.theta
@@ -87,7 +87,7 @@ baseDirectory = /projects/OceanClimate_2/yourUsername/path/here
 # option:
 #    mpas_analysis config.analysis --generate \
 #         all,no_ocean,all_timeSeries
-generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil b/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil
@@ -93,7 +93,8 @@ htmlSubdirectory = html
 #         all,no_ocean,all_timeSeries
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs',
+            'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/cori/config.20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl b/configs/cori/config.20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl
@@ -88,7 +88,7 @@ htmlSubdirectory = html
 # option:
 #    mpas_analysis config.analysis --generate \
 #         all,no_ocean,all_timeSeries
-generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/cori/config.20180129.DECKv1b_piControl.ne30_oEC.edison b/configs/cori/config.20180129.DECKv1b_piControl.ne30_oEC.edison
@@ -101,7 +101,8 @@ htmlSubdirectory = html
 #         all,no_ocean,all_timeSeries
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs',
+            'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/cori/config.20180209.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl.afterSalinityFix b/configs/cori/config.20180209.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl.afterSalinityFix
@@ -101,7 +101,7 @@ htmlSubdirectory = html
 #         all,no_ocean,all_timeSeries
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/cori/config.20180511.GMPAS-IAF.T62_oEC60to30v3wLI.edison b/configs/cori/config.20180511.GMPAS-IAF.T62_oEC60to30v3wLI.edison
@@ -101,7 +101,8 @@ htmlSubdirectory = html
 #         all,no_ocean,all_timeSeries
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_index']
+generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_index', 'no_min',
+            'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/cori/config.20180514.G.oQU240wLI.edison b/configs/cori/config.20180514.G.oQU240wLI.edison
@@ -101,7 +101,7 @@ htmlSubdirectory = html
 #         all,no_ocean,all_timeSeries
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/cori/config.20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl b/configs/cori/config.20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl
@@ -50,9 +50,9 @@ baseDirectory = /global/cscratch1/sd/dcomeau/acme_scratch/cori-knl/20190225.GMPA
 # subdirectory containing restart files
 runSubdirectory = run
 # subdirectory for ocean history files
-oceanHistorySubdirectory = run
+oceanHistorySubdirectory = /global/cscratch1/sd/dcomeau/acme_scratch/cori-knl/20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl/archive/ocn/hist
 # subdirectory for sea ice history files
-seaIceHistorySubdirectory = run
+seaIceHistorySubdirectory = /global/cscratch1/sd/dcomeau/acme_scratch/cori-knl/20190225.GMPAS-DIB-IAF-ISMF.T62_oEC60to30v3wLI.cori-knl/archive/ice/hist
 
 # names of ocean and sea ice meshes (e.g. oEC60to30v3, oQU240v3, oRRS30to10v3, etc.)
 mpasMeshName = oEC60to30v3wLI
@@ -103,7 +103,8 @@ htmlSubdirectory = html
 # All tasks with tag "BGC", "icebergs", "index", and "eke" are disabled because this run
 # did not include BGC or icebergs, the EKE analysis member was off and the El Nino analysis
 # is not meaningful (SSTs are prescribed).
-generate = ['all', 'no_BGC', 'no_icebergs', 'no_index', 'no_eke']
+generate = ['all', 'no_BGC', 'no_icebergs', 'no_index', 'no_eke', 'no_min',
+            'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/cori/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison b/configs/cori/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison
@@ -92,7 +92,7 @@ htmlSubdirectory = html
 # option:
 #    mpas_analysis config.analysis --generate \
 #         all,no_ocean,all_timeSeries
-generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/edison/job_script.edison.bash b/configs/edison/job_script.edison.bash
diff --git a/configs/lanl/config.CONUS.100km.NAEC60to30cr8.20181218 b/configs/lanl/config.CONUS.100km.NAEC60to30cr8.20181218
@@ -85,7 +85,7 @@ baseDirectory = /path/to/analysis/output
 generate = ['only_ocean', 'no_landIceCavities', 'no_mld', 'no_BGC',
             'no_meridionalHeatTransport', 'no_timeSeriesTemperatureAnomaly',
             'no_timeSeriesSalinityAnomaly', 'no_timeSeriesOHCAnomaly',
-            'no_timeSeriesSST', 'no_indexNino34']
+            'no_timeSeriesSST', 'no_indexNino34', 'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/lanl/config.MatchBoth_orig b/configs/lanl/config.MatchBoth_orig
@@ -89,7 +89,8 @@ baseDirectory = /dir/to/analysis/output
 #         all,no_ocean,all_timeSeries
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs',
+            'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/olcf/config.20170313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison b/configs/olcf/config.20170313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison
@@ -93,7 +93,8 @@ htmlSubdirectory = html
 #         all,no_ocean,all_timeSeries
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs',
+            'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/olcf/config.20170915.beta2.A_WCYCL1850S.ne30_oECv3_ICG.edison b/configs/olcf/config.20170915.beta2.A_WCYCL1850S.ne30_oECv3_ICG.edison
@@ -104,7 +104,8 @@ htmlSubdirectory = html
 # option:
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs',
+            'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan b/configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan
@@ -93,7 +93,8 @@ htmlSubdirectory = html
 #         all,no_ocean,all_timeSeries
 # All tasks with tag "landIceCavities" are disabled because this run did not
 # include land-ice cavities.
-generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs']
+generate = ['all', 'no_landIceCavities', 'no_eke', 'no_BGC', 'no_icebergs',
+            'no_min', 'no_max']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against

diff --git a/docs/.gitignore b/docs/.gitignore
@@ -3,3 +3,15 @@ generated
 quick_start.md
 all_obs.rst
 obs
+design_docs/analysis_task_template.rst
+design_docs/config_file_reorganization.rst
+design_docs/eddykineticenergy.rst
+design_docs/generalize_calendar.rst
+design_docs/generalized_horizontal_interpolation.rst
+design_docs/parallel_tasks.rst
+design_docs/prerequisite_tasks.rst
+design_docs/remapper.rst
+design_docs/template.rst
+design_docs/timekeeping_reorg.rst
+design_docs/variable_mapping_reorg.rst
+quick_start.rst
diff --git a/docs/analysis_tasks.rst b/docs/analysis_tasks.rst
@@ -5,6 +5,7 @@ Analysis Tasks
    :maxdepth: 1
 
    tasks/climatologyMapMLD
+   tasks/climatologyMapMLDMinMax
    tasks/climatologyMapSST
    tasks/climatologyMapSSS
    tasks/climatologyMapSSH
@@ -18,6 +19,7 @@ Analysis Tasks
    tasks/climatologyMapAntarcticMelt
 
    tasks/timeSeriesAntarcticMelt
+   tasks/timeSeriesOceanRegions
    tasks/timeSeriesTemperatureAnomaly
    tasks/timeSeriesSalinityAnomaly
    tasks/timeSeriesOHCAnomaly