Merge pull request #645 from MPAS-Dev/develop

Merge develop to master for v1.2.6 release

.travis.yml

@@ -7,18 +7,13 @@ notifications:
 matrix:
   fast_finish: true
   include:
-  - python: 2.7
   - python: 3.6
   - python: 3.7
     dist: xenial
     sudo: true
 
 before_install:
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r

README.md

@@ -39,6 +39,7 @@ conda activate mpas-analysis
 To use the latest version for developers, you will need to set up a conda
 environment with the following packages:
 
+ * python >= 3.6
  * numpy
  * scipy
  * matplotlib >= 3.0.2
@@ -59,14 +60,15 @@ environment with the following packages:
  * cartopy
  * geometric\_features
  * gsw
+ * pyremap
 
 These can be installed via the conda command:
 ```
 conda config --add channels conda-forge
 conda create -n mpas-analysis python=3.7 numpy scipy "matplotlib>=3.0.2" \
     netCDF4 "xarray>=0.10.0" dask bottleneck basemap lxml "nco>=4.8.1" pyproj \
     pillow cmocean progressbar2 requests setuptools shapely cartopy \
-    geometric_features gsw
+    geometric_features gsw pyremap
 conda activate mpas-analysis
 ```
 

ci/requirements.yml

@@ -22,3 +22,4 @@ dependencies:
   - cartopy
   - geometric_features
   - gsw
+  - pyremap

configs/README.md

@@ -9,3 +9,14 @@ the output `baseDirectory`) and using them to run the analysis.
 To run tasks in parallel via a job queue, copy and modify the machine-specific
 job script or the default job script.
 
+## Analysis focused on polar regions
+
+For analysis such as E3SM cryosphere simulations that is focused on polar
+regions, include polarRegions.conf *before* your custom config file on the
+command line.
+
+Example:
+```
+python -m mpas_analysis configs/polarRegions.conf my_favorite.conf --generate=climatologyMapSSH --purge
+```
+

configs/alcf/config.20190301.GMPAS-DIB-IAF-ISMF.T62_oRRS30to10v3wLI.theta → configs/alcf/20190405.GMPAS-DIB-IAF-ISMF.T62_oRRS30to10v3wLI.theta.yrs41-50.conf

@@ -3,7 +3,7 @@
 ## compared against
 
 # mainRunName is a name that identifies the simulation being analyzed.
-mainRunName = 20190301.GMPAS-DIB-IAF-ISMF.T62_oRRS30to10v3wLI.theta
+mainRunName = 20190405.GMPAS-DIB-IAF-ISMF.T62_oRRS30to10v3wLI.theta
 
 # config file for a control run to which this run will be compared.  The
 # analysis should have already been run to completion once with this config
@@ -23,7 +23,7 @@ mainRunName = 20190301.GMPAS-DIB-IAF-ISMF.T62_oRRS30to10v3wLI.theta
 ## options related to executing parallel tasks
 
 # the number of parallel tasks (1 means tasks run in serial, the default)
-parallelTaskCount = 8
+parallelTaskCount = 12
 
 # the parallelism mode in ncclimo ("serial" or "bck")
 # Set this to "bck" (background parallelism) if running on a machine that can
@@ -45,7 +45,7 @@ baseDirectory = /lus/theta-fs0/projects/ClimateEnergy_3/diagnostics
 ## options related to reading in the results to be analyzed
 
 # directory containing model results
-baseDirectory = /lus/theta-fs0/projects/OceanClimate_2/outputForExampleThetaAnalysisConfigs/20190301.GMPAS-DIB-IAF-ISMF.T62_oRRS30to10v3wLI.theta/run
+baseDirectory = /lus/theta-fs0/projects/OceanClimate_2/sprice/20190405.GMPAS-DIB-IAF-ISMF.T62_oRRS30to10v3wLI.theta/run
 
 # names of ocean and sea ice meshes (e.g. oEC60to30v3, oQU240v3, oRRS30to10v3, etc.)
 mpasMeshName = oRRS30to10v3wLI
@@ -62,10 +62,9 @@ seaIceStreamsFileName = streams.seaice
 ## etc.
 
 # directory where analysis should be written (**** MAKE SURE TO UPDATE WITH YOUR PREFERRED PATH ***)
-baseDirectory = /projects/OceanClimate_2/yourUsername/path/here
+baseDirectory = /projects/ClimateEnergy_3/yourUsername/path/here
 
-# a list of analyses to generate.  Valid names can be seen by running:
-#   mpas_analysis --list
+# a list of analyses to generate.  Valid names can be seen by running:#   mpas_analysis --list
 # This command also lists tags for each analysis.
 # Shortcuts exist to generate (or not generate) several types of analysis.
 # These include:
@@ -87,7 +86,7 @@ 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', 'no_min', 'no_max']
+generate = ['all', 'no_BGC', 'no_icebergs', 'no_min', 'no_max' ]
 
 [climatology]
 ## options related to producing climatologies, typically to compare against
@@ -97,9 +96,20 @@ generate = ['all', 'no_eke', 'no_BGC', 'no_icebergs', 'no_min', 'no_max']
 useNcclimo = False
 
 # the first year over which to average climatalogies
-startYear = 1
+startYear = 41
 # the last year over which to average climatalogies
-endYear = 2
+endYear = 50
+
+# if useNcclimo = False, the number of threads dask is allowed to spawn for each# process computing a climatology for a given month or season
+# Decrease this number if mpasClimatology* subtasks are running
+# out of available threads
+daskThreads = 2
+
+# if useNcclimo = False, the number of subprocesses that each climatology
+# subtask gets counted as occupying.
+# Increase this number if mpasClimatology* subtasks are running
+# out of memory, and fewer tasks will be allowed to run at once
+subprocessCount = 2
 
 [timeSeries]
 ## options related to producing time series plots, often to compare against
@@ -109,7 +119,7 @@ endYear = 2
 #   like start_year = 1 and end_year = 9999 will be clipped to the valid range
 #   of years, and is a good way of insuring that all values are used.
 startYear = 1
-endYear = 2
+endYear = 50
 
 [index]
 ## options related to producing nino index.
@@ -119,7 +129,7 @@ endYear = 2
 #   of years, and is a good way of insuring that all values are used.
 # For valid statistics, index times should include at least 30 years
 startYear = 1
-endYear = 2
+endYear = 50
 
 [streamfunctionMOC]
 ## options related to plotting the streamfunction of the meridional overturning
@@ -132,3 +142,4 @@ endYear = 2
 # NOTE: this is a temporary option that will be removed once the online
 # MOC takes into account the bolus velocity when GM is on.
 usePostprocessingScript = True
+

configs/cori/config.20180511.GMPAS-IAF.T62_oEC60to30v3wLI.edison

@@ -132,3 +132,4 @@ endYear = 30
 # For valid statistics, index times should include at least 30 years
 startYear = 1
 endYear = 30
+

configs/cori/job_script.cori-haswell.bash

@@ -42,7 +42,9 @@ if [ ! -f $run_config_file ]; then
     exit 1
 fi
 
-srun -N 1 -n 1 python -m mpas_analysis $run_config_file
+# For an E3SM cryosphere run, include configs/polarRegions.conf, or exclude
+# this extra config file for defalut parameters
+srun -N 1 -n 1 python -m mpas_analysis configs/polarRegions.conf $run_config_file
 
 # If running from the conda package, use this instead:
 #srun -N 1 -n 1 mpas_analysis $run_config_file

configs/cori/job_script.cori-knl.bash

@@ -42,8 +42,10 @@ if [ ! -f $run_config_file ]; then
     exit 1
 fi
 
-# if using the mpas_analysis conda package instead of the git repo, remove
-# "python -m"
+# For an E3SM cryosphere run, include configs/polarRegions.conf, or exclude
+# this extra config file for defalut parameters
+srun -N 1 -n 1 python -m mpas_analysis configs/polarRegions.conf $run_config_file
 
-srun -N 1 -n 1 python -m mpas_analysis $run_config_file
+# if using the mpas_analysis conda package instead of the git repo
+# srun -N 1 -n 1 mpas_analysis $run_config_file
 

configs/polarRegions.conf

@@ -0,0 +1,143 @@
+[climatologyMapWoa]
+## options related to plotting climatology maps of Temperature and Salinity
+## fields at various levels, including the sea floor against control model
+## results and WOA climatological data
+
+# list of depths in meters (positive up) at which to analyze, 'top' for the
+# sea surface. Note that, for seasons='ANN', depths can be as deep as 5500 m,
+# otherwise use a maximum depth of 1500 m.
+depths = ['top', -50, -200, -400, -600, -800]
+
+[climatologyMapWoaTemperature]
+## options related to plotting climatology maps of potential temperature
+## at various levels, including the sea floor against control model results
+## and WOA18 climatological data
+
+# A dictionary with keywords for the norm
+normArgsResult = {'vmin': -2., 'vmax': 2.}
+
+[climatologyMapWoaSalinity]
+## options related to plotting climatology maps of salinity
+## at various levels, including the sea floor against control model results
+## and WOA18 climatological data
+
+# A dictionary with keywords for the norm
+normArgsResult = {'vmin': 33.8, 'vmax': 35.0}
+
+
+[TSDiagramsForAntarcticRegions]
+## options related to plotting T/S diagrams of Antarctic regions
+
+# The minimum and maximum depth over which fields are plotted, default is
+# to take these values from the geojson feature's zmin and zmax properties.
+zmin = -1000
+zmax = 0
+
+
+[soseTransects]
+## options related to plotting model vs. Southern Ocean State Estimate (SOSE)
+## transects.
+
+# longitudes of transects
+# Western Weddell 1, Filchner (318=42W), Western Weddell 2 (325=35W),
+# West Maud Rise, Fimbul (0), Amery (75E), Totten (117E),
+# George V coast, Merzt (145E), Wilkes (160E), Western Ross (184=176W),
+# Center Ross (187=173W), Eastern Ross (198=162W),
+# Amudsen, Thwaites (253=107W), Bellingshausen (280=80W),
+# West Antarctica (288=72W)
+# Note: Transects at 325, 145, 160, 184, 198 and 288 are chosen for comparison with
+#       Whitworth et al. (1998) doi: 10.1029/AR075p0001, Figs. 3, 7, 6, 5, 4, 10, respectively.
+longitudes = [318., 325., 0., 75., 117., 145., 160., 184., 187., 198., 253.,
+              280., 288.]
+
+[soseTemperatureTransects]
+# options related to plotting SOSE transects of potential temperature
+
+# whether the colormap is indexed or continuous
+colormapTypeResult = indexed
+# color indices into colormapName for filled contours
+colormapIndicesResult = [0, 14, 28, 57, 85, 113, 125, 142, 170, 180, 198, 227,
+                         240, 255]
+# colormap levels/values for contour boundaries
+colorbarLevelsResult = [-1.6, -1.2, -0.4, 0.0, 0.4, 0.6, 0.8, 1.0, 1.5, 2.0,
+                        3.0, 4.0, 6.0]
+
+# whether the colormap is indexed or continuous
+colormapTypeDifference = indexed
+# color indices into colormapName for filled contours
+colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227,
+                             255]
+# colormap levels/values for contour boundaries
+colorbarLevelsDifference = [-2, -1.5, -1.25, -1, -0.2, 0, 0.2, 1, 1.25, 1.5, 2]
+
+[soseSalinityTransects]
+## options related to plotting SOSE transects of salinity
+
+# whether the colormap is indexed or continuous
+colormapTypeResult = indexed
+# color indices into colormapName for filled contours
+colormapIndicesResult = [0, 20, 40, 80, 120, 140, 160, 180, 200, 220, 240, 255]
+# colormap levels/values for contour boundaries
+colorbarLevelsResult = [34.1, 34.2,  34.3,  34.4,  34.5, 34.55, 34.6, 34.65,
+                        34.68, 34.7, 35.0]
+
+# whether the colormap is indexed or continuous
+colormapTypeDifference = indexed
+# color indices into colormapName for filled contours
+colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227,
+                             255]
+# colormap levels/values for contour boundaries
+colorbarLevelsDifference = [-0.5, -0.2, -0.1, -0.05, -0.02, 0,  0.02, 0.05,
+                            0.1, 0.2, 0.5]
+
+
+[woceTransects]
+## options related to plotting model vs. World Ocean Circulation Experiment
+## (WOCE) transects.
+
+# 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
+horizontalBounds = {'WOCE_A21': [630., 830.],
+                    'WOCE_A23': [0., 200.],
+                    'WOCE_A12': [4620., 4820.]}
+
+[woceTemperatureTransects]
+## options related to plotting WOCE transects of potential temperature
+
+# whether the colormap is indexed or continuous
+colormapTypeResult = indexed
+# color indices into colormapName for filled contours
+colormapIndicesResult = [0, 14, 28, 57, 85, 113, 125, 142, 170, 180, 198, 227,
+                         240, 255]
+# colormap levels/values for contour boundaries
+colorbarLevelsResult = [-1.6, -1.2, -0.4, 0.0, 0.4, 0.6, 0.8, 1.0, 1.5, 2.0,
+                        3.0, 4.0, 6.0]
+
+# whether the colormap is indexed or continuous
+colormapTypeDifference = indexed
+# color indices into colormapName for filled contours
+colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227,
+                             255]
+# colormap levels/values for contour boundaries
+colorbarLevelsDifference = [-2, -1.5, -1.25, -1, -0.2, 0, 0.2, 1, 1.25, 1.5, 2]
+
+[woceSalinityTransects]
+## options related to plotting WOCE transects of salinity
+
+# whether the colormap is indexed or continuous
+colormapTypeResult = indexed
+# color indices into colormapName for filled contours
+colormapIndicesResult = [0, 20, 40, 80, 120, 140, 160, 180, 200, 220, 240, 255]
+# colormap levels/values for contour boundaries
+colorbarLevelsResult = [34.1, 34.2,  34.3,  34.4,  34.5, 34.55, 34.6, 34.65,
+                        34.68, 34.7, 35.0]
+
+# whether the colormap is indexed or continuous
+colormapTypeDifference = indexed
+# color indices into colormapName for filled contours
+colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227,
+                             255]
+# colormap levels/values for contour boundaries
+colorbarLevelsDifference = [-0.5, -0.2, -0.1, -0.05, -0.02, 0,  0.02, 0.05,
+                            0.1, 0.2, 0.5]

docs/api.rst

@@ -21,7 +21,7 @@ Top-level script: mpas_analysis
    update_generate
    run_analysis
    wait_for_task
- 
+
 Downloading data
 ================
 
@@ -221,25 +221,6 @@ Time Series
 
     MpasTimeSeriesTask
 
-Interpolation
--------------
-.. currentmodule:: mpas_analysis.shared.interpolation
-
-.. autosummary::
-   :toctree: generated/
-
-   Remapper
-
-.. currentmodule:: mpas_analysis.shared.grid
-
-.. autosummary::
-   :toctree: generated/
-
-   MpasMeshDescriptor
-   LatLonGridDescriptor
-   ProjectionGridDescriptor
-
-
 Namelist and Streams Files
 --------------------------
 .. currentmodule:: mpas_analysis.shared.io.namelist_streams_interface

docs/conf.py

@@ -76,9 +76,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.2.5'
+version = u'1.2.6'
 # The full version, including alpha/beta/rc tags.
-release = u'1.2.5'
+release = u'1.2.6'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.