Merge develop to master

README.md

@@ -27,12 +27,12 @@ available:
  * scipy
  * matplotlib
  * netCDF4
- * xarray >= 0.9.1
+ * xarray >= 0.10.0
  * dask
  * bottleneck
  * basemap
  * lxml
- * nco >= 4.6.8
+ * nco >= 4.7.0
  * pyproj
  * pillow
 
@@ -169,8 +169,7 @@ another machine to fit your needs.
 
 To generate the `sphinx` documentation, run:
 ```bash
-conda install sphinx sphinx_rtd_theme numpydoc
-pip install recommonmark
+conda install sphinx sphinx_rtd_theme numpydoc recommonmark
 cd docs
 make html
 ```

configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil

@@ -11,6 +11,13 @@ mainRunName = 20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil
 # MPAS-Analysis)
 preprocessedReferenceRunName = B1850C5_ne30_v0.4
 
+# config file for a reference run to which this run will be compared.  The
+# analysis should have already been run to completion once with this config
+# file, so that the relevant MPAS climatologies already exist and have been
+# remapped to the comparison grid.  Leave this option commented out if no
+# reference run is desired.
+# referenceRunConfigFile = /path/to/config/file
+
 [input]
 ## options related to reading in the results to be analyzed
 
@@ -36,37 +43,32 @@ baseDirectory = /dir/to/analysis/output
 # to be copied elsewhere (e.g. NERSC web portal)
 htmlSubdirectory = html
 
-# a list of analyses to generate.  Valid names are:
-#   'timeSeriesOHC', 'timeSeriesSST', 'climatologyMapSST',
-#   'climatologyMapSSS', 'climatologyMapMLD', 'streamfunctionMOC',
-#   'indexNino34', 'meridionalHeatTransport',
-#   'timeSeriesSeaIceAreaVol', 'climatologyMapSeaIceConcNH',
-#   'climatologyMapSeaIceConcSH', 'climatologyMapSeaIceThickNH',
-#   'climatologyMapSeaIceThickSH'
-# the following shortcuts exist:
+# a list of analyses to generate.  Valid names can be seen by running:
+#   ./run_mpas_analysis --list
+# This command also lists tags for each analysis.
+# Shortcuts exist to generate (or not generate) several types of analysis.
+# These include:
 #   'all' -- all analyses will be run
-#   'all_timeSeries' -- all time-series analyses will be run
-#   'all_climatology' -- all analyses involving climatologies
-#   'all_horizontalMap' -- all analyses involving horizontal climatology maps
-#   'all_ocean' -- all ocean analyses will be run
-#   'all_seaIce' -- all sea-ice analyses will be run
-#   'no_timeSeriesOHC' -- skip 'timeSeriesOHC' (and similarly with the
-#                             other analyses).
-#   'no_ocean', 'no_timeSeries', etc. -- in analogy to 'all_*', skip the
-#                                            given category of analysis
+#   'all_<tag>' -- all analysis with a particular tag will be run
+#   'all_<component>' -- all analyses from a given component (either 'ocean'
+#                        or 'seaIce') will be run
+#   'only_<component>', 'only_<tag>' -- all analysis from this component or
+#                                       with this tag will be run, and all
+#                                       analysis for other components or
+#                                       without the tag will be skipped
+#   'no_<task_name>' -- skip the given task
+#   'no_<component>', 'no_<tag>' -- in analogy to 'all_*', skip all analysis
+#                                   tasks from the given compoonent or with
+#                                   the given tag.  Do
+#                                      ./run_mpas_analysis --list
+#                                   to list all task names and their tags
 # an equivalent syntax can be used on the command line to override this
 # option:
 #    ./run_mpas_analysis config.analysis --generate \
 #         all,no_ocean,all_timeSeries
-generate = ['all']
-
-# alternative examples that would perform all analysis except
-#   'timeSeriesOHC'
-#generate = ['all', 'no_timeSeriesOHC']
-# Each subsequent list entry can be used to alter previous list entries. For
-# example, the following would run all tasks that aren't ocean analyses,
-# except that it would also run ocean time series tasks:
-#generate = ['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']
 
 [climatology]
 ## options related to producing climatologies, typically to compare against
@@ -136,10 +138,8 @@ baseDirectory = /lcrc/group/acme/mpas_analysis/ACMEv0_lowres/B1850C5_ne30_v0.4/i
 # plot on polar plot
 polarPlot = False
 
-[streamfunctionMOC]
-## options related to plotting the streamfunction of the meridional overturning
-## circulation (MOC)
-maxChunkSize = 1000
+[regions]
+## options related to ocean regions used in several analysis modules
 
-# Mask file for ocean basin regional computation
-regionMaskFiles = /lcrc/group/acme/mpas_analysis/region_masks/oEC60to30v3_Atlantic_region_and_southern_transect.nc
+# Directory for region mask files
+regionMaskDirectory = /global/project/projectdirs/acme/mapping/grids/

configs/anvil/job_script.anvil.bash

@@ -13,7 +13,7 @@ cd $PBS_O_WORKDIR
 
 # needed to prevent interference with acme-unified
 unset LD_LIBRARY_PATH
-soft add +acme-unified-1.1.1-nox
+soft add +e3sm-unified-1.1.2-nox
 
 # MPAS/ACME job to be analyzed, including paths to simulation data and
 # observations. Change this name and path as needed
@@ -54,7 +54,7 @@ ncclimoParallelMode = $ncclimo_mode
 EOF
 
 # first, perform setup only without mpirun to create the mapping files
-$mpas_analysis_dir/run_mpas_analysis --purge --setup_only $run_config_file \
+$mpas_analysis_dir/run_mpas_analysis --setup_only $run_config_file \
     $job_config_file
 # next, do the full run now tht we have mapping files, but this time launching
 # with mpirun

configs/cori/config.20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl

@@ -0,0 +1,186 @@
+[runs]
+## options related to the run to be analyzed and reference runs to be
+## compared against
+
+# mainRunName is a name that identifies the simulation being analyzed.
+mainRunName = 20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl
+# preprocessedReferenceRunName is the name of a reference run that has been
+# preprocessed to compare against (or None to turn off comparison).  Reference
+# runs of this type would have preprocessed results because they were not
+# performed with MPAS components (so they cannot be easily ingested by
+# MPAS-Analysis)
+preprocessedReferenceRunName = B1850C5_ne30_v0.4
+
+# config file for a reference run to which this run will be compared.  The
+# analysis should have already been run to completion once with this config
+# file, so that the relevant MPAS climatologies already exist and have been
+# remapped to the comparison grid.  Leave this option commented out if no
+# reference run is desired.
+# referenceRunConfigFile = /path/to/config/file
+
+[execute]
+## options related to executing parallel tasks
+
+# the number of parallel tasks (1 means tasks run in serial, the default)
+parallelTaskCount = 1
+
+# the parallelism mode in ncclimo ("serial" or "bck")
+# Set this to "bck" (background parallelism) if running on a machine that can
+# handle 12 simultaneous processes, one for each monthly climatology.
+ncclimoParallelMode = serial
+
+[input]
+## options related to reading in the results to be analyzed
+
+# directory containing model results
+baseDirectory = /global/cscratch1/sd/mpeterse/acme_scratch/20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl/run
+
+# names of ocean and sea ice meshes (e.g. EC60to30, QU240, RRS30to10, etc.)
+mpasMeshName = oRRS30to10v3wLI
+
+# Directory for mapping files (if they have been generated already). If mapping
+# files needed by the analysis are not found here, they will be generated and
+# placed in the output mappingSubdirectory
+mappingDirectory = /global/project/projectdirs/acme/mpas_analysis/mapping
+
+[output]
+## options related to writing out plots, intermediate cached data sets, logs,
+## etc.
+
+# directory where analysis should be written
+baseDirectory = /dir/to/analysis/output
+
+# provide an absolute path to put HTML in an alternative location (e.g. a web
+# portal)
+# htmlSubdirectory = /global/project/projectdirs/acme/www/USERNAME/RUNNAME
+htmlSubdirectory = html
+
+# a list of analyses to generate.  Valid names can be seen by running:
+#   ./run_mpas_analysis --list
+# This command also lists tags for each analysis.
+# Shortcuts exist to generate (or not generate) several types of analysis.
+# These include:
+#   'all' -- all analyses will be run
+#   'all_<tag>' -- all analysis with a particular tag will be run
+#   'all_<component>' -- all analyses from a given component (either 'ocean'
+#                        or 'seaIce') will be run
+#   'no_<task_name>' -- skip the given task
+#   'no_<component>', 'no_<tag>' -- in analogy to 'all_*', skip all analysis
+#                                   tasks from the given compoonent or with
+#                                   the given tag.  Do
+#                                      ./run_mpas_analysis --list
+#                                   to list all task names and their tags
+# an equivalent syntax can be used on the command line to override this
+# option:
+#    ./run_mpas_analysis config.analysis --generate \
+#         all,no_ocean,all_timeSeries
+generate = ['all']
+
+[climatology]
+## options related to producing climatologies, typically to compare against
+## observations and previous runs
+
+# the first year over which to average climatalogies
+startYear = 5
+# the last year over which to average climatalogies
+endYear = 10
+
+[timeSeries]
+## options related to producing time series plots, often to compare against
+## observations and previous runs
+
+# start and end years for timeseries analysis. Using out-of-bounds values
+#   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 = 10
+
+[index]
+## options related to producing nino index.
+
+# start and end years for the nino 3.4 analysis.  Using out-of-bounds values
+#   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.
+# For valid statistics, index times should include at least 30 years
+startYear = 1
+endYear = 10
+
+[oceanObservations]
+## options related to ocean observations with which the results will be compared
+
+# directory where ocean observations are stored
+baseDirectory = /global/project/projectdirs/acme/observations/Ocean/
+sstSubdirectory = SST
+sssSubdirectory = SSS
+mldSubdirectory = MLD
+ninoSubdirectory = Nino
+mhtSubdirectory = MHT
+meltSubdirectory = Melt
+soseSubdirectory = SOSE
+
+[oceanPreprocessedReference]
+## options related to preprocessed ocean reference run with which the results
+## will be compared (e.g. a POP, CESM or ACME v0 run)
+
+# directory where ocean reference simulation results are stored
+baseDirectory = /global/project/projectdirs/acme/ACMEv0_lowres/B1850C5_ne30_v0.4/ocn/postprocessing
+
+[seaIceObservations]
+## options related to sea ice observations with which the results will be
+## compared
+
+# directory where sea ice observations are stored
+baseDirectory = /global/project/projectdirs/acme/observations/SeaIce
+
+[seaIcePreprocessedReference]
+## options related to preprocessed sea ice reference run with which the results
+## will be compared (e.g. a CICE, CESM or ACME v0 run)
+
+# directory where ocean reference simulation results are stored
+baseDirectory =  /global/project/projectdirs/acme/ACMEv0_lowres/B1850C5_ne30_v0.4/ice/postprocessing
+
+[climatologyMapSoseTemperature]
+## options related to plotting climatology maps of Antarctic
+## potential temperature at various levels, including the sea floor against
+## reference model results and SOSE reanalysis data
+
+# Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct,
+# Nov, Dec, JFM, AMJ, JAS, OND, ANN)
+seasons =  ['ANN']
+
+# list of depths in meters (positive up) at which to analyze, 'top' for the
+# sea surface, 'bot' for the sea floor
+depths = ['top', -200, -400, -600, -800, 'bot']
+
+[climatologyMapSoseSalinity]
+## options related to plotting climatology maps of Antarctic
+## salinity at various levels, including the sea floor against
+## reference model results and SOSE reanalysis data
+
+# Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct,
+# Nov, Dec, JFM, AMJ, JAS, OND, ANN)
+seasons =  ['ANN']
+
+# list of depths in meters (positive up) at which to analyze, 'top' for the
+# sea surface, 'bot' for the sea floor
+depths = ['top', -200, -400, -600, -800, 'bot']
+
+[timeSeriesSeaIceAreaVol]
+## options related to plotting time series of sea ice area and volume
+
+# plot on polar plot
+polarPlot = False
+
+[timeSeriesAntarcticMelt]
+## options related to plotting time series of melt below Antarctic ice shelves
+
+# list of ice shelves to plot or ['all'] for all 106 ice shelves and regions.
+# See "regionNames" in the ice shelf masks file in regionMaskDirectory for
+# details.
+iceShelvesToPlot = ['Peninsula', 'West Antarctica', 'East Antarctica', 'Larsen_C', 'Filchner', 'Ronne', 'Brunt_Stancomb', 'Fimbul', 'Amery', 'Totten', 'Ross_West', 'Ross_East', 'Getz', 'Thwaites', 'Pine_Island', 'Abbot', 'George_VI']
+
+[regions]
+## options related to ocean regions used in several analysis modules
+
+# Directory for region mask files
+regionMaskDirectory = /global/project/projectdirs/acme/mpas_analysis/region_masks

configs/cori/job_script.cori-haswell.bash

@@ -0,0 +1,41 @@
+#!/bin/bash -l
+
+# comment out if using debug queue
+#SBATCH --partition=regular
+# comment in to get premium queue
+##SBATCH --qos=premium
+# comment in to get the debug queue
+##SBATCH --partition=debug
+# comment in when run on cori haswell or knl
+#SBATCH -C haswell
+#SBATCH --nodes=1
+#SBATCH --time=1:00:00
+#SBATCH --account=acme
+#SBATCH --job-name=mpas_analysis
+#SBATCH --output=mpas_analysis.o%j
+#SBATCH --error=mpas_analysis.e%j
+#SBATCH -L cscratch1,SCRATCH,project
+
+cd $SLURM_SUBMIT_DIR   # optional, since this is the default behavior
+
+export OMP_NUM_THREADS=1
+
+module unload python python/base
+module use /global/project/projectdirs/acme/software/modulefiles/all
+module load e3sm-unified/1.1.2
+
+# MPAS/ACME job to be analyzed, including paths to simulation data and
+# observations. Change this name and path as needed
+run_config_file="config.run_name_here"
+
+if [ ! -f $run_config_file ]; then
+    echo "File $run_config_file not found!"
+    exit 1
+fi
+if [ ! -f ./run_mpas_analysis ]; then
+    echo "run_mpas_analysis not found in current directory!"
+    exit 1
+fi
+
+srun -N 1 -n 1 ./run_mpas_analysis $run_config_file
+