Add analysis tasks for plotting SOSE T and S

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

@@ -0,0 +1,171 @@
+[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
+
+[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
+
+[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 +1,42 @@
+#!/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 $SLURM_SUBMIT_DIR   # optional, since this is the default behavior
+
+export OMP_NUM_THREADS=1
+
+module unload python python/base
+module use /global/project/projectdirs/acme/software/modulefiles/all
+module load python/anaconda-2.7-acme
+export PATH=/global/homes/z/zender/bin_cori:${PATH}
+
+# 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_analysis.py ]; then
+    echo "run_analysis.py not found in current directory!"
+    exit 1
+fi
+
+srun -N 1 -n 1 ./run_analysis.py $run_config_file
+

configs/cori/job_script.cori-knl.bash

@@ -0,0 +1,42 @@
+#!/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 knl
+#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 $SLURM_SUBMIT_DIR   # optional, since this is the default behavior
+
+export OMP_NUM_THREADS=1
+
+module unload python python/base
+module use /global/project/projectdirs/acme/software/modulefiles/all
+module load python/anaconda-2.7-acme
+export PATH=/global/homes/z/zender/bin_cori:${PATH}
+
+# 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_analysis.py ]; then
+    echo "run_analysis.py not found in current directory!"
+    exit 1
+fi
+
+srun -N 1 -n 1 ./run_analysis.py $run_config_file
+

configs/edison/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison

@@ -136,6 +136,32 @@ baseDirectory = /global/project/projectdirs/acme/observations/SeaIce
 # 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
 

configs/theta/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta

@@ -143,22 +143,31 @@ polarPlot = False
 # Directory containing mask files for ocean basins and ice shelves
 regionMaskDirectory = /projects/OceanClimate/mpas-analysis_data/mpas_analysis/region_masks
 
+
 [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 =  ['JFM', 'JAS', 'ANN']
 
-# list of depths in meters (positive up) at which to analyze, 'bot' for the
-# bottom of the ocean
+# 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 =  ['JFM', 'JAS', 'ANN']
 
-# list of depths in meters (positive up) at which to analyze, 'bot' for the
-# bottom of the ocean
+# 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']
 
 [timeSeriesAntarcticMelt]