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‎README.md‎

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`--generate` flag on the command line. See the comments in
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`mpas_analysis/config.default` for more details on this option.
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## List of MPAS output files that are needed by MPAS-Analysis:
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* mpas-o files:
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* `mpaso.hist.am.timeSeriesStatsMonthly.*.nc` (Note: since OHC
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anomalies are computed wrt the first year of the simulation,
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if OHC diagnostics is activated, the analysis will need the
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first full year of `mpaso.hist.am.timeSeriesStatsMonthly.*.nc`
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files, no matter what `[timeSeries]/startYear` and
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`[timeSeries]/endYear` are. This is especially important to know if
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short term archiving is used in the run to analyze: in that case, set
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`[input]/runSubdirectory`, `[input]/oceanHistorySubdirectory` and
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`[input]/seaIceHistorySubdirectory` to the appropriate run and archive
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directories and choose `[timeSeries]/startYear` and
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`[timeSeries]/endYear` to include only data that have been short-term
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archived).
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* `mpaso.hist.am.meridionalHeatTransport.0001-03-01.nc` (or any
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`hist.am.meridionalHeatTransport` file)
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* `mpaso.rst.0002-01-01_00000.nc` (or any other mpas-o restart file)
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* `streams.ocean`
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* `mpas-o_in`
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* mpas-cice files:
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* `mpascice.hist.am.timeSeriesStatsMonthly.*.nc`
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* `mpascice.rst.0002-01-01_00000.nc` (or any other mpas-cice restart
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file)
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* `streams.cice`
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* `mpas-cice_in`
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## Purge Old Analysis
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To purge old analysis (delete the whole output directory) before running run

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

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[runs]
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## options related to the run to be analyzed and reference runs to be
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## compared against
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# mainRunName is a name that identifies the simulation being analyzed.
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mainRunName = 20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil
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# preprocessedReferenceRunName is the name of a reference run that has been
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# preprocessed to compare against (or None to turn off comparison). Reference
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# runs of this type would have preprocessed results because they were not
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# performed with MPAS components (so they cannot be easily ingested by
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# MPAS-Analysis)
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preprocessedReferenceRunName = B1850C5_ne30_v0.4
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[input]
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## options related to reading in the results to be analyzed
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# directory containing model results
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baseDirectory = /lcrc/group/acme/jwolfe/acme_scratch/20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil/run
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# names of ocean and sea ice meshes (e.g. oEC60to30v3, oQU240v3, oRRS30to10v3, etc.)
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mpasMeshName = oEC60to30v3
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# Directory for mapping files (if they have been generated already). If mapping
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# files needed by the analysis are not found here, they will be generated and
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# placed in the output mappingSubdirectory
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mappingDirectory = /lcrc/group/acme/mpas_analysis/mapping
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[output]
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## options related to writing out plots, intermediate cached data sets, logs,
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## etc.
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# directory where analysis should be written
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baseDirectory = /dir/to/analysis/output
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# Anvil doesn't have direct access to a web portal, so output will need
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# to be copied elsewhere (e.g. NERSC web portal)
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htmlSubdirectory = html
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# a list of analyses to generate. Valid names are:
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# 'timeSeriesOHC', 'timeSeriesSST', 'climatologyMapSST',
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# 'climatologyMapSSS', 'climatologyMapMLD', 'streamfunctionMOC',
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# 'indexNino34', 'meridionalHeatTransport',
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# 'timeSeriesSeaIceAreaVol', 'climatologyMapSeaIceConcNH',
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# 'climatologyMapSeaIceConcSH', 'climatologyMapSeaIceThickNH',
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# 'climatologyMapSeaIceThickSH'
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# the following shortcuts exist:
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# 'all' -- all analyses will be run
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# 'all_timeSeries' -- all time-series analyses will be run
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# 'all_climatology' -- all analyses involving climatologies
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# 'all_horizontalMap' -- all analyses involving horizontal climatology maps
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# 'all_ocean' -- all ocean analyses will be run
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# 'all_seaIce' -- all sea-ice analyses will be run
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# 'no_timeSeriesOHC' -- skip 'timeSeriesOHC' (and similarly with the
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# other analyses).
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# 'no_ocean', 'no_timeSeries', etc. -- in analogy to 'all_*', skip the
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# given category of analysis
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# an equivalent syntax can be used on the command line to override this
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# option:
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# ./run_mpas_analysis config.analysis --generate \
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# all,no_ocean,all_timeSeries
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generate = ['all']
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# alternative examples that would perform all analysis except
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# 'timeSeriesOHC'
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#generate = ['all', 'no_timeSeriesOHC']
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# Each subsequent list entry can be used to alter previous list entries. For
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# example, the following would run all tasks that aren't ocean analyses,
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# except that it would also run ocean time series tasks:
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#generate = ['all', 'no_ocean', 'all_timeSeries']
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[climatology]
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## options related to producing climatologies, typically to compare against
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## observations and previous runs
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# the first year over which to average climatalogies
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startYear = 11
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# the last year over which to average climatalogies
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endYear = 20
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[timeSeries]
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## options related to producing time series plots, often to compare against
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## observations and previous runs
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# start and end years for timeseries analysis. Using out-of-bounds values
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# like start_year = 1 and end_year = 9999 will be clipped to the valid range
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# of years, and is a good way of insuring that all values are used.
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startYear = 1
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endYear = 22
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[index]
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## options related to producing nino index.
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# start and end years for the nino 3.4 analysis. Using out-of-bounds values
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# like start_year = 1 and end_year = 9999 will be clipped to the valid range
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# of years, and is a good way of insuring that all values are used.
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# For valid statistics, index times should include at least 30 years
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startYear = 1
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endYear = 9999
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[oceanObservations]
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## options related to ocean observations with which the results will be compared
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# directory where ocean observations are stored
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baseDirectory = /lcrc/group/acme/mpas_analysis/observations/Ocean
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sstSubdirectory = SST
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sssSubdirectory = SSS
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mldSubdirectory = MLD
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ninoSubdirectory = Nino
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mhtSubdirectory = MHT
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[oceanPreprocessedReference]
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## options related to preprocessed ocean reference run with which the results
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## will be compared (e.g. a POP, CESM or ACME v0 run)
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# directory where ocean reference simulation results are stored
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baseDirectory = /lcrc/group/acme/mpas_analysis/ACMEv0_lowres/B1850C5_ne30_v0.4/ocn/postprocessing
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[seaIceObservations]
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## options related to sea ice observations with which the results will be
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## compared
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# directory where sea ice observations are stored
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baseDirectory = /lcrc/group/acme/mpas_analysis/observations/SeaIce
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[seaIcePreprocessedReference]
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## options related to preprocessed sea ice reference run with which the results
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## will be compared (e.g. a CICE, CESM or ACME v0 run)
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# directory where ocean reference simulation results are stored
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baseDirectory = /lcrc/group/acme/mpas_analysis/ACMEv0_lowres/B1850C5_ne30_v0.4/ice/postprocessing
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[timeSeriesSeaIceAreaVol]
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## options related to plotting time series of sea ice area and volume
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# plot on polar plot
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polarPlot = False
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[streamfunctionMOC]
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## options related to plotting the streamfunction of the meridional overturning
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## circulation (MOC)
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maxChunkSize = 1000
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# Mask file for ocean basin regional computation
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regionMaskFiles = /lcrc/group/acme/mpas_analysis/region_masks/oEC60to30v3_Atlantic_region_and_southern_transect.nc

‎configs/anvil/job_script.anvil.bash‎

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#!/bin/bash
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# comment out if using debug queue
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#PBS -q acme
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#PBS -A ACME
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#PBS -l nodes=1
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#PBS -l walltime=1:00:00
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#PBS -N mpas_analysis
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#PBS -o mpas_analysis.o$PBS_JOBID
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#PBS -e mpas_analysis.e$PBS_JOBID
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cd $PBS_O_WORKDIR
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# needed to prevent interference with acme-unified
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unset LD_LIBRARY_PATH
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soft add +acme-unified-1.1.1-nox
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# MPAS/ACME job to be analyzed, including paths to simulation data and
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# observations. Change this name and path as needed
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run_config_file="config.run_name_here"
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# change this if not submitting this script from the directory
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# containing run_mpas_analysis
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mpas_analysis_dir="."
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# one parallel task per node by default
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parallel_task_count=6
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# ncclimo can run with 1 (serial) or 12 (bck) threads
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ncclimo_mode=bck
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if [ ! -f $run_config_file ]; then
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echo "File $run_config_file not found!"
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exit 1
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fi
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if [ ! -f $mpas_analysis_dir/run_mpas_analysis ]; then
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echo "run_mpas_analysis not found in $mpas_analysis_dir!"
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exit 1
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fi
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job_config_file=config.output.$PBS_JOBID
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# write out the config file specific to this job
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cat <<EOF > $job_config_file
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[execute]
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## options related to executing parallel tasks
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# the number of parallel tasks (1 means tasks run in serial, the default)
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parallelTaskCount = $parallel_task_count
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# the parallelism mode in ncclimo ("serial" or "bck")
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# Set this to "bck" (background parallelism) if running on a machine that can
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# handle 12 simultaneous processes, one for each monthly climatology.
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ncclimoParallelMode = $ncclimo_mode
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EOF
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# first, perform setup only without mpirun to create the mapping files
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$mpas_analysis_dir/run_mpas_analysis --purge --setup_only $run_config_file \
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$job_config_file
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# next, do the full run now tht we have mapping files, but this time launching
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# with mpirun
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mpirun -n 1 $mpas_analysis_dir/run_mpas_analysis $run_config_file \
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$job_config_file
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‎configs/edison/config.20170807.beta1.G_oQU240.edison‎

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# directory containing model results
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baseDirectory = /scratch1/scratchdirs/xylar/acme_scratch/edison/G-QU240-master-intel/run
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# names of ocean and sea ice meshes (e.g. EC60to30, QU240, RRS30to10, etc.)
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# names of ocean and sea ice meshes (e.g. oEC60to30v3, oQU240v3, oRRS30to10v3, etc.)
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mpasMeshName = oQU240
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# Directory for mapping files (if they have been generated already). If mapping
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# files needed by the analysis are not found here, they will be generated and
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# placed in the output mappingSubdirectory
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# mappingDirectory = /dir/for/mapping/files
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[output]
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## options related to writing out plots, intermediate cached data sets, logs,
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## etc.
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# 'timeSeriesOHC', 'timeSeriesSST', 'climatologyMapSST',
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# 'climatologyMapSSS', 'climatologyMapMLD', 'streamfunctionMOC',
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# 'indexNino34', 'meridionalHeatTransport',
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# 'timeSeriesSeaIceAreaVol', 'climatologyMapSeaIceConcNH',
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# 'climatologyMapSeaIceConcSH', 'climatologyMapSeaIceThickNH',
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# 'timeSeriesSeaIceAreaVol', 'climatologyMapSeaIceConcNH',
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# 'climatologyMapSeaIceConcSH', 'climatologyMapSeaIceThickNH',
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# 'climatologyMapSeaIceThickSH'
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# the following shortcuts exist:
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# 'all' -- all analyses will be run
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# the last year over which to average climatalogies
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endYear = 5
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# The names of the mapping file used for interpolation. If a mapping file has
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# already been generated, supplying the absolute path can save the time of
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# generating a new one. If nothing is supplied, the file name is automatically
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# generated based on the MPAS mesh name, the comparison grid resolution, and
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# the interpolation method
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# mpasMappingFile =
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[timeSeries]
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## options related to producing time series plots, often to compare against
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## observations and previous runs

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