MPAS-Analysis

Analysis for simulations produced with Model for Prediction Across Scales (MPAS) components and the Energy Exascale Earth System Model (E3SM), which used those components.

Documentation

http://mpas-analysis.readthedocs.io

Installation

MPAS-Analysis is available as an anaconda package via the e3sm channel:

conda install -c conda-forge -c e3sm mpas_analysis

To use the latest version for developers, you will need to set up a conda environment with the following packages:

numpy
scipy
matplotlib
netCDF4
xarray >= 0.10.0
dask
bottleneck
basemap
lxml
nco >= 4.7.0
pyproj
pillow
cmocean
progressbar2
requests

These can be installed via the conda command:

conda install -c conda-forge numpy scipy matplotlib netCDF4 xarray dask \
    bottleneck basemap lxml nco pyproj pillow cmocean progressbar2 requests

Download analysis input data

To download the data that is necessary to MPAS-Analysis, run:

./download_analysis_data.py -o /path/to/output/directory

where /path/to/output/directory is the main folder that will contain two subdirectories:

mpas_analysis, which includes mapping and region mask files for standard resolution MPAS meshes
observations, which includes the pre-processed observations listed in the Observations table and used to evaluate the model results

List Analysis

To list the available analysis tasks, run:

./run_mpas_analysis --list

This lists all tasks and their tags. These can be used in the generate command-line option or config option. See mpas_analysis/config.default for more details.

Running the analysis

Create and empty config file (say config.myrun), copy config.example, or copy one of the example files in the configs directory.
Either modify config options in your new file or copy and modify config options from mpas_analysis/config.default.

Requirements for custom config files:
- At minimum you should set baseDirectory under [output] to the folder where output is stored. NOTE this value should be a unique directory for each run being analyzed. If multiple runs are analyzed in the same directory, cached results from a previous analysis will not be updated correctly.
- Any options you copy into the config file must include the appropriate section header (e.g. '[run]' or '[output]')
- You do not need to copy all options from mpas_analysis/config.default. This file will automatically be used for any options you do not include in your custom config file.
- You should not modify mpas_analysis/config.default directly.
run: ./run_mpas_analysis config.myrun. This will read the configuraiton first from mpas_analysis/config.default and then replace that configuraiton with any changes from from config.myrun
If you want to run a subset of the analysis, you can either set the generate option under [output] in your config file or use the --generate flag on the command line. See the comments in mpas_analysis/config.default for more details on this option.

List of MPAS output files that are needed by MPAS-Analysis:

mpas-o files:
- mpaso.hist.am.timeSeriesStatsMonthly.*.nc (Note: since OHC anomalies are computed wrt the first year of the simulation, if OHC diagnostics is activated, the analysis will need the first full year of mpaso.hist.am.timeSeriesStatsMonthly.*.nc files, no matter what [timeSeries]/startYear and [timeSeries]/endYear are. This is especially important to know if short term archiving is used in the run to analyze: in that case, set [input]/runSubdirectory, [input]/oceanHistorySubdirectory and [input]/seaIceHistorySubdirectory to the appropriate run and archive directories and choose [timeSeries]/startYear and [timeSeries]/endYear to include only data that have been short-term archived).
- mpaso.hist.am.meridionalHeatTransport.0001-03-01.nc (or any hist.am.meridionalHeatTransport file)
- mpaso.rst.0002-01-01_00000.nc (or any other mpas-o restart file)
- streams.ocean
- mpaso_in
mpas-seaice files:
- mpasseaice.hist.am.timeSeriesStatsMonthly.*.nc
- mpasseaice.rst.0002-01-01_00000.nc (or any other mpas-seaice restart file)
- streams.seaice
- mpassi_in

Note: for older runs, mpas-seaice files will be named:

mpascice.hist.am.timeSeriesStatsMonthly.*.nc
mpascice.rst.0002-01-01_00000.nc
streams.cice
mpas-cice_in Also, for older runs mpaso-in will be named:
mpas-o_in

Purge Old Analysis

To purge old analysis (delete the whole output directory) before running run the analysis, add the --purge flag:

./run_mpas_analysis --purge <config.file>

All of the subdirectories listed in output will be deleted along with the climatology subdirectories in oceanObservations and seaIceObservations.

It is a good policy to use the purge flag for most changes to the config file, for example, updating the start and/or end years of climatologies (and sometimes time series), changing the resolution of a comparison grid, renaming the run, changing the seasons over which climatologies are computed for a given task, updating the code to the latest version.

Cases where it is reasonable not to purge would be, for example, changing options that only affect plotting (color map, ticks, ranges, font sizes, etc.), rerunning with a different set of tasks specified by the generate option (though this will often cause climatologies to be re-computed with new variables and may not save time compared with purging), generating only the final website with --html_only, and re-running after the simulation has progressed to extend time series (however, not recommended for changing the bounds on climatologies, see above).

Running in parallel

Copy the appropriate job script file from configs/<machine_name> to the same directory as run_mpas_analysis (or another directory if preferred). The default script, configs/job_script.default.bash, is appropriate for a laptop or desktop computer with multiple cores.
Modify the number of nodes (equal to the number of parallel tasks), the run name and optionally the output directory and the path to the config file for the run (default: ./configs/<machine_name>/config.<run_name>) Note: in job_script.default.bash, the number of parallel tasks is set manually, since there are no nodes.
Note: the number of parallel tasks can be anything between 1 and the number of analysis tasks to be performed. If there are more tasks than parallel tasks, later tasks will simply wait until earlier tasks have finished.
Submit the job using the modified job script

If a job script for your machine is not available, try modifying the default job script in configs/job_script.default.bash or one of the job scripts for another machine to fit your needs.

Instructions for creating a new analysis task

Analysis tasks can be found in a directory corresponding to each component, e.g., mpas_analysis/ocean for MPAS-Ocean. Shared functionality is contained within the mpas_analysis/shared directory.

create a new task by copying mpas_analysis/analysis_task_template.py to the appropriate folder (ocean, sea_ice, etc.) and modifying it as described in the template. Take a look at mpas_analysis/shared/analysis_task.py for additional guidance.
note, no changes need to be made to mpas_analysis/shared/analysis_task.py
modify mpas_analysis/config.default (and possibly any machine-specific config files in configs/<machine>)
import new analysis task in mpas_analysis/<component>/__init__.py
add new analysis task to run_mpas_analysis under build_analysis_list:
```
   analyses.append(<component>.MyTask(config, myArg='argValue'))
```
This will add a new object of the MyTask class to a list of analysis tasks created in build_analysis_list. Later on in run_analysis, it will first go through the list to make sure each task needs to be generated (by calling check_generate, which is defined in AnalysisTask), then, will call setup_and_check on each task (to make sure the appropriate AM is on and files are present), and will finally call run on each task that is to be generated and is set up properly.

Generating Documentation

To generate the sphinx documentation, run:

conda install sphinx sphinx_rtd_theme numpydoc recommonmark tabulate
cd docs
make html

kevinrosa/MPAS-Analysis