MDTF-diagnostics: A Portable Framework for Weather and Climate Model Data Analysis

The MDTF-diagnostics package is a portable framework for running process-oriented diagnostics (PODs) on weather and climate model data.

What is a POD?

Each process-oriented diagnostic [POD; Maloney et al.(2019)] targets a specific physical process or emergent behavior to determine how well one or more models represent the process, ensure that models produce the right answers for the right reasons, and identify gaps in the understanding of phenomena. Each POD is independent of other PODs. PODs generate diagnostic figures that can be viewed as an html file using a web browser.

Available and Planned Diagnostics

The links in the table below show sample output, a brief description, and a link to the full documentation for each currently-supported POD.

Diagnostic	Contributor
AMOC 3D structure (implementation in progress)	Xiaobiao Xu (FSU/COAPS)
Blocking Neale	Rich Neale (NCAR), Dani Coleman (NCAR)
Convective Transition Diagnostics	J. David Neelin (UCLA)
Diurnal Cycle of Precipitation	Rich Neale (NCAR)
Eulerian Storm Track	James Booth (CUNY), Jeyavinoth Jeyaratnam
Extratropical Variance (EOF 500hPa Height)	CESM/AMWG (NCAR)
Mixed Layer Depth	Cecilia Bitz (U. Washington), Lettie Roach
MJO Propagation and Amplitude	Xianan Jiang (UCLA)
MJO Spectra and Phasing	CESM/AMWG (NCAR)
MJO Teleconnections	Eric Maloney (CSU)
Moist Static Energy Diagnostic Package	H. Annamalai (U. Hawaii), Jan Hafner (U. Hawaii)
Ocean Surface Flux Diagnostic	Charlotte A. DeMott (Colorado State University), Chia-Weh Hsu (GFDL)
Precipitation Buoyancy Diagnostic	J. David Neelin (UCLA), Fiaz Ahmed
Rossby Wave Sources Diagnostic Package	H. Annamalai (U. Hawaii), Jan Hafner (U. Hawaii)
Sea Ice Suite	Cecilia Bitz (U. Washington), Lettie Roach
Soil Moisture-Evapotranspiration coupling	Eric Wood (Princeton)
Stratosphere-Troposphere Coupling: Annular Modes	Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)
Stratosphere-Troposphere Coupling: Eddy Heat Fluxes	Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)
Stratosphere-Troposphere Coupling: Stratospheric Ozone and Circulation	Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)
Stratosphere-Troposphere Coupling: Stratospheric Polar Vortex Extremes	Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)
Stratosphere-Troposphere Coupling: Vertical Wave Coupling	Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)
Surface Albedo Feedback	Cecilia Bitz (U. Washington), Aaron Donahoe (U. Washington), Ed Blanchard, Wei Cheng, Lettie Roach
Surface Temperature Extremes and Distribution Shape	J. David Neelin (UCLA), Paul C Loikith (PSU), Arielle Catalano (PSU)
TC MSE Variance Budget Analysis	Allison Wing (Florida State University), Jarrett Starr (Florida State University)
Top Heaviness Metric	Zhuo Wang (U.Illinois Urbana-Champaign), Jiacheng Ye (U.Illinois Urbana-Champaign)
Tropical Cyclone Rain Rate Azimuthal Average	Daehyun Kim (U. Washington), Nelly Emlaw (U.Washington)
Tropical Pacific Sea Level	Jianjun Yin (U. Arizona), Chia-Weh Hsu (GFDL)
Warm Rain Microphysics (implementation in progress)	Kentaroh Suzuki (AORI, U. Tokyo)
Wavenumber-Frequency Spectra	CESM/AMWG (NCAR)

Example POD Analysis Results

• Historical run of NOAA-GFDL ESM4, 1980-2014 (Krasting et al. 2018)
• Historical run of NOAA-GFDL CM4, 1980-2014 (Guo et al. 2018)
• Historical run of NCAR CESM2/CAM4, 1977-1981

Quickstart installation instructions

See the documentation site for all other information, including more in-depth installation instructions.

Visit the GFDL Youtube Channel for tutorials on package installation and other MDTF-diagnostics-related topics

Prerequisites

• Anaconda3, Miniconda3, or micromamba.

• Installation instructions are available here.

• MDTF-diagnositics is developed for macOS and Linux systems. The package has been tested on, but is not fully supported for, the Windows Subsystem for Linux.

• Attention macOS M-series chip users: the MDTF-diagnostics base and python3 conda environments will only build with micromamba on machines running Apple M-series chips. The NCL and R environments will NOT build on M-series machines because the conda packages do not support them at this time.

Notes

• $ indicates strings to be substituted, e.g., the string $CODE_ROOT should be substituted by the actual path to the MDTF-diagnostics directory.
• Consult the Getting started section to learn how to run the framework on your own data and configure general settings.
• POD contributors can consult the Developer Cheatsheet for brief instructions and useful tips

1. Install MDTF-diagnostics

• Open a terminal and create a directory named mdtf, then $ cd mdtf

• Clone your fork of the MDTF repo on your machine: git clone https://github.com/[your fork name]/MDTF-diagnostics

• Check out the latest official release: git checkout tags/[version name]

• Run % conda info --base to determine the location of your Conda installation. This path will be referred to as $CONDA_ROOT.

• cd $CODE_ROOT, then run

ANACONADA/MINICONDA

% ./src/conda/conda_env_setup.sh --all --conda_root $CONDA_ROOT --env_dir $CONDA_ENV_DIR

MICROMAMBA on machines that do NOT have Apple M-series chips

% ./src/conda/micromamba_env_setup.sh --all --micromamba_root $MICROMAMBA_ROOT --micromamba_exe $MICROMAMBA_EXE --env_dir $CONDA_ENV_DIR

MICROMAMBA on machines with Apple M-series chips

% ./src/conda/micromamba_env_setup.sh --e base --micromamba_root $MICROMAMBA_ROOT --micromamba_exe $MICROMAMBA_EXE --env_dir $CONDA_ENV_DIR

% ./src/conda/micromamba_env_setup.sh --e python3_base --micromamba_root $MICROMAMBA_ROOT ---micromamba_exe $MICROMAMBA_EXE -env_dir $CONDA_ENV_DIR

• Substitute the actual paths for $CODE_ROOT, $CONDA_ROOT, $MICROMAMBA_ROOT, MICROMAMBA_EXE, and $CONDA_ENV_DIR.
• $MICROMAMBA_ROOT is the path to micromamba installation on your system (e.g., /home/${USER}/micromamba). This is defined by the $MAMBA_ROOT_PREFIX environment variable on your system when micromamba is installed
• $MICROMAMBA_EXE is full path to the micromamba executable on your system (e.g., /home/${USER}/.local/bin/micromamba). This is defined by the MAMBA_EXE environment variable on your system
• The --env_dir flag allows you to put the program files in a designated location $CONDA_ENV_DIR (for space reasons, or if you don’t have write access). You can omit this flag, and the environments will be installed within $CONDA_ROOT/envs/ by default.

2. Download the sample data

Supporting observational data and sample model data are available via anonymous FTP at ftp://ftp.cgd.ucar.edu/archive/mdtf.

• Digested observational data: run wget ftp://ftp.cgd.ucar.edu/archive/mdtf/obs_data_latest/\* or download the collection "NCAR CGD Anon" from Globus
• NCAR-CESM-CAM sample data (12.3 Gb): model.QBOi.EXP1.AMIP.001.tar (ftp://ftp.cgd.ucar.edu/archive/mdtf/model.QBOi.EXP1.AMIP.001.tar)
• NOAA-GFDL-CM4 sample data (4.8 Gb): model.GFDL.CM4.c96L32.am4g10r8.tar (ftp://ftp.cgd.ucar.edu/archive/mdtf/model.GFDL.CM4.c96L32.am4g10r8.tar)

Note that the above paths are symlinks to the most recent versions of the data and will be reported as zero bytes in an FTP client.

Running tar -xvf [filename].tar will extract the contents in the following hierarchy under the mdtf directory:

mdtf
 ├── MDTF-diagnostics
 ├── inputdata
     ├── model ( = $MODEL_DATA_ROOT)
     │   ├── GFDL.CM4.c96L32.am4g10r8
     │   │   └── day
     │   │       ├── GFDL.CM4.c96L32.am4g10r8.precip.day.nc
     │   │       └── (... other .nc files )
     │   └── QBOi.EXP1.AMIP.001
     │       ├── 1hr
     │       │   ├── QBOi.EXP1.AMIP.001.PRECT.1hr.nc
     │       │   └── (... other .nc files )
     │       ├── 3hr
     │       │   └── QBOi.EXP1.AMIP.001.PRECT.3hr.nc
     │       ├── day
     │       │   ├── QBOi.EXP1.AMIP.001.FLUT.day.nc
     │       │   └── (... other .nc files )
     │       └── mon
     │           ├── QBOi.EXP1.AMIP.001.PS.mon.nc
     │           └── (... other .nc files )
     └── obs_data ( = $OBS_DATA_ROOT)
         ├── (... supporting data for individual PODs )

The default test case uses the QBOi.EXP1.AMIP.001 sample data. The GFDL.CM4.c96L32.am4g10r8 sample data is only needed to test the MJO Propagation and Amplitude POD.

You can put the observational data and model output in different locations (e.g., for space reasons) by changing the values of OBS_DATA_ROOT and MODEL_DATA_ROOT as described below in section 3.

3. Configure framework paths

The MDTF framework supports setting configuration options in a file as well as on the command line. An example of the configuration file format is provided at src/default_tests.jsonc. We recommend configuring the following settings by editing a copy of this file.

• If you've saved the supporting data in the directory structure described in section 2, the default values for OBS_DATA_ROOT and MODEL_DATA_ROOT given in src/default_tests.jsonc (../inputdata/obs_data and ../inputdata/model, respectively) will be correct. If you put the data in a different location, these paths should be changed accordingly.
• WORKING_DIR is used as a scratch location for files generated by the PODs, and should have sufficient quota to handle the full set of model variables you plan to analyze. This includes the sample model and observational data (approx. 19 GB) PLUS data required for the POD(s) you are developing. No files are saved here, so your system's temp directory would be a good choice.
• OUTPUT_DIR should be set to the desired location for output files. OUTPUT_DIR and WORKING_DIR are set to the same locations by default. The output of each run of the framework will be saved in a different subdirectory in this location. As with the WORKING_DIR, ensure that OUTPUT_DIR has sufficient space for all POD output.
• conda_root should be set to the value of $CONDA_ROOT used in section 2.
• If you specified a non-default conda environment location with $CONDA_ENV_DIR, set conda_env_root to that value; otherwise, leave it blank.

We recommend using absolute paths in default_tests.jsonc, but relative paths are also allowed and should be relative to $CODE_ROOT.$CODE_ROOT contains the following subdirectories:

• diagnostics/: directory containing source code and documentation of individual PODs.
• doc/: directory containing documentation (a local mirror of the documentation site).
• src/: source code of the framework itself.
• tests/: unit tests for the framework.

4. Execute the MDTF package with default test settings in single_run mode

The MDTF framework is run via the wrapper script $CODE_ROOT/mdtf that is generated conda_env_install.sh. To test the installation, % $CODE_ROOT/mdtf --help will print help text on the command-line options. Note that, if your current working directory is $CODE_ROOT, you will need to run % ./mdtf --help.

This should print the current version of the framework.

To run the code in single_run mode on the test data using the version of default_tests.jsonc you modified:

cd $CODE_ROOT
./mdtf -f src/default_tests.jsonc -v

-v is the "verbose" flag, and will print additional information that may help with debugging if you have issues

Run time may be 10-20 minutes, depending on your system.

• If you edited/renamed default_tests.jsonc, pass that file instead.

• The output files for this test case will be written to $OUTPUT_DIR/QBOi.EXP1.AMIP.001_1977_1981. When the framework is finished, open $OUTPUT_DIR/QBOi.EXP1.AMIP.001_1977_1981/index.html in a web browser to view the output report.

• The above command will execute PODs included in pod_list of default_tests.jsonc.

• Currently the framework only analyzes data from one model run at a time. To run the MJO_prop_amp POD on the GFDL.CM4.c96L32.am4g10r8 sample data, delete or comment out the section for QBOi.EXP1.AMIP.001 in "caselist" of default_tests.jsonc, and uncomment the section for GFDL.CM4.c96L32.am4g10r8.

• If you re-run the above command, the result will be written to another subdirectory under $OUTPUT_DIR, i.e., output files saved previously will not be overwritten unless you change overwrite in the configuration file to true.

5. Run the framework in multi_run mode (under development)

The framework is ready to test on PODs that analyze multiple model and or observational datasets (cases) using the latest version of the main branch. To run the framework on the example_multicase POD, modify the example configuration file and run

./mdtf -f /diagnostics/multirun_config_template.jsonc -v

You can specify your own datasets in the caselist block, or run the example_multicase POD on the same synthetic data specified in the configuration file. To generate the synthetic CMIP data, run:

mamba env create --force -q -f ./src/conda/_env_synthetic_data.yml
conda activate _MDTF_synthetic_data
pip install mdtf-test-data
mkdir mdtf_test_data && cd mdtf_test_data
mdtf_synthetic.py -c CMIP --startyear 1980 --nyears 5
mdtf_synthetic.py -c CMIP --startyear 1985 --nyears 5

6. Next steps

For more detailed information, consult the documentation site. The "Getting Started" section has more detailed information on customizing your installation and running the framework on your own data. Users interested in contributing a POD should consult the "Developer Information" section.

Acknowledgements

Development of this code framework for process-oriented diagnostics was supported by the National Oceanic and Atmospheric Administration (NOAA) Climate Program Office Modeling, Analysis, Predictions and Projections (MAPP) Program (grant # NA18OAR4310280). Additional support was provided by University of California Los Angeles, the Geophysical Fluid Dynamics Laboratory, the National Center for Atmospheric Research, Colorado State University, Lawrence Livermore National Laboratory and the US Department of Energy.

Many of the process-oriented diagnostics modules (PODs) were contributed by members of the NOAA Model Diagnostics Task Force under MAPP support. Statements, findings or recommendations in these documents do not necessarily reflect the views of NOAA or the US Department of Commerce.

Citations

Guo, Huan; John, Jasmin G; Blanton, Chris; McHugh, Colleen; Nikonov, Serguei; Radhakrishnan, Aparna; Rand, Kristopher; Zadeh, Niki T.; Balaji, V; Durachta, Jeff; Dupuis, Christopher; Menzel, Raymond; Robinson, Thomas; Underwood, Seth; Vahlenkamp, Hans; Bushuk, Mitchell; Dunne, Krista A.; Dussin, Raphael; Gauthier, Paul PG; Ginoux, Paul; Griffies, Stephen M.; Hallberg, Robert; Harrison, Matthew; Hurlin, William; Lin, Pu; Malyshev, Sergey; Naik, Vaishali; Paulot, Fabien; Paynter, David J; Ploshay, Jeffrey; Reichl, Brandon G; Schwarzkopf, Daniel M; Seman, Charles J; Shao, Andrew; Silvers, Levi; Wyman, Bruce; Yan, Xiaoqin; Zeng, Yujin; Adcroft, Alistair; Dunne, John P.; Held, Isaac M; Krasting, John P.; Horowitz, Larry W.; Milly, P.C.D; Shevliakova, Elena; Winton, Michael; Zhao, Ming; Zhang, Rong (2018). NOAA-GFDL GFDL-CM4 model output historical. Version YYYYMMDD[1].Earth System Grid Federation. https://doi.org/10.22033/ESGF/CMIP6.8594

Krasting, John P.; John, Jasmin G; Blanton, Chris; McHugh, Colleen; Nikonov, Serguei; Radhakrishnan, Aparna; Rand, Kristopher; Zadeh, Niki T.; Balaji, V; Durachta, Jeff; Dupuis, Christopher; Menzel, Raymond; Robinson, Thomas; Underwood, Seth; Vahlenkamp, Hans; Dunne, Krista A.; Gauthier, Paul PG; Ginoux, Paul; Griffies, Stephen M.; Hallberg, Robert; Harrison, Matthew; Hurlin, William; Malyshev, Sergey; Naik, Vaishali; Paulot, Fabien; Paynter, David J; Ploshay, Jeffrey; Schwarzkopf, Daniel M; Seman, Charles J; Silvers, Levi; Wyman, Bruce; Zeng, Yujin; Adcroft, Alistair; Dunne, John P.; Dussin, Raphael; Guo, Huan; He, Jian; Held, Isaac M; Horowitz, Larry W.; Lin, Pu; Milly, P.C.D; Shevliakova, Elena; Stock, Charles; Winton, Michael; Xie, Yuanyu; Zhao, Ming (2018). NOAA-GFDL GFDL-ESM4 model output prepared for CMIP6 CMIP historical. Version YYYYMMDD[1].Earth System Grid Federation. https://doi.org/10.22033/ESGF/CMIP6.8597

E. D. Maloney et al. (2019): Process-Oriented Evaluation of Climate and Weather Forecasting Models. BAMS, 100 (9), 1665–1686, doi:10.1175/BAMS-D-18-0042.1.

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