Add mdsl POD to docs (#742)

* add MDSE info to the MDTF_Variable_Lists_table * add MDSL POD to readme add instructions to softlink CONDA_ENV_DIR when using central installations of conda
NOAA-GFDL · Jan 31, 2025 · 87d8884 · 87d8884
1 parent d2bc665
commit 87d8884
Show file tree

Hide file tree

Showing 2 changed files with 63 additions and 39 deletions.
diff --git a/README.md b/README.md
@@ -19,37 +19,38 @@ PODs. PODs generate diagnostic figures that can be viewed as an html file using
 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                                                          |
-|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------|                                      
-| [Blocking Neale](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/blocking_neale/doc/blocking_neale.rst)                                                                                             | Rich Neale (NCAR), Dani Coleman (NCAR) |
-| [Convective Transition Diagnostics](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/convective_transition_diag/convective_transition_diag.html) | J. David Neelin (UCLA) |
-| [Diurnal Cycle of Precipitation](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/precip_diurnal_cycle/precip_diurnal_cycle.html) | Rich Neale (NCAR) |
-| [Eulerian Storm Track](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/eulerian_storm_track/doc/eulerian_storm_track.rst)                                                                           | James Booth (CUNY), Jeyavinoth Jeyaratnam |
-| [Extratropical Variance (EOF 500hPa Height)](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/EOF_500hPa/EOF_500hPa.html) | CESM/AMWG (NCAR) |
-| [Forcing Feedback Diagnostic](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/forcing_feedback/doc/forcing_feedback.rst) | Brian Soden (U. Miami), Ryan Kramer|
-| [Mixed Layer Depth](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/mixed_layer_depth/doc/mixed_layer_depth.rst)                                                                                    | Cecilia Bitz (U. Washington), Lettie Roach |
-| [MJO Propagation and Amplitude ](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_GFDL.CM4.c96L32.am4g10r8/MJO_prop_amp/MJO_prop_amp.html)| Xianan Jiang (UCLA) |
-| [MJO Spectra and Phasing](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/MJO_suite/MJO_suite.html) | CESM/AMWG (NCAR) |
-| [MJO Teleconnections](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/MJO_teleconnection/MJO_teleconnection.html)                                                | Eric Maloney (CSU) |
-| [Moist Static Energy Diagnostic Package](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/ENSO_MSE/doc/ENSO_MSE.rst)                                                                                 | H. Annamalai (U. Hawaii), Jan Hafner (U. Hawaii)                     |
-| [Ocean Surface Flux Diagnostic](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/ocn_surf_flux_diag/doc/ocn_surf_flux_diag.rst)                                                                      | Charlotte A. DeMott (Colorado State University), Chia-Weh Hsu (GFDL) |
-| [Precipitation Buoyancy Diagnostic](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/precip_buoy_diag/doc/precip_buoy_diag.rst)                                                                      | J. David Neelin (UCLA), Fiaz Ahmed                                   |
-| [Rossby Wave Sources Diagnostic Package](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/ENSO_RWS/doc/ENSO_RWS.rst)                                                                                 | H. Annamalai (U. Hawaii), Jan Hafner (U. Hawaii)                     |
-| [Sea Ice Suite](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/seaice_suite/doc/seaice_suite.rst) | Cecilia Bitz (U. Washington), Lettie Roach |
-| [Soil Moisture-Evapotranspiration coupling](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/SM_ET_coupling/doc/SM_ET_coupling.rst)     | Eric Wood (Princeton) |
-| [Stratosphere-Troposphere Coupling: Annular Modes](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_annular_modes/doc/stc_annular_modes.rst) | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL) |
-| [Stratosphere-Troposphere Coupling: Eddy Heat Fluxes](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_eddy_heat_fluxes/doc/stc_eddy_heat_fluxes.rst) | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL) |
-| [Stratosphere-Troposphere Coupling: QBO and ENSO stratospheric teleconnections](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_qbo_enso/doc/stc_qbo_enso.rst) | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL), Dillon Elsbury (NOAA) |
-| [Stratosphere-Troposphere Coupling: Stratospheric Ozone and Circulation](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_eddy_heat_fluxes/doc/stc_ozone.rst) | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL) |
-| [Stratosphere-Troposphere Coupling: Stratospheric Polar Vortex Extremes](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_spv_extremes/doc/stc_spv_extremes.rst) | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL) |
-| [Stratosphere-Troposphere Coupling: Vertical Wave Coupling](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_vert_wave_coupling/doc/stc_vert_wave_coupling.rst) | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL) |
-| [Surface Albedo Feedback](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/albedofb/doc/surface_albedo_feedback.rst) | Cecilia Bitz (U. Washington), Aaron Donahoe (U. Washington), Ed Blanchard, Wei Cheng, Lettie Roach |
-| [Surface Temperature Extremes and Distribution Shape](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/temp_extremes_distshape/doc/temp_extremes_distshape.rst)                                      | J. David Neelin (UCLA), Paul C Loikith (PSU), Arielle Catalano (PSU) |
-| [TC MSE Variance Budget Analysis](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/TC_MSE/doc/TC_MSE.rst)                                                                      | Allison Wing (Florida State University), Jarrett Starr (Florida State University)|
-| [Top Heaviness Metric](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/top_heaviness_metric/doc/top_heaviness_metric.rst)                                                                      | Zhuo Wang (U.Illinois Urbana-Champaign), Jiacheng Ye (U.Illinois Urbana-Champaign)|
-| [Tropical Cyclone Rain Rate Azimuthal Average](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/TC_Rain/doc/TC_Rain.rst)                                                                      | Daehyun Kim (U. Washington), Nelly Emlaw (U.Washington) |
-| [Tropical Pacific Sea Level](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/tropical_pacific_sea_level/doc/tropical_pacific_sea_level.rst) | Jianjun Yin (U. Arizona), Chia-Weh Hsu (GFDL)|
-| [Wavenumber-Frequency Spectra](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/Wheeler_Kiladis/Wheeler_Kiladis.html) | CESM/AMWG (NCAR) |
+| Diagnostic                                                                                                                                                                                             | Contributor                                                                                        |
+|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------|                                      
+| [Blocking Neale](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/blocking_neale/doc/blocking_neale.rst)                                                                            | Rich Neale (NCAR), Dani Coleman (NCAR)                                                             |
+| [Convective Transition Diagnostics](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/convective_transition_diag/convective_transition_diag.html) | J. David Neelin (UCLA)                                                                             |
+| [Diurnal Cycle of Precipitation](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/precip_diurnal_cycle/precip_diurnal_cycle.html)                | Rich Neale (NCAR)                                                                                  |
+| [Eulerian Storm Track](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/eulerian_storm_track/doc/eulerian_storm_track.rst)                                                          | James Booth (CUNY), Jeyavinoth Jeyaratnam                                                          |
+| [Extratropical Variance (EOF 500hPa Height)](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/EOF_500hPa/EOF_500hPa.html)                        | CESM/AMWG (NCAR)                                                                                   |
+| [Forcing Feedback Diagnostic](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/forcing_feedback/doc/forcing_feedback.rst)                                                           | Brian Soden (U. Miami), Ryan Kramer                                                                |
+| [Mean Dynamic Sea Level Package](https://github.com/wrongkindofdoctor/MDTF-diagnostics/blob/main/diagnostics/MDSL/doc/MDSL.rst)                                             | C.Little (AER, Inc.), N. Etige, S. Vannah, M. Zhao                                                 |
+| [Mixed Layer Depth](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/mixed_layer_depth/doc/mixed_layer_depth.rst)                                                                   | Cecilia Bitz (U. Washington), Lettie Roach                                                         |
+| [MJO Propagation and Amplitude ](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_GFDL.CM4.c96L32.am4g10r8/MJO_prop_amp/MJO_prop_amp.html)                               | Xianan Jiang (UCLA)                                                                                |
+| [MJO Spectra and Phasing](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/MJO_suite/MJO_suite.html)                                             | CESM/AMWG (NCAR)                                                                                   |
+| [MJO Teleconnections](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/MJO_teleconnection/MJO_teleconnection.html)                               | Eric Maloney (CSU)                                                                                 |
+| [Moist Static Energy Diagnostic Package](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/ENSO_MSE/doc/ENSO_MSE.rst)                                                                | H. Annamalai (U. Hawaii), Jan Hafner (U. Hawaii)                                      |
+| [Ocean Surface Flux Diagnostic](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/ocn_surf_flux_diag/doc/ocn_surf_flux_diag.rst)                                                     | Charlotte A. DeMott (Colorado State University), Chia-Weh Hsu (GFDL)                               |
+| [Precipitation Buoyancy Diagnostic](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/precip_buoy_diag/doc/precip_buoy_diag.rst)                                                     | J. David Neelin (UCLA), Fiaz Ahmed                                                                 |
+| [Rossby Wave Sources Diagnostic Package](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/ENSO_RWS/doc/ENSO_RWS.rst)                                                                | H. Annamalai (U. Hawaii), Jan Hafner (U. Hawaii)                                     |
+| [Sea Ice Suite](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/seaice_suite/doc/seaice_suite.rst)                                                                                 | Cecilia Bitz (U. Washington), Lettie Roach                                                         |
+| [Soil Moisture-Evapotranspiration coupling](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/SM_ET_coupling/doc/SM_ET_coupling.rst)                                                 | Eric Wood (Princeton)                                                                              |
+| [Stratosphere-Troposphere Coupling: Annular Modes](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_annular_modes/doc/stc_annular_modes.rst)                                    | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)                                     |
+| [Stratosphere-Troposphere Coupling: Eddy Heat Fluxes](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_eddy_heat_fluxes/doc/stc_eddy_heat_fluxes.rst)                           | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)                                     |
+| [Stratosphere-Troposphere Coupling: QBO and ENSO stratospheric teleconnections](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_qbo_enso/doc/stc_qbo_enso.rst)                 | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL), Dillon Elsbury (NOAA)              |
+| [Stratosphere-Troposphere Coupling: Stratospheric Ozone and Circulation](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_eddy_heat_fluxes/doc/stc_ozone.rst)                   | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)                                     |
+| [Stratosphere-Troposphere Coupling: Stratospheric Polar Vortex Extremes](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_spv_extremes/doc/stc_spv_extremes.rst)                | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)                                     |
+| [Stratosphere-Troposphere Coupling: Vertical Wave Coupling](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/stc_vert_wave_coupling/doc/stc_vert_wave_coupling.rst)                 | Amy H. Butler (NOAA CSL), Zachary D. Lawrence (CIRES/NOAA PSL)                                     |
+| [Surface Albedo Feedback](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/albedofb/doc/surface_albedo_feedback.rst)                                                                | Cecilia Bitz (U. Washington), Aaron Donahoe (U. Washington), Ed Blanchard, Wei Cheng, Lettie Roach |
+| [Surface Temperature Extremes and Distribution Shape](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/temp_extremes_distshape/doc/temp_extremes_distshape.rst)                     | J. David Neelin (UCLA), Paul C Loikith (PSU), Arielle Catalano (PSU)                               |
+| [TC MSE Variance Budget Analysis](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/TC_MSE/doc/TC_MSE.rst)                                                                           | Allison Wing (Florida State University), Jarrett Starr (Florida State University)                  |
+| [Top Heaviness Metric](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/top_heaviness_metric/doc/top_heaviness_metric.rst)                                                          | Zhuo Wang (U.Illinois Urbana-Champaign), Jiacheng Ye (U.Illinois Urbana-Champaign)                 |
+| [Tropical Cyclone Rain Rate Azimuthal Average](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/TC_Rain/doc/TC_Rain.rst)                                                            | Daehyun Kim (U. Washington), Nelly Emlaw (U.Washington)                                            |
+| [Tropical Pacific Sea Level](https://github.com/NOAA-GFDL/MDTF-diagnostics/blob/main/diagnostics/tropical_pacific_sea_level/doc/tropical_pacific_sea_level.rst)                                        | Jianjun Yin (U. Arizona), Chia-Weh Hsu (GFDL)                                                      |
+| [Wavenumber-Frequency Spectra](https://www.cgd.ucar.edu/cms/bundy/Projects/diagnostics/mdtf/mdtf_figures/MDTF_QBOi.EXP1.AMIP.001.save/Wheeler_Kiladis/Wheeler_Kiladis.html)                            | CESM/AMWG (NCAR)                                                                                   |
 
 ## Example POD Analysis Results
 
@@ -109,12 +110,10 @@ for, the Windows Subsystem for Linux.
      (e.g., /home/${USER}/.local/bin/micromamba). This is defined by the `MAMBA_EXE` environment variable on your system
   - All flags noted for your system above must be supplied for the script to work.
 
-  #### NOTE: The micromamba environments may differ from the conda environments because of package compatibility discrepancies between solvers
-  `% ./src/conda/micromamba_env_setup.sh --all --micromamba_root $MICROMAMBA_ROOT --micromamba_exe $MICROMAMBA_EXE --env_dir $CONDA_ENV_DIR` builds
-  the **base** environment, **NCL_base** environment, and a limited version of the **python3_base** enviroment that excludes the following packages
-  and dependencies that may be required by the POD(s) you want to run:
-  - falwa
-  - gridfill
+  #### NOTE: The micromamba environments may differ from the conda environments because of package compatibility discrepancies between solvers `% ./src/conda/micromamba_env_setup.sh --all --micromamba_root $MICROMAMBA_ROOT --micromamba_exe $MICROMAMBA_EXE --env_dir $CONDA_ENV_DIR` builds the **base** environment, **NCL_base** environment, and the **python3_base** environment.
+
+  #### NOTE: If you are trying to install environments with a Conda package managed by your institution, you will need to set your environment directory to a location with write access, and symbolically link $CONDA_ROOT/envs to this environment directory: `% ln -s [ROOT_DIR]/miniconda3/envs [path to your environment directory]`
+
 ## 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](ftp://ftp.cgd.ucar.edu/archive/mdtf).
@@ -211,7 +210,8 @@ If you re-run the above command, the result will be written to another subdirect
 i.e., output files saved previously will not be overwritten unless you change `overwrite` in the configuration file
 to `true`.
 
-The output files for the test case will be written to `$OUTPUT_DIR/MDTF_Output/`. 
+The output files for the test case will be written to `$OUTPUT_DIR/MDTF_Output/` (_[v(number)] will be appended
+output directories if an existing MDTF_Output directory is present in the `$OUTPUT_DIR`). 
 When the framework is finished, open `$OUTPUT_DIR/MDTF_Output/[POD NAME]/index.html` in a web browser to view 
 the output report.