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[develop]: Add SRW-SD chapter to SRW App docs (#1128)
Adds documentation for the SRW-SD features. --------- Co-authored-by: Ben Koziol <[email protected]> Co-authored-by: Michael Lueken <[email protected]>
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| .. _srw-sd: | ||
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| ===================================== | ||
| SRW Smoke & Dust (SRW-SD) Features | ||
| ===================================== | ||
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| .. attention:: | ||
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| SRW-SD capabilities are a new SRW App feature supported on Hera and Orion/Hercules; on other systems, users can expect only limited support. | ||
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| This chapter provides instructions for running a simple, example six-hour forecast for July 22, 2019 at 0z using SRW Smoke & Dust (SRW-SD) features. These features have been merged into an SRW App feature branch from a UFS WM Rapid Refresh Forecast System (RRFS) production branch. This forecast uses RAP data for :term:`ICs` and :term:`LBCs`, the ``RRFS_CONUS_3km`` predefined grid, and the ``FV3_HRRR_gf`` physics suite. This physics suite is similar to the NOAA operational HRRR v4 suite (Dowell et al., 2022), with the addition of the Grell-Freitas deep convective parameterization. `Scientific documentation for the HRRR_gf suite <https://dtcenter.ucar.edu/GMTB/v7.0.0/sci_doc/_h_r_r_r_gf_page.html>`_ and `technical documentation <https://ccpp-techdoc.readthedocs.io/en/v7.0.0/>`_ are available with the CCPP v7.0.0 release but may differ slightly from the version available in the SRW App. | ||
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| .. note:: | ||
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| Although this chapter is the primary documentation resource for running the SRW-SD configuration, users may need to refer to :numref:`Chapter %s <BuildSRW>` and :numref:`Chapter %s <RunSRW>` for additional information on building and running the SRW App, respectively. | ||
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| Quick Start Guide (SRW-SD) | ||
| ============================= | ||
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| .. attention:: | ||
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| These instructions should work smoothly on Hera and Orion/Hercules, but users on other systems may need to make additional adjustments. | ||
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| Download the Code | ||
| ------------------- | ||
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| Clone the |branch| branch of the authoritative SRW App repository: | ||
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| .. code-block:: console | ||
| git clone -b main_aqm https://github.com/ufs-community/ufs-srweather-app | ||
| cd ufs-srweather-app/sorc | ||
| Checkout Externals | ||
| --------------------- | ||
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| Users must run the ``checkout_externals`` script to collect (or "check out") the individual components of the SRW App (AQM version) from their respective GitHub repositories. | ||
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| .. code-block:: console | ||
| ./manage_externals/checkout_externals -e Externals_smoke_dust.cfg | ||
| Build the SRW App | ||
| ------------------ | ||
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| .. code-block:: console | ||
| ./app_build.sh -p=<machine> | ||
| where ``<machine>`` is ``hera``, ``orion``, or ``hercules``. | ||
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| Building the SRW App with SRW-SD on other machines, including other :srw-wiki:`Level 1 <Supported-Platforms-and-Compilers>` platforms, is not currently guaranteed to work, and users may have to make adjustments to the modulefiles for their system. | ||
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| If SRW-SD builds correctly, users should see the standard executables listed in :numref:`Table %s <ExecDescription>` in the ``ufs-srweather-app/exec`` directory. | ||
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| Load the |wflow_env| Environment | ||
| -------------------------------------------- | ||
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| Load the workflow environment: | ||
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| .. code-block:: console | ||
| module purge | ||
| source /path/to/ufs-srweather-app/versions/run.ver_<machine> | ||
| module use /path/to/ufs-srweather-app/modulefiles | ||
| module load wflow_<machine> | ||
| where ``<machine>`` is ``hera``, ``orion``, or ``hercules``. The workflow should load on other platforms listed under the ``MACHINE`` variable in :numref:`Section %s <user>`, but users may need to adjust other elements of the process when running on those platforms. | ||
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| .. _srw-sd-config: | ||
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| Configure an Experiment | ||
| --------------------------- | ||
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| Users will need to configure their experiment by setting parameters in the ``config.yaml`` file. To start, users can copy a default experiment setting into ``config.yaml``: | ||
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| .. code-block:: console | ||
| cd /path/to/ufs-srweather-app/parm | ||
| cp config.smoke_dust.yaml config.yaml | ||
| Users will need to change the ``ACCOUNT`` variable in ``config.yaml`` to an account that they have access to. They will also need to indicate which ``MACHINE`` they are working on. Users may also wish to adjust other experiment settings. For more information on each task and variable, see :numref:`Section %s <ConfigWorkflow>`. | ||
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| If running on Orion or Hercules, users will need to change the data paths to :term:`ICs/LBCs` on the following lines in the ``task_get_extrn_*:`` sections of ``config.yaml`` by commenting out the Hera lines and uncommenting the Orion/Hercules lines: | ||
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| .. code-block:: console | ||
| task_get_extrn_ics: | ||
| # EXTRN_MDL_SOURCE_BASEDIR_ICS: /scratch2/NAGAPE/epic/SRW-AQM_DATA/data_smoke_dust/RAP_DATA_SD/${yyyymmddhh} # hera | ||
| EXTRN_MDL_SOURCE_BASEDIR_ICS: /work/noaa/epic/SRW-AQM_DATA/input_model_data/RAP/${yyyymmddhh} # orion/hercules | ||
| task_get_extrn_lbcs: | ||
| # EXTRN_MDL_SOURCE_BASEDIR_LBCS: /scratch2/NAGAPE/epic/SRW-AQM_DATA/data_smoke_dust/RAP_DATA_SD/${yyyymmddhh} # hera | ||
| EXTRN_MDL_SOURCE_BASEDIR_LBCS: /work/noaa/epic/SRW-AQM_DATA/input_model_data/RAP/${yyyymmddhh} # orion/hercules | ||
| In addition to the UFS SRW fixed files, additional data files are required to run the smoke and dust experiment: | ||
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| * ``fix_smoke``: Contains analysis grids, regridding weights, a vegetation map, and dummy emissions (used when no in situ emission files are available). | ||
| * ``data_smoke_dust/RAVE_fire``: Emission estimates and Fire Radiative Power (FRP) observations derived from `RAVE <https://www.ospo.noaa.gov/products/land/rave/>`_ satellite observations. | ||
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| .. note:: | ||
| Smoke and dust fixed file data has not been added to the `SRW App data bucket <https://registry.opendata.aws/noaa-ufs-shortrangeweather/>`_. Users and developers who would like access to the fixed file data necessary to run the application should reach out the UFS SRW team in a :srw-repo:`GitHub Discussion <discussions>`. | ||
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| Users may also wish to change :term:`cron`-related parameters in ``config.yaml``. In the ``config.smoke_dust.yaml`` file, which was copied into ``config.yaml``, cron can be used for automatic submission and resubmission of the workflow by setting the following variables: | ||
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| .. code-block:: console | ||
| workflow: | ||
| USE_CRON_TO_RELAUNCH: true | ||
| CRON_RELAUNCH_INTVL_MNTS: 3 | ||
| This means that cron will submit the launch script every 3 minutes. Users may choose not to submit using cron or to submit at a different frequency. Note that users should create a crontab by running ``crontab -e`` the first time they use cron. | ||
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| When using the basic ``config.smoke_dust.yaml`` experiment, the usual pre-processing and coldstart forecast tasks are used, because ``"parm/wflow/prep.yaml"`` appears in the list of workflow files in the ``rocoto: tasks: taskgroups:`` section of ``config.yaml`` (see :numref:`Section %s <TasksPrepAQM>` for task descriptions). To turn on AQM *post*-processing tasks in the workflow, include ``"parm/wflow/aqm_post.yaml"`` in the ``rocoto: tasks: taskgroups:`` section, too (see :numref:`Section %s <TasksPostAQM>` for task descriptions). | ||
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| .. _srw-sd-more-tasks: | ||
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| Additional SRW-SD Tasks | ||
| -------------------------- | ||
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| .. COMMENT: Add workflow diagram in the future. | ||
| Compared to the typical SRW App workflow, the SRW-SD has slightly different tasks for pre- and post-processing. As in the SRW App default workflow, the SRW-SD workflow uses the preprocessing tasks from ``prep.yaml``, but it adds smoke-and-dust-specific tasks from ``smoke_dust.yaml``. For post-processing, it uses the NCO-compliant ``upp_post.yaml`` instead of the usual ``post.yaml``. | ||
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| The new tasks for SRW-SD are shown in :numref:`Table %s <pre-srw-sd>`. | ||
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| .. _pre-srw-sd: | ||
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| .. list-table:: *Tasks for SRW-SD Pre- and Post-Processing* | ||
| :widths: 20 50 30 | ||
| :header-rows: 1 | ||
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| * - Task Name | ||
| - Description | ||
| - File | ||
| * - smoke_dust | ||
| - Generates the input data file for smoke and dust to be used in the UFS Weather Model. | ||
| - ``parm/wflow/smoke_dust.yaml`` | ||
| * - prepstart | ||
| - Adds the smoke and dust fields to the ICs file from the restart file in the previous cycle. | ||
| - ``parm/wflow/smoke_dust.yaml`` | ||
| * - upp_post | ||
| - Performs post-processing with UPP. | ||
| - ``parm/wflow/upp_post.yaml`` | ||
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| The Python scripts listed in :numref:`Table %s <sd-scripts>` are used to perform data processing and calculations required for the SRW-SD forecast. | ||
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| .. _sd-scripts: | ||
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| .. list-table:: *Python Scripts Used by Smoke and Dust Tasks* | ||
| :widths: 20 50 | ||
| :header-rows: 1 | ||
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| * - Script | ||
| - Description | ||
| * - ``ush/smoke_dust_add_smoke.py`` | ||
| - Transfers smoke and dust-related variables from FV3 tracer outputs to GFS initial conditions. | ||
| * - ``ush/smoke_dust_fire_emiss_tools.py`` | ||
| - Calculates fire behavior and emission variables and creates input for the smoke and dust tracers. | ||
| * - ``ush/smoke_dust_generate_fire_emissions.py`` | ||
| - Entry point for the smoke and dust fire-related initial conditions generated during the ``smoke_dust`` task. | ||
| * - ``ush/smoke_dust_hwp_tools.py`` | ||
| - Utilities for calculating Hourly Wildfire Potential (HWP). | ||
| * - ``ush/smoke_dust_interp_tools.py`` | ||
| - Regridding utilities using `esmpy <https://earthsystemmodeling.org/esmpy/>`_ that interpolate data from the RAVE observational grid to the RRFS grid. | ||
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| Generate the Workflow | ||
| ------------------------ | ||
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| Generate the workflow: | ||
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| .. code-block:: console | ||
| ./generate_FV3LAM_wflow.py | ||
| Run the Workflow | ||
| ------------------ | ||
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| If ``USE_CRON_TO_RELAUNCH`` is set to true in ``config.yaml`` (see :numref:`Section %s <srw-sd-config>`), the workflow will run automatically. If it was set to false, users must submit the workflow manually from the experiment directory: | ||
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| .. code-block:: console | ||
| cd ../../expt_dirs/smoke_dust_conus3km | ||
| ./launch_FV3LAM_wflow.sh | ||
| Repeat the launch command regularly until a SUCCESS or FAILURE message appears on the terminal window. | ||
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| Users may check experiment status from the experiment directory with either of the following commands: | ||
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| .. code-block:: console | ||
| # Check the experiment status (for cron jobs) | ||
| rocotostat -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 | ||
| # Check the experiment status and relaunch the workflow (for manual jobs) | ||
| ./launch_FV3LAM_wflow.sh; tail -n 40 log.launch_FV3LAM_wflow | ||
| .. _srw-sd-success: | ||
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| Experiment Output | ||
| -------------------- | ||
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| The workflow run is complete when all tasks display a "SUCCEEDED" message. If everything goes smoothly, users will eventually see a workflow status table similar to the following: | ||
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| .. code-block:: console | ||
| [orion-login smoke_dust_conus3km]$ rocotostat -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 | ||
| CYCLE TASK JOBID STATE EXIT STATUS TRIES DURATION | ||
| ============================================================================================== | ||
| 201907220000 make_grid 18984137 SUCCEEDED 0 1 29.0 | ||
| 201907220000 make_orog 18984148 SUCCEEDED 0 1 419.0 | ||
| 201907220000 make_sfc_climo 18984184 SUCCEEDED 0 1 82.0 | ||
| 201907220000 smoke_dust 18984186 SUCCEEDED 0 1 243.0 | ||
| 201907220000 prepstart 18984324 SUCCEEDED 0 1 24.0 | ||
| 201907220000 get_extrn_ics 18984138 SUCCEEDED 0 1 11.0 | ||
| 201907220000 get_extrn_lbcs 18984149 SUCCEEDED 0 1 12.0 | ||
| 201907220000 make_ics_mem000 18984185 SUCCEEDED 0 1 157.0 | ||
| 201907220000 make_lbcs_mem000 18984187 SUCCEEDED 0 1 85.0 | ||
| 201907220000 forecast_mem000 18984328 SUCCEEDED 0 1 6199.0 | ||
| 201907220000 upp_post_mem000_f000 18988282 SUCCEEDED 0 1 212.0 | ||
| 201907220000 upp_post_mem000_f001 18988283 SUCCEEDED 0 1 247.0 | ||
| 201907220000 upp_post_mem000_f002 18988284 SUCCEEDED 0 1 258.0 | ||
| 201907220000 upp_post_mem000_f003 18988285 SUCCEEDED 0 1 271.0 | ||
| 201907220000 upp_post_mem000_f004 18988286 SUCCEEDED 0 1 284.0 | ||
| 201907220000 upp_post_mem000_f005 18988287 SUCCEEDED 0 1 286.0 | ||
| 201907220000 upp_post_mem000_f006 18988288 SUCCEEDED 0 1 292.0 | ||
| ============================================================================================== | ||
| 201907220600 smoke_dust 18988289 SUCCEEDED 0 1 225.0 | ||
| 201907220600 prepstart 18988302 SUCCEEDED 0 1 112.0 | ||
| 201907220600 get_extrn_ics 18984150 SUCCEEDED 0 1 10.0 | ||
| 201907220600 get_extrn_lbcs 18984151 SUCCEEDED 0 1 14.0 | ||
| 201907220600 make_ics_mem000 18984188 SUCCEEDED 0 1 152.0 | ||
| 201907220600 make_lbcs_mem000 18984189 SUCCEEDED 0 1 79.0 | ||
| 201907220600 forecast_mem000 18988311 SUCCEEDED 0 1 6191.0 | ||
| 201907220600 upp_post_mem000_f000 18989105 SUCCEEDED 0 1 212.0 | ||
| 201907220600 upp_post_mem000_f001 18989106 SUCCEEDED 0 1 283.0 | ||
| 201907220600 upp_post_mem000_f002 18989107 SUCCEEDED 0 1 287.0 | ||
| 201907220600 upp_post_mem000_f003 18989108 SUCCEEDED 0 1 284.0 | ||
| 201907220600 upp_post_mem000_f004 18989109 SUCCEEDED 0 1 289.0 | ||
| 201907220600 upp_post_mem000_f005 18989110 SUCCEEDED 0 1 294.0 | ||
| 201907220600 upp_post_mem000_f006 18989111 SUCCEEDED 0 1 294.0 | ||
| If something goes wrong, users can check the log files, which are located by default in ``expt_dirs/smoke_dust_conus3km/nco_logs/20190722``. |
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