`mpas_init`

The uw mode for configuring and running the MPAS init_atmosphere tool. Each listed TASK may be called to generate the runtime asset(s) it is responsible for, and will call any task it depends on as needed. A provisioned_run_directory comprises everything needed for a run, and a run runs the init_atmosphere executable.

uw mpas_init --help

usage: uw mpas_init [-h] [--version] TASK ...

Execute mpas_init tasks

Optional arguments:
  -h, --help
      Show help and exit
  --version
      Show version info and exit

Positional arguments:
  TASK
    boundary_files
      Boundary files
    files_copied
      Files copied for run
    files_linked
      Files linked for run
    namelist_file
      The namelist file
    provisioned_run_directory
      Run directory provisioned with all required content
    run
      A run
    runscript
      The runscript
    streams_file
      The streams file
    validate
      Validate the UW driver config

All tasks take the same arguments. For example:

uw mpas_init run --help

usage: uw mpas_init run --cycle CYCLE [-h] [--version] [--config-file PATH]
                        [--batch] [--dry-run] [--graph-file PATH]
                        [--key-path KEY[.KEY...]] [--quiet] [--verbose]

A run

Required arguments:
  --cycle CYCLE
      The cycle in ISO8601 format (e.g. 2024-05-23T18)

Optional arguments:
  -h, --help
      Show help and exit
  --version
      Show version info and exit
  --config-file PATH, -c PATH
      Path to UW YAML config file (default: read from stdin)
  --batch
      Submit run to batch scheduler
  --dry-run
      Only log info, making no changes
  --graph-file PATH
      Path to Graphviz DOT output [experimental]
  --key-path KEY[.KEY...]
      Dot-separated path of keys leading through the config to the driver's
      configuration block
  --quiet, -q
      Print no logging messages
  --verbose, -v
      Print all logging messages

Examples

The examples use a configuration file named config.yaml with contents similar to:

mpas_init:
  boundary_conditions:
    interval_hours: 6
    length: 6
    offset: 0
    path: /path/to/boundary/condition/files
  execution:
    batchargs:
      cores: 4
      walltime: "01:30:00"
    executable: init_atmosphere
    mpiargs:
      - "--ntasks=4"
    mpicmd: srun
  files_to_copy:
    conus.graph.info.part.4: /path/to/conus.graph.info.part.4
    conus.static.nc: /path/to/conus.static.nc
    stream_list.atmosphere.diagnostics: "{{ user.mpas_app }}/MPAS-Model/stream_list.atmosphere.diagnostics"
    stream_list.atmosphere.output: "{{ user.mpas_app }}/MPAS-Model/stream_list.atmosphere.output"
    stream_list.atmosphere.surface: "{{ user.mpas_app }}/MPAS-Model/stream_list.atmosphere.surface"
  files_to_link:
    CAM_ABS_DATA.DBL: "{{ user.mpas_app }}/MPAS-Model/CAM_ABS_DATA.DBL"
    CAM_AEROPT_DATA.DBL: "{{ user.mpas_app }}/MPAS-Model/CAM_AEROPT_DATA.DBL"
    GENPARM.TBL: "{{ user.mpas_app }}/MPAS-Model/GENPARM.TBL"
    LANDUSE.TBL: "{{ user.mpas_app }}/MPAS-Model/LANDUSE.TBL"
    OZONE_DAT.TBL: "{{ user.mpas_app }}/MPAS-Model/OZONE_DAT.TBL"
    OZONE_LAT.TBL: "{{ user.mpas_app }}/MPAS-Model/OZONE_LAT.TBL"
    OZONE_PLEV.TBL: "{{ user.mpas_app }}/MPAS-Model/OZONE_PLEV.TBL"
    RRTMG_LW_DATA: "{{ user.mpas_app }}/MPAS-Model/RRTMG_LW_DATA"
    RRTMG_LW_DATA.DBL: "{{ user.mpas_app }}/MPAS-Model/RRTMG_LW_DATA.DBL"
    RRTMG_SW_DATA: "{{ user.mpas_app }}/MPAS-Model/RRTMG_SW_DATA"
    RRTMG_SW_DATA.DBL: "{{ user.mpas_app }}/MPAS-Model/RRTMG_SW_DATA.DBL"
    SOILPARM.TBL: "{{ user.mpas_app }}/MPAS-Model/SOILPARM.TBL"
    VEGPARM.TBL: "{{ user.mpas_app }}/MPAS-Model/VEGPARM.TBL"
  namelist:
    base_file: "{{ user.mpas_app }}/MPAS-Model/namelist.init_atmosphere"
    update_values:
      data_sources:
        config_fg_interval: !int "{{ mpas_init.boundary_conditions['interval_hours'] * 3600 }}"
        config_met_prefix: FILE
      decomposition:
        config_block_decomp_file_prefix: conus.graph.info.part.
      nhyd_model:
        config_init_case: 9
      preproc_stages:
        config_native_gwd_static: false
        config_static_interp: false
      vertical_grid:
        config_blend_bdy_terrain: true
    validate: true
  run_dir: /path/to/rundir
  streams:
    path: "{{ user.mpas_app }}/MPAS-Model/streams.init_atmosphere"
    values:
      input_filename: conus.init.nc
      output_filename: foo.nc
platform:
  account: me
  scheduler: slurm
user:
  mpas_app: /path/to/mpas/installation

Its contents are described in depth in section mpas_init.

Run init_atmosphere on an interactive node
```
$ uw mpas_init run --config-file config.yaml --cycle 2023-12-18T00
```
The driver creates a runscript.mpas_init file in the directory specified by run_dir: in the config and runs it, executing init_atmosphere.
Run init_atmosphere via a batch job
```
$ uw mpas_init run --config-file config.yaml --cycle 2023-12-18T00 --batch
```
The driver creates a runscript.mpas_init file in the directory specified by run_dir: in the config and submits it to the batch system. Running with --batch requires a correctly configured platform: block in config.yaml, as well as appropriate settings in the execution: block under mpas_init:.
Specifying the --dry-run flag results in the driver logging messages about actions it would have taken, without actually taking any.
```
$ uw mpas_init run --config-file config.yaml --cycle 2023-12-18T00 --batch --dry-run
```

The --key-path option can be used to navigate from the top of the config to the driver’s configuration block. For example, specifying --key-path foo.bar with config
```
foo:
  bar:
    driver:
      # driver config block
```
is equivalent to using config
```
driver:
  # driver config block
```
without specifying --key-path.
The run task depends on the other available tasks and executes them as prerequisites. It is possible to execute any task directly, which entails execution of any of its dependencies. For example, to create an mpas_init run directory provisioned with all the files, directories, symlinks, etc. required per the configuration file:
```
$ uw mpas_init provisioned_run_directory --config-file config.yaml --cycle 2023-12-18T00 --batch
```

mpas_init

Examples

`mpas_init`