Merge pull request #82 from oceanmodeling/feature/perturb_features

Add option to enable disable perturbation feature

pyproject.toml

@@ -35,7 +35,7 @@ dependencies = [
     "cmocean",
     "dask",
     "dask-jobqueue",
-    "ensembleperturbation>=1.3.0",  # rmax option
+    "ensembleperturbation>=1.3.4",  # perturb feature
     "fiona",
     "geoalchemy2",
     "geopandas",

stormworkflow/main.py

@@ -18,7 +18,7 @@
 
 _logger = logging.getLogger(__file__)
 
-CUR_INPUT_VER = Version('0.0.4')
+CUR_INPUT_VER = Version('0.0.5')
 VER_UPDATE_FUNCS = []
 
 
@@ -74,6 +74,15 @@ def _handle_input_v0_0_3_to_v0_0_4(inout_conf):
     inout_conf['NHC_OBS'] = ''
 
 
+@_input_version('0.0.4', '0.0.5')
+def _handle_input_v0_0_4_to_v0_0_5(inout_conf):
+
+    _logger.info("Adding perturbation features")
+    inout_conf['perturb_features'] = [
+      'isotach_adjustment',
+    ]
+
+
 def handle_input_version(inout_conf):
 
     if 'input_version' not in inout_conf:

stormworkflow/prep/setup_ensemble.py

@@ -22,7 +22,7 @@
 from coupledmodeldriver.generate import SCHISMRunConfiguration
 from coupledmodeldriver.generate.schism.script import SchismEnsembleGenerationJob
 from coupledmodeldriver.generate import generate_schism_configuration
-from ensembleperturbation.perturbation.atcf import perturb_tracks
+from ensembleperturbation.perturbation.atcf import perturb_tracks, PerturberFeatures
 from pylib_essentials.schism_file import (
     read_schism_hgrid_cached,
     schism_bpfile,
@@ -137,6 +137,9 @@ def main(args):
     use_wwm = args.use_wwm
     with_hydrology = args.with_hydrology
     pahm_model = args.pahm_model
+    setup_features = PerturberFeatures.NONE
+    for feat in args.perturb_features:
+        setup_features |= PerturberFeatures[feat.upper()]
 
     workdir = out_dir
     mesh_file = mesh_dir / 'mesh_w_bdry.grd'
@@ -208,6 +211,7 @@ def main(args):
         overwrite=True,
         file_deck=file_deck,
         advisories=[advisory],
+        features=setup_features,
     )
 
     if perturb_start != model_start_time:
@@ -345,6 +349,7 @@ def parse_arguments():
     argument_parser.add_argument('--use-wwm', action='store_true')
     argument_parser.add_argument('--with-hydrology', action='store_true')
     argument_parser.add_argument('--pahm-model', choices=['gahm', 'symmetric'], default='gahm')
+    argument_parser.add_argument('--perturb-features', nargs='+', type=str, default=[PerturberFeatures.ISOTACH_ADJUSTMENT.name])
     argument_parser.add_argument('--variables', nargs='+', type=str)
 
     argument_parser.add_argument('name', help='name of the storm', type=str)

stormworkflow/refs/input.yaml

@@ -1,5 +1,5 @@
 ---
-input_version: 0.0.4
+input_version: 0.0.5
 
 storm: "florence"
 year: 2018
@@ -19,6 +19,8 @@ perturb_vars:
   - "radius_of_maximum_winds_persistent"
   - "max_sustained_wind_speed"
 rmw_fill_method: "persistent"
+perturb_features:
+  - "isotach_adjustment"
 
 spinup_exec: "pschism_PAHM_TVD-VL"
 hotstart_exec: "pschism_PAHM_TVD-VL"

stormworkflow/scripts/workflow.sh

@@ -139,22 +139,22 @@ PREP_KWDS+=" --variables $perturb_vars"
 if [ $use_wwm == 1 ]; then PREP_KWDS+=" --use-wwm"; fi
 if [ $hydrology == 1 ]; then PREP_KWDS+=" --with-hydrology"; fi
 PREP_KWDS+=" --pahm-model $pahm_model"
+PREP_KWDS+=" --perturb-features $perturb_features"
 export PREP_KWDS
 # NOTE: We need to wait because run jobs depend on perturbation dirs!
 setup_id=$(sbatch \
     --output "${run_dir}/output/slurm-%j.setup.out" \
     --wait \
     --job-name=prep_$tag \
     --parsable \
-    --export=ALL,PREP_KWDS,STORM=$storm,YEAR=$year,IMG="$L_IMG_DIR/prep.sif" \
+    --export=ALL,PREP_KWDS,STORM=$storm,YEAR=$year \
     $run_dir/slurm/prep.sbatch \
 )
 
 
 echo "Launching runs"
 SCHISM_SHARED_ENV=""
 SCHISM_SHARED_ENV+="ALL"
-SCHISM_SHARED_ENV+=",IMG=$L_IMG_DIR/solve.sif"
 SCHISM_SHARED_ENV+=",MODULES=$L_SOLVE_MODULES"
 spinup_id=$(sbatch \
     --nodes $hpc_solver_nnodes --ntasks $hpc_solver_ntasks \
@@ -185,5 +185,5 @@ sbatch \
     --output "${run_dir}/output/slurm-%j.post.out" \
     --job-name=post_$tag \
     -d afterok${joblist} \
-    --export=ALL,IMG="$L_IMG_DIR/prep.sif",ENSEMBLE_DIR="$run_dir/setup/ensemble.dir/" \
+    --export=ALL,ENSEMBLE_DIR="$run_dir/setup/ensemble.dir/" \
     $run_dir/slurm/post.sbatch

tests/conftest.py

@@ -11,6 +11,7 @@
 input_v0_0_2 = test_refs.joinpath('input_v0.0.2.yaml')
 input_v0_0_3 = test_refs.joinpath('input_v0.0.3.yaml')
 input_v0_0_4 = test_refs.joinpath('input_v0.0.4.yaml')
+input_v0_0_5 = test_refs.joinpath('input_v0.0.5.yaml')
 input_latest = refs.joinpath('input.yaml')
 
 
@@ -38,6 +39,10 @@ def conf_v0_0_3():
 def conf_v0_0_4():
     return read_conf(input_v0_0_4)
 
+@pytest.fixture
+def conf_v0_0_5():
+    return read_conf(input_v0_0_5)
+
 @pytest.fixture
 def conf_latest():
     return read_conf(input_latest)

tests/data/refs/input_v0.0.5.yaml

@@ -0,0 +1,51 @@
+---
+input_version: 0.0.5
+
+storm: "florence"
+year: 2018
+suffix: ""
+subset_mesh: 1
+hr_prelandfall: -1
+past_forecast: 1
+hydrology: 0
+use_wwm: 0
+pahm_model: "gahm"
+num_perturb: 2
+sample_rule: "korobov"
+perturb_vars:
+  - "cross_track"
+  - "along_track"
+#  - "radius_of_maximum_winds"
+  - "radius_of_maximum_winds_persistent"
+  - "max_sustained_wind_speed"
+rmw_fill_method: "persistent"
+perturb_features:
+  - "isotach_adjustment"
+
+spinup_exec: "pschism_PAHM_TVD-VL"
+hotstart_exec: "pschism_PAHM_TVD-VL"
+
+hpc_solver_nnodes: 3
+hpc_solver_ntasks: 108
+hpc_account: ""
+hpc_partition: ""
+
+RUN_OUT: ""
+L_NWM_DATASET: ""
+L_TPXO_DATASET: ""
+L_LEADTIMES_DATASET: ""
+L_TRACK_DIR: ""
+L_DEM_HI: ""
+L_DEM_LO: ""
+L_MESH_HI: ""
+L_MESH_LO: ""
+L_SHP_DIR: ""
+NHC_OBS: ""
+
+TMPDIR: "/tmp"
+PATH_APPEND: ""
+
+L_SOLVE_MODULES:
+  - "intel/2022.1.2"
+  - "impi/2022.1.2"
+  - "netcdf"

tests/test_input_version.py

@@ -50,3 +50,8 @@ def test_v0_0_3_to_latest(conf_v0_0_3, conf_latest):
 def test_v0_0_4_to_latest(conf_v0_0_4, conf_latest):
     handle_input_version(conf_v0_0_4)
     assert conf_latest == conf_v0_0_4
+
+
+def test_v0_0_5_to_latest(conf_v0_0_5, conf_latest):
+    handle_input_version(conf_v0_0_5)
+    assert conf_latest == conf_v0_0_5