Merge pull request #54 from ACCESS-NRI/50-access-esm1p5-qa-ice-histor…

…y-nml-test

ACCESS-ESM1.5 QA test: CICE icefields_nml configuration

src/model_config_tests/qa/test_access_esm1p5_config.py

@@ -7,6 +7,7 @@
 import warnings
 from typing import Any
 
+import f90nml
 import pytest
 
 from model_config_tests.qa.test_config import check_manifest_exes_in_spack_location
@@ -17,6 +18,7 @@
 # Name of Model Repository - used for retrieving spack location files for released versions
 ACCESS_ESM1P5_REPOSITORY_NAME = "ACCESS-ESM1.5"
 
+
 ######################################
 # Bunch of expected values for tests #
 ######################################
@@ -30,6 +32,10 @@
 VALID_RESTART_FREQ: str = "10YS"
 VALID_MPPNCCOMBINE_EXE: str = "mppnccombine.spack"
 
+CICE_IN_NML_FNAME = "cice_in.nml"
+ICE_HISTORY_NML_FNAME = "ice_history.nml"
+ICEFIELDS_NML_NAME = "icefields_nml"
+
 
 ### Some functions to avoid copying assertion error text
 def error_field_nonexistence(field: str, file: str) -> str:
@@ -191,3 +197,50 @@ def test_mppnccombine_fast_collate_exe(self, config):
             assert isinstance(config["collate"]["mpi"], bool), error_field_incorrect(
                 "collate.mpi", "config.yaml", "true or false"
             )
+
+    def test_cice_configuration_icefields_nml_in_ice_history_nml(
+        self, config, control_path
+    ):
+        # Find CICE sub-model control path
+        model_name = None
+        for sub_model in config["submodels"]:
+            if sub_model["model"] == "cice":
+                model_name = sub_model["name"]
+        assert model_name
+        cice_control_path = control_path / model_name
+
+        icefields_nml_error_msg = (
+            f"Expected CICE configuration to have {ICE_HISTORY_NML_FNAME} that "
+            f"contains an {ICEFIELDS_NML_NAME} namelist. This is to keep icefields "
+            f"namelist separate from the {CICE_IN_NML_FNAME} to allow simpler changes."
+        )
+
+        # Check ice_history.nml exists
+        ice_history_nml_path = cice_control_path / ICE_HISTORY_NML_FNAME
+        assert ice_history_nml_path.is_file(), icefields_nml_error_msg
+
+        # Check icefields_nml in ice_history.nml
+        ice_history_nml = f90nml.read(ice_history_nml_path)
+        assert ICEFIELDS_NML_NAME in ice_history_nml, icefields_nml_error_msg
+
+        # Check icefields_nml not in cice_in.nml
+        cice_in_path = cice_control_path / CICE_IN_NML_FNAME
+        assert cice_in_path.is_file(), (
+            f"No {CICE_IN_NML_FNAME} file found. This is a required "
+            "configuration file for the CICE model component."
+        )
+        cice_in = f90nml.read(cice_in_path)
+        assert ICEFIELDS_NML_NAME not in cice_in, (
+            f"{ICEFIELDS_NML_NAME} namelist found in {CICE_IN_NML_FNAME}. "
+            f"This should only be in {ICE_HISTORY_NML_FNAME} to prevent duplication."
+        )
+
+        # Check no repeated fields between the two namelist files
+        common_nmls = set(cice_in) & set(ice_history_nml)
+        for nml in common_nmls:
+            repeated_fields = set(cice_in[nml]) & set(ice_history_nml[nml])
+            assert repeated_fields == set(), (
+                f"Found repeated fields for '{nml}' namelist"
+                f" in {CICE_IN_NML_FNAME} and {ICE_HISTORY_NML_FNAME}"
+                f": {repeated_fields}"
+            )

tests/common.py

@@ -0,0 +1,5 @@
+import os
+from pathlib import Path
+
+HERE = os.path.dirname(__file__)
+RESOURCES_DIR = Path(f"{HERE}/resources")

tests/qa/test_test_access_esm1p5_config.py

@@ -0,0 +1,30 @@
+import shlex
+import subprocess
+
+from tests.common import RESOURCES_DIR
+
+
+def test_test_access_esm1p5_config_release_release_preindustrial():
+    """Test ACCESS-ESM1.5 specific config tests"""
+    access_esm1p5_configs = RESOURCES_DIR / "access" / "configurations"
+    test_config = access_esm1p5_configs / "release-preindustrial+concentrations"
+
+    assert test_config.exists()
+
+    test_cmd = (
+        "model-config-tests -s "
+        # Run all access_esm1p5 specific tests
+        "-m access_esm1p5 "
+        f"--control-path {test_config} "
+        # Use target branch as can't mock get_git_branch function in utils
+        f"--target-branch release-preindustrial+concentrations"
+    )
+
+    result = subprocess.run(shlex.split(test_cmd), capture_output=True, text=True)
+
+    # Expect the tests to have passed
+    if result.returncode:
+        # Print out test logs if there are errors
+        print(f"Test stdout: {result.stdout}\nTest stderr: {result.stderr}")
+
+    assert result.returncode == 0

tests/test_test_access_om2_config.py → tests/qa/test_test_access_om2_config.py

@@ -1,13 +1,10 @@
-import os
 import shlex
 import shutil
 import subprocess
-from pathlib import Path
 
 import yaml
 
-HERE = os.path.dirname(__file__)
-RESOURCES_DIR = Path(f"{HERE}/resources")
+from tests.common import RESOURCES_DIR
 
 
 def test_test_access_om2_config_release_1deg_jra55_ryf():

tests/test_test_config.py → tests/qa/test_test_config.py

@@ -1,10 +1,7 @@
-import os
 import shlex
 import subprocess
-from pathlib import Path
 
-HERE = os.path.dirname(__file__)
-RESOURCES_DIR = Path(f"{HERE}/resources")
+from tests.common import RESOURCES_DIR
 
 
 def test_test_config_access_om2():

tests/resources/access/configurations/README.md

@@ -0,0 +1,4 @@
+# Example test configuration 
+
+This contains some files of configuration from the [ACCESS-NRI/access-esm1.5-configs](https://github.com/ACCESS-NRI/access-esm1.5-configs) repository. The configurations contain only the files
+checked with QA checks, so they are incomplete configurations.

tests/resources/access/configurations/release-preindustrial+concentrations/config.yaml

@@ -0,0 +1,163 @@
+# A tutorial for running ACCESS ESM1.5 can be found at
+# https://access-hive.org.au/models/run-a-model/run-access-esm
+# Full details about the payu configuration settings are available at
+# https://payu.readthedocs.io/en/latest/config.html
+
+
+# PBS configuration
+
+# If submitting to a different project to your default, uncomment line below
+# and replace PROJECT_CODE with appropriate code. This may require setting shortpath
+# project: PROJECT_CODE
+
+# Force payu to always find, and save, files in this scratch project directory
+# shortpath: /scratch/PROJECT_CODE
+
+# Note: if laboratory is relative path, it is relative to shortpath/$USER
+laboratory: access-esm
+
+jobname: pre-industrial
+queue: normal
+walltime: 2:30:00
+
+# Modules for loading model executables
+modules:
+  use:
+      - /g/data/vk83/modules
+  load:
+      - access-esm1p5/2024.05.0
+
+# Model configuration
+model: access
+
+submodels:
+    - name: atmosphere
+      model: um
+      ncpus: 192
+      exe: um_hg3.exe
+      input:
+        # Aerosols
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/aerosol/global.N96/2020.05.19/OCFF_1850_ESM1.anc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/aerosol/global.N96/2020.05.19/BC_hi_1850_ESM1.anc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/aerosol/global.N96/2020.05.19/scycl_1850_ESM1_v4.anc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/aerosol/global.N96/2020.05.19/Bio_1850_ESM1.anc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/aerosol/global.N96/2020.05.19/biogenic_351sm.N96L38
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/aerosol/global.N96/2020.05.19/sulpc_oxidants_N96_L38
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/aerosol/global.N96/2020.05.19/DMS_conc.N96
+        # Forcing
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/forcing/global.N96/2020.05.19/ozone_1850_ESM1.anc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/forcing/resolution_independent/2020.05.19/volcts_18502000ave.dat
+        # Land
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/land/biogeochemistry/global.N96/2020.05.19/Ndep_1850_ESM1.anc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/land/soiltype/global.N96/2020.05.19/qrparm.soil_igbp_vg
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/land/vegetation/global.N96/2020.05.19/cable_vegfunc_N96.anc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/land/biogeochemistry/resolution_independent/2020.05.19/modis_phenology_csiro.txt
+        - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/land/biogeochemistry/resolution_independent/2020.05.19/pftlookup_csiro_v16_17tiles_wtlnds.csv
+        - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/land/biogeophysics/resolution_independent/2020.05.19/def_soil_params.txt
+        - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/land/biogeophysics/resolution_independent/2020.05.19/def_veg_params.txt
+        # Spectral
+        - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/spectral/resolution_independent/2020.05.19/spec3a_sw_hadgem1_6on
+        - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/spectral/resolution_independent/2020.05.19/spec3a_lw_hadgem1_6on
+        # Grids
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/grids/global.N96/2020.05.19/qrparm.mask
+        - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/grids/resolution_independent/2020.05.19/vertlevs_G3
+        # STASH
+        - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/stash/2020.05.19/
+
+    - name: ocean
+      model: mom
+      ncpus: 180
+      exe: fms_ACCESS-CM.x
+      input:
+        # Biogeochemistry
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/biogeochemistry/global.1deg/2020.05.19/dust.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/biogeochemistry/global.1deg/2020.05.19/ocmip2_press_monthly_om1p5_bc.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/share/ocean/biogeochemistry/global.1deg/2024.07.12/bgc_param.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/unused/ocean/biogeochemistry/global.1deg/2020.05.19/ocmip2_fice_monthly_om1p5_bc.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/unused/ocean/biogeochemistry/global.1deg/2020.05.19/ocmip2_xkw_monthly_om1p5_bc.nc
+        # Tides
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/tides/global.1deg/2020.05.19/roughness_amp.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/tides/global.1deg/2020.05.19/tideamp.nc
+        # Shortwave
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/shortwave_penetration/global.1deg/2020.05.19/ssw_atten_depth.nc
+        # Grids
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/grids/mosaic/global.1deg/2020.05.19/grid_spec.nc
+
+    - name: ice
+      model: cice
+      ncpus: 12
+      exe: cice_access_360x300_12x1_12p.exe
+      input:
+        # Grids
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ice/grids/global.1deg/2020.05.19/kmt.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ice/grids/global.1deg/2020.05.19/grid.nc
+        # Climatology
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ice/climatology/global.1deg/2020.05.19/monthly_sstsss.nc
+
+    - name: coupler
+      model: oasis
+      ncpus: 0
+      input:
+        # Grids
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/grids/global.oi_1deg.a_N96/2020.05.19/grids.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/grids/global.oi_1deg.a_N96/2020.05.19/areas.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/grids/global.oi_1deg.a_N96/2020.05.19/masks.nc
+        # Remapping weights
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/remapping_weights/global.oi_1deg.a_N96/2020.05.19/rmp_cice_to_um1t_CONSERV_FRACNNEI.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/remapping_weights/global.oi_1deg.a_N96/2020.05.19/rmp_um1u_to_cice_CONSERV_FRACNNEI.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/remapping_weights/global.oi_1deg.a_N96/2020.05.19/rmp_um1t_to_cice_CONSERV_DESTAREA.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/remapping_weights/global.oi_1deg.a_N96/2020.05.19/rmp_cice_to_um1u_CONSERV_FRACNNEI.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/remapping_weights/global.oi_1deg.a_N96/2020.05.19/rmp_um1v_to_cice_CONSERV_FRACNNEI.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/remapping_weights/global.oi_1deg.a_N96/2020.05.19/rmp_um1t_to_cice_CONSERV_FRACNNEI.nc
+        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/coupler/remapping_weights/global.oi_1deg.a_N96/2020.05.19/rmp_cice_to_um1v_CONSERV_FRACNNEI.nc
+
+# Collation
+collate:
+    exe: mppnccombine.spack
+    restart: true
+    mem: 4GB
+    walltime: 1:00:00
+    mpi: false
+
+restart: /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/restart/
+
+# Timing controls
+calendar:
+    start:
+        year: 101
+        month: 1
+        days: 1
+
+    runtime:
+        years: 1
+        months: 0
+        days: 0
+
+runspersub: 1
+
+# Misc
+restart_freq: 10YS
+
+runlog: true
+manifest:
+  reproduce:
+    exe: True
+
+
+stacksize: unlimited
+qsub_flags: -W umask=027
+
+
+# Sync options for automatically copying data from ephemeral scratch space to
+# longer term storage
+sync:
+    enable: False # set path below and change to true
+    path: null # Set to location on /g/data or a remote server and path (rsync syntax)
+
+# If a postscript included (such as the automated netcdf conversion), the latest output and restart files will not
+# be automatically synced at the end of a run. To sync the latest output after a postscript has completed,
+#  manually run `payu sync` from the command line.
+
+# userscripts:
+
+postscript: -v PAYU_CURRENT_OUTPUT_DIR,PROJECT  -lstorage=${PBS_NCI_STORAGE} ./scripts/NetCDF-conversion/UM_conversion_job.sh

tests/resources/access/configurations/release-preindustrial+concentrations/ice/cice_in.nml

@@ -0,0 +1,5 @@
+&setup_nml
+    days_per_year  = 365
+  , year_init      = 0001
+  , istep0         = 0
+/

tests/resources/access/configurations/release-preindustrial+concentrations/ice/ice_history.nml

@@ -0,0 +1,9 @@
+&setup_nml
+  , histfreq       = 'd','m','x','x','x'
+  , histfreq_n     = 1, 1, 1, 1, 1
+  , hist_avg       = .true.
+/
+
+&icefields_nml
+    mock_field = .true.
+/

tests/resources/access/configurations/release-preindustrial+concentrations/manifests/exe.yaml

@@ -0,0 +1,18 @@
+format: yamanifest
+version: 1.0
+---
+work/atmosphere/um_hg3.exe:
+  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/um7-git.2024.07.03_access-esm1.5-kgxooyp2s476dd4zc5mgtwhxfknkhnoe/bin/um_hg3.exe
+  hashes:
+    binhash: 3180dda616c7dfe63d8134e00bff2641
+    md5: 1b7874ffb5e34ec50b6a68abbb7769a6
+work/ice/cice_access_360x300_12x1_12p.exe:
+  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/cice4-git.2024.05.21_access-esm1.5-hhtnigwxdyz7ta4dv3gvhwulze6hxqra/bin/cice_access_360x300_12x1_12p.exe
+  hashes:
+    binhash: 818f213e53d30fc307b565c35939382c
+    md5: 04fd88249ebc16e3f560fc265838e9d1
+work/ocean/fms_ACCESS-CM.x:
+  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/mom5-git.access-esm1.5_2024.06.20_access-esm1.5-wxxrc3ivrjz76yx565ddkuuiwoqpalko/bin/fms_ACCESS-CM.x
+  hashes:
+    binhash: a7a3151fb1b814f9e94f05e637b86a44
+    md5: 241db68e6164fac77c59da99ffb1d3b1

tests/resources/access/configurations/release-preindustrial+concentrations/metadata.yaml

@@ -0,0 +1,28 @@
+contact: Add your name here
+email: Add your email address here
+created: Add the date you started the experiment here (YYYY-MM-DD)
+description: |-
+  ACCESS-ESM1.5 global coupled model configuration running in co2 concentration driven mode under pre-industrial forcings, as described in Ziehn et al. (2020), https://doi.org/10.1071/ES19035.
+  Pre-industrial forcing data including atmospheric co2 concentrations are primarily sourced from UKMO versions of CMIP6 inputs, with additional atmospheric forcings sourced from CMIP5 and land cover data adapted from Lawrence et al. (2012), https://doi.org/10.1175/JCLI-D-11-00256.1.
+notes: |-
+  The developers of ACCESS-ESM1.5 request that users of these model configurations:
+   (a) Cite https://doi.org/10.1071/ES19035
+   (b) Include an acknowledgment such as the following:
+   "The authors thank CSIRO for developing the ACCESS-ESM1.5 model configuration and making it freely available to researchers."
+   ACCESS-NRI requests users follow the guidelines for acknowledging ACCESS-NRI and include a statement such as:
+   "This research used the ACCESS-ESM1.5 model infrastructure provided by ACCESS-NRI, which is enabled by the Australian Government's National Collaborative Research Infrastructure Strategy (NCRIS)."
+keywords:
+  - global
+  - access-esm1.5
+realm:
+  - atmos
+  - land
+  - ocean
+  - ocnBgchem
+  - seaIce
+nominal_resolution: 100 km
+reference: https://doi.org/10.1071/ES19035
+license: CC-BY-4.0
+model: ACCESS-ESM1.5
+version: '1.0'
+url: https://github.com/ACCESS-NRI/access-esm1.5-configs.git

tests/test_model_extract_checksums.py

@@ -1,5 +1,4 @@
 import json
-import os
 from pathlib import Path
 from unittest.mock import Mock
 
@@ -8,10 +7,9 @@
 import requests
 
 from model_config_tests.models import index as model_index
+from tests.common import RESOURCES_DIR
 
 MODEL_NAMES = model_index.keys()
-HERE = os.path.dirname(__file__)
-RESOURCES_DIR = Path(f"{HERE}/resources")
 
 
 @pytest.mark.parametrize("model_name", MODEL_NAMES)