Adapt workflow

conf/jobs-real-from-ideal.yaml

@@ -75,16 +75,29 @@ JOBS:
     FILE: templates/real-from-ideal/prepare_experiment.sh
     DEPENDENCIES: BUILD_ICON
     RUNNING: once
-    WALLCLOCK: 01:00
+    WALLCLOCK: 00:10
+
+  PREPARE_IDEAL_DIRECTORY:
+    FILE: templates/real-from-ideal/prepare_ideal_directory.sh
+    DEPENDENCIES: PREPARE_EXPERIMENT
+    RUNNING: date
+    WALLCLOCK: 00:10
 
-  PREPARE_DATE:
-    FILE: templates/real-from-ideal/prepare_date.sh
+  PREPARE_IDEAL_NAMELIST:
+    FILE: templates/real-from-ideal/prepare_ideal_namelist.sh
+    DEPENDENCIES: PREPARE_IDEAL_DIRECTORY
+    RUNNING: date
+    WALLCLOCK: 00:10
+
+  RUN_IDEAL:
+    FILE: templates/real-from-ideal/run_ideal.sh
+    DEPENDENCIES: PREPARE_IDEAL_NAMELIST
     RUNNING: date
     WALLCLOCK: 01:00
 
   PREPARE_MEMBER:
     FILE: templates/real-from-ideal/prepare_member.sh
-    DEPENDENCIES: PREPARE_EXPERIMENT PREPARE_DATE
+    DEPENDENCIES: RUN_IDEAL
     RUNNING: member
     WALLCLOCK: 01:00
 
@@ -96,7 +109,6 @@ JOBS:
     TYPE: python
     EXECUTABLE: "%HPCROOTDIR%/%python_environment.folder_name%/bin/python3"
 
-
   RUN_ICON:
     FILE: templates/run_icon.sh
     DEPENDENCIES: PREPARE_CHUNK

templates/real-from-ideal/prepare_date.sh

-#!/bin/bash -l
-
-# Get some variables provided by autosubmit.
-WORKDIR=%HPCROOTDIR%
-STARTDATE=%SDATE%
-
-# Define date directory, create it and go there
-COMMON_DATE_FOLDER=${WORKDIR}/${STARTDATE}/inidata
-# Create member folder and go there
-mkdir -p ${COMMON_DATE_FOLDER}
-cd ${COMMON_DATE_FOLDER} || exit
-
-# some settings
-AN_MEMBER=$(printf "%03d" %initial_conditions.member%)
-INITIAL_CONDITIONS_PARENT_FOLDER=%initial_conditions.parent_folder%
-
-INITIAL_CONDITIONS_PATH=${INITIAL_CONDITIONS_PARENT_FOLDER}/${STARTDATE:0:6}/${STARTDATE:0:8}T00
-
-AN_SOURCE=$(find ${INITIAL_CONDITIONS_PATH} -name "igaf*00.m${AN_MEMBER}.grb" | sort | tail -n 1)
-FG_SOURCE=$(find ${INITIAL_CONDITIONS_PATH} -name "igfff00030000.m${AN_MEMBER}.grb" | sort | tail -n 1)
-
-if [ ! -f "${AN_SOURCE}" ]; then
-  echo "Analysis file for date ${STARTDATE} not found!"
-  exit 1
-fi
-
-if [ ! -f "${FG_SOURCE}" ]; then
-  echo "FG file for date ${STARTDATE} not found!"
-  exit 1
-fi
-
-AN_FILE=$(basename "${AN_SOURCE}")
-FG_FILE=$(basename "${FG_SOURCE}")
-
-# Save filenames to be used later by other scripts.
-echo "${AN_FILE}" > an_file.txt
-echo "${FG_FILE}" > fg_file.txt
-
-# Copy the first-guess and analysis files.
-cp "${FG_SOURCE}" "${FG_FILE}"
-cp "${AN_SOURCE}" "${AN_FILE}"
-
-# Change permissions to read only.
-chmod 440 ./*

templates/real-from-ideal/prepare_experiment.sh

@@ -4,8 +4,6 @@
 WORKDIR=%HPCROOTDIR%
 DYNAMICS_GRID_FILENAME=%simulation.dynamics_grid_filename%
 RADIATION_GRID_FILE=%simulation.radiation_grid_filename%
-EXTERNAL_PARAMETERS_FILE=%simulation.external_parameters_filename%
-
 
 # Activate spack
 SPACK_ENV=${WORKDIR}/spack/share/spack/setup-env.sh
@@ -33,13 +31,10 @@ function download_file() {
 BASEURL=http://icon-downloads.mpimet.mpg.de/grids/public/edzw
 download_file $BASEURL/${DYNAMICS_GRID_FILENAME}
 download_file $BASEURL/${RADIATION_GRID_FILE}
-download_file $BASEURL/${EXTERNAL_PARAMETERS_FILE}
 
 # Link input for radiation
 ln -sf "${ICON_DATA_PATH}/rrtmg_lw.nc" .
 ln -sf "${ICON_DATA_PATH}/ECHAM6_CldOptProps.nc" .
-ln -sf "${ICON_BASE_PATH}/run/ana_varnames_map_file.txt" .
-
 
 # Change permissions to read only.
-chmod 440 ./*
+chmod 440 ./*
\ No newline at end of file

templates/real-from-ideal/prepare_ideal_directory.sh

+#!/bin/bash -l
+
+# Get some variables provided by autosubmit.
+WORKDIR=%HPCROOTDIR%
+STARTDATE=%SDATE%
+
+# Common folder with data needed for all simulations
+COMMON_INIDATA_FOLDER=${WORKDIR}/inidata
+
+# Ideal folder
+IDEAL_DIR=${WORKDIR}/${STARTDATE}/ideal
+
+# Create member folder and go there
+mkdir -p ${IDEAL_DIR}
+cd ${IDEAL_DIR} || exit
+
+# Link all files from the common inidata folder and the common date folder
+ln -sf ${COMMON_INIDATA_FOLDER}/* .

templates/real-from-ideal/prepare_ideal_namelist.py

+import logging
+import re
+from datetime import datetime, timedelta
+from pathlib import Path
+
+import f90nml
+
+logger = logging.getLogger("prepare_chunk")
+logger.setLevel(logging.INFO)
+
+# Get some autosubmit variables
+WORKDIR = "%HPCROOTDIR%"
+STARTDATE = "%SDATE%"
+
+# Example of date format "2018-06-01T00:00:00Z"
+date_format = "%simulation.date_format%"
+
+START_YEAR = "%Chunk_START_YEAR%"
+START_MONTH = "%Chunk_START_MONTH%"
+START_DAY = "%Chunk_START_DAY%"
+START_HOUR = "%Chunk_START_HOUR%"
+
+END_YEAR = "%Chunk_END_YEAR%"
+END_MONTH = "%Chunk_END_MONTH%"
+END_DAY = "%Chunk_END_DAY%"
+END_HOUR = "%Chunk_END_HOUR%"
+
+Chunk_START_DATE = datetime(year=int(START_YEAR), month=int(START_MONTH), day=int(START_DAY), hour=int(START_HOUR))
+Chunk_END_DATE = datetime(year=int(END_YEAR), month=int(END_MONTH), day=int(END_DAY), hour=int(END_HOUR))
+
+# Compute difference in seconds
+checkpoint_time = int((Chunk_END_DATE - Chunk_START_DATE).total_seconds())
+
+# TODO: Is that really necessary?
+# Add 10 minutes to allow the model to write the restarts
+Chunk_END_DATE = Chunk_END_DATE + timedelta(minutes=10)
+# Get run directory
+RUNDIR = Path(f"{WORKDIR}/{STARTDATE}/ideal")
+
+# Get some variable replacements from the proj.yml file through autosubmit
+variable_replacements = {
+    "dynamics_grid_filename": "%simulation.dynamics_grid_filename%",
+    "radiation_grid_filename": "%simulation.radiation_grid_filename%",
+    "external_parameters_filename": "%simulation.external_parameters_filename%",
+    "Chunk_START_DATE": Chunk_START_DATE.strftime(date_format),
+    "Chunk_END_DATE": Chunk_END_DATE.strftime(date_format),
+    "is_restart": False if "%CHUNK%" == "1" else True,
+    "checkpoint_time": checkpoint_time,
+}
+
+
+def adapt_namelist(input_namelist: str, output_namelist: str):
+    input_namelist = Path(input_namelist)
+    output_namelist = Path(output_namelist)
+
+    namelist = f90nml.read(input_namelist.as_posix())
+    group_keys = [gk for gk in namelist]
+
+    for group in group_keys:
+        variable_keys = [vk for vk in namelist[group]]
+        for variable in variable_keys:
+            value = namelist[group][variable]
+            m = re.match(r"%(.*)%", str(value))
+            if m:
+                key = m.group(1)
+
+                if key not in variable_replacements:
+                    raise AssertionError(f"The namelist {input_namelist.as_posix()!r} contains the variable {key!r} "
+                                         f"which is not in the list of provided replacements:\n"
+                                         f"{[v for v in variable_replacements]}")
+                logger.info(f"Replacing {group}>{variable}:{key} with {variable_replacements[key]!r}")
+                namelist[group][variable] = variable_replacements[key]
+
+    f90nml.write(nml=namelist, nml_path=output_namelist.as_posix(), force=True)
+
+
+if __name__ == '__main__':
+    atmosphere_namelist_path = "%simulation.namelist_paths.ideal.atmosphere%"
+    master_namelist_path = "%simulation.namelist_paths.master%"
+
+    # Adapt atmosphere namelist
+    adapt_namelist(input_namelist=atmosphere_namelist_path,
+                   output_namelist=(RUNDIR / "icon_atmosphere.namelist").as_posix())
+    # Adapt master namelist
+    adapt_namelist(input_namelist=master_namelist_path,
+                   output_namelist=(RUNDIR / "icon_master.namelist").as_posix())

templates/real-from-ideal/prepare_member.sh

@@ -7,8 +7,6 @@ MEMBER=%MEMBER%
 
 # Common folder with data needed for all simulations
 COMMON_INIDATA_FOLDER=${WORKDIR}/inidata
-# Common folder for the same start date
-COMMON_DATE_FOLDER=${WORKDIR}/${STARTDATE}/inidata
 
 # Member folder
 MEMBER_DIR=${WORKDIR}/${STARTDATE}/${MEMBER}
@@ -21,4 +19,3 @@ cd ${MEMBER_DIR} || exit
 
 # Link all files from the common inidata folder and the common date folder
 ln -sf ${COMMON_INIDATA_FOLDER}/* .
-ln -sf ${COMMON_DATE_FOLDER}/* .

templates/real-from-ideal/run_ideal.sh

+# Get some variables provided by autosubmit.
+WORKDIR=%HPCROOTDIR%
+ICON_VERSION=%ICON_VERSION%
+
+STARTDATE=%SDATE%
+
+# Define rundir
+RUNDIR=${WORKDIR}/${STARTDATE}/ideal
+
+# Go to the ideal rundir
+cd ${RUNDIR}
+
+# Activate spack
+SPACK_ENV=${WORKDIR}/spack/share/spack/setup-env.sh
+source ${SPACK_ENV}
+# Load icon module
+spack load icon-nwp@%ICON_VERSION%
+
+# Set environment variable for eccodes-dwd definitions:
+source ${WORKDIR}/eccodes_defs.env
+
+# Run icon
+srun icon