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‎docs/datasets/climate_model_data.md‎

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```
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- Status: frozen (2019-03)
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- Variables:
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```
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- Status: monthly updated
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- Resolution: 0.44° and 0.11°
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/nfs/atmos/c2sm/cordex-reklies
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```
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‎docs/datasets/obs_reanalysis_data.md‎

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- Time period: 1985-2020
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‎docs/models/icon/SUMMARY.md‎

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* [Validate Custom Namelist](validate_custom_namelist.md)
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* [Run Probtest on Säntis](probtest.md)
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* [ICON-CLM](icon-clm.md)
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* [Input Data](input_data.md)
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* [Known Bugs](known_bugs.md)

‎docs/models/icon/icon-clm.md‎

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```
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Now your Python environment for SPICE is ready to go! 🚀
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### Option 1) Use Template from C2SM's EURO-CORDEX Run
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### Use Experiment Template from C2SM's EURO-CORDEX Run
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The official ICON-CLM setups are part of the [spice-setups :material-open-in-new:](https://github.com/C2SM/spice-setups){:target="_blank"} repository.
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Please follow the instructions in the [README :material-open-in-new:](https://github.com/C2SM/spice-setups/blob/main/README.md){:target="_blank"} file.
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### Option 2) Manually Create ERA5-driven 12 km case
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??? note "Show instructions for manual ERA5-driven case setup"
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From the SPICE root directory, let's create an experiment folder and
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copy the `sp001` case in there. If you want a different name for your
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experiment, just modify the `EXP` variable.
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!!! note
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The `sp001` is the standard `gcm2icon` test case defined in SPICE.
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It is run on the EURO-CORDEX domain at 44 km horizontal resolution
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and uses ERAInterim data as initial and boundary conditions.
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If you want to run this case, skip the next subsections and continue
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with [Install Python virtual environment](#install-python-virtual-environment).
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```bash
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EXP=EVAL-EUR12-ERA5
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mkdir -p ${SPICE_DIR}/experiments
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cp -r ${SPICE_DIR}/chain/gcm2icon/sp001 ${SPICE_DIR}/experiments
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mv ${SPICE_DIR}/experiments/sp001 ${SPICE_DIR}/experiments/${EXP}
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```
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Navigate to the directory where our new case is located:
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```bash
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cd ${SPICE_DIR}/experiments/${EXP}
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```
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##### Adjust boundary data to ERA5
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Since the standard spice case `sp001` takes ERAInterim data as input,
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we need to replace this with ERA5.
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```bash
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# Extract lines 17-23 from the source file
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source_lines=$(sed -n '17,23p' ${SPICE_DIR}/chain/boundary_data_options/era5/job_settings)
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# Define job_settings_file
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job_settings_file=${SPICE_DIR}/experiments/${EXP}/job_settings
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# Replace lines 165-173 in the target file with the extracted lines
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sed -i '165,173d' ${job_settings_file}
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line_num=165
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while IFS= read -r line; do
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sed -i "${line_num}i $line" ${job_settings_file}
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line_num=$((line_num + 1))
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done <<< "$source_lines"
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# Replace DKRZ data folder with Alps one
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sed -i 's|/pool/data/CLMcom/CCLM/reanalyses|/capstor/store/cscs/c2sm/c2sme/reanalyses_dkrz|g' ${job_settings_file}
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```
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We also need to replace the `prep` job. This is simply done by copying
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the corresponding file from the boundary data options to our working
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directory:
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```bash
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cp -v ${SPICE_DIR}/chain/boundary_data_options/era5/prep.job.sh ${SPICE_DIR}/experiments/${EXP}/scripts
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```
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##### Adapt `job_settings` file and fix ICON run script
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Now, there are still some necessary adaptations to the `job_settings` file to be done,
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which includes changing paths, ICON executable, meta data and some other settings.
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```bash
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# General settings
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sed -i "s|icon-nwp|icon-model|g" ${job_settings_file}
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sed -i "s|nco-5.1.9-7pd2hhq2wllvietf2rvclejzxgcjwosq|nco-5.1.9-yykwws3dmcypjzraijgzagmkb6ml2zzo|g" ${job_settings_file}
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sed -i "s|netcdf-c-4.9.2-azccejv4b3ba227zys3e7mkdo6fxxhlq|netcdf-c-4.9.2-5ijnfossknlii33dnqn7asnlmzst3444|g" ${job_settings_file}
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sed -i "s|netcdf-tools/2024:v1-rc1|netcdf-tools/2024:v1|g" ${job_settings_file}
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sed -i "s|EMAIL_ADDRESS= |[email protected] |g" ${job_settings_file}
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# EURO-CORDEX 12 km
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sed -i "s|sp001|${EXP}|g" ${job_settings_file}
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sed -i "s|PFDIR=\${SPDIR}/chain/gcm2icon|PFDIR=\${SPDIR}/experiments|g" ${job_settings_file}
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sed -i "s|WORKDIR=\${SPDIR}/chain|WORKDIR=\${SPDIR}/experiments/work|g" ${job_settings_file}
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sed -i "s|SCRATCHDIR=\${SPDIR}/chain|SCRATCHDIR=\${SPDIR}/experiments/scratch|g" ${job_settings_file}
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sed -i "s|ARCHIVE_OUTDIR=\${SPDIR}/chain|ARCHIVE_OUTDIR=\${SPDIR}/experiments|g" ${job_settings_file}
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sed -i "s|1979-01-01|1940-01-01|g" ${job_settings_file}
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sed -i "s|1979-03-01|2024-01-01|g" ${job_settings_file}
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sed -i "s|europe044|europe011|g" ${job_settings_file}
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sed -i "s|0.44|0.11|g" ${job_settings_file}
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sed -i "s|TIME_ICON=00-00:30:00|TIME_ICON=00-01:00:00|g" ${job_settings_file}
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sed -i "s|TIME_ARCH=\"00-00:30:00\"|TIME_ARCH=\"00-01:30:00\"|g" ${job_settings_file}
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sed -i "s|ITYPE_TS=1|ITYPE_TS=2|g" ${job_settings_file}
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sed -i "s|ITYPE_COMPRESS_POST=0|ITYPE_COMPRESS_POST=1|g" ${job_settings_file}
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sed -i "s|ITYPE_COMPRESS_ARCH=0|ITYPE_COMPRESS_ARCH=1|g" ${job_settings_file}
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sed -i '/ZML_SOIL/c\ZML_SOIL="0.005,0.025,0.07,0.16,0.34,0.7,1.42,2.86,5.74,11.5" # soil level' ${job_settings_file}
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```
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For better readability, the following replacements are done:
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**General settings:**
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| Original String | Replacement String | Description |
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|------------------------------------|-------------------------------------------------|----------------------------------------------|
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| `icon-nwp` | `icon-model` | Root directory of ICON model |
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| `nco-5.1.9-7pd2hhq2wllvietf2rvclejzxgcjwosq` | `nco-5.1.9-yykwws3dmcypjzraijgzagmkb6ml2zzo` | New nco path due to uenv |
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| `netcdf-c-4.9.2-azccejv4b3ba227zys3e7mkdo6fxxhlq` | `netcdf-c-4.9.2-5ijnfossknlii33dnqn7asnlmzst3444` | New netcdf path due to uenv |
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| `netcdf-tools/2024:v1-rc1` | `netcdf-tools/2024:v1` | New uenv on santis |
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| `EMAIL_ADDRESS= ` | `[email protected] ` | Add email address for notifications |
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**EURO-CORDEX 12 km**:
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| Original String | Replacement String | Description |
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|------------------------------------|-------------------------------------------------|----------------------------------------------|
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| `sp001` | `EVAL-EUR12-ERA5` | Name of the experiment |
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| `PFDIR=${SPDIR}/chain/gcm2icon` | `PFDIR=${SPDIR}/experiments` | Base directory of experiment |
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| `WORKDIR=${SPDIR}/chain` | `WORKDIR=${SPDIR}/experiments/work` | Working directory of experiment |
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| `SCRATCHDIR=${SPDIR}/chain` | `SCRATCHDIR=${SPDIR}/experiments/scratch` | Scratch directory of experiment |
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| `ARCHIVE_OUTDIR=${SPDIR}/chain` | `ARCHIVE_OUTDIR=${SPDIR}/experiments` | Archive directory of experiment |
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| `1979-01-01` | `1940-01-01` | Start date |
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| `1979-03-01` | `2024-01-01` | End date |
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| `europe044` | `europe011` | Folder names for ERA5 data |
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| `0.44` | `0.11` | netCDF metadata for 11 km run |
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| `TIME_ICON=00-00:30:00` | `TIME_ICON=00-01:00:00` | Increase walltime for icon job |
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| `TIME_ARCH="00-00:30:00"` | `TIME_ARCH="00-01:30:00"` | Increase walltime for arch job |
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| `ITYPE_TS=1` | `ITYPE_TS=2` | Yearly time series |
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| `ITYPE_COMPRESS_POST=0` | `ITYPE_COMPRESS_POST=1` | netCDF compression for post data |
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| `ITYPE_COMPRESS_ARCH=0` | `ITYPE_COMPRESS_ARCH=1` | netCDF compression for arch data |
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| `${ICONDIR}/run` | `bash ${ICONDIR}/run` | Explicitly call bash for the wrapper script |
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| `ZML_SOIL` | `ZML_SOIL=...` | New soil height values |
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!!! tip
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There might be even more changes to the `job_settings` file, depending on your setup.
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For example, your CSCS project needs to be set for the `PROJECT_ACCOUNT` variable.
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Also, for production runs, all variables starting with `GA_` should be set accordingly,
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as they are important for the netCDF meta data.
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Furthermore, additional data paths for transient aerosols, ozone and
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solar irradiation need to be set.
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```bash
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sed -i '/^TARGET_GRID=/a \
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\
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# Additional directories for aerosol treatment\
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DATADIR_AERO=/capstor/store/cscs/c2sm/c2sme/ICON-CLM/rcm_new\
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\
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KINNE_DIR=${DATADIR_AERO}/europe011/interpolated_aeop_R13B05\
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VOLC_DIR=${DATADIR_AERO}/independent/volcanic_aeropt\
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SP_DIR=${DATADIR_AERO}/independent/MACv2_simple_plumes_merged\
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\
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# Additional directory for ozone treatment\
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OZONE_DIR=${DATADIR_AERO}/europe011/ozone_europe011\
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\
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# Additional directory for solar irradiation\
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SOLAR_DIR=${DATADIR_AERO}/independent/solar_radiation\n' ${job_settings_file}
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```
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#### Changing the ICON namelist to match the official CLM configuration
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The official setup can be copied from our `icon-clm_patch` repository, which should already
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be present in `${SPICE_DIR}/src`.
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This also includes a change for the ICON run script around the `srun` command.
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```shell
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cp -v ${SPICE_DIR}/src/icon-clm_patch/icon.job.sh ${SPICE_DIR}/experiments/${EXP}/scripts
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cp -v ${SPICE_DIR}/src/icon-clm_patch/post.job.sh ${SPICE_DIR}/experiments/${EXP}/scripts
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```
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#### Optional: Warm start run for official ICON-CLM EVAL run
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Replace the ICON run script:
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```bash
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cp -v ${SPICE_DIR}/src/icon-clm_patch/icon-warm.job.sh ${SPICE_DIR}/experiments/${EXP}/scripts/icon.job.sh
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```
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It takes the restart file directory (1950/01):
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```bash
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/capstor/store/cscs/c2sm/c2sme/ICON-CLM/multifile_restart_ATMO_19500101T000000Z.mfr
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```
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Note that the `START_DATE` in the `job_settings` file needs to be adapted.
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### Run the case
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Navigate into your experiment folder and start the simulation chain with

‎docs/models/icon/input_data.md‎

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# Input data
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There are two types in input data sets available for ICON:
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- General input data for use cases / production runs
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- Testing input data for CI
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## Santis
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On Säntis, all ICON input data is collected in the project `cws01`.
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```shell
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/capstor/store/cscs/userlab/cws01/
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```
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### Directory Tree
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!!! warning "Work in Progress"
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The directory tree below is a rough outline of the planned structure. It is subject
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to change and non-exhaustive. If you find data that is in the wrong place, or if you
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want to have your data added to the project, please contact
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[Michael Jähn :material-open-in-new:](https://c2sm.ethz.ch/the-center/people/person-detail.html?persid=286091){:target="_blank"}.
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```
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/capstor/store/cscs/userlab/cws01/
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│
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├── ci/ # CI
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│ ├── testing-input-data/ # Input data for CI (git lfs repo)
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│ └── buildbot_data/ # Buildbot data
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│ ├── nwp/ # nwp test case data
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│ └── ref/ # Reference data (hashed)
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│
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├── input/ # All input data
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│ ├── icon/ # ICON-specific input
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│ │ ├── clm/ # ICON-CLM input
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│ │ │ ├── independent/ # Input independent of case/domain
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│ │ │ │ ├── aerosols/ # ICON-CLM aerosol input datasets
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│ │ │ │ ├── gcm/ # Global climate model boundary data
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│ │ │ │ └── rcm/ # Regional climate model boundary data
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│ │ │ │
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│ │ │ └── europe11/ # EURO-CORDEX 0.11° domain-specific input
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│ │ │ ├── aerosols/
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│ │ │ ├── gcm/
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│ │ │ └── rcm/
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│ │ │
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│ │ ├── global/ # ICON global model input
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│ │ │ ├── grids/ # ICON global grids at different resolutions
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│ │ │ │ ├── R02B04/
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│ │ │ │ │ ├── icon_grid_0013_R02B04_G.nc
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│ │ │ │ │ └── index.txt
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│ │ │ │ ├── R02B05/
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│ │ │ │ │ ├── icon_grid_0019_R02B05_G.nc
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│ │ │ │ │ ├── aerosol_kinne/ # Aerosol climatologies
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│ │ │ │ │ ├── external_parameter/ # Surface and land-sea mask data
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│ │ │ │ │ ├── initial_conditions/ # Initial state for atmosphere/ocean
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│ │ │ │ │ ├── ozone/ # Ozone datasets
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│ │ │ │ │ ├── ozone_old/ # Legacy ozone datasets
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│ │ │ │ │ └── sst_and_seaice/ # SST & sea-ice boundary conditions
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│ │ │ │ └── ... # Other grids (R02B06, R02B07, ...)
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│ │ │ │
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│ │ │ └── misc/ # Other ICON global input data
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│ │ │
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│ │ ├── public/ # Public data
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│ │ │ └── grids/ # Public grids from MPI-M and DWD
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│ │ │ ├── edzw/
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│ │ │ └── mpim/
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│ │ └── regional/ # ICON regional model input
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│ │
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│ └── misc/ # Non-ICON input (placeholder for future)
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│
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└── reference/ # Reference datasets
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├── observations/ # Ground-based or in-situ observations
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| └── eObs/ # E-OBS daily gridded meteorological data for Europe
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| ├── eObs28.0/
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| ├── eObs29.0/
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| ├── eObs30.0/
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| └── eObs31.0/
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├── reanalysis/ # Reanalysis datasets (e.g. ERA5)
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| ├── ERA5/
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| └── dkrz/ # Synced from DKRZ, ready-to-use for SPICE (CLM runs)
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| ├── ERA5/ # ERA5 (updated as soon as new data is available)
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| └── ERAInterim/ # ERAInterim (static)
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├── satellite/ # Satellite observations for validation
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└── model_comparisons/ # Reference data from other models
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```
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## Input data pools
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=== "Santis"
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```shell
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/capstor/store/cscs/userlab/cws01/input/icon
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```
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=== "Balfrin"
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```shell
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/scratch/mch/jenkins/icon/pool/data/ICON
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```
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=== "Euler"
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```shell
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/cluster/work/climate/icon_input
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```
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## Testing input data pool
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The input data for standard ICON tests are stored in a [Git-lfs repository :material-open-in-new:](https://gitlab.dkrz.de/icon/testing-input-data){:target="_blank"}.
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=== "Santis"
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```shell
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/capstor/store/cscs/userlab/cws01/ci/testing-input-data
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```
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=== "Balfrin"
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```shell
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/scratch/mch/icontest/testing-input-data
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```
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=== "Euler"
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```shell
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/cluster/work/climate/icon_testing_input
119+
```

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