add first example script for 01_real-from-ideal.sh - currently not working for...

add first example script for 01_real-from-ideal.sh - currently not working for a couple of reasons but working on it to be able to run it via gitlab runners

examples/01_real-from-ideal.sh

+#!/bin bash
+set -euo pipefail
+
+STAGE=${1:-}
+
+function help() {
+  echo "Need to provide a integer for the stage we want to run."
+  echo " e.g."
+  echo " - 0: Build Icon and python environemnts"
+  echo " - 1: Run the ideal case used to initialize a real run from"
+  echo " - 2: Run the real case"
+  echo " - 3: postprocess outputs"
+}
+
+if [ -z "$STAGE" ]; then
+  help
+  exit 1
+fi
+
+if [[ "$STAGE" -lt 0 ]] || [[ "$STAGE" -gt 3 ]]; then
+  echo "invalid stage id: $STAGE"
+  help
+  exit 2
+fi
+
+
+AUTOSUBMIT_VERSION="4.0.76"
+
+SCRIPTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+PROJECT_ROOT=$(readlink -f $SCRIPTDIR/../)
+
+OUTPUTDIR=$PROJECT_ROOT/output
+mkdir -p $OUTPUTDIR
+
+WORKDIR=$SCRATCH/autosubmit_rundir
+PROJECTNAME='ls-mayer'
+mkdir -p $WORKDIR/$PROJECTNAME/$(whoami)
+
+virtualenv -p python3 pyenv
+. pyenv/bin/activate
+
+cat > requirements.txt <<EOF
+autosubmit==$AUTOSUBMIT_VERSION
+EOF
+pip install -r requirements.txt
+
+if [ ! -e ./.autosubmitrc ] || [ ! -e autosubmit ] ; then
+  # Note that we create autosubmit here with --local to create the .autosubmitrc not in the home dir
+  # This requires to run all autosubmit calls from within this root dir.
+  autosubmit configure --local -db $(pwd)/autosubmit -dbf autosubmit.db -lr $(pwd)/autosubmit
+fi
+
+if [ ! -e autosubmit/autosubmit.db ]; then
+  autosubmit install
+fi
+
+PROJECT_ORIGIN="https://gitlab.physik.uni-muenchen.de/w2w/autosubmit-icon-today.git"
+PROJECT_BRANCH="master"
+EXPID=rfi001
+
+if [ ! -e autosubmit/$EXPID/ ]; then
+  mkdir -p autosubmit/$EXPID/
+  autosubmit expid -min -H lmu -d myiconsim -repo $PROJECT_ORIGIN -b $PROJECT_BRANCH &> >(tee autosubmit/$EXPID/log.autosubmit.expid)
+  AUTOID=$(grep Experiment autosubmit/$EXPID/log.autosubmit.expid | awk '{print $2}')
+  mv -v autosubmit/$AUTOID/* autosubmit/$EXPID
+  rmdir -v autosubmit/$AUTOID
+fi
+
+cat > autosubmit/$EXPID/conf/minimal.yml <<EOF
+ICON_CASE: "real-from-ideal"
+
+CONFIG:
+  AUTOSUBMIT_VERSION: "$AUTOSUBMIT_VERSION"
+  TOTALJOBS: 20
+  MAXWAITINGJOBS: 20
+DEFAULT:
+  EXPID: "$EXPID"
+  HPCARCH: "LOCAL" # use LMU to run on cluster
+  CUSTOM_CONFIG:
+    PRE:
+      - "%PROJDIR%/conf/common"
+      - "%PROJDIR%/conf/%ICON_CASE%"
+
+PROJECT:
+  PROJECT_TYPE: "git"
+  PROJECT_DESTINATION: "autosubmit-icon-today"
+GIT:
+  PROJECT_ORIGIN: "$PROJECT_ORIGIN"
+  PROJECT_BRANCH: "$PROJECT_BRANCH"
+  PROJECT_COMMIT: ""
+  PROJECT_SUBMODULES: ""
+  FETCH_SINGLE_BRANCH: True
+EOF
+
+
+cat > autosubmit/${EXPID}/conf/myplatforms.yml <<EOF
+#Platforms:
+#  LMU:
+#    TYPE: slurm
+#    HOST: $HOSTNAME
+#    PROJECT: $PROJECTNAME
+#    USER: $(whoami)
+#    SCRATCH_DIR: $WORKDIR
+#    ADD_PROJECT_TO_HOST: False
+#    MAX_WALLCLOCK: '48:00'
+#    TEMP_DIR: ''
+#    CUSTOM_DIRECTIVES: "#SBATCH --export=ALL,OMPI_MCA_btl_tcp_if_include=10.0.0.0/8"
+#
+#  LRZ:
+#    # TYPE: slurm
+#    TYPE: ps
+#    HOST: LRZ-kcs
+#    PROJECT: lxcusers
+#    USER: ra57nun
+#    SCRATCH_DIR: /dss/dssfs02/lwp-dss-0001/uh211/uh211-dss-0000/ra57nun
+#    ADD_PROJECT_TO_HOST: False
+#    MAX_WALLCLOCK: '48:00'
+#    TEMP_DIR: ''
+EOF
+
+cat > autosubmit/${EXPID}/conf/myconf.yml <<EOF
+spack:
+  init: "module load spack/2023.02 gcc/11.3.0 openmpi/4.1.4-gcc-11.3.0 netcdf-fortran/4.6.0-gcc-11.3.0-openmpi" # command to load spack environment, e.g. module load spack, use spack/setup-env.sh if empty
+  url: https://github.com/spack/spack.git # url to download spack if necessary
+  branch: develop # if downloaded, branch name to use
+  compiler: "gcc@11.3.0" # desired compiler for spack
+  root: "%HPCROOTDIR%/../spack" # path to a spack install, will be downloaded to if not present
+  externals: "slurm"
+  user_cache_path:  "%HPCROOTDIR%/../spack_user_cache_path" # spack puts data here when bootstrapping, leave empty to use home folder
+  user_config_path: "%HPCROOTDIR%/../spack_user_config_path" # spack puts data here when bootstrapping, leave empty to use home folder
+  disable_local_config: false # if true, spack installs into spack source dir
+
+icon:
+  #build_cmd: "icon-nwp@%ICON.VERSION%% %SPACK.COMPILER%+debug+petsc target=x86_64_v2 ^openmpi+pmi+legacylaunchers schedulers=slurm fabrics=ucx ucx+dc+dm+ib_hw_tm+mlx5_dv+rc+rdmacm+thread_multiple+ud+verbs"
+  build_cmd: "icon-nwp@%ICON.VERSION%% %SPACK.COMPILER%+debug+petsc target=x86_64_v2"
+  version: psp
+
+data_management:
+  # Where do we put the output files afterwards?
+  local_destination_folder: $OUTPUTDIR/
+
+atmosphere_namelist: |
+  icon_nwp_phys:
+    psp_mode: 1
+atmosphere_namelist_ideal: |
+  icon_nwp_phys:
+    psp_mode: 1
+EOF
+
+if [ "$STAGE" -eq 0 ]; then
+  echo "Running Stage 0"
+  autosubmit create ${EXPID} -np
+  autosubmit refresh ${EXPID}
+  autosubmit setstatus ${EXPID} -ft PREPARE_EXPERIMENT -t SUSPENDED -s -np
+  autosubmit run ${EXPID}
+fi
+
+if [ "$STAGE" -eq 1 ]; then
+  echo "Running Stage 1"
+  autosubmit setstatus ${EXPID} -fs SUSPENDED -t WAITING -s -np
+  autosubmit setstatus ${EXPID} -ft EXTPAR_FROM_IDEALIZED FG_ANA_FROM_IDEALIZED -t SUSPENDED -s -np
+  autosubmit run ${EXPID}
+fi
+
+if [ "$STAGE" -eq 2 ]; then
+  echo "Running Stage 2"
+  autosubmit setstatus ${EXPID} -fs SUSPENDED -t WAITING -s -np
+  autosubmit setstatus ${EXPID} -ft TRANSFER -t SUSPENDED -s -np
+  autosubmit run ${EXPID}
+fi
+
+if [ "$STAGE" -eq 3 ]; then
+  echo "Running Stage 3"
+  autosubmit setstatus ${EXPID} -fs SUSPENDED -t WAITING -s -np
+  autosubmit run ${EXPID}
+fi