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add run-MDTF [GFDL driver script] (#784)
* add run-MDTF [GFDL driver script] * update pathing * update readme * remove unused os import --------- Co-authored-by: Jess <20195932+wrongkindofdoctor@users.noreply.github.com>
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‎tools/run-MDTF/README.md‎

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# run-MDTF
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MDTF shell driver to assist model development at the GFDL <br />
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Command-line usage:
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```
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run-mdtf.sh -i /path/to/pp/dir/pp -o out_dir/mdtf -s startyr -e endyr
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```
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This script requires a user inputted `pod_config.json`. One is supplied by default, but may need to be updated in order to launch more PODs or update realm information!
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A new one can be supplied with the `-l` OPTARG.

‎tools/run-MDTF/config/pod_config.json‎

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{
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"Wheeler_Kiladis": {
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"realm": "atmos_cmip",
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"frequency": "day",
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"vars": ["rlut","pr","wap500","ua200","ua850"]
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},
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"MJO_suite": {
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"realm": "atmos_cmip",
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"frequency": "day",
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"vars": ["rlut","pr","ua200","ua850","va200","va850"]
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},
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"ocn_surf_flux_diag": {
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"realm": "atmos_cmip",
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"frequency": "day",
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"vars": ["ts","psl","sfcWind","huss","hfls","pr"]
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},
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"forcing_feedback": {
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"realm": "atmos_cmip",
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"frequency": "mon",
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"vars": ["ts","ta","hus","rsus","rsuscs","rsds","rsdscs","rsdt","rsut","rsutcs","rlut","rlutcs"]
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}
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}

‎tools/run-MDTF/config/template_config.jsonc‎

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{
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"pod_list" : [],
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"case_list":
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{
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"case_name":
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{
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"model": "test",
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"convention": "CMIP",
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"startdate": "",
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"enddate": "",
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"realm": ""
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}
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},
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"DATA_CATALOG": "",
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"OBS_DATA_ROOT": "/home/oar.gfdl.mdtf/mdtf/inputdata/obs_data",
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"WORK_DIR": "",
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"OUTPUT_DIR": "",
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"conda_root": "/home/oar.gfdl.mdtf/miniconda3",
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"conda_env_root": "/home/oar.gfdl.mdtf/miniconda3/envs",
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"micromamba_exe": "",
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"run_pp": true,
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"translate_data": true,
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"save_ps": false,
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"large_file": false,
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"save_pp_data": false,
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"make_variab_tar": false,
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"make_multicase_figure_html": false,
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"overwrite": false,
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"user_pp_scripts" : [],
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"verbose": 1
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}

‎tools/run-MDTF/run-MDTF.sh‎

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#!/bin/bash -f
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#SBATCH --job-name=run-MDTF.sh
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#SBATCH --time=4:00:00
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#set -x
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# dir references
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run_dir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
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mdtf_dir=/home/oar.gfdl.mdtf/mdtf/MDTF-diagnostics
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#mdtf_dir=/home/Jacob.Mims/mdtf/MDTF-diagnostics
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activate=/home/oar.gfdl.mdtf/miniconda3/bin/activate
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#TEST: /archive/jpk/fre/FMS2024.02_OM5_20240819/CM4.5v01_om5b06_piC_noBLING_xrefine_test4/gfdl.ncrc5-intel23-prod-openmp/pp/ starts 0001
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#TEST 2: /archive/djp/am5/am5f7b12r1/c96L65_am5f7b12r1_amip/gfdl.ncrc5-intel23-classic-prod-openmp/pp/ starts 1990
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usage() {
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echo "USAGE: run-mdtf.sh -i /path/to/pp/dir/pp -o out_dir/mdtf -s startyr -e endyr"
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echo "ADDITONAL OPTS:"
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echo "-l: custom config file for pods (default: config/pod_config.json) this can be used to set which PODs you would like to run and define the realm to grab vars from"
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}
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# handle arguments
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tempdir=""
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pod_config=""
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declare -a pods=()
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while getopts "hi:o:s:e:p:t:l:" arg; do
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case "${arg}" in
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h)
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usage
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exit
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;;
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i)
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if [ -d $OPTARG ]; then
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ppdir="${OPTARG}"
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else
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echo "ERROR: $1 is not a directory"
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usage
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exit
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fi
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;;
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o)
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if [ -d "${OPTARG}" ]; then
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outdir="${OPTARG}"
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else
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mkdir -p "${OPTARG}"
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outdir="${OPTARG}"
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fi
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;;
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s)
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startyr="${OPTARG}"
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;;
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e)
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endyr="${OPTARG}"
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;;
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p)
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pods+=("$OPTARG")
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;;
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t)
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tempdir="${OPTARG}"
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;;
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l)
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pod_config="${OPTARG}"
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esac
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done
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shift $((OPTIND-1))
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if ! [ -d $outdir/config ]; then
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mkdir -p $outdir/config
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fi
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if [ -z $tempdir ]; then
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wkdir=$outdir
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else
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wkdir=$tempdir
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fi
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if [ -z $pod_config ]; then
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pod_config="$run_dir/config/pod_config.json"
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fi
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# check to see if catalog exists
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# ^..^
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# /o o\
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# oo--oo~~~
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echo "looking for catalog in $ppdir"
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cat=$(grep -s -H "esmcat_version" $ppdir/*.json | cut -d: -f1)
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if [[ "$cat" == "" ]]; then
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env=/nbhome/fms/conda/envs/fre-2025.01
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source $activate $env
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fre catalog builder --overwrite $ppdir $outdir/catalog
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cat=$outdir/catalog.json
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echo "new catalog generated: $cat"
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else
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echo "found catalog: $cat"
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fi
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# edit template config file
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cp $run_dir/config/template_config.jsonc $outdir
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f=$outdir/template_config.jsonc
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if [ ! -f $f ]; then
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echo "ERROR: failed to find $f"
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exit 0
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fi
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config='"DATA_CATALOG": "",'
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config_edit='"DATA_CATALOG": "'"${cat}"'",'
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sed -i "s|$config|$config_edit|ig" $f
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config='"WORK_DIR": "",'
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config_edit='"WORK_DIR": "'"${wkdir}"'",'
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sed -i "s|$config|$config_edit|ig" $f
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config='"OUTPUT_DIR": "",'
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config_edit='"OUTPUT_DIR": "'"${outdir}"'",'
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sed -i "s|$config|$config_edit|ig" $f
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config='"startdate": "",'
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config_edit='"startdate": "'"${startyr}"'",'
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sed -i "s|$config|$config_edit|ig" $f
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config='"enddate": ""'
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config_edit='"enddate": "'"${endyr}"'"'
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sed -i "s|$config|$config_edit|ig" $f
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echo "edited file $f"
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# load mdtf base conda env
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env=/home/oar.gfdl.mdtf/miniconda3/envs/_MDTF_base
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source $activate $env
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#generate config files
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python $run_dir/scripts/gen_config.py $outdir/ $pod_config
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# launch the mdtf with the config files
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for f in $(ls ${outdir}/config) ; do
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echo "launching MDTF with $f"
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"$mdtf_dir"/mdtf -f $outdir/config/$f
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done
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# consolidate outputs into index
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cp $run_dir/scripts/index.html $outdir/
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cp $run_dir/scripts/mdtf_diag_banner.png $outdir/
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python $run_dir/scripts/gen_index.py $outdir/ $pod_config
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exit 0

‎tools/run-MDTF/run-MDTF_frepp.csh‎

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#!/bin/csh -f
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#--------------------------------------
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#PBS -N mdtf_frepp_driver
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#PBS -l size=1
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#PBS -l walltime=60:00:00
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#PBS -r y
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#PBS -j oe
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#PBS -o
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#PBS -q batch
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#--------------------------------------
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# clean up tmpdir
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wipetmp
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# fields set by frepp
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set argu
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set descriptor
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set in_data_dir
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set out_dir
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set WORKDIR
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set mode
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set yr1
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set yr2
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set databegyr
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set dataendyr
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set datachunk
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set staticfile
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set script_path
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set fremodule
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set mode = "GFDL"
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if (-d ${out_dir}/mdtf) then
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echo "Output directory already exists, removing"
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rm -fr ${out_dir}/mdtf
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endif
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set ppdir = `echo ${in_data_dir} | sed 's|\(.*pp\).*|\1|'`
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/home/oar.gfdl.mdtf/mdtf/MDTF-diagnostics/tools/run-MDTF/run-MDTF.sh -i ${ppdir} -o ${out_dir}/mdtf -s $yr1 -e $yr2
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‎tools/run-MDTF/scripts/gen_config.py‎

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# script to make the MDTF runtime configs for each realm/freq to run requested PODs
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import sys
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import json
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import copy
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# load pod information
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with open(sys.argv[2]) as f:
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pods = json.load(f)
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# load template config information
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with open(sys.argv[1]+'template_config.jsonc') as f:
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template_config = json.load(f)
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# create dict object for each pod
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config_files = {}
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for p in pods:
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config_name = f'{p}_config'
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config_realm = pods[p]['realm']
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config_files[config_name] = copy.deepcopy(template_config)
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config_files[config_name]['case_list']['case_name']['realm'] = config_realm
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config_files[config_name]['case_list'][config_realm] = config_files[config_name]['case_list'].pop('case_name')
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# add pods to cooresponding config file
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for p in pods:
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config_file = f"{p}_config"
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config_files[config_file]['pod_list'].append(p)
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#write out config files
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for c in config_files:
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with open(sys.argv[1]+f"config/{c}.jsonc", "w") as f:
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f.write(json.dumps(config_files[c], indent=2))

‎tools/run-MDTF/scripts/gen_index.py‎

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# script to create a simple index.html for automated mdtf runs
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import sys
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import os
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import json
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out_dir = sys.argv[1]
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# load pod information
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with open(sys.argv[2]) as f:
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pods = json.load(f)
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index_file = open(f'{out_dir}/index.html', 'a')
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pod_htmls = {}
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pods = [p for p in pods]
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mdtf_outputs = [os.path.join(out_dir, d) for d in os.listdir(out_dir) if 'MDTF_output' in d]
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for d in mdtf_outputs:
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list_d = os.listdir(d)
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for p in pods:
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if p in list_d:
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pod_dir = os.path.join(d, p)
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file_path = os.path.join(pod_dir, f'{p}.html')
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if os.path.exists(file_path):
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print(p)
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index_file.write(f'<a href="{file_path}"> {p} </a>')
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index_file.close()

‎tools/run-MDTF/scripts/index.html‎

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<HTML>
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<HEAD>
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<meta http-equiv="expires" content="Fri, 01 Sep 00:00:00 EST 2025">
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<TITLE>MDTF-Diagnostics</TITLE>
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</HEAD>
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<BODY BGCOLOR="white">
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<IMG SRC="mdtf_diag_banner.png" border=0 usemap="#logo">
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<br clear=left>
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<p> Completed PODs </p>
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<HR SIZE=2 WIDTH="100%" ALIGN="LEFT" NOSHADE>
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‎tools/run-MDTF/scripts/mdtf_diag_banner.png‎

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