#!/bin/bash # This script sets up and launches a (series of) simulation(s). # RECOMMENDATION: use main.sh to drive it (do not run it directly) set -eu # EXPERT-LEVEL CHOICES, only available in setup.sh, not in main.sh : #################################################################### function define_expert_options() { # optim: either "" or "-debug" to compile in debug mode (slower but better diagnosis of segfaults) optim="" # "n" or "y". If testmode="y", then simulations run for a single day per period. # NOTE: you must set mthend accordingly ! testmode="n" # Radiative code: "oldrad" / "rrtm" / "ecrad" rad="rrtm" # !!! STRONG recommendation : experiments with DIFFERENT Orchidee or aerosol options should be performed in DIFFERENT LMDZ_Setup folders # !!! (especially as they may need different initial files) # AEROSOLS : "n" (=no) / "clim" (=average 1995-2014) / "spla" (interactive dust and sea salt) # (WARNING : if you first run the scripts with aerosols=n, then you want to change to =clim , # you'll need to remove the INIT and LIMIT folders that have been created, then run main.sh with init=1 # in order to re-run the initialisation job, which downloads the aerosol files and interpolates them) aerosols="clim" # SURFACE/VEGETATION SCHEME # - "none" (bucket scheme) / "CMIP6" (orchidee version used in CMIP exercise) / "7983" (orch2.2) / "7994" (trunk) # If you need other orch versions, and also require XIOS, you'll need to create the appropriate files in DEF/XMLfilesOR... veget="CMIP6" # New snow scheme INLANDSIS! "y" / "n" # This flag activates INLANDSIS compilation; not yet done : treatment of specific restart and def file inlandsis="n" # netcdf: 0 (use existing library) / 1 (recompile netcdf, slow) / le chemin vers la librarie netcdf netcdf=0 # --->>> ALSO PAY ATTENTION TO OUTPUT files, frequency, level ------------- # With IOIPSL : Choose your config.def among the versions available in DEF, # copy it as config.def (the copy is done automatically for "iso"), # edit it and set up output files, frequencies and levels. # NB : For aerosols=spla, output level minimum 4 is required to output the specific variables. # For aerosols=n, the corresponding flags will automatically be set to "n". # With XIOS : adjust DEF/XMLfiles*/file*xml } # /!\ DO NOT EDIT BELOW UNLESS YOU KNOW WHAT YOU ARE DOING /!\ function enable_platform() { # In job scripts, sed platform-specific headers local file="$1" local platform case ${hostname:0:5} in jean-) platform="JZ";; spiri) platform="SP";; adast) platform="ADS";; *) echo "Warning: $hostname is not a known job platform (ignore if running locally)"; return 0;; esac sed -i'' -e "s/^#@$platform//" "$file" } function load_install_lib() { # Fetch and source install_lmdz.sh to get `myget` if [[ ! -f "install_lmdz.sh" ]]; then wget --no-cache "http://svn.lmd.jussieu.fr/LMDZ/BOL/script_install/install_lmdz.sh" fi # shellcheck disable=SC1090 source <(sed 's/function \(.*\) {/function installlmdz_\1 {/g' install_lmdz.sh) # source with a namespace for functions function myget { installlmdz_myget "$@"; } } function set_default_params() { # Default value of script parameters SIM=$(basename "$local")CTL # name phylmd="lmd" #option -p $phylmd for makelmdz cosp="n" # COSP xios="n" #XIOS # Nudging : ok_guide="n" # With nudging, use real calendar (climato=0) and monthly integrations climato=1 freq="mo" # frequence mensuelle mo ou annuelle yr # NB : the run stops in the BEGINNING of mthend (test "next=stopsim") mthini=200001 mthend=200501 resol="144x142x79" version="20230412.trunk" svn="" init=1 LIMIT="LIMIT" case $rad in oldrad) iflag_rrtm=0; NSW=2;; rrtm) iflag_rrtm=1; NSW=6;; ecrad) iflag_rrtm=2; NSW=6;; esac } function read_cmdline_args() { while (($# > 0)); do case $1 in "-h") cat <<........fin setup.sh can be launched/driven by main.sh; some options can only be specified in setup.sh (ex: veget, aerosols). setup.sh [-v version] [-r svn_release] [-init INIT] [-d 96x95x79] [-f mo] [-nudging] -v "version" like 20150828.trunk; see https://lmdz.lmd.jussieu.fr/Distrib/LISMOI.trunk (default <$version>) -r "svn_release" either the svn release number or "last" (default <$svn>) -d IMxJMxLM to run in resolution IM x JM x LM (default <$resol>) -install pour installer et compiler le modele -f mo/yr pour tourner en mensuel ou annuel (default <$freq>) "INIT" 1: creates INIT and LIMIT 0: reads from INIT and LIMIT SIMU: reads from preexisting simulation SIMU and LIMIT (default <$init>) -nudging to run with nudging. Nudging files must be created independently -p the physics to use (default <$phylmd>) -name install folder name (default <$SIM>) Other options available (see "options" section in the script) ........fin exit;; "-v") version="$2"; shift; shift;; "-r") svn=$2; shift; shift;; "-d") resol=$2; shift; shift;; "-f") freq=$2; shift; shift;; "-p") phylmd=$2; shift; shift;; "-name") SIM=$2; shift; shift;; "-cosp") cosp=y; shift;; "-xios") xios=y; shift;; "-init") init=$2; shift; shift;; "-nudging") ok_guide=y; shift;; "-climato") climato=$2; shift; shift;; "-mthini") mthini=$2; shift; shift;; "-mthend") mthend=$2; shift; shift;; *) echo "unexpected $1"; $0 -h; exit esac done # Initialisation if [[ $init = 1 || $init = 0 ]]; then INIT="INIT" else INIT=$init fi yearini=$(echo "$mthini" | cut -c-4) if [[ $freq = yr ]]; then stopsim=$(echo "$mthend" | cut -c-4); else stopsim=$mthend; fi if [[ -d $SIM ]]; then echo "La simulation $SIM existe deja. Il est conseillé d'arrêter et de vérifier." echo "Si vous êtes sûr de vous, vous pouvez la prolonger. Voulez vous la prolonger ? (y/n)" read -r ans if [[ $ans != y ]]; then exit 1; fi fi ###################################################################### # Choix du nombre de processeurs # NOTES : # omp=8 by default (for Jean-Zay must be a divisor of 40 procs/node), but we need # omp=1 for SPLA (only MPI parallelisation) # omp=2 for veget=CMIP6+XIOS beacause of a bug in ORCHIDEE/src_xml/xios_orchidee.f90 ###################################################################### jm=$(echo "$resol" | cut -dx -f2) (( mpi = ( jm + 1 ) / 2 )) omp=8 if [[ $aerosols = "spla" ]]; then omp=1; fi if [[ $veget = "CMIP6" && $xios = "y" ]]; then omp=2; fi if [[ $mpi -gt $NB_MPI_MAX ]]; then mpi=$NB_MPI_MAX; fi if [[ $omp -gt $NB_OMP_MAX ]]; then omp=$NB_OMP_MAX; fi # Compute how many mpi per node (required e.g. for Adastra) mpi_per_node=0 if [[ $NB_CORE_PER_NODE_MAX -gt 0 ]]; then local N_omp_mt=1 if [[ $omp -gt 1 ]]; then (( N_omp_mt = omp / N_HYPERTHREADING )); fi # take into account hyperthreading (( mpi_per_node = NB_CORE_PER_NODE_MAX / N_omp_mt )) if [[ mpi_per_node -gt mpi ]]; then mpi_per_node=$mpi; fi fi echo "Total MPI=$mpi (PER NODE=$mpi_per_node), OMP=$omp" } function ensure_correct_option_combinations() { # AVOID COMBINATIONS OF OPTIONS THAT DON'T WORK in user choices if [[ $ok_guide = y && $climato = 1 ]]; then echo "STOP: Running nudged simulations with climatological SSTs is not planned. Change to <0> or modify the setup (experts)"; exit 1 fi if [[ $climato = 0 && $freq = "yr" ]]; then echo "STOP: Running simulations with interannual SSTs is possible only month by month and a true calendar." echo "Change to <1> or to or modify setup.sh (experts)"; exit 1 fi # (Temporary) Constraints for aerosols=spla : # --> resolution 128x88x79 and rad=rrtm if [[ $aerosols = "spla" && $resol != "128x88x79" ]]; then echo 'STOP: For now, requires , and uses the zoomed grid from gcm.def_zNAfrica_BiJe, for which forcing & initial files are available' echo "Right now resol=<$resol>" exit 1 fi if [[ $rad = "ecrad" && $phylmd != "lmd" ]]; then echo " is only supported for here" # (Amaury) I added this check because we fetch ecrad data from libf/phylmd/ecrad/data only. fi } function install_model() { mkdir -p "$LMDZD" local ins_xios ins_cosp ins_aero ins_inlandsis if [[ $xios = "y" ]]; then ins_xios="-xios"; else ins_xios=""; fi if [[ $cosp = "y" ]]; then ins_cosp="-cosp v1"; else ins_cosp=""; fi if [[ $aerosols = "spla" ]]; then ins_aero="-spla"; else ins_aero=""; fi if [[ $inlandsis = "y" ]]; then ins_inlandsis="-inlandsis"; else ins_inlandsis=""; fi if [[ -n $svn ]]; then svnopt="-r $svn"; else svnopt=""; fi version_name=LMDZ$(echo "$version" | sed -e 's/-v//g' -e 's/-unstable//' -e 's/-r/r/' -e 's/ //g') LMDZname="${version_name}${svn}OR$veget${ins_xios}" MODEL="$LMDZD/$LMDZname/modipsl/modeles/LMDZ" if [[ -d $MODEL ]]; then echo "Found existing install at MODEL=$MODEL"; fi echo "Installing model" cd "$LMDZD" cp "$local/install_lmdz.sh" . chmod +x install_lmdz.sh local make_j=8 # We launch using $MPICMD, except if it's using mpirun (no srun equivalent for bash script) => if supported, the compilation runs in a cluster job jobcmd="\"$RUNBASHCMD $make_j\"" if [[ ${hostname:0:5} = "jean-" ]]; then jobcmd="\"$RUNBASHCMD $make_j --partition=compil\""; fi # On JeanZay: compile on the partition if [[ $(echo "$RUNBASHCMD" | cut -c -4) = "bash" ]]; then jobcmd="bash" fi echo "./install_lmdz.sh -noclean $optim -v $version $svnopt -d $resol -rad $rad -bench 0 -parallel mpi_omp $ins_cosp $ins_xios $ins_aero $ins_inlandsis -name $LMDZname -veget $veget -netcdf $netcdf -arch $ARCH -make_j $make_j -jobcmd $jobcmd" >> install_lmdz_options.$$.sh chmod +x install_lmdz_options.$$.sh echo "Running install_lmdz_options.$$.sh" set -o pipefail gcm=$MODEL/$(./install_lmdz_options.$$.sh | tee /dev/tty | tail -n 1 | sed -n "s:.* executable is \(.*\.e\).*:\1:p") set +o pipefail mv install_lmdz.sh install_lmdz.$$.sh cd "$local" } function setup_def() { # modify various .def in ./DEF (+ xios xml as needed) cd "$local" # Utilisation des .def_iso pour LMDZ-ISOtopes if [[ $phylmd = "lmdiso" ]]; then for file_iso in $(ls DEF | grep _iso); do cp DEF/"$file_iso" DEF/"${file_iso%%_iso}" done fi ###################################################################### # Choix de la grille verticale ###################################################################### lm=$(echo "$resol" | cut -dx -f3) if [ ! -f "DEF/L$lm.def" ]; then echo "STOP: Résolution verticale non prévue - créer un fichier DEF/L$lm.def"; exit 1 else sed -i'' -e "s/INCLUDEDEF=L.*.def/INCLUDEDEF=L$lm.def/" DEF/run.def fi ###################################################################### # Changements dans les fichiers DEF/*def # (ils vont se repercuter dans les repertoires de simulation $local/$SIM et de run $SIMRUNDIR) ###################################################################### # Choix du fichier tracer.def coherent avec l'option "aerosols" # NOTE : Le nouveau tracer.def_nospla par defaut n'inclut pas Rn-Pb; # si on les veut, il faut utiliser ci-dessous; a la place, tracer_RN_PB.def #--------------------------------------------------------------------- # NB : Les traceurs absents de start* files sont initialises=0 dans le code if [[ $aerosols = "spla" ]]; then # nouveau tracer.def (remplace "traceur.def") cp DEF/tracer.def_spla DEF/tracer.def elif [[ $phylmd = "lmdiso" ]]; then # déjà copié si 'y' cp DEF/tracer.def_nospla DEF/tracer.def fi # TEMPORAIREMENT pour spla on force l'utilisation de gcm.def_zNAfrica_BiJe (avec resolution 128x88x79) #---------------------------------------------------------------------- if [[ $aerosols = "spla" ]]; then cp DEF/gcm.def_zNAfrica_BiJe DEF/gcm.def; fi # Inscription du choix ok_guide dans DEF/guide.def #--------------------------------------------------------------------- sed -i'' -e 's/ok_guide=.*.$/ok_guide='$ok_guide'/' DEF/guide.def # Inscription du type de calendrier (qui est fonction de $climato) dans DEF/run.def #--------------------------------------------------------------------- # NB Contrairement a ce qui est ecrit dans les fichiers run.def standard, # dans ce tutorial le choix earth_365d n'est pas disponible, et earth_366d s'appelle gregorian if [[ $climato = 0 ]]; then calend="gregorian"; else calend="earth_360d"; fi sed -i'' -e 's/calend=.*.$/calend='$calend'/' DEF/run.def # Changements dans config.def (pre-choisi, et regle pour output si utilisation avec IOIPSL) # cf options veget, aerosols, cosp, xios #--------------------------------------------------------------------- if [[ $veget = "none" ]]; then VEGET="n"; else VEGET="y"; fi sed -i'' -e 's/VEGET=.*.$/VEGET='$VEGET'/' DEF/config.def if [[ $aerosols = "n" ]]; then # set flag_aerosols=0 and flags ok_ade&co=n sed -i'' -e 's/^ok_cdnc=.*.$/ok_cdnc=n/' -e 's/^ok_ade=.*.$/ok_ade=n/' -e 's/^ok_aie=.*.$/ok_aie=n/' -e 's/^ok_alw=.*.$/ok_alw=n/' -e 's/^flag_aerosol=.*.$/flag_aerosol=0/' DEF/config.def fi # COSP : ok_cosp desactive COSP si on a compile avec; il ne l'active pas si on a compile sans sed -i'' -e 's/ok_cosp.*.$/ok_cosp='$cosp'/' DEF/config.def if [[ $cosp = "y" ]]; then \cp -f "$MODEL"/DefLists/cosp*.txt "$local"/DEF/; fi # Sorties LMDZ en fonction de l'option "xios" sed -i'' -e 's/ok_all_xml=.*.$/ok_all_xml='$xios'/' DEF/config.def # Ajuster physiq.def en fonction de radiative code (default: values for rad=rrtm) # Pour isotopes=y , mettre iflag_ice_thermo=0 au lieu de 1 #--------------------------------------------------------------------- sed -i'' -e "s/iflag_rrtm=.*.$/iflag_rrtm=$iflag_rrtm/" -e "s/NSW=.*.$/NSW=$NSW/" DEF/physiq.def sed -i"" -e "s:directory_name.*$:directory_name=\"$MODEL/libf/phylmd/ecrad/data\",:" DEF/namelist_ecrad if [[ $phylmd = "lmdiso" ]]; then iflag_ice_thermo=0; else iflag_ice_thermo=1; fi sed -i -e 's/iflag_ice_thermo=.*.$/iflag_ice_thermo='$iflag_ice_thermo'/' DEF/physiq.def # Choix de orchidee.def en fonction de orchidee_rev; modification pour xios # NOTE separate orchidee_pft.def file for ORCHIDEE trunk post-CMIP6 #--------------------------------------------------------------------- orchidee_def=orchidee.def_6.1 orchidee_pft_def="" if [[ $veget = "7983" ]]; then orchidee_def=orchidee.def_6.2work elif [[ $veget = "7994" ]]; then orchidee_def=orchidee.def_6.4work orchidee_pft_def=orchidee_pft.def_6.4work if ! grep "INCLUDEDEF=orchidee_pft.def" DEF/run.def; then sed -i'' -e 's/INCLUDEDEF=orchidee.def/INCLUDEDEF=orchidee.def\nINCLUDEDEF=orchidee_pft.def/' DEF/run.def; fi fi cp -f DEF/$orchidee_def DEF/orchidee.def if [[ $orchidee_pft_def != "" ]]; then cp -f DEF/$orchidee_pft_def DEF/orchidee_pft.def; fi # Only for veget=CMIP6 it is still possible to use IOIPSL; newer versions of orchidee.def have XIOS_ORCHIDEE_OK = y sed -i'' -e 's/XIOS_ORCHIDEE_OK =.*.$/XIOS_ORCHIDEE_OK = '$xios'/' DEF/orchidee.def ###################################################################### # Si on tourne avec XIOS, mise a jour des fichiers context et field* dans XMLfilesLMDZ # (ils vont se repercuter dans les repertoires de simulation $local/$SIM et de run $SIMRUNDIR) ###################################################################### if [[ $xios = y ]]; then cp -f "$MODEL"/DefLists/context_lmdz.xml "$local"/DEF/XMLfilesLMDZ/. cp -f "$MODEL"/DefLists/field_def_lmdz.xml "$local"/DEF/XMLfilesLMDZ/. if [[ $cosp = y ]]; then cp -f "$MODEL"/DefLists/field_def_cosp1.xml "$local"/DEF/XMLfilesLMDZ/.; fi fi } function setup_ce0l() { # Verification de l'existance de l'état initial, compilation eventuelle pour sa creation if [[ ! -d $INIT ]]; then if [[ $init = 0 ]]; then echo "STOP: Récuperer les repertoires $INIT ou lancer avec option -init"; exit 1 else # Compile ce0l cd "$MODEL" sed -e 's/gcm$/ce0l/' compile.sh > compile_ce0l.sh; chmod +x compile_ce0l.sh echo "Compiling ce0l" if ! ./compile_ce0l.sh &> ce0l.log; then echo "STOP: ce0l compilation failed, see $MODEL/ce0l.log"; exit 1; fi echo "Compiled ce0l" ce0l=${gcm/gcm/ce0l} cd "$local" fi elif [[ $init = 1 ]]; then echo "STOP: Vous essayez d initialiser le modele mais $INIT existe deja"; exit 1 fi } function setup_simu() { SIMRUNTOPDIR="$SIMRUNBASEDIR/$(basename "$local")" SIMRUNDIR=$SIMRUNTOPDIR mkdir -p "$SIMRUNDIR" cd "$SIMRUNDIR" echo "La simulation s'exécutera sur $SIMRUNDIR" ##################################################################### # Creation du repertoire $SIM s'il n'existe pas deja ##################################################################### if [[ ! -d $local/$SIM ]]; then mkdir "$local/$SIM" cd "$local" # Edit reb.sh cp reb.sh "$local/$SIM/reb.sh"; chmod +x "$local/$SIM/reb.sh" sed -i'' -e "s:^rebuild=.*.$:rebuild=$LMDZD/$LMDZname/modipsl/bin/rebuild:" "$local/$SIM/reb.sh" enable_platform "$local/$SIM/reb.sh" # Copy .def cp lmdz_env.sh "$local/$SIM/" mkdir "$local/$SIM/DEF"; cp DEF/*def DEF/namelis* "$local/$SIM/DEF/" #Pour XIOS, respectivement COSP, copier aussi les fichiers *xml / *txt if [[ $cosp = "y" ]]; then cp DEF/cosp*txt "$local/$SIM/DEF/"; fi if [[ $xios = "y" ]]; then cp DEF/XMLfilesLMDZ/*xml "$local/$SIM/DEF/" if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml "$local/$SIM/DEF/"; fi fi chmod u+w "$local/$SIM"/DEF/* # Gestion du calendrier ####################### cd "$SIM" sed -i'' -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def if [[ $freq = "yr" ]]; then date=$yearini; else date=$mthini; fi echo "$date a faire" >| etat # Recuperation des fichiers : executable initiaux et forcages ############################################################# echo "date: $date" for f in start startphy; do inf=../$INIT/$f.$date.nc if [[ -f $inf || $init = 1 ]]; then ln -s "$inf" ./; else echo "STOP: $inf missing"; exit ; fi; done for f in sechiba stomate; do if [[ -f ../$INIT/start_$f.$date.nc ]]; then ln -sf "../$INIT/start_$f.$date.nc" .; fi done cp "$gcm" gcm.e fi cd "$local"/.. ##################################################################### echo "Modification du script de lancement" ##################################################################### local cput if [[ $freq = "yr" ]]; then cput="04:00:00"; else cput="01:00:00"; fi local isotopes="n" if [[ $phylmd = "lmdiso" ]]; then isotopes="y"; fi sed -e "s/NOM_SIMU/$SIM/" \ -e "s/time=.*.$/time=$cput/" \ -e "s/ntasks=.*.$/ntasks=$mpi/" \ -e "s/ntasks-per-node=.*.$/ntasks-per-node=$mpi_per_node/" \ -e "s/cpus-per-task=.*.$/cpus-per-task=$omp/" \ -e "s/nthreads=.*./nthreads=$omp/" \ -e "s/MAINDIR=.*.$/MAINDIR=$(basename "$local")/" \ -e "s:STORED=.*.*:STORED=$(dirname "$local"):" \ -e "s:SCRATCHD=.*.*:SCRATCHD=$SIMRUNBASEDIR:" \ -e "s/stopsim=.*.$/stopsim=$stopsim/" \ -e "s/^veget=.*.$/veget=$veget/" \ -e "s/^aerosols=.*.$/aerosols=$aerosols/" \ -e "s/^isotopes=.*.$/isotopes=$isotopes/" \ -e "s/^climato=.*.$/climato=$climato/" \ -e "s/^ok_guide=.*.$/ok_guide=$ok_guide/" \ "$local/script_SIMU" >| "$SIMRUNDIR/tmp_$SIM" enable_platform "$SIMRUNDIR/tmp_$SIM" if [[ $testmode = "y" ]]; then sed -i'' -e "s/time=.*.$/time=00:10:00/" -e "s/#nday=1/nday=1/" -e "s/#@TESTQ//" "$SIMRUNTOPDIR/tmp_$SIM" fi } function fetch_simu_init_files() { ##################################################################### echo "Recuperation eventuelle de certains fichiers sur $LMDZ_INIT" ##################################################################### mkdir -p "$LMDZ_INIT" #------------------------------------------------------------------- # Fichiers ORCHIDEE #------------------------------------------------------------------- get="myget 3DInputData/Orchidee/" cd "$LMDZ_INIT"; for file in "PFTmap_IPCC_2000.nc" "cartepente2d_15min.nc" "routing.nc" "routing_simple.nc" "lai2D.nc" "soils_param.nc" "woodharvest_2000.nc" "PFTmap_15PFT.v1_2000.nc"; do if [[ ! -f $file ]]; then ${get}$file; fi done cd - > /dev/null # Additionnal files needed for ORCHIDEE trunk post-CMIP6 if [[ $veget = 7994 && ! -f $LMDZ_INIT/soil_bulk_and_ph.nc ]]; then cd "$LMDZ_INIT" ${get}soil_bulk_and_ph.nc; ${get}NITROGEN_for_ORtrunk.tar tar -xvf NITROGEN_for_ORtrunk.tar; cd - > /dev/null fi #------------------------------------------------------------------- # Fichiers aerosols/chimie #------------------------------------------------------------------- if [[ $aerosols = "clim" ]]; then get="myget 3DInputData/AerChem/" #liste_get="aerosols1850_from_inca.nc aerosols2000_from_inca.nc" #aerosols9999_from_inca.nc est un lien vers aerosols1995_2014_ensavg_from_inca.nc cd "$LMDZ_INIT" for file in "aerosols1850_from_inca.nc" "aerosols9999_from_inca.nc"; do if [[ ! -f $file ]]; then ${get}$file; fi done cd - > /dev/null fi # For SPLA #------------------- # Dans ${LMDZ_INIT} on cree folder SPLA_Init et dedans le INITIAL # Pour l'instant on copie là-dedans de chez Binta les fichiers a la res zoomNaf; # plus tard on y recupererea des fichiers a haute resolution reguliere depuis http:/LMDZ, # a regrider ensuite par un script interp_fichiers_spla.sh (comme pour aerosols="clim") # Les fichiers (regrides, sauf SOILSPEC.data utilise tel quel) seront mis dans $MAINDIR/INPUT_SPLA (equivalent de INPUT_DUST) # The Path below is for JEANZAY. See with the team how to adapt to your cluster. if [[ $aerosols = "spla" ]]; then mkdir -p "${LMDZ_INIT}/SPLA_Init"; mkdir -p "$LMDZ_INIT/SPLA_Init/INITIAL" get="cp -p /gpfsstore/rech/gzi/rgzi027/ergon/BIBIAERO/INPUTS_DUST/INITIAL/" liste_get="wth.dat cly.dat donnees_lisa.nc SOILSPEC.data \ carbon_emissions.nc sulphur_emissions_antro.nc \ sulphur_emissions_nat.nc sulphur_emissions_volc.nc" cd "$LMDZ_INIT/SPLA_Init/INITIAL" for file in $liste_get; do if [[ ! -f $file ]]; then ${get}$file .; fi done cd - > /dev/null ### #Cas particulier des fichiers mensuels dust.nc :A DECIDER : #C'est entre le cas des aerosols.clim= 1 seul fichier, annuel, # et le cas des vents guidage, pré-interpolés avec era2gcm pour toute la periode, dans MAINDIR/GUIDE. # On pourrait (a)demander de precalculer dust.nc aussi, dans MAINDIR/INPUT_SPLA - avec un script à adapter de Jeronimo. Rien a mettre dans SPLA_Init alors. # Ou (b) fournir dans SPLA_Init les 12 mois d'un dust.nc climato (an 2006 pour nous ici) à la res EC, et faire juste le regrid vers MAINDIR/INPUT_SPLA #ICI pour l'instant je copie les fichiers de chez Binta (repositoire==http...) dans LMDZ_INIT/SPLA_Init, avec test sur mois 01 if [[ ! -d ${LMDZ_INIT}/SPLA_Init/PERIOD0001 ]]; then if [[ ${hostname:0:5} != "jean-" ]]; then echo "PERIOD001 (aerosols=spla) IS ONLY AVAILABLE ON JEANZAY FOR NOW, CONTACT SUPPORT"; exit 1; fi cp -pr /gpfsstore/rech/gzi/rgzi027/ergon/BIBIAERO/INPUTS_DUST/PERIOD* "$LMDZ_INIT/SPLA_Init/."; fi #A la fin on doit avoir dans SPLA_Init les fichiers initiaux dans INITIAL plus les repertoires PERIOD00MM contenant dust.nc #Cela doit se retrouver dans script_SIMU qui les copie dans le repertoire de run sur $SCRATCH fi #------------------------------------------------------------------- # Fichiers Init #------------------------------------------------------------------- get="myget 3DInputData/Init/" liste_get="alb_bg_modisopt_2D_ESA_v2.nc reftemp.nc" cd "$LMDZ_INIT" for file in $liste_get; do if [[ ! -f $LMDZ_INIT/$file ]]; then ${get}$file; fi done cd - > /dev/null } function run_sim_or_init() { cd "$local" if [[ $init = 1 ]]; then ##################################################################### echo "Creation de l etat initial" ##################################################################### # Creation du repertoire INIT et mise en place de liens logiques vers les starts # en anticipation de leur création : mkdir "$local/$INIT"; cd "$local/$INIT" for an in $mthini $yearini; do for f in start startphy; do ln -s "$f.nc" "$f.$an.nc"; done; done # Creation du repertoire INIT temporaire et rapatriement des fichiers necessaires if [[ -d $SIMRUNDIR/$INIT ]]; then mv "$SIMRUNDIR/$INIT" "$SIMRUNDIR/$INIT$$"; fi mkdir "$SIMRUNDIR/$INIT"; cp -r "$local/DEF" "$SIMRUNDIR/$INIT/" cd "$SIMRUNDIR/$INIT"; cp DEF/*.def .; cp "$local/lmdz_env.sh" . if [[ $xios = "y" ]]; then cp DEF/XMLfilesLMDZ/*xml . if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml .; fi fi sed -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def >| run.def #------------------------------------------------------------------- # Fichiers Limit #------------------------------------------------------------------- local yrs suf if [[ $climato = 0 ]]; then # calend est choisi plus haut dans "Changements dans les fichiers DEF/*def" et ecrit dans $MAINDIR/DEF/run.def yrini=$(echo "$mthini" | cut -c-4) yrend=$(echo "$mthend" | cut -c-4) yrs=""; yr=$yrini while [[ $yr -le $yrend ]]; do yrs="$yrs $yr"; (( yr = yr + 1 )); done suf="360x180_" else yrs=2000 suf="1x1_clim" fi get="myget 3DInputData/Limit/" liste_get="Albedo.nc Relief.nc Rugos.nc landiceref.nc" for yr in $yrs; do if [[ $climato = 0 ]]; then sufyr=$suf$yr; else sufyr=$suf; fi liste_get="$liste_get amipbc_sic_$sufyr.nc amipbc_sst_$sufyr.nc" done echo LISTEGET "$liste_get" for file in $liste_get; do cd "$LMDZ_INIT" if [[ ! -f $LMDZ_INIT/$file ]]; then ${get}$file; fi cd - > /dev/null ln -s "$LMDZ_INIT/$file" . done #------------------------------------------------------------------- # ECDYN #------------------------------------------------------------------- get="myget 3DInputData/Init/" if [[ ! -f $LMDZ_INIT/ECDYN.nc ]]; then cd "$LMDZ_INIT"; ${get}ECDYN.nc; cd - > /dev/null; fi ln -s "$LMDZ_INIT"/ECDYN.nc . ln -sf ECDYN.nc ECPHY.nc # Creation du script d'initialisation cat << ...eod >| tmp #!/bin/bash #@JZ#JeanZay #@JZ#SBATCH --job-name=Init # nom du job #@JZ#SBATCH --ntasks=1 # Nombre de processus MPI #@JZ#SBATCH --cpus-per-task=1 # nombre de threads OpenMP #@JZ# /!\ Attention, la ligne suivante est trompeuse mais dans le vocabulaire #@JZ# de Slurm "multithread" fait bien référence à l'hyperthreading. #@JZ#SBATCH --hint=nomultithread # 1 thread par coeur physique (pas d'hyperthreading) #@JZ#SBATCH --time=00:10:00 # Temps d'exécution maximum demandé (HH:MM:SS) #@JZ#SBATCH --output=Init%j.out # Nom du fichier de sortie #@JZ#SBATCH --error=Init%j.out # Nom du fichier d'erreur (ici commun avec la sortie) #@JZ# To submit to dev queue; "time" (above) must be max 2h #@JZ#TESTQ#SBATCH --qos=qos_cpu-dev #@SP#Spirit #@SP#SBATCH --job-name=Init #@SP#SBATCH --ntasks=1 #@SP#SBATCH --cpus-per-task=1 #@SP#SBATCH --hint=nomultithread #@SP#SBATCH --time=00:10:00 #@SP#SBATCH --output=Init%j.out #@SP#SBATCH --error=Init%j.out #@ADS#Adastra #@ADS#SBATCH --job-name=Init #@ADS#SBATCH --ntasks=1 #@ADS#SBATCH --cpus-per-task=1 #@ADS#SBATCH --nodes=1 #@ADS#SBATCH --hint=nomultithread #@ADS#SBATCH --time=00:10:00 #@ADS#SBATCH --output=Init%j.out #@ADS#SBATCH --error=Init%j.out set -eu # ANCIEN MULTI STEP case \${LOADL_STEP_NAME} in # ANCIEN MULTI STEP init ) if [ ! -f lmdz_env.sh ]; then echo "manque fichier lmdz_env.sh"; ls; exit 1; fi . lmdz_env.sh ulimit -s unlimited cd $SIMRUNDIR/$INIT echo "Executable : $ce0l" for yr in $yrs; do if [ $climato = 0 ]; then sufyr=$suf\$yr; else sufyr=$suf; fi ln -sf amipbc_sic_\$sufyr.nc amipbc_sic_1x1.nc ln -sf amipbc_sst_\$sufyr.nc amipbc_sst_1x1.nc sed -e 's/anneeref=.*.$/anneeref='\$yr'/' DEF/run.def >| run.def echo Starting initialisation OMP_NUM_THREADS=1 $MPICMD 1 $ce0l # ce0l requires MPI=OMP=1 if [ $climato = 0 ]; then mv limit.nc limit.\$yr.nc; fi done # ANCIEN MULTI STEP ;; # ANCIEN MULTI STEP interp ) if [[ $aerosols = clim ]]; then cp $local/interp_aerosols.sh .; chmod +x interp_aerosols.sh # Les aerosols de l'annee 2000 ont été remplacés par "9999" qui pointe vers un fichier moyen sur 1995-2014 #for year in 2000 1850; do ./interp_aerosols.sh \$year; done #mv aerosols.2000.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc for year in 9999 1850; do ./interp_aerosols.sh \$year; done mv aerosols.9999.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc fi # AS : S'il etait possible d'automatiser l'interpolation de l'input SPLA, ce serait a lancer ici #en attendant, on passe au paragraphe suivant où on copie les fichiers à la res ZoomNaf depuis $LMDZ_INIT/SPLA_Init #if [ $aerosols = spla ]; then #cp $local/futur script interp_aerosols_SPLA.sh .; chmod +x interp_aerosols_SPLA.sh #for file in...; do ./interp_aerosols_SPLA.sh \$year; done #etc etc etc ... #fi # Copy initial and forcing files in $local/$INIT and $local/$LIMIT; also in $local/INPUT_SPLA if $aerosols=spla for f in sta* gri*nc; do cp \$f $local/$INIT/\$f; done if [[ $climato = 1 ]]; then cp limit.nc $local/$INIT/limit.nc; fi mkdir -p $local/$LIMIT for f in limit*.nc ; do cp \$f $local/$LIMIT/\$f; done if [ $aerosols = clim ]; then for f in aerosols[.0-9]*nc; do cp \$f $local/$LIMIT/\$f; done; fi # if [ $aerosols = spla ]; then #mkdir -p $local/INPUT_SPLA; pour l'instant on copie $LMDZ_INIT/SPLA_Init en block if [ ! -d $local/INPUT_SPLA ]; then cp -pr $LMDZ_INIT/SPLA_Init $local/INPUT_SPLA; fi fi cd $SIMRUNDIR ...eod if [[ $ok_guide != "y" ]]; then # Running first simulation automatically except for nudging cat << ...eod >> tmp echo "Submitting job tmp_$SIM" echo "\$SUBMITCMD tmp_$SIM" \$SUBMITCMD tmp_$SIM ...eod fi cat << ...eod >> tmp # ANCIEN MULTI STEP esac ...eod enable_platform tmp echo "###############################################################################" echo "Submitting initialisation job <$SUBMITCMD tmp> from $(pwd)" chmod +x tmp $SUBMITCMD tmp echo "###############################################################################" else #case [ $init != 1 ] cd "$SIMRUNDIR" echo "###############################################################################" echo "Submitting job tmp_$SIM" echo "$SUBMITCMD tmp_$SIM" $SUBMITCMD "tmp_$SIM" echo '###############################################################################' fi } function message_post_submit() { if [[ $ok_guide = "y" && $init = 1 ]]; then cd "$local" enable_platform era2gcm_tuto.sh echo "Once initialisation is finished, you have to create nudging files" echo "Edit era2gcm_tuto.sh and set the desired parameters in section " echo "Make sure you have acces to the chosen ERA files, and the required modules are loaded, then run : ./era2gcm_tuto.sh" if [[ $aerosols = "spla" ]]; then echo "Your aerosol choice is , so you need ERA 10m-winds interpolated on LMDZ grid. Use script era2gcm_uv10m.sh" fi else echo "Si tout se passe bien, vous avez initialisé et lancé automatiquement la simulation." echo "Le job qui a été lancé se trouve sur $SIMRUNTOPDIR/tmp_$SIM" fi } function setup_and_load_lmdz_env() { if [[ ! -f .lmdz_setup_root_dir ]]; then echo "STOP: setup.sh is not located in the root dir ??!!"; exit 1; fi # sed root_dir in lmdz_env.sh sed -i'' "s