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setup.sh @ 5859

Last change on this file since 5859 was 5858, checked in by idelkadi, 4 weeks ago
The "veget" key reset to CMIP6 by default following the previous modification
File size: 35.2 KB

Rev	Line
[5542]	1	#!/bin/bash
[5415]	2	# This script sets up and launches a (series of) simulation(s).
	3	# RECOMMENDATION: use main.sh to drive it (do not run it directly)
[4615]	4
[5415]	5	set -eu
[4615]	6
[5438]	7	#---------------------------------------------------------------------------
	8	function define_expert_options() { # Expert-level choices
	9	#---------------------------------------------------------------------------
	10
	11	# optim: either "" or "-debug" to compile in debug mode
	12	# (slower but better diagnosis of segfaults)
[5415]	13	optim=""
[4615]	14
[5438]	15	# "n" or "y". If testmode="y", then simulations run for a single day
	16	# per period.
[5415]	17	# NOTE: you must set mthend accordingly !
	18	testmode="n"
[4615]	19
[5722]	20	# instll : either "y" or "n"
	21	# default : y if n LMDZ will not be installed and compiled
[5723]	22	install="y"
[5722]	23
[5415]	24	# Radiative code: "oldrad" / "rrtm" / "ecrad"
	25	rad="rrtm"
[4615]	26
[5438]	27	# !!! STRONG recommendation : experiments with DIFFERENT Orchidee or
	28	# aerosol options should be performed in DIFFERENT LMDZ_Setup folders
[5415]	29	# !!! (especially as they may need different initial files)
[4615]	30
[5438]	31	# AEROSOLS : "n" (=no)/"clim" (=average 1995-2014) / "spla" (interactive)
	32	# (WARNING : if you first run the scripts with aerosols=n, then you want
	33	# to change to =clim, you must remove the INIT and LIMIT folders and
	34	# rerun main.sh with init=1 in order to create aerosol files
	35
[5415]	36	aerosols="clim"
[4615]	37
[5857]	38	# OZONE :
	39	# AI et ZE oct 2025
	40	# 0 => analytic formula fonction of altitude and latitude
	41	# 1 => ozonread a single ozone climatology that will be used day and night
	42	ozone=0
	43
[5415]	44	# SURFACE/VEGETATION SCHEME
[5438]	45	# - "none" : bucket scheme
	46	# CMIP6 : orchidee CMIP6 version
	47	# 7983/7994 : orchidee svn release 7983 (orch2.2) and 7994 (last tested)
	48	# If you need other orch versions, and also require XIOS, you'll need
	49	# to create the appropriate files in DEF/XMLfilesOR...
[5858]	50	veget="CMIP6"
[4615]	51
[5415]	52	# New snow scheme INLANDSIS! "y" / "n"
[5438]	53	# Activates INLANDSIS compilation
	54	# to be done : treatment of specific restart and def file
[5415]	55	inlandsis="n"
[4615]	56
[5415]	57	# netcdf: 0 (use existing library) / 1 (recompile netcdf, slow)
	58	netcdf=0
[4615]	59
[5438]	60	# --->>> ALSO PAY ATTENTION TO OUTPUT files, frequency, level ------------
	61	# With IOIPSL : Choose your config.def among versions available in DEF,
[5415]	62	# copy it as config.def (the copy is done automatically for "iso"),
	63	# edit it and set up output files, frequencies and levels.
[5438]	64	# NB : For aerosols=spla, output level minimum 4 is required to outpu
	65	# the specific variables.
	66	# For aerosols=n, aerosol flags will automatically be set to "n".
[5415]	67	# With XIOS : adjust DEF/XMLfiles/filexml
[5539]	68
	69	save_pub=0
	70
[5415]	71	}
[4615]	72
	73
[5438]	74	#---------------------------------------------------------------------------
	75	function enable_platform() { # Sed platform-specific headers
	76	#---------------------------------------------------------------------------
[5415]	77	local file="$1"
	78	local platform
[4615]	79
[5415]	80	case ${hostname:0:5} in
	81	jean-) platform="JZ";;
	82	spiri) platform="SP";;
	83	adast) platform="ADS";;
	84	*) echo "Warning: $hostname is not a known job platform (ignore if running locally)"; return 0;;
	85	esac
[4615]	86
[5415]	87	sed -i'' -e "s/^#@$platform//" "$file"
	88	}
[4615]	89
[5438]	90	#---------------------------------------------------------------------------
	91	function load_install_lib() { #Fetch and source install_lmdz.sh to get myget
	92	#---------------------------------------------------------------------------
[5415]	93	if [[ ! -f "install_lmdz.sh" ]]; then
	94	wget --no-cache "http://svn.lmd.jussieu.fr/LMDZ/BOL/script_install/install_lmdz.sh"
	95	fi
	96	# shellcheck disable=SC1090
	97	source <(sed 's/function $.*$ {/function installlmdz_\1 {/g' install_lmdz.sh) # source with a namespace for functions
	98	function myget { installlmdz_myget "$@"; }
[4615]	99	}
	100
[5438]	101	#---------------------------------------------------------------------------
	102	function set_default_params() { # Default value of script parameters
	103	#---------------------------------------------------------------------------
	104
[5464]	105	SIM=$(basename "$local_d")CTL # name
[5415]	106	phylmd="lmd" #option -p $phylmd for makelmdz
[4615]	107
[5415]	108	cosp="n" # COSP
	109	xios="n" #XIOS
[4615]	110
[5415]	111	# Nudging :
	112	ok_guide="n"
	113	# With nudging, use real calendar (climato=0) and monthly integrations
	114	climato=1
	115	freq="mo" # frequence mensuelle mo ou annuelle yr
[4615]	116
[5415]	117	# NB : the run stops in the BEGINNING of mthend (test "next=stopsim")
	118	mthini=200001
	119	mthend=200501
	120	resol="144x142x79"
[4615]	121
[5415]	122	version="20230412.trunk"
	123	svn=""
[4615]	124
[5415]	125	init=1
[4615]	126
[5415]	127	LIMIT="LIMIT"
[4615]	128
[5415]	129	}
[4615]	130
[5438]	131	#---------------------------------------------------------------------------
[5415]	132	function read_cmdline_args() {
[5438]	133	#---------------------------------------------------------------------------
[5415]	134	while (($# > 0)); do
	135	case $1 in
	136	"-h") cat <<........fin
[5428]	137	setup.sh can be launched/driven by main.sh
[5415]	138	setup.sh [-v version] [-r svn_release] [-init INIT] [-d 96x95x79] [-f mo] [-nudging]
	139	-v "version" like 20150828.trunk; see https://lmdz.lmd.jussieu.fr/Distrib/LISMOI.trunk (default <$version>)
[5428]	140	-r "svn_release" either the svn release number or "last" (default <$svn>)
	141	-d IMxJMxLM to run in resolution IM x JM x LM (default <$resol>)
[5722]	142	-install y/n pour installer et compiler le modele
[5428]	143	-f mo/yr pour tourner en mensuel ou annuel (default <$freq>)
	144	-rad RAD Radiation
	145	-netcdf 0/1/DIR Netcdf installation
	146	-aerosols n/clim/spla Aerosols : none / climatological / interactive with SPLA
[5857]	147	-ozone 0/1 Ozone : not read / read an ozone climatology
[5428]	148	-veget CMIP6 CMIP6 version of rchidee
	149	7983 orch2.2
	150	7994 trunk
	151	"INIT" 1: creates INIT and LIMIT
	152	0: reads from INIT and LIMIT
	153	SIMU: reads from preexisting simulation SIMU and LIMIT (default <$init>)
	154	-nudging to run with nudging. Nudging files must be created independently
	155	-p the physics to use (default <$phylmd>)
[5539]	156	-save_pub To files downlaoded with wget (default <$SIM>)
[5428]	157	-name install folder name (default <$SIM>)
[5415]	158	Other options available (see "options" section in the script)
[4615]	159	........fin
[5415]	160	exit;;
[5539]	161	"-v") version="$2"; shift 2;;
	162	"-r") svn=$2; shift 2;;
	163	"-d") resol=$2; shift 2;;
	164	"-f") freq=$2; shift 2;;
	165	"-p") phylmd=$2; shift 2;;
	166	"-name") SIM=$2; shift 2;;
	167	"-save_pub") save_pub=$2 ; shift 2 ;;
[5722]	168	"-install") install=$2; shift 2;;
[5539]	169	"-rad") rad=$2; shift 2;;
	170	"-netcdf") netcdf=$2; shift 2;;
	171	"-aerosols") aerosols=$2; shift 2;;
	172	"-veget") veget=$2; shift 2;;
[5415]	173	"-cosp") cosp=y; shift;;
	174	"-xios") xios=y; shift;;
[5539]	175	"-init") init=$2; shift 2;;
[5415]	176	"-nudging") ok_guide=y; shift;;
[5539]	177	"-climato") climato=$2; shift 2;;
[5857]	178	"-ozone") ozone=$2; shift 2;;
[5539]	179	"-mthini") mthini=$2; shift 2;;
	180	"-mthend") mthend=$2; shift 2;;
[5415]	181	*) echo "unexpected $1"; $0 -h; exit
	182	esac
	183	done
[4615]	184
[5415]	185	# Initialisation
	186	if [[ $init = 1 \|\| $init = 0 ]]; then
	187	INIT="INIT"
	188	else
	189	INIT=$init
	190	fi
[4615]	191
[5428]	192	case $rad in
	193	oldrad) iflag_rrtm=0; NSW=2;;
	194	rrtm) iflag_rrtm=1; NSW=6;;
	195	ecrad) iflag_rrtm=2; NSW=6;;
	196	esac
	197
[5432]	198	im=$(echo "$resol" \| cut -dx -f1)
	199	jm=$(echo "$resol" \| cut -dx -f2)
	200	lm=$(echo "$resol" \| cut -dx -f3)
	201
[5539]	202	case $save_pub in
	203	0) save_pub_opt=0 ;;
	204	1) save_pub_opt="-save_pub" ;;
	205	*) save_pub_opt="-save_pub -save_pub_dir $save_pub"
	206	mkdir -p $save_pub
	207	if [ $? != 0 ] ; then echo Cannot create directory $save_pub
	208	exit 1 ; fi
	209	esac
	210
[5415]	211	yearini=$(echo "$mthini" \| cut -c-4)
	212	if [[ $freq = yr ]]; then stopsim=$(echo "$mthend" \| cut -c-4); else stopsim=$mthend; fi
[4615]	213
[5415]	214	if [[ -d $SIM ]]; then
	215	echo "La simulation $SIM existe deja. Il est conseillé d'arrêter et de vérifier."
	216	echo "Si vous êtes sûr de vous, vous pouvez la prolonger. Voulez vous la prolonger ? (y/n)"
	217	read -r ans
	218	if [[ $ans != y ]]; then exit 1; fi
	219	fi
[4615]	220
[5415]	221	######################################################################
	222	# Choix du nombre de processeurs
	223	# NOTES :
[5438]	224	# omp=8 by default (for Jean-Zay must be a divisor of 40 procs/node)
	225	# omp=1 : required for SPLA (omp parallelism not ready)
	226	# omp=2 for veget=CMIP6+XIOS beacause of a bug in ORCHIDEE/src_xml/xios_orchidee.f90
[5415]	227	######################################################################
[5604]	228	(( mpi = jm / 2 ))
[5415]	229	omp=8
	230	if [[ $aerosols = "spla" ]]; then omp=1; fi
	231	if [[ $veget = "CMIP6" && $xios = "y" ]]; then omp=2; fi
	232	if [[ $mpi -gt $NB_MPI_MAX ]]; then mpi=$NB_MPI_MAX; fi
	233	if [[ $omp -gt $NB_OMP_MAX ]]; then omp=$NB_OMP_MAX; fi
[4615]	234
[5415]	235	# Compute how many mpi per node (required e.g. for Adastra)
	236	mpi_per_node=0
	237	if [[ $NB_CORE_PER_NODE_MAX -gt 0 ]]; then
	238	local N_omp_mt=1
	239	if [[ $omp -gt 1 ]]; then (( N_omp_mt = omp / N_HYPERTHREADING )); fi # take into account hyperthreading
	240	(( mpi_per_node = NB_CORE_PER_NODE_MAX / N_omp_mt ))
	241	if [[ mpi_per_node -gt mpi ]]; then mpi_per_node=$mpi; fi
	242	fi
[4615]	243
[5415]	244	echo "Total MPI=$mpi (PER NODE=$mpi_per_node), OMP=$omp"
	245	}
[4615]	246
[5438]	247	#---------------------------------------------------------------------------
[5415]	248	function ensure_correct_option_combinations() {
	249	# AVOID COMBINATIONS OF OPTIONS THAT DON'T WORK in user choices
[5438]	250	#---------------------------------------------------------------------------
[5415]	251	if [[ $ok_guide = y && $climato = 1 ]]; then
	252	echo "STOP: Running nudged simulations with climatological SSTs is not planned. Change <climato> to <0> or modify the setup (experts)"; exit 1
	253	fi
[4615]	254
[5415]	255	if [[ $climato = 0 && $freq = "yr" ]]; then
	256	echo "STOP: Running simulations with interannual SSTs is possible only month by month and a true calendar."
	257	echo "Change <climato> to <1> or <freq> to <mo> or modify setup.sh (experts)"; exit 1
	258	fi
[4615]	259
	260
[5415]	261	# (Temporary) Constraints for aerosols=spla :
	262	# --> resolution 128x88x79 and rad=rrtm
[5438]	263	if [[ $aerosols = "spla" && ( ${im}x${jm} != "128x88" \|\| $freq != mo ) ]]; then
	264	echo 'STOP: For now, <aerosols=spla> requires <resol=128x88x79>,'
	265	echo 'and uses the zoomed grid from gcm.def_zNAfrica_BiJe,'
	266	echo 'for which forcing & initial files are available'
[5415]	267	echo "Right now resol=<$resol>"
[5438]	268	echo 'Should be run in monthly mode'
[5415]	269	exit 1
	270	fi
[4615]	271
[5415]	272	if [[ $rad = "ecrad" && $phylmd != "lmd" ]]; then
	273	echo "<rad=ecrad> is only supported for <phy=phylmd> here" # (Amaury) I added this check because we fetch ecrad data from libf/phylmd/ecrad/data only.
	274	fi
	275	}
[4615]	276
[5438]	277	#---------------------------------------------------------------------------
[5415]	278	function install_model() {
[5438]	279	#---------------------------------------------------------------------------
[5415]	280	mkdir -p "$LMDZD"
[4615]	281
[5415]	282	local ins_xios ins_cosp ins_aero ins_inlandsis
	283	if [[ $xios = "y" ]]; then ins_xios="-xios"; else ins_xios=""; fi
	284	if [[ $cosp = "y" ]]; then ins_cosp="-cosp v1"; else ins_cosp=""; fi
	285	if [[ $aerosols = "spla" ]]; then ins_aero="-spla"; else ins_aero=""; fi
	286	if [[ $inlandsis = "y" ]]; then ins_inlandsis="-inlandsis"; else ins_inlandsis=""; fi
	287	if [[ -n $svn ]]; then svnopt="-r $svn"; else svnopt=""; fi
[4615]	288
[5465]	289	if [[ $PARALLEL == 0 ]] ; then parallel= ; parsuf=seq ; else parallel="-parallel mpi_omp" ; parsuf= ; fi
[5415]	290	version_name=LMDZ$(echo "$version" \| sed -e 's/-v//g' -e 's/-unstable//' -e 's/-r/r/' -e 's/ //g')
[5465]	291	LMDZname="${version_name}${svn}OR$veget${ins_xios}${parsuf}$( echo $optim \| sed -e 's/[\ -]//g' )"
[5415]	292	MODEL="$LMDZD/$LMDZname/modipsl/modeles/LMDZ"
[4615]	293
[5415]	294	if [[ -d $MODEL ]]; then echo "Found existing install at MODEL=$MODEL"; fi
[5722]	295	if [[ $install = "y" ]]; then
	296	echo "Installing model"
	297	cd "$LMDZD"
	298	cp "$local_d/install_lmdz.sh" .
	299	chmod +x install_lmdz.sh
	300	local make_j=8
	301	# We launch using $MPICMD, except if it's using mpirun (no srun equivalent for bash script) => if supported, the compilation runs in a cluster job
	302	jobcmd="\"$RUNBASHCMD $make_j\""
	303	if [[ ${hostname:0:5} = "jean-" ]]; then jobcmd="\"$RUNBASHCMD $make_j --partition=compil\""; fi # On JeanZay: compile on the <compil> partition
	304	if [[ $(echo "$RUNBASHCMD" \| cut -c -4) = "bash" ]]; then
	305	jobcmd="bash"
	306	fi
	307	echo "./install_lmdz.sh -noclean $optim -v $version $svnopt -d $resol -rad $rad -bench compile_only $parallel $ins_cosp $ins_xios $ins_aero $ins_inlandsis -name $LMDZname -veget $veget -netcdf $netcdf -arch $ARCH -make_j $make_j -jobcmd $jobcmd" $save_pub_opt >> install_lmdz_options.$$.sh
	308	chmod +x install_lmdz_options.$$.sh
	309	echo "Running install_lmdz_options.$$.sh"
	310	set -o pipefail
	311	./install_lmdz_options.$$.sh
	312	#gcm=$MODEL/$(./install_lmdz_options.$$.sh \| tee /dev/tty \| tail -n 1 \| sed -n "s:.* executable is $.\.e$.:\1:p")
	313	gcm=$MODEL/bin/gcm.e
	314	set +o pipefail
	315	mv install_lmdz.sh install_lmdz.$$.sh
	316	else
	317	echo "install=n no need to install and recompile the model (already done)"
[5534]	318	gcm=$MODEL/bin/gcm.e
[5722]	319	fi
[5464]	320	cd "$local_d"
[5415]	321	}
[4615]	322
[5438]	323	#---------------------------------------------------------------------------
	324	function setup_def() { # modify various .def in ./DEF (+ xios xml )
	325	#---------------------------------------------------------------------------
[5464]	326	cd "$local_d"
[4615]	327
[5415]	328	# Utilisation des .def_iso pour LMDZ-ISOtopes
	329	if [[ $phylmd = "lmdiso" ]]; then
	330	for file_iso in $(ls DEF \| grep _iso); do
	331	cp DEF/"$file_iso" DEF/"${file_iso%%_iso}"
	332	done
	333	fi
[4615]	334
[5415]	335	######################################################################
	336	# Choix de la grille verticale
	337	######################################################################
[5587]	338	if [ ! -f "DEF/DYN/L$lm.def" ]; then
	339	echo "STOP: Résolution verticale non prévue - créer un fichier DEF/DYN/L$lm.def"; exit 1
[5415]	340	else
	341	sed -i'' -e "s/INCLUDEDEF=L.*.def/INCLUDEDEF=L$lm.def/" DEF/run.def
[5608]	342	cp DEF/DYN/L$lm.def DEF/
[5415]	343	fi
[4615]	344
[5415]	345	######################################################################
	346	# Changements dans les fichiers DEF/*def
[5464]	347	# (ils vont se repercuter dans les repertoires de simulation $local_d/$SIM et de run $SIMRUNDIR)
[5415]	348	######################################################################
[4615]	349
[5415]	350	# Choix du fichier tracer.def coherent avec l'option "aerosols"
	351	# NOTE : Le nouveau tracer.def_nospla par defaut n'inclut pas Rn-Pb;
[5439]	352	# si on les veut, il faut utiliser ci-dessous; a la place, tracer_RN_PB.def
[5415]	353	#---------------------------------------------------------------------
	354	# NB : Les traceurs absents de start* files sont initialises=0 dans le code
	355	if [[ $aerosols = "spla" ]]; then
	356	# nouveau tracer.def (remplace "traceur.def")
[5632]	357	cp DEF/CONFIG/traceur.def_spla DEF/traceur.def
	358	\rm -f DEF/tracer.def
[5415]	359	elif [[ $phylmd = "lmdiso" ]]; then
	360	# déjà copié si 'y'
[5632]	361	cp DEF/CONFIG/tracer.def_nospla DEF/tracer.def
[5415]	362	fi
[4615]	363
[5415]	364	# TEMPORAIREMENT pour spla on force l'utilisation de gcm.def_zNAfrica_BiJe (avec resolution 128x88x79)
	365	#----------------------------------------------------------------------
[5438]	366	if [[ $aerosols = "spla" ]]; then
[5632]	367	cp DEF/DYN/gcm.def_zNAfrica_BiJe DEF/gcm.def; fi
[4615]	368
[5415]	369	# Inscription du choix ok_guide dans DEF/guide.def
	370	#---------------------------------------------------------------------
	371	sed -i'' -e 's/ok_guide=.*.$/ok_guide='$ok_guide'/' DEF/guide.def
[4615]	372
[5415]	373	# Inscription du type de calendrier (qui est fonction de $climato) dans DEF/run.def
	374	#---------------------------------------------------------------------
	375	# NB Contrairement a ce qui est ecrit dans les fichiers run.def standard,
	376	# dans ce tutorial le choix earth_365d n'est pas disponible, et earth_366d s'appelle gregorian
	377	if [[ $climato = 0 ]]; then calend="gregorian"; else calend="earth_360d"; fi
	378	sed -i'' -e 's/calend=.*.$/calend='$calend'/' DEF/run.def
[4615]	379
[5415]	380	# Changements dans config.def (pre-choisi, et regle pour output si utilisation avec IOIPSL)
	381	# cf options veget, aerosols, cosp, xios
	382	#---------------------------------------------------------------------
	383	if [[ $veget = "none" ]]; then VEGET="n"; else VEGET="y"; fi
	384	sed -i'' -e 's/VEGET=.*.$/VEGET='$VEGET'/' DEF/config.def
[4615]	385
[5438]	386	ok_cdnc=y ; ok_ade=y ; ok_aie=y ; ok_alw=y
	387	case $aerosols in
	388	clim) flag_aerosol=6 ;;
	389	spla) flag_aerosol=1 ;;
	390	n) flag_aerosol=0 ; ok_cdnc=n ; ok_ade=n ; ok_aie=n ; ok_alw=n ;;
	391	*) echo Option aerosols=$aerosols not available ; exit 1
	392	esac
	393	sed -i'' -e 's/^ok_cdnc=.*.$/ok_cdnc='$ok_cdnc'/' \
	394	-e 's/^ok_ade=.*.$/ok_ade='$ok_ade'/' \
	395	-e 's/^ok_aie=.*.$/ok_aie='$ok_aie'/' \
	396	-e 's/^ok_alw=.*.$/ok_alw='$ok_alw'/' \
	397	-e 's/^flag_aerosol=.*.$/flag_aerosol='$flag_aerosol'/' DEF/config.def
	398	pwd
[4615]	399
[5857]	400	# OZONE : modifier la cles logique pour ozone
	401	if [[ $ozone -eq 1 ]]; then
	402	sed -i'' -e 's/read_climoz=.*.$/read_climoz='$ozone'/' DEF/config.def
	403	fi
	404
[5415]	405	# COSP : ok_cosp desactive COSP si on a compile avec; il ne l'active pas si on a compile sans
	406	sed -i'' -e 's/ok_cosp.*.$/ok_cosp='$cosp'/' DEF/config.def
[5464]	407	if [[ $cosp = "y" ]]; then \cp -f "$MODEL"/DefLists/cosp*.txt "$local_d"/DEF/; fi
[4615]	408
[5415]	409	# Sorties LMDZ en fonction de l'option "xios"
	410	sed -i'' -e 's/ok_all_xml=.*.$/ok_all_xml='$xios'/' DEF/config.def
[4615]	411
[5415]	412	# Ajuster physiq.def en fonction de radiative code (default: values for rad=rrtm)
	413	# Pour isotopes=y , mettre iflag_ice_thermo=0 au lieu de 1
	414	#---------------------------------------------------------------------
	415	sed -i'' -e "s/iflag_rrtm=..$/iflag_rrtm=$iflag_rrtm/" -e "s/NSW=..$/NSW=$NSW/" DEF/physiq.def
	416	sed -i"" -e "s:directory_name.*$:directory_name=\"$MODEL/libf/phylmd/ecrad/data\",:" DEF/namelist_ecrad
[4615]	417
[5415]	418	if [[ $phylmd = "lmdiso" ]]; then iflag_ice_thermo=0; else iflag_ice_thermo=1; fi
	419	sed -i -e 's/iflag_ice_thermo=.*.$/iflag_ice_thermo='$iflag_ice_thermo'/' DEF/physiq.def
[4615]	420
[5415]	421	# Choix de orchidee.def en fonction de orchidee_rev; modification pour xios
	422	# NOTE separate orchidee_pft.def file for ORCHIDEE trunk post-CMIP6
	423	#---------------------------------------------------------------------
	424	orchidee_def=orchidee.def_6.1
	425	orchidee_pft_def=""
	426	if [[ $veget = "7983" ]]; then
	427	orchidee_def=orchidee.def_6.2work
[5564]	428	elif [[ $veget = "8758" ]]; then
[5415]	429	orchidee_def=orchidee.def_6.4work
	430	orchidee_pft_def=orchidee_pft.def_6.4work
	431	if ! grep "INCLUDEDEF=orchidee_pft.def" DEF/run.def; then
	432	sed -i'' -e 's/INCLUDEDEF=orchidee.def/INCLUDEDEF=orchidee.def\nINCLUDEDEF=orchidee_pft.def/' DEF/run.def; fi
	433	fi
[5587]	434	cp -f DEF/CONFIG/$orchidee_def DEF/orchidee.def
	435	if [[ $orchidee_pft_def != "" ]]; then cp -f DEF/CONFIG/$orchidee_pft_def DEF/orchidee_pft.def; fi
[4615]	436
[5415]	437	# Only for veget=CMIP6 it is still possible to use IOIPSL; newer versions of orchidee.def have XIOS_ORCHIDEE_OK = y
	438	sed -i'' -e 's/XIOS_ORCHIDEE_OK =.*.$/XIOS_ORCHIDEE_OK = '$xios'/' DEF/orchidee.def
[4615]	439
[5415]	440	######################################################################
	441	# Si on tourne avec XIOS, mise a jour des fichiers context et field* dans XMLfilesLMDZ
[5464]	442	# (ils vont se repercuter dans les repertoires de simulation $local_d/$SIM et de run $SIMRUNDIR)
[5415]	443	######################################################################
	444	if [[ $xios = y ]]; then
[5464]	445	cp -f "$MODEL"/DefLists/context_lmdz.xml "$local_d"/DEF/XMLfilesLMDZ/.
	446	cp -f "$MODEL"/DefLists/field_def_lmdz.xml "$local_d"/DEF/XMLfilesLMDZ/.
	447	if [[ $cosp = y ]]; then cp -f "$MODEL"/DefLists/field_def_cosp1.xml "$local_d"/DEF/XMLfilesLMDZ/.; fi
[5415]	448	fi
	449	}
[4615]	450
[5438]	451	#---------------------------------------------------------------------------
[5415]	452	function setup_ce0l() { # Verification de l'existance de l'état initial, compilation eventuelle pour sa creation
[5438]	453	#---------------------------------------------------------------------------
[5415]	454	if [[ ! -d $INIT ]]; then
	455	if [[ $init = 0 ]]; then
	456	echo "STOP: Récuperer les repertoires $INIT ou lancer avec option -init"; exit 1
	457	else
	458	# Compile ce0l
	459	cd "$MODEL"
[5534]	460	sed -e 's/gcm/ce0l/g' compile.sh > compile_ce0l.sh; chmod +x compile_ce0l.sh
[5415]	461	echo "Compiling ce0l"
	462	if ! ./compile_ce0l.sh &> ce0l.log; then echo "STOP: ce0l compilation failed, see $MODEL/ce0l.log"; exit 1; fi
	463	echo "Compiled ce0l"
	464	ce0l=${gcm/gcm/ce0l}
[4615]	465
[5464]	466	cd "$local_d"
[4615]	467	fi
[5415]	468	elif [[ $init = 1 ]]; then
	469	echo "STOP: Vous essayez d initialiser le modele mais $INIT existe deja"; exit 1
	470	fi
	471	}
[4615]	472
[5438]	473	#---------------------------------------------------------------------------
[5415]	474	function setup_simu() {
[5438]	475	#---------------------------------------------------------------------------
[5464]	476	#SIMRUNTOPDIR="$SIMRUNBASEDIR/$(basename "$local_d")"
[5420]	477	SIMRUNTOPDIR="$SIMRUNBASEDIR"
[5415]	478	SIMRUNDIR=$SIMRUNTOPDIR
	479	mkdir -p "$SIMRUNDIR"
	480	cd "$SIMRUNDIR"
	481	echo "La simulation s'exécutera sur $SIMRUNDIR"
[4615]	482
[5415]	483	#####################################################################
	484	# Creation du repertoire $SIM s'il n'existe pas deja
	485	#####################################################################
[5464]	486	if [[ ! -d $local_d/$SIM ]]; then
	487	mkdir "$local_d/$SIM"
	488	cd "$local_d"
[4615]	489
[5415]	490	# Edit reb.sh
[5464]	491	cp reb.sh "$local_d/$SIM/reb.sh"; chmod +x "$local_d/$SIM/reb.sh"
	492	sed -i'' -e "s:^rebuild=.*.$:rebuild=$LMDZD/$LMDZname/modipsl/bin/rebuild:" "$local_d/$SIM/reb.sh"
	493	enable_platform "$local_d/$SIM/reb.sh"
[4615]	494
[5415]	495	# Copy .def
[5464]	496	cp lmdz_env.sh "$local_d/$SIM/"
	497	mkdir "$local_d/$SIM/DEF"; cp DEF/def DEF/namelis "$local_d/$SIM/DEF/"
[5415]	498	#Pour XIOS, respectivement COSP, copier aussi les fichiers xml / txt
[5464]	499	if [[ $cosp = "y" ]]; then cp DEF/cosp*txt "$local_d/$SIM/DEF/"; fi
[5415]	500	if [[ $xios = "y" ]]; then
[5464]	501	cp DEF/XMLfilesLMDZ/*xml "$local_d/$SIM/DEF/"
	502	if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml "$local_d/$SIM/DEF/"; fi
[5415]	503	fi
[5464]	504	chmod u+w "$local_d/$SIM"/DEF/*
[4615]	505
[5415]	506	# Gestion du calendrier
	507	#######################
	508	cd "$SIM"
	509	sed -i'' -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def
	510	if [[ $freq = "yr" ]]; then date=$yearini; else date=$mthini; fi
	511	echo "$date a faire" >\| etat
[4615]	512
[5415]	513	# Recuperation des fichiers : executable initiaux et forcages
	514	#############################################################
	515	echo "date: $date"
	516	for f in start startphy; do
	517	inf=../$INIT/$f.$date.nc
	518	if [[ -f $inf \|\| $init = 1 ]]; then ln -s "$inf" ./; else echo "STOP: $inf missing"; exit ; fi;
	519	done
	520	for f in sechiba stomate; do
	521	if [[ -f ../$INIT/start_$f.$date.nc ]]; then ln -sf "../$INIT/start_$f.$date.nc" .; fi
	522	done
	523	cp "$gcm" gcm.e
	524	fi
[5464]	525	cd "$local_d"/..
[4615]	526
[5415]	527	#####################################################################
	528	echo "Modification du script de lancement"
	529	#####################################################################
	530	local cput
	531	if [[ $freq = "yr" ]]; then cput="04:00:00"; else cput="01:00:00"; fi
	532	local isotopes="n"
	533	if [[ $phylmd = "lmdiso" ]]; then isotopes="y"; fi
	534	sed -e "s/NOM_SIMU/$SIM/" \
	535	-e "s/time=.*.$/time=$cput/" \
	536	-e "s/ntasks=.*.$/ntasks=$mpi/" \
	537	-e "s/ntasks-per-node=.*.$/ntasks-per-node=$mpi_per_node/" \
	538	-e "s/cpus-per-task=.*.$/cpus-per-task=$omp/" \
	539	-e "s/nthreads=.*./nthreads=$omp/" \
[5464]	540	-e "s/MAINDIR=.*.$/MAINDIR=$(basename "$local_d")/" \
	541	-e "s:STORED=..:STORED=$(dirname "$local_d"):" \
[5415]	542	-e "s:SCRATCHD=..:SCRATCHD=$SIMRUNBASEDIR:" \
	543	-e "s/stopsim=.*.$/stopsim=$stopsim/" \
	544	-e "s/^veget=.*.$/veget=$veget/" \
	545	-e "s/^aerosols=.*.$/aerosols=$aerosols/" \
	546	-e "s/^isotopes=.*.$/isotopes=$isotopes/" \
	547	-e "s/^climato=.*.$/climato=$climato/" \
[5857]	548	-e "s/^ozone=.*.$/ozone=$ozone/" \
[5415]	549	-e "s/^ok_guide=.*.$/ok_guide=$ok_guide/" \
[5464]	550	"$local_d/script_SIMU" >\| "$SIMRUNDIR/tmp_$SIM"
[4615]	551
[5415]	552	enable_platform "$SIMRUNDIR/tmp_$SIM"
[4615]	553
[5415]	554	if [[ $testmode = "y" ]]; then
	555	sed -i'' -e "s/time=.*.$/time=00:10:00/" -e "s/#nday=1/nday=1/" -e "s/#@TESTQ//" "$SIMRUNTOPDIR/tmp_$SIM"
	556	fi
	557	}
[4615]	558
[5429]	559	#----------------------------------------------------------------------
[5439]	560	function list_yrmth() {
	561	#----------------------------------------------------------------------
	562	local liste=""
	563	local mthini=$1
	564	local mthend=$2
	565	local mo_=$mthini
	566	while [[ $mo_ != $mthend ]] ; do
	567	liste="$liste $mo_"
	568	yr__=$( echo $mo_ \| cut -c 1-4 )
	569	mo__=$( echo $mo_ \| cut -c 5-6 )
	570	echo YM $yr__ $mo__
	571	if [ $(( $mo__ +1 )) == 12 ] ; then
	572	yr__=$(( $yr__ + 1 )) ; mo_=$yr__$mo__
	573	else
	574	mo_=$(( $mo_ + 1 ))
	575	fi
	576	done
	577	echo $liste
	578
	579	}
	580
	581	#----------------------------------------------------------------------
	582	increment_month() {
	583	#----------------------------------------------------------------------
	584	local year=$( echo $1 \| cut -c 1-4 )
	585	local month=$(( $1 - ${year}00 ))
	586	if [ $(( $month - 12 )) -eq 0 ]; then
	587	year=$((year + 1))
	588	month=1
	589	else
	590	month=$((month + 1))
	591	fi
	592	if [[ $month -le 9 ]] ; then month=0$month ; fi
	593	echo $year$month
	594	}
	595
	596	#----------------------------------------------------------------------
[5415]	597	function fetch_simu_init_files() {
[5429]	598	#----------------------------------------------------------------------
[5415]	599	#####################################################################
[5426]	600	echo "Recuperation eventuelle de certains fichiers sur http:lmdz.lmd.jussieu.fr/pub"
[5415]	601	#####################################################################
[4615]	602
[5426]	603	# ORCHIDEE input files
[5429]	604	get_input_files wget_pub Orchidee
[5426]	605
	606	# Files for aerosols and chemistry
[5438]	607	if [[ $aerosols = "clim" ]]; then
	608	get_input_files wget_pub AerChem ; fi
[5426]	609
[5429]	610	# Files for SPLA
[5438]	611	if [[ $aerosols = "spla" ]]; then
	612	get_input_files wget_pub SPLA_WA/emissions
[5439]	613	mo_=$mthini
	614	while [[ $mo_ != $mthend ]] ; do
	615	# Code horrible duplique a cause de 08 (FH)
	616	local yr__=$( echo $mo_ \| cut -c 1-4 )
	617	local mo__=$(( $mo_ - ${yr__}00 ))
	618	if [[ $mo__ -le 9 ]] ; then mo__=0$mo__ ; fi
[5438]	619	for var in u10m v10m u v ; do
	620	echo wget_pub 3DInputData/SPLA_WA/ERA5/$yr__/$mo__ $var.nc
	621	wget_pub 3DInputData/SPLA_WA/ERA5/$yr__/$mo__ $var.nc
	622	done
[5439]	623	mo_=$( increment_month $mo_ )
[5438]	624	done
[5464]	625	cd $local_d ; ln -sf $LMDZ_INIT/3DInputData/SPLA_WA/ERA5 GUIDE
[5438]	626	fi
[5415]	627	}
[4615]	628
[5429]	629	#----------------------------------------------------------------------
[5415]	630	function run_sim_or_init() {
[5429]	631	#----------------------------------------------------------------------
[5464]	632	cd "$local_d"
[4615]	633
[5415]	634	if [[ $init = 1 ]]; then
	635	#####################################################################
	636	echo "Creation de l etat initial"
	637	#####################################################################
[4615]	638
[5415]	639	# Creation du repertoire INIT et mise en place de liens logiques vers les starts
	640	# en anticipation de leur création :
[5464]	641	mkdir "$local_d/$INIT"; cd "$local_d/$INIT"
[5415]	642	for an in $mthini $yearini; do for f in start startphy; do ln -s "$f.nc" "$f.$an.nc"; done; done
[4615]	643
[5415]	644	# Creation du repertoire INIT temporaire et rapatriement des fichiers necessaires
	645	if [[ -d $SIMRUNDIR/$INIT ]]; then mv "$SIMRUNDIR/$INIT" "$SIMRUNDIR/$INIT$$"; fi
[5464]	646	mkdir "$SIMRUNDIR/$INIT"; cp -r "$local_d/DEF" "$SIMRUNDIR/$INIT/"
	647	cd "$SIMRUNDIR/$INIT"; cp DEF/*.def .; cp "$local_d/lmdz_env.sh" .
[5415]	648	if [[ $xios = "y" ]]; then
	649	cp DEF/XMLfilesLMDZ/*xml .
	650	if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml .; fi
	651	fi
	652	sed -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def >\| run.def
[4615]	653
[5415]	654	#-------------------------------------------------------------------
	655	# Fichiers Limit
	656	#-------------------------------------------------------------------
	657	local yrs suf
	658	if [[ $climato = 0 ]]; then
	659	# calend est choisi plus haut dans "Changements dans les fichiers DEF/*def" et ecrit dans $MAINDIR/DEF/run.def
	660	yrini=$(echo "$mthini" \| cut -c-4)
	661	yrend=$(echo "$mthend" \| cut -c-4)
	662	yrs=""; yr=$yrini
	663	while [[ $yr -le $yrend ]]; do yrs="$yrs $yr"; (( yr = yr + 1 )); done
	664	suf="360x180_"
	665	else
	666	yrs=2000
	667	suf="1x1_clim"
	668	fi
[4615]	669
[5415]	670	liste_get="Albedo.nc Relief.nc Rugos.nc landiceref.nc"
	671	for yr in $yrs; do
	672	if [[ $climato = 0 ]]; then sufyr=$suf$yr; else sufyr=$suf; fi
	673	liste_get="$liste_get amipbc_sic_$sufyr.nc amipbc_sst_$sufyr.nc"
	674	done
	675	echo LISTEGET "$liste_get"
	676	for file in $liste_get; do
[5426]	677	wget_pub 3DInputData/Limit $file
	678	ln_from_pub 3DInputData/Limit $file
[5415]	679	done
[5857]	680
	681	# Ozone
	682	if [[ $ozone -eq 1 ]]; then
	683	if [[ $climato -eq 1 ]]; then
	684	echo LISTEGET tro3_1979_2008_clim.nc
	685	wget_pub 3DInputData/Ozone/original tro3_1979_2008_clim.nc
	686	ln_from_pub 3DInputData/Ozone/original tro3_1979_2008_clim.nc
	687	elif [[ $climato -eq 0 ]]; then
	688	yr=$yrini
	689	#while [[ $yr -le $yrend ]]; do
	690	echo LISTEGET tro3_${yr}.nc
	691	wget_pub 3DInputData/Ozone/original tro3_$(( $yr - 1 )).nc
	692	ln_from_pub 3DInputData/Ozone/original tro3_$(( $yr - 1 )).nc
	693	wget_pub 3DInputData/Ozone/original tro3_${yr}.nc
	694	ln_from_pub 3DInputData/Ozone/original tro3_$yr.nc
	695	wget_pub 3DInputData/Ozone/original tro3_$(( $yr + 1 )).nc
	696	ln_from_pub 3DInputData/Ozone/original tro3_$(( $yr + 1 )).nc
	697	#done
	698	fi
	699	fi
[5415]	700	#-------------------------------------------------------------------
[5426]	701	# Initial state ECDYN
[5415]	702	#-------------------------------------------------------------------
[5426]	703	wget_pub 3DInputData/Init ECDYN.nc
	704	ln_from_pub 3DInputData/Init ECDYN.nc
[5415]	705	ln -sf ECDYN.nc ECPHY.nc
[4615]	706
[5415]	707	# Creation du script d'initialisation
[5465]	708	if [ "$MPICMD" = "" ] ; then mpicmd='' ; else mpicmd='OMP_NUM_THREADS=1 '"$MPICMD"' 1' ; fi
[5415]	709	cat << ...eod >\| tmp
[4615]	710	#!/bin/bash
[5415]	711	#@JZ#JeanZay
	712	#@JZ#SBATCH --job-name=Init # nom du job
	713	#@JZ#SBATCH --ntasks=1 # Nombre de processus MPI
	714	#@JZ#SBATCH --cpus-per-task=1 # nombre de threads OpenMP
	715	#@JZ# /!\ Attention, la ligne suivante est trompeuse mais dans le vocabulaire
	716	#@JZ# de Slurm "multithread" fait bien référence à l'hyperthreading.
	717	#@JZ#SBATCH --hint=nomultithread # 1 thread par coeur physique (pas d'hyperthreading)
[5850]	718	#@JZ#SBATCH --time=01:00:00 # Temps d'exécution maximum demandé (HH:MM:SS)
[5415]	719	#@JZ#SBATCH --output=Init%j.out # Nom du fichier de sortie
	720	#@JZ#SBATCH --error=Init%j.out # Nom du fichier d'erreur (ici commun avec la sortie)
	721	#@JZ# To submit to dev queue; "time" (above) must be max 2h
	722	#@JZ#TESTQ#SBATCH --qos=qos_cpu-dev
	723	#@SP#Spirit
	724	#@SP#SBATCH --job-name=Init
	725	#@SP#SBATCH --ntasks=1
	726	#@SP#SBATCH --cpus-per-task=1
	727	#@SP#SBATCH --hint=nomultithread
[5850]	728	#@SP#SBATCH --time=01:00:00
[5415]	729	#@SP#SBATCH --output=Init%j.out
	730	#@SP#SBATCH --error=Init%j.out
	731	#@ADS#Adastra
	732	#@ADS#SBATCH --job-name=Init
	733	#@ADS#SBATCH --ntasks=1
	734	#@ADS#SBATCH --cpus-per-task=1
	735	#@ADS#SBATCH --nodes=1
	736	#@ADS#SBATCH --hint=nomultithread
	737	#@ADS#SBATCH --time=00:10:00
	738	#@ADS#SBATCH --output=Init%j.out
	739	#@ADS#SBATCH --error=Init%j.out
[4615]	740
[5415]	741	set -eu
[4615]	742
	743	# ANCIEN MULTI STEP case \${LOADL_STEP_NAME} in
	744
	745	# ANCIEN MULTI STEP init )
	746
[5415]	747	if [ ! -f lmdz_env.sh ]; then echo "manque fichier lmdz_env.sh"; ls; exit 1; fi
	748	. lmdz_env.sh
	749	ulimit -s unlimited
	750	cd $SIMRUNDIR/$INIT
	751	echo "Executable : $ce0l"
	752	for yr in $yrs; do
[5857]	753	# sst and sic
[5415]	754	if [ $climato = 0 ]; then sufyr=$suf\$yr; else sufyr=$suf; fi
	755	ln -sf amipbc_sic_\$sufyr.nc amipbc_sic_1x1.nc
	756	ln -sf amipbc_sst_\$sufyr.nc amipbc_sst_1x1.nc
[5857]	757	# ozone
	758	if [[ $ozone -eq 1 ]]; then
	759	if [[ $climato -eq 1 ]]; then
	760	ln -s tro3_1979_2008_clim.nc climoz.nc
	761	else
	762	ln -s tro3_${yr}.nc climoz.nc
	763	ln -s tro3_$(( $yr - 1 )).nc climoz_m.nc
	764	ln -s tro3_$(( $yr + 1 )).nc climoz_p.nc
	765	fi
	766	fi
	767	# modif annee dans run.def
[5415]	768	sed -e 's/anneeref=.*.$/anneeref='\$yr'/' DEF/run.def >\| run.def
	769	echo Starting initialisation
[5426]	770	# Runing ce0l.e
[5465]	771	$mpicmd $ce0l # ce0l requires MPI=OMP=1
[5857]	772	# Renomer limit et/ou climoz_LMDZ.nc si climato=0
[5415]	773	if [ $climato = 0 ]; then mv limit.nc limit.\$yr.nc; fi
[5857]	774	if [[ $ozone -eq 1 ]]; then
	775	if [ $climato = 0 ]; then mv climoz_LMDZ.nc climoz_LMDZ_\$yr.nc; fi
	776	fi
[5415]	777	done
	778	# ANCIEN MULTI STEP ;;
[4615]	779
	780	# ANCIEN MULTI STEP interp )
[5415]	781	if [[ $aerosols = clim ]]; then
[5464]	782	cp $local_d/interp_aerosols.sh .; chmod +x interp_aerosols.sh
[5415]	783	# Les aerosols de l'annee 2000 ont été remplacés par "9999" qui pointe vers un fichier moyen sur 1995-2014
	784	#for year in 2000 1850; do ./interp_aerosols.sh \$year; done
	785	#mv aerosols.2000.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc
	786	for year in 9999 1850; do ./interp_aerosols.sh \$year; done
	787	mv aerosols.9999.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc
	788	fi
[4615]	789
[5464]	790	for f in sta* gri*nc; do cp \$f $local_d/$INIT/\$f; done
	791	if [[ $climato = 1 ]]; then cp limit.nc $local_d/$INIT/limit.nc; fi
[5857]	792	if [[ $climato = 1 ]]; then
	793	if [[ $ozone -eq 1 ]]; then cp climoz_LMDZ.nc $local_d/$INIT/climoz_LMDZ_1979_2008_clim.nc; fi
	794	fi
[5464]	795	mkdir -p $local_d/$LIMIT
	796	for f in limit*.nc ; do cp \$f $local_d/$LIMIT/\$f; done
[5857]	797	# ozone
	798	if [[ $ozone -eq 1 ]]; then
	799	if [[ $climato -eq 1 ]]; then cp climoz_LMDZ.nc $local_d/$LIMIT/climoz_LMDZ_1979_2008_clim.nc; fi
	800	if [[ $climato -eq 0 ]]; then cp climoz_LMDZ_${yr}.nc $local_d/$LIMIT/.; fi
	801	fi
[5464]	802	if [ $aerosols = clim ]; then for f in aerosols[.0-9]*nc; do cp \$f $local_d/$LIMIT/\$f; done; fi
[5415]	803	#
	804	cd $SIMRUNDIR
[4615]	805	...eod
[5415]	806	if [[ $ok_guide != "y" ]]; then # Running first simulation automatically except for nudging
	807	cat << ...eod >> tmp
	808	echo "Submitting job tmp_$SIM"
[5422]	809	#echo "\$SUBMITCMD tmp_$SIM"
	810	#\$SUBMITCMD tmp_$SIM
[5424]	811	echo submitcmd tmp_$SIM
[5422]	812	submitcmd tmp_$SIM
[4615]	813	...eod
[5415]	814	fi
	815	cat << ...eod >> tmp
	816	# ANCIEN MULTI STEP esac
[4615]	817	...eod
[5415]	818	enable_platform tmp
[5438]	819	echo "#################################################################"
[5422]	820	#echo "Submitting initialisation job <$SUBMITCMD tmp> from $(pwd)"
	821	echo "Submitting initialisation job <submitcmd tmp> from $(pwd)"
[5415]	822	chmod +x tmp
[5422]	823	#$SUBMITCMD tmp
	824	submitcmd tmp
[5438]	825	echo "#################################################################"
[4615]	826
[5415]	827	else #case [ $init != 1 ]
	828	cd "$SIMRUNDIR"
[5438]	829	echo "################################################################"
[5415]	830	echo "Submitting job tmp_$SIM"
[5422]	831	#echo "$SUBMITCMD tmp_$SIM"
	832	#$SUBMITCMD "tmp_$SIM"
	833	echo "submitcmd tmp_$SIM"
	834	submitcmd "tmp_$SIM"
[5438]	835	echo '################################################################'
[5415]	836	fi
	837	}
[4615]	838
[5438]	839	#---------------------------------------------------------------------------
[5415]	840	function message_post_submit() {
[5438]	841	#---------------------------------------------------------------------------
[5415]	842	if [[ $ok_guide = "y" && $init = 1 ]]; then
[5464]	843	cd "$local_d"
[5415]	844	enable_platform era2gcm_tuto.sh
	845	echo "Once initialisation is finished, you have to create nudging files"
	846	echo "Edit era2gcm_tuto.sh and set the desired parameters in section <User choices>"
	847	echo "Make sure you have acces to the chosen ERA files, and the required modules are loaded, then run : ./era2gcm_tuto.sh"
	848	if [[ $aerosols = "spla" ]]; then
	849	echo "Your aerosol choice is <spla>, so you need ERA 10m-winds interpolated on LMDZ grid. Use script era2gcm_uv10m.sh"
	850	fi
	851	else
	852	echo "Si tout se passe bien, vous avez initialisé et lancé automatiquement la simulation."
	853	echo "Le job qui a été lancé se trouve sur $SIMRUNTOPDIR/tmp_$SIM"
	854	fi
	855	}
[4615]	856
[5438]	857	#---------------------------------------------------------------------------
[5415]	858	function setup_and_load_lmdz_env() {
[5438]	859	#---------------------------------------------------------------------------
[5415]	860	if [[ ! -f .lmdz_setup_root_dir ]]; then echo "STOP: setup.sh is not located in the root dir ??!!"; exit 1; fi
	861	# sed root_dir in lmdz_env.sh
[5464]	862	sed -i'' "s<root_dir=.*<root_dir=$local_d<" lmdz_env.sh
[4615]	863
[5415]	864	# Set up the appropriate environment
	865	source lmdz_env.sh
	866	}
[4615]	867
[5464]	868	local_d=$(pwd)
[4615]	869
[5415]	870	setup_and_load_lmdz_env
	871	load_install_lib
	872	define_expert_options
	873	set_default_params
	874	read_cmdline_args "$@"
	875	ensure_correct_option_combinations
	876	install_model
	877	setup_def
	878	setup_ce0l
	879	setup_simu
	880	fetch_simu_init_files
	881	run_sim_or_init
[5420]	882	message_post_submit

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source: BOL/LMDZ_Setup/setup.sh @ 5859

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