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setup.sh @ 5453

Last change on this file since 5453 was 5414, checked in by abarral, 10 days ago
add comment regarding netcdf
File size: 32.0 KB

Rev	Line
[4615]	1	#!/bin/bash
[4935]	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
[4935]	5	set -eu
[4615]	6
	7	# EXPERT-LEVEL CHOICES, only available in setup.sh, not in main.sh :
[4935]	8	####################################################################
[5175]	9	function define_expert_options() {
[4991]	10	# optim: either "" or "-debug" to compile in debug mode (slower but better diagnosis of segfaults)
	11	optim=""
[4615]	12
[4991]	13	# "n" or "y". If testmode="y", then simulations run for a single day per period.
	14	# NOTE: you must set mthend accordingly !
	15	testmode="n"
[4615]	16
[4991]	17	# Radiative code: "oldrad" / "rrtm" / "ecrad"
[4935]	18	rad="rrtm"
[4615]	19
[4991]	20	# !!! STRONG recommendation : experiments with DIFFERENT Orchidee or aerosol options should be performed in DIFFERENT LMDZ_Setup folders
	21	# !!! (especially as they may need different initial files)
	22
	23	# AEROSOLS : "n" (=no) / "clim" (=average 1995-2014) / "spla" (interactive dust and sea salt)
[4935]	24	# (WARNING : if you first run the scripts with aerosols=n, then you want to change to =clim ,
	25	# you'll need to remove the INIT and LIMIT folders that have been created, then run main.sh with init=1
	26	# in order to re-run the initialisation job, which downloads the aerosol files and interpolates them)
	27	aerosols="clim"
[4615]	28
[4935]	29	# SURFACE/VEGETATION SCHEME
[4993]	30	# - "none" (bucket scheme) / "CMIP6" (orchidee version used in CMIP exercise) / "7983" (orch2.2) / "7994" (trunk)
	31	# If you need other orch versions, and also require XIOS, you'll need to create the appropriate files in DEF/XMLfilesOR...
[4935]	32	veget="CMIP6"
[4986]	33
[4991]	34	# New snow scheme INLANDSIS! "y" / "n"
	35	# This flag activates INLANDSIS compilation; not yet done : treatment of specific restart and def file
[4935]	36	inlandsis="n"
[4615]	37
[5414]	38	# netcdf: 0 (use existing library) / 1 (recompile netcdf, slow) / le chemin vers la librarie netcdf
[4991]	39	netcdf=0
	40
[4935]	41	# --->>> ALSO PAY ATTENTION TO OUTPUT files, frequency, level -------------
	42	# With IOIPSL : Choose your config.def among the versions available in DEF,
	43	# copy it as config.def (the copy is done automatically for "iso"),
	44	# edit it and set up output files, frequencies and levels.
	45	# NB : For aerosols=spla, output level minimum 4 is required to output the specific variables.
	46	# For aerosols=n, the corresponding flags will automatically be set to "n".
	47	# With XIOS : adjust DEF/XMLfiles/filexml
	48	}
[4615]	49
[4935]	50	# /!\ DO NOT EDIT BELOW UNLESS YOU KNOW WHAT YOU ARE DOING /!\
[4615]	51
[5175]	52	function enable_platform() { # In job scripts, sed platform-specific headers
[4955]	53	local file="$1"
	54	local platform
	55
	56	case ${hostname:0:5} in
	57	jean-) platform="JZ";;
[4978]	58	spiri) platform="SP";;
	59	adast) platform="ADS";;
[4955]	60	*) echo "Warning: $hostname is not a known job platform (ignore if running locally)"; return 0;;
	61	esac
	62
	63	sed -i'' -e "s/^#@$platform//" "$file"
	64	}
	65
[5175]	66	function load_install_lib() {
[4954]	67	# Fetch and source install_lmdz.sh to get `myget`
[4940]	68	if [[ ! -f "install_lmdz.sh" ]]; then
[5389]	69	wget --no-cache "http://svn.lmd.jussieu.fr/LMDZ/BOL/script_install/install_lmdz.sh"
[4935]	70	fi
[4940]	71	# shellcheck disable=SC1090
	72	source <(sed 's/function $.*$ {/function installlmdz_\1 {/g' install_lmdz.sh) # source with a namespace for functions
	73	function myget { installlmdz_myget "$@"; }
[4935]	74	}
[4615]	75
[5175]	76	function set_default_params() {
[4935]	77	# Default value of script parameters
	78	SIM=$(basename "$local")CTL # name
	79	phylmd="lmd" #option -p $phylmd for makelmdz
[4615]	80
[4935]	81	cosp="n" # COSP
	82	xios="n" #XIOS
[4615]	83
[4935]	84	# Nudging :
	85	ok_guide="n"
	86	# With nudging, use real calendar (climato=0) and monthly integrations
	87	climato=1
	88	freq="mo" # frequence mensuelle mo ou annuelle yr
[4615]	89
[4935]	90	# NB : the run stops in the BEGINNING of mthend (test "next=stopsim")
	91	mthini=200001
	92	mthend=200501
	93	resol="144x142x79"
[4615]	94
[4935]	95	version="20230412.trunk"
	96	svn=""
[4615]	97
[4935]	98	init=1
[4615]	99
[4935]	100	LIMIT="LIMIT"
[4954]	101
	102	case $rad in
	103	oldrad) iflag_rrtm=0; NSW=2;;
	104	rrtm) iflag_rrtm=1; NSW=6;;
	105	ecrad) iflag_rrtm=2; NSW=6;;
	106	esac
[4935]	107	}
[4615]	108
[5175]	109	function read_cmdline_args() {
[4935]	110	while (($# > 0)); do
	111	case $1 in
	112	"-h") cat <<........fin
	113	setup.sh can be launched/driven by main.sh; some options can only be specified in setup.sh (ex: veget, aerosols).
	114	setup.sh [-v version] [-r svn_release] [-init INIT] [-d 96x95x79] [-f mo] [-nudging]
[4954]	115	-v "version" like 20150828.trunk; see https://lmdz.lmd.jussieu.fr/Distrib/LISMOI.trunk (default <$version>)
	116	-r "svn_release" either the svn release number or "last" (default <$svn>)
[4935]	117	-d IMxJMxLM to run in resolution IM x JM x LM (default <$resol>)
	118	-install pour installer et compiler le modele
	119	-f mo/yr pour tourner en mensuel ou annuel (default <$freq>)
	120	"INIT" 1: creates INIT and LIMIT
	121	0: reads from INIT and LIMIT
	122	SIMU: reads from preexisting simulation SIMU and LIMIT (default <$init>)
	123	-nudging to run with nudging. Nudging files must be created independently
	124	-p the physics to use (default <$phylmd>)
	125	-name install folder name (default <$SIM>)
	126	Other options available (see "options" section in the script)
	127	........fin
	128	exit;;
	129	"-v") version="$2"; shift; shift;;
	130	"-r") svn=$2; shift; shift;;
	131	"-d") resol=$2; shift; shift;;
	132	"-f") freq=$2; shift; shift;;
	133	"-p") phylmd=$2; shift; shift;;
	134	"-name") SIM=$2; shift; shift;;
	135	"-cosp") cosp=y; shift;;
	136	"-xios") xios=y; shift;;
	137	"-init") init=$2; shift; shift;;
	138	"-nudging") ok_guide=y; shift;;
	139	"-climato") climato=$2; shift; shift;;
	140	"-mthini") mthini=$2; shift; shift;;
	141	"-mthend") mthend=$2; shift; shift;;
[4954]	142	*) echo "unexpected $1"; $0 -h; exit
[4935]	143	esac
	144	done
[4615]	145
[4935]	146	# Initialisation
	147	if [[ $init = 1 \|\| $init = 0 ]]; then
	148	INIT="INIT"
	149	else
	150	INIT=$init
	151	fi
[4615]	152
[4935]	153	yearini=$(echo "$mthini" \| cut -c-4)
	154	if [[ $freq = yr ]]; then stopsim=$(echo "$mthend" \| cut -c-4); else stopsim=$mthend; fi
[4615]	155
[4935]	156	if [[ -d $SIM ]]; then
	157	echo "La simulation $SIM existe deja. Il est conseillé d'arrêter et de vérifier."
	158	echo "Si vous êtes sûr de vous, vous pouvez la prolonger. Voulez vous la prolonger ? (y/n)"
	159	read -r ans
	160	if [[ $ans != y ]]; then exit 1; fi
	161	fi
[4986]	162
	163	######################################################################
	164	# Choix du nombre de processeurs
	165	# NOTES :
	166	# omp=8 by default (for Jean-Zay must be a divisor of 40 procs/node), but we need
[5030]	167	# omp=1 for SPLA (only MPI parallelisation)
[5078]	168	# omp=2 for veget=CMIP6+XIOS beacause of a bug in ORCHIDEE/src_xml/xios_orchidee.f90
[4986]	169	######################################################################
	170	jm=$(echo "$resol" \| cut -dx -f2)
	171	(( mpi = ( jm + 1 ) / 2 ))
	172	omp=8
	173	if [[ $aerosols = "spla" ]]; then omp=1; fi
[5078]	174	if [[ $veget = "CMIP6" && $xios = "y" ]]; then omp=2; fi
[4986]	175	if [[ $mpi -gt $NB_MPI_MAX ]]; then mpi=$NB_MPI_MAX; fi
	176	if [[ $omp -gt $NB_OMP_MAX ]]; then omp=$NB_OMP_MAX; fi
[5013]	177
	178	# Compute how many mpi per node (required e.g. for Adastra)
[5030]	179	mpi_per_node=0
[5013]	180	if [[ $NB_CORE_PER_NODE_MAX -gt 0 ]]; then
	181	local N_omp_mt=1
	182	if [[ $omp -gt 1 ]]; then (( N_omp_mt = omp / N_HYPERTHREADING )); fi # take into account hyperthreading
	183	(( mpi_per_node = NB_CORE_PER_NODE_MAX / N_omp_mt ))
	184	if [[ mpi_per_node -gt mpi ]]; then mpi_per_node=$mpi; fi
	185	fi
	186
	187	echo "Total MPI=$mpi (PER NODE=$mpi_per_node), OMP=$omp"
[4935]	188	}
[4615]	189
[5175]	190	function ensure_correct_option_combinations() {
[4935]	191	# AVOID COMBINATIONS OF OPTIONS THAT DON'T WORK in user choices
	192	if [[ $ok_guide = y && $climato = 1 ]]; then
[4953]	193	echo "STOP: Running nudged simulations with climatological SSTs is not planned. Change <climato> to <0> or modify the setup (experts)"; exit 1
[4935]	194	fi
[4615]	195
[4991]	196	if [[ $climato = 0 && $freq = "yr" ]]; then
[4953]	197	echo "STOP: Running simulations with interannual SSTs is possible only month by month and a true calendar."
[4935]	198	echo "Change <climato> to <1> or <freq> to <mo> or modify setup.sh (experts)"; exit 1
	199	fi
[4953]	200
	201
	202	# (Temporary) Constraints for aerosols=spla :
	203	# --> resolution 128x88x79 and rad=rrtm
[4980]	204	if [[ $aerosols = "spla" && $resol != "128x88x79" ]]; then
[4953]	205	echo 'STOP: For now, <aerosols=spla> requires <resol=128x88x79>, and uses the zoomed grid from gcm.def_zNAfrica_BiJe, for which forcing & initial files are available'
	206	echo "Right now resol=<$resol>"
	207	exit 1
	208	fi
[4993]	209
	210	if [[ $rad = "ecrad" && $phylmd != "lmd" ]]; then
	211	echo "<rad=ecrad> is only supported for <phy=phylmd> here" # (Amaury) I added this check because we fetch ecrad data from libf/phylmd/ecrad/data only.
	212	fi
[4940]	213	}
[4615]	214
[5175]	215	function install_model() {
[4940]	216	mkdir -p "$LMDZD"
[4615]	217
[4953]	218	local ins_xios ins_cosp ins_aero ins_inlandsis
	219	if [[ $xios = "y" ]]; then ins_xios="-xios"; else ins_xios=""; fi
	220	if [[ $cosp = "y" ]]; then ins_cosp="-cosp v1"; else ins_cosp=""; fi
	221	if [[ $aerosols = "spla" ]]; then ins_aero="-spla"; else ins_aero=""; fi
	222	if [[ $inlandsis = "y" ]]; then ins_inlandsis="-inlandsis"; else ins_inlandsis=""; fi
	223	if [[ -n $svn ]]; then svnopt="-r $svn"; else svnopt=""; fi
	224
[4940]	225	version_name=LMDZ$(echo "$version" \| sed -e 's/-v//g' -e 's/-unstable//' -e 's/-r/r/' -e 's/ //g')
	226	LMDZname="${version_name}${svn}OR$veget${ins_xios}"
	227	MODEL="$LMDZD/$LMDZname/modipsl/modeles/LMDZ"
[4615]	228
[4953]	229	if [[ -d $MODEL ]]; then echo "Found existing install at MODEL=$MODEL"; fi
	230	echo "Installing model"
	231	cd "$LMDZD"
	232	cp "$local/install_lmdz.sh" .
	233	chmod +x install_lmdz.sh
[4993]	234	local make_j=8
[5000]	235	# We launch using $MPICMD, except if it's using mpirun (no srun equivalent for bash script) => if supported, the compilation runs in a cluster job
	236	jobcmd="\"$RUNBASHCMD $make_j\""
	237	if [[ ${hostname:0:5} = "jean-" ]]; then jobcmd="\"$RUNBASHCMD $make_j --partition=compil\""; fi # On JeanZay: compile on the <compil> partition
	238	if [[ $(echo "$RUNBASHCMD" \| cut -c -4) = "bash" ]]; then
	239	jobcmd="bash"
	240	fi
	241	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.$$.sh
[4953]	242	chmod +x install_lmdz_options.$$.sh
	243	echo "Running install_lmdz_options.$$.sh"
[4978]	244	set -o pipefail
[5000]	245	gcm=$MODEL/$(./install_lmdz_options.$$.sh \| tee /dev/tty \| tail -n 1 \| sed -n "s:.* executable is $.\.e$.:\1:p")
[4978]	246	set +o pipefail
[4953]	247	mv install_lmdz.sh install_lmdz.$$.sh
[4954]	248	cd "$local"
[4935]	249	}
[4615]	250
[5175]	251	function setup_def() { # modify various .def in ./DEF (+ xios xml as needed)
[4954]	252	cd "$local"
[4615]	253
[4954]	254	# Utilisation des .def_iso pour LMDZ-ISOtopes
	255	if [[ $phylmd = "lmdiso" ]]; then
	256	for file_iso in $(ls DEF \| grep _iso); do
	257	cp DEF/"$file_iso" DEF/"${file_iso%%_iso}"
	258	done
	259	fi
[4615]	260
[4954]	261	######################################################################
	262	# Choix de la grille verticale
	263	######################################################################
	264	lm=$(echo "$resol" \| cut -dx -f3)
	265	if [ ! -f "DEF/L$lm.def" ]; then
	266	echo "STOP: Résolution verticale non prévue - créer un fichier DEF/L$lm.def"; exit 1
	267	else
	268	sed -i'' -e "s/INCLUDEDEF=L.*.def/INCLUDEDEF=L$lm.def/" DEF/run.def
	269	fi
[4615]	270
[4954]	271	######################################################################
	272	# Changements dans les fichiers DEF/*def
[4955]	273	# (ils vont se repercuter dans les repertoires de simulation $local/$SIM et de run $SIMRUNDIR)
[4954]	274	######################################################################
[4615]	275
[5030]	276	# Choix du fichier tracer.def coherent avec l'option "aerosols"
[4954]	277	# NOTE : Le nouveau tracer.def_nospla par defaut n'inclut pas Rn-Pb;
	278	# si on les veut, il faut utiliser ci-dessous; a la place, tracer_RN_PB.def
	279	#---------------------------------------------------------------------
[5030]	280	# NB : Les traceurs absents de start* files sont initialises=0 dans le code
[4954]	281	if [[ $aerosols = "spla" ]]; then
[5030]	282	# nouveau tracer.def (remplace "traceur.def")
[5010]	283	cp DEF/tracer.def_spla DEF/tracer.def
[4954]	284	elif [[ $phylmd = "lmdiso" ]]; then
[5030]	285	# déjà copié si 'y'
[4954]	286	cp DEF/tracer.def_nospla DEF/tracer.def
	287	fi
[4615]	288
[4954]	289	# TEMPORAIREMENT pour spla on force l'utilisation de gcm.def_zNAfrica_BiJe (avec resolution 128x88x79)
	290	#----------------------------------------------------------------------
[4980]	291	if [[ $aerosols = "spla" ]]; then cp DEF/gcm.def_zNAfrica_BiJe DEF/gcm.def; fi
[4615]	292
[4954]	293	# Inscription du choix ok_guide dans DEF/guide.def
	294	#---------------------------------------------------------------------
	295	sed -i'' -e 's/ok_guide=.*.$/ok_guide='$ok_guide'/' DEF/guide.def
[4615]	296
[4954]	297	# Inscription du type de calendrier (qui est fonction de $climato) dans DEF/run.def
	298	#---------------------------------------------------------------------
	299	# NB Contrairement a ce qui est ecrit dans les fichiers run.def standard,
	300	# dans ce tutorial le choix earth_365d n'est pas disponible, et earth_366d s'appelle gregorian
	301	if [[ $climato = 0 ]]; then calend="gregorian"; else calend="earth_360d"; fi
	302	sed -i'' -e 's/calend=.*.$/calend='$calend'/' DEF/run.def
[4615]	303
[4954]	304	# Changements dans config.def (pre-choisi, et regle pour output si utilisation avec IOIPSL)
	305	# cf options veget, aerosols, cosp, xios
	306	#---------------------------------------------------------------------
[4980]	307	if [[ $veget = "none" ]]; then VEGET="n"; else VEGET="y"; fi
[4954]	308	sed -i'' -e 's/VEGET=.*.$/VEGET='$VEGET'/' DEF/config.def
[4953]	309
[4954]	310	if [[ $aerosols = "n" ]]; then
	311	# set flag_aerosols=0 and flags ok_ade&co=n
	312	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
	313	fi
[4953]	314
[4954]	315	# COSP : ok_cosp desactive COSP si on a compile avec; il ne l'active pas si on a compile sans
	316	sed -i'' -e 's/ok_cosp.*.$/ok_cosp='$cosp'/' DEF/config.def
	317	if [[ $cosp = "y" ]]; then \cp -f "$MODEL"/DefLists/cosp*.txt "$local"/DEF/; fi
[4615]	318
[4954]	319	# Sorties LMDZ en fonction de l'option "xios"
	320	sed -i'' -e 's/ok_all_xml=.*.$/ok_all_xml='$xios'/' DEF/config.def
[4615]	321
[4954]	322	# Ajuster physiq.def en fonction de radiative code (default: values for rad=rrtm)
	323	# Pour isotopes=y , mettre iflag_ice_thermo=0 au lieu de 1
	324	#---------------------------------------------------------------------
[5372]	325	sed -i'' -e "s/iflag_rrtm=..$/iflag_rrtm=$iflag_rrtm/" -e "s/NSW=..$/NSW=$NSW/" DEF/physiq.def
[4995]	326	sed -i"" -e "s:directory_name.*$:directory_name=\"$MODEL/libf/phylmd/ecrad/data\",:" DEF/namelist_ecrad
[4615]	327
[4954]	328	if [[ $phylmd = "lmdiso" ]]; then iflag_ice_thermo=0; else iflag_ice_thermo=1; fi
	329	sed -i -e 's/iflag_ice_thermo=.*.$/iflag_ice_thermo='$iflag_ice_thermo'/' DEF/physiq.def
[4615]	330
[4954]	331	# Choix de orchidee.def en fonction de orchidee_rev; modification pour xios
	332	# NOTE separate orchidee_pft.def file for ORCHIDEE trunk post-CMIP6
	333	#---------------------------------------------------------------------
	334	orchidee_def=orchidee.def_6.1
	335	orchidee_pft_def=""
	336	if [[ $veget = "7983" ]]; then
	337	orchidee_def=orchidee.def_6.2work
	338	elif [[ $veget = "7994" ]]; then
	339	orchidee_def=orchidee.def_6.4work
	340	orchidee_pft_def=orchidee_pft.def_6.4work
	341	if ! grep "INCLUDEDEF=orchidee_pft.def" DEF/run.def; then
	342	sed -i'' -e 's/INCLUDEDEF=orchidee.def/INCLUDEDEF=orchidee.def\nINCLUDEDEF=orchidee_pft.def/' DEF/run.def; fi
	343	fi
	344	cp -f DEF/$orchidee_def DEF/orchidee.def
	345	if [[ $orchidee_pft_def != "" ]]; then cp -f DEF/$orchidee_pft_def DEF/orchidee_pft.def; fi
[4615]	346
[4954]	347	# Only for veget=CMIP6 it is still possible to use IOIPSL; newer versions of orchidee.def have XIOS_ORCHIDEE_OK = y
	348	sed -i'' -e 's/XIOS_ORCHIDEE_OK =.*.$/XIOS_ORCHIDEE_OK = '$xios'/' DEF/orchidee.def
[4615]	349
[4954]	350	######################################################################
	351	# Si on tourne avec XIOS, mise a jour des fichiers context et field* dans XMLfilesLMDZ
[4955]	352	# (ils vont se repercuter dans les repertoires de simulation $local/$SIM et de run $SIMRUNDIR)
[4954]	353	######################################################################
	354	if [[ $xios = y ]]; then
	355	cp -f "$MODEL"/DefLists/context_lmdz.xml "$local"/DEF/XMLfilesLMDZ/.
	356	cp -f "$MODEL"/DefLists/field_def_lmdz.xml "$local"/DEF/XMLfilesLMDZ/.
	357	if [[ $cosp = y ]]; then cp -f "$MODEL"/DefLists/field_def_cosp1.xml "$local"/DEF/XMLfilesLMDZ/.; fi
	358	fi
	359	}
[4615]	360
[5175]	361	function setup_ce0l() { # Verification de l'existance de l'état initial, compilation eventuelle pour sa creation
[4954]	362	if [[ ! -d $INIT ]]; then
	363	if [[ $init = 0 ]]; then
	364	echo "STOP: Récuperer les repertoires $INIT ou lancer avec option -init"; exit 1
	365	else
	366	# Compile ce0l
	367	cd "$MODEL"
	368	sed -e 's/gcm$/ce0l/' compile.sh > compile_ce0l.sh; chmod +x compile_ce0l.sh
	369	echo "Compiling ce0l"
	370	if ! ./compile_ce0l.sh &> ce0l.log; then echo "STOP: ce0l compilation failed, see $MODEL/ce0l.log"; exit 1; fi
	371	echo "Compiled ce0l"
[4955]	372	ce0l=${gcm/gcm/ce0l}
[4615]	373
[4954]	374	cd "$local"
	375	fi
	376	elif [[ $init = 1 ]]; then
	377	echo "STOP: Vous essayez d initialiser le modele mais $INIT existe deja"; exit 1
	378	fi
	379	}
[4615]	380
[5175]	381	function setup_simu() {
[4956]	382	SIMRUNTOPDIR="$SIMRUNBASEDIR/$(basename "$local")"
[4955]	383	SIMRUNDIR=$SIMRUNTOPDIR
	384	mkdir -p "$SIMRUNDIR"
	385	cd "$SIMRUNDIR"
	386	echo "La simulation s'exécutera sur $SIMRUNDIR"
[4615]	387
[4955]	388	#####################################################################
	389	# Creation du repertoire $SIM s'il n'existe pas deja
	390	#####################################################################
	391	if [[ ! -d $local/$SIM ]]; then
	392	mkdir "$local/$SIM"
	393	cd "$local"
[4615]	394
[4955]	395	# Edit reb.sh
	396	cp reb.sh "$local/$SIM/reb.sh"; chmod +x "$local/$SIM/reb.sh"
[4958]	397	sed -i'' -e "s:^rebuild=.*.$:rebuild=$LMDZD/$LMDZname/modipsl/bin/rebuild:" "$local/$SIM/reb.sh"
[4991]	398	enable_platform "$local/$SIM/reb.sh"
[4615]	399
[4955]	400	# Copy .def
	401	cp lmdz_env.sh "$local/$SIM/"
	402	mkdir "$local/$SIM/DEF"; cp DEF/def DEF/namelis "$local/$SIM/DEF/"
	403	#Pour XIOS, respectivement COSP, copier aussi les fichiers xml / txt
	404	if [[ $cosp = "y" ]]; then cp DEF/cosp*txt "$local/$SIM/DEF/"; fi
	405	if [[ $xios = "y" ]]; then
	406	cp DEF/XMLfilesLMDZ/*xml "$local/$SIM/DEF/"
	407	if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml "$local/$SIM/DEF/"; fi
	408	fi
	409	chmod u+w "$local/$SIM"/DEF/*
[4615]	410
[4955]	411	# Gestion du calendrier
	412	#######################
	413	cd "$SIM"
	414	sed -i'' -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def
	415	if [[ $freq = "yr" ]]; then date=$yearini; else date=$mthini; fi
	416	echo "$date a faire" >\| etat
[4615]	417
[4955]	418	# Recuperation des fichiers : executable initiaux et forcages
	419	#############################################################
	420	echo "date: $date"
	421	for f in start startphy; do
	422	inf=../$INIT/$f.$date.nc
	423	if [[ -f $inf \|\| $init = 1 ]]; then ln -s "$inf" ./; else echo "STOP: $inf missing"; exit ; fi;
	424	done
	425	for f in sechiba stomate; do
	426	if [[ -f ../$INIT/start_$f.$date.nc ]]; then ln -sf "../$INIT/start_$f.$date.nc" .; fi
	427	done
	428	cp "$gcm" gcm.e
	429	fi
	430	cd "$local"/..
[4615]	431
[4955]	432	#####################################################################
	433	echo "Modification du script de lancement"
	434	#####################################################################
	435	local cput
	436	if [[ $freq = "yr" ]]; then cput="04:00:00"; else cput="01:00:00"; fi
	437	local isotopes="n"
	438	if [[ $phylmd = "lmdiso" ]]; then isotopes="y"; fi
[4958]	439	sed -e "s/NOM_SIMU/$SIM/" \
[4955]	440	-e "s/time=.*.$/time=$cput/" \
	441	-e "s/ntasks=.*.$/ntasks=$mpi/" \
[5030]	442	-e "s/ntasks-per-node=.*.$/ntasks-per-node=$mpi_per_node/" \
[4955]	443	-e "s/cpus-per-task=.*.$/cpus-per-task=$omp/" \
	444	-e "s/nthreads=.*./nthreads=$omp/" \
[4956]	445	-e "s/MAINDIR=.*.$/MAINDIR=$(basename "$local")/" \
[5000]	446	-e "s:STORED=..:STORED=$(dirname "$local"):" \
[4956]	447	-e "s:SCRATCHD=..:SCRATCHD=$SIMRUNBASEDIR:" \
[4955]	448	-e "s/stopsim=.*.$/stopsim=$stopsim/" \
	449	-e "s/^veget=.*.$/veget=$veget/" \
	450	-e "s/^aerosols=.*.$/aerosols=$aerosols/" \
	451	-e "s/^isotopes=.*.$/isotopes=$isotopes/" \
	452	-e "s/^climato=.*.$/climato=$climato/" \
	453	-e "s/^ok_guide=.*.$/ok_guide=$ok_guide/" \
	454	"$local/script_SIMU" >\| "$SIMRUNDIR/tmp_$SIM"
[4615]	455
[4991]	456	enable_platform "$SIMRUNDIR/tmp_$SIM"
[4615]	457
[4955]	458	if [[ $testmode = "y" ]]; then
[4986]	459	sed -i'' -e "s/time=.*.$/time=00:10:00/" -e "s/#nday=1/nday=1/" -e "s/#@TESTQ//" "$SIMRUNTOPDIR/tmp_$SIM"
[4955]	460	fi
	461	}
[4615]	462
[5175]	463	function fetch_simu_init_files() {
[4955]	464	#####################################################################
	465	echo "Recuperation eventuelle de certains fichiers sur $LMDZ_INIT"
	466	#####################################################################
	467	mkdir -p "$LMDZ_INIT"
[4615]	468
[4955]	469	#-------------------------------------------------------------------
	470	# Fichiers ORCHIDEE
	471	#-------------------------------------------------------------------
	472	get="myget 3DInputData/Orchidee/"
	473	cd "$LMDZ_INIT";
	474	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
	475	if [[ ! -f $file ]]; then ${get}$file; fi
	476	done
	477	cd - > /dev/null
	478	# Additionnal files needed for ORCHIDEE trunk post-CMIP6
	479	if [[ $veget = 7994 && ! -f $LMDZ_INIT/soil_bulk_and_ph.nc ]]; then
	480	cd "$LMDZ_INIT"
	481	${get}soil_bulk_and_ph.nc; ${get}NITROGEN_for_ORtrunk.tar
	482	tar -xvf NITROGEN_for_ORtrunk.tar; cd - > /dev/null
	483	fi
	484	#-------------------------------------------------------------------
	485	# Fichiers aerosols/chimie
	486	#-------------------------------------------------------------------
	487	if [[ $aerosols = "clim" ]]; then
	488	get="myget 3DInputData/AerChem/"
	489	#liste_get="aerosols1850_from_inca.nc aerosols2000_from_inca.nc"
	490	#aerosols9999_from_inca.nc est un lien vers aerosols1995_2014_ensavg_from_inca.nc
	491	cd "$LMDZ_INIT"
	492	for file in "aerosols1850_from_inca.nc" "aerosols9999_from_inca.nc"; do
	493	if [[ ! -f $file ]]; then ${get}$file; fi
	494	done
	495	cd - > /dev/null
	496	fi
	497	# For SPLA
	498	#-------------------
	499	# Dans ${LMDZ_INIT} on cree folder SPLA_Init et dedans le INITIAL
	500	# Pour l'instant on copie là-dedans de chez Binta les fichiers a la res zoomNaf;
	501	# plus tard on y recupererea des fichiers a haute resolution reguliere depuis http:/LMDZ,
	502	# a regrider ensuite par un script interp_fichiers_spla.sh (comme pour aerosols="clim")
	503	# Les fichiers (regrides, sauf SOILSPEC.data utilise tel quel) seront mis dans $MAINDIR/INPUT_SPLA (equivalent de INPUT_DUST)
[5010]	504	# The Path below is for JEANZAY. See with the team how to adapt to your cluster.
[4955]	505	if [[ $aerosols = "spla" ]]; then
	506	mkdir -p "${LMDZ_INIT}/SPLA_Init"; mkdir -p "$LMDZ_INIT/SPLA_Init/INITIAL"
	507	get="cp -p /gpfsstore/rech/gzi/rgzi027/ergon/BIBIAERO/INPUTS_DUST/INITIAL/"
	508	liste_get="wth.dat cly.dat donnees_lisa.nc SOILSPEC.data \
	509	carbon_emissions.nc sulphur_emissions_antro.nc \
	510	sulphur_emissions_nat.nc sulphur_emissions_volc.nc"
[4615]	511
[4955]	512	cd "$LMDZ_INIT/SPLA_Init/INITIAL"
	513	for file in $liste_get; do
	514	if [[ ! -f $file ]]; then ${get}$file .; fi
	515	done
	516	cd - > /dev/null
	517	###
	518	#Cas particulier des fichiers mensuels dust.nc :A DECIDER :
	519	#C'est entre le cas des aerosols.clim= 1 seul fichier, annuel,
	520	# et le cas des vents guidage, pré-interpolés avec era2gcm pour toute la periode, dans MAINDIR/GUIDE.
	521	# 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.
	522	# 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
	523	#ICI pour l'instant je copie les fichiers de chez Binta (repositoire==http...) dans LMDZ_INIT/SPLA_Init, avec test sur mois 01
[4615]	524
[4955]	525	if [[ ! -d ${LMDZ_INIT}/SPLA_Init/PERIOD0001 ]]; then
	526	if [[ ${hostname:0:5} != "jean-" ]]; then echo "PERIOD001 (aerosols=spla) IS ONLY AVAILABLE ON JEANZAY FOR NOW, CONTACT SUPPORT"; exit 1; fi
	527	cp -pr /gpfsstore/rech/gzi/rgzi027/ergon/BIBIAERO/INPUTS_DUST/PERIOD* "$LMDZ_INIT/SPLA_Init/.";
	528	fi
	529	#A la fin on doit avoir dans SPLA_Init les fichiers initiaux dans INITIAL plus les repertoires PERIOD00MM contenant dust.nc
	530	#Cela doit se retrouver dans script_SIMU qui les copie dans le repertoire de run sur $SCRATCH
	531	fi
	532	#-------------------------------------------------------------------
	533	# Fichiers Init
	534	#-------------------------------------------------------------------
	535	get="myget 3DInputData/Init/"
	536	liste_get="alb_bg_modisopt_2D_ESA_v2.nc reftemp.nc"
	537	cd "$LMDZ_INIT"
	538	for file in $liste_get; do
	539	if [[ ! -f $LMDZ_INIT/$file ]]; then ${get}$file; fi
	540	done
	541	cd - > /dev/null
	542	}
[4615]	543
[5175]	544	function run_sim_or_init() {
[4955]	545	cd "$local"
[4956]	546
[4955]	547	if [[ $init = 1 ]]; then
	548	#####################################################################
	549	echo "Creation de l etat initial"
	550	#####################################################################
[4615]	551
[4955]	552	# Creation du repertoire INIT et mise en place de liens logiques vers les starts
	553	# en anticipation de leur création :
	554	mkdir "$local/$INIT"; cd "$local/$INIT"
	555	for an in $mthini $yearini; do for f in start startphy; do ln -s "$f.nc" "$f.$an.nc"; done; done
[4615]	556
[4955]	557	# Creation du repertoire INIT temporaire et rapatriement des fichiers necessaires
	558	if [[ -d $SIMRUNDIR/$INIT ]]; then mv "$SIMRUNDIR/$INIT" "$SIMRUNDIR/$INIT$$"; fi
	559	mkdir "$SIMRUNDIR/$INIT"; cp -r "$local/DEF" "$SIMRUNDIR/$INIT/"
	560	cd "$SIMRUNDIR/$INIT"; cp DEF/*.def .; cp "$local/lmdz_env.sh" .
	561	if [[ $xios = "y" ]]; then
	562	cp DEF/XMLfilesLMDZ/*xml .
	563	if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml .; fi
	564	fi
	565	sed -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def >\| run.def
[4954]	566
[4955]	567	#-------------------------------------------------------------------
	568	# Fichiers Limit
	569	#-------------------------------------------------------------------
	570	local yrs suf
	571	if [[ $climato = 0 ]]; then
	572	# calend est choisi plus haut dans "Changements dans les fichiers DEF/*def" et ecrit dans $MAINDIR/DEF/run.def
	573	yrini=$(echo "$mthini" \| cut -c-4)
	574	yrend=$(echo "$mthend" \| cut -c-4)
	575	yrs=""; yr=$yrini
	576	while [[ $yr -le $yrend ]]; do yrs="$yrs $yr"; (( yr = yr + 1 )); done
	577	suf="360x180_"
	578	else
	579	yrs=2000
	580	suf="1x1_clim"
	581	fi
[4954]	582
[4955]	583	get="myget 3DInputData/Limit/"
	584	liste_get="Albedo.nc Relief.nc Rugos.nc landiceref.nc"
	585	for yr in $yrs; do
	586	if [[ $climato = 0 ]]; then sufyr=$suf$yr; else sufyr=$suf; fi
	587	liste_get="$liste_get amipbc_sic_$sufyr.nc amipbc_sst_$sufyr.nc"
	588	done
	589	echo LISTEGET "$liste_get"
	590	for file in $liste_get; do
	591	cd "$LMDZ_INIT"
	592	if [[ ! -f $LMDZ_INIT/$file ]]; then ${get}$file; fi
	593	cd - > /dev/null
	594	ln -s "$LMDZ_INIT/$file" .
	595	done
	596	#-------------------------------------------------------------------
	597	# ECDYN
	598	#-------------------------------------------------------------------
	599	get="myget 3DInputData/Init/"
	600	if [[ ! -f $LMDZ_INIT/ECDYN.nc ]]; then cd "$LMDZ_INIT"; ${get}ECDYN.nc; cd - > /dev/null; fi
	601	ln -s "$LMDZ_INIT"/ECDYN.nc .
	602	ln -sf ECDYN.nc ECPHY.nc
[4615]	603
[4955]	604	# Creation du script d'initialisation
	605	cat << ...eod >\| tmp
	606	#!/bin/bash
	607	#@JZ#JeanZay
	608	#@JZ#SBATCH --job-name=Init # nom du job
[4978]	609	#@JZ#SBATCH --ntasks=1 # Nombre de processus MPI
[4980]	610	#@JZ#SBATCH --cpus-per-task=1 # nombre de threads OpenMP
[4955]	611	#@JZ# /!\ Attention, la ligne suivante est trompeuse mais dans le vocabulaire
[4978]	612	#@JZ# de Slurm "multithread" fait bien référence à l'hyperthreading.
	613	#@JZ#SBATCH --hint=nomultithread # 1 thread par coeur physique (pas d'hyperthreading)
	614	#@JZ#SBATCH --time=00:10:00 # Temps d'exécution maximum demandé (HH:MM:SS)
[4955]	615	#@JZ#SBATCH --output=Init%j.out # Nom du fichier de sortie
	616	#@JZ#SBATCH --error=Init%j.out # Nom du fichier d'erreur (ici commun avec la sortie)
	617	#@JZ# To submit to dev queue; "time" (above) must be max 2h
[4995]	618	#@JZ#TESTQ#SBATCH --qos=qos_cpu-dev
[4978]	619	#@SP#Spirit
	620	#@SP#SBATCH --job-name=Init
	621	#@SP#SBATCH --ntasks=1
[4980]	622	#@SP#SBATCH --cpus-per-task=1
[4978]	623	#@SP#SBATCH --hint=nomultithread
	624	#@SP#SBATCH --time=00:10:00
	625	#@SP#SBATCH --output=Init%j.out
	626	#@SP#SBATCH --error=Init%j.out
	627	#@ADS#Adastra
	628	#@ADS#SBATCH --job-name=Init
	629	#@ADS#SBATCH --ntasks=1
[4980]	630	#@ADS#SBATCH --cpus-per-task=1
[5013]	631	#@ADS#SBATCH --nodes=1
[4978]	632	#@ADS#SBATCH --hint=nomultithread
	633	#@ADS#SBATCH --time=00:10:00
	634	#@ADS#SBATCH --output=Init%j.out
	635	#@ADS#SBATCH --error=Init%j.out
[4615]	636
[4995]	637	set -eu
	638
[4955]	639	# ANCIEN MULTI STEP case \${LOADL_STEP_NAME} in
[4615]	640
[4955]	641	# ANCIEN MULTI STEP init )
[4615]	642
[4955]	643	if [ ! -f lmdz_env.sh ]; then echo "manque fichier lmdz_env.sh"; ls; exit 1; fi
	644	. lmdz_env.sh
	645	ulimit -s unlimited
	646	cd $SIMRUNDIR/$INIT
	647	echo "Executable : $ce0l"
	648	for yr in $yrs; do
	649	if [ $climato = 0 ]; then sufyr=$suf\$yr; else sufyr=$suf; fi
	650	ln -sf amipbc_sic_\$sufyr.nc amipbc_sic_1x1.nc
	651	ln -sf amipbc_sst_\$sufyr.nc amipbc_sst_1x1.nc
	652	sed -e 's/anneeref=.*.$/anneeref='\$yr'/' DEF/run.def >\| run.def
	653	echo Starting initialisation
[5000]	654	OMP_NUM_THREADS=1 $MPICMD 1 $ce0l # ce0l requires MPI=OMP=1
[4955]	655	if [ $climato = 0 ]; then mv limit.nc limit.\$yr.nc; fi
	656	done
	657	# ANCIEN MULTI STEP ;;
[4615]	658
[4955]	659	# ANCIEN MULTI STEP interp )
[4956]	660	if [[ $aerosols = clim ]]; then
	661	cp $local/interp_aerosols.sh .; chmod +x interp_aerosols.sh
	662	# Les aerosols de l'annee 2000 ont été remplacés par "9999" qui pointe vers un fichier moyen sur 1995-2014
	663	#for year in 2000 1850; do ./interp_aerosols.sh \$year; done
	664	#mv aerosols.2000.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc
	665	for year in 9999 1850; do ./interp_aerosols.sh \$year; done
	666	mv aerosols.9999.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc
[4615]	667	fi
	668
[4955]	669	# AS : S'il etait possible d'automatiser l'interpolation de l'input SPLA, ce serait a lancer ici
	670	#en attendant, on passe au paragraphe suivant où on copie les fichiers à la res ZoomNaf depuis $LMDZ_INIT/SPLA_Init
	671	#if [ $aerosols = spla ]; then
	672	#cp $local/futur script interp_aerosols_SPLA.sh .; chmod +x interp_aerosols_SPLA.sh
	673	#for file in...; do ./interp_aerosols_SPLA.sh \$year; done
	674	#etc etc etc ...
	675	#fi
[4615]	676
[4955]	677	# Copy initial and forcing files in $local/$INIT and $local/$LIMIT; also in $local/INPUT_SPLA if $aerosols=spla
[4991]	678	for f in sta* gri*nc; do cp \$f $local/$INIT/\$f; done
	679	if [[ $climato = 1 ]]; then cp limit.nc $local/$INIT/limit.nc; fi
[4955]	680	mkdir -p $local/$LIMIT
	681	for f in limit*.nc ; do cp \$f $local/$LIMIT/\$f; done
	682	if [ $aerosols = clim ]; then for f in aerosols[.0-9]*nc; do cp \$f $local/$LIMIT/\$f; done; fi
	683	#
	684	if [ $aerosols = spla ]; then
	685	#mkdir -p $local/INPUT_SPLA; pour l'instant on copie $LMDZ_INIT/SPLA_Init en block
	686	if [ ! -d $local/INPUT_SPLA ]; then cp -pr $LMDZ_INIT/SPLA_Init $local/INPUT_SPLA; fi
[4615]	687	fi
[4955]	688	cd $SIMRUNDIR
	689	...eod
	690	if [[ $ok_guide != "y" ]]; then # Running first simulation automatically except for nudging
	691	cat << ...eod >> tmp
[5034]	692	echo "Submitting job tmp_$SIM"
	693	echo "\$SUBMITCMD tmp_$SIM"
	694	\$SUBMITCMD tmp_$SIM
[4955]	695	...eod
	696	fi
	697	cat << ...eod >> tmp
	698	# ANCIEN MULTI STEP esac
	699	...eod
[4991]	700	enable_platform tmp
[4955]	701	echo "###############################################################################"
	702	echo "Submitting initialisation job <$SUBMITCMD tmp> from $(pwd)"
	703	chmod +x tmp
	704	$SUBMITCMD tmp
	705	echo "###############################################################################"
[4615]	706
[4955]	707	else #case [ $init != 1 ]
	708	cd "$SIMRUNDIR"
	709	echo "###############################################################################"
	710	echo "Submitting job tmp_$SIM"
	711	echo "$SUBMITCMD tmp_$SIM"
	712	$SUBMITCMD "tmp_$SIM"
	713	echo '###############################################################################'
	714	fi
	715	}
[4615]	716
[5175]	717	function message_post_submit() {
[4991]	718	if [[ $ok_guide = "y" && $init = 1 ]]; then
[5006]	719	cd "$local"
[4993]	720	enable_platform era2gcm_tuto.sh
[4991]	721	echo "Once initialisation is finished, you have to create nudging files"
[4993]	722	echo "Edit era2gcm_tuto.sh and set the desired parameters in section <User choices>"
	723	echo "Make sure you have acces to the chosen ERA files, and the required modules are loaded, then run : ./era2gcm_tuto.sh"
[4991]	724	if [[ $aerosols = "spla" ]]; then
	725	echo "Your aerosol choice is <spla>, so you need ERA 10m-winds interpolated on LMDZ grid. Use script era2gcm_uv10m.sh"
	726	fi
	727	else
	728	echo "Si tout se passe bien, vous avez initialisé et lancé automatiquement la simulation."
[4993]	729	echo "Le job qui a été lancé se trouve sur $SIMRUNTOPDIR/tmp_$SIM"
[4991]	730	fi
	731	}
	732
[5175]	733	function setup_and_load_lmdz_env() {
	734	if [[ ! -f .lmdz_setup_root_dir ]]; then echo "STOP: setup.sh is not located in the root dir ??!!"; exit 1; fi
	735	# sed root_dir in lmdz_env.sh
	736	sed -i'' "s<root_dir=.*<root_dir=$local<" lmdz_env.sh
[4615]	737
[5175]	738	# Set up the appropriate environment
	739	source lmdz_env.sh
	740	}
	741
[4955]	742	local=$(pwd)
[4615]	743
[5175]	744	setup_and_load_lmdz_env
[4955]	745	load_install_lib
	746	define_expert_options
	747	set_default_params
	748	read_cmdline_args "$@"
	749	ensure_correct_option_combinations
	750	install_model
	751	setup_def
	752	setup_ce0l
	753	setup_simu
	754	fetch_simu_init_files
	755	run_sim_or_init
[4993]	756	message_post_submit

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source: BOL/LMDZ_Setup_amaury/setup.sh @ 5453

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