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source: BOL/LMDZ_Setup/setup.sh @ 5531

Last change on this file since 5531 was 5465, checked in by fhourdin, 7 weeks ago
For sequential and debug compilation
File size: 32.2 KB

Rev	Line
[4615]	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
[5415]	20	# Radiative code: "oldrad" / "rrtm" / "ecrad"
	21	rad="rrtm"
[4615]	22
[5438]	23	# !!! STRONG recommendation : experiments with DIFFERENT Orchidee or
	24	# aerosol options should be performed in DIFFERENT LMDZ_Setup folders
[5415]	25	# !!! (especially as they may need different initial files)
[4615]	26
[5438]	27	# AEROSOLS : "n" (=no)/"clim" (=average 1995-2014) / "spla" (interactive)
	28	# (WARNING : if you first run the scripts with aerosols=n, then you want
	29	# to change to =clim, you must remove the INIT and LIMIT folders and
	30	# rerun main.sh with init=1 in order to create aerosol files
	31
[5415]	32	aerosols="clim"
[4615]	33
[5415]	34	# SURFACE/VEGETATION SCHEME
[5438]	35	# - "none" : bucket scheme
	36	# CMIP6 : orchidee CMIP6 version
	37	# 7983/7994 : orchidee svn release 7983 (orch2.2) and 7994 (last tested)
	38	# If you need other orch versions, and also require XIOS, you'll need
	39	# to create the appropriate files in DEF/XMLfilesOR...
[5415]	40	veget="CMIP6"
[4615]	41
[5415]	42	# New snow scheme INLANDSIS! "y" / "n"
[5438]	43	# Activates INLANDSIS compilation
	44	# to be done : treatment of specific restart and def file
[5415]	45	inlandsis="n"
[4615]	46
[5415]	47	# netcdf: 0 (use existing library) / 1 (recompile netcdf, slow)
	48	netcdf=0
[4615]	49
[5438]	50	# --->>> ALSO PAY ATTENTION TO OUTPUT files, frequency, level ------------
	51	# With IOIPSL : Choose your config.def among versions available in DEF,
[5415]	52	# copy it as config.def (the copy is done automatically for "iso"),
	53	# edit it and set up output files, frequencies and levels.
[5438]	54	# NB : For aerosols=spla, output level minimum 4 is required to outpu
	55	# the specific variables.
	56	# For aerosols=n, aerosol flags will automatically be set to "n".
[5415]	57	# With XIOS : adjust DEF/XMLfiles/filexml
	58	}
[4615]	59
	60
[5438]	61	#---------------------------------------------------------------------------
	62	function enable_platform() { # Sed platform-specific headers
	63	#---------------------------------------------------------------------------
[5415]	64	local file="$1"
	65	local platform
[4615]	66
[5415]	67	case ${hostname:0:5} in
	68	jean-) platform="JZ";;
	69	spiri) platform="SP";;
	70	adast) platform="ADS";;
	71	*) echo "Warning: $hostname is not a known job platform (ignore if running locally)"; return 0;;
	72	esac
[4615]	73
[5415]	74	sed -i'' -e "s/^#@$platform//" "$file"
	75	}
[4615]	76
[5438]	77	#---------------------------------------------------------------------------
	78	function load_install_lib() { #Fetch and source install_lmdz.sh to get myget
	79	#---------------------------------------------------------------------------
[5415]	80	if [[ ! -f "install_lmdz.sh" ]]; then
	81	wget --no-cache "http://svn.lmd.jussieu.fr/LMDZ/BOL/script_install/install_lmdz.sh"
	82	fi
	83	# shellcheck disable=SC1090
	84	source <(sed 's/function \(.*\) {/function installlmdz_\1 {/g' install_lmdz.sh) # source with a namespace for functions
	85	function myget { installlmdz_myget "$@"; }
[4615]	86	}
	87
[5438]	88	#---------------------------------------------------------------------------
	89	function set_default_params() { # Default value of script parameters
	90	#---------------------------------------------------------------------------
	91
[5464]	92	SIM=$(basename "$local_d")CTL # name
[5415]	93	phylmd="lmd" #option -p $phylmd for makelmdz
[4615]	94
[5415]	95	cosp="n" # COSP
	96	xios="n" #XIOS
[4615]	97
[5415]	98	# Nudging :
	99	ok_guide="n"
	100	# With nudging, use real calendar (climato=0) and monthly integrations
	101	climato=1
	102	freq="mo" # frequence mensuelle mo ou annuelle yr
[4615]	103
[5415]	104	# NB : the run stops in the BEGINNING of mthend (test "next=stopsim")
	105	mthini=200001
	106	mthend=200501
	107	resol="144x142x79"
[4615]	108
[5415]	109	version="20230412.trunk"
	110	svn=""
[4615]	111
[5415]	112	init=1
[4615]	113
[5415]	114	LIMIT="LIMIT"
[4615]	115
[5415]	116	}
[4615]	117
[5438]	118	#---------------------------------------------------------------------------
[5415]	119	function read_cmdline_args() {
[5438]	120	#---------------------------------------------------------------------------
[5415]	121	while (($# > 0)); do
	122	case $1 in
	123	"-h") cat <<........fin
[5428]	124	setup.sh can be launched/driven by main.sh
[5415]	125	setup.sh [-v version] [-r svn_release] [-init INIT] [-d 96x95x79] [-f mo] [-nudging]
	126	-v "version" like 20150828.trunk; see https://lmdz.lmd.jussieu.fr/Distrib/LISMOI.trunk (default <$version>)
[5428]	127	-r "svn_release" either the svn release number or "last" (default <$svn>)
	128	-d IMxJMxLM to run in resolution IM x JM x LM (default <$resol>)
	129	-install pour installer et compiler le modele
	130	-f mo/yr pour tourner en mensuel ou annuel (default <$freq>)
	131	-rad RAD Radiation
	132	-netcdf 0/1/DIR Netcdf installation
	133	-aerosols n/clim/spla Aerosols : none / climatological / interactive with SPLA
	134	-veget CMIP6 CMIP6 version of rchidee
	135	7983 orch2.2
	136	7994 trunk
	137	"INIT" 1: creates INIT and LIMIT
	138	0: reads from INIT and LIMIT
	139	SIMU: reads from preexisting simulation SIMU and LIMIT (default <$init>)
	140	-nudging to run with nudging. Nudging files must be created independently
	141	-p the physics to use (default <$phylmd>)
	142	-name install folder name (default <$SIM>)
[5415]	143	Other options available (see "options" section in the script)
[4615]	144	........fin
[5415]	145	exit;;
	146	"-v") version="$2"; shift; shift;;
	147	"-r") svn=$2; shift; shift;;
	148	"-d") resol=$2; shift; shift;;
	149	"-f") freq=$2; shift; shift;;
	150	"-p") phylmd=$2; shift; shift;;
	151	"-name") SIM=$2; shift; shift;;
[5428]	152	"-rad") rad=$2; shift; shift;;
	153	"-netcdf") netcdf=$2; shift; shift;;
	154	"-aerosols") aerosols=$2; shift; shift;;
	155	"-veget") veget=$2; shift; shift;;
[5415]	156	"-cosp") cosp=y; shift;;
	157	"-xios") xios=y; shift;;
	158	"-init") init=$2; shift; shift;;
	159	"-nudging") ok_guide=y; shift;;
	160	"-climato") climato=$2; shift; shift;;
	161	"-mthini") mthini=$2; shift; shift;;
	162	"-mthend") mthend=$2; shift; shift;;
	163	*) echo "unexpected $1"; $0 -h; exit
	164	esac
	165	done
[4615]	166
[5415]	167	# Initialisation
	168	if [[ $init = 1 \|\| $init = 0 ]]; then
	169	INIT="INIT"
	170	else
	171	INIT=$init
	172	fi
[4615]	173
[5428]	174	case $rad in
	175	oldrad) iflag_rrtm=0; NSW=2;;
	176	rrtm) iflag_rrtm=1; NSW=6;;
	177	ecrad) iflag_rrtm=2; NSW=6;;
	178	esac
	179
[5432]	180	im=$(echo "$resol" \| cut -dx -f1)
	181	jm=$(echo "$resol" \| cut -dx -f2)
	182	lm=$(echo "$resol" \| cut -dx -f3)
	183
[5415]	184	yearini=$(echo "$mthini" \| cut -c-4)
	185	if [[ $freq = yr ]]; then stopsim=$(echo "$mthend" \| cut -c-4); else stopsim=$mthend; fi
[4615]	186
[5415]	187	if [[ -d $SIM ]]; then
	188	echo "La simulation $SIM existe deja. Il est conseillé d'arrêter et de vérifier."
	189	echo "Si vous êtes sûr de vous, vous pouvez la prolonger. Voulez vous la prolonger ? (y/n)"
	190	read -r ans
	191	if [[ $ans != y ]]; then exit 1; fi
	192	fi
[4615]	193
[5415]	194	######################################################################
	195	# Choix du nombre de processeurs
	196	# NOTES :
[5438]	197	# omp=8 by default (for Jean-Zay must be a divisor of 40 procs/node)
	198	# omp=1 : required for SPLA (omp parallelism not ready)
	199	# omp=2 for veget=CMIP6+XIOS beacause of a bug in ORCHIDEE/src_xml/xios_orchidee.f90
[5415]	200	######################################################################
	201	(( mpi = ( jm + 1 ) / 2 ))
	202	omp=8
	203	if [[ $aerosols = "spla" ]]; then omp=1; fi
	204	if [[ $veget = "CMIP6" && $xios = "y" ]]; then omp=2; fi
	205	if [[ $mpi -gt $NB_MPI_MAX ]]; then mpi=$NB_MPI_MAX; fi
	206	if [[ $omp -gt $NB_OMP_MAX ]]; then omp=$NB_OMP_MAX; fi
[4615]	207
[5415]	208	# Compute how many mpi per node (required e.g. for Adastra)
	209	mpi_per_node=0
	210	if [[ $NB_CORE_PER_NODE_MAX -gt 0 ]]; then
	211	local N_omp_mt=1
	212	if [[ $omp -gt 1 ]]; then (( N_omp_mt = omp / N_HYPERTHREADING )); fi # take into account hyperthreading
	213	(( mpi_per_node = NB_CORE_PER_NODE_MAX / N_omp_mt ))
	214	if [[ mpi_per_node -gt mpi ]]; then mpi_per_node=$mpi; fi
	215	fi
[4615]	216
[5415]	217	echo "Total MPI=$mpi (PER NODE=$mpi_per_node), OMP=$omp"
	218	}
[4615]	219
[5438]	220	#---------------------------------------------------------------------------
[5415]	221	function ensure_correct_option_combinations() {
	222	# AVOID COMBINATIONS OF OPTIONS THAT DON'T WORK in user choices
[5438]	223	#---------------------------------------------------------------------------
[5415]	224	if [[ $ok_guide = y && $climato = 1 ]]; then
	225	echo "STOP: Running nudged simulations with climatological SSTs is not planned. Change <climato> to <0> or modify the setup (experts)"; exit 1
	226	fi
[4615]	227
[5415]	228	if [[ $climato = 0 && $freq = "yr" ]]; then
	229	echo "STOP: Running simulations with interannual SSTs is possible only month by month and a true calendar."
	230	echo "Change <climato> to <1> or <freq> to <mo> or modify setup.sh (experts)"; exit 1
	231	fi
[4615]	232
	233
[5415]	234	# (Temporary) Constraints for aerosols=spla :
	235	# --> resolution 128x88x79 and rad=rrtm
[5438]	236	if [[ $aerosols = "spla" && ( ${im}x${jm} != "128x88" \|\| $freq != mo ) ]]; then
	237	echo 'STOP: For now, <aerosols=spla> requires <resol=128x88x79>,'
	238	echo 'and uses the zoomed grid from gcm.def_zNAfrica_BiJe,'
	239	echo 'for which forcing & initial files are available'
[5415]	240	echo "Right now resol=<$resol>"
[5438]	241	echo 'Should be run in monthly mode'
[5415]	242	exit 1
	243	fi
[4615]	244
[5415]	245	if [[ $rad = "ecrad" && $phylmd != "lmd" ]]; then
	246	echo "<rad=ecrad> is only supported for <phy=phylmd> here" # (Amaury) I added this check because we fetch ecrad data from libf/phylmd/ecrad/data only.
	247	fi
	248	}
[4615]	249
[5438]	250	#---------------------------------------------------------------------------
[5415]	251	function install_model() {
[5438]	252	#---------------------------------------------------------------------------
[5415]	253	mkdir -p "$LMDZD"
[4615]	254
[5415]	255	local ins_xios ins_cosp ins_aero ins_inlandsis
	256	if [[ $xios = "y" ]]; then ins_xios="-xios"; else ins_xios=""; fi
	257	if [[ $cosp = "y" ]]; then ins_cosp="-cosp v1"; else ins_cosp=""; fi
	258	if [[ $aerosols = "spla" ]]; then ins_aero="-spla"; else ins_aero=""; fi
	259	if [[ $inlandsis = "y" ]]; then ins_inlandsis="-inlandsis"; else ins_inlandsis=""; fi
	260	if [[ -n $svn ]]; then svnopt="-r $svn"; else svnopt=""; fi
[4615]	261
[5465]	262	if [[ $PARALLEL == 0 ]] ; then parallel= ; parsuf=seq ; else parallel="-parallel mpi_omp" ; parsuf= ; fi
[5415]	263	version_name=LMDZ$(echo "$version" \| sed -e 's/-v//g' -e 's/-unstable//' -e 's/-r/r/' -e 's/ //g')
[5465]	264	LMDZname="${version_name}${svn}OR$veget${ins_xios}${parsuf}$( echo $optim \| sed -e 's/[\ -]//g' )"
[5415]	265	MODEL="$LMDZD/$LMDZname/modipsl/modeles/LMDZ"
[4615]	266
[5415]	267	if [[ -d $MODEL ]]; then echo "Found existing install at MODEL=$MODEL"; fi
	268	echo "Installing model"
	269	cd "$LMDZD"
[5464]	270	cp "$local_d/install_lmdz.sh" .
[5415]	271	chmod +x install_lmdz.sh
	272	local make_j=8
	273	# We launch using $MPICMD, except if it's using mpirun (no srun equivalent for bash script) => if supported, the compilation runs in a cluster job
	274	jobcmd="\"$RUNBASHCMD $make_j\""
	275	if [[ ${hostname:0:5} = "jean-" ]]; then jobcmd="\"$RUNBASHCMD $make_j --partition=compil\""; fi # On JeanZay: compile on the <compil> partition
	276	if [[ $(echo "$RUNBASHCMD" \| cut -c -4) = "bash" ]]; then
	277	jobcmd="bash"
	278	fi
[5462]	279	echo "./install_lmdz.sh -noclean $optim -v $version $svnopt -d $resol -rad $rad -bench 0 $parallel $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.$$.sh
[5415]	280	chmod +x install_lmdz_options.$$.sh
	281	echo "Running install_lmdz_options.$$.sh"
	282	set -o pipefail
	283	gcm=$MODEL/$(./install_lmdz_options.$$.sh \| tee /dev/tty \| tail -n 1 \| sed -n "s:.* executable is \(.\.e\).:\1:p")
	284	set +o pipefail
	285	mv install_lmdz.sh install_lmdz.$$.sh
[5464]	286	cd "$local_d"
[5415]	287	}
[4615]	288
[5438]	289	#---------------------------------------------------------------------------
	290	function setup_def() { # modify various .def in ./DEF (+ xios xml )
	291	#---------------------------------------------------------------------------
[5464]	292	cd "$local_d"
[4615]	293
[5415]	294	# Utilisation des .def_iso pour LMDZ-ISOtopes
	295	if [[ $phylmd = "lmdiso" ]]; then
	296	for file_iso in $(ls DEF \| grep _iso); do
	297	cp DEF/"$file_iso" DEF/"${file_iso%%_iso}"
	298	done
	299	fi
[4615]	300
[5415]	301	######################################################################
	302	# Choix de la grille verticale
	303	######################################################################
	304	if [ ! -f "DEF/L$lm.def" ]; then
	305	echo "STOP: Résolution verticale non prévue - créer un fichier DEF/L$lm.def"; exit 1
	306	else
	307	sed -i'' -e "s/INCLUDEDEF=L.*.def/INCLUDEDEF=L$lm.def/" DEF/run.def
	308	fi
[4615]	309
[5415]	310	######################################################################
	311	# Changements dans les fichiers DEF/*def
[5464]	312	# (ils vont se repercuter dans les repertoires de simulation $local_d/$SIM et de run $SIMRUNDIR)
[5415]	313	######################################################################
[4615]	314
[5415]	315	# Choix du fichier tracer.def coherent avec l'option "aerosols"
	316	# NOTE : Le nouveau tracer.def_nospla par defaut n'inclut pas Rn-Pb;
[5439]	317	# si on les veut, il faut utiliser ci-dessous; a la place, tracer_RN_PB.def
[5415]	318	#---------------------------------------------------------------------
	319	# NB : Les traceurs absents de start* files sont initialises=0 dans le code
	320	if [[ $aerosols = "spla" ]]; then
	321	# nouveau tracer.def (remplace "traceur.def")
	322	cp DEF/tracer.def_spla DEF/tracer.def
	323	elif [[ $phylmd = "lmdiso" ]]; then
	324	# déjà copié si 'y'
	325	cp DEF/tracer.def_nospla DEF/tracer.def
	326	fi
[4615]	327
[5415]	328	# TEMPORAIREMENT pour spla on force l'utilisation de gcm.def_zNAfrica_BiJe (avec resolution 128x88x79)
	329	#----------------------------------------------------------------------
[5438]	330	if [[ $aerosols = "spla" ]]; then
	331	cp DEF/gcm.def_zNAfrica_BiJe DEF/gcm.def; fi
[4615]	332
[5415]	333	# Inscription du choix ok_guide dans DEF/guide.def
	334	#---------------------------------------------------------------------
	335	sed -i'' -e 's/ok_guide=.*.$/ok_guide='$ok_guide'/' DEF/guide.def
[4615]	336
[5415]	337	# Inscription du type de calendrier (qui est fonction de $climato) dans DEF/run.def
	338	#---------------------------------------------------------------------
	339	# NB Contrairement a ce qui est ecrit dans les fichiers run.def standard,
	340	# dans ce tutorial le choix earth_365d n'est pas disponible, et earth_366d s'appelle gregorian
	341	if [[ $climato = 0 ]]; then calend="gregorian"; else calend="earth_360d"; fi
	342	sed -i'' -e 's/calend=.*.$/calend='$calend'/' DEF/run.def
[4615]	343
[5415]	344	# Changements dans config.def (pre-choisi, et regle pour output si utilisation avec IOIPSL)
	345	# cf options veget, aerosols, cosp, xios
	346	#---------------------------------------------------------------------
	347	if [[ $veget = "none" ]]; then VEGET="n"; else VEGET="y"; fi
	348	sed -i'' -e 's/VEGET=.*.$/VEGET='$VEGET'/' DEF/config.def
[4615]	349
[5438]	350	ok_cdnc=y ; ok_ade=y ; ok_aie=y ; ok_alw=y
	351	case $aerosols in
	352	clim) flag_aerosol=6 ;;
	353	spla) flag_aerosol=1 ;;
	354	n) flag_aerosol=0 ; ok_cdnc=n ; ok_ade=n ; ok_aie=n ; ok_alw=n ;;
	355	*) echo Option aerosols=$aerosols not available ; exit 1
	356	esac
	357	sed -i'' -e 's/^ok_cdnc=.*.$/ok_cdnc='$ok_cdnc'/' \
	358	-e 's/^ok_ade=.*.$/ok_ade='$ok_ade'/' \
	359	-e 's/^ok_aie=.*.$/ok_aie='$ok_aie'/' \
	360	-e 's/^ok_alw=.*.$/ok_alw='$ok_alw'/' \
	361	-e 's/^flag_aerosol=.*.$/flag_aerosol='$flag_aerosol'/' DEF/config.def
	362	pwd
[4615]	363
[5415]	364	# COSP : ok_cosp desactive COSP si on a compile avec; il ne l'active pas si on a compile sans
	365	sed -i'' -e 's/ok_cosp.*.$/ok_cosp='$cosp'/' DEF/config.def
[5464]	366	if [[ $cosp = "y" ]]; then \cp -f "$MODEL"/DefLists/cosp*.txt "$local_d"/DEF/; fi
[4615]	367
[5415]	368	# Sorties LMDZ en fonction de l'option "xios"
	369	sed -i'' -e 's/ok_all_xml=.*.$/ok_all_xml='$xios'/' DEF/config.def
[4615]	370
[5415]	371	# Ajuster physiq.def en fonction de radiative code (default: values for rad=rrtm)
	372	# Pour isotopes=y , mettre iflag_ice_thermo=0 au lieu de 1
	373	#---------------------------------------------------------------------
	374	sed -i'' -e "s/iflag_rrtm=..$/iflag_rrtm=$iflag_rrtm/" -e "s/NSW=..$/NSW=$NSW/" DEF/physiq.def
	375	sed -i"" -e "s:directory_name.*$:directory_name=\"$MODEL/libf/phylmd/ecrad/data\",:" DEF/namelist_ecrad
[4615]	376
[5415]	377	if [[ $phylmd = "lmdiso" ]]; then iflag_ice_thermo=0; else iflag_ice_thermo=1; fi
	378	sed -i -e 's/iflag_ice_thermo=.*.$/iflag_ice_thermo='$iflag_ice_thermo'/' DEF/physiq.def
[4615]	379
[5415]	380	# Choix de orchidee.def en fonction de orchidee_rev; modification pour xios
	381	# NOTE separate orchidee_pft.def file for ORCHIDEE trunk post-CMIP6
	382	#---------------------------------------------------------------------
	383	orchidee_def=orchidee.def_6.1
	384	orchidee_pft_def=""
	385	if [[ $veget = "7983" ]]; then
	386	orchidee_def=orchidee.def_6.2work
	387	elif [[ $veget = "7994" ]]; then
	388	orchidee_def=orchidee.def_6.4work
	389	orchidee_pft_def=orchidee_pft.def_6.4work
	390	if ! grep "INCLUDEDEF=orchidee_pft.def" DEF/run.def; then
	391	sed -i'' -e 's/INCLUDEDEF=orchidee.def/INCLUDEDEF=orchidee.def\nINCLUDEDEF=orchidee_pft.def/' DEF/run.def; fi
	392	fi
	393	cp -f DEF/$orchidee_def DEF/orchidee.def
	394	if [[ $orchidee_pft_def != "" ]]; then cp -f DEF/$orchidee_pft_def DEF/orchidee_pft.def; fi
[4615]	395
[5415]	396	# Only for veget=CMIP6 it is still possible to use IOIPSL; newer versions of orchidee.def have XIOS_ORCHIDEE_OK = y
	397	sed -i'' -e 's/XIOS_ORCHIDEE_OK =.*.$/XIOS_ORCHIDEE_OK = '$xios'/' DEF/orchidee.def
[4615]	398
[5415]	399	######################################################################
	400	# Si on tourne avec XIOS, mise a jour des fichiers context et field* dans XMLfilesLMDZ
[5464]	401	# (ils vont se repercuter dans les repertoires de simulation $local_d/$SIM et de run $SIMRUNDIR)
[5415]	402	######################################################################
	403	if [[ $xios = y ]]; then
[5464]	404	cp -f "$MODEL"/DefLists/context_lmdz.xml "$local_d"/DEF/XMLfilesLMDZ/.
	405	cp -f "$MODEL"/DefLists/field_def_lmdz.xml "$local_d"/DEF/XMLfilesLMDZ/.
	406	if [[ $cosp = y ]]; then cp -f "$MODEL"/DefLists/field_def_cosp1.xml "$local_d"/DEF/XMLfilesLMDZ/.; fi
[5415]	407	fi
	408	}
[4615]	409
[5438]	410	#---------------------------------------------------------------------------
[5415]	411	function setup_ce0l() { # Verification de l'existance de l'état initial, compilation eventuelle pour sa creation
[5438]	412	#---------------------------------------------------------------------------
[5415]	413	if [[ ! -d $INIT ]]; then
	414	if [[ $init = 0 ]]; then
	415	echo "STOP: Récuperer les repertoires $INIT ou lancer avec option -init"; exit 1
	416	else
	417	# Compile ce0l
	418	cd "$MODEL"
	419	sed -e 's/gcm$/ce0l/' compile.sh > compile_ce0l.sh; chmod +x compile_ce0l.sh
	420	echo "Compiling ce0l"
	421	if ! ./compile_ce0l.sh &> ce0l.log; then echo "STOP: ce0l compilation failed, see $MODEL/ce0l.log"; exit 1; fi
	422	echo "Compiled ce0l"
	423	ce0l=${gcm/gcm/ce0l}
[4615]	424
[5464]	425	cd "$local_d"
[4615]	426	fi
[5415]	427	elif [[ $init = 1 ]]; then
	428	echo "STOP: Vous essayez d initialiser le modele mais $INIT existe deja"; exit 1
	429	fi
	430	}
[4615]	431
[5438]	432	#---------------------------------------------------------------------------
[5415]	433	function setup_simu() {
[5438]	434	#---------------------------------------------------------------------------
[5464]	435	#SIMRUNTOPDIR="$SIMRUNBASEDIR/$(basename "$local_d")"
[5420]	436	SIMRUNTOPDIR="$SIMRUNBASEDIR"
[5415]	437	SIMRUNDIR=$SIMRUNTOPDIR
	438	mkdir -p "$SIMRUNDIR"
	439	cd "$SIMRUNDIR"
	440	echo "La simulation s'exécutera sur $SIMRUNDIR"
[4615]	441
[5415]	442	#####################################################################
	443	# Creation du repertoire $SIM s'il n'existe pas deja
	444	#####################################################################
[5464]	445	if [[ ! -d $local_d/$SIM ]]; then
	446	mkdir "$local_d/$SIM"
	447	cd "$local_d"
[4615]	448
[5415]	449	# Edit reb.sh
[5464]	450	cp reb.sh "$local_d/$SIM/reb.sh"; chmod +x "$local_d/$SIM/reb.sh"
	451	sed -i'' -e "s:^rebuild=.*.$:rebuild=$LMDZD/$LMDZname/modipsl/bin/rebuild:" "$local_d/$SIM/reb.sh"
	452	enable_platform "$local_d/$SIM/reb.sh"
[4615]	453
[5415]	454	# Copy .def
[5464]	455	cp lmdz_env.sh "$local_d/$SIM/"
	456	mkdir "$local_d/$SIM/DEF"; cp DEF/def DEF/namelis "$local_d/$SIM/DEF/"
[5415]	457	#Pour XIOS, respectivement COSP, copier aussi les fichiers xml / txt
[5464]	458	if [[ $cosp = "y" ]]; then cp DEF/cosp*txt "$local_d/$SIM/DEF/"; fi
[5415]	459	if [[ $xios = "y" ]]; then
[5464]	460	cp DEF/XMLfilesLMDZ/*xml "$local_d/$SIM/DEF/"
	461	if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml "$local_d/$SIM/DEF/"; fi
[5415]	462	fi
[5464]	463	chmod u+w "$local_d/$SIM"/DEF/*
[4615]	464
[5415]	465	# Gestion du calendrier
	466	#######################
	467	cd "$SIM"
	468	sed -i'' -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def
	469	if [[ $freq = "yr" ]]; then date=$yearini; else date=$mthini; fi
	470	echo "$date a faire" >\| etat
[4615]	471
[5415]	472	# Recuperation des fichiers : executable initiaux et forcages
	473	#############################################################
	474	echo "date: $date"
	475	for f in start startphy; do
	476	inf=../$INIT/$f.$date.nc
	477	if [[ -f $inf \|\| $init = 1 ]]; then ln -s "$inf" ./; else echo "STOP: $inf missing"; exit ; fi;
	478	done
	479	for f in sechiba stomate; do
	480	if [[ -f ../$INIT/start_$f.$date.nc ]]; then ln -sf "../$INIT/start_$f.$date.nc" .; fi
	481	done
	482	cp "$gcm" gcm.e
	483	fi
[5464]	484	cd "$local_d"/..
[4615]	485
[5415]	486	#####################################################################
	487	echo "Modification du script de lancement"
	488	#####################################################################
	489	local cput
	490	if [[ $freq = "yr" ]]; then cput="04:00:00"; else cput="01:00:00"; fi
	491	local isotopes="n"
	492	if [[ $phylmd = "lmdiso" ]]; then isotopes="y"; fi
	493	sed -e "s/NOM_SIMU/$SIM/" \
	494	-e "s/time=.*.$/time=$cput/" \
	495	-e "s/ntasks=.*.$/ntasks=$mpi/" \
	496	-e "s/ntasks-per-node=.*.$/ntasks-per-node=$mpi_per_node/" \
	497	-e "s/cpus-per-task=.*.$/cpus-per-task=$omp/" \
	498	-e "s/nthreads=.*./nthreads=$omp/" \
[5464]	499	-e "s/MAINDIR=.*.$/MAINDIR=$(basename "$local_d")/" \
	500	-e "s:STORED=..:STORED=$(dirname "$local_d"):" \
[5415]	501	-e "s:SCRATCHD=..:SCRATCHD=$SIMRUNBASEDIR:" \
	502	-e "s/stopsim=.*.$/stopsim=$stopsim/" \
	503	-e "s/^veget=.*.$/veget=$veget/" \
	504	-e "s/^aerosols=.*.$/aerosols=$aerosols/" \
	505	-e "s/^isotopes=.*.$/isotopes=$isotopes/" \
	506	-e "s/^climato=.*.$/climato=$climato/" \
	507	-e "s/^ok_guide=.*.$/ok_guide=$ok_guide/" \
[5464]	508	"$local_d/script_SIMU" >\| "$SIMRUNDIR/tmp_$SIM"
[4615]	509
[5415]	510	enable_platform "$SIMRUNDIR/tmp_$SIM"
[4615]	511
[5415]	512	if [[ $testmode = "y" ]]; then
	513	sed -i'' -e "s/time=.*.$/time=00:10:00/" -e "s/#nday=1/nday=1/" -e "s/#@TESTQ//" "$SIMRUNTOPDIR/tmp_$SIM"
	514	fi
	515	}
[4615]	516
[5429]	517	#----------------------------------------------------------------------
[5439]	518	function list_yrmth() {
	519	#----------------------------------------------------------------------
	520	local liste=""
	521	local mthini=$1
	522	local mthend=$2
	523	local mo_=$mthini
	524	while [[ $mo_ != $mthend ]] ; do
	525	liste="$liste $mo_"
	526	yr__=$( echo $mo_ \| cut -c 1-4 )
	527	mo__=$( echo $mo_ \| cut -c 5-6 )
	528	echo YM $yr__ $mo__
	529	if [ $(( $mo__ +1 )) == 12 ] ; then
	530	yr__=$(( $yr__ + 1 )) ; mo_=$yr__$mo__
	531	else
	532	mo_=$(( $mo_ + 1 ))
	533	fi
	534	done
	535	echo $liste
	536
	537	}
	538
	539	#----------------------------------------------------------------------
	540	increment_month() {
	541	#----------------------------------------------------------------------
	542	local year=$( echo $1 \| cut -c 1-4 )
	543	local month=$(( $1 - ${year}00 ))
	544	if [ $(( $month - 12 )) -eq 0 ]; then
	545	year=$((year + 1))
	546	month=1
	547	else
	548	month=$((month + 1))
	549	fi
	550	if [[ $month -le 9 ]] ; then month=0$month ; fi
	551	echo $year$month
	552	}
	553
	554	#----------------------------------------------------------------------
[5415]	555	function fetch_simu_init_files() {
[5429]	556	#----------------------------------------------------------------------
[5415]	557	#####################################################################
[5426]	558	echo "Recuperation eventuelle de certains fichiers sur http:lmdz.lmd.jussieu.fr/pub"
[5415]	559	#####################################################################
[4615]	560
[5426]	561	# ORCHIDEE input files
[5429]	562	get_input_files wget_pub Orchidee
[5426]	563
	564	# Files for aerosols and chemistry
[5438]	565	if [[ $aerosols = "clim" ]]; then
	566	get_input_files wget_pub AerChem ; fi
[5426]	567
[5429]	568	# Files for SPLA
[5438]	569	if [[ $aerosols = "spla" ]]; then
	570	get_input_files wget_pub SPLA_WA/emissions
[5439]	571	mo_=$mthini
	572	while [[ $mo_ != $mthend ]] ; do
	573	# Code horrible duplique a cause de 08 (FH)
	574	local yr__=$( echo $mo_ \| cut -c 1-4 )
	575	local mo__=$(( $mo_ - ${yr__}00 ))
	576	if [[ $mo__ -le 9 ]] ; then mo__=0$mo__ ; fi
[5438]	577	for var in u10m v10m u v ; do
	578	echo wget_pub 3DInputData/SPLA_WA/ERA5/$yr__/$mo__ $var.nc
	579	wget_pub 3DInputData/SPLA_WA/ERA5/$yr__/$mo__ $var.nc
	580	done
[5439]	581	mo_=$( increment_month $mo_ )
[5438]	582	done
[5464]	583	cd $local_d ; ln -sf $LMDZ_INIT/3DInputData/SPLA_WA/ERA5 GUIDE
[5438]	584	fi
[5415]	585	}
[4615]	586
[5429]	587	#----------------------------------------------------------------------
[5415]	588	function run_sim_or_init() {
[5429]	589	#----------------------------------------------------------------------
[5464]	590	cd "$local_d"
[4615]	591
[5415]	592	if [[ $init = 1 ]]; then
	593	#####################################################################
	594	echo "Creation de l etat initial"
	595	#####################################################################
[4615]	596
[5415]	597	# Creation du repertoire INIT et mise en place de liens logiques vers les starts
	598	# en anticipation de leur création :
[5464]	599	mkdir "$local_d/$INIT"; cd "$local_d/$INIT"
[5415]	600	for an in $mthini $yearini; do for f in start startphy; do ln -s "$f.nc" "$f.$an.nc"; done; done
[4615]	601
[5415]	602	# Creation du repertoire INIT temporaire et rapatriement des fichiers necessaires
	603	if [[ -d $SIMRUNDIR/$INIT ]]; then mv "$SIMRUNDIR/$INIT" "$SIMRUNDIR/$INIT$$"; fi
[5464]	604	mkdir "$SIMRUNDIR/$INIT"; cp -r "$local_d/DEF" "$SIMRUNDIR/$INIT/"
	605	cd "$SIMRUNDIR/$INIT"; cp DEF/*.def .; cp "$local_d/lmdz_env.sh" .
[5415]	606	if [[ $xios = "y" ]]; then
	607	cp DEF/XMLfilesLMDZ/*xml .
	608	if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml .; fi
	609	fi
	610	sed -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def >\| run.def
[4615]	611
[5415]	612	#-------------------------------------------------------------------
	613	# Fichiers Limit
	614	#-------------------------------------------------------------------
	615	local yrs suf
	616	if [[ $climato = 0 ]]; then
	617	# calend est choisi plus haut dans "Changements dans les fichiers DEF/*def" et ecrit dans $MAINDIR/DEF/run.def
	618	yrini=$(echo "$mthini" \| cut -c-4)
	619	yrend=$(echo "$mthend" \| cut -c-4)
	620	yrs=""; yr=$yrini
	621	while [[ $yr -le $yrend ]]; do yrs="$yrs $yr"; (( yr = yr + 1 )); done
	622	suf="360x180_"
	623	else
	624	yrs=2000
	625	suf="1x1_clim"
	626	fi
[4615]	627
[5415]	628	liste_get="Albedo.nc Relief.nc Rugos.nc landiceref.nc"
	629	for yr in $yrs; do
	630	if [[ $climato = 0 ]]; then sufyr=$suf$yr; else sufyr=$suf; fi
	631	liste_get="$liste_get amipbc_sic_$sufyr.nc amipbc_sst_$sufyr.nc"
	632	done
	633	echo LISTEGET "$liste_get"
	634	for file in $liste_get; do
[5426]	635	wget_pub 3DInputData/Limit $file
	636	ln_from_pub 3DInputData/Limit $file
[5415]	637	done
	638	#-------------------------------------------------------------------
[5426]	639	# Initial state ECDYN
[5415]	640	#-------------------------------------------------------------------
[5426]	641	wget_pub 3DInputData/Init ECDYN.nc
	642	ln_from_pub 3DInputData/Init ECDYN.nc
[5415]	643	ln -sf ECDYN.nc ECPHY.nc
[4615]	644
[5415]	645	# Creation du script d'initialisation
[5465]	646	if [ "$MPICMD" = "" ] ; then mpicmd='' ; else mpicmd='OMP_NUM_THREADS=1 '"$MPICMD"' 1' ; fi
[5415]	647	cat << ...eod >\| tmp
[4615]	648	#!/bin/bash
[5415]	649	#@JZ#JeanZay
	650	#@JZ#SBATCH --job-name=Init # nom du job
	651	#@JZ#SBATCH --ntasks=1 # Nombre de processus MPI
	652	#@JZ#SBATCH --cpus-per-task=1 # nombre de threads OpenMP
	653	#@JZ# /!\ Attention, la ligne suivante est trompeuse mais dans le vocabulaire
	654	#@JZ# de Slurm "multithread" fait bien référence à l'hyperthreading.
	655	#@JZ#SBATCH --hint=nomultithread # 1 thread par coeur physique (pas d'hyperthreading)
	656	#@JZ#SBATCH --time=00:10:00 # Temps d'exécution maximum demandé (HH:MM:SS)
	657	#@JZ#SBATCH --output=Init%j.out # Nom du fichier de sortie
	658	#@JZ#SBATCH --error=Init%j.out # Nom du fichier d'erreur (ici commun avec la sortie)
	659	#@JZ# To submit to dev queue; "time" (above) must be max 2h
	660	#@JZ#TESTQ#SBATCH --qos=qos_cpu-dev
	661	#@SP#Spirit
	662	#@SP#SBATCH --job-name=Init
	663	#@SP#SBATCH --ntasks=1
	664	#@SP#SBATCH --cpus-per-task=1
	665	#@SP#SBATCH --hint=nomultithread
	666	#@SP#SBATCH --time=00:10:00
	667	#@SP#SBATCH --output=Init%j.out
	668	#@SP#SBATCH --error=Init%j.out
	669	#@ADS#Adastra
	670	#@ADS#SBATCH --job-name=Init
	671	#@ADS#SBATCH --ntasks=1
	672	#@ADS#SBATCH --cpus-per-task=1
	673	#@ADS#SBATCH --nodes=1
	674	#@ADS#SBATCH --hint=nomultithread
	675	#@ADS#SBATCH --time=00:10:00
	676	#@ADS#SBATCH --output=Init%j.out
	677	#@ADS#SBATCH --error=Init%j.out
[4615]	678
[5415]	679	set -eu
[4615]	680
	681	# ANCIEN MULTI STEP case \${LOADL_STEP_NAME} in
	682
	683	# ANCIEN MULTI STEP init )
	684
[5415]	685	if [ ! -f lmdz_env.sh ]; then echo "manque fichier lmdz_env.sh"; ls; exit 1; fi
	686	. lmdz_env.sh
	687	ulimit -s unlimited
	688	cd $SIMRUNDIR/$INIT
	689	echo "Executable : $ce0l"
	690	for yr in $yrs; do
	691	if [ $climato = 0 ]; then sufyr=$suf\$yr; else sufyr=$suf; fi
	692	ln -sf amipbc_sic_\$sufyr.nc amipbc_sic_1x1.nc
	693	ln -sf amipbc_sst_\$sufyr.nc amipbc_sst_1x1.nc
	694	sed -e 's/anneeref=.*.$/anneeref='\$yr'/' DEF/run.def >\| run.def
	695	echo Starting initialisation
[5426]	696	# Runing ce0l.e
[5465]	697	$mpicmd $ce0l # ce0l requires MPI=OMP=1
[5415]	698	if [ $climato = 0 ]; then mv limit.nc limit.\$yr.nc; fi
	699	done
	700	# ANCIEN MULTI STEP ;;
[4615]	701
	702	# ANCIEN MULTI STEP interp )
[5415]	703	if [[ $aerosols = clim ]]; then
[5464]	704	cp $local_d/interp_aerosols.sh .; chmod +x interp_aerosols.sh
[5415]	705	# Les aerosols de l'annee 2000 ont été remplacés par "9999" qui pointe vers un fichier moyen sur 1995-2014
	706	#for year in 2000 1850; do ./interp_aerosols.sh \$year; done
	707	#mv aerosols.2000.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc
	708	for year in 9999 1850; do ./interp_aerosols.sh \$year; done
	709	mv aerosols.9999.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc
	710	fi
[4615]	711
[5464]	712	for f in sta* gri*nc; do cp \$f $local_d/$INIT/\$f; done
	713	if [[ $climato = 1 ]]; then cp limit.nc $local_d/$INIT/limit.nc; fi
	714	mkdir -p $local_d/$LIMIT
	715	for f in limit*.nc ; do cp \$f $local_d/$LIMIT/\$f; done
	716	if [ $aerosols = clim ]; then for f in aerosols[.0-9]*nc; do cp \$f $local_d/$LIMIT/\$f; done; fi
[5415]	717	#
	718	cd $SIMRUNDIR
[4615]	719	...eod
[5415]	720	if [[ $ok_guide != "y" ]]; then # Running first simulation automatically except for nudging
	721	cat << ...eod >> tmp
	722	echo "Submitting job tmp_$SIM"
[5422]	723	#echo "\$SUBMITCMD tmp_$SIM"
	724	#\$SUBMITCMD tmp_$SIM
[5424]	725	echo submitcmd tmp_$SIM
[5422]	726	submitcmd tmp_$SIM
[4615]	727	...eod
[5415]	728	fi
	729	cat << ...eod >> tmp
	730	# ANCIEN MULTI STEP esac
[4615]	731	...eod
[5415]	732	enable_platform tmp
[5438]	733	echo "#################################################################"
[5422]	734	#echo "Submitting initialisation job <$SUBMITCMD tmp> from $(pwd)"
	735	echo "Submitting initialisation job <submitcmd tmp> from $(pwd)"
[5415]	736	chmod +x tmp
[5422]	737	#$SUBMITCMD tmp
	738	submitcmd tmp
[5438]	739	echo "#################################################################"
[4615]	740
[5415]	741	else #case [ $init != 1 ]
	742	cd "$SIMRUNDIR"
[5438]	743	echo "################################################################"
[5415]	744	echo "Submitting job tmp_$SIM"
[5422]	745	#echo "$SUBMITCMD tmp_$SIM"
	746	#$SUBMITCMD "tmp_$SIM"
	747	echo "submitcmd tmp_$SIM"
	748	submitcmd "tmp_$SIM"
[5438]	749	echo '################################################################'
[5415]	750	fi
	751	}
[4615]	752
[5438]	753	#---------------------------------------------------------------------------
[5415]	754	function message_post_submit() {
[5438]	755	#---------------------------------------------------------------------------
[5415]	756	if [[ $ok_guide = "y" && $init = 1 ]]; then
[5464]	757	cd "$local_d"
[5415]	758	enable_platform era2gcm_tuto.sh
	759	echo "Once initialisation is finished, you have to create nudging files"
	760	echo "Edit era2gcm_tuto.sh and set the desired parameters in section <User choices>"
	761	echo "Make sure you have acces to the chosen ERA files, and the required modules are loaded, then run : ./era2gcm_tuto.sh"
	762	if [[ $aerosols = "spla" ]]; then
	763	echo "Your aerosol choice is <spla>, so you need ERA 10m-winds interpolated on LMDZ grid. Use script era2gcm_uv10m.sh"
	764	fi
	765	else
	766	echo "Si tout se passe bien, vous avez initialisé et lancé automatiquement la simulation."
	767	echo "Le job qui a été lancé se trouve sur $SIMRUNTOPDIR/tmp_$SIM"
	768	fi
	769	}
[4615]	770
[5438]	771	#---------------------------------------------------------------------------
[5415]	772	function setup_and_load_lmdz_env() {
[5438]	773	#---------------------------------------------------------------------------
[5415]	774	if [[ ! -f .lmdz_setup_root_dir ]]; then echo "STOP: setup.sh is not located in the root dir ??!!"; exit 1; fi
	775	# sed root_dir in lmdz_env.sh
[5464]	776	sed -i'' "s<root_dir=.*<root_dir=$local_d<" lmdz_env.sh
[4615]	777
[5415]	778	# Set up the appropriate environment
	779	source lmdz_env.sh
	780	}
[4615]	781
[5464]	782	local_d=$(pwd)
[4615]	783
[5415]	784	setup_and_load_lmdz_env
	785	load_install_lib
	786	define_expert_options
	787	set_default_params
	788	read_cmdline_args "$@"
	789	ensure_correct_option_combinations
	790	install_model
	791	setup_def
	792	setup_ce0l
	793	setup_simu
	794	fetch_simu_init_files
	795	run_sim_or_init
[5420]	796	message_post_submit

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