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source: BOL/LMDZ_Setup/setup.sh @ 5632

Last change on this file since 5632 was 5632, checked in by fhourdin, 7 months ago
Bug fix LMDZ_Setup pour spla et iso
File size: 32.7 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
[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
[5539]	58
	59	save_pub=0
	60
[5415]	61	}
[4615]	62
	63
[5438]	64	#---------------------------------------------------------------------------
	65	function enable_platform() { # Sed platform-specific headers
	66	#---------------------------------------------------------------------------
[5415]	67	local file="$1"
	68	local platform
[4615]	69
[5415]	70	case ${hostname:0:5} in
	71	jean-) platform="JZ";;
	72	spiri) platform="SP";;
	73	adast) platform="ADS";;
	74	*) echo "Warning: $hostname is not a known job platform (ignore if running locally)"; return 0;;
	75	esac
[4615]	76
[5415]	77	sed -i'' -e "s/^#@$platform//" "$file"
	78	}
[4615]	79
[5438]	80	#---------------------------------------------------------------------------
	81	function load_install_lib() { #Fetch and source install_lmdz.sh to get myget
	82	#---------------------------------------------------------------------------
[5415]	83	if [[ ! -f "install_lmdz.sh" ]]; then
	84	wget --no-cache "http://svn.lmd.jussieu.fr/LMDZ/BOL/script_install/install_lmdz.sh"
	85	fi
	86	# shellcheck disable=SC1090
	87	source <(sed 's/function \(.*\) {/function installlmdz_\1 {/g' install_lmdz.sh) # source with a namespace for functions
	88	function myget { installlmdz_myget "$@"; }
[4615]	89	}
	90
[5438]	91	#---------------------------------------------------------------------------
	92	function set_default_params() { # Default value of script parameters
	93	#---------------------------------------------------------------------------
	94
[5464]	95	SIM=$(basename "$local_d")CTL # name
[5415]	96	phylmd="lmd" #option -p $phylmd for makelmdz
[4615]	97
[5415]	98	cosp="n" # COSP
	99	xios="n" #XIOS
[4615]	100
[5415]	101	# Nudging :
	102	ok_guide="n"
	103	# With nudging, use real calendar (climato=0) and monthly integrations
	104	climato=1
	105	freq="mo" # frequence mensuelle mo ou annuelle yr
[4615]	106
[5415]	107	# NB : the run stops in the BEGINNING of mthend (test "next=stopsim")
	108	mthini=200001
	109	mthend=200501
	110	resol="144x142x79"
[4615]	111
[5415]	112	version="20230412.trunk"
	113	svn=""
[4615]	114
[5415]	115	init=1
[4615]	116
[5415]	117	LIMIT="LIMIT"
[4615]	118
[5415]	119	}
[4615]	120
[5438]	121	#---------------------------------------------------------------------------
[5415]	122	function read_cmdline_args() {
[5438]	123	#---------------------------------------------------------------------------
[5415]	124	while (($# > 0)); do
	125	case $1 in
	126	"-h") cat <<........fin
[5428]	127	setup.sh can be launched/driven by main.sh
[5415]	128	setup.sh [-v version] [-r svn_release] [-init INIT] [-d 96x95x79] [-f mo] [-nudging]
	129	-v "version" like 20150828.trunk; see https://lmdz.lmd.jussieu.fr/Distrib/LISMOI.trunk (default <$version>)
[5428]	130	-r "svn_release" either the svn release number or "last" (default <$svn>)
	131	-d IMxJMxLM to run in resolution IM x JM x LM (default <$resol>)
	132	-install pour installer et compiler le modele
	133	-f mo/yr pour tourner en mensuel ou annuel (default <$freq>)
	134	-rad RAD Radiation
	135	-netcdf 0/1/DIR Netcdf installation
	136	-aerosols n/clim/spla Aerosols : none / climatological / interactive with SPLA
	137	-veget CMIP6 CMIP6 version of rchidee
	138	7983 orch2.2
	139	7994 trunk
	140	"INIT" 1: creates INIT and LIMIT
	141	0: reads from INIT and LIMIT
	142	SIMU: reads from preexisting simulation SIMU and LIMIT (default <$init>)
	143	-nudging to run with nudging. Nudging files must be created independently
	144	-p the physics to use (default <$phylmd>)
[5539]	145	-save_pub To files downlaoded with wget (default <$SIM>)
[5428]	146	-name install folder name (default <$SIM>)
[5415]	147	Other options available (see "options" section in the script)
[4615]	148	........fin
[5415]	149	exit;;
[5539]	150	"-v") version="$2"; shift 2;;
	151	"-r") svn=$2; shift 2;;
	152	"-d") resol=$2; shift 2;;
	153	"-f") freq=$2; shift 2;;
	154	"-p") phylmd=$2; shift 2;;
	155	"-name") SIM=$2; shift 2;;
	156	"-save_pub") save_pub=$2 ; shift 2 ;;
	157	"-rad") rad=$2; shift 2;;
	158	"-netcdf") netcdf=$2; shift 2;;
	159	"-aerosols") aerosols=$2; shift 2;;
	160	"-veget") veget=$2; shift 2;;
[5415]	161	"-cosp") cosp=y; shift;;
	162	"-xios") xios=y; shift;;
[5539]	163	"-init") init=$2; shift 2;;
[5415]	164	"-nudging") ok_guide=y; shift;;
[5539]	165	"-climato") climato=$2; shift 2;;
	166	"-mthini") mthini=$2; shift 2;;
	167	"-mthend") mthend=$2; shift 2;;
[5415]	168	*) echo "unexpected $1"; $0 -h; exit
	169	esac
	170	done
[4615]	171
[5415]	172	# Initialisation
	173	if [[ $init = 1 \|\| $init = 0 ]]; then
	174	INIT="INIT"
	175	else
	176	INIT=$init
	177	fi
[4615]	178
[5428]	179	case $rad in
	180	oldrad) iflag_rrtm=0; NSW=2;;
	181	rrtm) iflag_rrtm=1; NSW=6;;
	182	ecrad) iflag_rrtm=2; NSW=6;;
	183	esac
	184
[5432]	185	im=$(echo "$resol" \| cut -dx -f1)
	186	jm=$(echo "$resol" \| cut -dx -f2)
	187	lm=$(echo "$resol" \| cut -dx -f3)
	188
[5539]	189	case $save_pub in
	190	0) save_pub_opt=0 ;;
	191	1) save_pub_opt="-save_pub" ;;
	192	*) save_pub_opt="-save_pub -save_pub_dir $save_pub"
	193	mkdir -p $save_pub
	194	if [ $? != 0 ] ; then echo Cannot create directory $save_pub
	195	exit 1 ; fi
	196	esac
	197
[5415]	198	yearini=$(echo "$mthini" \| cut -c-4)
	199	if [[ $freq = yr ]]; then stopsim=$(echo "$mthend" \| cut -c-4); else stopsim=$mthend; fi
[4615]	200
[5415]	201	if [[ -d $SIM ]]; then
	202	echo "La simulation $SIM existe deja. Il est conseillé d'arrêter et de vérifier."
	203	echo "Si vous êtes sûr de vous, vous pouvez la prolonger. Voulez vous la prolonger ? (y/n)"
	204	read -r ans
	205	if [[ $ans != y ]]; then exit 1; fi
	206	fi
[4615]	207
[5415]	208	######################################################################
	209	# Choix du nombre de processeurs
	210	# NOTES :
[5438]	211	# omp=8 by default (for Jean-Zay must be a divisor of 40 procs/node)
	212	# omp=1 : required for SPLA (omp parallelism not ready)
	213	# omp=2 for veget=CMIP6+XIOS beacause of a bug in ORCHIDEE/src_xml/xios_orchidee.f90
[5415]	214	######################################################################
[5604]	215	(( mpi = jm / 2 ))
[5415]	216	omp=8
	217	if [[ $aerosols = "spla" ]]; then omp=1; fi
	218	if [[ $veget = "CMIP6" && $xios = "y" ]]; then omp=2; fi
	219	if [[ $mpi -gt $NB_MPI_MAX ]]; then mpi=$NB_MPI_MAX; fi
	220	if [[ $omp -gt $NB_OMP_MAX ]]; then omp=$NB_OMP_MAX; fi
[4615]	221
[5415]	222	# Compute how many mpi per node (required e.g. for Adastra)
	223	mpi_per_node=0
	224	if [[ $NB_CORE_PER_NODE_MAX -gt 0 ]]; then
	225	local N_omp_mt=1
	226	if [[ $omp -gt 1 ]]; then (( N_omp_mt = omp / N_HYPERTHREADING )); fi # take into account hyperthreading
	227	(( mpi_per_node = NB_CORE_PER_NODE_MAX / N_omp_mt ))
	228	if [[ mpi_per_node -gt mpi ]]; then mpi_per_node=$mpi; fi
	229	fi
[4615]	230
[5415]	231	echo "Total MPI=$mpi (PER NODE=$mpi_per_node), OMP=$omp"
	232	}
[4615]	233
[5438]	234	#---------------------------------------------------------------------------
[5415]	235	function ensure_correct_option_combinations() {
	236	# AVOID COMBINATIONS OF OPTIONS THAT DON'T WORK in user choices
[5438]	237	#---------------------------------------------------------------------------
[5415]	238	if [[ $ok_guide = y && $climato = 1 ]]; then
	239	echo "STOP: Running nudged simulations with climatological SSTs is not planned. Change <climato> to <0> or modify the setup (experts)"; exit 1
	240	fi
[4615]	241
[5415]	242	if [[ $climato = 0 && $freq = "yr" ]]; then
	243	echo "STOP: Running simulations with interannual SSTs is possible only month by month and a true calendar."
	244	echo "Change <climato> to <1> or <freq> to <mo> or modify setup.sh (experts)"; exit 1
	245	fi
[4615]	246
	247
[5415]	248	# (Temporary) Constraints for aerosols=spla :
	249	# --> resolution 128x88x79 and rad=rrtm
[5438]	250	if [[ $aerosols = "spla" && ( ${im}x${jm} != "128x88" \|\| $freq != mo ) ]]; then
	251	echo 'STOP: For now, <aerosols=spla> requires <resol=128x88x79>,'
	252	echo 'and uses the zoomed grid from gcm.def_zNAfrica_BiJe,'
	253	echo 'for which forcing & initial files are available'
[5415]	254	echo "Right now resol=<$resol>"
[5438]	255	echo 'Should be run in monthly mode'
[5415]	256	exit 1
	257	fi
[4615]	258
[5415]	259	if [[ $rad = "ecrad" && $phylmd != "lmd" ]]; then
	260	echo "<rad=ecrad> is only supported for <phy=phylmd> here" # (Amaury) I added this check because we fetch ecrad data from libf/phylmd/ecrad/data only.
	261	fi
	262	}
[4615]	263
[5438]	264	#---------------------------------------------------------------------------
[5415]	265	function install_model() {
[5438]	266	#---------------------------------------------------------------------------
[5415]	267	mkdir -p "$LMDZD"
[4615]	268
[5415]	269	local ins_xios ins_cosp ins_aero ins_inlandsis
	270	if [[ $xios = "y" ]]; then ins_xios="-xios"; else ins_xios=""; fi
	271	if [[ $cosp = "y" ]]; then ins_cosp="-cosp v1"; else ins_cosp=""; fi
	272	if [[ $aerosols = "spla" ]]; then ins_aero="-spla"; else ins_aero=""; fi
	273	if [[ $inlandsis = "y" ]]; then ins_inlandsis="-inlandsis"; else ins_inlandsis=""; fi
	274	if [[ -n $svn ]]; then svnopt="-r $svn"; else svnopt=""; fi
[4615]	275
[5465]	276	if [[ $PARALLEL == 0 ]] ; then parallel= ; parsuf=seq ; else parallel="-parallel mpi_omp" ; parsuf= ; fi
[5415]	277	version_name=LMDZ$(echo "$version" \| sed -e 's/-v//g' -e 's/-unstable//' -e 's/-r/r/' -e 's/ //g')
[5465]	278	LMDZname="${version_name}${svn}OR$veget${ins_xios}${parsuf}$( echo $optim \| sed -e 's/[\ -]//g' )"
[5415]	279	MODEL="$LMDZD/$LMDZname/modipsl/modeles/LMDZ"
[4615]	280
[5415]	281	if [[ -d $MODEL ]]; then echo "Found existing install at MODEL=$MODEL"; fi
	282	echo "Installing model"
	283	cd "$LMDZD"
[5464]	284	cp "$local_d/install_lmdz.sh" .
[5415]	285	chmod +x install_lmdz.sh
	286	local make_j=8
	287	# We launch using $MPICMD, except if it's using mpirun (no srun equivalent for bash script) => if supported, the compilation runs in a cluster job
	288	jobcmd="\"$RUNBASHCMD $make_j\""
	289	if [[ ${hostname:0:5} = "jean-" ]]; then jobcmd="\"$RUNBASHCMD $make_j --partition=compil\""; fi # On JeanZay: compile on the <compil> partition
	290	if [[ $(echo "$RUNBASHCMD" \| cut -c -4) = "bash" ]]; then
	291	jobcmd="bash"
	292	fi
[5539]	293	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.$$.sh
[5415]	294	chmod +x install_lmdz_options.$$.sh
	295	echo "Running install_lmdz_options.$$.sh"
	296	set -o pipefail
[5534]	297	./install_lmdz_options.$$.sh
	298	#gcm=$MODEL/$(./install_lmdz_options.$$.sh \| tee /dev/tty \| tail -n 1 \| sed -n "s:.* executable is \(.\.e\).:\1:p")
	299	gcm=$MODEL/bin/gcm.e
[5415]	300	set +o pipefail
	301	mv install_lmdz.sh install_lmdz.$$.sh
[5464]	302	cd "$local_d"
[5415]	303	}
[4615]	304
[5438]	305	#---------------------------------------------------------------------------
	306	function setup_def() { # modify various .def in ./DEF (+ xios xml )
	307	#---------------------------------------------------------------------------
[5464]	308	cd "$local_d"
[4615]	309
[5415]	310	# Utilisation des .def_iso pour LMDZ-ISOtopes
	311	if [[ $phylmd = "lmdiso" ]]; then
	312	for file_iso in $(ls DEF \| grep _iso); do
	313	cp DEF/"$file_iso" DEF/"${file_iso%%_iso}"
	314	done
	315	fi
[4615]	316
[5415]	317	######################################################################
	318	# Choix de la grille verticale
	319	######################################################################
[5587]	320	if [ ! -f "DEF/DYN/L$lm.def" ]; then
	321	echo "STOP: Résolution verticale non prévue - créer un fichier DEF/DYN/L$lm.def"; exit 1
[5415]	322	else
	323	sed -i'' -e "s/INCLUDEDEF=L.*.def/INCLUDEDEF=L$lm.def/" DEF/run.def
[5608]	324	cp DEF/DYN/L$lm.def DEF/
[5415]	325	fi
[4615]	326
[5415]	327	######################################################################
	328	# Changements dans les fichiers DEF/*def
[5464]	329	# (ils vont se repercuter dans les repertoires de simulation $local_d/$SIM et de run $SIMRUNDIR)
[5415]	330	######################################################################
[4615]	331
[5415]	332	# Choix du fichier tracer.def coherent avec l'option "aerosols"
	333	# NOTE : Le nouveau tracer.def_nospla par defaut n'inclut pas Rn-Pb;
[5439]	334	# si on les veut, il faut utiliser ci-dessous; a la place, tracer_RN_PB.def
[5415]	335	#---------------------------------------------------------------------
	336	# NB : Les traceurs absents de start* files sont initialises=0 dans le code
	337	if [[ $aerosols = "spla" ]]; then
	338	# nouveau tracer.def (remplace "traceur.def")
[5632]	339	cp DEF/CONFIG/traceur.def_spla DEF/traceur.def
	340	\rm -f DEF/tracer.def
[5415]	341	elif [[ $phylmd = "lmdiso" ]]; then
	342	# déjà copié si 'y'
[5632]	343	cp DEF/CONFIG/tracer.def_nospla DEF/tracer.def
[5415]	344	fi
[4615]	345
[5415]	346	# TEMPORAIREMENT pour spla on force l'utilisation de gcm.def_zNAfrica_BiJe (avec resolution 128x88x79)
	347	#----------------------------------------------------------------------
[5438]	348	if [[ $aerosols = "spla" ]]; then
[5632]	349	cp DEF/DYN/gcm.def_zNAfrica_BiJe DEF/gcm.def; fi
[4615]	350
[5415]	351	# Inscription du choix ok_guide dans DEF/guide.def
	352	#---------------------------------------------------------------------
	353	sed -i'' -e 's/ok_guide=.*.$/ok_guide='$ok_guide'/' DEF/guide.def
[4615]	354
[5415]	355	# Inscription du type de calendrier (qui est fonction de $climato) dans DEF/run.def
	356	#---------------------------------------------------------------------
	357	# NB Contrairement a ce qui est ecrit dans les fichiers run.def standard,
	358	# dans ce tutorial le choix earth_365d n'est pas disponible, et earth_366d s'appelle gregorian
	359	if [[ $climato = 0 ]]; then calend="gregorian"; else calend="earth_360d"; fi
	360	sed -i'' -e 's/calend=.*.$/calend='$calend'/' DEF/run.def
[4615]	361
[5415]	362	# Changements dans config.def (pre-choisi, et regle pour output si utilisation avec IOIPSL)
	363	# cf options veget, aerosols, cosp, xios
	364	#---------------------------------------------------------------------
	365	if [[ $veget = "none" ]]; then VEGET="n"; else VEGET="y"; fi
	366	sed -i'' -e 's/VEGET=.*.$/VEGET='$VEGET'/' DEF/config.def
[4615]	367
[5438]	368	ok_cdnc=y ; ok_ade=y ; ok_aie=y ; ok_alw=y
	369	case $aerosols in
	370	clim) flag_aerosol=6 ;;
	371	spla) flag_aerosol=1 ;;
	372	n) flag_aerosol=0 ; ok_cdnc=n ; ok_ade=n ; ok_aie=n ; ok_alw=n ;;
	373	*) echo Option aerosols=$aerosols not available ; exit 1
	374	esac
	375	sed -i'' -e 's/^ok_cdnc=.*.$/ok_cdnc='$ok_cdnc'/' \
	376	-e 's/^ok_ade=.*.$/ok_ade='$ok_ade'/' \
	377	-e 's/^ok_aie=.*.$/ok_aie='$ok_aie'/' \
	378	-e 's/^ok_alw=.*.$/ok_alw='$ok_alw'/' \
	379	-e 's/^flag_aerosol=.*.$/flag_aerosol='$flag_aerosol'/' DEF/config.def
	380	pwd
[4615]	381
[5415]	382	# COSP : ok_cosp desactive COSP si on a compile avec; il ne l'active pas si on a compile sans
	383	sed -i'' -e 's/ok_cosp.*.$/ok_cosp='$cosp'/' DEF/config.def
[5464]	384	if [[ $cosp = "y" ]]; then \cp -f "$MODEL"/DefLists/cosp*.txt "$local_d"/DEF/; fi
[4615]	385
[5415]	386	# Sorties LMDZ en fonction de l'option "xios"
	387	sed -i'' -e 's/ok_all_xml=.*.$/ok_all_xml='$xios'/' DEF/config.def
[4615]	388
[5415]	389	# Ajuster physiq.def en fonction de radiative code (default: values for rad=rrtm)
	390	# Pour isotopes=y , mettre iflag_ice_thermo=0 au lieu de 1
	391	#---------------------------------------------------------------------
	392	sed -i'' -e "s/iflag_rrtm=..$/iflag_rrtm=$iflag_rrtm/" -e "s/NSW=..$/NSW=$NSW/" DEF/physiq.def
	393	sed -i"" -e "s:directory_name.*$:directory_name=\"$MODEL/libf/phylmd/ecrad/data\",:" DEF/namelist_ecrad
[4615]	394
[5415]	395	if [[ $phylmd = "lmdiso" ]]; then iflag_ice_thermo=0; else iflag_ice_thermo=1; fi
	396	sed -i -e 's/iflag_ice_thermo=.*.$/iflag_ice_thermo='$iflag_ice_thermo'/' DEF/physiq.def
[4615]	397
[5415]	398	# Choix de orchidee.def en fonction de orchidee_rev; modification pour xios
	399	# NOTE separate orchidee_pft.def file for ORCHIDEE trunk post-CMIP6
	400	#---------------------------------------------------------------------
	401	orchidee_def=orchidee.def_6.1
	402	orchidee_pft_def=""
	403	if [[ $veget = "7983" ]]; then
	404	orchidee_def=orchidee.def_6.2work
[5564]	405	elif [[ $veget = "8758" ]]; then
[5415]	406	orchidee_def=orchidee.def_6.4work
	407	orchidee_pft_def=orchidee_pft.def_6.4work
	408	if ! grep "INCLUDEDEF=orchidee_pft.def" DEF/run.def; then
	409	sed -i'' -e 's/INCLUDEDEF=orchidee.def/INCLUDEDEF=orchidee.def\nINCLUDEDEF=orchidee_pft.def/' DEF/run.def; fi
	410	fi
[5587]	411	cp -f DEF/CONFIG/$orchidee_def DEF/orchidee.def
	412	if [[ $orchidee_pft_def != "" ]]; then cp -f DEF/CONFIG/$orchidee_pft_def DEF/orchidee_pft.def; fi
[4615]	413
[5415]	414	# Only for veget=CMIP6 it is still possible to use IOIPSL; newer versions of orchidee.def have XIOS_ORCHIDEE_OK = y
	415	sed -i'' -e 's/XIOS_ORCHIDEE_OK =.*.$/XIOS_ORCHIDEE_OK = '$xios'/' DEF/orchidee.def
[4615]	416
[5415]	417	######################################################################
	418	# Si on tourne avec XIOS, mise a jour des fichiers context et field* dans XMLfilesLMDZ
[5464]	419	# (ils vont se repercuter dans les repertoires de simulation $local_d/$SIM et de run $SIMRUNDIR)
[5415]	420	######################################################################
	421	if [[ $xios = y ]]; then
[5464]	422	cp -f "$MODEL"/DefLists/context_lmdz.xml "$local_d"/DEF/XMLfilesLMDZ/.
	423	cp -f "$MODEL"/DefLists/field_def_lmdz.xml "$local_d"/DEF/XMLfilesLMDZ/.
	424	if [[ $cosp = y ]]; then cp -f "$MODEL"/DefLists/field_def_cosp1.xml "$local_d"/DEF/XMLfilesLMDZ/.; fi
[5415]	425	fi
	426	}
[4615]	427
[5438]	428	#---------------------------------------------------------------------------
[5415]	429	function setup_ce0l() { # Verification de l'existance de l'état initial, compilation eventuelle pour sa creation
[5438]	430	#---------------------------------------------------------------------------
[5415]	431	if [[ ! -d $INIT ]]; then
	432	if [[ $init = 0 ]]; then
	433	echo "STOP: Récuperer les repertoires $INIT ou lancer avec option -init"; exit 1
	434	else
	435	# Compile ce0l
	436	cd "$MODEL"
[5534]	437	sed -e 's/gcm/ce0l/g' compile.sh > compile_ce0l.sh; chmod +x compile_ce0l.sh
[5415]	438	echo "Compiling ce0l"
	439	if ! ./compile_ce0l.sh &> ce0l.log; then echo "STOP: ce0l compilation failed, see $MODEL/ce0l.log"; exit 1; fi
	440	echo "Compiled ce0l"
	441	ce0l=${gcm/gcm/ce0l}
[4615]	442
[5464]	443	cd "$local_d"
[4615]	444	fi
[5415]	445	elif [[ $init = 1 ]]; then
	446	echo "STOP: Vous essayez d initialiser le modele mais $INIT existe deja"; exit 1
	447	fi
	448	}
[4615]	449
[5438]	450	#---------------------------------------------------------------------------
[5415]	451	function setup_simu() {
[5438]	452	#---------------------------------------------------------------------------
[5464]	453	#SIMRUNTOPDIR="$SIMRUNBASEDIR/$(basename "$local_d")"
[5420]	454	SIMRUNTOPDIR="$SIMRUNBASEDIR"
[5415]	455	SIMRUNDIR=$SIMRUNTOPDIR
	456	mkdir -p "$SIMRUNDIR"
	457	cd "$SIMRUNDIR"
	458	echo "La simulation s'exécutera sur $SIMRUNDIR"
[4615]	459
[5415]	460	#####################################################################
	461	# Creation du repertoire $SIM s'il n'existe pas deja
	462	#####################################################################
[5464]	463	if [[ ! -d $local_d/$SIM ]]; then
	464	mkdir "$local_d/$SIM"
	465	cd "$local_d"
[4615]	466
[5415]	467	# Edit reb.sh
[5464]	468	cp reb.sh "$local_d/$SIM/reb.sh"; chmod +x "$local_d/$SIM/reb.sh"
	469	sed -i'' -e "s:^rebuild=.*.$:rebuild=$LMDZD/$LMDZname/modipsl/bin/rebuild:" "$local_d/$SIM/reb.sh"
	470	enable_platform "$local_d/$SIM/reb.sh"
[4615]	471
[5415]	472	# Copy .def
[5464]	473	cp lmdz_env.sh "$local_d/$SIM/"
	474	mkdir "$local_d/$SIM/DEF"; cp DEF/def DEF/namelis "$local_d/$SIM/DEF/"
[5415]	475	#Pour XIOS, respectivement COSP, copier aussi les fichiers xml / txt
[5464]	476	if [[ $cosp = "y" ]]; then cp DEF/cosp*txt "$local_d/$SIM/DEF/"; fi
[5415]	477	if [[ $xios = "y" ]]; then
[5464]	478	cp DEF/XMLfilesLMDZ/*xml "$local_d/$SIM/DEF/"
	479	if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml "$local_d/$SIM/DEF/"; fi
[5415]	480	fi
[5464]	481	chmod u+w "$local_d/$SIM"/DEF/*
[4615]	482
[5415]	483	# Gestion du calendrier
	484	#######################
	485	cd "$SIM"
	486	sed -i'' -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def
	487	if [[ $freq = "yr" ]]; then date=$yearini; else date=$mthini; fi
	488	echo "$date a faire" >\| etat
[4615]	489
[5415]	490	# Recuperation des fichiers : executable initiaux et forcages
	491	#############################################################
	492	echo "date: $date"
	493	for f in start startphy; do
	494	inf=../$INIT/$f.$date.nc
	495	if [[ -f $inf \|\| $init = 1 ]]; then ln -s "$inf" ./; else echo "STOP: $inf missing"; exit ; fi;
	496	done
	497	for f in sechiba stomate; do
	498	if [[ -f ../$INIT/start_$f.$date.nc ]]; then ln -sf "../$INIT/start_$f.$date.nc" .; fi
	499	done
	500	cp "$gcm" gcm.e
	501	fi
[5464]	502	cd "$local_d"/..
[4615]	503
[5415]	504	#####################################################################
	505	echo "Modification du script de lancement"
	506	#####################################################################
	507	local cput
	508	if [[ $freq = "yr" ]]; then cput="04:00:00"; else cput="01:00:00"; fi
	509	local isotopes="n"
	510	if [[ $phylmd = "lmdiso" ]]; then isotopes="y"; fi
	511	sed -e "s/NOM_SIMU/$SIM/" \
	512	-e "s/time=.*.$/time=$cput/" \
	513	-e "s/ntasks=.*.$/ntasks=$mpi/" \
	514	-e "s/ntasks-per-node=.*.$/ntasks-per-node=$mpi_per_node/" \
	515	-e "s/cpus-per-task=.*.$/cpus-per-task=$omp/" \
	516	-e "s/nthreads=.*./nthreads=$omp/" \
[5464]	517	-e "s/MAINDIR=.*.$/MAINDIR=$(basename "$local_d")/" \
	518	-e "s:STORED=..:STORED=$(dirname "$local_d"):" \
[5415]	519	-e "s:SCRATCHD=..:SCRATCHD=$SIMRUNBASEDIR:" \
	520	-e "s/stopsim=.*.$/stopsim=$stopsim/" \
	521	-e "s/^veget=.*.$/veget=$veget/" \
	522	-e "s/^aerosols=.*.$/aerosols=$aerosols/" \
	523	-e "s/^isotopes=.*.$/isotopes=$isotopes/" \
	524	-e "s/^climato=.*.$/climato=$climato/" \
	525	-e "s/^ok_guide=.*.$/ok_guide=$ok_guide/" \
[5464]	526	"$local_d/script_SIMU" >\| "$SIMRUNDIR/tmp_$SIM"
[4615]	527
[5415]	528	enable_platform "$SIMRUNDIR/tmp_$SIM"
[4615]	529
[5415]	530	if [[ $testmode = "y" ]]; then
	531	sed -i'' -e "s/time=.*.$/time=00:10:00/" -e "s/#nday=1/nday=1/" -e "s/#@TESTQ//" "$SIMRUNTOPDIR/tmp_$SIM"
	532	fi
	533	}
[4615]	534
[5429]	535	#----------------------------------------------------------------------
[5439]	536	function list_yrmth() {
	537	#----------------------------------------------------------------------
	538	local liste=""
	539	local mthini=$1
	540	local mthend=$2
	541	local mo_=$mthini
	542	while [[ $mo_ != $mthend ]] ; do
	543	liste="$liste $mo_"
	544	yr__=$( echo $mo_ \| cut -c 1-4 )
	545	mo__=$( echo $mo_ \| cut -c 5-6 )
	546	echo YM $yr__ $mo__
	547	if [ $(( $mo__ +1 )) == 12 ] ; then
	548	yr__=$(( $yr__ + 1 )) ; mo_=$yr__$mo__
	549	else
	550	mo_=$(( $mo_ + 1 ))
	551	fi
	552	done
	553	echo $liste
	554
	555	}
	556
	557	#----------------------------------------------------------------------
	558	increment_month() {
	559	#----------------------------------------------------------------------
	560	local year=$( echo $1 \| cut -c 1-4 )
	561	local month=$(( $1 - ${year}00 ))
	562	if [ $(( $month - 12 )) -eq 0 ]; then
	563	year=$((year + 1))
	564	month=1
	565	else
	566	month=$((month + 1))
	567	fi
	568	if [[ $month -le 9 ]] ; then month=0$month ; fi
	569	echo $year$month
	570	}
	571
	572	#----------------------------------------------------------------------
[5415]	573	function fetch_simu_init_files() {
[5429]	574	#----------------------------------------------------------------------
[5415]	575	#####################################################################
[5426]	576	echo "Recuperation eventuelle de certains fichiers sur http:lmdz.lmd.jussieu.fr/pub"
[5415]	577	#####################################################################
[4615]	578
[5426]	579	# ORCHIDEE input files
[5429]	580	get_input_files wget_pub Orchidee
[5426]	581
	582	# Files for aerosols and chemistry
[5438]	583	if [[ $aerosols = "clim" ]]; then
	584	get_input_files wget_pub AerChem ; fi
[5426]	585
[5429]	586	# Files for SPLA
[5438]	587	if [[ $aerosols = "spla" ]]; then
	588	get_input_files wget_pub SPLA_WA/emissions
[5439]	589	mo_=$mthini
	590	while [[ $mo_ != $mthend ]] ; do
	591	# Code horrible duplique a cause de 08 (FH)
	592	local yr__=$( echo $mo_ \| cut -c 1-4 )
	593	local mo__=$(( $mo_ - ${yr__}00 ))
	594	if [[ $mo__ -le 9 ]] ; then mo__=0$mo__ ; fi
[5438]	595	for var in u10m v10m u v ; do
	596	echo wget_pub 3DInputData/SPLA_WA/ERA5/$yr__/$mo__ $var.nc
	597	wget_pub 3DInputData/SPLA_WA/ERA5/$yr__/$mo__ $var.nc
	598	done
[5439]	599	mo_=$( increment_month $mo_ )
[5438]	600	done
[5464]	601	cd $local_d ; ln -sf $LMDZ_INIT/3DInputData/SPLA_WA/ERA5 GUIDE
[5438]	602	fi
[5415]	603	}
[4615]	604
[5429]	605	#----------------------------------------------------------------------
[5415]	606	function run_sim_or_init() {
[5429]	607	#----------------------------------------------------------------------
[5464]	608	cd "$local_d"
[4615]	609
[5415]	610	if [[ $init = 1 ]]; then
	611	#####################################################################
	612	echo "Creation de l etat initial"
	613	#####################################################################
[4615]	614
[5415]	615	# Creation du repertoire INIT et mise en place de liens logiques vers les starts
	616	# en anticipation de leur création :
[5464]	617	mkdir "$local_d/$INIT"; cd "$local_d/$INIT"
[5415]	618	for an in $mthini $yearini; do for f in start startphy; do ln -s "$f.nc" "$f.$an.nc"; done; done
[4615]	619
[5415]	620	# Creation du repertoire INIT temporaire et rapatriement des fichiers necessaires
	621	if [[ -d $SIMRUNDIR/$INIT ]]; then mv "$SIMRUNDIR/$INIT" "$SIMRUNDIR/$INIT$$"; fi
[5464]	622	mkdir "$SIMRUNDIR/$INIT"; cp -r "$local_d/DEF" "$SIMRUNDIR/$INIT/"
	623	cd "$SIMRUNDIR/$INIT"; cp DEF/*.def .; cp "$local_d/lmdz_env.sh" .
[5415]	624	if [[ $xios = "y" ]]; then
	625	cp DEF/XMLfilesLMDZ/*xml .
	626	if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml .; fi
	627	fi
	628	sed -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def >\| run.def
[4615]	629
[5415]	630	#-------------------------------------------------------------------
	631	# Fichiers Limit
	632	#-------------------------------------------------------------------
	633	local yrs suf
	634	if [[ $climato = 0 ]]; then
	635	# calend est choisi plus haut dans "Changements dans les fichiers DEF/*def" et ecrit dans $MAINDIR/DEF/run.def
	636	yrini=$(echo "$mthini" \| cut -c-4)
	637	yrend=$(echo "$mthend" \| cut -c-4)
	638	yrs=""; yr=$yrini
	639	while [[ $yr -le $yrend ]]; do yrs="$yrs $yr"; (( yr = yr + 1 )); done
	640	suf="360x180_"
	641	else
	642	yrs=2000
	643	suf="1x1_clim"
	644	fi
[4615]	645
[5415]	646	liste_get="Albedo.nc Relief.nc Rugos.nc landiceref.nc"
	647	for yr in $yrs; do
	648	if [[ $climato = 0 ]]; then sufyr=$suf$yr; else sufyr=$suf; fi
	649	liste_get="$liste_get amipbc_sic_$sufyr.nc amipbc_sst_$sufyr.nc"
	650	done
	651	echo LISTEGET "$liste_get"
	652	for file in $liste_get; do
[5426]	653	wget_pub 3DInputData/Limit $file
	654	ln_from_pub 3DInputData/Limit $file
[5415]	655	done
	656	#-------------------------------------------------------------------
[5426]	657	# Initial state ECDYN
[5415]	658	#-------------------------------------------------------------------
[5426]	659	wget_pub 3DInputData/Init ECDYN.nc
	660	ln_from_pub 3DInputData/Init ECDYN.nc
[5415]	661	ln -sf ECDYN.nc ECPHY.nc
[4615]	662
[5415]	663	# Creation du script d'initialisation
[5465]	664	if [ "$MPICMD" = "" ] ; then mpicmd='' ; else mpicmd='OMP_NUM_THREADS=1 '"$MPICMD"' 1' ; fi
[5415]	665	cat << ...eod >\| tmp
[4615]	666	#!/bin/bash
[5415]	667	#@JZ#JeanZay
	668	#@JZ#SBATCH --job-name=Init # nom du job
	669	#@JZ#SBATCH --ntasks=1 # Nombre de processus MPI
	670	#@JZ#SBATCH --cpus-per-task=1 # nombre de threads OpenMP
	671	#@JZ# /!\ Attention, la ligne suivante est trompeuse mais dans le vocabulaire
	672	#@JZ# de Slurm "multithread" fait bien référence à l'hyperthreading.
	673	#@JZ#SBATCH --hint=nomultithread # 1 thread par coeur physique (pas d'hyperthreading)
	674	#@JZ#SBATCH --time=00:10:00 # Temps d'exécution maximum demandé (HH:MM:SS)
	675	#@JZ#SBATCH --output=Init%j.out # Nom du fichier de sortie
	676	#@JZ#SBATCH --error=Init%j.out # Nom du fichier d'erreur (ici commun avec la sortie)
	677	#@JZ# To submit to dev queue; "time" (above) must be max 2h
	678	#@JZ#TESTQ#SBATCH --qos=qos_cpu-dev
	679	#@SP#Spirit
	680	#@SP#SBATCH --job-name=Init
	681	#@SP#SBATCH --ntasks=1
	682	#@SP#SBATCH --cpus-per-task=1
	683	#@SP#SBATCH --hint=nomultithread
	684	#@SP#SBATCH --time=00:10:00
	685	#@SP#SBATCH --output=Init%j.out
	686	#@SP#SBATCH --error=Init%j.out
	687	#@ADS#Adastra
	688	#@ADS#SBATCH --job-name=Init
	689	#@ADS#SBATCH --ntasks=1
	690	#@ADS#SBATCH --cpus-per-task=1
	691	#@ADS#SBATCH --nodes=1
	692	#@ADS#SBATCH --hint=nomultithread
	693	#@ADS#SBATCH --time=00:10:00
	694	#@ADS#SBATCH --output=Init%j.out
	695	#@ADS#SBATCH --error=Init%j.out
[4615]	696
[5415]	697	set -eu
[4615]	698
	699	# ANCIEN MULTI STEP case \${LOADL_STEP_NAME} in
	700
	701	# ANCIEN MULTI STEP init )
	702
[5415]	703	if [ ! -f lmdz_env.sh ]; then echo "manque fichier lmdz_env.sh"; ls; exit 1; fi
	704	. lmdz_env.sh
	705	ulimit -s unlimited
	706	cd $SIMRUNDIR/$INIT
	707	echo "Executable : $ce0l"
	708	for yr in $yrs; do
	709	if [ $climato = 0 ]; then sufyr=$suf\$yr; else sufyr=$suf; fi
	710	ln -sf amipbc_sic_\$sufyr.nc amipbc_sic_1x1.nc
	711	ln -sf amipbc_sst_\$sufyr.nc amipbc_sst_1x1.nc
	712	sed -e 's/anneeref=.*.$/anneeref='\$yr'/' DEF/run.def >\| run.def
	713	echo Starting initialisation
[5426]	714	# Runing ce0l.e
[5465]	715	$mpicmd $ce0l # ce0l requires MPI=OMP=1
[5415]	716	if [ $climato = 0 ]; then mv limit.nc limit.\$yr.nc; fi
	717	done
	718	# ANCIEN MULTI STEP ;;
[4615]	719
	720	# ANCIEN MULTI STEP interp )
[5415]	721	if [[ $aerosols = clim ]]; then
[5464]	722	cp $local_d/interp_aerosols.sh .; chmod +x interp_aerosols.sh
[5415]	723	# Les aerosols de l'annee 2000 ont été remplacés par "9999" qui pointe vers un fichier moyen sur 1995-2014
	724	#for year in 2000 1850; do ./interp_aerosols.sh \$year; done
	725	#mv aerosols.2000.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc
	726	for year in 9999 1850; do ./interp_aerosols.sh \$year; done
	727	mv aerosols.9999.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc
	728	fi
[4615]	729
[5464]	730	for f in sta* gri*nc; do cp \$f $local_d/$INIT/\$f; done
	731	if [[ $climato = 1 ]]; then cp limit.nc $local_d/$INIT/limit.nc; fi
	732	mkdir -p $local_d/$LIMIT
	733	for f in limit*.nc ; do cp \$f $local_d/$LIMIT/\$f; done
	734	if [ $aerosols = clim ]; then for f in aerosols[.0-9]*nc; do cp \$f $local_d/$LIMIT/\$f; done; fi
[5415]	735	#
	736	cd $SIMRUNDIR
[4615]	737	...eod
[5415]	738	if [[ $ok_guide != "y" ]]; then # Running first simulation automatically except for nudging
	739	cat << ...eod >> tmp
	740	echo "Submitting job tmp_$SIM"
[5422]	741	#echo "\$SUBMITCMD tmp_$SIM"
	742	#\$SUBMITCMD tmp_$SIM
[5424]	743	echo submitcmd tmp_$SIM
[5422]	744	submitcmd tmp_$SIM
[4615]	745	...eod
[5415]	746	fi
	747	cat << ...eod >> tmp
	748	# ANCIEN MULTI STEP esac
[4615]	749	...eod
[5415]	750	enable_platform tmp
[5438]	751	echo "#################################################################"
[5422]	752	#echo "Submitting initialisation job <$SUBMITCMD tmp> from $(pwd)"
	753	echo "Submitting initialisation job <submitcmd tmp> from $(pwd)"
[5415]	754	chmod +x tmp
[5422]	755	#$SUBMITCMD tmp
	756	submitcmd tmp
[5438]	757	echo "#################################################################"
[4615]	758
[5415]	759	else #case [ $init != 1 ]
	760	cd "$SIMRUNDIR"
[5438]	761	echo "################################################################"
[5415]	762	echo "Submitting job tmp_$SIM"
[5422]	763	#echo "$SUBMITCMD tmp_$SIM"
	764	#$SUBMITCMD "tmp_$SIM"
	765	echo "submitcmd tmp_$SIM"
	766	submitcmd "tmp_$SIM"
[5438]	767	echo '################################################################'
[5415]	768	fi
	769	}
[4615]	770
[5438]	771	#---------------------------------------------------------------------------
[5415]	772	function message_post_submit() {
[5438]	773	#---------------------------------------------------------------------------
[5415]	774	if [[ $ok_guide = "y" && $init = 1 ]]; then
[5464]	775	cd "$local_d"
[5415]	776	enable_platform era2gcm_tuto.sh
	777	echo "Once initialisation is finished, you have to create nudging files"
	778	echo "Edit era2gcm_tuto.sh and set the desired parameters in section <User choices>"
	779	echo "Make sure you have acces to the chosen ERA files, and the required modules are loaded, then run : ./era2gcm_tuto.sh"
	780	if [[ $aerosols = "spla" ]]; then
	781	echo "Your aerosol choice is <spla>, so you need ERA 10m-winds interpolated on LMDZ grid. Use script era2gcm_uv10m.sh"
	782	fi
	783	else
	784	echo "Si tout se passe bien, vous avez initialisé et lancé automatiquement la simulation."
	785	echo "Le job qui a été lancé se trouve sur $SIMRUNTOPDIR/tmp_$SIM"
	786	fi
	787	}
[4615]	788
[5438]	789	#---------------------------------------------------------------------------
[5415]	790	function setup_and_load_lmdz_env() {
[5438]	791	#---------------------------------------------------------------------------
[5415]	792	if [[ ! -f .lmdz_setup_root_dir ]]; then echo "STOP: setup.sh is not located in the root dir ??!!"; exit 1; fi
	793	# sed root_dir in lmdz_env.sh
[5464]	794	sed -i'' "s<root_dir=.*<root_dir=$local_d<" lmdz_env.sh
[4615]	795
[5415]	796	# Set up the appropriate environment
	797	source lmdz_env.sh
	798	}
[4615]	799
[5464]	800	local_d=$(pwd)
[4615]	801
[5415]	802	setup_and_load_lmdz_env
	803	load_install_lib
	804	define_expert_options
	805	set_default_params
	806	read_cmdline_args "$@"
	807	ensure_correct_option_combinations
	808	install_model
	809	setup_def
	810	setup_ce0l
	811	setup_simu
	812	fetch_simu_init_files
	813	run_sim_or_init
[5420]	814	message_post_submit

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