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CreateRestartOce4Oasis.bash @ 6690

Last change on this file since 6690 was 6669, checked in by omamce, 9 months ago

O.M. : CPLRESTART

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Python cleanup
More use of nemo.py functionalities

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Property svn:keywords set to Date Revision HeadURL Author Id

File size: 15.2 KB

Rev	Line
[5155]	1	#!/usr/bin/env bash
[3707]	2	### ===========================================================================
	3	###
	4	### Creates initial state for coupler, ocean side
	5	### Take data from NEMO grid_T and icemod files
	6	###
	7	### ===========================================================================
	8	##
	9	## Warning, to install, configure, run, use any of Olivier Marti's
	10	## software or to read the associated documentation you'll need at least
	11	## one (1) brain in a reasonably working order. Lack of this implement
	12	## will void any warranties (either express or implied).
	13	## O. Marti assumes no responsability for errors, omissions,
	14	## data loss, or any other consequences caused directly or indirectly by
	15	## the usage of his software by incorrectly or partially configured
	16	## personal.
	17	##
	18	###
	19	### Documentation : https://forge.ipsl.jussieu.fr/igcmg/wiki/IPSLCM6/MOSAIX
	20	###
	21	## SVN information
	22	# $Author$
	23	# $Date$
	24	# $Revision$
	25	# $Id$
	26	# $HeadURL$
	27
[4289]	28	## Usage exemples :
	29	#
	30	# CreateRestartOce4Oasis.bash --ocefile /ccc/store/cont003/dsm/p25sepul/IGCM_OUT/IPSLCM5A2/PROD/piControl/CM5A2.1.pi.00/OCE/Output/MO/CM5A2.1.pi.00_40100101_40191231_1M_grid_T.nc --icefile /ccc/store/cont003/dsm/p25sepul/IGCM_OUT/IPSLCM5A2/PROD/piControl/CM5A2.1.pi.00/ICE/Output/MO/CM5A2.1.pi.00_40100101_40191231_1M_icemod.nc --icefrc ice_pres --icetem tsice --icealb ialb
[6669]	31
[6228]	32	# CreateRestartOce4Oasis.bash --ocefile /ccc/store/cont003/gencmip6/p86mart/IGCM_OUT/IPSLCM6/DEVT/pdControl/CM6010.2.rivgeo-LR-pdCtrl/OCE/Output/MO/CM6010.2.rivgeo-LR-pdCtrl_22400101_22491231_1M_grid_T.nc --icefrc siconc
[6669]	33
[6228]	34	# CreateRestartOce4Oasis.bash --ocefile /ccc/store/cont003/gencmip6/p86maf/IGCM_OUT/IPSLCM6/PROD/piControl/CM61-LR-pi-03/OCE/Output/MO/CM61-LR-pi-03_23400101_23491231_1M_grid_T.nc --icefile /ccc/store/cont003/gencmip6/p86maf/IGCM_OUT/IPSLCM6/PROD/piControl/CM61-LR-pi-03/ICE/Output/MO/CM61-LR-pi-03_23400101_23491231_1M_icemod.nc --icefrc siconc
[6669]	35
[4289]	36	# CreateRestartOce4Oasis.bash --ocefile /ccc/store/cont003/gen7451/personr/IGCM_OUT/ORCA025_LIM3_PISCES/DEVT/ORCA025ia/eOR025L3P-IA-REF07-MUSCL/OCE/Output/MO/eOR025L3P-IA-REF07-MUSCL_20090101_20091231_1M_grid_T.nc
[6669]	37
[4289]	38	# CreateRestartOce4Oasis.bash --ocefile /ccc/work/cont003/gencmip6/p48ethe/ICMC-TOOLS/DATA/eOR025L3P-IA-REF07-MUSCL_20090101_20091231_1M_grid_T.nc --icefile /ccc/work/cont003/gencmip6/p48ethe/ICMC-TOOLS/DATA/eOR025L3P-IA-REF07-MUSCL_20090101_20091231_1M_icemod.nc --icefrc siconc/oce --icetem sistem
	39	#
	40	#
[3707]	41	## ===========================================================================
	42	##
	43	## You should not change anything below this line ....
	44	##
	45	## ===========================================================================
	46
[6669]	47	## Creates colors for petty prints
	48	## ===============================
	49	export Bold=$(tput bold)
	50	export Unde=$(tput smul) ; export OffUnde=$(tput rmul)
	51	export Stou=$(tput smso) ; export OffStou=$(tput rmso)
	52	export Reve=$(tput rev )
	53	declare -a couleurs=( "Black" "Blue" "Green" "Cyan" "Red" "Magenta" "Yellow" "White" )
	54	[[ "${bash_debug}" = "true" ]] && echod ".bash_login Couleurs : ${couleurs[*]}"
	55	[[ "${bash_debug}" = "true" ]] && echod "Demmarrage de la boucle"
	56	for i in $(seq 1 7)
	57	do
	58	[[ "${bash_debug}" = "true" ]] && echod i:${i}
	59	[[ "${bash_debug}" = "true" ]] && echod ".bashrc Couleur ${i} : ${couleurs[${i}]}"
	60	eval "export ${couleurs[$i]}=$(tput setf $i)"
	61	eval "export ${couleurs[$i]}F=$(tput setb $i)"
	62	done
	63	export Norm=$(tput sgr0 )
[3707]	64	##
	65	## Command line parameters
	66	## ===========================================================================
	67	# Default values
	68	Comment="Preliminary attempt - Do not trust !"
[4289]	69	#
	70	# --ocefile : file in which sea surface temperature is read
[6228]	71	# --icefile : file in which sea ice fraction, albedo and ice surface temperature are read.
[4289]	72	# if not specified, these variables are readed in the ocean file
	73	#
	74	## Variable in ocean file :
	75	OceSst=tos #> Variable containing sea surface temperature (Â°C) : --ocesst tos
	76	## Variables in ice file
	77	IceFrc=ice_pres #> Variable containing sea ice fraction [0-1] : --icefrc ice_pres
	78	IceAlb=none #> Variable containing sea ice albedo [0-1]. If 'none', set to 0.65 : --icealb ialb
	79	IceTem=none #> Variable containing sea ice surface temperature (Â°C). If 'none', set to -20Â°C : --icetem tsice
[3707]	80
[4289]	81	# Complementary syntaxes for variables names
	82	# --icefrc siconc/oce means that siconc variable should be taken in the ocean file ...
	83	# --icealb ialb/oce
	84	# --icetem tsice/oce
	85
	86	## Filling
	87	# If the ocean in the coupled model has a different geometry that the one in the files.
	88	# In general, the forced ocean does run with no closed sea, when the coupled model does.
	89	# This step is he mandatory
	90	Fill=yes # If yes, fill the continents. --fill / --nofill
	91
	92	# nperio parameter for ORCA. Normally guess from name or dimensions. For ORCA2, set to nperio=4, but should be set to nperio=6 for some paleo configs
	93	# --nperio 4
	94
	95	DefaultIceAlb=0.65
	96	DefaultIceTem=-20.0
	97
	98	#OceFile=/ccc/store/cont003/dsm/p25sepul/IGCM_OUT/IPSLCM5A2/PROD/piControl/CM5A2.1.pi.00/OCE/Output/MO/CM5A2.1.pi.00_40100101_40191231_1M_grid_T.nc
	99	#OceFile=/ccc/store/cont003/gencmip6/p86mart/IGCM_OUT/IPSLCM6/DEVT/pdControl/CM6010.2.rivgeo-LR-pdCtrl/OCE/Output/MO/CM6010.2.rivgeo-LR-pdCtrl_22400101_22491231_1M_grid_T.nc
[3707]	100	#
[4289]	101
	102	#
[3707]	103	# Defines computer
	104	# ================
	105	if [[ $(hostname) = irene* ]] ; then arch=irene ; center=tgcc ; fi
	106
	107	case ${arch} in
[4289]	108	( irene )
[6228]	109	set +e
	110	R_IN=$(ccc_home -u igcmg --cccwork)/IGCM
[6669]	111	TMPDIR=$(ccc_home --cccwork)/TMP/CPLRESTART
[6228]	112	SUBMIT_DIR=${BRIDGE_MSUB_PWD:-${SUBMIT_DIR}}
	113	MpiRun="time ccc_mprun"
	114	PyRun="time ccc_mprun -n 1" # Needed to force python to run on one process only
[6669]	115	source $(ccc_home -u igcmg)/MachineEnvironment/irene/env_atlas_irene
[6228]	116	set -e
[3707]	117	;;
[6228]	118	( spip )
	119	R_IN=${HOME}/Scratch/IGCM
	120	TMPDIR=${HOME}/Scratch/TMP
	121	SUBMIT_DIR=$(pwd)
	122	MpiRun="/opt/local/bin/mpirun -n 1"
	123	PyRun="time"
	124	;;
[3707]	125	( * )
	126	exit -1
	127	;;
	128	esac
	129
[6669]	130	Nperio=''
	131	bVerbose='Yes'
	132	bXtrace='Yes'
	133	bError='Yes'
	134	Fill='yes'
[4289]	135
[6669]	136	while [[ ${1} = -* \|\| ${1} = +* ]] ; do
[3707]	137	case ${1} in
	138	( -- ) shift ; break ;;
[4289]	139	( -c \| --comment ) shift ; Comment=${1} ;;
	140	( --ocefile ) shift ; OceFile=${1} ;;
	141	( --icefile ) shift ; IceFile=${1} ;;
	142	( --ocesst ) shift ; OceSst=${1} ;;
	143	( --icefrc ) shift ; IceFrc=${1} ;;
	144	( --icetem ) shift ; IceTem=${1} ;;
	145	( --icealb ) shift ; IceAlb=${1} ;;
	146	( --fill ) Fill="yes" ;;
	147	( --nofill ) Fill="no" ;;
	148	( --nperio ) shift ; Nperio="--nperio ${1}" ;;
[6669]	149	( -v \| --verbose ) bVerbose='Yes' ;;
	150	( -x \| --xtrace ) bXtrace='Yes' ;;
	151	( -xv \| -vx ) bVerbose='Yes' ; bXtrace='Yes' ;;
	152	( -e ) bError='Yes' ;;
	153	( -V \| +v \| --noverbose ) bVerbose='No' ;;
	154	( -X \| +x \| --noxtrace ) bXtrace='No' ;;
	155	( -XV \| -VX \| +vx \| +xv ) bVerbose='No'; bXtrace='No' ;;
	156	( -E \| +e ) bError='No' ;;
	157	( -* ) echo ${Bold}${Red}"Unknown option : ${1}"${Norm} ; exit 1 ;;
[3707]	158	esac
	159	shift
	160	done
	161
[6669]	162	[[ "X${bVerbose}" = "XYes" ]] && set -o verbose
	163	[[ "X${bVerbose}" = "XNo" ]] && set +o verbose
	164	[[ "X${bXtrace}" = "XYes" ]] && set -o xtrace
	165	[[ "X${bXtrace}" = "XNo" ]] && set +o xtrace
	166	[[ "X${bError}" = "XYes" ]] && set -o errexit
	167	[[ "X${bError}" = "XNo" ]] && set +o errexit
[3707]	168	#
	169	# Format for OASIS files : should be NetCDF3 classic or NetCDF3 64 bits
	170	# ---------------------------------------------------------------------------
	171	FL_FMT=64bit
	172
	173	##
	174	## Defines associated sea ice file
	175	## ===========================================================================
[4289]	176	if [[ -z ${IceFile} ]] ; then IceFile=${OceFile} ; fi
	177	IceFrcFile=${IceFile}
	178	IceTemFile=${IceFile}
	179	IceAlbFile=${IceFile}
[3707]	180
[4289]	181	## Select file for each variable
	182	OceSstFile=${OceFile}
	183	if [[ ${OceSst} = */ice ]] ; then
	184	OceSstFile=${IceFile}
	185	OceSst=${OceSst%%/*}
	186	fi
	187
	188
	189	if [[ ${IceAlb} = */oce ]] ; then
	190	IceAlbFile=${OceFile}
	191	IceAlb=${IceFrc%%/*}
	192	fi
	193	if [[ ${IceFrc} = */oce ]] ; then
	194	IceFrcFile=${OceFile}
	195	IceFrc=${IceFrc%%/*}
	196	fi
	197	if [[ ${IceTem} = */oce ]] ; then
	198	IceTemFile=${OceFile}
	199	IceTem=${IceTem%%/*}
	200	fi
	201
	202
[6669]	203	echo ${Blue}"Oce sst - Variable ${OceSst} - File ${OceSstFile}"${Norm}
	204	echo ${Blue}"Ice fraction - Variable ${IceFrc} - File ${IceFrcFile}"${Norm}
	205	echo ${Blue}"Ice albedo - Variable ${IceAlb} - File ${IceAlbFile}"${Norm}
	206	echo ${Blue}"Ice temperature - Variable ${IceTem} - File ${IcetemFile}"${Norm}
[4289]	207
	208
[6669]	209	if [[ ! -f ${OceSstFile} ]] ; then
	210	echo ${Red}"Not found : ${OceSstFile}"${Norm}
	211	fi
	212
	213	if [[ ! -f ${IceFrcFile} ]] ; then
	214	echo ${Red}"Not found : ${IceFrcFile}"${Norm}
	215	fi
	216
[3707]	217	##
	218	## Extract variables
	219	## ===========================================================================
[6669]	220	ncks --overwrite --fl_fmt=${FL_FMT} --history -d time_counter,0,0 --variable ${IceFrc} ${IceFrcFile} ${TMPDIR}/sstoce_fields.nc
	221	ncks --overwrite --fl_fmt=${FL_FMT} --history -d time_counter,0,0 --variable ${OceSst} ${OceSstFile} ${TMPDIR}/oce_sst.nc
[4289]	222
[6669]	223	ncks --append --fl_fmt=${FL_FMT} --history ${TMPDIR}/oce_sst.nc ${TMPDIR}/sstoce_fields.nc
[4289]	224	if [[ "X${IceAlb}" != "Xnone" ]] ; then
[6669]	225	ncks --overwrite --fl_fmt=${FL_FMT} --history -d time_counter,0,0 --variable ${IceAlb} ${IceAlbFile} ${TMPDIR}/ice_alb.nc
	226	ncks --append --fl_fmt=${FL_FMT} --history ${TMPDIR}/ice_alb.nc ${TMPDIR}/sstoce_fields.nc
[4289]	227	fi
	228	if [[ "X${IceTem}" != "Xnone" ]] ; then
[6669]	229	ncks --overwrite --fl_fmt=${FL_FMT} --history -d time_counter,0,0 --variable ${IceTem} ${IceTemFile} ${TMPDIR}/ice_tem.nc
	230	ncks --append --fl_fmt=${FL_FMT} --history ${TMPDIR}/ice_tem.nc ${TMPDIR}/sstoce_fields.nc
[4289]	231	fi
[3707]	232
[6669]	233	#
	234	## Remove time dimension
	235	## ===========================================================================
	236
	237	ncwa --overwrite --fl_fmt=${FL_FMT} --history --average time_counter ${TMPDIR}/sstoce_fields.nc ${TMPDIR}/sstoce_fields_notime.nc
	238
	239	# Clean attributes
	240	ncatted --history --attribute history,global,d,c,"" ${TMPDIR}/sstoce_fields_notime.nc
	241
[3707]	242	##
	243	## Find ocean name
	244	## ===========================================================================
[6669]	245	dim_y=$(ncdump -h ${TMPDIR}/sstoce_fields_notime.nc \| grep "y *=" \| grep -v "nvertex" \| awk '{print $3}' )
	246	dim_x=$(ncdump -h ${TMPDIR}/sstoce_fields_notime.nc \| grep "x *=" \| grep -v "nvertex" \| awk '{print $3}' )
[3707]	247	echo ${dim_x} ${dim_y}
	248
[4289]	249	[[ ${dim_x} = 182 && ${dim_y} = 149 ]] && OCE=ORCA2.3
	250	[[ ${dim_x} = 362 && ${dim_y} = 332 ]] && OCE=eORCA1.2
[6228]	251	[[ ${dim_x} = 360 && ${dim_y} = 331 ]] && OCE=eORCA1.4
[4249]	252	[[ ${dim_x} = 1442 && ${dim_y} = 1207 ]] && OCE=eORCA025.1
[3707]	253
	254	##
	255	## Creates sstoce file
	256	## ===========================================================================
[6669]	257	cat <<EOF > ${TMPDIR}/create_sstoce.nco
[6228]	258	*OceSst[y,x] = double ( ${OceSst}(:,:) + 273.15d ) ;
	259	OIceFrc[y,x] = double ( ${IceFrc}(:,:) ) ;
[4289]	260	//
	261	EOF
[3707]	262
[4289]	263	if [[ "X${IceAlb}" != "Xnone" ]] ; then
[6669]	264	cat <<EOF >> ${TMPDIR}/create_sstoce.nco
[6228]	265	*IceAlb[y,x] = double ( ${IceAlb}(:,:) ) ;
[4289]	266	//
	267	EOF
	268	else
[6669]	269	cat <<EOF >> ${TMPDIR}/create_sstoce.nco
[4289]	270	*IceAlb[y,x] = double ( ${DefaultIceAlb}d ) ;
	271	//
	272	EOF
	273	fi
	274
	275	if [[ "X${IceTem}" != "Xnone" ]] ; then
[6669]	276	cat <<EOF >> ${TMPDIR}/create_sstoce.nco
[4289]	277	*IceTem[y,x] = double ( ${IceTem}(:,:) + 273.15d ) ;
	278	//
	279	EOF
	280	else
[6669]	281	cat <<EOF >> ${TMPDIR}/create_sstoce.nco
[4289]	282	*IceTem[y,x] = double ( ${DefaultIceTem}d + 273.15d ) ;
	283	//
	284	EOF
	285	fi
	286
[6669]	287	cat <<EOF >> ${TMPDIR}/create_sstoce.nco
[6228]	288	O_SSTSST[y,x] = OceSst (:,:) * (1.0d-OIceFrc(:,:)) ;
	289	O_AlbIce[y,x] = IceAlb (:,:) * OIceFrc(:,:) ;
	290	O_TepIce[y,x] = IceTem (:,:) * OIceFrc(:,:) ;
	291	O_OCurx1[y,x] = 0.0d ;
	292	O_OCury1[y,x] = 0.0d ;
	293	O_OCurz1[y,x] = 0.0d ;
[3707]	294	EOF
	295
[6669]	296	ncap2 --overwrite --fl_fmt=${FL_FMT} --history --script-file ${TMPDIR}/create_sstoce.nco ${TMPDIR}/sstoce_fields_notime.nc ${TMPDIR}/tmp_sstoc.nc
	297	ncks --fl_fmt=${FL_FMT} --overwrite --history --variable OIceFrc,O_SSTSST,O_AlbIce,O_TepIce,O_OCurx1,O_OCury1,O_OCurz1 ${TMPDIR}/tmp_sstoc.nc ${TMPDIR}/sstoc.nc
	298	ncatted --history --attribute long_name,O_SSTSST,o,c,"SST weighted by fraction of open ocean" ${TMPDIR}/sstoc.nc
	299	ncatted --history --attribute long_name,O_AlbIce,o,c,"Albedo weighted by fraction of sea ice" ${TMPDIR}/sstoc.nc
	300	ncatted --history --attribute long_name,O_TepIce,o,c,"Ice temperature weighted by fraction of sea ice" ${TMPDIR}/sstoc.nc
[3707]	301
[6669]	302	ncatted --history --attribute comment,O_SSTSST,o,c,"Variable ${OceSst} taken in ${OceSstFile}" ${TMPDIR}/sstoc.nc
	303	ncatted --history --attribute comment,OIceFrc,o,c,"Variable ${IceFrc} taken in ${IceFrcFile}" ${TMPDIR}/sstoc.nc
[4289]	304
[6669]	305	if [[ ${IceAlb} = none ]] ; then
	306	ncatted --history --attribute comment,O_AlbIce,o,c,"Set to ${DefaultIceAlb}" ${TMPDIR}/sstoc.nc
	307	else
	308	ncatted --history --attribute comment,O_AlbIce,o,c,"Variable ${IceAlb} taken in ${IceAlbFile}" ${TMPDIR}/sstoc.nc
[4289]	309	fi
[6669]	310
	311	if [[ ${IceTem} = none ]] ; then
	312	ncatted --history --attribute comment,O_TepIce,o,c,"Set to ${DefaultIceTem}" ${TMPDIR}/sstoc.nc
	313	else
	314	ncatted --history --attribute comment,O_TepIce,o,c,"Variable ${IceTem} taken in ${IceTemFile}" ${TMPDIR}/sstoc.nc
[4289]	315	fi
	316
[3707]	317	##
[4289]	318	## Filling the fields
[3707]	319	## ===========================================================================
[4289]	320	if [[ ${Fill} = yes ]] ; then
[6669]	321	mv ${TMPDIR}/sstoc.nc ${TMPDIR}/sstoc_nofilled.nc
	322	python3 FillOceRestart.py --input ${TMPDIR}/sstoc_nofilled.nc --output ${TMPDIR}/sstoc.nc ${Nperio}
[4289]	323	fi
[3707]	324
[4289]	325	##
	326	## Add some information in file header
	327	## ===========================================================================
	328
[3707]	329	UUID=$(uuid)
	330	NCO="$(ncks --version \|& tail -1\|sed 's/ncks //')"
	331	ncatted --history \
	332	--attribute nco_openmp_thread_number,global,d,, \
	333	--attribute source,global,o,c,"IPSL Earth system model" \
	334	--attribute group,global,o,c,"ICMC IPSL Climate Modelling Center" \
	335	--attribute Institution,global,o,c,"IPSL https://www.ipsl.fr" \
	336	--attribute Model,global,o,c,"${OCE} https://www.nemo-ocean.eu" \
	337	--attribute originalFiles,global,o,c,"${OceFile} ${IceFile}" \
	338	--attribute directory,global,o,c,"$(pwd)" \
	339	--attribute description,global,o,c,"Fields needed by OASIS-MCT" \
	340	--attribute timeStamp,global,o,c,"$(date)" \
	341	--attribute uuid,global,o,c,"${UUID}" \
	342	--attribute Program,global,o,c,"Generated by ${0}" \
	343	--attribute HOSTNAME,global,o,c,"$(hostname)" \
	344	--attribute LOGNAME,global,o,c,"$(whoami)" \
	345	--attribute NCO,global,o,c,"NCO netCDF Operator ${NCO} http://nco.sourceforge.net" \
	346	--attribute OS,global,o,c,"$(uname -o)" \
	347	--attribute release,global,o,c,"$(uname -r)" \
	348	--attribute hardware,global,o,c,"$(uname -i)" \
	349	--attribute directory,global,o,c,"$(pwd)" \
	350	--attribute Comment,global,o,c,"${Comment}" \
	351	--attribute SVN_Author,global,o,c,"$Author$" \
	352	--attribute SVN_Date,global,o,c,"$Date$" \
	353	--attribute SVN_Revision,global,o,c,"$Revision$" \
	354	--attribute SVN_Id,global,o,c,"$Id$" \
[6669]	355	${TMPDIR}/sstoc.nc
[3707]	356
	357	##
	358	## Cleaning
	359	## ===========================================================================
[4289]	360	#rm -f sstoce_fields.nc sstoce_fields_notime.nc tmp_sstoce.nc oce_fields.nc
[3707]	361
[6669]	362	mv ${TMPDIR}/sstoc.nc ${TMPDIR}/sstoc_${OCE}.nc
[3707]	363
[6512]	364	##
	365
[6669]	366	echo ${Blue}"TMPDIR : ${TMPDIR}"${Norm}
[3707]	367	## ===========================================================================
	368	##
	369	## That's all folk's !!!
	370	##
	371	## ===========================================================================

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