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source: trunk/libIGCM/AA_create_se @ 1456

Last change on this file since 1456 was 1448, checked in by jgipsl, 6 years ago
Change in headers at irene : temporary remove option -m and use a workaround given by the TGCC. This change is done to avoid problems with resubmitting from job when submitting the main job from workdir.
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
File size: 28.4 KB

Rev	Line
[622]	1	#-Q- curie ######################
	2	#-Q- curie ## CURIE TGCC/CEA ##
	3	#-Q- curie ######################
[904]	4	#-Q- curie #MSUB -r SE # Nom du job
[622]	5	#-Q- curie #MSUB -eo
	6	#-Q- curie #MSUB -n 1 # Reservation du processus
[880]	7	#-Q- curie #MSUB -T 36000 # Limite de temps elapsed du job
[1154]	8	#-Q- curie #MSUB -q ::default_node::
[1274]	9	#-Q- curie #MSUB -c ::default_core::
[704]	10	#-Q- curie #MSUB -Q normal
[837]	11	#-Q- curie #MSUB -A ::default_project::
[681]	12	#-Q- curie set +x
[1437]	13	#-Q- irene ######################
	14	#-Q- irene ## IRENE TGCC/CEA ##
	15	#-Q- irene ######################
	16	#-Q- irene #MSUB -r SE # Job name
	17	#-Q- irene #MSUB -eo
	18	#-Q- irene #MSUB -n 1
	19	#-Q- irene #MSUB -T 36000 # Maximum elapsed time
	20	#-Q- irene #MSUB -q skylake
	21	#-Q- irene #MSUB -c 4
	22	#-Q- irene #MSUB -Q normal
	23	#-Q- irene #MSUB -A ::default_project::
[1448]	24	#-Q- irene ###MSUB -m store,work,scratch
	25	#-Q- irene #MSUB -E '--licenses=fs_unshare,fs_work,fs_store,fs_scratch'
[1437]	26	#-Q- irene set +x
[770]	27	#-Q- ada #!/bin/ksh
	28	#-Q- ada #######################
[929]	29	#-Q- ada ## ADA IDRIS ##
[770]	30	#-Q- ada #######################
[1409]	31	#-Q- ada # @ job_type = mpich
[848]	32	#-Q- ada # @ requirements = (Feature == "prepost")
[770]	33	#-Q- ada # Temps Elapsed max. d'une requete hh:mm:ss
	34	#-Q- ada # @ wall_clock_limit = 10:00:00
[1336]	35	#-Q- ada # Memory required for ncrcat
	36	#-Q- ada # @ as_limit = 30Gb
[770]	37	#-Q- ada # Nom du travail LoadLeveler
	38	#-Q- ada # @ job_name = SE
[904]	39	#-Q- ada # Fichier de sortie standard du travail
[770]	40	#-Q- ada # @ output = $(job_name).$(jobid)
	41	#-Q- ada # Fichier de sortie d'erreur du travail
	42	#-Q- ada # @ error = $(job_name).$(jobid)
	43	#-Q- ada # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
	44	#-Q- ada # @ notification = error
[1290]	45	#-Q- ada # @ environment = $DEBUG_debug ; $BigBrother ; $postProcessingStopLevel ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $POST_DIR ; $Script_Post_Output ; $MASTER ; $DateBegin ; $PeriodDateEnd ; $StandAlone ; $RESOL_ATM ; $RESOL_OCE ; $RESOL_ICE ; $RESOL_MBG ; $RESOL_SRF ; $RESOL_SBG ; wall_clock_limit=$(wall_clock_limit)
[770]	46	#-Q- ada # @ queue
[281]	47	#-Q- lxiv8 ######################
	48	#-Q- lxiv8 ## OBELIX LSCE ##
	49	#-Q- lxiv8 ######################
	50	#-Q- lxiv8 #PBS -N SE
	51	#-Q- lxiv8 #PBS -m a
	52	#-Q- lxiv8 #PBS -j oe
	53	#-Q- lxiv8 #PBS -q medium
	54	#-Q- lxiv8 #PBS -o SE.$$
	55	#-Q- lxiv8 #PBS -S /bin/ksh
[1184]	56	#-Q- ifort_CICLAD ######################
	57	#-Q- ifort_CICLAD ## CICLAD IPSL ##
	58	#-Q- ifort_CICLAD ######################
	59	#-Q- ifort_CICLAD #PBS -N SE
	60	#-Q- ifort_CICLAD #PBS -m a
	61	#-Q- ifort_CICLAD #PBS -j oe
[1314]	62	#-Q- ifort_CICLAD ###PBS -q h12 # Queue for 12 hours at ciclad only
[1184]	63	#-Q- ifort_CICLAD #PBS -S /bin/ksh
[2]	64	#-Q- default #!/bin/ksh
	65	#-Q- default ##################
	66	#-Q- default ## DEFAULT HOST ##
	67	#-Q- default ##################
	68
[373]	69	#**************************************************************
	70	# Author: Sebastien Denvil
	71	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
	72	# $Revision:: $ Revision of last commit
	73	# $Author:: $ Author of last commit
	74	# $Date:: $ Date of last commit
[108]	75	# IPSL (2006)
	76	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
[373]	77	#
	78	#**************************************************************
[108]	79
	80	#set -eu
[2]	81	#set -vx
	82
	83	date
	84
[770]	85	#-Q- ada export OMP_NUM_THREADS=1
[2]	86
[1356]	87	#D- Task type DO NOT CHANGE (computing, post-processing or checking)
[712]	88	TaskType=post-processing
	89
[2]	90	########################################################################
	91
	92	#D- Flag to determine if this job in a standalone mode
	93	#D- Default : value from AA_job if any
	94	StandAlone=${StandAlone:=true}
	95
[554]	96	#D- Path to libIGCM
[206]	97	#D- Default : value from AA_job if any
[229]	98	libIGCM=${libIGCM:=::modipsl::/libIGCM}
[206]	99
[213]	100	#D- Flag to determine if rebuild process has been performed asynchronously
[904]	101	#D- Possible value true or false.
[213]	102	#D- If true raw files has allready been patched by rebuild job
	103	#D- If false create_ts will patch the raw files
	104	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
	105	RebuildFrequency=${RebuildFrequency:=true}
	106
[2]	107	#D- Flag to determine atlas job's output directory
	108	#D- Default : value from libIGCM_post.ksh if any
[370]	109	POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
[2]	110
	111	#D- Increased verbosity (1, 2, 3)
	112	#D- Default : value from AA_job if any
	113	Verbosity=${Verbosity:=3}
	114
	115	#D- Low level debug : to bypass lib test checks and stack construction
	116	#D- Default : value from AA_job if any
	117	DEBUG_debug=${DEBUG_debug:=false}
	118
	119	#D- TEMPORARY Flag to determine atmospheric resolution
	120	#D- Default : value from atmospheric driver if any
[135]	121	RESOL_ATM=${RESOL_ATM:=ALL}
[2]	122
[257]	123	#D- Flag to determine surface resolution
	124	#D- Default : value from surface driver if any
	125	RESOL_SRF=ALL
	126
	127	#D- Flag to determine surface resolution
	128	#D- Default : value from surface driver if any
	129	RESOL_SBG=ALL
	130
[2]	131	#D- TEMPORARY Flag to determine ocean resolution
	132	#D- Default : value from ocean driver if any
	133	RESOL_OCE=${RESOL_OCE:=ORCA2}
	134
	135	#D- TEMPORARY Flag to determine ice resolution
	136	#D- Default : value from ice driver if any
[1326]	137	RESOL_ICE=${RESOL_OCE:=ORCA2}
[2]	138
[178]	139	#D- TEMPORARY Flag to determine marine biogeochemistry resolution
	140	#D- Default : value from ice driver if any
[1326]	141	RESOL_MBG=${RESOL_OCE:=ORCA2}
[178]	142
[2]	143	########################################################################
	144
[108]	145	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
	146	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
	147	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
	148	#-------
	149	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
[731]	150	. ${libIGCM}/libIGCM_config/libIGCM_config.ksh
[832]	151	#-------
[1192]	152	IGCM_sys_MkdirWork ${RUN_DIR_PATH}
	153	IGCM_sys_Cd ${RUN_DIR_PATH}
	154	#-------
[832]	155	( ${DEBUG_debug} ) && IGCM_debug_Check
	156	( ${DEBUG_debug} ) && IGCM_card_Check
	157	( ${DEBUG_debug} ) && IGCM_date_Check
[2]	158
	159	########################################################################
	160
	161	#set -vx
	162
[436]	163	# ------------------------------------------------------------------
	164	# Test if all was right before proceeding further
	165	# ------------------------------------------------------------------
[1206]	166	IGCM_debug_Verif_Exit
[436]	167
[2]	168	if [ ${StandAlone} = true ] ; then
	169	CARD_DIR=${SUBMIT_DIR}
	170	else
[647]	171	CARD_DIR=${RUN_DIR_PATH}
[640]	172	IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
	173	IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card ${RUN_DIR_PATH}
	174	IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP ${RUN_DIR_PATH}
	175	IGCM_sys_Get_Master ${SUBMIT_DIR}/POST ${RUN_DIR_PATH}
[2]	176	fi
	177
[616]	178	#==================================
[2]	179	# First of all
	180	#
[727]	181	# Read libIGCM compatibility version in config.card
	182	# Read UserChoices section
	183	# Read Ensemble section
	184	# Read Post section
	185	# Define all netcdf output directories
[616]	186	#==================================
[727]	187	IGCM_config_CommonConfiguration ${CARD_DIR}/config.card
[616]	188
[1198]	189	# ------------------------------------------------------------------
	190	# Activate BigBrother so as to supervise this job
	191	# ------------------------------------------------------------------
	192	IGCM_debug_BigBro_Initialize
	193
[616]	194	#==================================
[633]	195	# Define default value to keep compatibility with previous card: means before changes due to TGCC
	196	if [ X${PackDefault} = Xtrue ] ; then
	197	[ X${config_Post_PackFrequency} = X ] && config_Post_PackFrequency=${config_Post_RebuildFrequency}
	198	else
	199	config_Post_PackFrequency=NONE
	200	fi
[616]	201
	202	#==================================
	203	# If pack is active then PackFrequency overule the config_UserChoices_PeriodLength
	204	if ( [ ! X${config_Post_PackFrequency} = X${NULL_STR} ] && [ ! X${config_Post_PackFrequency} = XNONE ] ) ; then
	205	config_UserChoices_PeriodLength=${config_Post_PackFrequency}
	206	fi
	207
	208	#==================================
[727]	209	# Read ListOfComponents section:
[2]	210	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
[727]	211
	212	#==================================
	213	# Read SeasonalFrequency:
[2]	214	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post SeasonalFrequency
[727]	215
[2]	216	#
	217	# Determine period for seasonnal average. Default : value from AA_job if any
	218	#
	219	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
	220	#
	221	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
	222	#
	223	freq=$( echo ${config_Post_SeasonalFrequency} \| sed -e "s/[yY]//" )
	224	#
[149]	225	an_fin=$(( $( IGCM_date_ConvertGregorianDateToJulian ${PeriodDateEnd} ) / 1000 ))
[2]	226	an_deb=$( IGCM_date_YearDigit $(( an_fin - freq + 1 )) )
	227	an_fin=$( IGCM_date_YearDigit ${an_fin} )
	228	#
	229	# For each component selected determine which files need post-processing
	230	#
	231	for comp in ${config_ListOfComponents[*]} ; do
[785]	232	#
	233	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
	234	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	235	#
	236	card=${CARD_DIR}/COMP/${compname}.card
	237	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	238	#
	239	ListFilesName=${compname}_OutputFiles_List
	240	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
	241	#
	242	if [ X${FileName0} != X${NULL_STR} ] ; then
[2]	243	#
[785]	244	# INITIALISATION
[2]	245	#
[785]	246	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
	247	typeset i=2
[2]	248	#
[785]	249	until [ $i -gt $NbFiles ]; do
	250	#
	251	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
	252	#
	253	if [ X${flag_post} != XNONE ] ; then
	254	#
	255	# Check if seasonal is required for this file
	256	#
	257	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
	258	#
	259	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
	260	#
	261	# variable option allready typeset above
	262	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
	263	if [ ${option} = Seasonal ] ; then
	264	FoundSeasonal=true
	265	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
	266	fi
	267	done
	268	#
	269	if [ ! X${FoundSeasonal} = Xtrue ] ; then
	270	eval ${compname}_${flag_post}_Seasonal=ON
	271	fi
	272	#
	273	if [ ! X$( eval echo \${${compname}_${flag_post}_Seasonal} ) = XON ] ; then
	274	(( i=i+3 ))
	275	continue
	276	fi
	277	#
	278	# CREATE LIST
	279	#
	280	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
	281	#
	282	DIRECTORY=${R_SAVE}/${comp}/Analyse/SE
	283	#
	284	TestedFile=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${FILE}.nc
	285	#
	286	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
	287	if [ ! $? = 0 ] ; then
	288	eval set +A LISTE_FILE_${comp} \$\{LISTE_FILE_${comp}[*]} ${FILE}
	289	if [ ! ${RebuildFrequency} = true ] ; then
	290	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
	291	eval set +A LISTE_PATCHES_${FILE} \$\{${compname}_Post_${FILE}_Patches[*]}
	292	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
	293	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
	294	if [ Xload${Patch} != X ] ; then
	295	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
	296	eval load${Patch}=loaded
	297	fi
	298	done
	299	fi
	300	fi
	301	fi
	302	fi
	303	(( i=i+3 ))
	304	done # until [ $i -eq $NbFiles ]
	305	fi
[150]	306	done # for comp
[2]	307
	308	for comp in ${config_ListOfComponents[*]} ; do
[785]	309	#
	310	eval R_OUT_${comp}=${R_SAVE}/${comp}
	311	#
	312	i=0
	313	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
[2]	314	#
[785]	315	# Determine in which output can we find file
	316	# IE : Output/MO or Output/DA or ...
[2]	317	#
[785]	318	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
	319	case ${FlagDir} in
	320	1Y) FreqDir=YE ;;
	321	1M) FreqDir=MO ;;
	322	5D\|1D) FreqDir=DA ;;
	323	HF) FreqDir=HF ;;
	324	3H) FreqDir=HF ;;
	325	INS) FreqDir=INS ;;
	326	esac
	327	#
	328	RESULT_SE=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${file}.nc
	329	# Do not redoo an existing SE
	330	IGCM_sys_TestFileArchive ${R_SAVE}/${comp}/Analyse/SE/${RESULT_SE}
	331	if [ $? = 0 ] ; then
	332	continue
	333	fi
	334	#
	335	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
	336	#
	337	case ${config_UserChoices_PeriodLength} in
	338	# For Yearly simulation :
[904]	339	Y\|y)
	340	PeriodLengthInYears=$( echo ${config_UserChoices_PeriodLength} \| sed -e 's/[yY]//' )
[785]	341	(( an = an_deb ))
	342	# Initialize array
	343	unset liste_file_se
	344	unset liste_file_se_tmp
	345	while [ ${an} -le ${an_fin} ] ; do
	346	#
	347	an4=$(printf "%04i\n" ${an} )
	348	#
[905]	349	diy=$( IGCM_date_DaysInCurrentPeriod ${an4}0101 ${config_UserChoices_PeriodLength} )
	350	afin=$( IGCM_date_AddDaysToGregorianDate ${an4}0101 $(( diy - 1 )) )
[904]	351	#
[785]	352	date=${an4}0101_${afin}
[905]	353	#
[785]	354	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
	355	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
[904]	356	(( an = an + ${PeriodLengthInYears} ))
[785]	357	done
	358	#
	359	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
[1206]	360	IGCM_debug_Verif_Exit
[785]	361
	362	# Apply IGCM_Patch if needed
	363	if [ ! ${RebuildFrequency} = true ] ; then
	364	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
	365	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
	366	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
	367	IGCM_${Patch} ${file_t}
	368	done
	369	done
	370	fi
	371	fi
	372
	373	# Search of common list of variables to be treated
	374	nbfile=0
	375	for file_common_var in ${liste_file_se_tmp[*]} ; do
	376	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
	377	(( nbfile = nbfile + 1 ))
	378	done
	379	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
	380	IGCM_sys_Rm tmpfile_ncra
	381
	382	# detect time counter : time or time_counter ie unlimited variable
[951]	383	var_unlim=$(ncdump -h ${liste_file_se_tmp[0]}\|grep UNLIMITED\|awk '{print $1}')
[785]	384
	385	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
	386	#
	387	(( nb = ${mois} - 1 ))
	388	#
	389	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
	390	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d ${var_unlim},${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
	391	done
	392	IGCM_sys_Rm ${liste_file_se_tmp[*]}
	393	;;
	394	# For Monthly simulation :
	395	1M\|1m)
	396	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
	397	#
	398	(( nb = ${mois} - 1 ))
	399	#
	400	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
	401	#
	402	(( an = an_deb ))
[2]	403	# Initialize array
[785]	404	unset liste_file_se
	405	unset liste_file_se_tmp
	406	while [ ${an} -le ${an_fin} ] ; do
	407	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
	408	#
	409	an4=$(printf "%04i\n" ${an} )
	410	#
	411	date=${an4}${mois}01_${an4}${mois}${moisL}
[905]	412	#
[785]	413	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
	414	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
[2]	415
[785]	416	(( an = an + 1 ))
	417	done
	418	#
	419	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
[1206]	420	IGCM_debug_Verif_Exit
[370]	421
[785]	422	# Apply IGCM_Patch if needed
	423	if [ ! ${RebuildFrequency} = true ] ; then
	424	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
	425	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
	426	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
	427	IGCM_${Patch} ${file_t}
	428	done
	429	done
	430	fi
	431	fi
[66]	432
[785]	433	# Search of common list of variables to be treated
	434	nbfile=0
	435	for file_common_var in ${liste_file_se_tmp[*]} ; do
	436	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
	437	(( nbfile = nbfile + 1 ))
	438	done
	439	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
	440	IGCM_sys_Rm tmpfile_ncra
[370]	441
[785]	442	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
[231]	443
[785]	444	IGCM_sys_Rm ${liste_file_se_tmp[*]}
	445	done
	446	;;
	447	D\|d)
	448	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
	449	#
	450	(( nb = ${mois} - 1 ))
	451	#
	452	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
	453	#
	454	(( an = an_deb ))
	455	# Initialize array
	456	unset liste_file_se
	457	unset liste_file_se_tmp
	458	while [ ${an} -le ${an_fin} ] ; do
	459	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
	460	#
	461	an4=$(printf "%04i\n" ${an} )
	462	#
	463	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
	464	# for one day
	465	if [ ${length_d} -eq 1 ] ; then
	466	(( length_d = 0 ))
	467	fi
	468	(( day = 1 ))
	469	while [ ${day} -le ${moisL} ] ; do
	470	day2=$(printf "%02i\n" ${day} )
	471	day_beg=${an4}${mois}${day2}
	472	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
	473	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
[905]	474	#
[785]	475	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
	476	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
	477	(( day = day + 1 ))
	478	done
	479	(( an = an + 1 ))
	480	done
	481	#
	482	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
[1206]	483	IGCM_debug_Verif_Exit
[2]	484
[785]	485	# Apply IGCM_Patch if needed
	486	if [ ! ${RebuildFrequency} = true ] ; then
	487	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
	488	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
	489	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
	490	IGCM_${Patch} ${file_t}
	491	done
	492	done
	493	fi
	494	fi
[231]	495
[785]	496	# Search of common list of variables to be treated
	497	nbfile=0
	498	for file_common_var in ${liste_file_se_tmp[*]} ; do
	499	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
	500	(( nbfile = nbfile + 1 ))
	501	done
	502	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
	503	IGCM_sys_Rm tmpfile_ncra
[231]	504
[785]	505	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
	506	IGCM_sys_Rm ${liste_file_se_tmp[*]}
[231]	507	done
[785]	508	;;
	509	esac
	510	#
[231]	511
[785]	512	# Search of common list of variables to be treated
	513	nbfile=0
	514	for file_common_var in ${OUT_SE[*]} ; do
	515	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncrcat
	516	(( nbfile = nbfile + 1 ))
	517	done
[1219]	518	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| grep -v ^time_ \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
[785]	519	IGCM_sys_Rm tmpfile_ncrcat
[370]	520
[785]	521	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
	522	#
	523	IGCM_sys_Rm ${OUT_SE[*]}
	524	#
	525	# detect time counter : time or time_counter ie unlimited variable
[1304]	526	var_unlim=$( ncdump -h ${RESULT_SE} \| grep UNLIMITED \| cut -d ' ' -f 1 \| sed -e 's/^[[:space:]]*//' )
[785]	527
[904]	528	# Put correct climatological axis following calendar
[785]	529	case ${config_UserChoices_CalendarType} in
	530	360d\|360_day)
	531	# 360 days
	532	ncap2cmd="'defdim(\"tbnds\",2) ; ${var_unlim}[${var_unlim}]={15, 45, 75, 105, 135, 165, 195, 225, 255, 285, 315, 345.} ; ${var_unlim}_bnds[${var_unlim},tbnds]={0, 30, 30, 60, 60, 90, 90, 120, 120, 150, 150, 180, 180, 210, 210, 240, 240, 270, 270, 300, 300, 330, 330, 360.} ; ${var_unlim}@units=\"days since 0000-01-01 00:00:00\" ; ${var_unlim}@time_origin=\"01-JAN-0000 00:00:00\" ; ${var_unlim}@calendar=\"360_day\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
	533	;;
	534	noleap\|365_day)
	535	# 365 days
	536	ncap2cmd="'defdim(\"tbnds\",2) ; ${var_unlim}[${var_unlim}]={15.5, 45, 74.5, 105, 135.5, 166, 196.5, 227.5, 258, 288.5, 319, 349.5} ; ${var_unlim}_bnds[${var_unlim},tbnds]={0, 31, 31, 59, 59, 90, 90, 120, 120, 151, 151, 181, 181, 212, 212, 243, 243, 273, 273, 304, 304, 334, 334, 365.} ; ${var_unlim}@units=\"days since 0000-01-01 00:00:00\" ; ${var_unlim}@time_origin=\"01-JAN-0000 00:00:00\" ; ${var_unlim}@calendar=\"365_day\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
	537	;;
	538	all_leap\|366_day)
	539	# 366 days
	540	ncap2cmd="'defdim(\"tbnds\",2) ; ${var_unlim}[${var_unlim}]={15.5, 45.5, 75.5, 106, 136.5, 167, 197.5, 228.5, 259, 289.5, 320, 350.5} ; ${var_unlim}_bnds[${var_unlim},tbnds]={0, 31, 31, 60, 60, 91, 91, 121, 121, 152, 152, 182, 182, 213, 213, 244, 244, 274, 274, 305, 305, 335, 335, 366.} ; ${var_unlim}@units=\"days since 0000-01-01 00:00:00\" ; ${var_unlim}@time_origin=\"01-JAN-0000 00:00:00\" ; ${var_unlim}@calendar=\"366_day\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
	541	;;
	542	leap\|gregorian\|standard)
	543	# 365.2425 days
	544	ncap2cmd="'defdim(\"tbnds\",2) ; ${var_unlim}[${var_unlim}]={15.5, 45.12125, 74.7425, 105.2425, 135.7425, 166.2425, 196.7425, 227.7425, 258.2425, 288.7425, 319.2425, 349.7425} ; ${var_unlim}_bnds[${var_unlim},tbnds]={0, 31, 31, 59.2425, 59.2425, 90.2425, 90.2425, 120.2425, 120.2425, 151.2425, 151.2425, 181.2425, 181.2425, 212.2425, 212.2425, 243.2425, 243.2425, 273.2425, 273.2425, 304.2425, 304.2425, 334.2425, 334.2425, 365.2425} ; ${var_unlim}@units=\"days since 0000-01-01 00:00:00\" ; ${var_unlim}@time_origin=\"01-JAN-0000 00:00:00\" ; ${var_unlim}@calendar=\"gregorian\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
	545	;;
	546	esac
	547	eval IGCM_sys_ncap2 -Oh -s $ncap2cmd ${RESULT_SE} tmp.nc
	548	IGCM_sys_Rm ${RESULT_SE}
	549	IGCM_sys_Mv tmp.nc ${RESULT_SE}
	550	#
	551	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
[1040]	552	[ -f ${RESULT_SE} ] && IGCM_sys_Rm ${RESULT_SE}
[785]	553	#
	554	done
[2]	555	done
	556
	557	# DODS copy
[903]	558	if [ X${config_Post_DodsCopy} = XTRUE ] ; then
	559	for comp in ${config_ListOfComponents[*]} ; do
	560	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
	561	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
	562	done
	563	fi
[2]	564
[903]	565	# Temporal coverage id for atlas
[2]	566	YEARS=${an_deb}_${an_fin}
[370]	567	DIR_OUT=SE
[2]	568
[1112]	569	export DEBUG_debug; export BigBrother ; export libIGCM; export SUBMIT_DIR; export POST_DIR; export Script_Output ;
	570	export StandAlone ; export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ;
	571	export RESOL_SBG ; export YEARS; export DIR_OUT
	572	listVarEnv="DEBUG_debug,BigBrother,libIGCM,SUBMIT_DIR,POST_DIR,Script_Post_Output,StandAlone,RESOL_ATM,RESOL_OCE,RESOL_ICE,RESOL_MBG,RESOL_SRF,RESOL_SBG,YEARS,DIR_OUT"
[2]	573	export listVarEnv;
	574
	575	#D-
	576	# --------------------------------------------------------------------
	577	#D- Test if all was right before ATLAS
	578	# --------------------------------------------------------------------
[1206]	579	IGCM_debug_Verif_Exit
[2]	580
	581	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
[15]	582	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
[2]	583	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
[1366]	584	# ATLAS
	585	if [ X${config_Post_AtlasIPSL} = XTRUE ] ; then
	586	export Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
	587	IGCM_sys_QsubPost atlas_ORCHIDEE ;
	588	export Script_Post_Output=atlas_LMDZ.${PeriodDateEnd} ;
	589	IGCM_sys_QsubPost atlas_LMDZ ;
	590	export Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
	591	IGCM_sys_QsubPost atlas_ORCA_LIM ;
	592	export Script_Post_Output=additionnal.${PeriodDateEnd} ;
	593	IGCM_sys_QsubPost additionnal ;
	594	fi
[785]	595	#
[1112]	596	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
	597	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] \|\| \
	598	[ ${config_UserChoices_TagName} = "IPSLCM5B" ] \|\| \
	599	[ ${config_UserChoices_TagName} = "IPSLCM5A-MR" ] \|\| \
[1377]	600	[ ${config_UserChoices_TagName} = "IPSLCM5A2" ] \|\| \
[957]	601	[ ${config_UserChoices_TagName} = "IPSLCM6" ] ; then
[1225]	602	# METRICS
[1335]	603	if [ X${config_Post_MetricsPCMDI} = XTRUE ] ; then
	604	export Script_Post_Output=metrics_LMDZ.${PeriodDateEnd} ;
	605	IGCM_sys_QsubPost metrics_LMDZ ;
	606	export Script_Post_Output=metrics_NEMO.${PeriodDateEnd} ;
	607	IGCM_sys_QsubPost metrics_NEMO ;
	608	fi
[1225]	609	# ATLAS
[1366]	610	if [ X${config_Post_AtlasIPSL} = XTRUE ] ; then
	611	export Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
	612	IGCM_sys_QsubPost atlas_ORCHIDEE ;
	613	export Script_Post_Output=atlas_LMDZ.${PeriodDateEnd} ;
	614	IGCM_sys_QsubPost atlas_LMDZ ;
	615	export Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
	616	IGCM_sys_QsubPost atlas_ORCA_LIM ;
	617	export Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
	618	IGCM_sys_QsubPost atlas_PISCES ;
	619	fi
[1112]	620	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
	621	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
[25]	622	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
[1225]	623	# METRICS
[1335]	624	if [ X${config_Post_MetricsPCMDI} = XTRUE ] ; then
	625	export Script_Post_Output=metrics_LMDZ.${PeriodDateEnd} ;
	626	IGCM_sys_QsubPost metrics_LMDZ ;
	627	fi
[1225]	628	# ATLAS
[1366]	629	if [ X${config_Post_AtlasIPSL} = XTRUE ] ; then
	630	export Script_Post_Output=atlas_LMDZ.${PeriodDateEnd} ;
	631	IGCM_sys_QsubPost atlas_LMDZ ;
	632	export Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
	633	IGCM_sys_QsubPost atlas_ORCHIDEE ;
	634	fi
[45]	635	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
[1225]	636	# METRICS
[1335]	637	if [ X${config_Post_MetricsPCMDI} = XTRUE ] ; then
	638	export Script_Post_Output=metrics_LMDZ.${PeriodDateEnd} ;
	639	IGCM_sys_QsubPost metrics_LMDZ ;
	640	fi
[1225]	641	# ATLAS
[1366]	642	if [ X${config_Post_AtlasIPSL} = XTRUE ] ; then
	643	export Script_Post_Output=atlas_LMDZ.${PeriodDateEnd} ;
	644	IGCM_sys_QsubPost atlas_LMDZ ;
	645	fi
[1112]	646	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
[2]	647	[ ${config_UserChoices_TagName} = "OL2" ] ; then
[1225]	648	# METRICS
	649	# ATLAS
[1366]	650	if [ X${config_Post_AtlasIPSL} = XTRUE ] ; then
	651	export Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
	652	IGCM_sys_QsubPost atlas_ORCHIDEE ;
	653	fi
[1112]	654	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\| \
	655	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] \|\| \
[1309]	656	[ ${config_UserChoices_TagName} = "ORCA2_LIM3" ] \|\| \
	657	[ ${config_UserChoices_TagName} = "ORCA1_LIM2" ] \|\| \
	658	[ ${config_UserChoices_TagName} = "ORCA1_LIM3" ] ; then
[1225]	659	# METRICS
[1335]	660	if [ X${config_Post_MetricsPCMDI} = XTRUE ] ; then
	661	export Script_Post_Output=metrics_NEMO.${PeriodDateEnd} ;
	662	IGCM_sys_QsubPost metrics_NEMO ;
	663	fi
[1225]	664	# ATLAS
[1366]	665	if [ X${config_Post_AtlasIPSL} = XTRUE ] ; then
	666	export Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
	667	IGCM_sys_QsubPost atlas_ORCA_LIM ;
	668	fi
[957]	669	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] \|\| \
[1309]	670	[ ${config_UserChoices_TagName} = "ORCA2_LIM3_PISCES" ] \|\| \
	671	[ ${config_UserChoices_TagName} = "ORCA1_LIM2_PISCES" ] \|\| \
	672	[ ${config_UserChoices_TagName} = "ORCA1_LIM3_PISCES" ] ; then
[1225]	673	# METRICS
[1335]	674	if [ X${config_Post_MetricsPCMDI} = XTRUE ] ; then
	675	export Script_Post_Output=metrics_NEMO.${PeriodDateEnd} ;
	676	IGCM_sys_QsubPost metrics_NEMO ;
	677	fi
[1225]	678	# ATLAS
[1366]	679	if [ X${config_Post_AtlasIPSL} = XTRUE ] ; then
	680	export Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
	681	IGCM_sys_QsubPost atlas_ORCA_LIM ;
	682	export Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
	683	IGCM_sys_QsubPost atlas_PISCES ;
	684	fi
[1112]	685	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
[1225]	686	# METRICS
	687	# ATLAS
[1366]	688	if [ X${config_Post_AtlasIPSL} = XTRUE ] ; then
[1112]	689	export Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
	690	IGCM_sys_QsubPost atlas_PISCES ;
[1366]	691	fi
[2]	692	fi
[203]	693
[590]	694	# Clean RUN_DIR_PATH (necessary for cesium and titane only)
[203]	695	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
[1198]	696
	697	# ------------------------------------------------------------------
	698	# Finalize BigBrother to inform that the jobs end
	699	# ------------------------------------------------------------------
	700	IGCM_debug_BigBro_Finalize

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