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source: trunk/libIGCM/AA_create_se @ 380

Last change on this file since 380 was 379, checked in by brocksce, 14 years ago
Correction on calendar can now be applied for any var_unlim
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`
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1	#-Q- cesium #!/bin/ksh
2	#-Q- cesium ######################
3	#-Q- cesium ## CESIUM CEA ##
4	#-Q- cesium ######################
5	#-Q- cesium #MSUB -r SE # Nom du job
6	#-Q- cesium #MSUB -N 1 # Reservation du noeud
7	#-Q- cesium #MSUB -n 1 # Reservation du processus
8	#-Q- cesium #MSUB -T 86400 # Limite de temps elapsed du job
9	#-Q- cesium #MSUB -E "-j o"
10	#-Q- cesium #MSUB -E "-S /bin/ksh"
11	#-Q- platine #!/usr/bin/ksh
12	#-Q- platine ###################
13	#-Q- platine ## PLATINE CEA ##
14	#-Q- platine ###################
15	#-Q- platine #BSUB -J SE # Nom du job
16	#-Q- platine #BSUB -N # message a la fin du job
17	#-Q- platine #BSUB -n 1 # reservation des processeurs pour le job
18	#-Q- platine #BSUB -W 1:00 # Limite temps
19	#-Q- platine #BSUB -q post # Passage en queue post
20	#-Q- sx8brodie #!/bin/ksh
21	#-Q- sx8brodie #######################
22	#-Q- sx8brodie ## SX8BRODIE IDRIS ##
23	#-Q- sx8brodie #######################
24	#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
25	#-Q- sx8brodie # @ wall_clock_limit = 20:00:00
26	#-Q- sx8brodie # Nom du travail LoadLeveler
27	#-Q- sx8brodie # @ job_name = SE
28	#-Q- sx8brodie # Fichier de sortie standard du travail
29	#-Q- sx8brodie # @ output = $(job_name).$(jobid)
30	#-Q- sx8brodie # Fichier de sortie d'erreur du travail
31	#-Q- sx8brodie # @ error = $(job_name).$(jobid)
32	#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
33	#-Q- sx8brodie # @ notification = error
34	#-Q- sx8brodie # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $REBUILD_DIR ; $RebuildFromArchive ; $POST_DIR ; $MASTER ; $DateBegin ; $PeriodDateBegin ; $PeriodDateEnd ; $NbRebuildDir ; $StandAlone ; $RESOL_ATM ; $RESOL_OCE ; $RESOL_ICE ; $RESOL_MBG ; $RESOL_SRF ; $RESOL_SBG ; $MASTER
35	#-Q- sx8brodie # @ queue
36	#-Q- aix6 #!/bin/ksh
37	#-Q- aix6 #######################
38	#-Q- aix6 ## VARGAS IDRIS ##
39	#-Q- aix6 #######################
40	#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
41	#-Q- aix6 # @ wall_clock_limit = 20:00:00
42	#-Q- aix6 # Nom du travail LoadLeveler
43	#-Q- aix6 # @ job_name = SE
44	#-Q- aix6 # Fichier de sortie standard du travail
45	#-Q- aix6 # @ output = $(job_name).$(jobid)
46	#-Q- aix6 # Fichier de sortie d'erreur du travail
47	#-Q- aix6 # @ error = $(job_name).$(jobid)
48	#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
49	#-Q- aix6 # @ notification = error
50	#-Q- aix6 # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $REBUILD_DIR ; $RebuildFromArchive ; $POST_DIR ; $MASTER ; $DateBegin ; $PeriodDateBegin ; $PeriodDateEnd ; $NbRebuildDir ; $StandAlone ; $RESOL_ATM ; $RESOL_OCE ; $RESOL_ICE ; $RESOL_MBG ; $RESOL_SRF ; $RESOL_SBG ; $MASTER
51	#-Q- aix6 # @ queue
52	#-Q- sx8mercure #!/bin/ksh
53	#-Q- sx8mercure ######################
54	#-Q- sx8mercure ## SX8MERCURE CEA ##
55	#-Q- sx8mercure ######################
56	#-Q- sx8mercure #PBS -N SE # Nom du job
57	#-Q- sx8mercure #PBS -j o # regroupement des stdout et stderr
58	#-Q- sx8mercure #PBS -S /usr/bin/ksh # shell de soumission
59	#-Q- sx8mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go
60	#-Q- sx8mercure #PBS -l cputim_job=1:00:00 # Limite temps a 1 heures
61	#-Q- sx8mercure #PBS -q scalaire
62	#-Q- sx9mercure #!/bin/ksh
63	#-Q- sx9mercure #########################
64	#-Q- sx9mercure ## CESIUM FOR SX9 CEA ##
65	#-Q- sx9mercure #########################
66	#-Q- sx9mercure #MSUB -r SE # Nom du job
67	#-Q- sx9mercure #MSUB -N 1 # Reservation du noeud
68	#-Q- sx9mercure #MSUB -n 1 # Reservation du processus
69	#-Q- sx9mercure #MSUB -T 86400 # Limite de temps elapsed du job
70	#-Q- sx9mercure #MSUB -E "-j o"
71	#-Q- sx9mercure #MSUB -E "-S /bin/ksh"
72	#-Q- titane #!/bin/ksh
73	#-Q- titane ######################
74	#-Q- titane ## TITANE CEA ##
75	#-Q- titane ######################
76	#-Q- titane #MSUB -r SE # Nom du job
77	#-Q- titane #MSUB -N 1 # Reservation du noeud
78	#-Q- titane #MSUB -n 1 # Reservation du processus
79	#-Q- titane #MSUB -T 86400 # Limite de temps elapsed du job
80	#-Q- titane #MSUB -E "-j o"
81	#-Q- titane #MSUB -E "-S /bin/ksh"
82	#-Q- titane ##MSUB -e nco.out # Sortie standard
83	#-Q- titane ##MSUB -o nco.out # Sortie standard
84	#-Q- lxiv8 ######################
85	#-Q- lxiv8 ## OBELIX LSCE ##
86	#-Q- lxiv8 ######################
87	#-Q- lxiv8 #PBS -N SE
88	#-Q- lxiv8 #PBS -m a
89	#-Q- lxiv8 #PBS -j oe
90	#-Q- lxiv8 #PBS -q medium
91	#-Q- lxiv8 #PBS -o SE.$$
92	#-Q- lxiv8 #PBS -S /bin/ksh
93	#-Q- default #!/bin/ksh
94	#-Q- default ##################
95	#-Q- default ## DEFAULT HOST ##
96	#-Q- default ##################
97
98	#**************************************************************
99	# Author: Sebastien Denvil
100	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
101	# $Revision:: $ Revision of last commit
102	# $Author:: $ Author of last commit
103	# $Date:: $ Date of last commit
104	# IPSL (2006)
105	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
106	#
107	#**************************************************************
108
109	#set -eu
110	#set -vx
111
112	date
113
114	#-Q- sx8brodie export OMP_NUM_THREADS=1
115	#-Q- aix6 export OMP_NUM_THREADS=1
116
117	########################################################################
118
119	#D- Flag to determine if this job in a standalone mode
120	#D- Default : value from AA_job if any
121	StandAlone=${StandAlone:=true}
122
123	#D- Low level debug : to bypass lib test checks and stack construction
124	#D- Default : value from AA_job if any
125	libIGCM=${libIGCM:=::modipsl::/libIGCM}
126	# WARNING for StandAlone used : To run this script on some machine,
127	# you must check MirrorlibIGCM variable in sys library.
128	# If this variable is true, you must use libIGCM_POST path instead
129	# of your running libIGCM directory.
130
131	#D- Flag to determine if rebuild process has been performed asynchronously
132	#D- Possible value true or false.
133	#D- If true raw files has allready been patched by rebuild job
134	#D- If false create_ts will patch the raw files
135	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
136	RebuildFrequency=${RebuildFrequency:=true}
137
138	#D- Flag to determine atlas job's output directory
139	#D- Default : value from libIGCM_post.ksh if any
140	POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
141
142	#D- Increased verbosity (1, 2, 3)
143	#D- Default : value from AA_job if any
144	Verbosity=${Verbosity:=3}
145
146	#D- Low level debug : to bypass lib test checks and stack construction
147	#D- Default : value from AA_job if any
148	DEBUG_debug=${DEBUG_debug:=false}
149
150	#D- TEMPORARY Flag to determine atmospheric resolution
151	#D- Default : value from atmospheric driver if any
152	RESOL_ATM=${RESOL_ATM:=ALL}
153
154	#D- Flag to determine surface resolution
155	#D- Default : value from surface driver if any
156	RESOL_SRF=ALL
157
158	#D- Flag to determine surface resolution
159	#D- Default : value from surface driver if any
160	RESOL_SBG=ALL
161
162	#D- TEMPORARY Flag to determine ocean resolution
163	#D- Default : value from ocean driver if any
164	RESOL_OCE=${RESOL_OCE:=ORCA2}
165
166	#D- TEMPORARY Flag to determine ice resolution
167	#D- Default : value from ice driver if any
168	RESOL_ICE=${RESOL_ICE:=ORCA2}
169
170	#D- TEMPORARY Flag to determine marine biogeochemistry resolution
171	#D- Default : value from ice driver if any
172	RESOL_MBG=${RESOL_MBG:=ORCA2}
173
174	########################################################################
175
176	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
177	( ${DEBUG_debug} ) && IGCM_debug_Check
178	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
179	( ${DEBUG_debug} ) && IGCM_card_Check
180	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
181	( ${DEBUG_debug} ) && IGCM_date_Check
182	#-------
183	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
184
185	########################################################################
186
187	#set -vx
188
189	IGCM_sys_MkdirWork ${RUN_DIR_PATH}
190	IGCM_sys_Cd ${RUN_DIR_PATH}
191
192	if [ ${StandAlone} = true ] ; then
193	CARD_DIR=${SUBMIT_DIR}
194	else
195	CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
196	IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH}
197	fi
198
199	#
200	# First of all
201	#
202	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card UserChoices
203	typeset option
204	for option in ${config_UserChoices[*]} ; do
205	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
206	done
207	#
208	echo
209	IGCM_debug_Print 1 "DefineArrayFromOption : config_UserChoices"
210	IGCM_debug_PrintVariables 3 config_UserChoices_JobName
211	IGCM_debug_PrintVariables 3 config_UserChoices_LongName
212	IGCM_debug_PrintVariables 3 config_UserChoices_TagName
213	IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
214	IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
215	IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
216	IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
217	IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
218	IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
219	echo
220
221	#==================================
222	#R_SAVE : Job output directory
223	if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
224	FreeName=$( echo ${config_UserChoices_JobName} \| sed 's/.*_//' )
225	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
226	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
227	else
228	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
229	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_JobName}
230	fi
231	#
232	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
233	#
234	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post SeasonalFrequency
235	#
236	# Determine period for seasonnal average. Default : value from AA_job if any
237	#
238	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
239	#
240	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
241	#
242	freq=$( echo ${config_Post_SeasonalFrequency} \| sed -e "s/[yY]//" )
243	#
244	an_fin=$(( $( IGCM_date_ConvertGregorianDateToJulian ${PeriodDateEnd} ) / 1000 ))
245	an_deb=$( IGCM_date_YearDigit $(( an_fin - freq + 1 )) )
246	an_fin=$( IGCM_date_YearDigit ${an_fin} )
247	#
248	# For each component selected determine which files need post-processing
249	#
250	for comp in ${config_ListOfComponents[*]} ; do
251	#
252	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
253	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
254	#
255	card=${CARD_DIR}/COMP/${compname}.card
256	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
257	#
258	ListFilesName=${compname}_OutputFiles_List
259	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
260	#
261	if [ X${FileName0} != X${NULL_STR} ] ; then
262	#
263	# INITIALISATION
264	#
265	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
266	typeset i=2
267	#
268	until [ $i -gt $NbFiles ]; do
269	#
270	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
271	#
272	if [ X${flag_post} != XNONE ] ; then
273	#
274	# Check if seasonal is required for this file
275	#
276	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
277	#
278	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
279	#
280	# variable option allready typeset above
281	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
282	if [ ${option} = Seasonal ] ; then
283	FoundSeasonal=true
284	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
285	fi
286	done
287	#
288	if [ ! X${FoundSeasonal} = Xtrue ] ; then
289	eval ${compname}_${flag_post}_Seasonal=ON
290	fi
291	#
292	if [ ! X$( eval echo \${${compname}_${flag_post}_Seasonal} ) = XON ] ; then
293	(( i=i+3 ))
294	continue
295	fi
296	#
297	# CREATE LIST
298	#
299	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
300	#
301	DIRECTORY=${R_SAVE}/${comp}/Analyse/SE
302	#
303	TestedFile=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${FILE}.nc
304	#
305	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
306	if [ ! $? = 0 ] ; then
307	eval set +A LISTE_FILE_${comp} \$\{LISTE_FILE_${comp}[*]} ${FILE}
308	if [ ! ${RebuildFrequency} = true ] ; then
309	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
310	eval set +A LISTE_PATCHES_${FILE} \$\{${compname}_Post_${FILE}_Patches[*]}
311	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
312	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
313	if [ Xload${Patch} != X ] ; then
314	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
315	eval load${Patch}=loaded
316	fi
317	done
318	fi
319	fi
320	fi
321	fi
322	(( i=i+3 ))
323	done # until [ $i -eq $NbFiles ]
324	fi
325	done # for comp
326
327	for comp in ${config_ListOfComponents[*]} ; do
328	#
329	eval R_OUT_${comp}=${R_SAVE}/${comp}
330	#
331	i=0
332	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
333	#
334	# Determine in which output can we find file
335	# IE : Output/MO or Output/DA or ...
336	#
337	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
338	case ${FlagDir} in
339	1Y) FreqDir=YE ;;
340	1M) FreqDir=MO ;;
341	5D\|1D) FreqDir=DA ;;
342	HF) FreqDir=HF ;;
343	3H) FreqDir=HF ;;
344	INS) FreqDir=INS ;;
345	esac
346	#
347	RESULT_SE=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${file}.nc
348	# Do not redoo an existing SE
349	IGCM_sys_TestFileArchive ${R_SAVE}/${comp}/Analyse/SE/${RESULT_SE}
350	if [ $? = 0 ] ; then
351	continue
352	fi
353	#
354	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
355	#
356	case ${config_UserChoices_PeriodLength} in
357	# For Yearly simulation :
358	1Y\|1y)
359	(( an = an_deb ))
360	# Initialize array
361	#set -A liste_file_se
362	#set -A liste_file_se_tmp
363	unset liste_file_se
364	unset liste_file_se_tmp
365	while [ ${an} -le ${an_fin} ] ; do
366	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
367	#
368	an4=$(printf "%04i\n" ${an} )
369	#
370	diy=$( IGCM_date_DaysInYear $an4 )
371	afin=$( IGCM_date_AddDaysToGregorianDate ${an4}0101 $(( diy - 1 )) )
372	date=${an4}0101_${afin}
373	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
374	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
375	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
376	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
377	(( an = an + 1 ))
378	done
379	#
380	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
381	eval ExitFlag=false
382	IGCM_debug_Verif_Exit_Post
383
384	# Apply IGCM_Patch if needed
385	if [ ! ${RebuildFrequency} = true ] ; then
386	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
387	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
388	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
389	IGCM_${Patch} ${file_t}
390	done
391	done
392	fi
393	fi
394
395	# Search of common list of variables to be treated
396	nbfile=0
397	for file_common_var in ${liste_file_se_tmp[*]} ; do
398	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
399	(( nbfile = nbfile + 1 ))
400	done
401	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
402	IGCM_sys_Rm tmpfile_ncra
403
404	# detect time counter : time or time_counter ie unlimited variable
405	var_unlim=$(ncdump -h ${liste_file_se_tmp[1]}\|grep UNLIMITED\| cut -d ' ' -f 1)
406
407	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
408	#
409	(( nb = ${mois} - 1 ))
410	#
411	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
412	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d ${var_unlim},${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
413	done
414	IGCM_sys_Rm ${liste_file_se_tmp[*]}
415	eval ExitFlag=false
416	IGCM_debug_Verif_Exit_Post
417	;;
418	# For Monthly simulation :
419	1M\|1m)
420	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
421	#
422	(( nb = ${mois} - 1 ))
423	#
424	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
425	#
426	(( an = an_deb ))
427	# Initialize array
428	#set -A liste_file_se
429	#set -A liste_file_se_tmp
430	unset liste_file_se
431	unset liste_file_se_tmp
432	while [ ${an} -le ${an_fin} ] ; do
433	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
434	#
435	an4=$(printf "%04i\n" ${an} )
436	#
437	date=${an4}${mois}01_${an4}${mois}${moisL}
438	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
439	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
440	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
441	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
442
443	(( an = an + 1 ))
444	done
445	#
446	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
447	eval ExitFlag=false
448	IGCM_debug_Verif_Exit_Post
449
450	# Apply IGCM_Patch if needed
451	if [ ! ${RebuildFrequency} = true ] ; then
452	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
453	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
454	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
455	IGCM_${Patch} ${file_t}
456	done
457	done
458	fi
459	fi
460
461	# Search of common list of variables to be treated
462	nbfile=0
463	for file_common_var in ${liste_file_se_tmp[*]} ; do
464	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
465	(( nbfile = nbfile + 1 ))
466	done
467	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
468	IGCM_sys_Rm tmpfile_ncra
469
470	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
471
472	IGCM_sys_Rm ${liste_file_se_tmp[*]}
473	eval ExitFlag=false
474	IGCM_debug_Verif_Exit_Post
475	done
476	;;
477	D\|d)
478	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
479	#
480	(( nb = ${mois} - 1 ))
481	#
482	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
483	#
484	(( an = an_deb ))
485	# Initialize array
486	#set -A liste_file_se
487	#set -A liste_file_se_tmp
488	unset liste_file_se
489	unset liste_file_se_tmp
490	while [ ${an} -le ${an_fin} ] ; do
491	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
492	#
493	an4=$(printf "%04i\n" ${an} )
494	#
495	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
496	# for one day
497	if [ ${length_d} -eq 1 ] ; then
498	(( length_d = 0 ))
499	fi
500	(( day = 1 ))
501	while [ ${day} -le ${moisL} ] ; do
502	day2=$(printf "%02i\n" ${day} )
503	day_beg=${an4}${mois}${day2}
504	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
505	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
506	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
507	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
508	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
509	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
510	(( day = day + 1 ))
511	done
512	(( an = an + 1 ))
513	done
514	#
515	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
516	eval ExitFlag=false
517	IGCM_debug_Verif_Exit_Post
518
519	# Apply IGCM_Patch if needed
520	if [ ! ${RebuildFrequency} = true ] ; then
521	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
522	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
523	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
524	IGCM_${Patch} ${file_t}
525	done
526	done
527	fi
528	fi
529
530	# Search of common list of variables to be treated
531	nbfile=0
532	for file_common_var in ${liste_file_se_tmp[*]} ; do
533	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
534	(( nbfile = nbfile + 1 ))
535	done
536	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
537	IGCM_sys_Rm tmpfile_ncra
538
539	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
540	IGCM_sys_Rm ${liste_file_se_tmp[*]}
541	eval ExitFlag=false
542	IGCM_debug_Verif_Exit_Post
543	done
544	;;
545	esac
546	#
547
548	# Search of common list of variables to be treated
549	nbfile=0
550	for file_common_var in ${OUT_SE[*]} ; do
551	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncrcat
552	(( nbfile = nbfile + 1 ))
553	done
554	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
555	IGCM_sys_Rm tmpfile_ncrcat
556
557	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
558	#
559	IGCM_sys_Rm ${OUT_SE[*]}
560	#
561	# detect time counter : time or time_counter ie unlimited variable
562	var_unlim=$(ncdump -h ${RESULT_SE}\|grep UNLIMITED\| cut -d ' ' -f 1)
563
564	# Put correct climatological axis following calendar
565	case ${config_UserChoices_CalendarType} in
566	360d)
567	# 360 days
568	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\"'"
569	;;
570	noleap)
571	# 365 days
572	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=\"noleap\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
573	;;
574	all_leap)
575	# 366 days
576	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=\"all_leap\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
577	;;
578	leap\|gregorian)
579	# 365.2425 days
580	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\"'"
581	;;
582	esac
583	eval IGCM_sys_ncap2 -Oh -s $ncap2cmd ${RESULT_MULTI_SE} tmp.nc
584	IGCM_sys_Rm ${RESULT_SE}
585	IGCM_sys_Mv tmp.nc ${RESULT_SE}
586	#
587	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
588	IGCM_sys_Rm ${RESULT_SE}
589	#
590	eval ExitFlag=false
591	IGCM_debug_Verif_Exit_Post
592	done
593	done
594
595	# DODS copy
596	for comp in ${config_ListOfComponents[*]} ; do
597	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
598	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
599	done
600
601	YEARS=${an_deb}_${an_fin}
602	DIR_OUT=SE
603
604	export POST_DIR; export SUBMIT_DIR; export libIGCM; export R_INIT; export R_BC; export StandAlone
605	export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ; export RESOL_SBG
606	export R_SAVE; export config_UserChoices_JobName; export config_UserChoices_TagName; export YEARS; export DIR_OUT
607	listVarEnv="POST_DIR,SUBMIT_DIR,libIGCM,R_INIT,R_BC,StandAlone,RESOL_ATM,RESOL_OCE,RESOL_ICE,RESOL_MBG,RESOL_SRF,RESOL_SBG,R_SAVE,config_UserChoices_JobName,config_UserChoices_TagName,YEARS,DIR_OUT"
608	export listVarEnv;
609
610	#D-
611	# --------------------------------------------------------------------
612	#D- Test if all was right before ATLAS
613	# --------------------------------------------------------------------
614	IGCM_debug_Verif_Exit_Post
615
616	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
617	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
618	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
619	#
620	IGCM_sys_QsubPost atlas_ORCHIDEE ;
621	IGCM_sys_QsubPost atlas_LMDZ ;
622	IGCM_sys_QsubPost atlas_ORCA_LIM ;
623	IGCM_sys_QsubPost additionnal ;
624	#
625	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
626	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] \|\| \
627	[ ${config_UserChoices_TagName} = "IPSLCM5A-MR" ] ; then
628	IGCM_sys_QsubPost atlas_ORCHIDEE ;
629	IGCM_sys_QsubPost atlas_LMDZ ;
630	IGCM_sys_QsubPost atlas_ORCA_LIM ;
631	IGCM_sys_QsubPost atlas_PISCES ;
632	#
633	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
634	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
635	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
636	#
637	IGCM_sys_QsubPost atlas_LMDZ ;
638	IGCM_sys_QsubPost atlas_ORCHIDEE ;
639	#
640	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
641	#
642	IGCM_sys_QsubPost atlas_LMDZ ;
643	#
644	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
645	[ ${config_UserChoices_TagName} = "OL2" ] ; then
646	#
647	IGCM_sys_QsubPost atlas_ORCHIDEE ;
648	#
649	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\|
650	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] ; then
651	#
652	IGCM_sys_QsubPost atlas_ORCA_LIM ;
653	# IGCM_sys_QsubPost additionnal ;
654	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] ; then
655	#
656	IGCM_sys_QsubPost atlas_ORCA_LIM ;
657	IGCM_sys_QsubPost atlas_PISCES ;
658	# IGCM_sys_QsubPost additionnal ;
659	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
660	#
661	IGCM_sys_QsubPost atlas_PISCES ;
662	#
663	fi
664
665	# Clean RUN_DIR_PATH (necessary for cesium)
666	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}

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