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source: trunk/libIGCM/AA_create_se @ 370

Last change on this file since 370 was 370, checked in by mafoipsl, 14 years ago
Add AA_create_multi_se script to build SE_nnnY based on previous SE. Use optionnal MultiSeasonalFrequency?[=50 by default] parameter in config.card Post Section. Use climatological time axis for SE and SE_nnnY files. Add DIR_OUT to allow atlas to work with SE_nnnY. Add POST_DIR default value for interactive session.
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 `Date Author Revision`
File size: 23.9 KB

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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	# $Date$
99	# $Author$
100	# $Revision$
101	# IPSL (2006)
102	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
103
104	#set -eu
105	#set -vx
106
107	date
108
109	#-Q- sx8brodie export OMP_NUM_THREADS=1
110	#-Q- aix6 export OMP_NUM_THREADS=1
111
112	########################################################################
113
114	#D- Flag to determine if this job in a standalone mode
115	#D- Default : value from AA_job if any
116	StandAlone=${StandAlone:=true}
117
118	#D- Low level debug : to bypass lib test checks and stack construction
119	#D- Default : value from AA_job if any
120	libIGCM=${libIGCM:=::modipsl::/libIGCM}
121	# WARNING for StandAlone used : To run this script on some machine,
122	# you must check MirrorlibIGCM variable in sys library.
123	# If this variable is true, you must use libIGCM_POST path instead
124	# of your running libIGCM directory.
125
126	#D- Flag to determine if rebuild process has been performed asynchronously
127	#D- Possible value true or false.
128	#D- If true raw files has allready been patched by rebuild job
129	#D- If false create_ts will patch the raw files
130	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
131	RebuildFrequency=${RebuildFrequency:=true}
132
133	#D- Flag to determine atlas job's output directory
134	#D- Default : value from libIGCM_post.ksh if any
135	POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
136
137	#D- Increased verbosity (1, 2, 3)
138	#D- Default : value from AA_job if any
139	Verbosity=${Verbosity:=3}
140
141	#D- Low level debug : to bypass lib test checks and stack construction
142	#D- Default : value from AA_job if any
143	DEBUG_debug=${DEBUG_debug:=false}
144
145	#D- TEMPORARY Flag to determine atmospheric resolution
146	#D- Default : value from atmospheric driver if any
147	RESOL_ATM=${RESOL_ATM:=ALL}
148
149	#D- Flag to determine surface resolution
150	#D- Default : value from surface driver if any
151	RESOL_SRF=ALL
152
153	#D- Flag to determine surface resolution
154	#D- Default : value from surface driver if any
155	RESOL_SBG=ALL
156
157	#D- TEMPORARY Flag to determine ocean resolution
158	#D- Default : value from ocean driver if any
159	RESOL_OCE=${RESOL_OCE:=ORCA2}
160
161	#D- TEMPORARY Flag to determine ice resolution
162	#D- Default : value from ice driver if any
163	RESOL_ICE=${RESOL_ICE:=ORCA2}
164
165	#D- TEMPORARY Flag to determine marine biogeochemistry resolution
166	#D- Default : value from ice driver if any
167	RESOL_MBG=${RESOL_MBG:=ORCA2}
168
169	########################################################################
170
171	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
172	( ${DEBUG_debug} ) && IGCM_debug_Check
173	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
174	( ${DEBUG_debug} ) && IGCM_card_Check
175	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
176	( ${DEBUG_debug} ) && IGCM_date_Check
177	#-------
178	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
179
180	########################################################################
181
182	#set -vx
183
184	IGCM_sys_MkdirWork ${RUN_DIR_PATH}
185	IGCM_sys_Cd ${RUN_DIR_PATH}
186
187	if [ ${StandAlone} = true ] ; then
188	CARD_DIR=${SUBMIT_DIR}
189	else
190	CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
191	IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH}
192	fi
193
194	#
195	# First of all
196	#
197	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card UserChoices
198	typeset option
199	for option in ${config_UserChoices[*]} ; do
200	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
201	done
202	#
203	echo
204	IGCM_debug_Print 1 "DefineArrayFromOption : config_UserChoices"
205	IGCM_debug_PrintVariables 3 config_UserChoices_JobName
206	IGCM_debug_PrintVariables 3 config_UserChoices_LongName
207	IGCM_debug_PrintVariables 3 config_UserChoices_TagName
208	IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
209	IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
210	IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
211	IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
212	IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
213	IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
214	echo
215
216	#==================================
217	#R_SAVE : Job output directory
218	if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
219	FreeName=$( echo ${config_UserChoices_JobName} \| sed 's/.*_//' )
220	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
221	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
222	else
223	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
224	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_JobName}
225	fi
226	#
227	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
228	#
229	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post SeasonalFrequency
230	#
231	# Determine period for seasonnal average. Default : value from AA_job if any
232	#
233	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
234	#
235	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
236	#
237	freq=$( echo ${config_Post_SeasonalFrequency} \| sed -e "s/[yY]//" )
238	#
239	an_fin=$(( $( IGCM_date_ConvertGregorianDateToJulian ${PeriodDateEnd} ) / 1000 ))
240	an_deb=$( IGCM_date_YearDigit $(( an_fin - freq + 1 )) )
241	an_fin=$( IGCM_date_YearDigit ${an_fin} )
242	#
243	# For each component selected determine which files need post-processing
244	#
245	for comp in ${config_ListOfComponents[*]} ; do
246	#
247	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
248	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
249	#
250	card=${CARD_DIR}/COMP/${compname}.card
251	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
252	#
253	ListFilesName=${compname}_OutputFiles_List
254	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
255	#
256	if [ X${FileName0} != X${NULL_STR} ] ; then
257	#
258	# INITIALISATION
259	#
260	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
261	typeset i=2
262	#
263	until [ $i -gt $NbFiles ]; do
264	#
265	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
266	#
267	if [ X${flag_post} != XNONE ] ; then
268	#
269	# Check if seasonal is required for this file
270	#
271	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
272	#
273	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
274	#
275	# variable option allready typeset above
276	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
277	if [ ${option} = Seasonal ] ; then
278	FoundSeasonal=true
279	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
280	fi
281	done
282	#
283	if [ ! X${FoundSeasonal} = Xtrue ] ; then
284	eval ${compname}_${flag_post}_Seasonal=ON
285	fi
286	#
287	if [ ! X$( eval echo \${${compname}_${flag_post}_Seasonal} ) = XON ] ; then
288	(( i=i+3 ))
289	continue
290	fi
291	#
292	# CREATE LIST
293	#
294	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
295	#
296	DIRECTORY=${R_SAVE}/${comp}/Analyse/SE
297	#
298	TestedFile=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${FILE}.nc
299	#
300	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
301	if [ ! $? = 0 ] ; then
302	eval set +A LISTE_FILE_${comp} \$\{LISTE_FILE_${comp}[*]} ${FILE}
303	if [ ! ${RebuildFrequency} = true ] ; then
304	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
305	eval set +A LISTE_PATCHES_${FILE} \$\{${compname}_Post_${FILE}_Patches[*]}
306	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
307	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
308	if [ Xload${Patch} != X ] ; then
309	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
310	eval load${Patch}=loaded
311	fi
312	done
313	fi
314	fi
315	fi
316	fi
317	(( i=i+3 ))
318	done # until [ $i -eq $NbFiles ]
319	fi
320	done # for comp
321
322	for comp in ${config_ListOfComponents[*]} ; do
323	#
324	eval R_OUT_${comp}=${R_SAVE}/${comp}
325	#
326	i=0
327	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
328	#
329	# Determine in which output can we find file
330	# IE : Output/MO or Output/DA or ...
331	#
332	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
333	case ${FlagDir} in
334	1Y) FreqDir=YE ;;
335	1M) FreqDir=MO ;;
336	5D\|1D) FreqDir=DA ;;
337	HF) FreqDir=HF ;;
338	3H) FreqDir=HF ;;
339	INS) FreqDir=INS ;;
340	esac
341	#
342	RESULT_SE=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${file}.nc
343	# Do not redoo an existing SE
344	IGCM_sys_TestFileArchive ${R_SAVE}/${comp}/Analyse/SE/${RESULT_SE}
345	if [ $? = 0 ] ; then
346	continue
347	fi
348	#
349	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
350	#
351	case ${config_UserChoices_PeriodLength} in
352	# For Yearly simulation :
353	1Y\|1y)
354	(( an = an_deb ))
355	# Initialize array
356	#set -A liste_file_se
357	#set -A liste_file_se_tmp
358	unset liste_file_se
359	unset liste_file_se_tmp
360	while [ ${an} -le ${an_fin} ] ; do
361	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
362	#
363	an4=$(printf "%04i\n" ${an} )
364	#
365	diy=$( IGCM_date_DaysInYear $an4 )
366	afin=$( IGCM_date_AddDaysToGregorianDate ${an4}0101 $(( diy - 1 )) )
367	date=${an4}0101_${afin}
368	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
369	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
370	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
371	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
372	(( an = an + 1 ))
373	done
374	#
375	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
376	eval ExitFlag=false
377	IGCM_debug_Verif_Exit_Post
378
379	# Apply IGCM_Patch if needed
380	if [ ! ${RebuildFrequency} = true ] ; then
381	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
382	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
383	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
384	IGCM_${Patch} ${file_t}
385	done
386	done
387	fi
388	fi
389
390	# Search of common list of variables to be treated
391	nbfile=0
392	for file_common_var in ${liste_file_se_tmp[*]} ; do
393	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
394	(( nbfile = nbfile + 1 ))
395	done
396	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
397	IGCM_sys_Rm tmpfile_ncra
398
399	# detect time counter : time or time_counter ie unlimited variable
400	var_unlim=$(ncdump -h ${liste_file_se_tmp[1]}\|grep UNLIMITED\| cut -d ' ' -f 1)
401
402	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
403	#
404	(( nb = ${mois} - 1 ))
405	#
406	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
407	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d ${var_unlim},${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
408	done
409	IGCM_sys_Rm ${liste_file_se_tmp[*]}
410	eval ExitFlag=false
411	IGCM_debug_Verif_Exit_Post
412	;;
413	# For Monthly simulation :
414	1M\|1m)
415	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
416	#
417	(( nb = ${mois} - 1 ))
418	#
419	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
420	#
421	(( an = an_deb ))
422	# Initialize array
423	#set -A liste_file_se
424	#set -A liste_file_se_tmp
425	unset liste_file_se
426	unset liste_file_se_tmp
427	while [ ${an} -le ${an_fin} ] ; do
428	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
429	#
430	an4=$(printf "%04i\n" ${an} )
431	#
432	date=${an4}${mois}01_${an4}${mois}${moisL}
433	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
434	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
435	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
436	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
437
438	(( an = an + 1 ))
439	done
440	#
441	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
442	eval ExitFlag=false
443	IGCM_debug_Verif_Exit_Post
444
445	# Apply IGCM_Patch if needed
446	if [ ! ${RebuildFrequency} = true ] ; then
447	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
448	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
449	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
450	IGCM_${Patch} ${file_t}
451	done
452	done
453	fi
454	fi
455
456	# Search of common list of variables to be treated
457	nbfile=0
458	for file_common_var in ${liste_file_se_tmp[*]} ; do
459	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
460	(( nbfile = nbfile + 1 ))
461	done
462	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
463	IGCM_sys_Rm tmpfile_ncra
464
465	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
466
467	IGCM_sys_Rm ${liste_file_se_tmp[*]}
468	eval ExitFlag=false
469	IGCM_debug_Verif_Exit_Post
470	done
471	;;
472	D\|d)
473	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
474	#
475	(( nb = ${mois} - 1 ))
476	#
477	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
478	#
479	(( an = an_deb ))
480	# Initialize array
481	#set -A liste_file_se
482	#set -A liste_file_se_tmp
483	unset liste_file_se
484	unset liste_file_se_tmp
485	while [ ${an} -le ${an_fin} ] ; do
486	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
487	#
488	an4=$(printf "%04i\n" ${an} )
489	#
490	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
491	# for one day
492	if [ ${length_d} -eq 1 ] ; then
493	(( length_d = 0 ))
494	fi
495	(( day = 1 ))
496	while [ ${day} -le ${moisL} ] ; do
497	day2=$(printf "%02i\n" ${day} )
498	day_beg=${an4}${mois}${day2}
499	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
500	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
501	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
502	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
503	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
504	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
505	(( day = day + 1 ))
506	done
507	(( an = an + 1 ))
508	done
509	#
510	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
511	eval ExitFlag=false
512	IGCM_debug_Verif_Exit_Post
513
514	# Apply IGCM_Patch if needed
515	if [ ! ${RebuildFrequency} = true ] ; then
516	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
517	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
518	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
519	IGCM_${Patch} ${file_t}
520	done
521	done
522	fi
523	fi
524
525	# Search of common list of variables to be treated
526	nbfile=0
527	for file_common_var in ${liste_file_se_tmp[*]} ; do
528	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
529	(( nbfile = nbfile + 1 ))
530	done
531	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
532	IGCM_sys_Rm tmpfile_ncra
533
534	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
535	IGCM_sys_Rm ${liste_file_se_tmp[*]}
536	eval ExitFlag=false
537	IGCM_debug_Verif_Exit_Post
538	done
539	;;
540	esac
541	#
542
543	# Search of common list of variables to be treated
544	nbfile=0
545	for file_common_var in ${OUT_SE[*]} ; do
546	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncrcat
547	(( nbfile = nbfile + 1 ))
548	done
549	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
550	IGCM_sys_Rm tmpfile_ncrcat
551
552	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
553	#
554	IGCM_sys_Rm ${OUT_SE[*]}
555	#
556	# detect time counter : time or time_counter ie unlimited variable
557	var_unlim=$(ncdump -h ${RESULT_SE}\|grep UNLIMITED\| cut -d ' ' -f 1)
558
559	# add modulo attribute on time axis
560	${ncatted} -a modulo,${var_unlim},c,c," " ${RESULT_SE}
561	#
562	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
563	IGCM_sys_Rm ${RESULT_SE}
564	#
565	eval ExitFlag=false
566	IGCM_debug_Verif_Exit_Post
567	done
568	done
569
570	# DODS copy
571	for comp in ${config_ListOfComponents[*]} ; do
572	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
573	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
574	done
575
576	YEARS=${an_deb}_${an_fin}
577	DIR_OUT=SE
578
579	export POST_DIR; export SUBMIT_DIR; export libIGCM; export R_INIT; export R_BC; export StandAlone
580	export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ; export RESOL_SBG
581	export R_SAVE; export config_UserChoices_JobName; export config_UserChoices_TagName; export YEARS; export DIR_OUT
582	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"
583	export listVarEnv;
584
585	#D-
586	# --------------------------------------------------------------------
587	#D- Test if all was right before ATLAS
588	# --------------------------------------------------------------------
589	IGCM_debug_Verif_Exit_Post
590
591	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
592	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
593	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
594	#
595	IGCM_sys_QsubPost atlas_ORCHIDEE ;
596	IGCM_sys_QsubPost atlas_LMDZ ;
597	IGCM_sys_QsubPost atlas_ORCA_LIM ;
598	IGCM_sys_QsubPost additionnal ;
599	#
600	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
601	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] \|\| \
602	[ ${config_UserChoices_TagName} = "IPSLCM5A-MR" ] ; then
603	IGCM_sys_QsubPost atlas_ORCHIDEE ;
604	IGCM_sys_QsubPost atlas_LMDZ ;
605	IGCM_sys_QsubPost atlas_ORCA_LIM ;
606	IGCM_sys_QsubPost atlas_PISCES ;
607	#
608	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
609	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
610	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
611	#
612	IGCM_sys_QsubPost atlas_LMDZ ;
613	IGCM_sys_QsubPost atlas_ORCHIDEE ;
614	#
615	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
616	#
617	IGCM_sys_QsubPost atlas_LMDZ ;
618	#
619	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
620	[ ${config_UserChoices_TagName} = "OL2" ] ; then
621	#
622	IGCM_sys_QsubPost atlas_ORCHIDEE ;
623	#
624	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\|
625	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] ; then
626	#
627	IGCM_sys_QsubPost atlas_ORCA_LIM ;
628	# IGCM_sys_QsubPost additionnal ;
629	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] ; then
630	#
631	IGCM_sys_QsubPost atlas_ORCA_LIM ;
632	IGCM_sys_QsubPost atlas_PISCES ;
633	# IGCM_sys_QsubPost additionnal ;
634	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
635	#
636	IGCM_sys_QsubPost atlas_PISCES ;
637	#
638	fi
639
640	# Clean RUN_DIR_PATH (necessary for cesium)
641	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}

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