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source: tags/libIGCM_v1_7/AA_create_se

Last change on this file was 299, checked in by mafoipsl, 14 years ago
Use mercure (scalaire) new front end for SX8 post-processing.
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`
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1	#-Q- platine #!/usr/bin/ksh
2	#-Q- platine ###################
3	#-Q- platine ## PLATINE CEA ##
4	#-Q- platine ###################
5	#-Q- platine #BSUB -J SE # Nom du job
6	#-Q- platine #BSUB -N # message a la fin du job
7	#-Q- platine #BSUB -n 1 # reservation des processeurs pour le job
8	#-Q- platine #BSUB -W 1:00 # Limite temps
9	#-Q- platine #BSUB -q post # Passage en queue post
10	#-Q- sx8brodie #!/bin/ksh
11	#-Q- sx8brodie #######################
12	#-Q- sx8brodie ## SX8BRODIE IDRIS ##
13	#-Q- sx8brodie #######################
14	#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
15	#-Q- sx8brodie # @ wall_clock_limit = 20:00:00
16	#-Q- sx8brodie # Nom du travail LoadLeveler
17	#-Q- sx8brodie # @ job_name = SE
18	#-Q- sx8brodie # Fichier de sortie standard du travail
19	#-Q- sx8brodie # @ output = $(job_name).$(jobid)
20	#-Q- sx8brodie # Fichier de sortie d'erreur du travail
21	#-Q- sx8brodie # @ error = $(job_name).$(jobid)
22	#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
23	#-Q- sx8brodie # @ notification = error
24	#-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
25	#-Q- sx8brodie # @ queue
26	#-Q- aix6 #!/bin/ksh
27	#-Q- aix6 #######################
28	#-Q- aix6 ## VARGAS IDRIS ##
29	#-Q- aix6 #######################
30	#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
31	#-Q- aix6 # @ wall_clock_limit = 20:00:00
32	#-Q- aix6 # Nom du travail LoadLeveler
33	#-Q- aix6 # @ job_name = SE
34	#-Q- aix6 # Fichier de sortie standard du travail
35	#-Q- aix6 # @ output = $(job_name).$(jobid)
36	#-Q- aix6 # Fichier de sortie d'erreur du travail
37	#-Q- aix6 # @ error = $(job_name).$(jobid)
38	#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
39	#-Q- aix6 # @ notification = error
40	#-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
41	#-Q- aix6 # @ queue
42	#-Q- sx8mercure #!/bin/ksh
43	#-Q- sx8mercure ######################
44	#-Q- sx8mercure ## SX8MERCURE CEA ##
45	#-Q- sx8mercure ######################
46	#-Q- sx8mercure #PBS -N SE # Nom du job
47	#-Q- sx8mercure #PBS -j o # regroupement des stdout et stderr
48	#-Q- sx8mercure #PBS -S /usr/bin/ksh # shell de soumission
49	#-Q- sx8mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go
50	#-Q- sx8mercure #PBS -l cputim_job=1:00:00 # Limite temps a 1 heures
51	#-Q- sx8mercure #PBS -q scalaire
52	#-Q- sx9mercure ######################
53	#-Q- sx9mercure ## SX9MERCURE CEA ##
54	#-Q- sx9mercure ######################
55	#-Q- sx9mercure #PBS -N SE # Nom du job
56	#-Q- sx9mercure #PBS -j o # regroupement des stdout et stderr
57	#-Q- sx9mercure #PBS -S /usr/bin/ksh # shell de soumission
58	#-Q- sx9mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go
59	#-Q- sx9mercure #PBS -l cputim_job=1:00:00 # Limite temps a 1 heures
60	#-Q- sx9mercure #PBS -q scalaire
61	#-Q- titane #!/bin/ksh
62	#-Q- titane ######################
63	#-Q- titane ## TITANE CEA ##
64	#-Q- titane ######################
65	#-Q- titane #MSUB -r SE # Nom du job
66	#-Q- titane #MSUB -N 1 # Reservation du noeud
67	#-Q- titane #MSUB -n 1 # Reservation du processus
68	#-Q- titane #MSUB -T 86400 # Limite de temps elapsed du job
69	#-Q- titane #MSUB -E "-j o"
70	#-Q- titane #MSUB -E "-S /bin/ksh"
71	#-Q- titane ##MSUB -e nco.out # Sortie standard
72	#-Q- titane ##MSUB -o nco.out # Sortie standard
73	#-Q- lxiv8 ######################
74	#-Q- lxiv8 ## OBELIX LSCE ##
75	#-Q- lxiv8 ######################
76	#-Q- lxiv8 #PBS -N SE
77	#-Q- lxiv8 #PBS -m a
78	#-Q- lxiv8 #PBS -j oe
79	#-Q- lxiv8 #PBS -q medium
80	#-Q- lxiv8 #PBS -o SE.$$
81	#-Q- lxiv8 #PBS -S /bin/ksh
82	#-Q- default #!/bin/ksh
83	#-Q- default ##################
84	#-Q- default ## DEFAULT HOST ##
85	#-Q- default ##################
86
87	# $Date$
88	# $Author$
89	# $Revision$
90	# IPSL (2006)
91	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
92
93	#set -eu
94	#set -vx
95
96	date
97
98	#-Q- sx8brodie export OMP_NUM_THREADS=1
99	#-Q- aix6 export OMP_NUM_THREADS=1
100
101	########################################################################
102
103	#D- Flag to determine if this job in a standalone mode
104	#D- Default : value from AA_job if any
105	StandAlone=${StandAlone:=true}
106
107	#D- Low level debug : to bypass lib test checks and stack construction
108	#D- Default : value from AA_job if any
109	libIGCM=${libIGCM:=::modipsl::/libIGCM}
110	# WARNING for StandAlone used : To run this script on some machine,
111	# you must check MirrorlibIGCM variable in sys library.
112	# If this variable is true, you must use libIGCM_POST path instead
113	# of your running libIGCM directory.
114
115	#D- Flag to determine if rebuild process has been performed asynchronously
116	#D- Possible value true or false.
117	#D- If true raw files has allready been patched by rebuild job
118	#D- If false create_ts will patch the raw files
119	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
120	RebuildFrequency=${RebuildFrequency:=true}
121
122	#D- Flag to determine atlas job's output directory
123	#D- Default : value from libIGCM_post.ksh if any
124	POST_DIR=${POST_DIR:=${PBS_O_WORKDIR}}
125
126	#D- Increased verbosity (1, 2, 3)
127	#D- Default : value from AA_job if any
128	Verbosity=${Verbosity:=3}
129
130	#D- Low level debug : to bypass lib test checks and stack construction
131	#D- Default : value from AA_job if any
132	DEBUG_debug=${DEBUG_debug:=false}
133
134	#D- TEMPORARY Flag to determine atmospheric resolution
135	#D- Default : value from atmospheric driver if any
136	RESOL_ATM=${RESOL_ATM:=ALL}
137
138	#D- Flag to determine surface resolution
139	#D- Default : value from surface driver if any
140	RESOL_SRF=ALL
141
142	#D- Flag to determine surface resolution
143	#D- Default : value from surface driver if any
144	RESOL_SBG=ALL
145
146	#D- TEMPORARY Flag to determine ocean resolution
147	#D- Default : value from ocean driver if any
148	RESOL_OCE=${RESOL_OCE:=ORCA2}
149
150	#D- TEMPORARY Flag to determine ice resolution
151	#D- Default : value from ice driver if any
152	RESOL_ICE=${RESOL_ICE:=ORCA2}
153
154	#D- TEMPORARY Flag to determine marine biogeochemistry resolution
155	#D- Default : value from ice driver if any
156	RESOL_MBG=${RESOL_MBG:=ORCA2}
157
158	########################################################################
159
160	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
161	( ${DEBUG_debug} ) && IGCM_debug_Check
162	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
163	( ${DEBUG_debug} ) && IGCM_card_Check
164	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
165	( ${DEBUG_debug} ) && IGCM_date_Check
166	#-------
167	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
168
169	########################################################################
170
171	#set -vx
172
173	IGCM_sys_MkdirWork ${RUN_DIR_PATH}
174	IGCM_sys_Cd ${RUN_DIR_PATH}
175
176	if [ ${StandAlone} = true ] ; then
177	CARD_DIR=${SUBMIT_DIR}
178	else
179	CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
180	IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH}
181	fi
182
183	#
184	# First of all
185	#
186	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card UserChoices
187	typeset option
188	for option in ${config_UserChoices[*]} ; do
189	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
190	done
191	#
192	echo
193	IGCM_debug_Print 1 "DefineArrayFromOption : config_UserChoices"
194	IGCM_debug_PrintVariables 3 config_UserChoices_JobName
195	IGCM_debug_PrintVariables 3 config_UserChoices_LongName
196	IGCM_debug_PrintVariables 3 config_UserChoices_TagName
197	IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
198	IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
199	IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
200	IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
201	IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
202	IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
203	echo
204
205	#==================================
206	#R_SAVE : Job output directory
207	if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
208	FreeName=$( echo ${config_UserChoices_JobName} \| sed 's/.*_//' )
209	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
210	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
211	else
212	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
213	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_JobName}
214	fi
215	#
216	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
217	#
218	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post SeasonalFrequency
219	#
220	# Determine period for seasonnal average. Default : value from AA_job if any
221	#
222	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
223	#
224	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
225	#
226	freq=$( echo ${config_Post_SeasonalFrequency} \| sed -e "s/[yY]//" )
227	#
228	an_fin=$(( $( IGCM_date_ConvertGregorianDateToJulian ${PeriodDateEnd} ) / 1000 ))
229	an_deb=$( IGCM_date_YearDigit $(( an_fin - freq + 1 )) )
230	an_fin=$( IGCM_date_YearDigit ${an_fin} )
231	#
232	# For each component selected determine which files need post-processing
233	#
234	for comp in ${config_ListOfComponents[*]} ; do
235	#
236	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
237	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
238	#
239	card=${CARD_DIR}/COMP/${compname}.card
240	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
241	#
242	ListFilesName=${compname}_OutputFiles_List
243	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
244	#
245	if [ X${FileName0} != X${NULL_STR} ] ; then
246	#
247	# INITIALISATION
248	#
249	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
250	typeset i=2
251	#
252	until [ $i -gt $NbFiles ]; do
253	#
254	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
255	#
256	if [ X${flag_post} != XNONE ] ; then
257	#
258	# Check if seasonal is required for this file
259	#
260	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
261	#
262	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
263	#
264	# variable option allready typeset above
265	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
266	if [ ${option} = Seasonal ] ; then
267	FoundSeasonal=true
268	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
269	fi
270	done
271	#
272	if [ ! X${FoundSeasonal} = Xtrue ] ; then
273	eval ${compname}_${flag_post}_Seasonal=ON
274	fi
275	#
276	if [ ! X$( eval echo \${${compname}_${flag_post}_Seasonal} ) = XON ] ; then
277	(( i=i+3 ))
278	continue
279	fi
280	#
281	# CREATE LIST
282	#
283	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
284	#
285	DIRECTORY=${R_SAVE}/${comp}/Analyse/SE
286	#
287	TestedFile=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${FILE}.nc
288	#
289	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
290	if [ ! $? = 0 ] ; then
291	eval set +A LISTE_FILE_${comp} \$\{LISTE_FILE_${comp}[*]} ${FILE}
292	if [ ! ${RebuildFrequency} = true ] ; then
293	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
294	eval set +A LISTE_PATCHES_${FILE} \$\{${compname}_Post_${FILE}_Patches[*]}
295	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
296	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
297	if [ Xload${Patch} != X ] ; then
298	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
299	eval load${Patch}=loaded
300	fi
301	done
302	fi
303	fi
304	fi
305	fi
306	(( i=i+3 ))
307	done # until [ $i -eq $NbFiles ]
308	fi
309	done # for comp
310
311	for comp in ${config_ListOfComponents[*]} ; do
312	#
313	eval R_OUT_${comp}=${R_SAVE}/${comp}
314	#
315	i=0
316	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
317	#
318	# Determine in which output can we find file
319	# IE : Output/MO or Output/DA or ...
320	#
321	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
322	case ${FlagDir} in
323	1Y) FreqDir=YE ;;
324	1M) FreqDir=MO ;;
325	5D\|1D) FreqDir=DA ;;
326	HF) FreqDir=HF ;;
327	3H) FreqDir=HF ;;
328	INS) FreqDir=INS ;;
329	esac
330	#
331	RESULT_SE=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${file}.nc
332	# Do not redoo an existing SE
333	IGCM_sys_TestFileArchive ${R_SAVE}/${comp}/Analyse/SE/${RESULT_SE}
334	if [ $? = 0 ] ; then
335	continue
336	fi
337	#
338	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
339	#
340	case ${config_UserChoices_PeriodLength} in
341	# For Yearly simulation :
342	1Y\|1y)
343	(( an = an_deb ))
344	# Initialize array
345	#set -A liste_file_se
346	#set -A liste_file_se_tmp
347	unset liste_file_se
348	unset liste_file_se_tmp
349	while [ ${an} -le ${an_fin} ] ; do
350	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
351	#
352	an4=$(printf "%04i\n" ${an} )
353	#
354	diy=$( IGCM_date_DaysInYear $an4 )
355	afin=$( IGCM_date_AddDaysToGregorianDate ${an4}0101 $(( diy - 1 )) )
356	date=${an4}0101_${afin}
357	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
358	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
359	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
360	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
361	(( an = an + 1 ))
362	done
363	#
364	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
365	eval ExitFlag=false
366	IGCM_debug_Verif_Exit_Post
367
368	# Apply IGCM_Patch if needed
369	if [ ! ${RebuildFrequency} = true ] ; then
370	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
371	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
372	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
373	IGCM_${Patch} ${file_t}
374	done
375	done
376	fi
377	fi
378
379	# Search of common list of variables to be treated
380	nbfile=0
381	for file_common_var in ${liste_file_se_tmp[*]} ; do
382	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
383	(( nbfile = nbfile + 1 ))
384	done
385	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
386	IGCM_sys_Rm tmpfile_ncra
387
388	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
389	#
390	(( nb = ${mois} - 1 ))
391	#
392	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
393	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d time_counter,${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
394	done
395	IGCM_sys_Rm ${liste_file_se_tmp[*]}
396	eval ExitFlag=false
397	IGCM_debug_Verif_Exit_Post
398	;;
399	# For Monthly simulation :
400	1M\|1m)
401	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
402	#
403	(( nb = ${mois} - 1 ))
404	#
405	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
406	#
407	(( an = an_deb ))
408	# Initialize array
409	#set -A liste_file_se
410	#set -A liste_file_se_tmp
411	unset liste_file_se
412	unset liste_file_se_tmp
413	while [ ${an} -le ${an_fin} ] ; do
414	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
415	#
416	an4=$(printf "%04i\n" ${an} )
417	#
418	date=${an4}${mois}01_${an4}${mois}${moisL}
419	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
420	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
421	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
422	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
423
424	(( an = an + 1 ))
425	done
426	#
427	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
428	eval ExitFlag=false
429	IGCM_debug_Verif_Exit_Post
430
431	# Apply IGCM_Patch if needed
432	if [ ! ${RebuildFrequency} = true ] ; then
433	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
434	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
435	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
436	IGCM_${Patch} ${file_t}
437	done
438	done
439	fi
440	fi
441
442	# Search of common list of variables to be treated
443	nbfile=0
444	for file_common_var in ${liste_file_se_tmp[*]} ; do
445	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
446	(( nbfile = nbfile + 1 ))
447	done
448	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
449	IGCM_sys_Rm tmpfile_ncra
450	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
451
452	IGCM_sys_Rm ${liste_file_se_tmp[*]}
453	eval ExitFlag=false
454	IGCM_debug_Verif_Exit_Post
455	done
456	;;
457	D\|d)
458	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
459	#
460	(( nb = ${mois} - 1 ))
461	#
462	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
463	#
464	(( an = an_deb ))
465	# Initialize array
466	#set -A liste_file_se
467	#set -A liste_file_se_tmp
468	unset liste_file_se
469	unset liste_file_se_tmp
470	while [ ${an} -le ${an_fin} ] ; do
471	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
472	#
473	an4=$(printf "%04i\n" ${an} )
474	#
475	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
476	# for one day
477	if [ ${length_d} -eq 1 ] ; then
478	(( length_d = 0 ))
479	fi
480	(( day = 1 ))
481	while [ ${day} -le ${moisL} ] ; do
482	day2=$(printf "%02i\n" ${day} )
483	day_beg=${an4}${mois}${day2}
484	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
485	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
486	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
487	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
488	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
489	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
490	(( day = day + 1 ))
491	done
492	(( an = an + 1 ))
493	done
494	#
495	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
496	eval ExitFlag=false
497	IGCM_debug_Verif_Exit_Post
498
499	# Apply IGCM_Patch if needed
500	if [ ! ${RebuildFrequency} = true ] ; then
501	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
502	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
503	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
504	IGCM_${Patch} ${file_t}
505	done
506	done
507	fi
508	fi
509
510	# Search of common list of variables to be treated
511	nbfile=0
512	for file_common_var in ${liste_file_se_tmp[*]} ; do
513	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
514	(( nbfile = nbfile + 1 ))
515	done
516	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
517	IGCM_sys_Rm tmpfile_ncra
518
519	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
520	IGCM_sys_Rm ${liste_file_se_tmp[*]}
521	eval ExitFlag=false
522	IGCM_debug_Verif_Exit_Post
523	done
524	;;
525	esac
526	#
527
528	# Search of common list of variables to be treated
529	nbfile=0
530	for file_common_var in ${OUT_SE[*]} ; do
531	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncrcat
532	(( nbfile = nbfile + 1 ))
533	done
534	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
535	IGCM_sys_Rm tmpfile_ncrcat
536
537	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
538	#
539	IGCM_sys_Rm ${OUT_SE[*]}
540	#
541	if [ ${comp} = "CPL" ] ; then
542	${ncatted} -a modulo,time,c,c," " ${RESULT_SE}
543	else
544	${ncatted} -a modulo,time_counter,c,c," " ${RESULT_SE}
545	fi
546	#
547	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
548	IGCM_sys_Rm ${RESULT_SE}
549	#
550	eval ExitFlag=false
551	IGCM_debug_Verif_Exit_Post
552	done
553	done
554
555	# DODS copy
556	for comp in ${config_ListOfComponents[*]} ; do
557	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
558	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
559	done
560
561	YEARS=${an_deb}_${an_fin}
562
563	export POST_DIR; export SUBMIT_DIR; export libIGCM; export R_INIT; export R_BC; export StandAlone
564	export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ; export RESOL_SBG
565	export R_SAVE; export config_UserChoices_JobName; export config_UserChoices_TagName; export YEARS;
566	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"
567	export listVarEnv;
568
569	#D-
570	# --------------------------------------------------------------------
571	#D- Test if all was right before ATLAS
572	# --------------------------------------------------------------------
573	IGCM_debug_Verif_Exit_Post
574
575	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
576	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
577	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
578	#
579	IGCM_sys_QsubPost atlas_ORCHIDEE ;
580	IGCM_sys_QsubPost atlas_LMDZ ;
581	IGCM_sys_QsubPost atlas_ORCA_LIM ;
582	IGCM_sys_QsubPost additionnal ;
583	#
584	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
585	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] ; then
586	IGCM_sys_QsubPost atlas_ORCHIDEE ;
587	IGCM_sys_QsubPost atlas_LMDZ ;
588	IGCM_sys_QsubPost atlas_ORCA_LIM ;
589	IGCM_sys_QsubPost atlas_PISCES ;
590	#
591	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
592	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
593	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
594	#
595	IGCM_sys_QsubPost atlas_LMDZ ;
596	IGCM_sys_QsubPost atlas_ORCHIDEE ;
597	#
598	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
599	#
600	IGCM_sys_QsubPost atlas_LMDZ ;
601	#
602	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
603	[ ${config_UserChoices_TagName} = "OL2" ] ; then
604	#
605	IGCM_sys_QsubPost atlas_ORCHIDEE ;
606	#
607	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\|
608	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] ; then
609	#
610	IGCM_sys_QsubPost atlas_ORCA_LIM ;
611	# IGCM_sys_QsubPost additionnal ;
612	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] ; then
613	#
614	IGCM_sys_QsubPost atlas_ORCA_LIM ;
615	IGCM_sys_QsubPost atlas_PISCES ;
616	# IGCM_sys_QsubPost additionnal ;
617	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
618	#
619	IGCM_sys_QsubPost atlas_PISCES ;
620	#
621	fi
622
623	# Clean RUN_DIR_PATH (necessary for cesium)
624	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}

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