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source: trunk/libIGCM/AA_create_se @ 263

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

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