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source: trunk/libIGCM/AA_create_se @ 315

Last change on this file since 315 was 315, checked in by mafoipsl, 14 years ago
Add mail when job aborts in mercure front-end header. Correct SendMail? function on mercurex9.
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- 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 ######################
63	#-Q- sx9mercure ## SX9MERCURE CEA ##
64	#-Q- sx9mercure ######################
65	#-Q- sx9mercure #PBS -N SE # Nom du job
66	#-Q- sx9mercure #PBS -m a # message si abort
67	#-Q- sx9mercure #PBS -j o # regroupement des stdout et stderr
68	#-Q- sx9mercure #PBS -S /usr/bin/ksh # shell de soumission
69	#-Q- sx9mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go
70	#-Q- sx9mercure #PBS -l cputim_job=1:00:00 # Limite temps a 1 heures
71	#-Q- sx9mercure #PBS -q scalaire
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:=${PBS_O_WORKDIR}}
136
137	#D- Increased verbosity (1, 2, 3)
138	#D- Default : value from AA_job if any
139	Verbosity=${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	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
400	#
401	(( nb = ${mois} - 1 ))
402	#
403	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
404	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d time_counter,${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
405	done
406	IGCM_sys_Rm ${liste_file_se_tmp[*]}
407	eval ExitFlag=false
408	IGCM_debug_Verif_Exit_Post
409	;;
410	# For Monthly simulation :
411	1M\|1m)
412	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
413	#
414	(( nb = ${mois} - 1 ))
415	#
416	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
417	#
418	(( an = an_deb ))
419	# Initialize array
420	#set -A liste_file_se
421	#set -A liste_file_se_tmp
422	unset liste_file_se
423	unset liste_file_se_tmp
424	while [ ${an} -le ${an_fin} ] ; do
425	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
426	#
427	an4=$(printf "%04i\n" ${an} )
428	#
429	date=${an4}${mois}01_${an4}${mois}${moisL}
430	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
431	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
432	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
433	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
434
435	(( an = an + 1 ))
436	done
437	#
438	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
439	eval ExitFlag=false
440	IGCM_debug_Verif_Exit_Post
441
442	# Apply IGCM_Patch if needed
443	if [ ! ${RebuildFrequency} = true ] ; then
444	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
445	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
446	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
447	IGCM_${Patch} ${file_t}
448	done
449	done
450	fi
451	fi
452
453	# Search of common list of variables to be treated
454	nbfile=0
455	for file_common_var in ${liste_file_se_tmp[*]} ; do
456	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
457	(( nbfile = nbfile + 1 ))
458	done
459	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
460	IGCM_sys_Rm tmpfile_ncra
461	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
462
463	IGCM_sys_Rm ${liste_file_se_tmp[*]}
464	eval ExitFlag=false
465	IGCM_debug_Verif_Exit_Post
466	done
467	;;
468	D\|d)
469	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
470	#
471	(( nb = ${mois} - 1 ))
472	#
473	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
474	#
475	(( an = an_deb ))
476	# Initialize array
477	#set -A liste_file_se
478	#set -A liste_file_se_tmp
479	unset liste_file_se
480	unset liste_file_se_tmp
481	while [ ${an} -le ${an_fin} ] ; do
482	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
483	#
484	an4=$(printf "%04i\n" ${an} )
485	#
486	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
487	# for one day
488	if [ ${length_d} -eq 1 ] ; then
489	(( length_d = 0 ))
490	fi
491	(( day = 1 ))
492	while [ ${day} -le ${moisL} ] ; do
493	day2=$(printf "%02i\n" ${day} )
494	day_beg=${an4}${mois}${day2}
495	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
496	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
497	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
498	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
499	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
500	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
501	(( day = day + 1 ))
502	done
503	(( an = an + 1 ))
504	done
505	#
506	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
507	eval ExitFlag=false
508	IGCM_debug_Verif_Exit_Post
509
510	# Apply IGCM_Patch if needed
511	if [ ! ${RebuildFrequency} = true ] ; then
512	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
513	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
514	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
515	IGCM_${Patch} ${file_t}
516	done
517	done
518	fi
519	fi
520
521	# Search of common list of variables to be treated
522	nbfile=0
523	for file_common_var in ${liste_file_se_tmp[*]} ; do
524	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncra
525	(( nbfile = nbfile + 1 ))
526	done
527	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
528	IGCM_sys_Rm tmpfile_ncra
529
530	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
531	IGCM_sys_Rm ${liste_file_se_tmp[*]}
532	eval ExitFlag=false
533	IGCM_debug_Verif_Exit_Post
534	done
535	;;
536	esac
537	#
538
539	# Search of common list of variables to be treated
540	nbfile=0
541	for file_common_var in ${OUT_SE[*]} ; do
542	ncks -m ${file_common_var} \| grep '# dim. =' \| cut -d ':' -f 1 >> tmpfile_ncrcat
543	(( nbfile = nbfile + 1 ))
544	done
545	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
546	IGCM_sys_Rm tmpfile_ncrcat
547
548	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
549	#
550	IGCM_sys_Rm ${OUT_SE[*]}
551	#
552	if [ ${comp} = "CPL" ] ; then
553	${ncatted} -a modulo,time,c,c," " ${RESULT_SE}
554	else
555	${ncatted} -a modulo,time_counter,c,c," " ${RESULT_SE}
556	fi
557	#
558	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
559	IGCM_sys_Rm ${RESULT_SE}
560	#
561	eval ExitFlag=false
562	IGCM_debug_Verif_Exit_Post
563	done
564	done
565
566	# DODS copy
567	for comp in ${config_ListOfComponents[*]} ; do
568	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
569	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
570	done
571
572	YEARS=${an_deb}_${an_fin}
573
574	export POST_DIR; export SUBMIT_DIR; export libIGCM; export R_INIT; export R_BC; export StandAlone
575	export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ; export RESOL_SBG
576	export R_SAVE; export config_UserChoices_JobName; export config_UserChoices_TagName; export YEARS;
577	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"
578	export listVarEnv;
579
580	#D-
581	# --------------------------------------------------------------------
582	#D- Test if all was right before ATLAS
583	# --------------------------------------------------------------------
584	IGCM_debug_Verif_Exit_Post
585
586	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
587	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
588	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
589	#
590	IGCM_sys_QsubPost atlas_ORCHIDEE ;
591	IGCM_sys_QsubPost atlas_LMDZ ;
592	IGCM_sys_QsubPost atlas_ORCA_LIM ;
593	IGCM_sys_QsubPost additionnal ;
594	#
595	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
596	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] ; then
597	IGCM_sys_QsubPost atlas_ORCHIDEE ;
598	IGCM_sys_QsubPost atlas_LMDZ ;
599	IGCM_sys_QsubPost atlas_ORCA_LIM ;
600	IGCM_sys_QsubPost atlas_PISCES ;
601	#
602	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
603	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
604	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
605	#
606	IGCM_sys_QsubPost atlas_LMDZ ;
607	IGCM_sys_QsubPost atlas_ORCHIDEE ;
608	#
609	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
610	#
611	IGCM_sys_QsubPost atlas_LMDZ ;
612	#
613	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
614	[ ${config_UserChoices_TagName} = "OL2" ] ; then
615	#
616	IGCM_sys_QsubPost atlas_ORCHIDEE ;
617	#
618	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\|
619	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] ; then
620	#
621	IGCM_sys_QsubPost atlas_ORCA_LIM ;
622	# IGCM_sys_QsubPost additionnal ;
623	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] ; then
624	#
625	IGCM_sys_QsubPost atlas_ORCA_LIM ;
626	IGCM_sys_QsubPost atlas_PISCES ;
627	# IGCM_sys_QsubPost additionnal ;
628	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
629	#
630	IGCM_sys_QsubPost atlas_PISCES ;
631	#
632	fi
633
634	# Clean RUN_DIR_PATH (necessary for cesium)
635	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}

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