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source: branches/libIGCM_MPI_OpenMP/AA_create_se @ 593

Last change on this file since 593 was 592, checked in by mafoipsl, 12 years ago
Second merge of libIGCM_MPI_OpenMP branch with libIGCM trunk, revision 591.
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
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1	#-Q- cesium #!/bin/ksh
2	#-Q- cesium ######################
3	#-Q- cesium ## CESIUM CEA ##
4	#-Q- cesium ######################
5	#-Q- cesium #MSUB -r SE # Nom du job
6	#-Q- cesium #MSUB -N 1 # Reservation du noeud
7	#-Q- cesium #MSUB -n 1 # Reservation du processus
8	#-Q- cesium #MSUB -T 86400 # Limite de temps elapsed du job
9	#-Q- cesium #MSUB -E "-j o"
10	#-Q- cesium #MSUB -E "-S /bin/ksh"
11	#-Q- curie ######################
12	#-Q- curie ## CURIE TGCC/CEA ##
13	#-Q- curie ######################
14	#-Q- curie #MSUB -r TS # Nom du job
15	#-Q- curie #MSUB -eo
16	#-Q- curie #MSUB -n 1 # Reservation du processus
17	#-Q- curie #MSUB -T 86400 # Limite de temps elapsed du job
18	#-Q- platine #!/usr/bin/ksh
19	#-Q- platine ###################
20	#-Q- platine ## PLATINE CEA ##
21	#-Q- platine ###################
22	#-Q- platine #BSUB -J SE # Nom du job
23	#-Q- platine #BSUB -N # message a la fin du job
24	#-Q- platine #BSUB -n 1 # reservation des processeurs pour le job
25	#-Q- platine #BSUB -W 1:00 # Limite temps
26	#-Q- platine #BSUB -q post # Passage en queue post
27	#-Q- platine #BSUB -L /bin/ksh
28	#-Q- sx8brodie #!/bin/ksh
29	#-Q- sx8brodie #######################
30	#-Q- sx8brodie ## SX8BRODIE IDRIS ##
31	#-Q- sx8brodie #######################
32	#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
33	#-Q- sx8brodie # @ wall_clock_limit = 10:00:00
34	#-Q- sx8brodie # Nom du travail LoadLeveler
35	#-Q- sx8brodie # @ job_name = SE
36	#-Q- sx8brodie # Fichier de sortie standard du travail
37	#-Q- sx8brodie # @ output = $(job_name).$(jobid)
38	#-Q- sx8brodie # Fichier de sortie d'erreur du travail
39	#-Q- sx8brodie # @ error = $(job_name).$(jobid)
40	#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
41	#-Q- sx8brodie # @ notification = error
42	#-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
43	#-Q- sx8brodie # @ queue
44	#-Q- aix6 #!/bin/ksh
45	#-Q- aix6 #######################
46	#-Q- aix6 ## VARGAS IDRIS ##
47	#-Q- aix6 #######################
48	#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
49	#-Q- aix6 # @ wall_clock_limit = 10:00:00
50	#-Q- aix6 # Nom du travail LoadLeveler
51	#-Q- aix6 # @ job_name = SE
52	#-Q- aix6 # Fichier de sortie standard du travail
53	#-Q- aix6 # @ output = $(job_name).$(jobid)
54	#-Q- aix6 # Fichier de sortie d'erreur du travail
55	#-Q- aix6 # @ error = $(job_name).$(jobid)
56	#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
57	#-Q- aix6 # @ notification = error
58	#-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
59	#-Q- aix6 # @ queue
60	#-Q- ulam #!/bin/ksh
61	#-Q- ulam #######################
62	#-Q- ulam ## ULAM IDRIS ##
63	#-Q- ulam #######################
64	#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
65	#-Q- ulam # @ wall_clock_limit = 10:00:00
66	#-Q- ulam # Nom du travail LoadLeveler
67	#-Q- ulam # @ job_name = SE
68	#-Q- ulam # Fichier de sortie standard du travail
69	#-Q- ulam # @ output = $(job_name).$(jobid)
70	#-Q- ulam # Fichier de sortie d'erreur du travail
71	#-Q- ulam # @ error = $(job_name).$(jobid)
72	#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
73	#-Q- ulam # @ notification = error
74	#-Q- ulam # @ 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
75	#-Q- ulam # @ queue
76	#-Q- sx8mercure #!/bin/ksh
77	#-Q- sx8mercure ######################
78	#-Q- sx8mercure ## SX8MERCURE CEA ##
79	#-Q- sx8mercure ######################
80	#-Q- sx8mercure #PBS -N SE # Nom du job
81	#-Q- sx8mercure #PBS -j o # regroupement des stdout et stderr
82	#-Q- sx8mercure #PBS -S /usr/bin/ksh # shell de soumission
83	#-Q- sx8mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go
84	#-Q- sx8mercure #PBS -l cputim_job=1:00:00 # Limite temps a 1 heures
85	#-Q- sx8mercure #PBS -q scalaire
86	#-Q- sx9mercure #!/bin/ksh
87	#-Q- sx9mercure #########################
88	#-Q- sx9mercure ## CESIUM FOR SX9 CEA ##
89	#-Q- sx9mercure #########################
90	#-Q- sx9mercure #MSUB -r SE # Nom du job
91	#-Q- sx9mercure #MSUB -N 1 # Reservation du noeud
92	#-Q- sx9mercure #MSUB -n 1 # Reservation du processus
93	#-Q- sx9mercure #MSUB -T 86400 # Limite de temps elapsed du job
94	#-Q- sx9mercure #MSUB -E "-j o"
95	#-Q- sx9mercure #MSUB -E "-S /bin/ksh"
96	#-Q- titane #!/bin/ksh
97	#-Q- titane ######################
98	#-Q- titane ## TITANE CEA ##
99	#-Q- titane ######################
100	#-Q- titane #MSUB -r SE # Nom du job
101	#-Q- titane #MSUB -eo
102	#-Q- titane #MSUB -n 1 # Reservation du processus
103	#-Q- titane #MSUB -T 86400 # Limite de temps elapsed du job
104	#-Q- titane #MSUB -q mono
105	#-Q- lxiv8 ######################
106	#-Q- lxiv8 ## OBELIX LSCE ##
107	#-Q- lxiv8 ######################
108	#-Q- lxiv8 #PBS -N SE
109	#-Q- lxiv8 #PBS -m a
110	#-Q- lxiv8 #PBS -j oe
111	#-Q- lxiv8 #PBS -q medium
112	#-Q- lxiv8 #PBS -o SE.$$
113	#-Q- lxiv8 #PBS -S /bin/ksh
114	#-Q- default #!/bin/ksh
115	#-Q- default ##################
116	#-Q- default ## DEFAULT HOST ##
117	#-Q- default ##################
118
119	#**************************************************************
120	# Author: Sebastien Denvil
121	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
122	# $Revision:: $ Revision of last commit
123	# $Author:: $ Author of last commit
124	# $Date:: $ Date of last commit
125	# IPSL (2006)
126	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
127	#
128	#**************************************************************
129
130	#set -eu
131	#set -vx
132
133	date
134
135	#-Q- sx8brodie export OMP_NUM_THREADS=1
136	#-Q- aix6 export OMP_NUM_THREADS=1
137	#-Q- ulam export OMP_NUM_THREADS=1
138
139	########################################################################
140
141	#D- Flag to determine if this job in a standalone mode
142	#D- Default : value from AA_job if any
143	StandAlone=${StandAlone:=true}
144
145	#D- Path to libIGCM
146	#D- Default : value from AA_job if any
147	# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
148	# WARNING you must check MirrorlibIGCM variable in sys library.
149	# WARNING If this variable is true, you must use libIGCM_POST path instead
150	# WARNING of your running libIGCM directory.
151	libIGCM=${libIGCM:=::modipsl::/libIGCM}
152
153	#D- Flag to determine if rebuild process has been performed asynchronously
154	#D- Possible value true or false.
155	#D- If true raw files has allready been patched by rebuild job
156	#D- If false create_ts will patch the raw files
157	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
158	RebuildFrequency=${RebuildFrequency:=true}
159
160	#D- Flag to determine atlas job's output directory
161	#D- Default : value from libIGCM_post.ksh if any
162	POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
163
164	#D- Increased verbosity (1, 2, 3)
165	#D- Default : value from AA_job if any
166	Verbosity=${Verbosity:=3}
167
168	#D- Low level debug : to bypass lib test checks and stack construction
169	#D- Default : value from AA_job if any
170	DEBUG_debug=${DEBUG_debug:=false}
171
172	#D- TEMPORARY Flag to determine atmospheric resolution
173	#D- Default : value from atmospheric driver if any
174	RESOL_ATM=${RESOL_ATM:=ALL}
175
176	#D- Flag to determine surface resolution
177	#D- Default : value from surface driver if any
178	RESOL_SRF=ALL
179
180	#D- Flag to determine surface resolution
181	#D- Default : value from surface driver if any
182	RESOL_SBG=ALL
183
184	#D- TEMPORARY Flag to determine ocean resolution
185	#D- Default : value from ocean driver if any
186	RESOL_OCE=${RESOL_OCE:=ORCA2}
187
188	#D- TEMPORARY Flag to determine ice resolution
189	#D- Default : value from ice driver if any
190	RESOL_ICE=${RESOL_ICE:=ORCA2}
191
192	#D- TEMPORARY Flag to determine marine biogeochemistry resolution
193	#D- Default : value from ice driver if any
194	RESOL_MBG=${RESOL_MBG:=ORCA2}
195
196	########################################################################
197
198	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
199	( ${DEBUG_debug} ) && IGCM_debug_Check
200	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
201	( ${DEBUG_debug} ) && IGCM_card_Check
202	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
203	( ${DEBUG_debug} ) && IGCM_date_Check
204	#-------
205	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
206
207	########################################################################
208
209	#set -vx
210
211	IGCM_sys_MkdirWork ${RUN_DIR_PATH}
212	IGCM_sys_Cd ${RUN_DIR_PATH}
213
214	# ------------------------------------------------------------------
215	# Test if all was right before proceeding further
216	# ------------------------------------------------------------------
217	IGCM_debug_Verif_Exit_Post
218
219	if [ ${StandAlone} = true ] ; then
220	CARD_DIR=${SUBMIT_DIR}
221	else
222	CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
223	IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH}
224	fi
225
226	#
227	# First of all
228	#
229	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card UserChoices
230	typeset option
231	for option in ${config_UserChoices[*]} ; do
232	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
233	done
234	#
235	echo
236	IGCM_debug_Print 1 "DefineArrayFromOption : config_UserChoices"
237	IGCM_debug_PrintVariables 3 config_UserChoices_JobName
238	IGCM_debug_PrintVariables 3 config_UserChoices_LongName
239	IGCM_debug_PrintVariables 3 config_UserChoices_TagName
240	IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
241	IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
242	IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
243	IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
244	IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
245	IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
246	echo
247
248	#==================================
249	#R_SAVE : Job output directory
250	#R_BUFR : Job output buffered directory
251	if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
252	FreeName=$( echo ${config_UserChoices_JobName} \| sed 's/.*_//' )
253	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
254	R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
255	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
256	else
257	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
258	R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
259	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_JobName}
260	fi
261	#
262	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
263	#
264	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post SeasonalFrequency
265	#
266	# Determine period for seasonnal average. Default : value from AA_job if any
267	#
268	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
269	#
270	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
271	#
272	freq=$( echo ${config_Post_SeasonalFrequency} \| sed -e "s/[yY]//" )
273	#
274	an_fin=$(( $( IGCM_date_ConvertGregorianDateToJulian ${PeriodDateEnd} ) / 1000 ))
275	an_deb=$( IGCM_date_YearDigit $(( an_fin - freq + 1 )) )
276	an_fin=$( IGCM_date_YearDigit ${an_fin} )
277	#
278	# For each component selected determine which files need post-processing
279	#
280	for comp in ${config_ListOfComponents[*]} ; do
281	#
282	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
283	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
284	#
285	card=${CARD_DIR}/COMP/${compname}.card
286	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
287	#
288	ListFilesName=${compname}_OutputFiles_List
289	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
290	#
291	if [ X${FileName0} != X${NULL_STR} ] ; then
292	#
293	# INITIALISATION
294	#
295	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
296	typeset i=2
297	#
298	until [ $i -gt $NbFiles ]; do
299	#
300	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
301	#
302	if [ X${flag_post} != XNONE ] ; then
303	#
304	# Check if seasonal is required for this file
305	#
306	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
307	#
308	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
309	#
310	# variable option allready typeset above
311	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
312	if [ ${option} = Seasonal ] ; then
313	FoundSeasonal=true
314	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
315	fi
316	done
317	#
318	if [ ! X${FoundSeasonal} = Xtrue ] ; then
319	eval ${compname}_${flag_post}_Seasonal=ON
320	fi
321	#
322	if [ ! X$( eval echo \${${compname}_${flag_post}_Seasonal} ) = XON ] ; then
323	(( i=i+3 ))
324	continue
325	fi
326	#
327	# CREATE LIST
328	#
329	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
330	#
331	DIRECTORY=${R_SAVE}/${comp}/Analyse/SE
332	#
333	TestedFile=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${FILE}.nc
334	#
335	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
336	if [ ! $? = 0 ] ; then
337	eval set +A LISTE_FILE_${comp} \$\{LISTE_FILE_${comp}[*]} ${FILE}
338	if [ ! ${RebuildFrequency} = true ] ; then
339	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
340	eval set +A LISTE_PATCHES_${FILE} \$\{${compname}_Post_${FILE}_Patches[*]}
341	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
342	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
343	if [ Xload${Patch} != X ] ; then
344	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
345	eval load${Patch}=loaded
346	fi
347	done
348	fi
349	fi
350	fi
351	fi
352	(( i=i+3 ))
353	done # until [ $i -eq $NbFiles ]
354	fi
355	done # for comp
356
357	for comp in ${config_ListOfComponents[*]} ; do
358	#
359	eval R_OUT_${comp}=${R_SAVE}/${comp}
360	#
361	i=0
362	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
363	#
364	# Determine in which output can we find file
365	# IE : Output/MO or Output/DA or ...
366	#
367	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
368	case ${FlagDir} in
369	1Y) FreqDir=YE ;;
370	1M) FreqDir=MO ;;
371	5D\|1D) FreqDir=DA ;;
372	HF) FreqDir=HF ;;
373	3H) FreqDir=HF ;;
374	INS) FreqDir=INS ;;
375	esac
376	#
377	RESULT_SE=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${file}.nc
378	# Do not redoo an existing SE
379	IGCM_sys_TestFileArchive ${R_SAVE}/${comp}/Analyse/SE/${RESULT_SE}
380	if [ $? = 0 ] ; then
381	continue
382	fi
383	#
384	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
385	#
386	case ${config_UserChoices_PeriodLength} in
387	# For Yearly simulation :
388	1Y\|1y)
389	(( an = an_deb ))
390	# Initialize array
391	#set -A liste_file_se
392	#set -A liste_file_se_tmp
393	unset liste_file_se
394	unset liste_file_se_tmp
395	while [ ${an} -le ${an_fin} ] ; do
396	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
397	#
398	an4=$(printf "%04i\n" ${an} )
399	#
400	diy=$( IGCM_date_DaysInYear $an4 )
401	afin=$( IGCM_date_AddDaysToGregorianDate ${an4}0101 $(( diy - 1 )) )
402	date=${an4}0101_${afin}
403	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
404	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
405	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
406	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
407	(( an = an + 1 ))
408	done
409	#
410	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
411	IGCM_debug_Verif_Exit_Post
412
413	# Apply IGCM_Patch if needed
414	if [ ! ${RebuildFrequency} = true ] ; then
415	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
416	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
417	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
418	IGCM_${Patch} ${file_t}
419	done
420	done
421	fi
422	fi
423
424	# Search of common list of variables to be treated
425	nbfile=0
426	for file_common_var in ${liste_file_se_tmp[*]} ; do
427	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
428	(( nbfile = nbfile + 1 ))
429	done
430	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
431	IGCM_sys_Rm tmpfile_ncra
432
433	# detect time counter : time or time_counter ie unlimited variable
434	var_unlim=$(ncdump -h ${liste_file_se_tmp[1]}\|grep UNLIMITED\| cut -d ' ' -f 1)
435
436	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
437	#
438	(( nb = ${mois} - 1 ))
439	#
440	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
441	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d ${var_unlim},${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
442	done
443	IGCM_sys_Rm ${liste_file_se_tmp[*]}
444	;;
445	# For Monthly simulation :
446	1M\|1m)
447	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
448	#
449	(( nb = ${mois} - 1 ))
450	#
451	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
452	#
453	(( an = an_deb ))
454	# Initialize array
455	#set -A liste_file_se
456	#set -A liste_file_se_tmp
457	unset liste_file_se
458	unset liste_file_se_tmp
459	while [ ${an} -le ${an_fin} ] ; do
460	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
461	#
462	an4=$(printf "%04i\n" ${an} )
463	#
464	date=${an4}${mois}01_${an4}${mois}${moisL}
465	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
466	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
467	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
468	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
469
470	(( an = an + 1 ))
471	done
472	#
473	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
474	IGCM_debug_Verif_Exit_Post
475
476	# Apply IGCM_Patch if needed
477	if [ ! ${RebuildFrequency} = true ] ; then
478	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
479	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
480	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
481	IGCM_${Patch} ${file_t}
482	done
483	done
484	fi
485	fi
486
487	# Search of common list of variables to be treated
488	nbfile=0
489	for file_common_var in ${liste_file_se_tmp[*]} ; do
490	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
491	(( nbfile = nbfile + 1 ))
492	done
493	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
494	IGCM_sys_Rm tmpfile_ncra
495
496	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
497
498	IGCM_sys_Rm ${liste_file_se_tmp[*]}
499	done
500	;;
501	D\|d)
502	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
503	#
504	(( nb = ${mois} - 1 ))
505	#
506	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
507	#
508	(( an = an_deb ))
509	# Initialize array
510	#set -A liste_file_se
511	#set -A liste_file_se_tmp
512	unset liste_file_se
513	unset liste_file_se_tmp
514	while [ ${an} -le ${an_fin} ] ; do
515	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
516	#
517	an4=$(printf "%04i\n" ${an} )
518	#
519	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
520	# for one day
521	if [ ${length_d} -eq 1 ] ; then
522	(( length_d = 0 ))
523	fi
524	(( day = 1 ))
525	while [ ${day} -le ${moisL} ] ; do
526	day2=$(printf "%02i\n" ${day} )
527	day_beg=${an4}${mois}${day2}
528	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
529	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
530	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
531	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
532	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
533	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
534	(( day = day + 1 ))
535	done
536	(( an = an + 1 ))
537	done
538	#
539	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
540	IGCM_debug_Verif_Exit_Post
541
542	# Apply IGCM_Patch if needed
543	if [ ! ${RebuildFrequency} = true ] ; then
544	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
545	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
546	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
547	IGCM_${Patch} ${file_t}
548	done
549	done
550	fi
551	fi
552
553	# Search of common list of variables to be treated
554	nbfile=0
555	for file_common_var in ${liste_file_se_tmp[*]} ; do
556	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
557	(( nbfile = nbfile + 1 ))
558	done
559	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
560	IGCM_sys_Rm tmpfile_ncra
561
562	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
563	IGCM_sys_Rm ${liste_file_se_tmp[*]}
564	done
565	;;
566	esac
567	#
568
569	# Search of common list of variables to be treated
570	nbfile=0
571	for file_common_var in ${OUT_SE[*]} ; do
572	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncrcat
573	(( nbfile = nbfile + 1 ))
574	done
575	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
576	IGCM_sys_Rm tmpfile_ncrcat
577
578	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
579	#
580	IGCM_sys_Rm ${OUT_SE[*]}
581	#
582	# detect time counter : time or time_counter ie unlimited variable
583	var_unlim=$(ncdump -h ${RESULT_SE}\|grep UNLIMITED\| cut -d ' ' -f 1)
584
585	# Put correct climatological axis following calendar
586	case ${config_UserChoices_CalendarType} in
587	360d\|360_day)
588	# 360 days
589	ncap2cmd="'defdim(\"tbnds\",2) ; ${var_unlim}[${var_unlim}]={15, 45, 75, 105, 135, 165, 195, 225, 255, 285, 315, 345.} ; ${var_unlim}_bnds[${var_unlim},tbnds]={0, 30, 30, 60, 60, 90, 90, 120, 120, 150, 150, 180, 180, 210, 210, 240, 240, 270, 270, 300, 300, 330, 330, 360.} ; ${var_unlim}@units=\"days since 0000-01-01 00:00:00\" ; ${var_unlim}@time_origin=\"01-JAN-0000 00:00:00\" ; ${var_unlim}@calendar=\"360_day\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
590	;;
591	noleap\|365_day)
592	# 365 days
593	ncap2cmd="'defdim(\"tbnds\",2) ; ${var_unlim}[${var_unlim}]={15.5, 45, 74.5, 105, 135.5, 166, 196.5, 227.5, 258, 288.5, 319, 349.5} ; ${var_unlim}_bnds[${var_unlim},tbnds]={0, 31, 31, 59, 59, 90, 90, 120, 120, 151, 151, 181, 181, 212, 212, 243, 243, 273, 273, 304, 304, 334, 334, 365.} ; ${var_unlim}@units=\"days since 0000-01-01 00:00:00\" ; ${var_unlim}@time_origin=\"01-JAN-0000 00:00:00\" ; ${var_unlim}@calendar=\"365_day\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
594	;;
595	all_leap\|366_day)
596	# 366 days
597	ncap2cmd="'defdim(\"tbnds\",2) ; ${var_unlim}[${var_unlim}]={15.5, 45.5, 75.5, 106, 136.5, 167, 197.5, 228.5, 259, 289.5, 320, 350.5} ; ${var_unlim}_bnds[${var_unlim},tbnds]={0, 31, 31, 60, 60, 91, 91, 121, 121, 152, 152, 182, 182, 213, 213, 244, 244, 274, 274, 305, 305, 335, 335, 366.} ; ${var_unlim}@units=\"days since 0000-01-01 00:00:00\" ; ${var_unlim}@time_origin=\"01-JAN-0000 00:00:00\" ; ${var_unlim}@calendar=\"366_day\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
598	;;
599	leap\|gregorian\|standard)
600	# 365.2425 days
601	ncap2cmd="'defdim(\"tbnds\",2) ; ${var_unlim}[${var_unlim}]={15.5, 45.12125, 74.7425, 105.2425, 135.7425, 166.2425, 196.7425, 227.7425, 258.2425, 288.7425, 319.2425, 349.7425} ; ${var_unlim}_bnds[${var_unlim},tbnds]={0, 31, 31, 59.2425, 59.2425, 90.2425, 90.2425, 120.2425, 120.2425, 151.2425, 151.2425, 181.2425, 181.2425, 212.2425, 212.2425, 243.2425, 243.2425, 273.2425, 273.2425, 304.2425, 304.2425, 334.2425, 334.2425, 365.2425} ; ${var_unlim}@units=\"days since 0000-01-01 00:00:00\" ; ${var_unlim}@time_origin=\"01-JAN-0000 00:00:00\" ; ${var_unlim}@calendar=\"gregorian\" ; ${var_unlim}@bounds=\"${var_unlim}_bnds\"'"
602	;;
603	esac
604	eval IGCM_sys_ncap2 -Oh -s $ncap2cmd ${RESULT_SE} tmp.nc
605	IGCM_sys_Rm ${RESULT_SE}
606	IGCM_sys_Mv tmp.nc ${RESULT_SE}
607	#
608	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
609	IGCM_sys_Rm ${RESULT_SE}
610	#
611	done
612	done
613
614	# DODS copy
615	for comp in ${config_ListOfComponents[*]} ; do
616	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
617	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
618	done
619
620	YEARS=${an_deb}_${an_fin}
621	DIR_OUT=SE
622
623	export POST_DIR; export SUBMIT_DIR; export libIGCM; export R_INIT; export R_BC; export StandAlone
624	export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ; export RESOL_SBG
625	export R_SAVE; export config_UserChoices_JobName; export config_UserChoices_TagName; export YEARS; export DIR_OUT
626	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"
627	export listVarEnv;
628
629	#D-
630	# --------------------------------------------------------------------
631	#D- Test if all was right before ATLAS
632	# --------------------------------------------------------------------
633	IGCM_debug_Verif_Exit_Post
634
635	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
636	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
637	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
638	#
639	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
640	IGCM_sys_QsubPost atlas_ORCHIDEE ;
641	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
642	IGCM_sys_QsubPost atlas_LMDZ ;
643	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
644	IGCM_sys_QsubPost atlas_ORCA_LIM ;
645	Script_Post_Output=additionnal.${PeriodDateEnd} ;
646	IGCM_sys_QsubPost additionnal ;
647	#
648	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
649	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] \|\| \
650	[ ${config_UserChoices_TagName} = "IPSLCM5B" ] \|\| \
651	[ ${config_UserChoices_TagName} = "IPSLCM5A-MR" ] ; then
652	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
653	IGCM_sys_QsubPost atlas_ORCHIDEE ;
654	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
655	IGCM_sys_QsubPost atlas_LMDZ ;
656	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
657	IGCM_sys_QsubPost atlas_ORCA_LIM ;
658	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
659	IGCM_sys_QsubPost atlas_PISCES ;
660	#
661	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
662	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
663	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
664	#
665	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
666	IGCM_sys_QsubPost atlas_LMDZ ;
667	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
668	IGCM_sys_QsubPost atlas_ORCHIDEE ;
669	#
670	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
671	#
672	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
673	IGCM_sys_QsubPost atlas_LMDZ ;
674	#
675	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
676	[ ${config_UserChoices_TagName} = "OL2" ] ; then
677	#
678	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
679	IGCM_sys_QsubPost atlas_ORCHIDEE ;
680	#
681	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\|
682	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] ; then
683	#
684	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
685	IGCM_sys_QsubPost atlas_ORCA_LIM ;
686	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] ; then
687	#
688	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
689	IGCM_sys_QsubPost atlas_ORCA_LIM ;
690	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
691	IGCM_sys_QsubPost atlas_PISCES ;
692	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
693	#
694	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
695	IGCM_sys_QsubPost atlas_PISCES ;
696	#
697	fi
698
699	# Clean RUN_DIR_PATH (necessary for cesium and titane only)
700	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}

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