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source: tags/libIGCM_v2.0_rc1/AA_create_se @ 1137

Last change on this file since 1137 was 741, checked in by sdipsl, 12 years ago
use xlarge class on curie comment header tweaking for ensemble due to bas side effect
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 SE # 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- curie #MSUB -E '--no-requeue'
19	#-Q- curie #MSUB -q xlarge
20	#-Q- curie #MSUB -Q normal
21	#-Q- curie set +x
22	#-Q- platine #!/usr/bin/ksh
23	#-Q- platine ###################
24	#-Q- platine ## PLATINE CEA ##
25	#-Q- platine ###################
26	#-Q- platine #BSUB -J SE # Nom du job
27	#-Q- platine #BSUB -N # message a la fin du job
28	#-Q- platine #BSUB -n 1 # reservation des processeurs pour le job
29	#-Q- platine #BSUB -W 1:00 # Limite temps
30	#-Q- platine #BSUB -q post # Passage en queue post
31	#-Q- platine #BSUB -L /bin/ksh
32	#-Q- sx8brodie #!/bin/ksh
33	#-Q- sx8brodie #######################
34	#-Q- sx8brodie ## SX8BRODIE IDRIS ##
35	#-Q- sx8brodie #######################
36	#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
37	#-Q- sx8brodie # @ wall_clock_limit = 10:00:00
38	#-Q- sx8brodie # Nom du travail LoadLeveler
39	#-Q- sx8brodie # @ job_name = SE
40	#-Q- sx8brodie # Fichier de sortie standard du travail
41	#-Q- sx8brodie # @ output = $(job_name).$(jobid)
42	#-Q- sx8brodie # Fichier de sortie d'erreur du travail
43	#-Q- sx8brodie # @ error = $(job_name).$(jobid)
44	#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
45	#-Q- sx8brodie # @ notification = error
46	#-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
47	#-Q- sx8brodie # @ queue
48	#-Q- aix6 #!/bin/ksh
49	#-Q- aix6 #######################
50	#-Q- aix6 ## VARGAS IDRIS ##
51	#-Q- aix6 #######################
52	#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
53	#-Q- aix6 # @ wall_clock_limit = 10:00:00
54	#-Q- aix6 # Nom du travail LoadLeveler
55	#-Q- aix6 # @ job_name = SE
56	#-Q- aix6 # Fichier de sortie standard du travail
57	#-Q- aix6 # @ output = $(job_name).$(jobid)
58	#-Q- aix6 # Fichier de sortie d'erreur du travail
59	#-Q- aix6 # @ error = $(job_name).$(jobid)
60	#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
61	#-Q- aix6 # @ notification = error
62	#-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
63	#-Q- aix6 # @ queue
64	#-Q- ulam #!/bin/ksh
65	#-Q- ulam #######################
66	#-Q- ulam ## ULAM IDRIS ##
67	#-Q- ulam #######################
68	#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
69	#-Q- ulam # @ wall_clock_limit = 10:00:00
70	#-Q- ulam # Nom du travail LoadLeveler
71	#-Q- ulam # @ job_name = SE
72	#-Q- ulam # Fichier de sortie standard du travail
73	#-Q- ulam # @ output = $(job_name).$(jobid)
74	#-Q- ulam # Fichier de sortie d'erreur du travail
75	#-Q- ulam # @ error = $(job_name).$(jobid)
76	#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
77	#-Q- ulam # @ notification = error
78	#-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
79	#-Q- ulam # @ queue
80	#-Q- sx8mercure #!/bin/ksh
81	#-Q- sx8mercure ######################
82	#-Q- sx8mercure ## SX8MERCURE CEA ##
83	#-Q- sx8mercure ######################
84	#-Q- sx8mercure #PBS -N SE # Nom du job
85	#-Q- sx8mercure #PBS -j o # regroupement des stdout et stderr
86	#-Q- sx8mercure #PBS -S /usr/bin/ksh # shell de soumission
87	#-Q- sx8mercure #PBS -l memsz_job=8gb # Limite memoire a 1 Go
88	#-Q- sx8mercure #PBS -l cputim_job=24:00:00 # Limite temps a 1 heures
89	#-Q- sx8mercure #PBS -q scalaire
90	#-Q- sx8mercure #PBS -r n
91	#-Q- sx9mercure #!/bin/ksh
92	#-Q- sx9mercure ######################
93	#-Q- sx9mercure ## SX9MERCURE CCRT ##
94	#-Q- sx9mercure ######################
95	#-Q- sx9mercure #PBS -N SE # Nom du job
96	#-Q- sx9mercure #PBS -j o # regroupement des stdout et stderr
97	#-Q- sx9mercure #PBS -S /usr/bin/ksh # shell de soumission
98	#-Q- sx9mercure #PBS -l memsz_job=8gb # Limite memoire a 1 Go
99	#-Q- sx9mercure #PBS -l elapstim_req=24:00:00 # Limite temps a 1 heures
100	#-Q- sx9mercure #PBS -q scalaire
101	#-Q- sx9mercure #PBS -r n
102	#-Q- titane #!/bin/ksh
103	#-Q- titane ######################
104	#-Q- titane ## TITANE CEA ##
105	#-Q- titane ######################
106	#-Q- titane #MSUB -r SE # Nom du job
107	#-Q- titane #MSUB -eo
108	#-Q- titane #MSUB -n 1 # Reservation du processus
109	#-Q- titane #MSUB -T 86400 # Limite de temps elapsed du job
110	#-Q- titane #MSUB -q mono
111	#-Q- titane #MSUB -E '-rn'
112	#-Q- lxiv8 ######################
113	#-Q- lxiv8 ## OBELIX LSCE ##
114	#-Q- lxiv8 ######################
115	#-Q- lxiv8 #PBS -N SE
116	#-Q- lxiv8 #PBS -m a
117	#-Q- lxiv8 #PBS -j oe
118	#-Q- lxiv8 #PBS -q medium
119	#-Q- lxiv8 #PBS -o SE.$$
120	#-Q- lxiv8 #PBS -S /bin/ksh
121	#-Q- default #!/bin/ksh
122	#-Q- default ##################
123	#-Q- default ## DEFAULT HOST ##
124	#-Q- default ##################
125
126	#**************************************************************
127	# Author: Sebastien Denvil
128	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
129	# $Revision:: $ Revision of last commit
130	# $Author:: $ Author of last commit
131	# $Date:: $ Date of last commit
132	# IPSL (2006)
133	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
134	#
135	#**************************************************************
136
137	#set -eu
138	#set -vx
139
140	date
141
142	#-Q- sx8brodie export OMP_NUM_THREADS=1
143	#-Q- aix6 export OMP_NUM_THREADS=1
144	#-Q- ulam export OMP_NUM_THREADS=1
145
146	#D- Task type (computing or post-processing)
147	TaskType=post-processing
148
149	########################################################################
150
151	#D- Flag to determine if this job in a standalone mode
152	#D- Default : value from AA_job if any
153	StandAlone=${StandAlone:=true}
154
155	#D- Path to libIGCM
156	#D- Default : value from AA_job if any
157	# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
158	# WARNING you must check MirrorlibIGCM variable in sys library.
159	# WARNING If this variable is true, you must use libIGCM_POST path instead
160	# WARNING of your running libIGCM directory.
161	libIGCM=${libIGCM:=::modipsl::/libIGCM}
162
163	#D- Flag to determine if rebuild process has been performed asynchronously
164	#D- Possible value true or false.
165	#D- If true raw files has allready been patched by rebuild job
166	#D- If false create_ts will patch the raw files
167	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
168	RebuildFrequency=${RebuildFrequency:=true}
169
170	#D- Flag to determine atlas job's output directory
171	#D- Default : value from libIGCM_post.ksh if any
172	POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
173
174	#D- Increased verbosity (1, 2, 3)
175	#D- Default : value from AA_job if any
176	Verbosity=${Verbosity:=3}
177
178	#D- Low level debug : to bypass lib test checks and stack construction
179	#D- Default : value from AA_job if any
180	DEBUG_debug=${DEBUG_debug:=false}
181
182	#D- TEMPORARY Flag to determine atmospheric resolution
183	#D- Default : value from atmospheric driver if any
184	RESOL_ATM=${RESOL_ATM:=ALL}
185
186	#D- Flag to determine surface resolution
187	#D- Default : value from surface driver if any
188	RESOL_SRF=ALL
189
190	#D- Flag to determine surface resolution
191	#D- Default : value from surface driver if any
192	RESOL_SBG=ALL
193
194	#D- TEMPORARY Flag to determine ocean resolution
195	#D- Default : value from ocean driver if any
196	RESOL_OCE=${RESOL_OCE:=ORCA2}
197
198	#D- TEMPORARY Flag to determine ice resolution
199	#D- Default : value from ice driver if any
200	RESOL_ICE=${RESOL_ICE:=ORCA2}
201
202	#D- TEMPORARY Flag to determine marine biogeochemistry resolution
203	#D- Default : value from ice driver if any
204	RESOL_MBG=${RESOL_MBG:=ORCA2}
205
206	########################################################################
207
208	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
209	( ${DEBUG_debug} ) && IGCM_debug_Check
210	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
211	( ${DEBUG_debug} ) && IGCM_card_Check
212	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
213	( ${DEBUG_debug} ) && IGCM_date_Check
214	#-------
215	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
216	. ${libIGCM}/libIGCM_config/libIGCM_config.ksh
217
218	########################################################################
219
220	#set -vx
221
222	IGCM_sys_MkdirWork ${RUN_DIR_PATH}
223	IGCM_sys_Cd ${RUN_DIR_PATH}
224
225	# ------------------------------------------------------------------
226	# Test if all was right before proceeding further
227	# ------------------------------------------------------------------
228	IGCM_debug_Verif_Exit_Post
229
230	if [ ${StandAlone} = true ] ; then
231	CARD_DIR=${SUBMIT_DIR}
232	else
233	CARD_DIR=${RUN_DIR_PATH}
234	IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
235	IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card ${RUN_DIR_PATH}
236	IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP ${RUN_DIR_PATH}
237	IGCM_sys_Get_Master ${SUBMIT_DIR}/POST ${RUN_DIR_PATH}
238	fi
239
240	#==================================
241	# First of all
242	#
243	# Read libIGCM compatibility version in config.card
244	# Read UserChoices section
245	# Read Ensemble section
246	# Read Post section
247	# Define all netcdf output directories
248	#==================================
249	IGCM_config_CommonConfiguration ${CARD_DIR}/config.card
250
251	#==================================
252	# Define default value to keep compatibility with previous card: means before changes due to TGCC
253	if [ X${PackDefault} = Xtrue ] ; then
254	[ X${config_Post_PackFrequency} = X ] && config_Post_PackFrequency=${config_Post_RebuildFrequency}
255	else
256	config_Post_PackFrequency=NONE
257	fi
258
259	#==================================
260	# If pack is active then PackFrequency overule the config_UserChoices_PeriodLength
261	if ( [ ! X${config_Post_PackFrequency} = X${NULL_STR} ] && [ ! X${config_Post_PackFrequency} = XNONE ] ) ; then
262	config_UserChoices_PeriodLength=${config_Post_PackFrequency}
263	fi
264
265	#==================================
266	# Read ListOfComponents section:
267	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
268
269	#==================================
270	# Read SeasonalFrequency:
271	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post SeasonalFrequency
272
273	#
274	# Determine period for seasonnal average. Default : value from AA_job if any
275	#
276	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
277	#
278	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
279	#
280	freq=$( echo ${config_Post_SeasonalFrequency} \| sed -e "s/[yY]//" )
281	#
282	an_fin=$(( $( IGCM_date_ConvertGregorianDateToJulian ${PeriodDateEnd} ) / 1000 ))
283	an_deb=$( IGCM_date_YearDigit $(( an_fin - freq + 1 )) )
284	an_fin=$( IGCM_date_YearDigit ${an_fin} )
285	#
286	# For each component selected determine which files need post-processing
287	#
288	for comp in ${config_ListOfComponents[*]} ; do
289	#
290	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
291	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
292	#
293	card=${CARD_DIR}/COMP/${compname}.card
294	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
295	#
296	ListFilesName=${compname}_OutputFiles_List
297	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
298	#
299	if [ X${FileName0} != X${NULL_STR} ] ; then
300	#
301	# INITIALISATION
302	#
303	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
304	typeset i=2
305	#
306	until [ $i -gt $NbFiles ]; do
307	#
308	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
309	#
310	if [ X${flag_post} != XNONE ] ; then
311	#
312	# Check if seasonal is required for this file
313	#
314	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
315	#
316	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
317	#
318	# variable option allready typeset above
319	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
320	if [ ${option} = Seasonal ] ; then
321	FoundSeasonal=true
322	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
323	fi
324	done
325	#
326	if [ ! X${FoundSeasonal} = Xtrue ] ; then
327	eval ${compname}_${flag_post}_Seasonal=ON
328	fi
329	#
330	if [ ! X$( eval echo \${${compname}_${flag_post}_Seasonal} ) = XON ] ; then
331	(( i=i+3 ))
332	continue
333	fi
334	#
335	# CREATE LIST
336	#
337	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
338	#
339	DIRECTORY=${R_SAVE}/${comp}/Analyse/SE
340	#
341	TestedFile=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${FILE}.nc
342	#
343	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
344	if [ ! $? = 0 ] ; then
345	eval set +A LISTE_FILE_${comp} \$\{LISTE_FILE_${comp}[*]} ${FILE}
346	if [ ! ${RebuildFrequency} = true ] ; then
347	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
348	eval set +A LISTE_PATCHES_${FILE} \$\{${compname}_Post_${FILE}_Patches[*]}
349	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
350	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
351	if [ Xload${Patch} != X ] ; then
352	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
353	eval load${Patch}=loaded
354	fi
355	done
356	fi
357	fi
358	fi
359	fi
360	(( i=i+3 ))
361	done # until [ $i -eq $NbFiles ]
362	fi
363	done # for comp
364
365	for comp in ${config_ListOfComponents[*]} ; do
366	#
367	eval R_OUT_${comp}=${R_SAVE}/${comp}
368	#
369	i=0
370	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
371	#
372	# Determine in which output can we find file
373	# IE : Output/MO or Output/DA or ...
374	#
375	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
376	case ${FlagDir} in
377	1Y) FreqDir=YE ;;
378	1M) FreqDir=MO ;;
379	5D\|1D) FreqDir=DA ;;
380	HF) FreqDir=HF ;;
381	3H) FreqDir=HF ;;
382	INS) FreqDir=INS ;;
383	esac
384	#
385	RESULT_SE=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${file}.nc
386	# Do not redoo an existing SE
387	IGCM_sys_TestFileArchive ${R_SAVE}/${comp}/Analyse/SE/${RESULT_SE}
388	if [ $? = 0 ] ; then
389	continue
390	fi
391	#
392	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
393	#
394	case ${config_UserChoices_PeriodLength} in
395	# For Yearly simulation :
396	1Y\|1y)
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" ${an} )
407	#
408	diy=$( IGCM_date_DaysInYear $an4 )
409	afin=$( IGCM_date_AddDaysToGregorianDate ${an4}0101 $(( diy - 1 )) )
410	date=${an4}0101_${afin}
411	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
412	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
413	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
414	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
415	(( an = an + 1 ))
416	done
417	#
418	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
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	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
436	(( nbfile = nbfile + 1 ))
437	done
438	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
439	IGCM_sys_Rm tmpfile_ncra
440
441	# detect time counter : time or time_counter ie unlimited variable
442	var_unlim=$(ncdump -h ${liste_file_se_tmp[1]}\|grep UNLIMITED\|awk '{print $1}')
443
444	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
445	#
446	(( nb = ${mois} - 1 ))
447	#
448	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
449	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d ${var_unlim},${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
450	done
451	IGCM_sys_Rm ${liste_file_se_tmp[*]}
452	;;
453	# For Monthly simulation :
454	1M\|1m)
455	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
456	#
457	(( nb = ${mois} - 1 ))
458	#
459	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
460	#
461	(( an = an_deb ))
462	# Initialize array
463	#set -A liste_file_se
464	#set -A liste_file_se_tmp
465	unset liste_file_se
466	unset liste_file_se_tmp
467	while [ ${an} -le ${an_fin} ] ; do
468	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
469	#
470	an4=$(printf "%04i\n" ${an} )
471	#
472	date=${an4}${mois}01_${an4}${mois}${moisL}
473	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
474	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
475	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
476	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
477
478	(( an = an + 1 ))
479	done
480	#
481	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
482	IGCM_debug_Verif_Exit_Post
483
484	# Apply IGCM_Patch if needed
485	if [ ! ${RebuildFrequency} = true ] ; then
486	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
487	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
488	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
489	IGCM_${Patch} ${file_t}
490	done
491	done
492	fi
493	fi
494
495	# Search of common list of variables to be treated
496	nbfile=0
497	for file_common_var in ${liste_file_se_tmp[*]} ; do
498	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
499	(( nbfile = nbfile + 1 ))
500	done
501	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
502	IGCM_sys_Rm tmpfile_ncra
503
504	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
505
506	IGCM_sys_Rm ${liste_file_se_tmp[*]}
507	done
508	;;
509	D\|d)
510	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
511	#
512	(( nb = ${mois} - 1 ))
513	#
514	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
515	#
516	(( an = an_deb ))
517	# Initialize array
518	#set -A liste_file_se
519	#set -A liste_file_se_tmp
520	unset liste_file_se
521	unset liste_file_se_tmp
522	while [ ${an} -le ${an_fin} ] ; do
523	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
524	#
525	an4=$(printf "%04i\n" ${an} )
526	#
527	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
528	# for one day
529	if [ ${length_d} -eq 1 ] ; then
530	(( length_d = 0 ))
531	fi
532	(( day = 1 ))
533	while [ ${day} -le ${moisL} ] ; do
534	day2=$(printf "%02i\n" ${day} )
535	day_beg=${an4}${mois}${day2}
536	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
537	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
538	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
539	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
540	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
541	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
542	(( day = day + 1 ))
543	done
544	(( an = an + 1 ))
545	done
546	#
547	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
548	IGCM_debug_Verif_Exit_Post
549
550	# Apply IGCM_Patch if needed
551	if [ ! ${RebuildFrequency} = true ] ; then
552	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
553	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
554	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
555	IGCM_${Patch} ${file_t}
556	done
557	done
558	fi
559	fi
560
561	# Search of common list of variables to be treated
562	nbfile=0
563	for file_common_var in ${liste_file_se_tmp[*]} ; do
564	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
565	(( nbfile = nbfile + 1 ))
566	done
567	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
568	IGCM_sys_Rm tmpfile_ncra
569
570	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
571	IGCM_sys_Rm ${liste_file_se_tmp[*]}
572	done
573	;;
574	esac
575	#
576
577	# Search of common list of variables to be treated
578	nbfile=0
579	for file_common_var in ${OUT_SE[*]} ; do
580	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncrcat
581	(( nbfile = nbfile + 1 ))
582	done
583	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
584	IGCM_sys_Rm tmpfile_ncrcat
585
586	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
587	#
588	IGCM_sys_Rm ${OUT_SE[*]}
589	#
590	# detect time counter : time or time_counter ie unlimited variable
591	var_unlim=$(ncdump -h ${RESULT_SE}\|grep UNLIMITED\| cut -d ' ' -f 1)
592
593	# Put correct climatological axis following calendar
594	case ${config_UserChoices_CalendarType} in
595	360d\|360_day)
596	# 360 days
597	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\"'"
598	;;
599	noleap\|365_day)
600	# 365 days
601	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\"'"
602	;;
603	all_leap\|366_day)
604	# 366 days
605	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\"'"
606	;;
607	leap\|gregorian\|standard)
608	# 365.2425 days
609	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\"'"
610	;;
611	esac
612	eval IGCM_sys_ncap2 -Oh -s $ncap2cmd ${RESULT_SE} tmp.nc
613	IGCM_sys_Rm ${RESULT_SE}
614	IGCM_sys_Mv tmp.nc ${RESULT_SE}
615	#
616	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
617	IGCM_sys_Rm ${RESULT_SE}
618	#
619	done
620	done
621
622	# DODS copy
623	for comp in ${config_ListOfComponents[*]} ; do
624	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
625	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
626	done
627
628	YEARS=${an_deb}_${an_fin}
629	DIR_OUT=SE
630
631	export POST_DIR; export SUBMIT_DIR; export libIGCM; export R_INIT; export R_BC; export StandAlone
632	export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ; export RESOL_SBG
633	export R_SAVE; export config_UserChoices_JobName; export config_UserChoices_TagName; export YEARS; export DIR_OUT
634	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"
635	export listVarEnv;
636
637	#D-
638	# --------------------------------------------------------------------
639	#D- Test if all was right before ATLAS
640	# --------------------------------------------------------------------
641	IGCM_debug_Verif_Exit_Post
642
643	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
644	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
645	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
646	#
647	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
648	IGCM_sys_QsubPost atlas_ORCHIDEE ;
649	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
650	IGCM_sys_QsubPost atlas_LMDZ ;
651	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
652	IGCM_sys_QsubPost atlas_ORCA_LIM ;
653	Script_Post_Output=additionnal.${PeriodDateEnd} ;
654	IGCM_sys_QsubPost additionnal ;
655	#
656	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
657	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] \|\| \
658	[ ${config_UserChoices_TagName} = "IPSLCM5B" ] \|\| \
659	[ ${config_UserChoices_TagName} = "IPSLCM5A-MR" ] ; then
660	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
661	IGCM_sys_QsubPost atlas_ORCHIDEE ;
662	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
663	IGCM_sys_QsubPost atlas_LMDZ ;
664	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
665	IGCM_sys_QsubPost atlas_ORCA_LIM ;
666	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
667	IGCM_sys_QsubPost atlas_PISCES ;
668	#
669	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
670	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
671	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
672	#
673	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
674	IGCM_sys_QsubPost atlas_LMDZ ;
675	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
676	IGCM_sys_QsubPost atlas_ORCHIDEE ;
677	#
678	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
679	#
680	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
681	IGCM_sys_QsubPost atlas_LMDZ ;
682	#
683	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
684	[ ${config_UserChoices_TagName} = "OL2" ] ; then
685	#
686	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
687	IGCM_sys_QsubPost atlas_ORCHIDEE ;
688	#
689	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\|
690	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] ; then
691	#
692	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
693	IGCM_sys_QsubPost atlas_ORCA_LIM ;
694	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] ; then
695	#
696	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
697	IGCM_sys_QsubPost atlas_ORCA_LIM ;
698	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
699	IGCM_sys_QsubPost atlas_PISCES ;
700	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
701	#
702	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
703	IGCM_sys_QsubPost atlas_PISCES ;
704	#
705	fi
706
707	# Clean RUN_DIR_PATH (necessary for cesium and titane only)
708	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}

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