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source: trunk/libIGCM/AA_create_se @ 426

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

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