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source: trunk/libIGCM/AA_create_se @ 416

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

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