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source: trunk/libIGCM/AA_create_se @ 617

Last change on this file since 617 was 616, checked in by sdipsl, 12 years ago
Merge libIGCM_MPI_OpenMP branch within the trunk trunk will shortly be tagged libIGCM_2.0_beta
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 = 10:00:00
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 = 10:00:00
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 = 10:00:00
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 ## SX9MERCURE CCRT ##
82	#-Q- sx9mercure ######################
83	#-Q- sx9mercure #PBS -N SE # Nom du job
84	#-Q- sx9mercure #PBS -j o # regroupement des stdout et stderr
85	#-Q- sx9mercure #PBS -S /usr/bin/ksh # shell de soumission
86	#-Q- sx9mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go
87	#-Q- sx9mercure #PBS -l elapstim_req=1:00:00 # Limite temps a 1 heures
88	#-Q- sx9mercure #PBS -q scalaire
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 -eo
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 -q mono
98	#-Q- lxiv8 ######################
99	#-Q- lxiv8 ## OBELIX LSCE ##
100	#-Q- lxiv8 ######################
101	#-Q- lxiv8 #PBS -N SE
102	#-Q- lxiv8 #PBS -m a
103	#-Q- lxiv8 #PBS -j oe
104	#-Q- lxiv8 #PBS -q medium
105	#-Q- lxiv8 #PBS -o SE.$$
106	#-Q- lxiv8 #PBS -S /bin/ksh
107	#-Q- default #!/bin/ksh
108	#-Q- default ##################
109	#-Q- default ## DEFAULT HOST ##
110	#-Q- default ##################
111
112	#**************************************************************
113	# Author: Sebastien Denvil
114	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
115	# $Revision:: $ Revision of last commit
116	# $Author:: $ Author of last commit
117	# $Date:: $ Date of last commit
118	# IPSL (2006)
119	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
120	#
121	#**************************************************************
122
123	#set -eu
124	#set -vx
125
126	date
127
128	#-Q- sx8brodie export OMP_NUM_THREADS=1
129	#-Q- aix6 export OMP_NUM_THREADS=1
130	#-Q- ulam export OMP_NUM_THREADS=1
131
132	########################################################################
133
134	#D- Flag to determine if this job in a standalone mode
135	#D- Default : value from AA_job if any
136	StandAlone=${StandAlone:=true}
137
138	#D- Path to libIGCM
139	#D- Default : value from AA_job if any
140	# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
141	# WARNING you must check MirrorlibIGCM variable in sys library.
142	# WARNING If this variable is true, you must use libIGCM_POST path instead
143	# WARNING of your running libIGCM directory.
144	libIGCM=${libIGCM:=::modipsl::/libIGCM}
145
146	#D- Flag to determine if rebuild process has been performed asynchronously
147	#D- Possible value true or false.
148	#D- If true raw files has allready been patched by rebuild job
149	#D- If false create_ts will patch the raw files
150	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
151	RebuildFrequency=${RebuildFrequency:=true}
152
153	#D- Flag to determine atlas job's output directory
154	#D- Default : value from libIGCM_post.ksh if any
155	POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
156
157	#D- Increased verbosity (1, 2, 3)
158	#D- Default : value from AA_job if any
159	Verbosity=${Verbosity:=3}
160
161	#D- Low level debug : to bypass lib test checks and stack construction
162	#D- Default : value from AA_job if any
163	DEBUG_debug=${DEBUG_debug:=false}
164
165	#D- TEMPORARY Flag to determine atmospheric resolution
166	#D- Default : value from atmospheric driver if any
167	RESOL_ATM=${RESOL_ATM:=ALL}
168
169	#D- Flag to determine surface resolution
170	#D- Default : value from surface driver if any
171	RESOL_SRF=ALL
172
173	#D- Flag to determine surface resolution
174	#D- Default : value from surface driver if any
175	RESOL_SBG=ALL
176
177	#D- TEMPORARY Flag to determine ocean resolution
178	#D- Default : value from ocean driver if any
179	RESOL_OCE=${RESOL_OCE:=ORCA2}
180
181	#D- TEMPORARY Flag to determine ice resolution
182	#D- Default : value from ice driver if any
183	RESOL_ICE=${RESOL_ICE:=ORCA2}
184
185	#D- TEMPORARY Flag to determine marine biogeochemistry resolution
186	#D- Default : value from ice driver if any
187	RESOL_MBG=${RESOL_MBG:=ORCA2}
188
189	########################################################################
190
191	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
192	( ${DEBUG_debug} ) && IGCM_debug_Check
193	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
194	( ${DEBUG_debug} ) && IGCM_card_Check
195	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
196	( ${DEBUG_debug} ) && IGCM_date_Check
197	#-------
198	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
199
200	########################################################################
201
202	#set -vx
203
204	IGCM_sys_MkdirWork ${RUN_DIR_PATH}
205	IGCM_sys_Cd ${RUN_DIR_PATH}
206
207	# ------------------------------------------------------------------
208	# Test if all was right before proceeding further
209	# ------------------------------------------------------------------
210	IGCM_debug_Verif_Exit_Post
211
212	if [ ${StandAlone} = true ] ; then
213	CARD_DIR=${SUBMIT_DIR}
214	else
215	CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
216	IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH}
217	fi
218
219	#==================================
220	# First of all
221	#
222	typeset option
223
224	#==================================
225	# Read UserChoices section:
226	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card UserChoices
227	echo
228	IGCM_debug_Print 1 "DefineArrayFromOption : config_UserChoices"
229	for option in ${config_UserChoices[*]} ; do
230	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
231	eval auxprint=\${config_UserChoices_${option}}
232	IGCM_debug_Print 3 "${option} : ${auxprint}"
233	done
234	#
235	echo
236
237	#==================================
238	# Read Post section:
239	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card Post
240	echo
241	IGCM_debug_Print 1 "DefineArrayFromOption : config_Post"
242	for option in ${config_Post[*]} ; do
243	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post ${option}
244	eval auxprint=\${config_Post_${option}}
245	IGCM_debug_Print 3 "${option} : ${auxprint}"
246	done
247	#
248	echo
249
250	#==================================
251	# Define default value to keep compatibility with previous card: means before changes due to TGCC
252	[ X${config_Post_PackFrequency} = X ] && config_Post_PackFrequency=${config_Post_RebuildFrequency}
253
254	#==================================
255	# If pack is active then PackFrequency overule the config_UserChoices_PeriodLength
256	if ( [ ! X${config_Post_PackFrequency} = X${NULL_STR} ] && [ ! X${config_Post_PackFrequency} = XNONE ] ) ; then
257	config_UserChoices_PeriodLength=${config_Post_PackFrequency}
258	fi
259
260	#==================================
261	#R_SAVE : Job output directory
262	#R_BUFR : Job output buffered directory
263	if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
264	FreeName=$( echo ${config_UserChoices_JobName} \| sed 's/.*_//' )
265	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
266	R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
267	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
268	else
269	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
270	R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
271	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_JobName}
272	fi
273	#
274	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
275	#
276	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post SeasonalFrequency
277	#
278	# Determine period for seasonnal average. Default : value from AA_job if any
279	#
280	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
281	#
282	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
283	#
284	freq=$( echo ${config_Post_SeasonalFrequency} \| sed -e "s/[yY]//" )
285	#
286	an_fin=$(( $( IGCM_date_ConvertGregorianDateToJulian ${PeriodDateEnd} ) / 1000 ))
287	an_deb=$( IGCM_date_YearDigit $(( an_fin - freq + 1 )) )
288	an_fin=$( IGCM_date_YearDigit ${an_fin} )
289	#
290	# For each component selected determine which files need post-processing
291	#
292	for comp in ${config_ListOfComponents[*]} ; do
293	#
294	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
295	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
296	#
297	card=${CARD_DIR}/COMP/${compname}.card
298	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
299	#
300	ListFilesName=${compname}_OutputFiles_List
301	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
302	#
303	if [ X${FileName0} != X${NULL_STR} ] ; then
304	#
305	# INITIALISATION
306	#
307	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
308	typeset i=2
309	#
310	until [ $i -gt $NbFiles ]; do
311	#
312	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
313	#
314	if [ X${flag_post} != XNONE ] ; then
315	#
316	# Check if seasonal is required for this file
317	#
318	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
319	#
320	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
321	#
322	# variable option allready typeset above
323	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
324	if [ ${option} = Seasonal ] ; then
325	FoundSeasonal=true
326	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
327	fi
328	done
329	#
330	if [ ! X${FoundSeasonal} = Xtrue ] ; then
331	eval ${compname}_${flag_post}_Seasonal=ON
332	fi
333	#
334	if [ ! X$( eval echo \${${compname}_${flag_post}_Seasonal} ) = XON ] ; then
335	(( i=i+3 ))
336	continue
337	fi
338	#
339	# CREATE LIST
340	#
341	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
342	#
343	DIRECTORY=${R_SAVE}/${comp}/Analyse/SE
344	#
345	TestedFile=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${FILE}.nc
346	#
347	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
348	if [ ! $? = 0 ] ; then
349	eval set +A LISTE_FILE_${comp} \$\{LISTE_FILE_${comp}[*]} ${FILE}
350	if [ ! ${RebuildFrequency} = true ] ; then
351	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
352	eval set +A LISTE_PATCHES_${FILE} \$\{${compname}_Post_${FILE}_Patches[*]}
353	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
354	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
355	if [ Xload${Patch} != X ] ; then
356	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
357	eval load${Patch}=loaded
358	fi
359	done
360	fi
361	fi
362	fi
363	fi
364	(( i=i+3 ))
365	done # until [ $i -eq $NbFiles ]
366	fi
367	done # for comp
368
369	for comp in ${config_ListOfComponents[*]} ; do
370	#
371	eval R_OUT_${comp}=${R_SAVE}/${comp}
372	#
373	i=0
374	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
375	#
376	# Determine in which output can we find file
377	# IE : Output/MO or Output/DA or ...
378	#
379	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
380	case ${FlagDir} in
381	1Y) FreqDir=YE ;;
382	1M) FreqDir=MO ;;
383	5D\|1D) FreqDir=DA ;;
384	HF) FreqDir=HF ;;
385	3H) FreqDir=HF ;;
386	INS) FreqDir=INS ;;
387	esac
388	#
389	RESULT_SE=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${file}.nc
390	# Do not redoo an existing SE
391	IGCM_sys_TestFileArchive ${R_SAVE}/${comp}/Analyse/SE/${RESULT_SE}
392	if [ $? = 0 ] ; then
393	continue
394	fi
395	#
396	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
397	#
398	case ${config_UserChoices_PeriodLength} in
399	# For Yearly simulation :
400	1Y\|1y)
401	(( an = an_deb ))
402	# Initialize array
403	#set -A liste_file_se
404	#set -A liste_file_se_tmp
405	unset liste_file_se
406	unset liste_file_se_tmp
407	while [ ${an} -le ${an_fin} ] ; do
408	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
409	#
410	an4=$(printf "%04i\n" ${an} )
411	#
412	diy=$( IGCM_date_DaysInYear $an4 )
413	afin=$( IGCM_date_AddDaysToGregorianDate ${an4}0101 $(( diy - 1 )) )
414	date=${an4}0101_${afin}
415	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
416	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
417	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
418	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
419	(( an = an + 1 ))
420	done
421	#
422	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
423	IGCM_debug_Verif_Exit_Post
424
425	# Apply IGCM_Patch if needed
426	if [ ! ${RebuildFrequency} = true ] ; then
427	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
428	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
429	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
430	IGCM_${Patch} ${file_t}
431	done
432	done
433	fi
434	fi
435
436	# Search of common list of variables to be treated
437	nbfile=0
438	for file_common_var in ${liste_file_se_tmp[*]} ; do
439	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
440	(( nbfile = nbfile + 1 ))
441	done
442	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
443	IGCM_sys_Rm tmpfile_ncra
444
445	# detect time counter : time or time_counter ie unlimited variable
446	var_unlim=$(ncdump -h ${liste_file_se_tmp[1]}\|grep UNLIMITED\| cut -d ' ' -f 1)
447
448	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
449	#
450	(( nb = ${mois} - 1 ))
451	#
452	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
453	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d ${var_unlim},${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
454	done
455	IGCM_sys_Rm ${liste_file_se_tmp[*]}
456	;;
457	# For Monthly simulation :
458	1M\|1m)
459	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
460	#
461	(( nb = ${mois} - 1 ))
462	#
463	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
464	#
465	(( an = an_deb ))
466	# Initialize array
467	#set -A liste_file_se
468	#set -A liste_file_se_tmp
469	unset liste_file_se
470	unset liste_file_se_tmp
471	while [ ${an} -le ${an_fin} ] ; do
472	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
473	#
474	an4=$(printf "%04i\n" ${an} )
475	#
476	date=${an4}${mois}01_${an4}${mois}${moisL}
477	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
478	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
479	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
480	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
481
482	(( an = an + 1 ))
483	done
484	#
485	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
486	IGCM_debug_Verif_Exit_Post
487
488	# Apply IGCM_Patch if needed
489	if [ ! ${RebuildFrequency} = true ] ; then
490	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
491	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
492	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
493	IGCM_${Patch} ${file_t}
494	done
495	done
496	fi
497	fi
498
499	# Search of common list of variables to be treated
500	nbfile=0
501	for file_common_var in ${liste_file_se_tmp[*]} ; do
502	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
503	(( nbfile = nbfile + 1 ))
504	done
505	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
506	IGCM_sys_Rm tmpfile_ncra
507
508	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
509
510	IGCM_sys_Rm ${liste_file_se_tmp[*]}
511	done
512	;;
513	D\|d)
514	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
515	#
516	(( nb = ${mois} - 1 ))
517	#
518	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
519	#
520	(( an = an_deb ))
521	# Initialize array
522	#set -A liste_file_se
523	#set -A liste_file_se_tmp
524	unset liste_file_se
525	unset liste_file_se_tmp
526	while [ ${an} -le ${an_fin} ] ; do
527	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
528	#
529	an4=$(printf "%04i\n" ${an} )
530	#
531	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
532	# for one day
533	if [ ${length_d} -eq 1 ] ; then
534	(( length_d = 0 ))
535	fi
536	(( day = 1 ))
537	while [ ${day} -le ${moisL} ] ; do
538	day2=$(printf "%02i\n" ${day} )
539	day_beg=${an4}${mois}${day2}
540	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
541	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
542	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
543	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
544	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
545	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
546	(( day = day + 1 ))
547	done
548	(( an = an + 1 ))
549	done
550	#
551	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
552	IGCM_debug_Verif_Exit_Post
553
554	# Apply IGCM_Patch if needed
555	if [ ! ${RebuildFrequency} = true ] ; then
556	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
557	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
558	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
559	IGCM_${Patch} ${file_t}
560	done
561	done
562	fi
563	fi
564
565	# Search of common list of variables to be treated
566	nbfile=0
567	for file_common_var in ${liste_file_se_tmp[*]} ; do
568	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
569	(( nbfile = nbfile + 1 ))
570	done
571	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
572	IGCM_sys_Rm tmpfile_ncra
573
574	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
575	IGCM_sys_Rm ${liste_file_se_tmp[*]}
576	done
577	;;
578	esac
579	#
580
581	# Search of common list of variables to be treated
582	nbfile=0
583	for file_common_var in ${OUT_SE[*]} ; do
584	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncrcat
585	(( nbfile = nbfile + 1 ))
586	done
587	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
588	IGCM_sys_Rm tmpfile_ncrcat
589
590	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
591	#
592	IGCM_sys_Rm ${OUT_SE[*]}
593	#
594	# detect time counter : time or time_counter ie unlimited variable
595	var_unlim=$(ncdump -h ${RESULT_SE}\|grep UNLIMITED\| cut -d ' ' -f 1)
596
597	# Put correct climatological axis following calendar
598	case ${config_UserChoices_CalendarType} in
599	360d\|360_day)
600	# 360 days
601	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\"'"
602	;;
603	noleap\|365_day)
604	# 365 days
605	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\"'"
606	;;
607	all_leap\|366_day)
608	# 366 days
609	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\"'"
610	;;
611	leap\|gregorian\|standard)
612	# 365.2425 days
613	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\"'"
614	;;
615	esac
616	eval IGCM_sys_ncap2 -Oh -s $ncap2cmd ${RESULT_SE} tmp.nc
617	IGCM_sys_Rm ${RESULT_SE}
618	IGCM_sys_Mv tmp.nc ${RESULT_SE}
619	#
620	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
621	IGCM_sys_Rm ${RESULT_SE}
622	#
623	done
624	done
625
626	# DODS copy
627	for comp in ${config_ListOfComponents[*]} ; do
628	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
629	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
630	done
631
632	YEARS=${an_deb}_${an_fin}
633	DIR_OUT=SE
634
635	export POST_DIR; export SUBMIT_DIR; export libIGCM; export R_INIT; export R_BC; export StandAlone
636	export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ; export RESOL_SBG
637	export R_SAVE; export config_UserChoices_JobName; export config_UserChoices_TagName; export YEARS; export DIR_OUT
638	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"
639	export listVarEnv;
640
641	#D-
642	# --------------------------------------------------------------------
643	#D- Test if all was right before ATLAS
644	# --------------------------------------------------------------------
645	IGCM_debug_Verif_Exit_Post
646
647	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
648	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
649	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
650	#
651	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
652	IGCM_sys_QsubPost atlas_ORCHIDEE ;
653	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
654	IGCM_sys_QsubPost atlas_LMDZ ;
655	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
656	IGCM_sys_QsubPost atlas_ORCA_LIM ;
657	Script_Post_Output=additionnal.${PeriodDateEnd} ;
658	IGCM_sys_QsubPost additionnal ;
659	#
660	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
661	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] \|\| \
662	[ ${config_UserChoices_TagName} = "IPSLCM5B" ] \|\| \
663	[ ${config_UserChoices_TagName} = "IPSLCM5A-MR" ] ; then
664	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
665	IGCM_sys_QsubPost atlas_ORCHIDEE ;
666	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
667	IGCM_sys_QsubPost atlas_LMDZ ;
668	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
669	IGCM_sys_QsubPost atlas_ORCA_LIM ;
670	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
671	IGCM_sys_QsubPost atlas_PISCES ;
672	#
673	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
674	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
675	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
676	#
677	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
678	IGCM_sys_QsubPost atlas_LMDZ ;
679	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
680	IGCM_sys_QsubPost atlas_ORCHIDEE ;
681	#
682	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
683	#
684	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
685	IGCM_sys_QsubPost atlas_LMDZ ;
686	#
687	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
688	[ ${config_UserChoices_TagName} = "OL2" ] ; then
689	#
690	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
691	IGCM_sys_QsubPost atlas_ORCHIDEE ;
692	#
693	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\|
694	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] ; then
695	#
696	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
697	IGCM_sys_QsubPost atlas_ORCA_LIM ;
698	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] ; then
699	#
700	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
701	IGCM_sys_QsubPost atlas_ORCA_LIM ;
702	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
703	IGCM_sys_QsubPost atlas_PISCES ;
704	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
705	#
706	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
707	IGCM_sys_QsubPost atlas_PISCES ;
708	#
709	fi
710
711	# Clean RUN_DIR_PATH (necessary for cesium and titane only)
712	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}

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