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source: trunk/libIGCM/AA_create_se @ 636

Last change on this file since 636 was 633, checked in by sdipsl, 12 years ago
Take into account PackDefault? to adapt post-processing behaviour
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
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1	#-Q- cesium #!/bin/ksh
2	#-Q- cesium ######################
3	#-Q- cesium ## CESIUM CEA ##
4	#-Q- cesium ######################
5	#-Q- cesium #MSUB -r SE # Nom du job
6	#-Q- cesium #MSUB -N 1 # Reservation du noeud
7	#-Q- cesium #MSUB -n 1 # Reservation du processus
8	#-Q- cesium #MSUB -T 86400 # Limite de temps elapsed du job
9	#-Q- cesium #MSUB -E "-j o"
10	#-Q- cesium #MSUB -E "-S /bin/ksh"
11	#-Q- curie ######################
12	#-Q- curie ## CURIE TGCC/CEA ##
13	#-Q- curie ######################
14	#-Q- curie #MSUB -r SE # Nom du job
15	#-Q- curie #MSUB -eo
16	#-Q- curie #MSUB -n 1 # Reservation du processus
17	#-Q- curie #MSUB -T 86400 # Limite de temps elapsed du job
18	#-Q- platine #!/usr/bin/ksh
19	#-Q- platine ###################
20	#-Q- platine ## PLATINE CEA ##
21	#-Q- platine ###################
22	#-Q- platine #BSUB -J SE # Nom du job
23	#-Q- platine #BSUB -N # message a la fin du job
24	#-Q- platine #BSUB -n 1 # reservation des processeurs pour le job
25	#-Q- platine #BSUB -W 1:00 # Limite temps
26	#-Q- platine #BSUB -q post # Passage en queue post
27	#-Q- platine #BSUB -L /bin/ksh
28	#-Q- sx8brodie #!/bin/ksh
29	#-Q- sx8brodie #######################
30	#-Q- sx8brodie ## SX8BRODIE IDRIS ##
31	#-Q- sx8brodie #######################
32	#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
33	#-Q- sx8brodie # @ wall_clock_limit = 10:00:00
34	#-Q- sx8brodie # Nom du travail LoadLeveler
35	#-Q- sx8brodie # @ job_name = SE
36	#-Q- sx8brodie # Fichier de sortie standard du travail
37	#-Q- sx8brodie # @ output = $(job_name).$(jobid)
38	#-Q- sx8brodie # Fichier de sortie d'erreur du travail
39	#-Q- sx8brodie # @ error = $(job_name).$(jobid)
40	#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
41	#-Q- sx8brodie # @ notification = error
42	#-Q- sx8brodie # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $REBUILD_DIR ; $RebuildFromArchive ; $POST_DIR ; $MASTER ; $DateBegin ; $PeriodDateBegin ; $PeriodDateEnd ; $NbRebuildDir ; $StandAlone ; $RESOL_ATM ; $RESOL_OCE ; $RESOL_ICE ; $RESOL_MBG ; $RESOL_SRF ; $RESOL_SBG ; $MASTER
43	#-Q- sx8brodie # @ queue
44	#-Q- aix6 #!/bin/ksh
45	#-Q- aix6 #######################
46	#-Q- aix6 ## VARGAS IDRIS ##
47	#-Q- aix6 #######################
48	#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
49	#-Q- aix6 # @ wall_clock_limit = 10:00:00
50	#-Q- aix6 # Nom du travail LoadLeveler
51	#-Q- aix6 # @ job_name = SE
52	#-Q- aix6 # Fichier de sortie standard du travail
53	#-Q- aix6 # @ output = $(job_name).$(jobid)
54	#-Q- aix6 # Fichier de sortie d'erreur du travail
55	#-Q- aix6 # @ error = $(job_name).$(jobid)
56	#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
57	#-Q- aix6 # @ notification = error
58	#-Q- aix6 # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $REBUILD_DIR ; $RebuildFromArchive ; $POST_DIR ; $MASTER ; $DateBegin ; $PeriodDateBegin ; $PeriodDateEnd ; $NbRebuildDir ; $StandAlone ; $RESOL_ATM ; $RESOL_OCE ; $RESOL_ICE ; $RESOL_MBG ; $RESOL_SRF ; $RESOL_SBG ; $MASTER
59	#-Q- aix6 # @ queue
60	#-Q- ulam #!/bin/ksh
61	#-Q- ulam #######################
62	#-Q- ulam ## ULAM IDRIS ##
63	#-Q- ulam #######################
64	#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
65	#-Q- ulam # @ wall_clock_limit = 10:00:00
66	#-Q- ulam # Nom du travail LoadLeveler
67	#-Q- ulam # @ job_name = SE
68	#-Q- ulam # Fichier de sortie standard du travail
69	#-Q- ulam # @ output = $(job_name).$(jobid)
70	#-Q- ulam # Fichier de sortie d'erreur du travail
71	#-Q- ulam # @ error = $(job_name).$(jobid)
72	#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
73	#-Q- ulam # @ notification = error
74	#-Q- ulam # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $REBUILD_DIR ; $RebuildFromArchive ; $POST_DIR ; $MASTER ; $DateBegin ; $PeriodDateBegin ; $PeriodDateEnd ; $NbRebuildDir ; $StandAlone ; $RESOL_ATM ; $RESOL_OCE ; $RESOL_ICE ; $RESOL_MBG ; $RESOL_SRF ; $RESOL_SBG ; $MASTER
75	#-Q- ulam # @ queue
76	#-Q- sx8mercure #!/bin/ksh
77	#-Q- sx8mercure ######################
78	#-Q- sx8mercure ## SX8MERCURE CEA ##
79	#-Q- sx8mercure ######################
80	#-Q- sx8mercure #PBS -N SE # Nom du job
81	#-Q- sx8mercure #PBS -j o # regroupement des stdout et stderr
82	#-Q- sx8mercure #PBS -S /usr/bin/ksh # shell de soumission
83	#-Q- sx8mercure #PBS -l memsz_job=8gb # Limite memoire a 1 Go
84	#-Q- sx8mercure #PBS -l cputim_job=24:00:00 # Limite temps a 1 heures
85	#-Q- sx8mercure #PBS -q scalaire
86	#-Q- sx9mercure #!/bin/ksh
87	#-Q- sx9mercure ######################
88	#-Q- sx9mercure ## SX9MERCURE CCRT ##
89	#-Q- sx9mercure ######################
90	#-Q- sx9mercure #PBS -N SE # Nom du job
91	#-Q- sx9mercure #PBS -j o # regroupement des stdout et stderr
92	#-Q- sx9mercure #PBS -S /usr/bin/ksh # shell de soumission
93	#-Q- sx9mercure #PBS -l memsz_job=8gb # Limite memoire a 1 Go
94	#-Q- sx9mercure #PBS -l elapstim_req=24:00:00 # Limite temps a 1 heures
95	#-Q- sx9mercure #PBS -q scalaire
96	#-Q- titane #!/bin/ksh
97	#-Q- titane ######################
98	#-Q- titane ## TITANE CEA ##
99	#-Q- titane ######################
100	#-Q- titane #MSUB -r SE # Nom du job
101	#-Q- titane #MSUB -eo
102	#-Q- titane #MSUB -n 1 # Reservation du processus
103	#-Q- titane #MSUB -T 86400 # Limite de temps elapsed du job
104	#-Q- titane #MSUB -q mono
105	#-Q- lxiv8 ######################
106	#-Q- lxiv8 ## OBELIX LSCE ##
107	#-Q- lxiv8 ######################
108	#-Q- lxiv8 #PBS -N SE
109	#-Q- lxiv8 #PBS -m a
110	#-Q- lxiv8 #PBS -j oe
111	#-Q- lxiv8 #PBS -q medium
112	#-Q- lxiv8 #PBS -o SE.$$
113	#-Q- lxiv8 #PBS -S /bin/ksh
114	#-Q- default #!/bin/ksh
115	#-Q- default ##################
116	#-Q- default ## DEFAULT HOST ##
117	#-Q- default ##################
118
119	#**************************************************************
120	# Author: Sebastien Denvil
121	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
122	# $Revision:: $ Revision of last commit
123	# $Author:: $ Author of last commit
124	# $Date:: $ Date of last commit
125	# IPSL (2006)
126	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
127	#
128	#**************************************************************
129
130	#set -eu
131	#set -vx
132
133	date
134
135	#-Q- sx8brodie export OMP_NUM_THREADS=1
136	#-Q- aix6 export OMP_NUM_THREADS=1
137	#-Q- ulam export OMP_NUM_THREADS=1
138
139	########################################################################
140
141	#D- Flag to determine if this job in a standalone mode
142	#D- Default : value from AA_job if any
143	StandAlone=${StandAlone:=true}
144
145	#D- Path to libIGCM
146	#D- Default : value from AA_job if any
147	# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
148	# WARNING you must check MirrorlibIGCM variable in sys library.
149	# WARNING If this variable is true, you must use libIGCM_POST path instead
150	# WARNING of your running libIGCM directory.
151	libIGCM=${libIGCM:=::modipsl::/libIGCM}
152
153	#D- Flag to determine if rebuild process has been performed asynchronously
154	#D- Possible value true or false.
155	#D- If true raw files has allready been patched by rebuild job
156	#D- If false create_ts will patch the raw files
157	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
158	RebuildFrequency=${RebuildFrequency:=true}
159
160	#D- Flag to determine atlas job's output directory
161	#D- Default : value from libIGCM_post.ksh if any
162	POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
163
164	#D- Increased verbosity (1, 2, 3)
165	#D- Default : value from AA_job if any
166	Verbosity=${Verbosity:=3}
167
168	#D- Low level debug : to bypass lib test checks and stack construction
169	#D- Default : value from AA_job if any
170	DEBUG_debug=${DEBUG_debug:=false}
171
172	#D- TEMPORARY Flag to determine atmospheric resolution
173	#D- Default : value from atmospheric driver if any
174	RESOL_ATM=${RESOL_ATM:=ALL}
175
176	#D- Flag to determine surface resolution
177	#D- Default : value from surface driver if any
178	RESOL_SRF=ALL
179
180	#D- Flag to determine surface resolution
181	#D- Default : value from surface driver if any
182	RESOL_SBG=ALL
183
184	#D- TEMPORARY Flag to determine ocean resolution
185	#D- Default : value from ocean driver if any
186	RESOL_OCE=${RESOL_OCE:=ORCA2}
187
188	#D- TEMPORARY Flag to determine ice resolution
189	#D- Default : value from ice driver if any
190	RESOL_ICE=${RESOL_ICE:=ORCA2}
191
192	#D- TEMPORARY Flag to determine marine biogeochemistry resolution
193	#D- Default : value from ice driver if any
194	RESOL_MBG=${RESOL_MBG:=ORCA2}
195
196	########################################################################
197
198	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
199	( ${DEBUG_debug} ) && IGCM_debug_Check
200	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
201	( ${DEBUG_debug} ) && IGCM_card_Check
202	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
203	( ${DEBUG_debug} ) && IGCM_date_Check
204	#-------
205	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
206
207	########################################################################
208
209	#set -vx
210
211	IGCM_sys_MkdirWork ${RUN_DIR_PATH}
212	IGCM_sys_Cd ${RUN_DIR_PATH}
213
214	# ------------------------------------------------------------------
215	# Test if all was right before proceeding further
216	# ------------------------------------------------------------------
217	IGCM_debug_Verif_Exit_Post
218
219	if [ ${StandAlone} = true ] ; then
220	CARD_DIR=${SUBMIT_DIR}
221	else
222	CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
223	IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH}
224	fi
225
226	#==================================
227	# First of all
228	#
229	typeset option
230
231	#==================================
232	# Read UserChoices section:
233	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card UserChoices
234	echo
235	IGCM_debug_Print 1 "DefineArrayFromOption : config_UserChoices"
236	for option in ${config_UserChoices[*]} ; do
237	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
238	eval auxprint=\${config_UserChoices_${option}}
239	IGCM_debug_Print 3 "${option} : ${auxprint}"
240	done
241	#
242	echo
243
244	#==================================
245	# Read Post section:
246	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card Post
247	echo
248	IGCM_debug_Print 1 "DefineArrayFromOption : config_Post"
249	for option in ${config_Post[*]} ; do
250	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post ${option}
251	eval auxprint=\${config_Post_${option}}
252	IGCM_debug_Print 3 "${option} : ${auxprint}"
253	done
254	#
255	echo
256
257	#==================================
258	# Define default value to keep compatibility with previous card: means before changes due to TGCC
259	if [ X${PackDefault} = Xtrue ] ; then
260	[ X${config_Post_PackFrequency} = X ] && config_Post_PackFrequency=${config_Post_RebuildFrequency}
261	else
262	config_Post_PackFrequency=NONE
263	fi
264
265	#==================================
266	# If pack is active then PackFrequency overule the config_UserChoices_PeriodLength
267	if ( [ ! X${config_Post_PackFrequency} = X${NULL_STR} ] && [ ! X${config_Post_PackFrequency} = XNONE ] ) ; then
268	config_UserChoices_PeriodLength=${config_Post_PackFrequency}
269	fi
270
271	#==================================
272	#R_SAVE : Job output directory
273	#R_BUFR : Job output buffered directory
274	if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
275	FreeName=$( echo ${config_UserChoices_JobName} \| sed 's/.*_//' )
276	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
277	R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
278	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
279	else
280	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
281	R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
282	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_JobName}
283	fi
284	#
285	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
286	#
287	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post SeasonalFrequency
288	#
289	# Determine period for seasonnal average. Default : value from AA_job if any
290	#
291	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
292	#
293	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
294	#
295	freq=$( echo ${config_Post_SeasonalFrequency} \| sed -e "s/[yY]//" )
296	#
297	an_fin=$(( $( IGCM_date_ConvertGregorianDateToJulian ${PeriodDateEnd} ) / 1000 ))
298	an_deb=$( IGCM_date_YearDigit $(( an_fin - freq + 1 )) )
299	an_fin=$( IGCM_date_YearDigit ${an_fin} )
300	#
301	# For each component selected determine which files need post-processing
302	#
303	for comp in ${config_ListOfComponents[*]} ; do
304	#
305	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
306	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
307	#
308	card=${CARD_DIR}/COMP/${compname}.card
309	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
310	#
311	ListFilesName=${compname}_OutputFiles_List
312	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
313	#
314	if [ X${FileName0} != X${NULL_STR} ] ; then
315	#
316	# INITIALISATION
317	#
318	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
319	typeset i=2
320	#
321	until [ $i -gt $NbFiles ]; do
322	#
323	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
324	#
325	if [ X${flag_post} != XNONE ] ; then
326	#
327	# Check if seasonal is required for this file
328	#
329	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
330	#
331	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
332	#
333	# variable option allready typeset above
334	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
335	if [ ${option} = Seasonal ] ; then
336	FoundSeasonal=true
337	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
338	fi
339	done
340	#
341	if [ ! X${FoundSeasonal} = Xtrue ] ; then
342	eval ${compname}_${flag_post}_Seasonal=ON
343	fi
344	#
345	if [ ! X$( eval echo \${${compname}_${flag_post}_Seasonal} ) = XON ] ; then
346	(( i=i+3 ))
347	continue
348	fi
349	#
350	# CREATE LIST
351	#
352	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
353	#
354	DIRECTORY=${R_SAVE}/${comp}/Analyse/SE
355	#
356	TestedFile=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${FILE}.nc
357	#
358	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
359	if [ ! $? = 0 ] ; then
360	eval set +A LISTE_FILE_${comp} \$\{LISTE_FILE_${comp}[*]} ${FILE}
361	if [ ! ${RebuildFrequency} = true ] ; then
362	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
363	eval set +A LISTE_PATCHES_${FILE} \$\{${compname}_Post_${FILE}_Patches[*]}
364	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
365	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
366	if [ Xload${Patch} != X ] ; then
367	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
368	eval load${Patch}=loaded
369	fi
370	done
371	fi
372	fi
373	fi
374	fi
375	(( i=i+3 ))
376	done # until [ $i -eq $NbFiles ]
377	fi
378	done # for comp
379
380	for comp in ${config_ListOfComponents[*]} ; do
381	#
382	eval R_OUT_${comp}=${R_SAVE}/${comp}
383	#
384	i=0
385	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
386	#
387	# Determine in which output can we find file
388	# IE : Output/MO or Output/DA or ...
389	#
390	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
391	case ${FlagDir} in
392	1Y) FreqDir=YE ;;
393	1M) FreqDir=MO ;;
394	5D\|1D) FreqDir=DA ;;
395	HF) FreqDir=HF ;;
396	3H) FreqDir=HF ;;
397	INS) FreqDir=INS ;;
398	esac
399	#
400	RESULT_SE=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${file}.nc
401	# Do not redoo an existing SE
402	IGCM_sys_TestFileArchive ${R_SAVE}/${comp}/Analyse/SE/${RESULT_SE}
403	if [ $? = 0 ] ; then
404	continue
405	fi
406	#
407	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
408	#
409	case ${config_UserChoices_PeriodLength} in
410	# For Yearly simulation :
411	1Y\|1y)
412	(( an = an_deb ))
413	# Initialize array
414	#set -A liste_file_se
415	#set -A liste_file_se_tmp
416	unset liste_file_se
417	unset liste_file_se_tmp
418	while [ ${an} -le ${an_fin} ] ; do
419	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
420	#
421	an4=$(printf "%04i\n" ${an} )
422	#
423	diy=$( IGCM_date_DaysInYear $an4 )
424	afin=$( IGCM_date_AddDaysToGregorianDate ${an4}0101 $(( diy - 1 )) )
425	date=${an4}0101_${afin}
426	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
427	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
428	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
429	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
430	(( an = an + 1 ))
431	done
432	#
433	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
434	IGCM_debug_Verif_Exit_Post
435
436	# Apply IGCM_Patch if needed
437	if [ ! ${RebuildFrequency} = true ] ; then
438	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
439	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
440	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
441	IGCM_${Patch} ${file_t}
442	done
443	done
444	fi
445	fi
446
447	# Search of common list of variables to be treated
448	nbfile=0
449	for file_common_var in ${liste_file_se_tmp[*]} ; do
450	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
451	(( nbfile = nbfile + 1 ))
452	done
453	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
454	IGCM_sys_Rm tmpfile_ncra
455
456	# detect time counter : time or time_counter ie unlimited variable
457	var_unlim=$(ncdump -h ${liste_file_se_tmp[1]}\|grep UNLIMITED\| cut -d ' ' -f 1)
458
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	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d ${var_unlim},${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
465	done
466	IGCM_sys_Rm ${liste_file_se_tmp[*]}
467	;;
468	# For Monthly simulation :
469	1M\|1m)
470	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
471	#
472	(( nb = ${mois} - 1 ))
473	#
474	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
475	#
476	(( an = an_deb ))
477	# Initialize array
478	#set -A liste_file_se
479	#set -A liste_file_se_tmp
480	unset liste_file_se
481	unset liste_file_se_tmp
482	while [ ${an} -le ${an_fin} ] ; do
483	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
484	#
485	an4=$(printf "%04i\n" ${an} )
486	#
487	date=${an4}${mois}01_${an4}${mois}${moisL}
488	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
489	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
490	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
491	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
492
493	(( an = an + 1 ))
494	done
495	#
496	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
497	IGCM_debug_Verif_Exit_Post
498
499	# Apply IGCM_Patch if needed
500	if [ ! ${RebuildFrequency} = true ] ; then
501	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
502	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
503	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
504	IGCM_${Patch} ${file_t}
505	done
506	done
507	fi
508	fi
509
510	# Search of common list of variables to be treated
511	nbfile=0
512	for file_common_var in ${liste_file_se_tmp[*]} ; do
513	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
514	(( nbfile = nbfile + 1 ))
515	done
516	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
517	IGCM_sys_Rm tmpfile_ncra
518
519	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
520
521	IGCM_sys_Rm ${liste_file_se_tmp[*]}
522	done
523	;;
524	D\|d)
525	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
526	#
527	(( nb = ${mois} - 1 ))
528	#
529	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
530	#
531	(( an = an_deb ))
532	# Initialize array
533	#set -A liste_file_se
534	#set -A liste_file_se_tmp
535	unset liste_file_se
536	unset liste_file_se_tmp
537	while [ ${an} -le ${an_fin} ] ; do
538	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
539	#
540	an4=$(printf "%04i\n" ${an} )
541	#
542	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
543	# for one day
544	if [ ${length_d} -eq 1 ] ; then
545	(( length_d = 0 ))
546	fi
547	(( day = 1 ))
548	while [ ${day} -le ${moisL} ] ; do
549	day2=$(printf "%02i\n" ${day} )
550	day_beg=${an4}${mois}${day2}
551	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
552	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
553	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
554	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
555	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
556	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
557	(( day = day + 1 ))
558	done
559	(( an = an + 1 ))
560	done
561	#
562	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
563	IGCM_debug_Verif_Exit_Post
564
565	# Apply IGCM_Patch if needed
566	if [ ! ${RebuildFrequency} = true ] ; then
567	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
568	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
569	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
570	IGCM_${Patch} ${file_t}
571	done
572	done
573	fi
574	fi
575
576	# Search of common list of variables to be treated
577	nbfile=0
578	for file_common_var in ${liste_file_se_tmp[*]} ; do
579	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
580	(( nbfile = nbfile + 1 ))
581	done
582	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
583	IGCM_sys_Rm tmpfile_ncra
584
585	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
586	IGCM_sys_Rm ${liste_file_se_tmp[*]}
587	done
588	;;
589	esac
590	#
591
592	# Search of common list of variables to be treated
593	nbfile=0
594	for file_common_var in ${OUT_SE[*]} ; do
595	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncrcat
596	(( nbfile = nbfile + 1 ))
597	done
598	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
599	IGCM_sys_Rm tmpfile_ncrcat
600
601	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
602	#
603	IGCM_sys_Rm ${OUT_SE[*]}
604	#
605	# detect time counter : time or time_counter ie unlimited variable
606	var_unlim=$(ncdump -h ${RESULT_SE}\|grep UNLIMITED\| cut -d ' ' -f 1)
607
608	# Put correct climatological axis following calendar
609	case ${config_UserChoices_CalendarType} in
610	360d\|360_day)
611	# 360 days
612	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\"'"
613	;;
614	noleap\|365_day)
615	# 365 days
616	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\"'"
617	;;
618	all_leap\|366_day)
619	# 366 days
620	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\"'"
621	;;
622	leap\|gregorian\|standard)
623	# 365.2425 days
624	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\"'"
625	;;
626	esac
627	eval IGCM_sys_ncap2 -Oh -s $ncap2cmd ${RESULT_SE} tmp.nc
628	IGCM_sys_Rm ${RESULT_SE}
629	IGCM_sys_Mv tmp.nc ${RESULT_SE}
630	#
631	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
632	IGCM_sys_Rm ${RESULT_SE}
633	#
634	done
635	done
636
637	# DODS copy
638	for comp in ${config_ListOfComponents[*]} ; do
639	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
640	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
641	done
642
643	YEARS=${an_deb}_${an_fin}
644	DIR_OUT=SE
645
646	export POST_DIR; export SUBMIT_DIR; export libIGCM; export R_INIT; export R_BC; export StandAlone
647	export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ; export RESOL_SBG
648	export R_SAVE; export config_UserChoices_JobName; export config_UserChoices_TagName; export YEARS; export DIR_OUT
649	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"
650	export listVarEnv;
651
652	#D-
653	# --------------------------------------------------------------------
654	#D- Test if all was right before ATLAS
655	# --------------------------------------------------------------------
656	IGCM_debug_Verif_Exit_Post
657
658	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
659	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
660	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
661	#
662	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
663	IGCM_sys_QsubPost atlas_ORCHIDEE ;
664	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
665	IGCM_sys_QsubPost atlas_LMDZ ;
666	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
667	IGCM_sys_QsubPost atlas_ORCA_LIM ;
668	Script_Post_Output=additionnal.${PeriodDateEnd} ;
669	IGCM_sys_QsubPost additionnal ;
670	#
671	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
672	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] \|\| \
673	[ ${config_UserChoices_TagName} = "IPSLCM5B" ] \|\| \
674	[ ${config_UserChoices_TagName} = "IPSLCM5A-MR" ] ; then
675	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
676	IGCM_sys_QsubPost atlas_ORCHIDEE ;
677	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
678	IGCM_sys_QsubPost atlas_LMDZ ;
679	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
680	IGCM_sys_QsubPost atlas_ORCA_LIM ;
681	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
682	IGCM_sys_QsubPost atlas_PISCES ;
683	#
684	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
685	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
686	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
687	#
688	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
689	IGCM_sys_QsubPost atlas_LMDZ ;
690	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
691	IGCM_sys_QsubPost atlas_ORCHIDEE ;
692	#
693	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
694	#
695	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
696	IGCM_sys_QsubPost atlas_LMDZ ;
697	#
698	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
699	[ ${config_UserChoices_TagName} = "OL2" ] ; then
700	#
701	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
702	IGCM_sys_QsubPost atlas_ORCHIDEE ;
703	#
704	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\|
705	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] ; then
706	#
707	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
708	IGCM_sys_QsubPost atlas_ORCA_LIM ;
709	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] ; then
710	#
711	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
712	IGCM_sys_QsubPost atlas_ORCA_LIM ;
713	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
714	IGCM_sys_QsubPost atlas_PISCES ;
715	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
716	#
717	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
718	IGCM_sys_QsubPost atlas_PISCES ;
719	#
720	fi
721
722	# Clean RUN_DIR_PATH (necessary for cesium and titane only)
723	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}

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