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AA_create_se

Last change on this file was 605, checked in by mafoipsl, 12 years ago
Tttttt use elapstim_req instead of cpu_time on mercure front-end.
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`
File size: 29.7 KB

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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 TS # 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=1gb # Limite memoire a 1 Go
84	#-Q- sx8mercure #PBS -l cputim_job=1:00:00 # 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=1gb # Limite memoire a 1 Go
94	#-Q- sx9mercure #PBS -l elapstim_req=1:00:00 # 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} : ${auxprint}"
253	done
254	#
255	echo
256
257	#==================================
258	# Define default value to keep compatibility with previous card: means before changes due to TGCC
259	[ X${config_Post_PackFrequency} = X ] && config_Post_PackFrequency=${config_Post_RebuildFrequency}
260
261	#==================================
262	# If pack is active then PackFrequency overule the config_UserChoices_PeriodLength
263	if ( [ ! X${config_Post_PackFrequency} = X${NULL_STR} ] && [ ! X${config_Post_PackFrequency} = XNONE ] ) ; then
264	config_UserChoices_PeriodLength=${config_Post_PackFrequency}
265	fi
266
267	#==================================
268	#R_SAVE : Job output directory
269	#R_BUFR : Job output buffered directory
270	if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
271	FreeName=$( echo ${config_UserChoices_JobName} \| sed 's/.*_//' )
272	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
273	R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
274	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
275	else
276	R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
277	R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
278	R_DODS=${config_UserChoices_TagName}/${config_UserChoices_JobName}
279	fi
280	#
281	IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
282	#
283	IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post SeasonalFrequency
284	#
285	# Determine period for seasonnal average. Default : value from AA_job if any
286	#
287	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
288	#
289	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
290	#
291	freq=$( echo ${config_Post_SeasonalFrequency} \| sed -e "s/[yY]//" )
292	#
293	an_fin=$(( $( IGCM_date_ConvertGregorianDateToJulian ${PeriodDateEnd} ) / 1000 ))
294	an_deb=$( IGCM_date_YearDigit $(( an_fin - freq + 1 )) )
295	an_fin=$( IGCM_date_YearDigit ${an_fin} )
296	#
297	# For each component selected determine which files need post-processing
298	#
299	for comp in ${config_ListOfComponents[*]} ; do
300	#
301	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
302	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
303	#
304	card=${CARD_DIR}/COMP/${compname}.card
305	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
306	#
307	ListFilesName=${compname}_OutputFiles_List
308	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
309	#
310	if [ X${FileName0} != X${NULL_STR} ] ; then
311	#
312	# INITIALISATION
313	#
314	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
315	typeset i=2
316	#
317	until [ $i -gt $NbFiles ]; do
318	#
319	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
320	#
321	if [ X${flag_post} != XNONE ] ; then
322	#
323	# Check if seasonal is required for this file
324	#
325	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
326	#
327	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
328	#
329	# variable option allready typeset above
330	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
331	if [ ${option} = Seasonal ] ; then
332	FoundSeasonal=true
333	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
334	fi
335	done
336	#
337	if [ ! X${FoundSeasonal} = Xtrue ] ; then
338	eval ${compname}_${flag_post}_Seasonal=ON
339	fi
340	#
341	if [ ! X$( eval echo \${${compname}_${flag_post}_Seasonal} ) = XON ] ; then
342	(( i=i+3 ))
343	continue
344	fi
345	#
346	# CREATE LIST
347	#
348	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
349	#
350	DIRECTORY=${R_SAVE}/${comp}/Analyse/SE
351	#
352	TestedFile=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${FILE}.nc
353	#
354	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
355	if [ ! $? = 0 ] ; then
356	eval set +A LISTE_FILE_${comp} \$\{LISTE_FILE_${comp}[*]} ${FILE}
357	if [ ! ${RebuildFrequency} = true ] ; then
358	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
359	eval set +A LISTE_PATCHES_${FILE} \$\{${compname}_Post_${FILE}_Patches[*]}
360	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
361	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
362	if [ Xload${Patch} != X ] ; then
363	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
364	eval load${Patch}=loaded
365	fi
366	done
367	fi
368	fi
369	fi
370	fi
371	(( i=i+3 ))
372	done # until [ $i -eq $NbFiles ]
373	fi
374	done # for comp
375
376	for comp in ${config_ListOfComponents[*]} ; do
377	#
378	eval R_OUT_${comp}=${R_SAVE}/${comp}
379	#
380	i=0
381	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
382	#
383	# Determine in which output can we find file
384	# IE : Output/MO or Output/DA or ...
385	#
386	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
387	case ${FlagDir} in
388	1Y) FreqDir=YE ;;
389	1M) FreqDir=MO ;;
390	5D\|1D) FreqDir=DA ;;
391	HF) FreqDir=HF ;;
392	3H) FreqDir=HF ;;
393	INS) FreqDir=INS ;;
394	esac
395	#
396	RESULT_SE=${config_UserChoices_JobName}_SE_${an_deb}_${an_fin}_${file}.nc
397	# Do not redoo an existing SE
398	IGCM_sys_TestFileArchive ${R_SAVE}/${comp}/Analyse/SE/${RESULT_SE}
399	if [ $? = 0 ] ; then
400	continue
401	fi
402	#
403	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
404	#
405	case ${config_UserChoices_PeriodLength} in
406	# For Yearly simulation :
407	1Y\|1y)
408	(( an = an_deb ))
409	# Initialize array
410	#set -A liste_file_se
411	#set -A liste_file_se_tmp
412	unset liste_file_se
413	unset liste_file_se_tmp
414	while [ ${an} -le ${an_fin} ] ; do
415	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
416	#
417	an4=$(printf "%04i\n" ${an} )
418	#
419	diy=$( IGCM_date_DaysInYear $an4 )
420	afin=$( IGCM_date_AddDaysToGregorianDate ${an4}0101 $(( diy - 1 )) )
421	date=${an4}0101_${afin}
422	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
423	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
424	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
425	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
426	(( an = an + 1 ))
427	done
428	#
429	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
430	IGCM_debug_Verif_Exit_Post
431
432	# Apply IGCM_Patch if needed
433	if [ ! ${RebuildFrequency} = true ] ; then
434	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
435	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
436	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
437	IGCM_${Patch} ${file_t}
438	done
439	done
440	fi
441	fi
442
443	# Search of common list of variables to be treated
444	nbfile=0
445	for file_common_var in ${liste_file_se_tmp[*]} ; do
446	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
447	(( nbfile = nbfile + 1 ))
448	done
449	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
450	IGCM_sys_Rm tmpfile_ncra
451
452	# detect time counter : time or time_counter ie unlimited variable
453	var_unlim=$(ncdump -h ${liste_file_se_tmp[1]}\|grep UNLIMITED\| cut -d ' ' -f 1)
454
455	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
456	#
457	(( nb = ${mois} - 1 ))
458	#
459	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
460	IGCM_sys_ncra -O -v ${list_var_final_ncra} -d ${var_unlim},${nb},,12 ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
461	done
462	IGCM_sys_Rm ${liste_file_se_tmp[*]}
463	;;
464	# For Monthly simulation :
465	1M\|1m)
466	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
467	#
468	(( nb = ${mois} - 1 ))
469	#
470	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
471	#
472	(( an = an_deb ))
473	# Initialize array
474	#set -A liste_file_se
475	#set -A liste_file_se_tmp
476	unset liste_file_se
477	unset liste_file_se_tmp
478	while [ ${an} -le ${an_fin} ] ; do
479	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
480	#
481	an4=$(printf "%04i\n" ${an} )
482	#
483	date=${an4}${mois}01_${an4}${mois}${moisL}
484	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
485	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
486	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
487	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
488
489	(( an = an + 1 ))
490	done
491	#
492	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
493	IGCM_debug_Verif_Exit_Post
494
495	# Apply IGCM_Patch if needed
496	if [ ! ${RebuildFrequency} = true ] ; then
497	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
498	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
499	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
500	IGCM_${Patch} ${file_t}
501	done
502	done
503	fi
504	fi
505
506	# Search of common list of variables to be treated
507	nbfile=0
508	for file_common_var in ${liste_file_se_tmp[*]} ; do
509	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
510	(( nbfile = nbfile + 1 ))
511	done
512	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
513	IGCM_sys_Rm tmpfile_ncra
514
515	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
516
517	IGCM_sys_Rm ${liste_file_se_tmp[*]}
518	done
519	;;
520	D\|d)
521	for mois in 01 02 03 04 05 06 07 08 09 10 11 12 ; do
522	#
523	(( nb = ${mois} - 1 ))
524	#
525	OUT_SE[${nb}]=${config_UserChoices_JobName}_SE${mois}_${an_deb}_${an_fin}_${file}.nc
526	#
527	(( an = an_deb ))
528	# Initialize array
529	#set -A liste_file_se
530	#set -A liste_file_se_tmp
531	unset liste_file_se
532	unset liste_file_se_tmp
533	while [ ${an} -le ${an_fin} ] ; do
534	moisL=$( IGCM_date_DaysInMonth ${an} ${mois} )
535	#
536	an4=$(printf "%04i\n" ${an} )
537	#
538	length_d=$(( ${config_UserChoices_PeriodLength} - 1 ))
539	# for one day
540	if [ ${length_d} -eq 1 ] ; then
541	(( length_d = 0 ))
542	fi
543	(( day = 1 ))
544	while [ ${day} -le ${moisL} ] ; do
545	day2=$(printf "%02i\n" ${day} )
546	day_beg=${an4}${mois}${day2}
547	day_end=$( IGCM_date_AddDaysToGregorianDate ${day_beg} ${length_d} )
548	date=${an4}${mois}${day_beg}_${an4}${mois}${day_end}
549	#set +A liste_file_se ${liste_file_se[*]} ${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
550	#set +A liste_file_se_tmp ${liste_file_se_tmp[*]} ${config_UserChoices_JobName}_${date}_${file}.nc
551	liste_file_se[${#liste_file_se[*]}]=${file_path}${config_UserChoices_JobName}_${date}_${file}.nc
552	liste_file_se_tmp[${#liste_file_se_tmp[*]}]=${config_UserChoices_JobName}_${date}_${file}.nc
553	(( day = day + 1 ))
554	done
555	(( an = an + 1 ))
556	done
557	#
558	IGCM_sys_Get /l liste_file_se[*] ${RUN_DIR_PATH}
559	IGCM_debug_Verif_Exit_Post
560
561	# Apply IGCM_Patch if needed
562	if [ ! ${RebuildFrequency} = true ] ; then
563	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
564	for file_t in $( eval echo ${liste_file_se_tmp[*]} ); do
565	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
566	IGCM_${Patch} ${file_t}
567	done
568	done
569	fi
570	fi
571
572	# Search of common list of variables to be treated
573	nbfile=0
574	for file_common_var in ${liste_file_se_tmp[*]} ; do
575	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncra
576	(( nbfile = nbfile + 1 ))
577	done
578	list_var_final_ncra=`cat tmpfile_ncra \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
579	IGCM_sys_Rm tmpfile_ncra
580
581	IGCM_sys_ncra -O -v ${list_var_final_ncra} ${liste_file_se_tmp[*]} ${OUT_SE[${nb}]}
582	IGCM_sys_Rm ${liste_file_se_tmp[*]}
583	done
584	;;
585	esac
586	#
587
588	# Search of common list of variables to be treated
589	nbfile=0
590	for file_common_var in ${OUT_SE[*]} ; do
591	ncdump -h ${file_common_var} \| grep -E 'float\|double' \| cut -f 1 -d '(' \| cut -f 2 -d ' ' >> tmpfile_ncrcat
592	(( nbfile = nbfile + 1 ))
593	done
594	list_var_final_ncrcat=`cat tmpfile_ncrcat \| sort \| uniq -c \| awk -v nbfile=$nbfile '{if ($1 == nbfile) {print $2}}' \| paste -s -d ','`
595	IGCM_sys_Rm tmpfile_ncrcat
596
597	IGCM_sys_ncrcat -O -v ${list_var_final_ncrcat} ${OUT_SE[*]} ${RESULT_SE}
598	#
599	IGCM_sys_Rm ${OUT_SE[*]}
600	#
601	# detect time counter : time or time_counter ie unlimited variable
602	var_unlim=$(ncdump -h ${RESULT_SE}\|grep UNLIMITED\| cut -d ' ' -f 1)
603
604	# Put correct climatological axis following calendar
605	case ${config_UserChoices_CalendarType} in
606	360d\|360_day)
607	# 360 days
608	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\"'"
609	;;
610	noleap\|365_day)
611	# 365 days
612	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\"'"
613	;;
614	all_leap\|366_day)
615	# 366 days
616	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\"'"
617	;;
618	leap\|gregorian\|standard)
619	# 365.2425 days
620	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\"'"
621	;;
622	esac
623	eval IGCM_sys_ncap2 -Oh -s $ncap2cmd ${RESULT_SE} tmp.nc
624	IGCM_sys_Rm ${RESULT_SE}
625	IGCM_sys_Mv tmp.nc ${RESULT_SE}
626	#
627	eval IGCM_sys_Put_Out ${RESULT_SE} \${R_OUT_${comp}}/Analyse/SE/${RESULT_SE}
628	IGCM_sys_Rm ${RESULT_SE}
629	#
630	done
631	done
632
633	# DODS copy
634	for comp in ${config_ListOfComponents[*]} ; do
635	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/SE
636	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/SE
637	done
638
639	YEARS=${an_deb}_${an_fin}
640	DIR_OUT=SE
641
642	export POST_DIR; export SUBMIT_DIR; export libIGCM; export R_INIT; export R_BC; export StandAlone
643	export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ; export RESOL_SBG
644	export R_SAVE; export config_UserChoices_JobName; export config_UserChoices_TagName; export YEARS; export DIR_OUT
645	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"
646	export listVarEnv;
647
648	#D-
649	# --------------------------------------------------------------------
650	#D- Test if all was right before ATLAS
651	# --------------------------------------------------------------------
652	IGCM_debug_Verif_Exit_Post
653
654	if [ ${config_UserChoices_TagName} = "IPSLCM4_v1_OASIS3" ] \|\| \
655	[ ${config_UserChoices_TagName} = "IPSLCM4_v2" ] \|\| \
656	[ ${config_UserChoices_TagName} = "IPSL_ESM_V1" ] ; then
657	#
658	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
659	IGCM_sys_QsubPost atlas_ORCHIDEE ;
660	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
661	IGCM_sys_QsubPost atlas_LMDZ ;
662	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
663	IGCM_sys_QsubPost atlas_ORCA_LIM ;
664	Script_Post_Output=additionnal.${PeriodDateEnd} ;
665	IGCM_sys_QsubPost additionnal ;
666	#
667	elif [ ${config_UserChoices_TagName} = "IPSLCM5" ] \|\| \
668	[ ${config_UserChoices_TagName} = "IPSLCM5A" ] \|\| \
669	[ ${config_UserChoices_TagName} = "IPSLCM5B" ] \|\| \
670	[ ${config_UserChoices_TagName} = "IPSLCM5A-MR" ] ; then
671	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
672	IGCM_sys_QsubPost atlas_ORCHIDEE ;
673	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
674	IGCM_sys_QsubPost atlas_LMDZ ;
675	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
676	IGCM_sys_QsubPost atlas_ORCA_LIM ;
677	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
678	IGCM_sys_QsubPost atlas_PISCES ;
679	#
680	elif [ ${config_UserChoices_TagName} = "LMDZ4OR" ] \|\| \
681	[ ${config_UserChoices_TagName} = "LMDZOR" ] \|\| \
682	[ ${config_UserChoices_TagName} = "LMDZ4OR_v2" ] ; then
683	#
684	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
685	IGCM_sys_QsubPost atlas_LMDZ ;
686	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
687	IGCM_sys_QsubPost atlas_ORCHIDEE ;
688	#
689	elif [ ${config_UserChoices_TagName} = "LMDZ" ] ; then
690	#
691	Script_Post_Output=atlas_LDMZ.${PeriodDateEnd} ;
692	IGCM_sys_QsubPost atlas_LMDZ ;
693	#
694	elif [ ${config_UserChoices_TagName} = "OL" ] \|\| \
695	[ ${config_UserChoices_TagName} = "OL2" ] ; then
696	#
697	Script_Post_Output=atlas_ORCHIDEE.${PeriodDateEnd} ;
698	IGCM_sys_QsubPost atlas_ORCHIDEE ;
699	#
700	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM" ] \|\|
701	[ ${config_UserChoices_TagName} = "ORCA2_LIM2" ] ; then
702	#
703	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
704	IGCM_sys_QsubPost atlas_ORCA_LIM ;
705	elif [ ${config_UserChoices_TagName} = "ORCA2_LIM2_PISCES" ] ; then
706	#
707	Script_Post_Output=atlas_ORCA_LIM.${PeriodDateEnd} ;
708	IGCM_sys_QsubPost atlas_ORCA_LIM ;
709	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
710	IGCM_sys_QsubPost atlas_PISCES ;
711	elif [ ${config_UserChoices_TagName} = "ORCA2_OFF_PISCES" ] ; then
712	#
713	Script_Post_Output=atlas_PISCES.${PeriodDateEnd} ;
714	IGCM_sys_QsubPost atlas_PISCES ;
715	#
716	fi
717
718	# Clean RUN_DIR_PATH (necessary for cesium and titane only)
719	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}

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