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AA_create_ts @ 1449

Last change on this file since 1449 was 1448, checked in by jgipsl, 6 years ago
Change in headers at irene : temporary remove option -m and use a workaround given by the TGCC. This change is done to avoid problems with resubmitting from job when submitting the main job from workdir.
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- curie ######################
2	#-Q- curie ## CURIE TGCC/CEA ##
3	#-Q- curie ######################
4	#-Q- curie #MSUB -r TS # Nom du job
5	#-Q- curie #MSUB -eo
6	#-Q- curie #MSUB -n 1 # Reservation du processus
7	#-Q- curie #MSUB -T 80000 # Limite de temps elapsed du job
8	#-Q- curie #MSUB -q ::default_node::
9	#-Q- curie #MSUB -c ::default_core::
10	#-Q- curie #MSUB -Q normal
11	#-Q- curie #MSUB -A ::default_project::
12	#-Q- curie set +x
13	#-Q- irene ######################
14	#-Q- irene ## IRENE TGCC/CEA ##
15	#-Q- irene ######################
16	#-Q- irene #MSUB -r TS # Job name
17	#-Q- irene #MSUB -eo
18	#-Q- irene #MSUB -n 1 # Number of cores
19	#-Q- irene #MSUB -T 80000 # Maximum elapsed time
20	#-Q- irene #MSUB -q skylake
21	#-Q- irene #MSUB -c 4
22	#-Q- irene #MSUB -Q normal
23	#-Q- irene #MSUB -A ::default_project::
24	#-Q- irene ###MSUB -m store,work,scratch
25	#-Q- irene #MSUB -E '--licenses=fs_unshare,fs_work,fs_store,fs_scratch'
26	#-Q- irene set +x
27	#-Q- ada #!/bin/ksh
28	#-Q- ada #######################
29	#-Q- ada ## ADA IDRIS ##
30	#-Q- ada #######################
31	#-Q- ada # @ job_type = mpich
32	#-Q- ada # @ requirements = (Feature == "prepost")
33	#-Q- ada # Temps Elapsed max. d'une requete hh:mm:ss
34	#-Q- ada # @ wall_clock_limit = 20:00:00
35	#-Q- ada # Nom du travail LoadLeveler
36	#-Q- ada # @ job_name = TS
37	#-Q- ada # Fichier de sortie standard du travail
38	#-Q- ada # @ output = $(job_name).$(jobid)
39	#-Q- ada # Fichier de sortie d'erreur du travail
40	#-Q- ada # @ error = $(job_name).$(jobid)
41	#-Q- ada # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
42	#-Q- ada # @ notification = error
43	#-Q- ada # @ environment = $DEBUG_debug ; $BigBrother ; $postProcessingStopLevel ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $POST_DIR ; $Script_Post_Output ; $MASTER ; $RebuildFrequency ; $DateBegin ; $PeriodDateEnd ; $StandAlone ; $CompletedFlag ; $TsTask ; $CompToRead ; $FlagToRead ; $RESOL_ATM ; $RESOL_OCE ; $RESOL_ICE ; $RESOL_MBG ; $RESOL_SRF ; $RESOL_SBG ; wall_clock_limit=$(wall_clock_limit)
44	#-Q- ada # @ queue
45	#-Q- lxiv8 ######################
46	#-Q- lxiv8 ## OBELIX LSCE ##
47	#-Q- lxiv8 ######################
48	#-Q- lxiv8 #PBS -N TS
49	#-Q- lxiv8 #PBS -m a
50	#-Q- lxiv8 #PBS -j oe
51	#-Q- lxiv8 #PBS -q medium
52	#-Q- lxiv8 #PBS -o TS.$$
53	#-Q- lxiv8 #PBS -S /bin/ksh
54	#-Q- ifort_CICLAD ######################
55	#-Q- ifort_CICLAD ## CICLAD IPSL ##
56	#-Q- ifort_CICLAD ######################
57	#-Q- ifort_CICLAD #PBS -N TS
58	#-Q- ifort_CICLAD #PBS -m a
59	#-Q- ifort_CICLAD #PBS -j oe
60	#-Q- ifort_CICLAD ###PBS -q h12 # Queue for 12 hours at ciclad only
61	#-Q- ifort_CICLAD #PBS -S /bin/ksh
62	#-Q- default #!/bin/ksh
63	#-Q- default ##################
64	#-Q- default ## DEFAULT HOST ##
65	#-Q- default ##################
66
67	#**************************************************************
68	# Author: Sebastien Denvil
69	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
70	# $Revision:: $ Revision of last commit
71	# $Author:: $ Author of last commit
72	# $Date:: $ Date of last commit
73	# IPSL (2006)
74	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
75	#
76	#**************************************************************
77
78	#set -eu
79	#set -vx
80
81	date
82
83	#-Q- ada export OMP_NUM_THREADS=1
84
85	#D- Task type DO NOT CHANGE (computing, post-processing or checking)
86	TaskType=post-processing
87
88	########################################################################
89
90	#D- Flag to determine if this job in a standalone mode
91	#D- Default : value from AA_job if any
92	StandAlone=${StandAlone:=true}
93
94	#D- Path to libIGCM
95	#D- Default : value from AA_job if any
96	libIGCM=${libIGCM:=::modipsl::/libIGCM}
97
98	#D- Flag to determine allready produced time series. Empty if you start from the beginning
99	#D- Default : Value from AA_job if any. Usefull in StandAlone case if you want to continue a time series
100	CompletedFlag=${CompletedFlag:=}
101
102	#D- Flag to determine task type this script will perform.
103	#D- Possible Value : 2D, 3D, Chunck2D, Chunck3D
104	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
105	TsTask=${TsTask:=2D}
106	if [ X${TsTask} = Xempty ] ; then
107	TsTask=""
108	fi
109
110	#D- Flag to determine if rebuild process has been performed asynchronously
111	#D- Possible value true or false.
112	#D- If true raw files has allready been patched by rebuild job
113	#D- If false create_ts will patch the raw files
114	#D- Default : Value from AA_job if any. Usefull in StandAlone case.
115	RebuildFrequency=${RebuildFrequency:=true}
116
117	#D- Flag to determine job's output directory
118	#D- Default : value from libIGCM_post.ksh if any
119	POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
120
121	#D- Increased verbosity (1, 2, 3)
122	#D- Default : value from AA_job if any
123	Verbosity=${Verbosity:=3}
124
125	#D- Low level debug : to bypass lib test checks and stack construction
126	#D- Default : value from AA_job if any
127	DEBUG_debug=${DEBUG_debug:=false}
128
129	#D- TEMPORARY Flag to determine atmospheric resolution
130	#D- Default : value from atmospheric driver if any
131	RESOL_ATM=ALL
132
133	#D- Flag to determine surface resolution
134	#D- Default : value from surface driver if any
135	RESOL_SRF=ALL
136
137	#D- Flag to determine surface resolution
138	#D- Default : value from surface driver if any
139	RESOL_SBG=ALL
140
141	#D- TEMPORARY Flag to determine ocean resolution
142	#D- Default : value from ocean driver if any
143	RESOL_OCE=${RESOL_OCE:=ORCA2}
144
145	#D- TEMPORARY Flag to determine ice resolution
146	#D- Default : value from ice driver if any
147	RESOL_ICE=${RESOL_OCE:=ORCA2}
148
149	#D- TEMPORARY Flag to determine marine biogeochemistry resolution
150	#D- Default : value from ice driver if any
151	RESOL_MBG=${RESOL_OCE:=ORCA2}
152
153	########################################################################
154
155	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
156	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
157	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
158	#-------
159	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
160	. ${libIGCM}/libIGCM_config/libIGCM_config.ksh
161	#-------
162	IGCM_sys_MkdirWork ${RUN_DIR_PATH}
163	IGCM_sys_Cd ${RUN_DIR_PATH}
164	#-------
165	( ${DEBUG_debug} ) && IGCM_debug_Check
166	( ${DEBUG_debug} ) && IGCM_card_Check
167	( ${DEBUG_debug} ) && IGCM_date_Check
168
169	########################################################################
170
171	#set -vx
172
173	# Useful cleaning function
174	MENAGE ()
175	{
176	typeset ExistFlag
177	ExistFlag=$( IGCM_sys_RshArchive "[ -f $1/$3 ] && echo 0 \|\| echo 1" )
178	[ ${ExistFlag} -eq 0 ] && ( IGCM_sys_RshArchive rm -f $1/$2 ;)
179	}
180
181	########################################################################
182
183	# ------------------------------------------------------------------
184	# Test if all was right before proceeding further
185	# ------------------------------------------------------------------
186	IGCM_debug_Verif_Exit
187
188	if [ ${StandAlone} = true ] ; then
189	CARD_DIR=${SUBMIT_DIR}
190	else
191	CARD_DIR=${RUN_DIR_PATH}
192
193	IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
194
195	IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card ${RUN_DIR_PATH}
196
197	IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP ${RUN_DIR_PATH}
198
199	IGCM_sys_Get_Master ${SUBMIT_DIR}/POST ${RUN_DIR_PATH}
200	fi
201
202	#==================================
203	# First of all
204	#
205	# Read libIGCM compatibility version in config.card
206	# Read UserChoices section
207	# Read Ensemble section
208	# Read Post section
209	# Define all netcdf output directories
210	#==================================
211	IGCM_config_CommonConfiguration ${CARD_DIR}/config.card
212
213	# ------------------------------------------------------------------
214	# Activate BigBrother so as to supervise this job
215	# ------------------------------------------------------------------
216	IGCM_debug_BigBro_Initialize
217
218	#==================================
219	# Define default value to keep compatibility with previous card: means before changes due to TGCC
220	if [ X${PackDefault} = Xtrue ] ; then
221	[ X${config_Post_PackFrequency} = X ] && config_Post_PackFrequency=${config_Post_RebuildFrequency}
222	else
223	config_Post_PackFrequency=NONE
224	fi
225
226	#==================================
227	# If pack is active then PackFrequency overule the config_UserChoices_PeriodLength
228	if ( [ ! X${config_Post_PackFrequency} = X${NULL_STR} ] && [ ! X${config_Post_PackFrequency} = XNONE ] ) ; then
229	config_UserChoices_PeriodLength=${config_Post_PackFrequency}
230	fi
231
232	#
233	# Determine component to take care of depending on kind of task create_ts will perform
234	#
235	[ ${CompToRead} ] && set -A config_ListOfComponents ${CompToRead} \|\| IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
236	#
237	# Determine period for time series. Default : value from AA_job or from launch_TS if any
238	#
239	[ X${CompletedFlag} = X ] \|\| CompletedFlag=$( IGCM_date_ConvertFormatToGregorian ${CompletedFlag} )
240
241	DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
242	#
243	PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
244	#
245	# Determine Dimension of the produced time series : 2D or 3D
246	if ( [ X${TsTask} = XChunck2D ] \|\| [ X${TsTask} = X2D ] ) ; then
247	Dimension=2D
248	elif ( [ X${TsTask} = XChunck3D ] \|\| [ X${TsTask} = X3D ] ) ; then
249	Dimension=3D
250	else
251	Dimension=""
252	fi
253
254	# ------------------------------------------------------------------
255	#D- Test if all was right before entering the loop
256	# ------------------------------------------------------------------
257	IGCM_debug_Verif_Exit
258
259	########################################################################
260	# Depending on requested time series fill following variables :
261	#
262	# - LISTE_FILE_${comp}[*]
263	# - LISTE_VARS_${file}[*]
264	# - LISTE_AXIS_${file}[*]
265	# - LISTE_PATCH_${file}[*]
266	########################################################################
267
268	#
269	# For each selected component determine which files need post-processing
270	#
271	DoJob=false
272	for comp in ${config_ListOfComponents[*]} ; do
273	#
274	ActiveComp=false
275	#
276	IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
277	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
278	#
279	card=${CARD_DIR}/COMP/${compname}.card
280
281	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
282	#
283	ListFilesName=${compname}_OutputFiles_List
284	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
285	#
286	if [ X${FileName0} != X${NULL_STR} ] ; then
287	#
288	#IGCM_debug_Print 1 "Component : ${compname}"
289	#
290	# INITIALISATION
291	#
292	typeset i
293	if [ ${FlagToRead} ] ; then
294	((NbFiles=${FlagToRead}))
295	((i=${NbFiles}))
296	else
297	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
298	i=2
299	fi
300	#
301	until [ $i -gt $NbFiles ]; do
302	#
303	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
304	#
305	if [ X${flag_post} != XNONE ] ; then
306	#
307	# For each comp and each file who needs post-processing
308	# determine which variables need time series.
309	#
310	FILE=$( echo ${flag_post} \| awk "-FPost_" '{print $2}' )
311	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} TimeSeriesVars${Dimension}
312	IGCM_card_DefineVariableFromOption ${card} Post_${FILE} ChunckJob${Dimension}
313	#
314	# If TimeSeriesVars list is empty we skip
315	#
316	if [ $( eval echo \${${compname}_Post_${FILE}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
317	#
318	IGCM_debug_Print 3 "Nothing to do for ${FILE} according to ${card}"
319	IGCM_debug_Print 3 "TimeSeriesVars${Dimension} for ${FILE} is empty"
320	(( i=i+3 ))
321	continue
322	#
323	fi
324	#
325	# If files/variables has been switch off by ChunckJob${Dimension}=0 we skip
326	#
327	if [ X$( eval echo \${${compname}_Post_${FILE}_ChunckJob${Dimension}} ) = XOFF ] ; then
328	IGCM_debug_Print 3 "Nothing to do for ${FILE} according to ${card}"
329	IGCM_debug_Print 3 "ChunckJob${Dimension}=OFF for ${FILE} so it has been switched off"
330	(( i=i+3 ))
331	continue
332	fi
333	#
334	# If we are not a Chunck type task, we skip files/variables handled by chunck task
335	#
336	if ( [ ! X${TsTask} = XChunck${Dimension} ] && [ ! X${TsTask} = X ] && [ ! XChunck${Dimension} = XChunck ] ) ; then
337	if [ ! $( eval echo \${${compname}_Post_${FILE}_ChunckJob${Dimension}} ) = NONE ] ; then
338	IGCM_debug_Print 3 "Nothing to do for ${FILE} TimeSeriesVars${Dimension} according to ${card}"
339	IGCM_debug_Print 3 "Let another chunck task do the job $( eval echo \${${compname}_Post_${FILE}_ChunckJob${Dimension}} )"
340	(( i=i+3 ))
341	continue
342	fi
343	fi
344	#
345	# Now on we know we have things to do
346	#
347
348	#
349	# We need coordinates axis to properly fill produced time series
350	#
351	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} GatherWithInternal
352	#
353	if [ $( eval echo \${${compname}_Post_${FILE}_GatherWithInternal} ) = ${NULL_STR} ] ; then
354	#
355	IGCM_debug_Print 1 "ERROR !! We miss coordinate axis for ${FILE} according to ${card}"
356	IGCM_debug_Print 1 "So no time series will be produced for ${FILE} !!"
357	(( i=i+3 ))
358	continue
359	#
360	fi
361	#
362	# We need LIST of variables not allready produced (useful for standalone mode)
363	#
364	FlagDir=$( echo ${FILE} \| awk -F "_" '{print $1}' )
365	case ${FlagDir} in
366	*Y) TS_Dir=TS_YE ;;
367	*M) TS_Dir=TS_MO ;;
368	*D) TS_Dir=TS_DA ;;
369	HF) TS_Dir=TS_HF ;;
370	3H) TS_Dir=TS_HF ;;
371	INS) TS_Dir=TS_INS ;;
372	esac
373	#
374	count=0
375	for var in $( eval echo \${${compname}_Post_${FILE}_TimeSeriesVars${Dimension}[*]} ) ; do
376	#
377	DIRECTORY=${R_SAVE}/${comp}/Analyse/${TS_Dir}
378	TestedFile=${config_UserChoices_JobName}_${DateBegin}_${PeriodDateEnd}_${FlagDir}_${var}.nc
379	#
380	IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
381	if [ ! $? = 0 ] ; then
382	eval set +A LISTE_VARS_${FILE} \${LISTE_VARS_${FILE}[*]} ${var}
383	ActiveComp=true
384	(( count = count + 1 ))
385	fi
386	done
387	#
388	if [ ${count} -gt 0 ] ; then
389	#
390	eval set +A LISTE_FILE_${comp} \${LISTE_FILE_${comp}[*]} ${FILE}
391	eval set +A LISTE_AXIS_${FILE} \${${compname}_Post_${FILE}_GatherWithInternal[*]}
392	#
393	if [ ! X${RebuildFrequency} = Xtrue ] ; then
394	IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
395	eval set +A LISTE_PATCHES_${FILE} \${${compname}_Post_${FILE}_Patches[*]}
396	if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) != X${NULL_STR} ]; then
397	for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
398	if [ Xload${Patch} != X ] ; then
399	. ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
400	eval load${Patch}=loaded
401	fi
402	done
403	fi
404	fi
405	fi
406	fi
407	(( i=i+3 ))
408	done
409	fi
410	#
411	if [ ${ActiveComp} = true ] ; then
412	set +A ActiveListOfComponents ${ActiveListOfComponents[*]} ${comp}
413	fi
414	done
415
416	set -A config_ListOfComponents ${ActiveListOfComponents[*]}
417	[ ! -z "${ActiveListOfComponents}" ] && DoJob=true
418
419	########################################################################
420	#
421	# IS THERE SOME ALLREADY PRODUCED TIME SERIES ?
422	# IF SO BRING THEM IN THE WORKING DIRECTORY
423	#
424	# PS : Keep in mind that IGCM_sys_Get here is a weak link :
425	# - especially for IDRiS
426	# - no special protection against "command too long" !
427	# - libIGCM_sys should handle that or modify following code part
428	#
429	########################################################################
430
431	if [ ${StandAlone} != true ] ; then
432	Running_Flag=$( IGCM_sys_RshMaster "IGCM_card_DefineVariableFromOption \
433	${SUBMIT_DIR}/run.card PostProcessing TimeSeriesRunning ; \
434	echo \${run_PostProcessing_TimeSeriesRunning}" )
435
436	#if [ X${Running_Flag} = Xy ] ; then
437	# # Time Series Job allready running
438	# IGCM_debug_Print 1 "Time Series Job allready running exit"
439	# exit
440	#fi
441	# Now run.card know we are running
442
443
444
445
446	IGCM_sys_RshMaster IGCM_card_WriteOption ${SUBMIT_DIR}/run.card PostProcessing TimeSeriesRunning "y"
447
448
449
450
451
452	# Get information from last execution
453	#CompletedFlag=$( IGCM_sys_RshMaster \
454	# "IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/run.card PostProcessing TimeSeriesCompleted ;\
455	# echo \${run_PostProcessing_TimeSeriesCompleted}" )
456	fi
457
458	# Is it the first submission or not ?
459
460	if ( [ X${CompletedFlag} = X ] \|\| [ X${CompletedFlag} = X$( IGCM_date_AddDaysToGregorianDate ${DateBegin} -1 ) ] ) ; then
461	# First Time Series Submission
462	FIRST_PASS=TRUE
463	Length=$( IGCM_date_DaysInPreviousPeriod ${DateBegin} ${config_UserChoices_PeriodLength} begin)
464	DATE_FIN_JOB_B=$( IGCM_date_AddDaysToGregorianDate ${DateBegin} $(( Length - 1 )) )
465	else
466	# Last Completed Time Series
467	FIRST_PASS=FALSE
468	DATE_FIN_JOB_B=${CompletedFlag}
469	date=${DateBegin}_${DATE_FIN_JOB_B}
470	#
471	for comp in ${config_ListOfComponents[*]} ; do
472	#
473	IGCM_sys_Mkdir ${RUN_DIR_PATH}/${comp}
474	#
475	IGCM_sys_Cd ${RUN_DIR_PATH}/${comp}
476	#
477	unset liste_file
478	#
479	file_path=${R_SAVE}/${comp}/Analyse
480	#
481	i=0
482	file=${NULL_STR}
483	#
484	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
485	#
486	# Determine in which output can we find file
487	# IE : Analyse/TS or Analyse/DA2TS or ...
488	#
489	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
490	case ${FlagDir} in
491	*Y) TS_Dir=TS_YE ;;
492	*M) TS_Dir=TS_MO ;;
493	*D) TS_Dir=TS_DA ;;
494	HF) TS_Dir=TS_HF ;;
495	3H) TS_Dir=TS_HF ;;
496	INS) TS_Dir=TS_INS ;;
497	esac
498	for var in $( eval echo \${LISTE_VARS_${file}[*]} ) ; do
499	#
500	IGCM_sys_TestFileArchive ${file_path}/${TS_Dir}/${config_UserChoices_JobName}_${date}_${FlagDir}_${var}.nc
501	if [ $? = 0 ] ; then
502	liste_file[${#liste_file[*]}]=${file_path}/${TS_Dir}/${config_UserChoices_JobName}_${date}_${FlagDir}_${var}.nc
503	else
504	IGCM_debug_Print 1 "WARNING ${file_path}/${TS_Dir}/${config_UserChoices_JobName}_${date}_${FlagDir}_${var}.nc dont exist"
505	fi
506	#
507	done
508	done
509	if [ X${file} != X${NULL_STR} ] ; then
510	IGCM_sys_Get /l liste_file[*] ${RUN_DIR_PATH}/${comp}
511	IGCM_debug_Verif_Exit
512	fi
513	done
514	#
515	LEVEL=0
516	#
517	fi
518
519	########################################################################
520	#
521	# DEFINE LOOP PARAMETERS
522	#
523	########################################################################
524
525	DATE_COUNT=${DATE_FIN_JOB_B}
526	DATE_FIN_JOB_B_LOOP=${DATE_FIN_JOB_B}
527
528	( [ -n "${LEVEL}" ] && [ ${LEVEL} -eq 0 ] ) && NBRE_FILE_TOT=0 \|\| NBRE_FILE_TOT=1
529
530	if [ ${DoJob} = true ] ; then
531	while [ ${DATE_COUNT} -lt ${PeriodDateEnd} ] ; do
532	(( NBRE_FILE_TOT = NBRE_FILE_TOT + 1 ))
533	Length=$( IGCM_date_DaysInNextPeriod ${DATE_COUNT} ${config_UserChoices_PeriodLength} )
534	DATE_COUNT=$( IGCM_date_AddDaysToGregorianDate ${DATE_COUNT} ${Length} )
535	done
536	else
537	NBRE_FILE_TOT=0
538	fi
539
540	if [ ${NBRE_FILE_TOT} -le ${UNIX_MAX_LIMIT} ] ; then
541	NBRE_TOUR=1
542	elif [ ${NBRE_FILE_TOT}%${UNIX_MAX_LIMIT} -eq 0 ] ; then
543	let NBRE_TOUR=${NBRE_FILE_TOT}/${UNIX_MAX_LIMIT}
544	else
545	let NBRE_TOUR=${NBRE_FILE_TOT}/${UNIX_MAX_LIMIT}+1
546	fi
547
548	CURRENT_LOOP=1
549	# THIS LOOP GIVES PARAMETERS FOR THE DATE'S LOOP ie : DATE_COURANTE, DATE_FIN.
550	# WE HAVE 3 LEVELS
551	# - LEVEL 1 : JUST ONE LOOP TO COMPLETE
552	# - LEVEL 2 : WE ARE IN THE "DEEP" LOOP
553	# - LEVEL 3 : WE ARE IN THE LAST LOOP
554
555	while [ ${CURRENT_LOOP} -le ${NBRE_TOUR} ] ; do
556
557	if [ ${NBRE_FILE_TOT} -le ${UNIX_MAX_LIMIT} ] ; then
558	# - LEVEL 1 : JUST ONE LOOP TO COMPLETE
559	NBRE_FILE_LOOP=${NBRE_FILE_TOT}
560
561	if [ ${FIRST_PASS} = TRUE ] ; then
562	DATE_COURANTE=${DATE_FIN_JOB_B_LOOP}
563	else
564	Length=$( IGCM_date_DaysInNextPeriod ${DATE_FIN_JOB_B_LOOP} ${config_UserChoices_PeriodLength} )
565	DATE_COURANTE=$( IGCM_date_AddDaysToGregorianDate ${DATE_FIN_JOB_B_LOOP} ${Length} )
566	fi
567
568	DATE_FIN=${PeriodDateEnd}
569	DATE_FIN_JOB_B_LOOP_PREC=${DATE_FIN_JOB_B_LOOP}
570
571	[ -n "${DATE_LOOP}" ] && DATE_FIN_JOB_B_LOOP=${DATE_LOOP}
572	[ -n "${LEVEL}" ] && FLAG_B="TRUE" \|\| FLAG_B="FALSE"
573
574	LEVEL=1
575	DEPOT="TRUE"
576	elif [ ${CURRENT_LOOP} -ne ${NBRE_TOUR} ] ; then
577	# - LEVEL 2 : WE ARE IN THE "DEEP" LOOP
578	NBRE_FILE_LOOP=${UNIX_MAX_LIMIT}
579
580	if [ ! ${FIRST_PASS} = TRUE ] && [ ${CURRENT_LOOP} -eq 1 ] ; then
581	Length=$( IGCM_date_DaysInNextPeriod ${DATE_FIN_JOB_B_LOOP} ${config_UserChoices_PeriodLength} )
582	DATE_COURANTE=$( IGCM_date_AddDaysToGregorianDate ${DATE_FIN_JOB_B_LOOP} ${Length} )
583	elif [ -z "${DATE_COURANTE}" ] ; then
584	DATE_COURANTE=${DATE_FIN_JOB_B}
585	else
586	Length=$( IGCM_date_DaysInNextPeriod ${DATE_FIN} ${config_UserChoices_PeriodLength} )
587	DATE_COURANTE=$( IGCM_date_AddDaysToGregorianDate ${DATE_FIN} ${Length} )
588	fi
589
590	(( TotLength = 0 ))
591	COMPTEUR=1
592	DATE_LOOP=${DATE_COURANTE}
593
594	while [ ${COMPTEUR} -lt ${NBRE_FILE_LOOP} ] ; do
595	#
596	Length=$( IGCM_date_DaysInNextPeriod ${DATE_LOOP} ${config_UserChoices_PeriodLength} )
597	DATE_LOOP=$( IGCM_date_AddDaysToGregorianDate ${DATE_LOOP} ${Length} )
598	(( TotLength = TotLength + Length ))
599	(( COMPTEUR = COMPTEUR + 1 ))
600	#
601	done # while [ ${COMPTEUR} -le ${NBRE_FILE_LOOP} ] done
602	DATE_FIN=$( IGCM_date_AddDaysToGregorianDate ${DATE_COURANTE} ${TotLength} )
603
604	[ -n "${DATE_LOOP}" ] && DATE_FIN_JOB_B_LOOP_PREC=${DATE_FIN_JOB_B_LOOP} ; DATE_FIN_JOB_B_LOOP=${DATE_LOOP}
605	[ -n "${LEVEL}" ] && [ ${LEVEL} -eq 0 ] && FLAG_B="TRUE" \|\| [ ${CURRENT_LOOP} -gt 1 ] && FLAG_B="TRUE" \|\| FLAG_B="FALSE"
606	DEPOT="FALSE"
607	LEVEL=2
608	else
609	# - LEVEL 3 : WE ARE IN THE LAST LOOP
610	NBRE_FILE_LOOP=$(( ${NBRE_FILE_TOT} % ( ${UNIX_MAX_LIMIT} * ( ${CURRENT_LOOP} - 1 ) ) ))
611	[ ${NBRE_FILE_LOOP} -eq 0 ] && NBRE_FILE_LOOP=${UNIX_MAX_LIMIT}
612
613	Length=$( IGCM_date_DaysInNextPeriod ${DATE_FIN} ${config_UserChoices_PeriodLength} )
614	DATE_COURANTE=$(IGCM_date_AddDaysToGregorianDate ${DATE_FIN} ${Length} )
615	DATE_FIN=${PeriodDateEnd}
616	[ -n "${DATE_LOOP}" ] && DATE_FIN_JOB_B_LOOP_PREC=${DATE_FIN_JOB_B_LOOP} ; DATE_FIN_JOB_B_LOOP=${DATE_LOOP}
617
618	LEVEL=3
619	DEPOT="TRUE"
620	FLAG_B="TRUE"
621	fi
622
623	# THEN FOR EACH FILE TYPE WE LOOP BETWEEN DATE_COURANTE AND DATE_FIN.
624	for comp in ${config_ListOfComponents[*]} ; do
625	#
626	IGCM_sys_Mkdir ${RUN_DIR_PATH}/${comp}
627	#
628	IGCM_sys_Cd ${RUN_DIR_PATH}/${comp}
629	#
630	eval R_OUT_${comp}=${R_SAVE}/${comp}
631	#
632	i=0
633	#
634	for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
635	#
636	# Determine in which output we can find file
637	# IE : Output/MO or Output/DA or ...
638	#
639	FlagDir=$( echo ${file} \| awk -F "_" '{print $1}' )
640	case ${FlagDir} in
641	*Y) TS_Dir=TS_YE ; FreqDir=YE ;;
642	*M) TS_Dir=TS_MO ; FreqDir=MO ;;
643	*D) TS_Dir=TS_DA ; FreqDir=DA ;;
644	HF) TS_Dir=TS_HF ; FreqDir=HF ;;
645	3H) TS_Dir=TS_HF ; FreqDir=HF ;;
646	INS) TS_Dir=TS_INS ; FreqDir=INS ;;
647	*) IGCM_debug_Print 1 "Error in FlagDir=${FlagDir} for file ${file}."
648	IGCM_debug_Exit "Job create_ts" ;;
649	esac
650
651	# Initialize array
652	unset liste_file
653	unset liste_file_tmp
654	eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
655
656	COMPTEUR=1
657	MissingFile=FALSE
658	DATE_LOOP=${DATE_COURANTE}
659
660	while [ ${COMPTEUR} -le ${NBRE_FILE_LOOP} ] ; do
661	#
662	Length1=$( IGCM_date_DaysInPreviousPeriod ${DATE_LOOP} ${config_UserChoices_PeriodLength} end)
663	DATE_TAB=$( IGCM_date_AddDaysToGregorianDate ${DATE_LOOP} $(( 1 - Length1 )) )_${DATE_LOOP}
664
665	Length2=$( IGCM_date_DaysInNextPeriod ${DATE_LOOP} ${config_UserChoices_PeriodLength} )
666	DATE_LOOP=$( IGCM_date_AddDaysToGregorianDate ${DATE_LOOP} ${Length2} )
667
668	IGCM_sys_TestFileArchive ${file_path}${config_UserChoices_JobName}_${DATE_TAB}_${file}.nc
669	if [ $? = 0 ] ; then
670	liste_file[${#liste_file[*]}]=${file_path}${config_UserChoices_JobName}_${DATE_TAB}_${file}.nc
671	liste_file_tmp[${#liste_file_tmp[*]}]=${config_UserChoices_JobName}_${DATE_TAB}_${file}.nc
672	else
673	IGCM_debug_Print 1 "WARNING ${file_path}${config_UserChoices_JobName}_${DATE_TAB}_${file}.nc dont exist"
674	MissingFile=TRUE
675	fi
676	(( COMPTEUR = COMPTEUR + 1 ))
677	#
678	done # while [ ${COMPTEUR} -le ${NBRE_FILE_LOOP} ] done
679
680	# We skip this file type if one of them is missing.
681	if [ "${MissingFile}" = "TRUE" ] ; then
682	IGCM_debug_Print 1 "WARNING We skip ${file} type processing"
683	continue
684	fi
685
686	DATE_LOOP=$( IGCM_date_AddDaysToGregorianDate ${DATE_LOOP} -${Length2} )
687
688	# Get selected files
689	IGCM_sys_Get /l liste_file[*] ${RUN_DIR_PATH}/${comp}
690	IGCM_debug_Verif_Exit
691
692	# Apply IGCM_Patch if needed
693	if [ ! X${RebuildFrequency} = Xtrue ] ; then
694	if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) != X${NULL_STR} ]; then
695	for file_t in $( eval echo ${liste_file_tmp[*]} ); do
696	for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
697	IGCM_${Patch} ${file_t}
698	IGCM_debug_Verif_Exit
699	done
700	done
701	fi
702	fi
703
704	# WE CAN CONCATENATE FILES AT THIS POINT
705	[ "${FLAG_B}" = "TRUE" ] && DATE_BUILD_B=${DateBegin}_${DATE_FIN_JOB_B_LOOP_PREC}
706	Length=$( IGCM_date_DaysInPreviousPeriod ${DATE_COURANTE} ${config_UserChoices_PeriodLength} end)
707	DATE_BUILD1=$( IGCM_date_AddDaysToGregorianDate ${DATE_COURANTE} -$(( Length - 1 )) )
708	DATE_BUILD=${DATE_BUILD1}_${DATE_FIN}
709	DATE_BUILD_END=${DateBegin}_${DATE_FIN}
710
711	liste_coord=" "
712	for axis in $( eval echo \${LISTE_AXIS_${file}[*]} ); do
713	liste_coord=${liste_coord}${axis}","
714	done
715
716	# Time axis must be the last dimension
717	time_axis=${axis}
718
719	# SWITCH BETWEEN MODEL TO FIT PARTICULAR CASE
720	for var in $( eval echo \${LISTE_VARS_${file}[*]} ) ; do
721	#
722	# We skip variables not in the first file of the list.
723	# Seems overkill to test thel all... but will do if needed
724	ncdump -hv ${var} ${liste_file_tmp[0]} > /dev/null 2>&1
725	if [ ! $? = 0 ] ; then
726	IGCM_debug_Print 1 "WARNING We skip ${var}, not present within ${liste_file_tmp[0]}"
727	continue
728	fi
729	#
730	if [ "${FLAG_B}" = "TRUE" ] ; then
731	# WE CONCATENATE WITH EXISTING FILES
732	file1=${config_UserChoices_JobName}_${DATE_BUILD_B}_${FlagDir}_${var}.nc
733	file_out=${config_UserChoices_JobName}_${DATE_BUILD_END}_${FlagDir}_${var}.nc
734	IGCM_sys_ncrcat --hst -v ${liste_coord}${var} ${file1} ${liste_file_tmp[*]} ${file_out}
735	IGCM_debug_Verif_Exit
736	#
737	IGCM_sys_Rm ${file1}
738	if [ ! "${DEPOT}" = "TRUE" ] ; then
739	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}}/Analyse/${TS_Dir}/${file_out}
740	# "${file1} = file_before ?
741	[ ! "${file1}" = "${config_UserChoices_JobName}_${DateBegin}_${DATE_FIN_JOB_B}_${FlagDir}_${var}.nc" ] && eval MENAGE \${R_OUT_${comp}}/Analyse/${TS_Dir} ${file1} ${file_out}
742	fi
743	else
744	# OR NOT
745	file_out=${config_UserChoices_JobName}_${DATE_BUILD}_${FlagDir}_${var}.nc
746	IGCM_sys_ncrcat --hst -v ${liste_coord}${var} ${liste_file_tmp[*]} ${file_out}
747	IGCM_debug_Verif_Exit
748	fi
749
750	#
751	if [ "${DEPOT}" = "TRUE" ] ; then
752	# WE PUT FINAL FILE ON FILE SYSTEM
753	[ "${FLAG_B}" = "FALSE" ] && file_out=${config_UserChoices_JobName}_${DATE_BUILD}_${FlagDir}_${var}.nc
754	file_before=${config_UserChoices_JobName}_${DateBegin}_${DATE_FIN_JOB_B}_${FlagDir}_${var}.nc
755	#
756	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}}/Analyse/${TS_Dir}/${file_out}
757	[ "${FLAG_B}" = "TRUE" ] && eval MENAGE \${R_OUT_${comp}}/Analyse/${TS_Dir} ${file_before} ${file_out}
758	if [ ! "X${file1}" = "X" ] ; then
759	[ ! "${file1}" = "${config_UserChoices_JobName}_${DateBegin}_${DATE_FIN_JOB_B}_${FlagDir}_${var}.nc" ] && eval MENAGE \${R_OUT_${comp}}/Analyse/${TS_Dir} ${file1} ${file_out}
760	fi
761	#
762	[ -f ${file_out} ] && IGCM_sys_Rm ${file_out}
763	#
764	fi
765	#
766	done # for var in ${liste_var} ; do
767	IGCM_sys_Rm ${liste_file_tmp[*]}
768	done # for file in ${liste_file_brut} do
769	done # for comp in ${config_ListOfComponents[*]} ; do
770	# GO AHEAD IN DEEPEST LOOP
771	(( CURRENT_LOOP = CURRENT_LOOP + 1 ))
772	done # while [ ${CURRENT_LOOP} -le ${NBRE_TOUR} ] do
773	# FINISH
774
775	# DODS copy
776	for comp in ${config_ListOfComponents[*]} ; do
777	for TS_Dir in TS_YE TS_MO TS_DA TS_HF TS_INS ; do
778	IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/${TS_Dir}
779	[ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/${TS_Dir}
780	done
781	done
782
783	export DEBUG_debug; export BigBrother ; export libIGCM; export SUBMIT_DIR; export POST_DIR; export Script_Output ;
784	export StandAlone ; export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ;
785	export RESOL_SBG
786	listVarEnv="DEBUG_debug,BigBrother,libIGCM,SUBMIT_DIR,POST_DIR,Script_Post_Output,StandAlone,RESOL_ATM,RESOL_OCE,RESOL_ICE,RESOL_MBG,RESOL_SRF,RESOL_SBG"
787	export listVarEnv
788
789	#D-
790	# --------------------------------------------------------------------
791	#D- Test if all was right
792	# --------------------------------------------------------------------
793	IGCM_debug_Verif_Exit
794	# --------------------------------------------------------------------
795	#D- Submit MONITORING
796	# --------------------------------------------------------------------
797	if ( [ X${TsTask} = X2D ] \|\| [ X${TsTask} = X3D ] \|\| [ X${TsTask} = X ] ) ; then
798	# From 2D and 3D it is the last one to finish that will submit the monitoring.
799	if [ ! "X$( grep "IGCM_sys_RmRunDir" ${POST_DIR}/create_ts.${PeriodDateEnd}.[23]D.out 2> /dev/null )" = "X" ] ; then
800	Script_Post_Output=monitoring.${PeriodDateEnd}
801	IGCM_sys_QsubPost monitoring
802	fi
803	fi
804
805	#D-
806	# --------------------------------------------------------------------
807	#D- Update the run.card
808	# --------------------------------------------------------------------
809	if [ ${StandAlone} != true ] ; then
810	# Put in run.card end period of time series
811	[ X"${DATE_FIN}" = X ] \|\| IGCM_sys_RshMaster IGCM_card_WriteOption ${SUBMIT_DIR}/run.card PostProcessing TimeSeriesCompleted "${DATE_FIN}"
812	# We have finish the job !
813	IGCM_sys_RshMaster IGCM_card_WriteOption ${SUBMIT_DIR}/run.card PostProcessing TimeSeriesRunning "n"
814	fi
815
816	# Clean RUN_DIR_PATH (necessary for cesium and titane only)
817	IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
818
819	# ------------------------------------------------------------------
820	# Finalize BigBrother to inform that the jobs end
821	# ------------------------------------------------------------------
822	IGCM_debug_BigBro_Finalize
823
824	date

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