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source: CONFIG_DEVT/IPSLCM6.5_work_ENSEMBLES/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 6031

Last change on this file since 6031 was 6031, checked in by aclsce, 2 years ago
Update of ensembles development configuration.
File size: 84.8 KB

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1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
6	# $Revision:: 1545 $ Revision of last commit
7	# $Author:: aclsce $ Author of last commit
8	# $Date:: 2021-01-18 14:16:13 +0100 (Mon, 18 Jan 2021) $ Date of last commit
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	#
12	#**************************************************************
13
14	#========================================================================
15	function IGCM_comp_Initialize
16	{
17	IGCM_debug_PushStack "IGCM_comp_Initialize"
18
19	# Debug Print :
20	echo
21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
22	echo
23
24	typeset comp compname comptagname auxprint card_UserChoices first_option option i j
25	for comp in ${config_ListOfComponents[*]} ; do
26
27	# Define component
28	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
29	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
30	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
31
32	# Debug Print
33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
34
35	# ${compname}.card PATH
36	card=${SUBMIT_DIR}/COMP/${compname}.card
37
38	# Manage component executable
39	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
40
41	# Define all options in section [comp]
42	IGCM_debug_Print 3 " DefineArrayFromSection : ${comp}"
43	IGCM_card_DefineArrayFromSection ${SUBMIT_DIR}/config.card ${comp}
44	eval config_comp=\${config_${comp}[*]} > /dev/null 2>&1
45	for option in ${config_comp[*]} ; do
46	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
47	done
48	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
49
50	# Debug Print :
51	eval auxprint=\${config_${comp}_WriteFrequency}
52	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
53	#2> /dev/null
54
55	# Debug Print :
56	IGCM_debug_Print 2 "Initialize following component library"
57
58	# Source drivers in directory DRIVER if it exist
59	# else source them from directory COMP
60	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
61	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
62	# Source component library
63	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
64	else
65	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
66	# Source component library
67	. ${SUBMIT_DIR}/COMP/${compname}.driver
68	fi
69	IGCM_debug_Print 3 "With tag : ${comptagname}"
70
71	# Debug Print
72	IGCM_debug_Print 3 "Initialize ${comp} output directory."
73
74	# Define ARCHIVED Dirs
75	eval R_OUT_${comp}=${R_SAVE}/${comp}
76	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
77
78	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
79	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
80
81	eval R_OUT_${comp}_A=\${R_OUT_${comp}}/Analyse
82	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_A}
83
84	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
86
87	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
88	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
89
90	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
91	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
92	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
93	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
94
95	eval R_OUT_${comp}_A_H=\${R_OUT_${comp}_A}/TS_HF
96	eval R_OUT_${comp}_A_D=\${R_OUT_${comp}_A}/TS_DA
97	eval R_OUT_${comp}_A_M=\${R_OUT_${comp}_A}/TS_MO
98	eval R_OUT_${comp}_A_Y=\${R_OUT_${comp}_A}/TS_YE
99
100	# Define BUFFERED Dirs
101	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
102	eval R_BUF_${comp}=${R_BUFR}/${comp}
103	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
104
105	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
107
108	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
110
111	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
112
113	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
114
115	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
116
117	for (( pool_rank_comp_Init=0 ; pool_rank_comp_Init < $(($config_Ensemble_PoolNumber)) ; pool_rank_comp_Init++ ))
118	do
119
120	for (( pool_member_rank=0 ; pool_member_rank < $config_Ensemble_PoolSize ; pool_member_rank++ ))
121	do
122	whole_ensemble_rank=$(($config_Ensemble_PoolSize*$pool_rank_comp_Init+$pool_member_rank))
123	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}/MEMBER_$whole_ensemble_rank
124	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}/MEMBER_$whole_ensemble_rank
125	done
126	done
127	fi
128
129	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
130	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
131	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
132	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
133
134	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
135	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
136	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
137	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
138
139	# Define CMIP6 Dirs
140	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
141	fi
142
143	# Read UserChoices section of component card
144	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
145	IGCM_card_DefineArrayFromSection ${card} UserChoices
146	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
147
148	# If section is not empty we define corresponding variables
149	if [ X${first_option} != X"Error:" ] ; then
150	if [ X${card_UserChoices[0]} != X ] ; then
151	unset card_UserChoices
152	fi
153	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
154	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
155	for option in ${card_UserChoices[*]} ; do
156	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
157	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
158	done
159	fi
160
161	# Read and Build Output File stuff
162	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
163	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
164	ListFilesName=${compname}_OutputFiles_List
165	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
166	#
167	if [ X${FileName0} != X${NULL_STR} ] ; then
168	#
169	#IGCM_debug_Print 1 "Component : ${compname}"
170	#
171	# INITIALISATION
172	#
173	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
174	#
175	i=2
176	#
177	until [ $i -ge $NbFiles ]; do
178	#
179	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
180	#
181	if [ X${flag_post} != XNONE ] ; then
182	#
183	# First of all
184	#
185	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
186	# This section is mandatory
187	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
188	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
189	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
190	IGCM_debug_Verif_Exit
191	fi
192	#
193	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
194	#
195	# variable option allready typeset above
196	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
197	if [ ${option} = Seasonal ] ; then
198	FoundSeasonal=true
199	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
200	fi
201	done
202	#
203	if [ ! X${FoundSeasonal} = Xtrue ] ; then
204	eval ${compname}_${flag_post}_Seasonal=ON
205	fi
206	#
207	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
208	Seasonal=true
209	fi
210
211	# Dimension = vide si vieille card.
212	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
213	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
214	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
215	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
216	ListDimension[0]=2D
217	ListDimension[1]=3D
218	TimeSeries=false
219	iLoop=${#ListDimension[*]}
220	j=0
221	until [ $j -ge ${iLoop} ]; do
222	Dimension=${ListDimension[${j}]}
223	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
224	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
225	#
226	# Time series WITHOUT chunk
227	#
228	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
229	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
230	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
231	eval TimeSeries${Dimension}=true
232	fi
233	fi
234	#
235	# Time series WITH chunk
236	#
237	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
238	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
239	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
240	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
241	eval TimeSeriesChunck${Dimension}=true
242	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
243	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
244	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
245	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
246	fi
247	fi
248	(( j=j+1 ))
249	done
250	else
251	ListDimension[0]=""
252	TimeSeries=true
253	TimeSeries2D=false
254	TimeSeries3D=false
255	TimeSeriesChunck2D=false
256	TimeSeriesChunck3D=false
257	fi
258	fi
259	(( i=i+3 ))
260	done
261	fi
262	# Debug Print
263	IGCM_debug_Print 3 "Initialize ${compname} with driver."
264	# INIT component
265	${comp}_Initialize
266	echo
267	done
268
269	IGCM_debug_PopStack "IGCM_comp_Initialize"
270	}
271
272	#=======================================================================
273	function IGCM_comp_PrepareDeletedFiles
274	{
275	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
276
277	if [ X${2} != X. ] ; then
278	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
279	else
280	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
281	fi
282
283	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
284	}
285
286	#=======================================================================
287	function IGCM_comp_PrepareXiosFiles
288	{
289	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
290
291	typeset file
292	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
293
294	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
295	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
296	fi
297	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
298	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
299	fi
300	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
301	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
302	fi
303
304	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
305	}
306
307	#=======================================================================
308	function IGCM_comp_GetInputInitialStateFiles
309	{
310	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
311
312	# Debug Print :
313	echo
314	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
315	echo
316
317	# Only the first time step need InitialStateFiles
318	# otherwise it's BoundaryConditions
319	if ( ${FirstInitialize} ) ; then
320	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
321	typeset file_in_ file_in file_out_ file_out do_init
322	for comp in ${config_ListOfComponents[*]} ; do
323	# Initialize
324	do_init="y"
325	# Do we need to bring initial state file for this component
326	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
327	eval do_init="n"
328	else
329	# Read component Restarts parameters
330	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
331	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
332	if [ "${do_start}" = "y" ] ; then
333	do_init="n"
334	else
335	do_init="y"
336	fi
337	fi
338
339	if [ "${do_init}" = "y" ] ; then
340	# Define component
341	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
342	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
343
344	# Debug Print :
345	IGCM_debug_Print 3 "Initialisation files ${compname}"
346
347	card=${SUBMIT_DIR}/COMP/${compname}.card
348
349	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
350	ListFilesName=${compname}_InitialStateFiles_List
351
352	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
353	if [ X${FileName0} != X${NULL_STR} ] ; then
354	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
355	(( i=0 ))
356	until [ $i -ge $NbFiles ]; do
357	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
358	eval file_in=${file_in_}
359	(( i_ = i+1 ))
360	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
361	eval file_out=${file_out_}
362
363	IGCM_sys_IsFileArchived ${file_in}
364	if [ $? = 0 ] ; then
365	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
366	IGCM_sys_Cp_ensembleXIOS ${file_in} ${file_out} $1
367	else
368	IGCM_sys_Get ${file_in} ${file_out}
369	fi
370	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
371	else
372	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
373	IGCM_sys_Cp_ensembleXIOS ${file_in} ${file_out} $1
374	else
375	IGCM_sys_Cp ${file_in} ${file_out}
376	fi
377	fi
378	(( i=i+2 ))
379	done
380	fi
381	fi
382	done
383	fi
384	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
385	}
386
387	#=======================================================================
388	# Definition of Smooth modulo function
389	# usage :
390	# IGCM_SmoothModulo StringModulo value
391	#
392	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
393	# [min]:[modulo:][max]
394	# where :
395	# [] value are optionnals;
396	# empty min equal 1
397	# empty max equal infinity
398	# modulo not given or empty equal 1
399	# empty string or just ':' equal always.
400	#
401	# value : the value to test with the definition
402	#
403	# return : true(1)/false(0)
404	function IGCM_SmoothModulo
405	{
406	IGCM_debug_PushStack "IGCM_SmoothModulo"
407	typeset defVector ModValue
408
409	eval set +A defVector -- $( echo "${1}" \| \
410	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
411
412	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
413	arr[1]=${defVector[0]}
414	arr[2]=${defVector[2]}
415
416	# Test limits :
417	# ${defVector[0]} <= ${2} <= ${defVector[2]}
418	# or ${defVector[2]} == -1
419	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
420	# Test modulo
421	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
422	if [ ${ModValue} -eq 0 ] ; then
423	arr[3]=true
424	echo ${arr[@]}
425	IGCM_debug_PopStack "IGCM_SmoothModulo"
426	return 1
427	else
428	arr[3]=false
429	echo ${arr[@]}
430	IGCM_debug_PopStack "IGCM_SmoothModulo"
431	return 0
432	fi
433	else
434	arr[3]=false
435	echo ${arr[@]}
436	IGCM_debug_PopStack "IGCM_SmoothModulo"
437	return 0
438	fi
439	}
440
441	#=======================================================================
442	function IGCM_comp_GetInputSmoothFiles
443	{
444	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
445
446	# Debug Print :
447	echo
448	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
449	echo
450
451	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
452	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
453
454	for comp in ${config_ListOfComponents[*]} ; do
455	# Define component
456	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
457	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
458
459	# Debug Print :
460	IGCM_debug_Print 3 "Smooth files ${compname}"
461
462	card=${SUBMIT_DIR}/COMP/${compname}.card
463
464	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
465	ListFilesName=${compname}_SmoothFiles_List
466	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
467
468	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
469	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
470
471	(( i=0 ))
472	until [ $i -ge $NbFiles ]; do
473	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
474	eval file_in=${file_in_}
475	(( i_ = i+1 ))
476	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
477	eval file_out=${file_out_}
478
479	# define CumulPeriod definition for this file
480	(( i__ = i+2 ))
481	eval SmoothDef=\${${ListFilesName}[$i__]}
482	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
483	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
484	j=1
485	for val in ${aux} ; do
486	[ ${j} -eq 1 ] && SmoothMin=${val}
487	[ ${j} -eq 2 ] && SmoothMax=${val}
488	[ ${j} -eq 3 ] && ret=${val}
489	(( j=j+1 ))
490	done
491	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
492	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
493
494	IGCM_sys_IsFileArchived ${file_in}
495	if [ $? = 0 ] ; then
496	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
497	IGCM_sys_Cp_ensembleXIOS ${file_in} ${file_out} $1
498	else
499	IGCM_sys_Get ${file_in} ${file_out}
500	fi
501	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
502	else
503	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
504	IGCM_sys_Cp_ensembleXIOS ${file_in} ${file_out} $1
505	else
506	IGCM_sys_Cp ${file_in} ${file_out}
507	fi
508	fi
509	fi
510	(( i=i+3 ))
511	done
512	fi
513	done
514
515	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
516	}
517
518	#=======================================================================
519	function IGCM_comp_GetInputBoundaryFiles
520	{
521	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
522
523	# Debug Print :
524	echo
525	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
526	echo
527
528	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
529	typeset file_in_ file_in file_out_ file_out
530
531	if [ ${Period} = 1 ]; then
532	ListFixBoundary=" "
533	fi
534
535	for comp in ${config_ListOfComponents[*]} ; do
536
537	# Define component
538	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
539	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
540
541	# Debug Print :
542	IGCM_debug_Print 3 "Boundary files ${compname}"
543
544	card=${SUBMIT_DIR}/COMP/${compname}.card
545
546	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
547	ListFilesName=${compname}_BoundaryFiles_List
548	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
549
550	if [ X${FileName0} != X${NULL_STR} ] ; then
551	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
552
553	(( i=0 ))
554	until [ $i -ge $NbFiles ]; do
555	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
556	eval file_in=${file_in_}
557	(( i_ = i+1 ))
558	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
559	eval file_out=${file_out_}
560
561	IGCM_sys_IsFileArchived ${file_in}
562	if [ $? = 0 ] ; then
563	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
564	IGCM_sys_Cp_ensembleXIOS ${file_in} ${file_out} $1
565	else
566	IGCM_sys_Get ${file_in} ${file_out}
567	fi
568	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
569	else
570	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
571	IGCM_sys_Cp_ensembleXIOS ${file_in} ${file_out} $1
572	else
573	IGCM_sys_Cp ${file_in} ${file_out}
574	fi
575	fi
576
577	(( i=i+2 ))
578	done
579	fi
580
581	# Get non deleted files
582	if [ ${Period} = 1 ]; then
583
584	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
585	ListFilesName=${compname}_BoundaryFiles_ListNonDel
586	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
587
588	if [ X${FileName0} != X${NULL_STR} ] ; then
589	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
590
591	(( i=0 ))
592	until [ $i -ge $NbFiles ]; do
593	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
594	eval file_in=${file_in_}
595	(( i_ = i+1 ))
596	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
597	eval file_out=${file_out_}
598
599	IGCM_sys_IsFileArchived ${file_in}
600	if [ $? = 0 ] ; then
601	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
602	IGCM_sys_Cp_ensembleXIOS ${file_in} ${file_out} $1
603	else
604	IGCM_sys_Get ${file_in} ${file_out}
605	fi
606	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
607	else
608	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
609	IGCM_sys_Cp_ensembleXIOS ${file_in} ${file_out} $1
610	else
611	IGCM_sys_Cp ${file_in} ${file_out}
612	fi
613	fi
614
615	if [ X${file_out} != X. ] ; then
616	ListFixBoundary=${ListFixBoundary}" "${file_out}
617	else
618	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
619	fi
620
621	(( i=i+2 ))
622	done
623	fi
624	fi
625	done
626
627	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
628	}
629
630	#=======================================================================
631	function IGCM_comp_DelFixeBoundaryFiles
632	{
633	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
634
635	# Debug Print :
636	echo
637	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
638	echo
639
640	ls -l ${ListFixBoundary}
641	rm -f ${ListFixBoundary}
642
643	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
644	}
645
646	#=======================================================================
647	function IGCM_comp_GetInputParametersFiles
648	{
649	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
650
651	# Debug Print :
652	echo
653	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
654	echo
655
656	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
657	for comp in ${config_ListOfComponents[*]} ; do
658	# Define component
659	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
660	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
661
662	# Initialize array hosting file_def and field_def files to check and/or modify
663	unset FieldDef
664	unset FileDef
665
666	# Debug Print :
667	IGCM_debug_Print 3 "Parameters ${compname}"
668
669	card=${SUBMIT_DIR}/COMP/${compname}.card
670
671	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
672	ListFilesName=${compname}_ParametersFiles_List
673	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
674
675	if [ X${FileName0} != X${NULL_STR} ] ; then
676	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
677
678	(( i=0 ))
679	until [ $i -ge $NbFiles ]; do
680	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
681	eval file_in=${file_in_}
682	(( i_ = i+1 ))
683	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
684	eval file_out=${file_out_}
685	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
686	IGCM_sys_Cp_ensembleXIOS ${file_in} ${file_out} $1
687	else
688	IGCM_sys_Cp ${file_in} ${file_out}
689	fi
690	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
691	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
692
693	(( i=i+2 ))
694	done
695	fi
696
697	done
698
699	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
700	}
701
702	#=======================================================================
703	function IGCM_comp_GetInputRestartFiles
704	{
705	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
706
707	# Debug Print :
708	echo
709	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
710	echo
711
712	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
713	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
714	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
715	typeset file_in file_out file_in_ file_out_ file_in_Name
716	typeset -Z4 j4
717	#BASH declare j4
718
719	IsMatching=""
720
721	for comp in ${config_ListOfComponents[*]} ; do
722	# Define component
723	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
724	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
725	#
726	card=${SUBMIT_DIR}/COMP/${compname}.card
727	#
728	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
729	ListFilesName=${compname}_RestartFiles_List
730	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
731
732	# Debug Print :
733	IGCM_debug_Print 3 "restart ${compname}"
734
735	if ( ${FirstInitialize} ) ; then
736
737	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
738	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
739	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
740	CompOldName=IOS
741	config_IOS_Restart="n"
742	do_start="n"
743	config_IOS_RestartDate=-1
744	config_IOS_RestartJobName=${NULL_STR}
745	config_IOS_RestartPath=${NULL_STR}
746	else
747	eval config_${comp}_Restart="y"
748	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
749	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
750	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
751	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
752	eval CompOldName=${comp}
753	fi
754	else
755	# Read component Restarts parameters
756	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
757	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
758
759	if [ "${do_start}" = "y" ] ; then
760	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
761	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
762	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
763	else
764	eval config_${comp}_RestartDate=-1
765	eval config_${comp}_RestartJobName=${NULL_STR}
766	eval config_${comp}_RestartPath=${NULL_STR}
767	fi
768
769	eval CompOldName=\${config_${comp}_OldName}
770	if [ X${CompOldName} = X ] ; then
771	eval CompOldName=${comp}
772	fi
773
774	# Reinitialize IsMatching to allow searching for a different tar file for each component.
775	IsMatching=""
776	TarFileFound=""
777	fi
778
779	if [ "${do_start}" = "y" ] ; then
780
781	# Restore Restarts files
782	#-----------------------
783	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
784	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
785
786	(( i=1 ))
787	until [ $i -gt $NbFiles ]; do
788	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
789	eval file_in=${file_in_}
790	(( i_ = i+1 ))
791	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
792	eval file_out=${file_out_}
793
794	eval Date_tmp=\${config_${comp}_RestartDate}
795	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
796	# will be re-use
797	eval RestartPath=\${config_${comp}_RestartPath}
798	eval RestartJobName=\${config_${comp}_RestartJobName}
799	#
800	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
801	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
802
803	extension_in=$( echo ${file_in_Name##*.} )
804	extension_out=$( echo ${file_out##*.} )
805
806	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
807	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
808	Path_OUT=${Path_r}/${generic_restart_file_name_in}
809
810	path_restart_tmp=`dirname $Path_OUT`
811	base_restart_tmp=`basename $Path_OUT`
812
813	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
814	for (( pool_member_rank=0 ; pool_member_rank < $config_Ensemble_PoolSize ; pool_member_rank++ ))
815	do
816	whole_ensemble_rank=$(($config_Ensemble_PoolSize*$1+$pool_member_rank))
817	Path_OUT="$path_restart_tmp/MEMBER_$whole_ensemble_rank/$base_restart_tmp"
818	Path_r="$path_restart_tmp/MEMBER_$whole_ensemble_rank"
819	cd MEMBER_$whole_ensemble_rank
820
821	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
822	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
823	Buffered=true
824	Archived=false
825	Tared=false
826	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
827	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
828	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
829	Buffered=false
830	Archived=true
831	Tared=false
832	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
833	else
834	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
835	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
836	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
837	Buffered=false
838	Archived=false
839	Tared=true
840	# Look after the tar file we want if we did not found it already
841	if [ X${IsMatching} = X ] ; then
842	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
843	if [ $? ] ; then
844	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
845	IsMatching=$( echo ${PotentialTarFile##*/} \| \
846	sed "s:_restart::" \| \
847	sed "s:^${RestartJobName}_::" \| \
848	sed "s:\.tar$::" \| \
849	gawk -F_ -v restartdate=${Date_r} \
850	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
851	if [ ! X${IsMatching} = X ] ; then
852	TarFileFound=${PotentialTarFile}
853	break
854	fi
855	done
856	fi
857	# Stop here if nothing has been found
858	if [ X${TarFileFound} = X ] ; then
859	IGCM_debug_Print 3 "Restart files were not found!"
860	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
861	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
862	IGCM_debug_Exit "Please double check restart settings in config.card"
863	IGCM_debug_Verif_Exit
864	fi
865	fi
866	IGCM_sys_PrepareTaredRestart ${TarFileFound}
867	TarFileLocation=$( basename ${TarFileFound} )
868	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
869	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
870	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
871	fi
872
873	if [ ${nb_restart_file} -gt 1 ] ; then
874	j=0 # BASH LINE NOT NEEDED
875	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
876	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
877	j4=${j} # BASH LINE NOT NEEDED
878	if [ X${Buffered} = Xtrue ] ; then
879	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
880	elif [ X${Archived} = Xtrue ] ; then
881	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
882	elif [ X${Tared} = Xtrue ] ; then
883	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
884	fi
885	(( j=j+1 )) #BASH LINE NOT NEEDED
886	done
887
888	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
889	if [ X${OCE_PROC_MPI} != X ] ; then
890	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
891	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
892	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
893	fi
894	fi
895	else
896	if [ X${Buffered} = Xtrue ] ; then
897	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
898	elif [ X${Archived} = Xtrue ] ; then
899	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
900	elif [ X${Tared} = Xtrue ] ; then
901	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
902	fi
903	fi
904	cd ..
905	done
906	fi
907	(( i=i+3 ))
908	done
909	else
910	if [ X${FileName0} != XNONE ] ; then
911	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
912	else
913	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
914	fi
915	fi
916	fi
917	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
918	# if not FirstInitialize and first loop of this job
919
920	# Restore Restarts files
921	#-----------------------
922	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
923	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
924
925	index_j=0
926	for index_member in $(cut -d: -f2 ${SUBMIT_DIR}/ensemble.txt); do
927	member[$index_j]=$index_member
928	index_j=$index_j+1
929	done
930
931	(( i=1 ))
932	until [ $i -gt $NbFiles ]; do
933	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
934	eval file_in=${file_in_}
935	(( i_ = i+1 ))
936	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
937	eval file_out=${file_out_}
938
939	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
940
941	extension_in=$( echo ${file_in_Name##*.} )
942	extension_out=$( echo ${file_out##*.} )
943
944	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
945	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
946
947	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
948	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
949
950	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
951	path_restart_tmp=`dirname $Path_BUF`
952	base_restart_tmp=`basename $Path_BUF`
953
954	for (( pool_member_rank=0 ; pool_member_rank < $config_Ensemble_PoolSize ; pool_member_rank++ ))
955	do
956	whole_ensemble_rank=$(($config_Ensemble_PoolSize*$1+$pool_member_rank))
957	Path_BUF=$path_restart_tmp/MEMBER_${member[$whole_ensemble_rank]}/$base_restart_tmp
958	Path_r=$path_restart_tmp/MEMBER_${member[$whole_ensemble_rank]}
959	cd MEMBER_$whole_ensemble_rank
960
961
962	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
963	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
964	Buffered=true
965	Archived=false
966	Tared=false
967	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
968	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
969	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
970	Buffered=false
971	Archived=true
972	Tared=false
973	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
974	else
975	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
976	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
977	Buffered=false
978	Archived=false
979	Tared=true
980	# Look after the tar file we want if we did not found it already
981	if [ X${IsMatching} = X ] ; then
982	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
983	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
984	if [ ! X${IsMatching} = X ] ; then
985	TarFileFound=${PotentialTarFile}
986	break
987	fi
988	done
989	fi
990	# Stop here if nothing has been found
991	if [ X${TarFileFound} = X ] ; then
992	IGCM_debug_Print 3 "Restart files were not found!"
993	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
994	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
995	IGCM_debug_Exit "Please double check restart settings in config.card"
996	IGCM_debug_Verif_Exit
997	fi
998	IGCM_sys_PrepareTaredRestart ${TarFileFound}
999	TarFileLocation=$( basename ${TarFileFound} )
1000	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
1001	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
1002	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
1003	fi
1004
1005	if [ ${nb_restart_file} -gt 1 ] ; then
1006	j=0 # BASH LINE NOT NEEDED
1007	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1008	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1009	j4=${j} # BASH LINE NOT NEEDED
1010	if [ X${Buffered} = Xtrue ] ; then
1011	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1012	elif [ X${Archived} = Xtrue ] ; then
1013	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1014	elif [ X${Tared} = Xtrue ] ; then
1015	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1016	fi
1017	(( j=j+1 )) # BASH LINE NOT NEEDED
1018	done
1019	else
1020	if [ X${Buffered} = Xtrue ] ; then
1021	eval IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
1022	elif [ X${Archived} = Xtrue ] ; then
1023	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
1024	elif [ X${Tared} = Xtrue ] ; then
1025	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
1026	fi
1027	fi
1028	cd ..
1029	done
1030	fi
1031	(( i=i+3 ))
1032	done
1033	else
1034	if [ X${FileName0} != XNONE ] ; then
1035	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
1036	else
1037	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
1038	fi
1039	fi
1040	fi
1041	done
1042
1043	NbFiles=$( ls * 2> /dev/null \| wc -l )
1044	if [ ${NbFiles} -gt 0 ] ; then
1045	IGCM_sys_Chmod u+rw *
1046	fi
1047
1048	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
1049	}
1050
1051	#=======================================================================
1052	function IGCM_comp_GetInputBinaryFiles
1053	{
1054	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
1055
1056	# Debug Print :
1057	echo
1058	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
1059	echo
1060
1061	# Clean up previous pass
1062	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
1063
1064	typeset comp ExeNameIn ExeNameOut byPass
1065	typeset compilerNmbr compilerUnit compilerFull
1066	byPass=false
1067	for comp in ${config_ListOfComponents[*]} ; do
1068	# Define component
1069
1070	# Copy executable for this component
1071	eval ExeNameIn=\${config_Executable_${comp}[0]}
1072	eval ExeNameOut=\${config_Executable_${comp}[1]}
1073	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
1074	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
1075	# The executable is set in config.card and is different from ""
1076	# Use eval to expand ExeNameIn if variables are used in the name
1077	eval ExeNameIn=${ExeNameIn}
1078	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1079	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1080	fi
1081	fi
1082
1083	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1084	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1085	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1086	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1087	fi
1088	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1089	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1090	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1091	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1092	fi
1093	fi
1094
1095	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1096	# Get the compiler version
1097	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1098	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1099	# Save it
1100	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1101	[ X${compilerFull} = X ] && byPass=true
1102	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1103	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1104	fi
1105	done
1106
1107	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1108	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1109
1110	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1111	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1112	fi
1113
1114	# Test on compiler version for IPSLCM6* configuration on irene (only for CMIP6 production)
1115	if [ ${SYSTEM} = irene ]; then
1116	if ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.13 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.14 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.15 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.1 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM5A2.1 )" != "X" ] && [ X${compilerFull} != XV17 ] ) ; then
1117	IGCM_debug_Exit "IPSLCM6.0.13, IPSLCM6.0.14, IPSLCM6.0.15, IPSLCM6.1 and IPSLCM5A2.1 must be compiled with intel 2017 compiler"
1118	fi
1119	fi
1120
1121	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1122	}
1123
1124	#=======================================================================
1125	function IGCM_comp_PeriodStart
1126	{
1127	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1128
1129	# Debug Print :
1130	echo
1131	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1132	echo
1133
1134	typeset ExeNameIn ExeNameOut
1135	typeset comp compname comptagname
1136	for comp in ${config_ListOfComponents[*]} ; do
1137	# Define component
1138	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1139	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1140
1141	# Copy executable for this component
1142	eval ExeNameIn=\${config_Executable_${comp}[0]}
1143	eval ExeNameIn=${ExeNameIn}
1144	eval ExeNameOut=\${config_Executable_${comp}[1]}
1145
1146	# Debug Print
1147	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1148	# UPDATE component
1149	${comp}_PeriodStart 2> /dev/null
1150
1151	done
1152
1153	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1154	}
1155
1156
1157
1158	#=======================================================================
1159	function IGCM_comp_modifyFile
1160	{
1161	#
1162	# syntax: IGCM_comp_modifyFile filein key [value]
1163	#
1164	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1165	#
1166	# This function is used to replace a pattern in a file for a specific variable.
1167	#
1168	# Arguments:
1169	# - filein : the file in run directory in which the variable should be set
1170	# - key : the variable to modify
1171	# - value : the value to set the key equal to
1172	#
1173	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1174
1175	typeset filein key value pattern
1176
1177	# Set local variables and test the arguments
1178	if [ $# = 3 ] ; then
1179	# Normal case with 3 arguments
1180	filein=$1 ; key=$2 ; value=$3
1181	else
1182	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1183	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1184	return
1185	fi
1186	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1187
1188	# Test if the file exist
1189	if [ ! -f ${filein} ] ; then
1190	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1191	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1192	return
1193	fi
1194
1195	# Read the line with key in the file without the comments
1196	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1197
1198	# Verify the existance of the pattern
1199	if [ X"${pattern}" = X ] ; then
1200	# Variable key is not set in filein, stop.
1201	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1202	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1203	return
1204	fi
1205
1206	# Now change key in filein
1207	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1208	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1209	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1210	\mv ${filein}.tmp ${filein}
1211
1212	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1213	}
1214
1215	#=======================================================================
1216	function IGCM_comp_modifyDefFile
1217	{
1218	#
1219	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1220	#
1221	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1222	#
1223	# This function is used to modify a parameter file for a specific variable.
1224	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1225	# This function can be used in the comp.driver files for the components.
1226	#
1227	# Arguments:
1228	# - type : first argument must be blocker, nonblocker or force
1229	# For "blocker" case, the variable must be attributed the keyworld AUTO
1230	# otherwise this function will exit.
1231	# For "nonblocker" case, the user can remove or modify the variable. For
1232	# this case, as long as AUTO is not set, no modification will be done.
1233	# For "force" case, the variable will be modified even if it is not set to AUTO
1234	# - filein : the file in run directory of .def type in which the variable should be set
1235	# - key : the variable to modify
1236	# - value : the value to set the key equal to, optional. If value is not set or if
1237	# value=DEFAULT, then a default value must be given in filein using syntax :
1238	# key= AUTO : DEFAULT=def_value
1239	#
1240	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1241
1242	typeset type filein key value
1243	typeset filelist nb_occ modify
1244
1245	# Set local variables and test the arguments
1246	if [ $# = 4 ] ; then
1247	# Normal case with 4 arguments
1248	type=$1 ; filein=$2 ; key=$3 ; value=$4
1249	elif [ $# = 3 ] ; then
1250	# Normal case with 3 arguments
1251	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1252	else
1253	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1254	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1255	return
1256	fi
1257	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1258
1259	# Test if first argument is correct
1260	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1261	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1262	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1263	return
1264	fi
1265
1266	# Test if the file exist.
1267	# Exit with error if the file does not exist for the case blocker or force.
1268	# Only return for the case nonblocker.
1269	if [ ! -f ${filein} ] ; then
1270	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1271	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1272	else
1273	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1274	fi
1275	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1276	return
1277	fi
1278
1279	# Define list of files to test using all files with suffix .def (except used*.def)
1280	filelist=$( ls *def \| grep -v used )
1281
1282	# Count number of occurances for the key in all files
1283	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1284
1285	# Test if key is set several times
1286	if [ ${nb_occ} -gt 1 ] ; then
1287	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1288	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1289	return
1290	fi
1291
1292	# Treatement according to different cases
1293	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1294	# Stop if the key is never set and the function is blocker
1295	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1296	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1297	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1298	# The key is not set but it is a nonblocker call so nothing is done.
1299	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1300	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1301	modify=no
1302	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1303	# Variable key is not set in filein, stop.
1304	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1305	fi
1306
1307	# Check if AUTO is set in the filein on the same line as the key variable
1308	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1309	# Modification will be done for all cases
1310	modify=yes
1311	else
1312	# The variable was not set to AUTO
1313	if [ ${type} = blocker ] ; then
1314	# Exit because this is a blocker call
1315	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1316	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1317	return
1318	elif [ ${type} = nonblocker ] ; then
1319	# Do nothing. Suppose that the user did set the variable correct
1320	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1321	modify=no
1322	elif [ ${type} = force ] ; then
1323	# Force modification
1324	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1325	modify=yes
1326	fi
1327	fi
1328
1329	# Do the modifcation now
1330	if [ ${modify} = yes ] ; then
1331
1332	# For option DEFAULT, read default value from file.
1333	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1334	# Case to set DEFAULT value
1335	# Read default value from filein
1336	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1337
1338	if [ X"${value}" = X ] ; then
1339	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1340	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1341	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1342	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1343	return
1344	fi
1345	fi
1346
1347	# Now change key in filein
1348	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1349	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1350	\mv ${filein}.tmp ${filein}
1351	fi
1352	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1353	}
1354
1355	#=======================================================================
1356	function IGCM_comp_modifyNamelist
1357	{
1358	#
1359	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1360	#
1361	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1362	#
1363	# This function is used to modify a parameter file for a specific variable.
1364	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1365	# This function can be used in the comp.driver files for the components.
1366	#
1367	# Arguments:
1368	# - type : first argument must be blocker, nonblocker or force
1369	# For "blocker" case, the variable must be attributed the keyworld AUTO
1370	# otherwise this function will exit.
1371	# For "nonblocker" case, the user can remove or modify the variable. For
1372	# this case, as long as AUTO is not set, no modification will be done.
1373	# For "force" case, the variable will be modified even if it is not set to AUTO
1374	# - filein : the file in run directory of .def type in which the variable should be set
1375	# - key : the variable to modify
1376	# - value : the value to set the key equal to, optional. If value is not set or if
1377	# value=DEFAULT, then a default value must be given in filein using syntax :
1378	# key= AUTO : DEFAULT=def_value
1379	#
1380	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1381
1382	typeset type filein key value pattern modify
1383
1384	# Set local variables and test the arguments
1385	if [ $# = 4 ] ; then
1386	# Normal case with 4 arguments
1387	type=$1 ; filein=$2 ; key=$3 ; value=$4
1388	elif [ $# = 3 ] ; then
1389	# Normal case with 3 arguments
1390	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1391	else
1392	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1393	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1394	return
1395	fi
1396	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1397
1398	# Test if first argument is correct
1399	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1400	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1401	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1402	return
1403	fi
1404
1405	# Test if the file exist.
1406	# Exit with error if the file does not exist for the case blocker or force.
1407	# Only return for the case nonblocker.
1408	if [ ! -f ${filein} ] ; then
1409	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1410	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1411	else
1412	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1413	fi
1414	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1415	return
1416	fi
1417
1418	# Read the line with key in the file without the comments
1419	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1420
1421	# Verify the existance of the pattern
1422	if [ X"$pattern" = X ] ; then
1423	# Variable key is not set in filein, stop.
1424	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1425	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1426	return
1427	fi
1428
1429	# Check if the variable is set to AUTO in the filein
1430	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1431	# Modification will be done for all cases
1432	modify=yes
1433	else
1434	# The variable was not set to AUTO
1435	if [ ${type} = blocker ] ; then
1436	# Exit because this is a blocker call
1437	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1438	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1439	return
1440	elif [ ${type} = nonblocker ] ; then
1441	# Do nothing. Suppose that the user did set the variable correct
1442	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1443	modify=no
1444	elif [ ${type} = force ] ; then
1445	# Force modification
1446	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1447	modify=yes
1448	fi
1449	fi
1450
1451	# Do the modifcation now
1452	if [ ${modify} = yes ] ; then
1453
1454	# For option DEFAULT, read default value from file.
1455	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1456	# Case to set DEFAULT value
1457	# Read default value from filein
1458	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1459
1460	if [ X"${value}" = X ] ; then
1461	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1462	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1463	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1464	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1465	return
1466	fi
1467	fi
1468
1469	# Now change key in filein
1470	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1471	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1472	\mv ${filein}.tmp ${filein}
1473	fi
1474	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1475	}
1476
1477	#=======================================================================
1478	function IGCM_comp_modifyXmlFile
1479	{
1480	#
1481	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1482	#
1483	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1484	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1485	#
1486	# This function is used to modify the value for a specific attribute and variable id.
1487	# The file must be a valid xml file.
1488	# This function can be used in the comp.driver files for the components.
1489	#
1490	# Arguments:
1491	# - type : first argument must be blocker, nonblocker or force.
1492	# For "blocker" case, the variable must be attributed the keyworld AUTO
1493	# otherwise this function will exit.
1494	# For "nonblocker" case, the user can remove or modify the variable. For
1495	# this case, as long as AUTO is not set, no modification will be done.
1496	# For "force" case, the variable will be modified even if it is not set to AUTO
1497	# - filein : the file in run directory of .xml type in which the variable should be set
1498	# - keyid : the variable to modify
1499	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1500	# - value : the value to set in the filein
1501	#
1502	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1503
1504	typeset type filein keyid keyattrib value modify
1505
1506	# Set local variables and test the arguments
1507	if [ $# = 5 ] ; then
1508	# Normal case with 4 arguments
1509	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1510	else
1511	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1512	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1513	return
1514	fi
1515	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1516
1517	# Test if first argument is correct
1518	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1519	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1520	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1521	return
1522	fi
1523
1524	# Test if the file exist.
1525	# Exit with error if the file does not exist for the case blocker or force.
1526	# Only return for the case nonblocker.
1527	if [ ! -f ${filein} ] ; then
1528	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1529	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1530	else
1531	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1532	fi
1533	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1534	return
1535	fi
1536
1537	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1538	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1539	if [ ${type} = nonblocker ] ; then
1540	# This is a nonblocker case, print warning but do nothing else
1541	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1542	else
1543	# This is a blocker or force case : stop now
1544	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1545	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1546	return
1547	fi
1548	fi
1549
1550	# Check if AUTO is set on the same line as keyid and keyattrib
1551	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1552	# Modification will be done
1553	modify=yes
1554	else
1555	if [ ${type} = blocker ] ; then
1556	# Exit, the variable must be set to AUTO
1557	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1558	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1559	return
1560	elif [ ${type} = nonblocker ] ; then
1561	# Nothing will be done
1562	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1563	modify=no
1564	elif [ ${type} = force ] ; then
1565	# Force modification
1566	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1567	modify=yes
1568	fi
1569	fi
1570
1571	# Do the modifcation now
1572	if [ ${modify} = yes ] ; then
1573	if [ ${keyattrib} = NONE ] ; then
1574	# Case to modify the variable itself
1575	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1576	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1577	else
1578	# Check if keyattrib is set on the same line as keyid
1579	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1580	# Case to modify the attribute value
1581	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1582	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1583	else
1584	# Case to add the attribute and its value
1585	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1586	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1587	fi
1588	fi
1589	\mv ${filein}.tmp ${filein}
1590	fi
1591	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1592	}
1593
1594	#=======================================================================
1595	function IGCM_comp_Update
1596	{
1597	IGCM_debug_PushStack "IGCM_comp_Update"
1598
1599	# Debug Print :
1600	echo
1601	IGCM_debug_Print 1 "IGCM_comp_Update"
1602	echo
1603	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
1604	cd ENSEMBLE_TEMPLATE
1605	fi
1606
1607	typeset comp compname comptagname
1608	for comp in ${config_ListOfComponents[*]} ; do
1609	# Define component
1610	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1611	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1612
1613	# Debug Print
1614	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1615	# UPDATE component
1616	${comp}_Update
1617
1618	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1619	if [ -f timeseries_def_${compname}.xml ]; then
1620	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1621	for line in $( cat ts.temp.${compname}.txt ); do
1622	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1623	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1624	case ${output_freq} in
1625	Y\|y)
1626	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1627	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1628	;;
1629	MO\|mo)
1630	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1631	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1632	;;
1633	D\|d)
1634	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1635	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1636	;;
1637	S\|s)
1638	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1639	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1640	;;
1641	esac
1642	done
1643	fi
1644
1645	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1646	if [ -f dr2xml_${compname}.xml ]; then
1647	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
1648	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1649	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1650	# Modify path from dr2xml_{compname}.xml
1651	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
1652	${libIGCM}/libIGCM_post/xios_parser.py -v modifydr2xmlIPSL --newPath ${CMIP6_DIR} --splitLastDate ${EndYear_p1} --JobName ${config_UserChoices_JobName} --ModelName ${config_UserChoices_ModelName} --ModelVersion ${config_UserChoices_LongName} --file dr2xml_${compname}.xml
1653	else
1654	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1655	fi
1656	# Overwrite the original file
1657	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1658	fi
1659	fi
1660	done
1661	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
1662	cd ..
1663	fi
1664
1665
1666	IGCM_debug_PopStack "IGCM_comp_Update"
1667	}
1668
1669	#=======================================================================
1670	function IGCM_comp_Finalize
1671	{
1672	IGCM_debug_PushStack "IGCM_comp_Finalize"
1673
1674	# Debug Print :
1675	echo
1676	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1677	echo
1678
1679	typeset ListTextName TextName0
1680	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1681	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1682	typeset -Z4 j4 #BASH declare j4
1683	typeset list_file nlist_file
1684	typeset compactoutputs
1685
1686	# Initialize array hosting list of rebuilded files to copy
1687	unset rebuildedActionsList
1688
1689	# Text compacting options
1690	compactoutputs=false
1691	if [ X${JobType} != XRUN ] ; then
1692	compactoutputs=true
1693	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1694	compactoutputs=true
1695	fi
1696
1697	# Prepare headers for the shell dedicated to offline rebuild
1698	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1699	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1700	if [ ${DRYRUN} -le 1 ] ; then
1701	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1702	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1703	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1704	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1705	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1706	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1707	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1708	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1709	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1710	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1711	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1712	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1713	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1714	fi
1715	fi
1716
1717	for comp in ${config_ListOfComponents[*]} ; do
1718	# Define component
1719	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1720	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1721
1722	# Debug Print
1723	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1724	# FINALIZE component
1725	${comp}_Finalize
1726
1727	card=${SUBMIT_DIR}/COMP/${compname}.card
1728
1729	# Save Output Text files of models
1730	#---------------------------------
1731	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1732	IGCM_card_DefineArrayFromOption ${card} OutputText List
1733	ListTextName=${compname}_OutputText_List
1734
1735	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1736	if [ X${TextName0} != X${NULL_STR} ] ; then
1737	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1738
1739	(( i=0 ))
1740	until [ $i -eq $NbFiles ]; do
1741	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1742	eval file_out=${PREFIX}_${file_in}
1743
1744	(( i=i+1 ))
1745
1746	unset list_file
1747
1748	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
1749	for (( pool_member_rank=0 ; pool_member_rank < $config_Ensemble_PoolSize ; pool_member_rank++ ))
1750	do
1751	whole_ensemble_rank=$(($config_Ensemble_PoolSize*$1+$pool_member_rank))
1752	Path_OUT="\${R_BUF_${comp}_D}/MEMBER_$whole_ensemble_rank"
1753	cd MEMBER_$whole_ensemble_rank
1754
1755	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1756	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1757	set +A list_file -- $( [ -f ${file_in} ] && ls ${file_in} ; for i in $(ls ${file_in}* 2>/dev/null \| sed "s/${file_in}//" \| sort -n) ; do ls ${file_in}$i ; done )
1758	nlist_file=${#list_file[@]}
1759	if [ ${nlist_file} -gt 1 ] ; then
1760	if ( ${compactoutputs} ) ; then
1761	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1762	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1763	echo ${list_file[*]} > ${file_out}
1764	echo "" >> ${file_out}
1765
1766	(( i_ = 0 ))
1767	for file in ${list_file[@]} ; do
1768	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1769	echo "\| " ${i_} " " ${file} >> ${file_out}
1770	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1771	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1772	echo "" >> ${file_out}
1773	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1774	(( i_ = i_ + 1 ))
1775	done
1776	if ( ${ExecutionFail} ) ; then
1777	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1778	fi
1779
1780	if [ X${Pack} = Xtrue ] ; then
1781	eval IGCM_sys_PutBuffer_Out ${file_out} $Path_OUT/${file_out}
1782	else
1783	eval IGCM_sys_Put_Out ${file_out} $Path_OUT/${file_out}
1784	fi
1785
1786	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1787	else
1788	for file in ${list_file[@]} ; do
1789	if ( ${ExecutionFail} ) ; then
1790	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1791	fi
1792
1793	if [ X${Pack} = Xtrue ] ; then
1794	eval IGCM_sys_PutBuffer_Out ${file} $Path_OUT/${PREFIX}_${file}
1795	else
1796	eval IGCM_sys_Put_Out ${file} $Path_OUT/${PREFIX}_${file}
1797	fi
1798
1799	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1800	done
1801	fi
1802	else
1803	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1804	eval IGCM_sys_Mv ${file_in}* ${file_in}
1805	fi
1806
1807	if ( ${ExecutionFail} ) ; then
1808	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1809	fi
1810
1811	if [ X${Pack} = Xtrue ] ; then
1812	eval IGCM_sys_PutBuffer_Out ${file_in} $Path_OUT/${file_out}
1813	else
1814	eval IGCM_sys_Put_Out ${file_in} $Path_OUT/${file_out}
1815	fi
1816	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1817	fi
1818	cd ..
1819	done
1820	fi
1821	done
1822	fi
1823
1824	# Save Restarts files
1825	#--------------------
1826	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1827	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1828	ListFilesName=${compname}_RestartFiles_List
1829	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1830
1831	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1832	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1833
1834	(( i=0 ))
1835	until [ $i -ge $NbFiles ]; do
1836	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1837	eval file_in=${file_in_}
1838
1839	(( i_ = i+1 ))
1840	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1841	eval file_out=${file_out_}
1842
1843	(( i_ = i+2 ))
1844	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1845	eval file_outin=${file_outin_}
1846
1847	generic_restart_file_name_in=$( basename ${file_in} .nc )
1848	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1849	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1850
1851	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
1852
1853	generic_restart_file_name_in_tmp=${generic_restart_file_name_in}
1854	for (( pool_member_rank=0 ; pool_member_rank < $config_Ensemble_PoolSize ; pool_member_rank++ ))
1855	do
1856	whole_ensemble_rank=$(($config_Ensemble_PoolSize*$1+$pool_member_rank))
1857	Path_OUT="\${R_BUF_${comp}_R}/MEMBER_$whole_ensemble_rank"
1858	cd MEMBER_$whole_ensemble_rank
1859	if [ X${comp} = XCPL ] ; then
1860	generic_restart_file_name_in="${generic_restart_file_name_in_tmp}__$pool_member_rank"
1861	file_in="${generic_restart_file_name_in}.nc"
1862
1863	if [ X${file_in} = Xsstoc__${pool_member_rank}.nc ] ; then
1864
1865	for varname in O_SSTSST OIceFrc O_AlbIce O_TepIce O_OCurx1 O_OCury1 O_OCurz1
1866	do
1867	ncrename -O -v .${varname}__${pool_member_rank},${varname} ${file_in}
1868	done
1869
1870	else
1871
1872	for varname in COTAUXXU COTAUYYU COTAUZZU COTAUXXV COTAUYYV COTAUZZV COTOTRAI COTOTSNO COTOTEVA COICEVAP COQSRMIX COQNSMIX COSHFICE CONSFICE CODFLXDT COCALVIN COLIQRUN COWINDSP COTAUMOD
1873	do
1874	ncrename -O -v .${varname}__${pool_member_rank},${varname} ${file_in}
1875	done
1876	fi
1877	fi
1878	echo $generic_restart_file_name_in
1879	echo $file_in
1880
1881	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1882	if [ ${nb_restart_file} -gt 1 ] ; then
1883	IGCM_sys_rebuild_nemo ${generic_restart_file_name_in} ${nb_restart_file}
1884	IGCM_sys_Rm ${generic_restart_file_name_in}_????.nc
1885	if [ X${Pack} = Xtrue ] ; then
1886	eval IGCM_sys_PutBuffer_Rest ${file_in} $Path_OUT/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1887	else
1888	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1889	fi
1890	if [ ! ${file_in} = ${file_outin} ] ; then
1891	if ( ${ExitFlag} ) ; then
1892	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1893	else
1894	IGCM_sys_Mv ${file_in} ${file_outin}
1895	fi
1896	fi
1897	else
1898	if [ X${Pack} = Xtrue ] ; then
1899	eval IGCM_sys_PutBuffer_Rest ${file_in} $Path_OUT/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1900	else
1901	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1902	fi
1903	if [ ! ${file_in} = ${file_outin} ] ; then
1904	if ( ${ExitFlag} ) ; then
1905	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1906	else
1907	IGCM_sys_Mv ${file_in} ${file_outin}
1908	fi
1909	fi
1910	fi
1911	cd ..
1912	done
1913	fi
1914	(( i=i+3 ))
1915	done
1916	else
1917	if [ X${FileName0} != XNONE ] ; then
1918	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1919	else
1920	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1921	fi
1922	fi
1923
1924	# Save Output files
1925	#------------------
1926	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1927	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1928	ListFilesName=${compname}_OutputFiles_List
1929	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1930
1931	if [ X${FileName0} != X${NULL_STR} ] ; then
1932	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1933
1934	(( i=0 ))
1935	until [ $i -ge $NbFiles ]; do
1936	SaveOnArchive=true
1937	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1938	eval file_in=${file_in_}
1939	(( i_ = i+1 ))
1940	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1941	eval file_out=${file_out_}
1942	#
1943	# Override file_out path remplacing R_SAVE by R_BUFR
1944	#
1945	if [ X${Pack} = Xtrue ] ; then
1946	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1947	fi
1948	#
1949	# Not necessarily the best option. /!\ Potential side effects /!\
1950	#
1951	(( i_ = i+2 ))
1952	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1953	#
1954
1955	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
1956	cd XIOS
1957	fi
1958
1959	generic_file_name=$( basename ${file_in} .nc )
1960	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1961	#
1962	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1963	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1964	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1965	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1966	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1967	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1968	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1969	#
1970	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
1971	if [ ${file_in} = output.abort.nc ] ; then
1972	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
1973	else
1974	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
1975	fi
1976	else
1977	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1978	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1979
1980	# Prepare the shell dedicated to offline rebuild
1981	if [ $DRYRUN -le 1 ]; then
1982	if [ ${file_in} = histstn.nc ] ; then
1983	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1984	else
1985	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1986	fi
1987	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1988	fi
1989	#
1990	# Load Patch we need to apply and apply
1991	if [ $DRYRUN -le 1 ]; then
1992	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1993	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1994	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1995	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1996	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1997	done
1998	fi
1999	fi
2000	#
2001	if [ $DRYRUN -le 1 ]; then
2002	if [ X${Pack} = Xtrue ] ; then
2003	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
2004	else
2005	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
2006	fi
2007	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
2008	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
2009	fi
2010	SaveOnArchive=false
2011	fi
2012	fi
2013	#
2014	if [ ${SaveOnArchive} = true ] ; then
2015	#
2016	# Rebuild has been done online or it was not needed
2017	#
2018	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
2019	#
2020	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
2021	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
2022	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
2023	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
2024	#
2025	if [ $DRYRUN -le 1 ]; then
2026	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2027	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2028	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2029	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2030	done
2031	#
2032	if [ X${Pack} = Xtrue ] ; then
2033	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2034	else
2035	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2036	fi
2037	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2038	#
2039	fi
2040	else
2041	#
2042	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
2043	#
2044	if [ X${Pack} = Xtrue ] ; then
2045	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
2046	else
2047	IGCM_sys_Put_Out ${file_in} ${file_out}
2048	fi
2049	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
2050	if [ ${nb_rebuild_file} -gt 1 ] ; then
2051	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
2052	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
2053	done
2054	fi
2055	fi
2056	fi
2057	(( i=i+3 ))
2058	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
2059	cd ..
2060	fi
2061	done
2062	fi
2063	echo
2064	done
2065	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
2066	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
2067	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2068	i=0
2069	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
2070	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2071	(( i=i+1 ))
2072	done
2073	fi
2074	IGCM_debug_PopStack "IGCM_comp_Finalize"
2075	}

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