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libIGCM_comp.ksh @ 6206

Last change on this file since 6206 was 6206, checked in by aclsce, 2 years ago
Fixed some problems.
File size: 88.2 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	for comp in ${config_ListOfComponents[*]} ; do
721	# Define component
722	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
723	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
724	#
725	card=${SUBMIT_DIR}/COMP/${compname}.card
726	#
727	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
728	ListFilesName=${compname}_RestartFiles_List
729	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
730
731	# Debug Print :
732	IGCM_debug_Print 3 "restart ${compname}"
733
734	if ( ${FirstInitialize} ) ; then
735
736	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
737	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
738	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
739	CompOldName=IOS
740	config_IOS_Restart="n"
741	do_start="n"
742	config_IOS_RestartDate=-1
743	config_IOS_RestartJobName=${NULL_STR}
744	config_IOS_RestartPath=${NULL_STR}
745	else
746	eval config_${comp}_Restart="y"
747	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
748	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
749	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
750	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
751	eval CompOldName=${comp}
752	fi
753	else
754	# Read component Restarts parameters
755	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
756	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
757
758	if [ "${do_start}" = "y" ] ; then
759	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
760	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
761	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
762	else
763	eval config_${comp}_RestartDate=-1
764	eval config_${comp}_RestartJobName=${NULL_STR}
765	eval config_${comp}_RestartPath=${NULL_STR}
766	fi
767
768	eval CompOldName=\${config_${comp}_OldName}
769	if [ X${CompOldName} = X ] ; then
770	eval CompOldName=${comp}
771	fi
772
773	# Reinitialize IsMatching to allow searching for a different tar file for each component.
774	IsMatching=""
775	TarFileFound=""
776	fi
777
778	if [ "${do_start}" = "y" ] ; then
779
780	# Restore Restarts files
781	#-----------------------
782	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
783	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
784
785	(( i=1 ))
786	until [ $i -gt $NbFiles ]; do
787	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
788	eval file_in=${file_in_}
789	(( i_ = i+1 ))
790	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
791	eval file_out=${file_out_}
792
793	eval Date_tmp=\${config_${comp}_RestartDate}
794	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
795	# will be re-use
796	eval RestartPath=\${config_${comp}_RestartPath}
797	eval RestartJobName=\${config_${comp}_RestartJobName}
798	#
799	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
800	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
801
802	extension_in=$( echo ${file_in_Name##*.} )
803	extension_out=$( echo ${file_out##*.} )
804
805	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
806	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
807	Path_OUT=${Path_r}/${generic_restart_file_name_in}
808
809	path_restart_tmp=`dirname $Path_OUT`
810	base_restart_tmp=`basename $Path_OUT`
811
812	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
813	for (( pool_member_rank=0 ; pool_member_rank < $config_Ensemble_PoolSize ; pool_member_rank++ ))
814	do
815	whole_ensemble_rank=$(($config_Ensemble_PoolSize*$1+$pool_member_rank))
816	Path_OUT="$path_restart_tmp/MEMBER_$whole_ensemble_rank/$base_restart_tmp"
817	Path_r="$path_restart_tmp/MEMBER_$whole_ensemble_rank"
818	cd MEMBER_$whole_ensemble_rank
819
820	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
821	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
822	Buffered=true
823	Archived=false
824	Tared=false
825	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
826	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
827	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
828	Buffered=false
829	Archived=true
830	Tared=false
831	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
832	else
833	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
834	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
835	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
836	Buffered=false
837	Archived=false
838	Tared=true
839	# Look after the tar file we want if we did not found it already
840	if [ X${IsMatching} = X ] ; then
841	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
842	if [ $? ] ; then
843	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
844	IsMatching=$( echo ${PotentialTarFile##*/} \| \
845	sed "s:_restart::" \| \
846	sed "s:^${RestartJobName}_::" \| \
847	sed "s:\.tar$::" \| \
848	gawk -F_ -v restartdate=${Date_r} \
849	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
850	if [ ! X${IsMatching} = X ] ; then
851	TarFileFound=${PotentialTarFile}
852	break
853	fi
854	done
855	fi
856	# Stop here if nothing has been found
857	if [ X${TarFileFound} = X ] ; then
858	IGCM_debug_Print 3 "Restart files were not found!"
859	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
860	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
861	IGCM_debug_Exit "Please double check restart settings in config.card"
862	IGCM_debug_Verif_Exit
863	fi
864	fi
865	IGCM_sys_PrepareTaredRestart ${TarFileFound}
866	TarFileLocation=$( basename ${TarFileFound} )
867	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
868	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
869	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
870	fi
871
872	if [ ${nb_restart_file} -gt 1 ] ; then
873	j=0 # BASH LINE NOT NEEDED
874	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
875	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
876	j4=${j} # BASH LINE NOT NEEDED
877	if [ X${Buffered} = Xtrue ] ; then
878	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
879	elif [ X${Archived} = Xtrue ] ; then
880	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
881	elif [ X${Tared} = Xtrue ] ; then
882	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
883	fi
884	(( j=j+1 )) #BASH LINE NOT NEEDED
885	done
886
887	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
888	if [ X${OCE_PROC_MPI} != X ] ; then
889	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
890	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
891	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
892	fi
893	fi
894	else
895	if [ X${Buffered} = Xtrue ] ; then
896	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
897	elif [ X${Archived} = Xtrue ] ; then
898	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
899	elif [ X${Tared} = Xtrue ] ; then
900	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
901	fi
902	fi
903	cd ..
904	done
905	fi
906	(( i=i+3 ))
907	done
908	else
909	if [ X${FileName0} != XNONE ] ; then
910	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
911	else
912	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
913	fi
914	fi
915	fi
916	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
917	# if not FirstInitialize and first loop of this job
918
919	# Restore Restarts files
920	#-----------------------
921	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
922	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
923
924	index_j=0
925	for index_member in $(cut -d: -f2 ${SUBMIT_DIR}/ensemble.txt); do
926	member[$index_j]=$index_member
927	index_j=$index_j+1
928	done
929
930	(( i=1 ))
931	until [ $i -gt $NbFiles ]; do
932	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
933	eval file_in=${file_in_}
934	(( i_ = i+1 ))
935	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
936	eval file_out=${file_out_}
937
938	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
939
940	extension_in=$( echo ${file_in_Name##*.} )
941	extension_out=$( echo ${file_out##*.} )
942
943	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
944	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
945
946	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
947	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
948
949	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
950	path_restart_tmp=`dirname $Path_BUF`
951	base_restart_tmp=`basename $Path_BUF`
952
953	for (( pool_member_rank=0 ; pool_member_rank < $config_Ensemble_PoolSize ; pool_member_rank++ ))
954	do
955	whole_ensemble_rank=$(($config_Ensemble_PoolSize*$1+$pool_member_rank))
956	Path_BUF=$path_restart_tmp/MEMBER_${member[$whole_ensemble_rank]}/$base_restart_tmp
957	Path_r=$path_restart_tmp/MEMBER_${member[$whole_ensemble_rank]}
958	cd MEMBER_$whole_ensemble_rank
959
960
961	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
962	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
963	Buffered=true
964	Archived=false
965	Tared=false
966	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
967	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
968	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
969	Buffered=false
970	Archived=true
971	Tared=false
972	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
973	else
974	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
975	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
976	Buffered=false
977	Archived=false
978	Tared=true
979	# Look after the tar file we want if we did not found it already
980	if [ X${IsMatching} = X ] ; then
981	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
982	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
983	if [ ! X${IsMatching} = X ] ; then
984	TarFileFound=${PotentialTarFile}
985	break
986	fi
987	done
988	fi
989	# Stop here if nothing has been found
990	if [ X${TarFileFound} = X ] ; then
991	IGCM_debug_Print 3 "Restart files were not found!"
992	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
993	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
994	IGCM_debug_Exit "Please double check restart settings in config.card"
995	IGCM_debug_Verif_Exit
996	fi
997	IGCM_sys_PrepareTaredRestart ${TarFileFound}
998	TarFileLocation=$( basename ${TarFileFound} )
999	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
1000	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
1001	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
1002	fi
1003
1004	if [ ${nb_restart_file} -gt 1 ] ; then
1005	j=0 # BASH LINE NOT NEEDED
1006	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1007	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1008	j4=${j} # BASH LINE NOT NEEDED
1009	if [ X${Buffered} = Xtrue ] ; then
1010	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1011	elif [ X${Archived} = Xtrue ] ; then
1012	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1013	elif [ X${Tared} = Xtrue ] ; then
1014	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1015	fi
1016	(( j=j+1 )) # BASH LINE NOT NEEDED
1017	done
1018	else
1019	if [ X${Buffered} = Xtrue ] ; then
1020	eval IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
1021	elif [ X${Archived} = Xtrue ] ; then
1022	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
1023	elif [ X${Tared} = Xtrue ] ; then
1024	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
1025	fi
1026	fi
1027	cd ..
1028	done
1029	fi
1030	(( i=i+3 ))
1031	done
1032	else
1033	if [ X${FileName0} != XNONE ] ; then
1034	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
1035	else
1036	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
1037	fi
1038	fi
1039	fi
1040	done
1041
1042	NbFiles=$( ls * 2> /dev/null \| wc -l )
1043	if [ ${NbFiles} -gt 0 ] ; then
1044	IGCM_sys_Chmod u+rw *
1045	fi
1046	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
1047	}
1048
1049	#=======================================================================
1050	function IGCM_comp_GetInputBinaryFiles
1051	{
1052	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
1053
1054	# Debug Print :
1055	echo
1056	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
1057	echo
1058
1059	# Clean up previous pass
1060	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
1061
1062	typeset comp ExeNameIn ExeNameOut byPass
1063	typeset compilerNmbr compilerUnit compilerFull
1064	byPass=false
1065	for comp in ${config_ListOfComponents[*]} ; do
1066	# Define component
1067
1068	# Copy executable for this component
1069	eval ExeNameIn=\${config_Executable_${comp}[0]}
1070	eval ExeNameOut=\${config_Executable_${comp}[1]}
1071	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
1072	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
1073	# The executable is set in config.card and is different from ""
1074	# Use eval to expand ExeNameIn if variables are used in the name
1075	eval ExeNameIn=${ExeNameIn}
1076	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1077	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1078	fi
1079	fi
1080
1081	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1082	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1083	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1084	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1085	fi
1086	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1087	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1088	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1089	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1090	fi
1091	fi
1092
1093	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1094	# Get the compiler version
1095	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1096	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1097	# Save it
1098	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1099	[ X${compilerFull} = X ] && byPass=true
1100	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1101	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1102	fi
1103	done
1104
1105	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1106	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1107
1108	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1109	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1110	fi
1111
1112	# Test on compiler version for IPSLCM6* configuration on irene (only for CMIP6 production)
1113	if [ ${SYSTEM} = irene ]; then
1114	if ( [ X"$( 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
1115	IGCM_debug_Exit "IPSLCM6.0.13, IPSLCM6.0.14, IPSLCM6.0.15, IPSLCM6.1 and IPSLCM5A2.1 must be compiled with intel 2017 compiler"
1116	fi
1117	fi
1118
1119	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1120	}
1121
1122	#=======================================================================
1123	function IGCM_comp_PeriodStart
1124	{
1125	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1126
1127	# Debug Print :
1128	echo
1129	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1130	echo
1131
1132	typeset ExeNameIn ExeNameOut
1133	typeset comp compname comptagname
1134	for comp in ${config_ListOfComponents[*]} ; do
1135	# Define component
1136	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1137	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1138
1139	# Copy executable for this component
1140	eval ExeNameIn=\${config_Executable_${comp}[0]}
1141	eval ExeNameIn=${ExeNameIn}
1142	eval ExeNameOut=\${config_Executable_${comp}[1]}
1143
1144	# Debug Print
1145	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1146	# UPDATE component
1147	${comp}_PeriodStart 2> /dev/null
1148
1149	done
1150
1151	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1152	}
1153
1154
1155
1156	#=======================================================================
1157	function IGCM_comp_modifyFile
1158	{
1159	#
1160	# syntax: IGCM_comp_modifyFile filein key [value]
1161	#
1162	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1163	#
1164	# This function is used to replace a pattern in a file for a specific variable.
1165	#
1166	# Arguments:
1167	# - filein : the file in run directory in which the variable should be set
1168	# - key : the variable to modify
1169	# - value : the value to set the key equal to
1170	#
1171	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1172
1173	typeset filein key value pattern
1174
1175	# Set local variables and test the arguments
1176	if [ $# = 3 ] ; then
1177	# Normal case with 3 arguments
1178	filein=$1 ; key=$2 ; value=$3
1179	else
1180	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1181	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1182	return
1183	fi
1184	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1185
1186	# Test if the file exist
1187	if [ ! -f ${filein} ] ; then
1188	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1189	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1190	return
1191	fi
1192
1193	# Read the line with key in the file without the comments
1194	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1195
1196	# Verify the existance of the pattern
1197	if [ X"${pattern}" = X ] ; then
1198	# Variable key is not set in filein, stop.
1199	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1200	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1201	return
1202	fi
1203
1204	# Now change key in filein
1205	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1206	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1207	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1208	\mv ${filein}.tmp ${filein}
1209
1210	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1211	}
1212
1213	#=======================================================================
1214	function IGCM_comp_modifyDefFile
1215	{
1216	#
1217	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1218	#
1219	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1220	#
1221	# This function is used to modify a parameter file for a specific variable.
1222	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1223	# This function can be used in the comp.driver files for the components.
1224	#
1225	# Arguments:
1226	# - type : first argument must be blocker, nonblocker or force
1227	# For "blocker" case, the variable must be attributed the keyworld AUTO
1228	# otherwise this function will exit.
1229	# For "nonblocker" case, the user can remove or modify the variable. For
1230	# this case, as long as AUTO is not set, no modification will be done.
1231	# For "force" case, the variable will be modified even if it is not set to AUTO
1232	# - filein : the file in run directory of .def type in which the variable should be set
1233	# - key : the variable to modify
1234	# - value : the value to set the key equal to, optional. If value is not set or if
1235	# value=DEFAULT, then a default value must be given in filein using syntax :
1236	# key= AUTO : DEFAULT=def_value
1237	#
1238	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1239
1240	typeset type filein key value
1241	typeset filelist nb_occ modify
1242
1243	# Set local variables and test the arguments
1244	if [ $# = 4 ] ; then
1245	# Normal case with 4 arguments
1246	type=$1 ; filein=$2 ; key=$3 ; value=$4
1247	elif [ $# = 3 ] ; then
1248	# Normal case with 3 arguments
1249	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1250	else
1251	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1252	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1253	return
1254	fi
1255	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1256
1257	# Test if first argument is correct
1258	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1259	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1260	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1261	return
1262	fi
1263
1264	# Test if the file exist.
1265	# Exit with error if the file does not exist for the case blocker or force.
1266	# Only return for the case nonblocker.
1267	if [ ! -f ${filein} ] ; then
1268	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1269	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1270	else
1271	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1272	fi
1273	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1274	return
1275	fi
1276
1277	# Define list of files to test using all files with suffix .def (except used*.def)
1278	filelist=$( ls *def \| grep -v used )
1279
1280	# Count number of occurances for the key in all files
1281	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1282
1283	# Test if key is set several times
1284	if [ ${nb_occ} -gt 1 ] ; then
1285	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1286	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1287	return
1288	fi
1289
1290	# Treatement according to different cases
1291	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1292	# Stop if the key is never set and the function is blocker
1293	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1294	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1295	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1296	# The key is not set but it is a nonblocker call so nothing is done.
1297	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1298	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1299	modify=no
1300	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1301	# Variable key is not set in filein, stop.
1302	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1303	fi
1304
1305	# Check if AUTO is set in the filein on the same line as the key variable
1306	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1307	# Modification will be done for all cases
1308	modify=yes
1309	else
1310	# The variable was not set to AUTO
1311	if [ ${type} = blocker ] ; then
1312	# Exit because this is a blocker call
1313	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1314	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1315	return
1316	elif [ ${type} = nonblocker ] ; then
1317	# Do nothing. Suppose that the user did set the variable correct
1318	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1319	modify=no
1320	elif [ ${type} = force ] ; then
1321	# Force modification
1322	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1323	modify=yes
1324	fi
1325	fi
1326
1327	# Do the modifcation now
1328	if [ ${modify} = yes ] ; then
1329
1330	# For option DEFAULT, read default value from file.
1331	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1332	# Case to set DEFAULT value
1333	# Read default value from filein
1334	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1335
1336	if [ X"${value}" = X ] ; then
1337	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1338	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1339	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1340	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1341	return
1342	fi
1343	fi
1344
1345	# Now change key in filein
1346	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1347	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1348	\mv ${filein}.tmp ${filein}
1349	fi
1350	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1351	}
1352
1353	#=======================================================================
1354	function IGCM_comp_modifyNamelist
1355	{
1356	#
1357	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1358	#
1359	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1360	#
1361	# This function is used to modify a parameter file for a specific variable.
1362	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1363	# This function can be used in the comp.driver files for the components.
1364	#
1365	# Arguments:
1366	# - type : first argument must be blocker, nonblocker or force
1367	# For "blocker" case, the variable must be attributed the keyworld AUTO
1368	# otherwise this function will exit.
1369	# For "nonblocker" case, the user can remove or modify the variable. For
1370	# this case, as long as AUTO is not set, no modification will be done.
1371	# For "force" case, the variable will be modified even if it is not set to AUTO
1372	# - filein : the file in run directory of .def type in which the variable should be set
1373	# - key : the variable to modify
1374	# - value : the value to set the key equal to, optional. If value is not set or if
1375	# value=DEFAULT, then a default value must be given in filein using syntax :
1376	# key= AUTO : DEFAULT=def_value
1377	#
1378	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1379
1380	typeset type filein key value pattern modify
1381
1382	# Set local variables and test the arguments
1383	if [ $# = 4 ] ; then
1384	# Normal case with 4 arguments
1385	type=$1 ; filein=$2 ; key=$3 ; value=$4
1386	elif [ $# = 3 ] ; then
1387	# Normal case with 3 arguments
1388	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1389	else
1390	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1391	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1392	return
1393	fi
1394	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1395
1396	# Test if first argument is correct
1397	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1398	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1399	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1400	return
1401	fi
1402
1403	# Test if the file exist.
1404	# Exit with error if the file does not exist for the case blocker or force.
1405	# Only return for the case nonblocker.
1406	if [ ! -f ${filein} ] ; then
1407	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1408	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1409	else
1410	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1411	fi
1412	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1413	return
1414	fi
1415
1416	# Read the line with key in the file without the comments
1417	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1418
1419	# Verify the existance of the pattern
1420	if [ X"$pattern" = X ] ; then
1421	# Variable key is not set in filein, stop.
1422	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1423	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1424	return
1425	fi
1426
1427	# Check if the variable is set to AUTO in the filein
1428	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1429	# Modification will be done for all cases
1430	modify=yes
1431	else
1432	# The variable was not set to AUTO
1433	if [ ${type} = blocker ] ; then
1434	# Exit because this is a blocker call
1435	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1436	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1437	return
1438	elif [ ${type} = nonblocker ] ; then
1439	# Do nothing. Suppose that the user did set the variable correct
1440	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1441	modify=no
1442	elif [ ${type} = force ] ; then
1443	# Force modification
1444	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1445	modify=yes
1446	fi
1447	fi
1448
1449	# Do the modifcation now
1450	if [ ${modify} = yes ] ; then
1451
1452	# For option DEFAULT, read default value from file.
1453	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1454	# Case to set DEFAULT value
1455	# Read default value from filein
1456	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1457
1458	if [ X"${value}" = X ] ; then
1459	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1460	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1461	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1462	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1463	return
1464	fi
1465	fi
1466
1467	# Now change key in filein
1468	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1469	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1470	\mv ${filein}.tmp ${filein}
1471	fi
1472	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1473	}
1474
1475	#=======================================================================
1476	function IGCM_comp_modifyXmlFile
1477	{
1478	#
1479	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1480	#
1481	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1482	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1483	#
1484	# This function is used to modify the value for a specific attribute and variable id.
1485	# The file must be a valid xml file.
1486	# This function can be used in the comp.driver files for the components.
1487	#
1488	# Arguments:
1489	# - type : first argument must be blocker, nonblocker or force.
1490	# For "blocker" case, the variable must be attributed the keyworld AUTO
1491	# otherwise this function will exit.
1492	# For "nonblocker" case, the user can remove or modify the variable. For
1493	# this case, as long as AUTO is not set, no modification will be done.
1494	# For "force" case, the variable will be modified even if it is not set to AUTO
1495	# - filein : the file in run directory of .xml type in which the variable should be set
1496	# - keyid : the variable to modify
1497	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1498	# - value : the value to set in the filein
1499	#
1500	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1501
1502	typeset type filein keyid keyattrib value modify
1503
1504	# Set local variables and test the arguments
1505	if [ $# = 5 ] ; then
1506	# Normal case with 4 arguments
1507	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1508	else
1509	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1510	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1511	return
1512	fi
1513	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1514
1515	# Test if first argument is correct
1516	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1517	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1518	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1519	return
1520	fi
1521
1522	# Test if the file exist.
1523	# Exit with error if the file does not exist for the case blocker or force.
1524	# Only return for the case nonblocker.
1525	if [ ! -f ${filein} ] ; then
1526	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1527	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1528	else
1529	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1530	fi
1531	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1532	return
1533	fi
1534
1535	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1536	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1537	if [ ${type} = nonblocker ] ; then
1538	# This is a nonblocker case, print warning but do nothing else
1539	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1540	else
1541	# This is a blocker or force case : stop now
1542	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1543	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1544	return
1545	fi
1546	fi
1547
1548	# Check if AUTO is set on the same line as keyid and keyattrib
1549	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1550	# Modification will be done
1551	modify=yes
1552	else
1553	if [ ${type} = blocker ] ; then
1554	# Exit, the variable must be set to AUTO
1555	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1556	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1557	return
1558	elif [ ${type} = nonblocker ] ; then
1559	# Nothing will be done
1560	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1561	modify=no
1562	elif [ ${type} = force ] ; then
1563	# Force modification
1564	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1565	modify=yes
1566	fi
1567	fi
1568
1569	# Do the modifcation now
1570	if [ ${modify} = yes ] ; then
1571	if [ ${keyattrib} = NONE ] ; then
1572	# Case to modify the variable itself
1573	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1574	sed -e "s/$<[^\"]\"${keyid}\".>$$[^<]$$<[^>]$/\1${value}\3/" ${filein} > ${filein}.tmp
1575	else
1576	# Check if keyattrib is set on the same line as keyid
1577	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1578	# Case to modify the attribute value
1579	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1580	sed -e "/id=\"${keyid}\"/s/$${keyattrib}=\"$[^\"]*$\"$/\1${value}\2/" ${filein} > ${filein}.tmp
1581	else
1582	# Case to add the attribute and its value
1583	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1584	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1585	fi
1586	fi
1587	\mv ${filein}.tmp ${filein}
1588	fi
1589	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1590	}
1591
1592	#=======================================================================
1593	function IGCM_comp_Update
1594	{
1595	IGCM_debug_PushStack "IGCM_comp_Update"
1596
1597	# Debug Print :
1598	echo
1599	IGCM_debug_Print 1 "IGCM_comp_Update"
1600	echo
1601	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
1602	cd ENSEMBLE_TEMPLATE
1603	fi
1604
1605	typeset comp compname comptagname
1606	for comp in ${config_ListOfComponents[*]} ; do
1607	# Define component
1608	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1609	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1610
1611	# Debug Print
1612	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1613	# UPDATE component
1614	${comp}_Update
1615
1616	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1617	if [ -f timeseries_def_${compname}.xml ]; then
1618	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1619	for line in $( cat ts.temp.${compname}.txt ); do
1620	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1621	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1622	case ${output_freq} in
1623	Y\|y)
1624	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1625	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1626	;;
1627	MO\|mo)
1628	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1629	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1630	;;
1631	D\|d)
1632	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1633	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1634	;;
1635	S\|s)
1636	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1637	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1638	;;
1639	esac
1640	done
1641	fi
1642
1643	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1644	if [ -f dr2xml_${compname}.xml ]; then
1645	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
1646	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1647	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1648	# Modify path from dr2xml_{compname}.xml
1649	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
1650	${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
1651	else
1652	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1653	fi
1654	# Overwrite the original file
1655	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1656	fi
1657	fi
1658	done
1659	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
1660	cd ..
1661	fi
1662
1663
1664	IGCM_debug_PopStack "IGCM_comp_Update"
1665	}
1666
1667	#=======================================================================
1668	function IGCM_comp_Finalize
1669	{
1670	IGCM_debug_PushStack "IGCM_comp_Finalize"
1671
1672	# Debug Print :
1673	echo
1674	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1675	echo
1676
1677	typeset ListTextName TextName0
1678	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1679	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1680	typeset -Z4 j4 #BASH declare j4
1681	typeset list_file nlist_file
1682	typeset compactoutputs
1683
1684	# Initialize array hosting list of rebuilded files to copy
1685	unset rebuildedActionsList
1686
1687	# Text compacting options
1688	compactoutputs=false
1689	if [ X${JobType} != XRUN ] ; then
1690	compactoutputs=true
1691	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1692	compactoutputs=true
1693	fi
1694
1695	# Prepare headers for the shell dedicated to offline rebuild
1696	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1697	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1698	if [ ${DRYRUN} -le 1 ] ; then
1699	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1700	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1701	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1702	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1703	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1704	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1705	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1706	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1707	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1708	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1709	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1710	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1711	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1712	fi
1713	fi
1714
1715	for comp in ${config_ListOfComponents[*]} ; do
1716	# Define component
1717	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1718	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1719
1720	# Debug Print
1721	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1722	# FINALIZE component
1723	${comp}_Finalize
1724
1725	card=${SUBMIT_DIR}/COMP/${compname}.card
1726
1727	# Save Output Text files of models
1728	#---------------------------------
1729	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1730	IGCM_card_DefineArrayFromOption ${card} OutputText List
1731	ListTextName=${compname}_OutputText_List
1732
1733	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1734	if [ X${TextName0} != X${NULL_STR} ] ; then
1735	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1736
1737	(( i=0 ))
1738	until [ $i -eq $NbFiles ]; do
1739	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1740	eval file_out=${PREFIX}_${file_in}
1741
1742	(( i=i+1 ))
1743
1744	unset list_file
1745
1746	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
1747	for (( pool_member_rank=0 ; pool_member_rank < $config_Ensemble_PoolSize ; pool_member_rank++ ))
1748	do
1749	whole_ensemble_rank=$(($config_Ensemble_PoolSize*$1+$pool_member_rank))
1750	Path_OUT="\${R_BUF_${comp}_D}/MEMBER_$whole_ensemble_rank"
1751	cd MEMBER_$whole_ensemble_rank
1752
1753	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1754	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1755	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 )
1756	nlist_file=${#list_file[@]}
1757	if [ ${nlist_file} -gt 1 ] ; then
1758	if ( ${compactoutputs} ) ; then
1759	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1760	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1761	echo ${list_file[*]} > ${file_out}
1762	echo "" >> ${file_out}
1763
1764	(( i_ = 0 ))
1765	for file in ${list_file[@]} ; do
1766	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1767	echo "\| " ${i_} " " ${file} >> ${file_out}
1768	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1769	cat ${file} \| sed "s/$.*$/${i_}\1/" >> ${file_out}
1770	echo "" >> ${file_out}
1771	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1772	(( i_ = i_ + 1 ))
1773	done
1774	if ( ${ExecutionFail} ) ; then
1775	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1776	fi
1777
1778	if [ X${Pack} = Xtrue ] ; then
1779	eval IGCM_sys_PutBuffer_Out ${file_out} $Path_OUT/${file_out}
1780	else
1781	eval IGCM_sys_Put_Out ${file_out} $Path_OUT/${file_out}
1782	fi
1783
1784	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1785	else
1786	for file in ${list_file[@]} ; do
1787	if ( ${ExecutionFail} ) ; then
1788	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1789	fi
1790
1791	if [ X${Pack} = Xtrue ] ; then
1792	eval IGCM_sys_PutBuffer_Out ${file} $Path_OUT/${PREFIX}_${file}
1793	else
1794	eval IGCM_sys_Put_Out ${file} $Path_OUT/${PREFIX}_${file}
1795	fi
1796
1797	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1798	done
1799	fi
1800	else
1801	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1802	eval IGCM_sys_Mv ${file_in}* ${file_in}
1803	fi
1804
1805	if ( ${ExecutionFail} ) ; then
1806	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1807	fi
1808
1809	if [ X${Pack} = Xtrue ] ; then
1810	eval IGCM_sys_PutBuffer_Out ${file_in} $Path_OUT/${file_out}
1811	else
1812	eval IGCM_sys_Put_Out ${file_in} $Path_OUT/${file_out}
1813	fi
1814	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1815	fi
1816	cd ..
1817	done
1818	fi
1819	done
1820	fi
1821
1822	# Save Restarts files
1823	#--------------------
1824	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1825	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1826
1827	# for i in $(cut -d: -f3 ${SUBMIT_DIR}/ensemble.txt); do
1828	# noise_teta[$j]=$i
1829	# j=$j+1
1830	# done
1831
1832	# j=0
1833	# for CouplingField in O_SSTSST OIceFrc O_AlbIce O_TepIce O_OCurx1 O_OCury1 O_OCurz1
1834	# ListCouplingFieldSstoc[$CouplingField]
1835	# for j in $(seq '1 $
1836	# NumberCOCALVINicshf[$j]
1837
1838	ListFilesName=${compname}_RestartFiles_List
1839	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1840
1841	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1842	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1843
1844	(( i=0 ))
1845	until [ $i -ge $NbFiles ]; do
1846	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1847	eval file_in=${file_in_}
1848
1849	(( i_ = i+1 ))
1850	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1851	eval file_out=${file_out_}
1852
1853	(( i_ = i+2 ))
1854	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1855	eval file_outin=${file_outin_}
1856
1857	generic_restart_file_name_in=$( basename ${file_in} .nc )
1858	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1859	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1860	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
1861
1862	generic_restart_file_name_in_tmp=${generic_restart_file_name_in}
1863	for (( pool_member_rank=0 ; pool_member_rank < $config_Ensemble_PoolSize ; pool_member_rank++ ))
1864	do
1865	whole_ensemble_rank=$(($config_Ensemble_PoolSize*$1+$pool_member_rank))
1866	Path_OUT="\${R_BUF_${comp}_R}/MEMBER_$whole_ensemble_rank"
1867	cd MEMBER_$whole_ensemble_rank
1868	if [ X${comp} = XCPL ] ; then
1869	generic_restart_file_name_in="${generic_restart_file_name_in_tmp}__$pool_member_rank"
1870	file_in="${generic_restart_file_name_in}.nc"
1871
1872	if [ X${file_in} = Xsstoc__${pool_member_rank}.nc ] ; then
1873
1874	for varname in O_SSTSST OIceFrc O_AlbIce O_TepIce O_OCurx1 O_OCury1 O_OCurz1
1875	do
1876	ncrename -O -v .${varname}__${pool_member_rank},${varname} ${file_in}
1877
1878	done
1879
1880	elif [ X${file_in} = Xflxat__${pool_member_rank}.nc ] ; then
1881
1882	for varname in COTAUXXU COTAUYYU COTAUZZU COTAUXXV COTAUYYV COTAUZZV COTOTRAI COTOTSNO COTOTEVA COICEVAP COQSRMIX COQNSMIX COSHFICE CONSFICE CODFLXDT COCALVIN COLIQRUN COWINDSP COTAUMOD
1883	do
1884	ncrename -O -v .${varname}__${pool_member_rank},${varname} ${file_in}
1885	done
1886
1887	NumberCOLIQRUNflxat=$((27*${pool_member_rank}+27))
1888	NumberCOLIQRUNflxat_4dgts=$(printf "%04i\n" ${NumberCOLIQRUNflxat})
1889
1890	NumberCOCALVINflxat=$((27*${pool_member_rank}+24))
1891	NumberCOCALVINflxat_4dgts=$(printf "%04i\n" ${NumberCOCALVINflxat})
1892
1893	ncrename -O -d loc00${NumberCOLIQRUNflxat_4dgts}_cnt_ncnt,loc000000_COLIQRUN_cnt_ncnt ${file_in}
1894	ncrename -O -d loc00${NumberCOLIQRUNflxat_4dgts}_COLIQRUN__${pool_member_rank}_nx,loc000000_COLIQRUN_nx ${file_in}
1895	ncrename -O -d loc00${NumberCOLIQRUNflxat_4dgts}_COLIQRUN__${pool_member_rank}_ny,loc000000_COLIQRUN_ny ${file_in}
1896	ncrename -O -v loc00${NumberCOLIQRUNflxat_4dgts}_cnt,loc000000_COLIQRUN_cnt ${file_in}
1897	ncrename -O -v loc00${NumberCOLIQRUNflxat_4dgts}_COLIQRUN__${pool_member_rank},loc000000_COLIQRUN ${file_in}
1898
1899	ncrename -O -d loc00${NumberCOCALVINflxat_4dgts}_cnt_ncnt,loc000000_COCALVIN_cnt_ncnt ${file_in}
1900	ncrename -O -d loc00${NumberCOCALVINflxat_4dgts}_COCALVIN__${pool_member_rank}_nx,loc000000_COCALVIN_nx ${file_in}
1901	ncrename -O -d loc00${NumberCOCALVINflxat_4dgts}_COCALVIN__${pool_member_rank}_ny,loc000000_COCALVIN_ny ${file_in}
1902	ncrename -O -v loc00${NumberCOCALVINflxat_4dgts}_cnt,loc000000_COCALVIN_cnt ${file_in}
1903	ncrename -O -v loc00${NumberCOCALVINflxat_4dgts}_COCALVIN__${pool_member_rank},loc000000_COCALVIN ${file_in}
1904
1905	elif [ X${file_in} = Xicbrg__${pool_member_rank}.nc ] ; then
1906
1907	NumberCOCALVINicbrg=$((27*${pool_member_rank}+25))
1908	NumberCOCALVINicbrg_4dgts=$(printf "%04i\n" ${NumberCOCALVINicbrg})
1909
1910	ncrename -O -d loc00${NumberCOCALVINicbrg_4dgts}_cnt_ncnt,loc000000_cnt_ncnt ${file_in}
1911	ncrename -O -d loc00${NumberCOCALVINicbrg_4dgts}_COCALVIN__${pool_member_rank}_nx,loc000000_COCALVIN_nx ${file_in}
1912	ncrename -O -d loc00${NumberCOCALVINicbrg_4dgts}_COCALVIN__${pool_member_rank}_ny,loc000000_COCALVIN_ny ${file_in}
1913	ncrename -O -v loc00${NumberCOCALVINicbrg_4dgts}_cnt,loc000000_cnt ${file_in}
1914	ncrename -O -v loc00${NumberCOCALVINicbrg_4dgts}_COCALVIN__${pool_member_rank},loc000000_COCALVIN ${file_in}
1915	ncrename -O -v .COCALVIN__${pool_member_rank},COCALVIN ${file_in}
1916
1917	elif [ X${file_in} = Xicshf__${pool_member_rank}.nc ] ; then
1918
1919	NumberCOCALVINicshf=$((27*${pool_member_rank}+26))
1920	NumberCOCALVINicshf_4dgts=$(printf "%04i\n" ${NumberCOCALVINicshf})
1921	ncrename -O -d loc00${NumberCOCALVINicshf_4dgts}_cnt_ncnt,loc000000_cnt_ncnt ${file_in}
1922	ncrename -O -d loc00${NumberCOCALVINicshf_4dgts}_COCALVIN__${pool_member_rank}_nx,loc000000_COCALVIN_nx ${file_in}
1923	ncrename -O -d loc00${NumberCOCALVINicshf_4dgts}_COCALVIN__${pool_member_rank}_ny,loc000000_COCALVIN_ny ${file_in}
1924	ncrename -O -v loc00${NumberCOCALVINicshf_4dgts}_cnt,loc000000_cnt ${file_in}
1925	ncrename -O -v loc00${NumberCOCALVINicshf_4dgts}_COCALVIN__${pool_member_rank},loc000000_COCALVIN ${file_in}
1926	ncrename -O -v .COCALVIN__${pool_member_rank},COCALVIN ${file_in}
1927	fi
1928
1929	fi
1930	echo $generic_restart_file_name_in
1931	echo $file_in
1932	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1933	if [ ${nb_restart_file} -gt 1 ] ; then
1934	IGCM_sys_rebuild_nemo ${generic_restart_file_name_in} ${nb_restart_file}
1935	IGCM_sys_Rm ${generic_restart_file_name_in}_????.nc
1936	if [ X${Pack} = Xtrue ] ; then
1937	eval IGCM_sys_PutBuffer_Rest ${file_in} $Path_OUT/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1938	else
1939	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1940	fi
1941	if [ ! ${file_in} = ${file_outin} ] ; then
1942	if ( ${ExitFlag} ) ; then
1943	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1944	else
1945	IGCM_sys_Mv ${file_in} ${file_outin}
1946	fi
1947	fi
1948	else
1949	if [ X${Pack} = Xtrue ] ; then
1950	eval IGCM_sys_PutBuffer_Rest ${file_in} $Path_OUT/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1951	else
1952	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1953	fi
1954	if [ ! ${file_in} = ${file_outin} ] ; then
1955	if ( ${ExitFlag} ) ; then
1956	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1957	else
1958	IGCM_sys_Mv ${file_in} ${file_outin}
1959	fi
1960	fi
1961	fi
1962	cd ..
1963	done
1964	fi
1965	(( i=i+3 ))
1966	done
1967	else
1968	if [ X${FileName0} != XNONE ] ; then
1969	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1970	else
1971	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1972	fi
1973	fi
1974
1975	# Save Output files
1976	#------------------
1977	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1978	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1979	ListFilesName=${compname}_OutputFiles_List
1980	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1981
1982	if [ X${FileName0} != X${NULL_STR} ] ; then
1983	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1984
1985	nb_member_dir=$( ls \| grep "MEMBER" \| wc -l )
1986	(( total_number_member = config_Ensemble_PoolSize * config_Ensemble_PoolNumber ))
1987	OutputCopy=FALSE
1988	if [ ${nb_member_dir} = ${total_number_member} ] ; then
1989	OutputCopy=TRUE
1990	fi
1991	(( i=0 ))
1992	until [ $i -ge $NbFiles ]; do
1993	SaveOnArchive=true
1994	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1995	eval file_in=${file_in_}
1996	(( i_ = i+1 ))
1997	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1998	eval file_out=${file_out_}
1999	#
2000	# Override file_out path remplacing R_SAVE by R_BUFR
2001	#
2002	if [ X${Pack} = Xtrue ] ; then
2003	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
2004	fi
2005	#
2006	# Not necessarily the best option. /!\ Potential side effects /!\
2007	#
2008	(( i_ = i+2 ))
2009	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
2010	#
2011
2012	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
2013	cd XIOS
2014	fi
2015
2016	generic_file_name=$( basename ${file_in} .nc )
2017	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
2018	#
2019	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
2020	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
2021	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
2022	elif [ ${nb_rebuild_file} -gt 1 ] ; then
2023	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
2024	if [ X${AsynchronousRebuild} = Xfalse ] ; then
2025	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
2026	#
2027	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
2028	if [ ${file_in} = output.abort.nc ] ; then
2029	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
2030	else
2031	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
2032	fi
2033	else
2034	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
2035	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
2036
2037	# Prepare the shell dedicated to offline rebuild
2038	if [ $DRYRUN -le 1 ]; then
2039	if [ ${file_in} = histstn.nc ] ; then
2040	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2041	else
2042	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2043	fi
2044	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2045	fi
2046	#
2047	# Load Patch we need to apply and apply
2048	if [ $DRYRUN -le 1 ]; then
2049	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
2050	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2051	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2052	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2053	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2054	done
2055	fi
2056	fi
2057	#
2058	if [ $DRYRUN -le 1 ]; then
2059	if [ X${Pack} = Xtrue ] ; then
2060	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
2061	else
2062	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
2063	fi
2064	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
2065	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
2066	fi
2067	SaveOnArchive=false
2068	fi
2069	fi
2070	#
2071	if [ ${SaveOnArchive} = true ] ; then
2072	#
2073	# Rebuild has been done online or it was not needed
2074	#
2075	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
2076	#
2077	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
2078	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
2079	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
2080	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
2081	#
2082	if [ $DRYRUN -le 1 ]; then
2083	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2084	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2085	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2086	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2087	done
2088	#
2089	if [ X${Pack} = Xtrue ] ; then
2090	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2091	else
2092	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2093	fi
2094	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2095	#
2096	fi
2097	else
2098	#
2099	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
2100	#
2101	if [ X${OutputCopy} = XTRUE ] ; then
2102	if [ X${Pack} = Xtrue ] ; then
2103	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
2104	else
2105	IGCM_sys_Put_Out ${file_in} ${file_out}
2106	fi
2107	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
2108	if [ ${nb_rebuild_file} -gt 1 ] ; then
2109	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
2110	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
2111	done
2112	fi
2113	fi
2114	fi
2115	fi
2116	(( i=i+3 ))
2117	if [ ${config_Ensemble_EnsembleXIOS} = TRUE ] ; then
2118	cd ..
2119	fi
2120	done
2121	fi
2122	echo
2123	done
2124	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
2125	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
2126	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2127	i=0
2128	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
2129	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2130	(( i=i+1 ))
2131	done
2132	fi
2133	IGCM_debug_PopStack "IGCM_comp_Finalize"
2134	}

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source: CONFIG_DEVT/IPSLCM6.2.2_ENSEMBLES/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 6206

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