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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1506

Last change on this file since 1506 was 1504, checked in by aclsce, 5 years ago
Modified test on compiler version for IPSLCM6* configuration to be applied only on irene (only for CMIP6 production)
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
File size: 80.2 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:: $ Revision of last commit
7	# $Author:: $ Author of last commit
8	# $Date:: $ 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	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
113
114	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
115	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
116
117	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
118	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
119	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
120	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
121
122	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
123	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
124	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
125	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
126
127	# Define CMIP6 Dirs
128	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
129	fi
130
131	# Read UserChoices section of component card
132	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
133	IGCM_card_DefineArrayFromSection ${card} UserChoices
134	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
135
136	# If section is not empty we define corresponding variables
137	if [ X${first_option} != X"Error:" ] ; then
138	if [ X${card_UserChoices[0]} != X ] ; then
139	unset card_UserChoices
140	fi
141	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
142	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
143	for option in ${card_UserChoices[*]} ; do
144	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
145	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
146	done
147	fi
148
149	# Read and Build Output File stuff
150	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
151	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
152	ListFilesName=${compname}_OutputFiles_List
153	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
154	#
155	if [ X${FileName0} != X${NULL_STR} ] ; then
156	#
157	#IGCM_debug_Print 1 "Component : ${compname}"
158	#
159	# INITIALISATION
160	#
161	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
162	#
163	i=2
164	#
165	until [ $i -ge $NbFiles ]; do
166	#
167	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
168	#
169	if [ X${flag_post} != XNONE ] ; then
170	#
171	# First of all
172	#
173	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
174	# This section is mandatory
175	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
176	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
177	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
178	IGCM_debug_Verif_Exit
179	fi
180	#
181	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
182	#
183	# variable option allready typeset above
184	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
185	if [ ${option} = Seasonal ] ; then
186	FoundSeasonal=true
187	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
188	fi
189	done
190	#
191	if [ ! X${FoundSeasonal} = Xtrue ] ; then
192	eval ${compname}_${flag_post}_Seasonal=ON
193	fi
194	#
195	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
196	Seasonal=true
197	fi
198
199	# Dimension = vide si vieille card.
200	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
201	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
202	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
203	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
204	ListDimension[0]=2D
205	ListDimension[1]=3D
206	TimeSeries=false
207	iLoop=${#ListDimension[*]}
208	j=0
209	until [ $j -ge ${iLoop} ]; do
210	Dimension=${ListDimension[${j}]}
211	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
212	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
213	#
214	# Time series WITHOUT chunk
215	#
216	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
217	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
218	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
219	eval TimeSeries${Dimension}=true
220	fi
221	fi
222	#
223	# Time series WITH chunk
224	#
225	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
226	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
227	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
228	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
229	eval TimeSeriesChunck${Dimension}=true
230	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
231	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
232	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
233	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
234	fi
235	fi
236	(( j=j+1 ))
237	done
238	else
239	ListDimension[0]=""
240	TimeSeries=true
241	TimeSeries2D=false
242	TimeSeries3D=false
243	TimeSeriesChunck2D=false
244	TimeSeriesChunck3D=false
245	fi
246	fi
247	(( i=i+3 ))
248	done
249	fi
250	# Debug Print
251	IGCM_debug_Print 3 "Initialize ${compname} with driver."
252	# INIT component
253	${comp}_Initialize
254	echo
255	done
256
257	IGCM_debug_PopStack "IGCM_comp_Initialize"
258	}
259
260	#=======================================================================
261	function IGCM_comp_PrepareDeletedFiles
262	{
263	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
264
265	if [ X${2} != X. ] ; then
266	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
267	else
268	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
269	fi
270
271	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
272	}
273
274	#=======================================================================
275	function IGCM_comp_PrepareXiosFiles
276	{
277	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
278
279	typeset file
280	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
281
282	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
283	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
284	fi
285	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
286	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
287	fi
288	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
289	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
290	fi
291
292	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
293	}
294
295	#=======================================================================
296	function IGCM_comp_GetInputInitialStateFiles
297	{
298	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
299
300	# Debug Print :
301	echo
302	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
303	echo
304
305	# Only the first time step need InitialStateFiles
306	# otherwise it's BoundaryConditions
307	if ( ${FirstInitialize} ) ; then
308	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
309	typeset file_in_ file_in file_out_ file_out do_init
310	for comp in ${config_ListOfComponents[*]} ; do
311	# Initialize
312	do_init="y"
313	# Do we need to bring initial state file for this component
314	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
315	eval do_init="n"
316	else
317	# Read component Restarts parameters
318	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
319	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
320	if [ "${do_start}" = "y" ] ; then
321	do_init="n"
322	else
323	do_init="y"
324	fi
325	fi
326
327	if [ "${do_init}" = "y" ] ; then
328	# Define component
329	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
330	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
331
332	# Debug Print :
333	IGCM_debug_Print 3 "Initialisation files ${compname}"
334
335	card=${SUBMIT_DIR}/COMP/${compname}.card
336
337	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
338	ListFilesName=${compname}_InitialStateFiles_List
339
340	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
341	if [ X${FileName0} != X${NULL_STR} ] ; then
342	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
343	(( i=0 ))
344	until [ $i -ge $NbFiles ]; do
345	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
346	eval file_in=${file_in_}
347	(( i_ = i+1 ))
348	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
349	eval file_out=${file_out_}
350
351	IGCM_sys_IsFileArchived ${file_in}
352	if [ $? = 0 ] ; then
353	IGCM_sys_Get ${file_in} ${file_out}
354	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
355	else
356	IGCM_sys_Cp ${file_in} ${file_out}
357	fi
358	(( i=i+2 ))
359	done
360	fi
361	fi
362	done
363	fi
364	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
365	}
366
367	#=======================================================================
368	# Definition of Smooth modulo function
369	# usage :
370	# IGCM_SmoothModulo StringModulo value
371	#
372	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
373	# [min]:[modulo:][max]
374	# where :
375	# [] value are optionnals;
376	# empty min equal 1
377	# empty max equal infinity
378	# modulo not given or empty equal 1
379	# empty string or just ':' equal always.
380	#
381	# value : the value to test with the definition
382	#
383	# return : true(1)/false(0)
384	function IGCM_SmoothModulo
385	{
386	IGCM_debug_PushStack "IGCM_SmoothModulo"
387	typeset defVector ModValue
388
389	eval set +A defVector -- $( echo "${1}" \| \
390	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
391
392	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
393	arr[1]=${defVector[0]}
394	arr[2]=${defVector[2]}
395
396	# Test limits :
397	# ${defVector[0]} <= ${2} <= ${defVector[2]}
398	# or ${defVector[2]} == -1
399	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
400	# Test modulo
401	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
402	if [ ${ModValue} -eq 0 ] ; then
403	arr[3]=true
404	echo ${arr[@]}
405	IGCM_debug_PopStack "IGCM_SmoothModulo"
406	return 1
407	else
408	arr[3]=false
409	echo ${arr[@]}
410	IGCM_debug_PopStack "IGCM_SmoothModulo"
411	return 0
412	fi
413	else
414	arr[3]=false
415	echo ${arr[@]}
416	IGCM_debug_PopStack "IGCM_SmoothModulo"
417	return 0
418	fi
419	}
420
421	#=======================================================================
422	function IGCM_comp_GetInputSmoothFiles
423	{
424	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
425
426	# Debug Print :
427	echo
428	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
429	echo
430
431	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
432	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
433
434	for comp in ${config_ListOfComponents[*]} ; do
435	# Define component
436	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
437	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
438
439	# Debug Print :
440	IGCM_debug_Print 3 "Smooth files ${compname}"
441
442	card=${SUBMIT_DIR}/COMP/${compname}.card
443
444	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
445	ListFilesName=${compname}_SmoothFiles_List
446	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
447
448	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
449	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
450
451	(( i=0 ))
452	until [ $i -ge $NbFiles ]; do
453	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
454	eval file_in=${file_in_}
455	(( i_ = i+1 ))
456	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
457	eval file_out=${file_out_}
458
459	# define CumulPeriod definition for this file
460	(( i__ = i+2 ))
461	eval SmoothDef=\${${ListFilesName}[$i__]}
462	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
463	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
464	j=1
465	for val in ${aux} ; do
466	[ ${j} -eq 1 ] && SmoothMin=${val}
467	[ ${j} -eq 2 ] && SmoothMax=${val}
468	[ ${j} -eq 3 ] && ret=${val}
469	(( j=j+1 ))
470	done
471	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
472	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
473
474	IGCM_sys_IsFileArchived ${file_in}
475	if [ $? = 0 ] ; then
476	IGCM_sys_Get ${file_in} ${file_out}
477	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
478	else
479	IGCM_sys_Cp ${file_in} ${file_out}
480	fi
481	fi
482	(( i=i+3 ))
483	done
484	fi
485	done
486
487	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
488	}
489
490	#=======================================================================
491	function IGCM_comp_GetInputBoundaryFiles
492	{
493	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
494
495	# Debug Print :
496	echo
497	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
498	echo
499
500	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
501	typeset file_in_ file_in file_out_ file_out
502
503	if [ ${Period} = 1 ]; then
504	ListFixBoundary=" "
505	fi
506
507	for comp in ${config_ListOfComponents[*]} ; do
508
509	# Define component
510	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
511	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
512
513	# Debug Print :
514	IGCM_debug_Print 3 "Boundary files ${compname}"
515
516	card=${SUBMIT_DIR}/COMP/${compname}.card
517
518	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
519	ListFilesName=${compname}_BoundaryFiles_List
520	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
521
522	if [ X${FileName0} != X${NULL_STR} ] ; then
523	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
524
525	(( i=0 ))
526	until [ $i -ge $NbFiles ]; do
527	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
528	eval file_in=${file_in_}
529	(( i_ = i+1 ))
530	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
531	eval file_out=${file_out_}
532
533	IGCM_sys_IsFileArchived ${file_in}
534	if [ $? = 0 ] ; then
535	IGCM_sys_Get ${file_in} ${file_out}
536	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
537	else
538	IGCM_sys_Cp ${file_in} ${file_out}
539	fi
540
541	(( i=i+2 ))
542	done
543	fi
544
545	# Get non deleted files
546	if [ ${Period} = 1 ]; then
547
548	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
549	ListFilesName=${compname}_BoundaryFiles_ListNonDel
550	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
551
552	if [ X${FileName0} != X${NULL_STR} ] ; then
553	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
554
555	(( i=0 ))
556	until [ $i -ge $NbFiles ]; do
557	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
558	eval file_in=${file_in_}
559	(( i_ = i+1 ))
560	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
561	eval file_out=${file_out_}
562
563	IGCM_sys_IsFileArchived ${file_in}
564	if [ $? = 0 ] ; then
565	IGCM_sys_Get ${file_in} ${file_out}
566	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
567	else
568	IGCM_sys_Cp ${file_in} ${file_out}
569	fi
570
571	if [ X${file_out} != X. ] ; then
572	ListFixBoundary=${ListFixBoundary}" "${file_out}
573	else
574	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
575	fi
576
577	(( i=i+2 ))
578	done
579	fi
580	fi
581	done
582
583	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
584	}
585
586	#=======================================================================
587	function IGCM_comp_DelFixeBoundaryFiles
588	{
589	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
590
591	# Debug Print :
592	echo
593	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
594	echo
595
596	ls -l ${ListFixBoundary}
597	rm -f ${ListFixBoundary}
598
599	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
600	}
601
602	#=======================================================================
603	function IGCM_comp_GetInputParametersFiles
604	{
605	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
606
607	# Debug Print :
608	echo
609	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
610	echo
611
612	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
613	for comp in ${config_ListOfComponents[*]} ; do
614	# Define component
615	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
616	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
617
618	# Initialize array hosting file_def and field_def files to check and/or modify
619	unset FieldDef
620	unset FileDef
621
622	# Debug Print :
623	IGCM_debug_Print 3 "Parameters ${compname}"
624
625	card=${SUBMIT_DIR}/COMP/${compname}.card
626
627	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
628	ListFilesName=${compname}_ParametersFiles_List
629	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
630
631	if [ X${FileName0} != X${NULL_STR} ] ; then
632	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
633
634	(( i=0 ))
635	until [ $i -ge $NbFiles ]; do
636	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
637	eval file_in=${file_in_}
638	(( i_ = i+1 ))
639	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
640	eval file_out=${file_out_}
641
642	IGCM_sys_Cp ${file_in} ${file_out}
643	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
644	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
645
646	(( i=i+2 ))
647	done
648	fi
649
650	if [ ${#FileDef[@]} -ne 0 ] ; then
651	# Check XMLs coherency now
652	IGCM_debug_Print 1 "${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}"
653	${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}
654	if [ $? = 0 ] ; then
655	IGCM_debug_Print 1 "${compname} XIOS XMLs are consistent"
656	else
657	IGCM_debug_Print 1 "${compname} XIOS XMLs ARE NOT consistent"
658	if [ X${config_Post_ParserXIOS} = XTRUE ] ; then
659	IGCM_debug_Print 1 "Try to fix it:"
660	IGCM_debug_Print 3 "${libIGCM}/libIGCM_post/xios_parser.py -v modify --field ${FieldDef[]} --file ${FileDef[]}"
661	${libIGCM}/libIGCM_post/xios_parser.py -vv modify --field ${FieldDef[]} --file ${FileDef[]}
662	[ $? != 0 ] && IGCM_debug_Exit "Failed to fix XIOS xml files for ${compname}"
663	fi
664	fi
665	fi
666	done
667
668	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
669	}
670
671	#=======================================================================
672	function IGCM_comp_GetInputRestartFiles
673	{
674	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
675
676	# Debug Print :
677	echo
678	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
679	echo
680
681	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
682	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
683	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
684	typeset file_in file_out file_in_ file_out_ file_in_Name
685	typeset -Z4 j4
686	#BASH declare j4
687
688	IsMatching=""
689
690	for comp in ${config_ListOfComponents[*]} ; do
691	# Define component
692	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
693	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
694	#
695	card=${SUBMIT_DIR}/COMP/${compname}.card
696	#
697	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
698	ListFilesName=${compname}_RestartFiles_List
699	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
700
701	# Debug Print :
702	IGCM_debug_Print 3 "restart ${compname}"
703
704	if ( ${FirstInitialize} ) ; then
705
706	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
707	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
708	if ( [ X${comp} = XIOS ] && [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] ) ; then
709	CompOldName=IOS
710	config_IOS_Restart="n"
711	do_start="n"
712	config_IOS_RestartDate=-1
713	config_IOS_RestartJobName=${NULL_STR}
714	config_IOS_RestartPath=${NULL_STR}
715	else
716	eval config_${comp}_Restart="y"
717	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
718	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
719	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
720	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
721	eval CompOldName=${comp}
722	fi
723	else
724	# Read component Restarts parameters
725	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
726	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
727
728	if [ "${do_start}" = "y" ] ; then
729	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
730	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
731	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
732	else
733	eval config_${comp}_RestartDate=-1
734	eval config_${comp}_RestartJobName=${NULL_STR}
735	eval config_${comp}_RestartPath=${NULL_STR}
736	fi
737
738	eval CompOldName=\${config_${comp}_OldName}
739	if [ X${CompOldName} = X ] ; then
740	eval CompOldName=${comp}
741	fi
742
743	# Reinitialize IsMatching to allow searching for a different tar file for each component.
744	IsMatching=""
745	TarFileFound=""
746	fi
747
748	if [ "${do_start}" = "y" ] ; then
749
750	# Restore Restarts files
751	#-----------------------
752	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
753	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
754
755	(( i=1 ))
756	until [ $i -gt $NbFiles ]; do
757	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
758	eval file_in=${file_in_}
759	(( i_ = i+1 ))
760	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
761	eval file_out=${file_out_}
762
763	eval Date_tmp=\${config_${comp}_RestartDate}
764	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
765	# will be re-use
766	eval RestartPath=\${config_${comp}_RestartPath}
767	eval RestartJobName=\${config_${comp}_RestartJobName}
768	#
769	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
770	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
771
772	extension_in=$( echo ${file_in_Name##*.} )
773	extension_out=$( echo ${file_out##*.} )
774
775	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
776	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
777
778	Path_OUT=${Path_r}/${generic_restart_file_name_in}
779
780	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
781	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
782	Buffered=true
783	Archived=false
784	Tared=false
785	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
786	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
787	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
788	Buffered=false
789	Archived=true
790	Tared=false
791	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
792	else
793	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
794	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
795	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
796	Buffered=false
797	Archived=false
798	Tared=true
799	# Look after the tar file we want if we did not found it already
800	if [ X${IsMatching} = X ] ; then
801	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
802	if [ $? ] ; then
803	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
804	IsMatching=$( echo ${PotentialTarFile##*/} \| \
805	sed "s:_restart::" \| \
806	sed "s:^${RestartJobName}_::" \| \
807	sed "s:\.tar$::" \| \
808	gawk -F_ -v restartdate=${Date_r} \
809	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
810	if [ ! X${IsMatching} = X ] ; then
811	TarFileFound=${PotentialTarFile}
812	break
813	fi
814	done
815	fi
816	# Stop here if nothing has been found
817	if [ X${TarFileFound} = X ] ; then
818	IGCM_debug_Print 3 "Restart files were not found!"
819	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
820	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
821	IGCM_debug_Exit "Please double check restart settings in config.card"
822	IGCM_debug_Verif_Exit
823	fi
824	fi
825	IGCM_sys_PrepareTaredRestart ${TarFileFound}
826	TarFileLocation=$( basename ${TarFileFound} )
827	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
828	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
829	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
830	fi
831
832	if [ ${nb_restart_file} -gt 1 ] ; then
833	j=0 # BASH LINE NOT NEEDED
834	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
835	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
836	j4=${j} # BASH LINE NOT NEEDED
837	if [ X${Buffered} = Xtrue ] ; then
838	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
839	elif [ X${Archived} = Xtrue ] ; then
840	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
841	elif [ X${Tared} = Xtrue ] ; then
842	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
843	fi
844	(( j=j+1 )) #BASH LINE NOT NEEDED
845	done
846
847	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
848	if [ X${OCE_PROC_MPI} != X ] ; then
849	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
850	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
851	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
852	fi
853	fi
854	else
855	if [ X${Buffered} = Xtrue ] ; then
856	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
857	elif [ X${Archived} = Xtrue ] ; then
858	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
859	elif [ X${Tared} = Xtrue ] ; then
860	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
861	fi
862	fi
863	(( i=i+3 ))
864	done
865	else
866	if [ X${FileName0} != XNONE ] ; then
867	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
868	else
869	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
870	fi
871	fi
872	fi
873	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
874	# if not FirstInitialize and first loop of this job
875
876	# Restore Restarts files
877	#-----------------------
878	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
879	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
880
881	(( i=1 ))
882	until [ $i -gt $NbFiles ]; do
883	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
884	eval file_in=${file_in_}
885	(( i_ = i+1 ))
886	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
887	eval file_out=${file_out_}
888
889	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
890
891	extension_in=$( echo ${file_in_Name##*.} )
892	extension_out=$( echo ${file_out##*.} )
893
894	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
895	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
896
897	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
898	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
899
900	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
901	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
902	Buffered=true
903	Archived=false
904	Tared=false
905	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
906	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
907	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
908	Buffered=false
909	Archived=true
910	Tared=false
911	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
912	else
913	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
914	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
915	Buffered=false
916	Archived=false
917	Tared=true
918	# Look after the tar file we want if we did not found it already
919	if [ X${IsMatching} = X ] ; then
920	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
921	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
922	if [ ! X${IsMatching} = X ] ; then
923	TarFileFound=${PotentialTarFile}
924	break
925	fi
926	done
927	fi
928	# Stop here if nothing has been found
929	if [ X${TarFileFound} = X ] ; then
930	IGCM_debug_Print 3 "Restart files were not found!"
931	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
932	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
933	IGCM_debug_Exit "Please double check restart settings in config.card"
934	IGCM_debug_Verif_Exit
935	fi
936	IGCM_sys_PrepareTaredRestart ${TarFileFound}
937	TarFileLocation=$( basename ${TarFileFound} )
938	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
939	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
940	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
941	fi
942
943	if [ ${nb_restart_file} -gt 1 ] ; then
944	j=0 # BASH LINE NOT NEEDED
945	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
946	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
947	j4=${j} # BASH LINE NOT NEEDED
948	if [ X${Buffered} = Xtrue ] ; then
949	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
950	elif [ X${Archived} = Xtrue ] ; then
951	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
952	elif [ X${Tared} = Xtrue ] ; then
953	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
954	fi
955	(( j=j+1 )) # BASH LINE NOT NEEDED
956	done
957	else
958	if [ X${Buffered} = Xtrue ] ; then
959	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
960	elif [ X${Archived} = Xtrue ] ; then
961	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
962	elif [ X${Tared} = Xtrue ] ; then
963	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
964	fi
965	fi
966	(( i=i+3 ))
967	done
968	else
969	if [ X${FileName0} != XNONE ] ; then
970	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
971	else
972	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
973	fi
974	fi
975	fi
976	done
977
978	NbFiles=$( ls * 2> /dev/null \| wc -l )
979	if [ ${NbFiles} -gt 0 ] ; then
980	IGCM_sys_Chmod u+rw *
981	fi
982
983	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
984	}
985
986	#=======================================================================
987	function IGCM_comp_GetInputBinaryFiles
988	{
989	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
990
991	# Debug Print :
992	echo
993	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
994	echo
995
996	# Clean up previous pass
997	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
998
999	typeset comp ExeNameIn ExeNameOut byPass
1000	typeset compilerNmbr compilerUnit compilerFull
1001	byPass=false
1002	for comp in ${config_ListOfComponents[*]} ; do
1003	# Define component
1004
1005	# Copy executable for this component
1006	eval ExeNameIn=\${config_Executable_${comp}[0]}
1007	eval ExeNameOut=\${config_Executable_${comp}[1]}
1008	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
1009	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
1010	# The executable is set in config.card and is different from ""
1011	# Use eval to expand ExeNameIn if variables are used in the name
1012	eval ExeNameIn=${ExeNameIn}
1013	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1014	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1015	fi
1016	fi
1017
1018	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1019	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1020	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1021	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1022	fi
1023	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1024	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1025	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1026	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1027	fi
1028	fi
1029
1030	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1031	# Get the compiler version
1032	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1033	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1034	# Save it
1035	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1036	[ X${compilerFull} = X ] && byPass=true
1037	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1038	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1039	fi
1040	done
1041
1042	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1043	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1044
1045	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1046	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1047	fi
1048
1049	# Test on compiler version for IPSLCM6* configuration on irene (only for CMIP6 production)
1050	if [ ${SYSTEM} = irene ]; then
1051	if ( [ X"$( 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 ] ) ; then
1052	IGCM_debug_Exit "IPSLCM6.0.13, IPSLCM6.0.14, IPSLCM6.0.15 and IPSLCM6.1 must be compiled with intel 2017 compiler"
1053	fi
1054	fi
1055
1056	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1057	}
1058
1059	#=======================================================================
1060	function IGCM_comp_PeriodStart
1061	{
1062	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1063
1064	# Debug Print :
1065	echo
1066	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1067	echo
1068
1069	typeset ExeNameIn ExeNameOut
1070	typeset comp compname comptagname
1071	for comp in ${config_ListOfComponents[*]} ; do
1072	# Define component
1073	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1074	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1075
1076	# Copy executable for this component
1077	eval ExeNameIn=\${config_Executable_${comp}[0]}
1078	eval ExeNameIn=${ExeNameIn}
1079	eval ExeNameOut=\${config_Executable_${comp}[1]}
1080
1081	# Debug Print
1082	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1083	# UPDATE component
1084	${comp}_PeriodStart 2> /dev/null
1085
1086	done
1087
1088	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1089	}
1090
1091
1092
1093	#=======================================================================
1094	function IGCM_comp_modifyFile
1095	{
1096	#
1097	# syntax: IGCM_comp_modifyFile filein key [value]
1098	#
1099	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1100	#
1101	# This function is used to replace a pattern in a file for a specific variable.
1102	#
1103	# Arguments:
1104	# - filein : the file in run directory in which the variable should be set
1105	# - key : the variable to modify
1106	# - value : the value to set the key equal to
1107	#
1108	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1109
1110	typeset filein key value pattern
1111
1112	# Set local variables and test the arguments
1113	if [ $# = 3 ] ; then
1114	# Normal case with 3 arguments
1115	filein=$1 ; key=$2 ; value=$3
1116	else
1117	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1118	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1119	return
1120	fi
1121	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1122
1123	# Test if the file exist
1124	if [ ! -f ${filein} ] ; then
1125	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1126	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1127	return
1128	fi
1129
1130	# Read the line with key in the file without the comments
1131	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1132
1133	# Verify the existance of the pattern
1134	if [ X"${pattern}" = X ] ; then
1135	# Variable key is not set in filein, stop.
1136	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1137	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1138	return
1139	fi
1140
1141	# Now change key in filein
1142	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1143	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1144	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1145	\mv ${filein}.tmp ${filein}
1146
1147	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1148	}
1149
1150	#=======================================================================
1151	function IGCM_comp_modifyDefFile
1152	{
1153	#
1154	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1155	#
1156	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1157	#
1158	# This function is used to modify a parameter file for a specific variable.
1159	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1160	# This function can be used in the comp.driver files for the components.
1161	#
1162	# Arguments:
1163	# - type : first argument must be blocker, nonblocker or force
1164	# For "blocker" case, the variable must be attributed the keyworld AUTO
1165	# otherwise this function will exit.
1166	# For "nonblocker" case, the user can remove or modify the variable. For
1167	# this case, as long as AUTO is not set, no modification will be done.
1168	# For "force" case, the variable will be modified even if it is not set to AUTO
1169	# - filein : the file in run directory of .def type in which the variable should be set
1170	# - key : the variable to modify
1171	# - value : the value to set the key equal to, optional. If value is not set or if
1172	# value=DEFAULT, then a default value must be given in filein using syntax :
1173	# key= AUTO : DEFAULT=def_value
1174	#
1175	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1176
1177	typeset type filein key value
1178	typeset filelist nb_occ modify
1179
1180	# Set local variables and test the arguments
1181	if [ $# = 4 ] ; then
1182	# Normal case with 4 arguments
1183	type=$1 ; filein=$2 ; key=$3 ; value=$4
1184	elif [ $# = 3 ] ; then
1185	# Normal case with 3 arguments
1186	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1187	else
1188	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1189	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1190	return
1191	fi
1192	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1193
1194	# Test if first argument is correct
1195	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1196	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1197	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1198	return
1199	fi
1200
1201	# Test if the file exist.
1202	# Exit with error if the file does not exist for the case blocker or force.
1203	# Only return for the case nonblocker.
1204	if [ ! -f ${filein} ] ; then
1205	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1206	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1207	else
1208	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1209	fi
1210	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1211	return
1212	fi
1213
1214	# Define list of files to test using all files with suffix .def (except used*.def)
1215	filelist=$( ls *def \| grep -v used )
1216
1217	# Count number of occurances for the key in all files
1218	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1219
1220	# Test if key is set several times
1221	if [ ${nb_occ} -gt 1 ] ; then
1222	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1223	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1224	return
1225	fi
1226
1227	# Treatement according to different cases
1228	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1229	# Stop if the key is never set and the function is blocker
1230	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1231	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1232	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1233	# The key is not set but it is a nonblocker call so nothing is done.
1234	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1235	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1236	modify=no
1237	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1238	# Variable key is not set in filein, stop.
1239	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1240	fi
1241
1242	# Check if AUTO is set in the filein on the same line as the key variable
1243	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1244	# Modification will be done for all cases
1245	modify=yes
1246	else
1247	# The variable was not set to AUTO
1248	if [ ${type} = blocker ] ; then
1249	# Exit because this is a blocker call
1250	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1251	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1252	return
1253	elif [ ${type} = nonblocker ] ; then
1254	# Do nothing. Suppose that the user did set the variable correct
1255	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1256	modify=no
1257	elif [ ${type} = force ] ; then
1258	# Force modification
1259	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1260	modify=yes
1261	fi
1262	fi
1263
1264	# Do the modifcation now
1265	if [ ${modify} = yes ] ; then
1266
1267	# For option DEFAULT, read default value from file.
1268	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1269	# Case to set DEFAULT value
1270	# Read default value from filein
1271	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1272
1273	if [ X"${value}" = X ] ; then
1274	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1275	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1276	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1277	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1278	return
1279	fi
1280	fi
1281
1282	# Now change key in filein
1283	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1284	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1285	\mv ${filein}.tmp ${filein}
1286	fi
1287	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1288	}
1289
1290	#=======================================================================
1291	function IGCM_comp_modifyNamelist
1292	{
1293	#
1294	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1295	#
1296	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1297	#
1298	# This function is used to modify a parameter file for a specific variable.
1299	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1300	# This function can be used in the comp.driver files for the components.
1301	#
1302	# Arguments:
1303	# - type : first argument must be blocker, nonblocker or force
1304	# For "blocker" case, the variable must be attributed the keyworld AUTO
1305	# otherwise this function will exit.
1306	# For "nonblocker" case, the user can remove or modify the variable. For
1307	# this case, as long as AUTO is not set, no modification will be done.
1308	# For "force" case, the variable will be modified even if it is not set to AUTO
1309	# - filein : the file in run directory of .def type in which the variable should be set
1310	# - key : the variable to modify
1311	# - value : the value to set the key equal to, optional. If value is not set or if
1312	# value=DEFAULT, then a default value must be given in filein using syntax :
1313	# key= AUTO : DEFAULT=def_value
1314	#
1315	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1316
1317	typeset type filein key value pattern modify
1318
1319	# Set local variables and test the arguments
1320	if [ $# = 4 ] ; then
1321	# Normal case with 4 arguments
1322	type=$1 ; filein=$2 ; key=$3 ; value=$4
1323	elif [ $# = 3 ] ; then
1324	# Normal case with 3 arguments
1325	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1326	else
1327	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1328	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1329	return
1330	fi
1331	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1332
1333	# Test if first argument is correct
1334	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1335	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1336	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1337	return
1338	fi
1339
1340	# Test if the file exist.
1341	# Exit with error if the file does not exist for the case blocker or force.
1342	# Only return for the case nonblocker.
1343	if [ ! -f ${filein} ] ; then
1344	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1345	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1346	else
1347	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1348	fi
1349	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1350	return
1351	fi
1352
1353	# Read the line with key in the file without the comments
1354	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1355
1356	# Verify the existance of the pattern
1357	if [ X"$pattern" = X ] ; then
1358	# Variable key is not set in filein, stop.
1359	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1360	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1361	return
1362	fi
1363
1364	# Check if the variable is set to AUTO in the filein
1365	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1366	# Modification will be done for all cases
1367	modify=yes
1368	else
1369	# The variable was not set to AUTO
1370	if [ ${type} = blocker ] ; then
1371	# Exit because this is a blocker call
1372	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1373	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1374	return
1375	elif [ ${type} = nonblocker ] ; then
1376	# Do nothing. Suppose that the user did set the variable correct
1377	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1378	modify=no
1379	elif [ ${type} = force ] ; then
1380	# Force modification
1381	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1382	modify=yes
1383	fi
1384	fi
1385
1386	# Do the modifcation now
1387	if [ ${modify} = yes ] ; then
1388
1389	# For option DEFAULT, read default value from file.
1390	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1391	# Case to set DEFAULT value
1392	# Read default value from filein
1393	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1394
1395	if [ X"${value}" = X ] ; then
1396	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1397	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1398	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1399	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1400	return
1401	fi
1402	fi
1403
1404	# Now change key in filein
1405	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1406	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1407	\mv ${filein}.tmp ${filein}
1408	fi
1409	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1410	}
1411
1412	#=======================================================================
1413	function IGCM_comp_modifyXmlFile
1414	{
1415	#
1416	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1417	#
1418	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1419	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1420	#
1421	# This function is used to modify the value for a specific attribute and variable id.
1422	# The file must be a valid xml file.
1423	# This function can be used in the comp.driver files for the components.
1424	#
1425	# Arguments:
1426	# - type : first argument must be blocker, nonblocker or force.
1427	# For "blocker" case, the variable must be attributed the keyworld AUTO
1428	# otherwise this function will exit.
1429	# For "nonblocker" case, the user can remove or modify the variable. For
1430	# this case, as long as AUTO is not set, no modification will be done.
1431	# For "force" case, the variable will be modified even if it is not set to AUTO
1432	# - filein : the file in run directory of .xml type in which the variable should be set
1433	# - keyid : the variable to modify
1434	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1435	# - value : the value to set in the filein
1436	#
1437	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1438
1439	typeset type filein keyid keyattrib value modify
1440
1441	# Set local variables and test the arguments
1442	if [ $# = 5 ] ; then
1443	# Normal case with 4 arguments
1444	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1445	else
1446	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1447	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1448	return
1449	fi
1450	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1451
1452	# Test if first argument is correct
1453	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1454	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1455	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1456	return
1457	fi
1458
1459	# Test if the file exist.
1460	# Exit with error if the file does not exist for the case blocker or force.
1461	# Only return for the case nonblocker.
1462	if [ ! -f ${filein} ] ; then
1463	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1464	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1465	else
1466	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1467	fi
1468	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1469	return
1470	fi
1471
1472	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1473	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1474	if [ ${type} = nonblocker ] ; then
1475	# This is a nonblocker case, print warning but do nothing else
1476	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1477	else
1478	# This is a blocker or force case : stop now
1479	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1480	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1481	return
1482	fi
1483	fi
1484
1485	# Check if AUTO is set on the same line as keyid and keyattrib
1486	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1487	# Modification will be done
1488	modify=yes
1489	else
1490	if [ ${type} = blocker ] ; then
1491	# Exit, the variable must be set to AUTO
1492	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1493	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1494	return
1495	elif [ ${type} = nonblocker ] ; then
1496	# Nothing will be done
1497	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1498	modify=no
1499	elif [ ${type} = force ] ; then
1500	# Force modification
1501	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1502	modify=yes
1503	fi
1504	fi
1505
1506	# Do the modifcation now
1507	if [ ${modify} = yes ] ; then
1508	if [ ${keyattrib} = NONE ] ; then
1509	# Case to modify the variable itself
1510	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1511	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1512	else
1513	# Check if keyattrib is set on the same line as keyid
1514	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1515	# Case to modify the attribute value
1516	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1517	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1518	else
1519	# Case to add the attribute and its value
1520	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1521	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1522	fi
1523	fi
1524	\mv ${filein}.tmp ${filein}
1525	fi
1526	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1527	}
1528
1529	#=======================================================================
1530	function IGCM_comp_Update
1531	{
1532	IGCM_debug_PushStack "IGCM_comp_Update"
1533
1534	# Debug Print :
1535	echo
1536	IGCM_debug_Print 1 "IGCM_comp_Update"
1537	echo
1538
1539	typeset comp compname comptagname
1540	for comp in ${config_ListOfComponents[*]} ; do
1541	# Define component
1542	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1543	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1544
1545	# Debug Print
1546	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1547	# UPDATE component
1548	${comp}_Update
1549
1550	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1551	if [ -f timeseries_def_${compname}.xml ]; then
1552	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1553	for line in $( cat ts.temp.${compname}.txt ); do
1554	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1555	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1556	case ${output_freq} in
1557	Y\|y)
1558	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1559	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1560	;;
1561	MO\|mo)
1562	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1563	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1564	;;
1565	D\|d)
1566	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1567	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1568	;;
1569	S\|s)
1570	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1571	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1572	;;
1573	esac
1574	done
1575	fi
1576
1577	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1578	if [ -f dr2xml_${compname}.xml ]; then
1579	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1580	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1581	# Modify path from dr2xml_{compname}.xml
1582	if [ X${config_Post_dr2xmlFilePrefix} = XTRUE ]; then
1583	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --filePrefix ${config_UserChoices_JobName} --file dr2xml_${compname}.xml
1584	else
1585	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1586	fi
1587	# Overwrite the original file
1588	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1589	fi
1590	done
1591
1592	IGCM_debug_PopStack "IGCM_comp_Update"
1593	}
1594
1595	#=======================================================================
1596	function IGCM_comp_Finalize
1597	{
1598	IGCM_debug_PushStack "IGCM_comp_Finalize"
1599
1600	# Debug Print :
1601	echo
1602	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1603	echo
1604
1605	typeset ListTextName TextName0
1606	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1607	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1608	typeset -Z4 j4 #BASH declare j4
1609	typeset list_file nlist_file
1610	typeset compactoutputs
1611
1612	# Initialize array hosting list of rebuilded files to copy
1613	unset rebuildedActionsList
1614
1615	# Text compacting options
1616	compactoutputs=false
1617	if [ X${JobType} != XRUN ] ; then
1618	compactoutputs=true
1619	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1620	compactoutputs=true
1621	fi
1622
1623	# Prepare headers for the shell dedicated to offline rebuild
1624	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1625	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1626	if [ ${DRYRUN} -le 1 ] ; then
1627	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1628	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1629	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1630	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1631	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1632	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1633	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1634	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1635	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1636	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1637	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1638	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1639	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1640	fi
1641	fi
1642
1643	for comp in ${config_ListOfComponents[*]} ; do
1644	# Define component
1645	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1646	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1647
1648	# Debug Print
1649	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1650	# FINALIZE component
1651	${comp}_Finalize
1652
1653	card=${SUBMIT_DIR}/COMP/${compname}.card
1654
1655	# Save Output Text files of models
1656	#---------------------------------
1657	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1658	IGCM_card_DefineArrayFromOption ${card} OutputText List
1659	ListTextName=${compname}_OutputText_List
1660
1661	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1662	if [ X${TextName0} != X${NULL_STR} ] ; then
1663	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1664
1665	(( i=0 ))
1666	until [ $i -eq $NbFiles ]; do
1667	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1668	eval file_out=${PREFIX}_${file_in}
1669
1670	(( i=i+1 ))
1671
1672	unset list_file
1673	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1674	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1675	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 )
1676	nlist_file=${#list_file[@]}
1677	if [ ${nlist_file} -gt 1 ] ; then
1678	if ( ${compactoutputs} ) ; then
1679	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1680	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1681	echo ${list_file[*]} > ${file_out}
1682	echo "" >> ${file_out}
1683
1684	(( i_ = 0 ))
1685	for file in ${list_file[@]} ; do
1686	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1687	echo "\| " ${i_} " " ${file} >> ${file_out}
1688	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1689	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1690	echo "" >> ${file_out}
1691	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1692	(( i_ = i_ + 1 ))
1693	done
1694	if ( ${ExecutionFail} ) ; then
1695	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1696	fi
1697
1698	if [ X${Pack} = Xtrue ] ; then
1699	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1700	else
1701	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1702	fi
1703
1704	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1705	else
1706	for file in ${list_file[@]} ; do
1707	if ( ${ExecutionFail} ) ; then
1708	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1709	fi
1710
1711	if [ X${Pack} = Xtrue ] ; then
1712	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1713	else
1714	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1715	fi
1716
1717	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1718	done
1719	fi
1720	else
1721	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1722	eval IGCM_sys_Mv ${file_in}* ${file_in}
1723	fi
1724
1725	if ( ${ExecutionFail} ) ; then
1726	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1727	fi
1728
1729	if [ X${Pack} = Xtrue ] ; then
1730	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1731	else
1732	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1733	fi
1734	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1735	fi
1736	done
1737	fi
1738
1739	# Save Restarts files
1740	#--------------------
1741	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1742	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1743	ListFilesName=${compname}_RestartFiles_List
1744	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1745
1746	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1747	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1748
1749	(( i=0 ))
1750	until [ $i -ge $NbFiles ]; do
1751	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1752	eval file_in=${file_in_}
1753
1754	(( i_ = i+1 ))
1755	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1756	eval file_out=${file_out_}
1757
1758	(( i_ = i+2 ))
1759	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1760	eval file_outin=${file_outin_}
1761
1762	generic_restart_file_name_in=$( basename ${file_in} .nc )
1763	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1764	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1765
1766	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1767	if [ ${nb_restart_file} -gt 1 ] ; then
1768	j=0 # BASH LINE NOT NEEDED
1769	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1770	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1771	j4=${j} # BASH LINE NOT NEEDED
1772	if [ X${Pack} = Xtrue ] ; then
1773	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1774	else
1775	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1776	fi
1777	if [ ! ${file_in} = ${file_outin} ] ; then
1778	if ( ${ExitFlag} ) ; then
1779	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1780	else
1781	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1782	fi
1783	fi
1784	(( j=j+1 )) # BASH LINE NOT NEEDED
1785	done
1786	else
1787	if [ X${Pack} = Xtrue ] ; then
1788	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1789	else
1790	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1791	fi
1792	if [ ! ${file_in} = ${file_outin} ] ; then
1793	if ( ${ExitFlag} ) ; then
1794	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1795	else
1796	IGCM_sys_Mv ${file_in} ${file_outin}
1797	fi
1798	fi
1799	fi
1800
1801	(( i=i+3 ))
1802	done
1803	else
1804	if [ X${FileName0} != XNONE ] ; then
1805	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1806	else
1807	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1808	fi
1809	fi
1810
1811	# Save Output files
1812	#------------------
1813	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1814	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1815	ListFilesName=${compname}_OutputFiles_List
1816	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1817
1818	if [ X${FileName0} != X${NULL_STR} ] ; then
1819	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1820
1821	(( i=0 ))
1822	until [ $i -ge $NbFiles ]; do
1823	SaveOnArchive=true
1824	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1825	eval file_in=${file_in_}
1826	(( i_ = i+1 ))
1827	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1828	eval file_out=${file_out_}
1829	#
1830	# Override file_out path remplacing R_SAVE by R_BUFR
1831	#
1832	if [ X${Pack} = Xtrue ] ; then
1833	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1834	fi
1835	#
1836	# Not necessarily the best option. /!\ Potential side effects /!\
1837	#
1838	(( i_ = i+2 ))
1839	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1840	#
1841	generic_file_name=$( basename ${file_in} .nc )
1842	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1843	#
1844	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1845	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1846	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1847	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1848	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1849	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1850	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1851	#
1852	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
1853	if [ ${file_in} = output.abort.nc ] ; then
1854	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
1855	else
1856	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
1857	fi
1858	else
1859	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1860	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1861
1862	# Prepare the shell dedicated to offline rebuild
1863	if [ $DRYRUN -le 1 ]; then
1864	if [ ${file_in} = histstn.nc ] ; then
1865	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1866	else
1867	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1868	fi
1869	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1870	fi
1871	#
1872	# Load Patch we need to apply and apply
1873	if [ $DRYRUN -le 1 ]; then
1874	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1875	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1876	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1877	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1878	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1879	done
1880	fi
1881	fi
1882	#
1883	if [ $DRYRUN -le 1 ]; then
1884	if [ X${Pack} = Xtrue ] ; then
1885	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1886	else
1887	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1888	fi
1889	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1890	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1891	fi
1892	SaveOnArchive=false
1893	fi
1894	fi
1895	#
1896	if [ ${SaveOnArchive} = true ] ; then
1897	#
1898	# Rebuild has been done online or it was not needed
1899	#
1900	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1901	#
1902	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1903	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1904	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1905	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1906	#
1907	if [ $DRYRUN -le 1 ]; then
1908	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1909	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1910	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1911	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1912	done
1913	#
1914	if [ X${Pack} = Xtrue ] ; then
1915	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1916	else
1917	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1918	fi
1919	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1920	#
1921	fi
1922	else
1923	#
1924	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1925	#
1926	if [ X${Pack} = Xtrue ] ; then
1927	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1928	else
1929	IGCM_sys_Put_Out ${file_in} ${file_out}
1930	fi
1931	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1932	if [ ${nb_rebuild_file} -gt 1 ] ; then
1933	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1934	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1935	done
1936	fi
1937	fi
1938	fi
1939	(( i=i+3 ))
1940	done
1941	fi
1942	echo
1943	done
1944	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1945	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1946	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1947	i=0
1948	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1949	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1950	(( i=i+1 ))
1951	done
1952	fi
1953	IGCM_debug_PopStack "IGCM_comp_Finalize"
1954	}

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