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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1452

Last change on this file since 1452 was 1449, checked in by sdipsl, 6 years ago
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Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
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1	#!/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
1009	# If missing executable and DRYRUN is set to 0 or 1 then stop!
1010	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1011	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1012	fi
1013
1014	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1015	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1016	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1017	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1018	fi
1019	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1020	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1021	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1022	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1023	fi
1024	fi
1025
1026	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1027	# Get the compiler version
1028	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1029	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1030	# Save it
1031	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1032	[ X${compilerFull} = X ] && byPass=true
1033	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1034	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1035	fi
1036	done
1037
1038	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1039	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1040
1041	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1042	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1043	fi
1044
1045	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
1046	IGCM_debug_Exit "IPSLCM6.0.13, IPSLCM6.0.14, IPSLCM6.0.15 and IPSLCM6.1 must be compiled with intel 2017 compiler"
1047	fi
1048
1049	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1050	}
1051
1052	#=======================================================================
1053	function IGCM_comp_PeriodStart
1054	{
1055	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1056
1057	# Debug Print :
1058	echo
1059	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1060	echo
1061
1062	typeset ExeNameIn ExeNameOut
1063	typeset comp compname comptagname
1064	for comp in ${config_ListOfComponents[*]} ; do
1065	# Define component
1066	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1067	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1068
1069	# Copy executable for this component
1070	eval ExeNameIn=\${config_Executable_${comp}[0]}
1071	eval ExeNameOut=\${config_Executable_${comp}[1]}
1072
1073	# Debug Print
1074	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1075	# UPDATE component
1076	${comp}_PeriodStart 2> /dev/null
1077
1078	done
1079
1080	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1081	}
1082
1083
1084
1085	#=======================================================================
1086	function IGCM_comp_modifyFile
1087	{
1088	#
1089	# syntax: IGCM_comp_modifyFile filein key [value]
1090	#
1091	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1092	#
1093	# This function is used to replace a pattern in a file for a specific variable.
1094	#
1095	# Arguments:
1096	# - filein : the file in run directory in which the variable should be set
1097	# - key : the variable to modify
1098	# - value : the value to set the key equal to
1099	#
1100	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1101
1102	typeset filein key value pattern
1103
1104	# Set local variables and test the arguments
1105	if [ $# = 3 ] ; then
1106	# Normal case with 3 arguments
1107	filein=$1 ; key=$2 ; value=$3
1108	else
1109	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1110	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1111	return
1112	fi
1113	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1114
1115	# Test if the file exist
1116	if [ ! -f ${filein} ] ; then
1117	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1118	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1119	return
1120	fi
1121
1122	# Read the line with key in the file without the comments
1123	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1124
1125	# Verify the existance of the pattern
1126	if [ X"${pattern}" = X ] ; then
1127	# Variable key is not set in filein, stop.
1128	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1129	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1130	return
1131	fi
1132
1133	# Now change key in filein
1134	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1135	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1136	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1137	\mv ${filein}.tmp ${filein}
1138
1139	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1140	}
1141
1142	#=======================================================================
1143	function IGCM_comp_modifyDefFile
1144	{
1145	#
1146	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1147	#
1148	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1149	#
1150	# This function is used to modify a parameter file for a specific variable.
1151	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1152	# This function can be used in the comp.driver files for the components.
1153	#
1154	# Arguments:
1155	# - type : first argument must be blocker, nonblocker or force
1156	# For "blocker" case, the variable must be attributed the keyworld AUTO
1157	# otherwise this function will exit.
1158	# For "nonblocker" case, the user can remove or modify the variable. For
1159	# this case, as long as AUTO is not set, no modification will be done.
1160	# For "force" case, the variable will be modified even if it is not set to AUTO
1161	# - filein : the file in run directory of .def type in which the variable should be set
1162	# - key : the variable to modify
1163	# - value : the value to set the key equal to, optional. If value is not set or if
1164	# value=DEFAULT, then a default value must be given in filein using syntax :
1165	# key= AUTO : DEFAULT=def_value
1166	#
1167	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1168
1169	typeset type filein key value
1170	typeset filelist nb_occ modify
1171
1172	# Set local variables and test the arguments
1173	if [ $# = 4 ] ; then
1174	# Normal case with 4 arguments
1175	type=$1 ; filein=$2 ; key=$3 ; value=$4
1176	elif [ $# = 3 ] ; then
1177	# Normal case with 3 arguments
1178	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1179	else
1180	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1181	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1182	return
1183	fi
1184	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1185
1186	# Test if first argument is correct
1187	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1188	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1189	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1190	return
1191	fi
1192
1193	# Test if the file exist.
1194	# Exit with error if the file does not exist for the case blocker or force.
1195	# Only return for the case nonblocker.
1196	if [ ! -f ${filein} ] ; then
1197	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1198	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1199	else
1200	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1201	fi
1202	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1203	return
1204	fi
1205
1206	# Define list of files to test using all files with suffix .def (except used*.def)
1207	filelist=$( ls *def \| grep -v used )
1208
1209	# Count number of occurances for the key in all files
1210	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1211
1212	# Test if key is set several times
1213	if [ ${nb_occ} -gt 1 ] ; then
1214	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1215	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1216	return
1217	fi
1218
1219	# Treatement according to different cases
1220	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1221	# Stop if the key is never set and the function is blocker
1222	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1223	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1224	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1225	# The key is not set but it is a nonblocker call so nothing is done.
1226	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1227	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1228	modify=no
1229	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1230	# Variable key is not set in filein, stop.
1231	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1232	fi
1233
1234	# Check if AUTO is set in the filein on the same line as the key variable
1235	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1236	# Modification will be done for all cases
1237	modify=yes
1238	else
1239	# The variable was not set to AUTO
1240	if [ ${type} = blocker ] ; then
1241	# Exit because this is a blocker call
1242	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1243	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1244	return
1245	elif [ ${type} = nonblocker ] ; then
1246	# Do nothing. Suppose that the user did set the variable correct
1247	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1248	modify=no
1249	elif [ ${type} = force ] ; then
1250	# Force modification
1251	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1252	modify=yes
1253	fi
1254	fi
1255
1256	# Do the modifcation now
1257	if [ ${modify} = yes ] ; then
1258
1259	# For option DEFAULT, read default value from file.
1260	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1261	# Case to set DEFAULT value
1262	# Read default value from filein
1263	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1264
1265	if [ X"${value}" = X ] ; then
1266	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1267	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1268	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1269	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1270	return
1271	fi
1272	fi
1273
1274	# Now change key in filein
1275	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1276	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1277	\mv ${filein}.tmp ${filein}
1278	fi
1279	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1280	}
1281
1282	#=======================================================================
1283	function IGCM_comp_modifyNamelist
1284	{
1285	#
1286	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1287	#
1288	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1289	#
1290	# This function is used to modify a parameter file for a specific variable.
1291	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1292	# This function can be used in the comp.driver files for the components.
1293	#
1294	# Arguments:
1295	# - type : first argument must be blocker, nonblocker or force
1296	# For "blocker" case, the variable must be attributed the keyworld AUTO
1297	# otherwise this function will exit.
1298	# For "nonblocker" case, the user can remove or modify the variable. For
1299	# this case, as long as AUTO is not set, no modification will be done.
1300	# For "force" case, the variable will be modified even if it is not set to AUTO
1301	# - filein : the file in run directory of .def type in which the variable should be set
1302	# - key : the variable to modify
1303	# - value : the value to set the key equal to, optional. If value is not set or if
1304	# value=DEFAULT, then a default value must be given in filein using syntax :
1305	# key= AUTO : DEFAULT=def_value
1306	#
1307	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1308
1309	typeset type filein key value pattern modify
1310
1311	# Set local variables and test the arguments
1312	if [ $# = 4 ] ; then
1313	# Normal case with 4 arguments
1314	type=$1 ; filein=$2 ; key=$3 ; value=$4
1315	elif [ $# = 3 ] ; then
1316	# Normal case with 3 arguments
1317	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1318	else
1319	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1320	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1321	return
1322	fi
1323	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1324
1325	# Test if first argument is correct
1326	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1327	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1328	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1329	return
1330	fi
1331
1332	# Test if the file exist.
1333	# Exit with error if the file does not exist for the case blocker or force.
1334	# Only return for the case nonblocker.
1335	if [ ! -f ${filein} ] ; then
1336	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1337	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1338	else
1339	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1340	fi
1341	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1342	return
1343	fi
1344
1345	# Read the line with key in the file without the comments
1346	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1347
1348	# Verify the existance of the pattern
1349	if [ X"$pattern" = X ] ; then
1350	# Variable key is not set in filein, stop.
1351	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1352	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1353	return
1354	fi
1355
1356	# Check if the variable is set to AUTO in the filein
1357	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1358	# Modification will be done for all cases
1359	modify=yes
1360	else
1361	# The variable was not set to AUTO
1362	if [ ${type} = blocker ] ; then
1363	# Exit because this is a blocker call
1364	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1365	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1366	return
1367	elif [ ${type} = nonblocker ] ; then
1368	# Do nothing. Suppose that the user did set the variable correct
1369	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1370	modify=no
1371	elif [ ${type} = force ] ; then
1372	# Force modification
1373	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1374	modify=yes
1375	fi
1376	fi
1377
1378	# Do the modifcation now
1379	if [ ${modify} = yes ] ; then
1380
1381	# For option DEFAULT, read default value from file.
1382	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1383	# Case to set DEFAULT value
1384	# Read default value from filein
1385	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1386
1387	if [ X"${value}" = X ] ; then
1388	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1389	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1390	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1391	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1392	return
1393	fi
1394	fi
1395
1396	# Now change key in filein
1397	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1398	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1399	\mv ${filein}.tmp ${filein}
1400	fi
1401	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1402	}
1403
1404	#=======================================================================
1405	function IGCM_comp_modifyXmlFile
1406	{
1407	#
1408	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1409	#
1410	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1411	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1412	#
1413	# This function is used to modify the value for a specific attribute and variable id.
1414	# The file must be a valid xml file.
1415	# This function can be used in the comp.driver files for the components.
1416	#
1417	# Arguments:
1418	# - type : first argument must be blocker, nonblocker or force.
1419	# For "blocker" case, the variable must be attributed the keyworld AUTO
1420	# otherwise this function will exit.
1421	# For "nonblocker" case, the user can remove or modify the variable. For
1422	# this case, as long as AUTO is not set, no modification will be done.
1423	# For "force" case, the variable will be modified even if it is not set to AUTO
1424	# - filein : the file in run directory of .xml type in which the variable should be set
1425	# - keyid : the variable to modify
1426	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1427	# - value : the value to set in the filein
1428	#
1429	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1430
1431	typeset type filein keyid keyattrib value modify
1432
1433	# Set local variables and test the arguments
1434	if [ $# = 5 ] ; then
1435	# Normal case with 4 arguments
1436	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1437	else
1438	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1439	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1440	return
1441	fi
1442	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1443
1444	# Test if first argument is correct
1445	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1446	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1447	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1448	return
1449	fi
1450
1451	# Test if the file exist.
1452	# Exit with error if the file does not exist for the case blocker or force.
1453	# Only return for the case nonblocker.
1454	if [ ! -f ${filein} ] ; then
1455	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1456	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1457	else
1458	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1459	fi
1460	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1461	return
1462	fi
1463
1464	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1465	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1466	if [ ${type} = nonblocker ] ; then
1467	# This is a nonblocker case, print warning but do nothing else
1468	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1469	else
1470	# This is a blocker or force case : stop now
1471	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1472	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1473	return
1474	fi
1475	fi
1476
1477	# Check if AUTO is set on the same line as keyid and keyattrib
1478	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1479	# Modification will be done
1480	modify=yes
1481	else
1482	if [ ${type} = blocker ] ; then
1483	# Exit, the variable must be set to AUTO
1484	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1485	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1486	return
1487	elif [ ${type} = nonblocker ] ; then
1488	# Nothing will be done
1489	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1490	modify=no
1491	elif [ ${type} = force ] ; then
1492	# Force modification
1493	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1494	modify=yes
1495	fi
1496	fi
1497
1498	# Do the modifcation now
1499	if [ ${modify} = yes ] ; then
1500	if [ ${keyattrib} = NONE ] ; then
1501	# Case to modify the variable itself
1502	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1503	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1504	else
1505	# Check if keyattrib is set on the same line as keyid
1506	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1507	# Case to modify the attribute value
1508	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1509	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1510	else
1511	# Case to add the attribute and its value
1512	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1513	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1514	fi
1515	fi
1516	\mv ${filein}.tmp ${filein}
1517	fi
1518	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1519	}
1520
1521	#=======================================================================
1522	function IGCM_comp_Update
1523	{
1524	IGCM_debug_PushStack "IGCM_comp_Update"
1525
1526	# Debug Print :
1527	echo
1528	IGCM_debug_Print 1 "IGCM_comp_Update"
1529	echo
1530
1531	typeset comp compname comptagname
1532	for comp in ${config_ListOfComponents[*]} ; do
1533	# Define component
1534	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1535	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1536
1537	# Debug Print
1538	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1539	# UPDATE component
1540	${comp}_Update
1541
1542	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1543	if [ -f timeseries_def_${compname}.xml ]; then
1544	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1545	for line in $( cat ts.temp.${compname}.txt ); do
1546	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1547	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1548	case ${output_freq} in
1549	Y\|y)
1550	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1551	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1552	;;
1553	MO\|mo)
1554	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1555	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1556	;;
1557	D\|d)
1558	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1559	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1560	;;
1561	S\|s)
1562	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1563	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1564	;;
1565	esac
1566	done
1567	fi
1568
1569	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1570	if [ -f dr2xml_${compname}.xml ]; then
1571	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1572	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1573
1574	# Modify path from dr2xml_{compname}.xml
1575	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1576
1577	# Overwrite the original file
1578	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1579	fi
1580	done
1581
1582	IGCM_debug_PopStack "IGCM_comp_Update"
1583	}
1584
1585	#=======================================================================
1586	function IGCM_comp_Finalize
1587	{
1588	IGCM_debug_PushStack "IGCM_comp_Finalize"
1589
1590	# Debug Print :
1591	echo
1592	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1593	echo
1594
1595	typeset ListTextName TextName0
1596	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1597	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1598	typeset -Z4 j4 #BASH declare j4
1599	typeset list_file nlist_file
1600	typeset compactoutputs
1601
1602	# Initialize array hosting list of rebuilded files to copy
1603	unset rebuildedActionsList
1604
1605	# Text compacting options
1606	compactoutputs=false
1607	if [ X${JobType} != XRUN ] ; then
1608	compactoutputs=true
1609	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1610	compactoutputs=true
1611	fi
1612
1613	# Prepare headers for the shell dedicated to offline rebuild
1614	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1615	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1616	if [ ${DRYRUN} -le 1 ] ; then
1617	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1618	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1619	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1620	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1621	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1622	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1623	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1624	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1625	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1626	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1627	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1628	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1629	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1630	fi
1631	fi
1632
1633	for comp in ${config_ListOfComponents[*]} ; do
1634	# Define component
1635	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1636	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1637
1638	# Debug Print
1639	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1640	# FINALIZE component
1641	${comp}_Finalize
1642
1643	card=${SUBMIT_DIR}/COMP/${compname}.card
1644
1645	# Save Output Text files of models
1646	#---------------------------------
1647	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1648	IGCM_card_DefineArrayFromOption ${card} OutputText List
1649	ListTextName=${compname}_OutputText_List
1650
1651	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1652	if [ X${TextName0} != X${NULL_STR} ] ; then
1653	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1654
1655	(( i=0 ))
1656	until [ $i -eq $NbFiles ]; do
1657	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1658	eval file_out=${PREFIX}_${file_in}
1659
1660	(( i=i+1 ))
1661
1662	unset list_file
1663	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1664	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1665	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 )
1666	nlist_file=${#list_file[@]}
1667	if [ ${nlist_file} -gt 1 ] ; then
1668	if ( ${compactoutputs} ) ; then
1669	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1670	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1671	echo ${list_file[*]} > ${file_out}
1672	echo "" >> ${file_out}
1673
1674	(( i_ = 0 ))
1675	for file in ${list_file[@]} ; do
1676	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1677	echo "\| " ${i_} " " ${file} >> ${file_out}
1678	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1679	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1680	echo "" >> ${file_out}
1681	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1682	(( i_ = i_ + 1 ))
1683	done
1684	if ( ${ExecutionFail} ) ; then
1685	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1686	fi
1687
1688	if [ X${Pack} = Xtrue ] ; then
1689	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1690	else
1691	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1692	fi
1693
1694	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1695	else
1696	for file in ${list_file[@]} ; do
1697	if ( ${ExecutionFail} ) ; then
1698	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1699	fi
1700
1701	if [ X${Pack} = Xtrue ] ; then
1702	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1703	else
1704	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1705	fi
1706
1707	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1708	done
1709	fi
1710	else
1711	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1712	eval IGCM_sys_Mv ${file_in}* ${file_in}
1713	fi
1714
1715	if ( ${ExecutionFail} ) ; then
1716	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1717	fi
1718
1719	if [ X${Pack} = Xtrue ] ; then
1720	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1721	else
1722	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1723	fi
1724	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1725	fi
1726	done
1727	fi
1728
1729	# Save Restarts files
1730	#--------------------
1731	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1732	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1733	ListFilesName=${compname}_RestartFiles_List
1734	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1735
1736	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1737	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1738
1739	(( i=0 ))
1740	until [ $i -ge $NbFiles ]; do
1741	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1742	eval file_in=${file_in_}
1743
1744	(( i_ = i+1 ))
1745	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1746	eval file_out=${file_out_}
1747
1748	(( i_ = i+2 ))
1749	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1750	eval file_outin=${file_outin_}
1751
1752	generic_restart_file_name_in=$( basename ${file_in} .nc )
1753	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1754	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1755
1756	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1757	if [ ${nb_restart_file} -gt 1 ] ; then
1758	j=0 # BASH LINE NOT NEEDED
1759	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1760	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1761	j4=${j} # BASH LINE NOT NEEDED
1762	if [ X${Pack} = Xtrue ] ; then
1763	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1764	else
1765	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1766	fi
1767	if [ ! ${file_in} = ${file_outin} ] ; then
1768	if ( ${ExitFlag} ) ; then
1769	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1770	else
1771	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1772	fi
1773	fi
1774	(( j=j+1 )) # BASH LINE NOT NEEDED
1775	done
1776	else
1777	if [ X${Pack} = Xtrue ] ; then
1778	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1779	else
1780	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1781	fi
1782	if [ ! ${file_in} = ${file_outin} ] ; then
1783	if ( ${ExitFlag} ) ; then
1784	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1785	else
1786	IGCM_sys_Mv ${file_in} ${file_outin}
1787	fi
1788	fi
1789	fi
1790
1791	(( i=i+3 ))
1792	done
1793	else
1794	if [ X${FileName0} != XNONE ] ; then
1795	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1796	else
1797	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1798	fi
1799	fi
1800
1801	# Save Output files
1802	#------------------
1803	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1804	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1805	ListFilesName=${compname}_OutputFiles_List
1806	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1807
1808	if [ X${FileName0} != X${NULL_STR} ] ; then
1809	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1810
1811	(( i=0 ))
1812	until [ $i -ge $NbFiles ]; do
1813	SaveOnArchive=true
1814	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1815	eval file_in=${file_in_}
1816	(( i_ = i+1 ))
1817	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1818	eval file_out=${file_out_}
1819	#
1820	# Override file_out path remplacing R_SAVE by R_BUFR
1821	#
1822	if [ X${Pack} = Xtrue ] ; then
1823	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1824	fi
1825	#
1826	# Not necessarily the best option. /!\ Potential side effects /!\
1827	#
1828	(( i_ = i+2 ))
1829	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1830	#
1831	generic_file_name=$( basename ${file_in} .nc )
1832	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1833	#
1834	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1835	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1836	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1837	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1838	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1839	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1840	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1841	#
1842	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
1843	if [ ${file_in} = output.abort.nc ] ; then
1844	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
1845	else
1846	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
1847	fi
1848	else
1849	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1850	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1851
1852	# Prepare the shell dedicated to offline rebuild
1853	if [ $DRYRUN -le 1 ]; then
1854	if [ ${file_in} = histstn.nc ] ; then
1855	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1856	else
1857	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1858	fi
1859	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1860	fi
1861	#
1862	# Load Patch we need to apply and apply
1863	if [ $DRYRUN -le 1 ]; then
1864	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1865	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1866	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1867	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1868	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1869	done
1870	fi
1871	fi
1872	#
1873	if [ $DRYRUN -le 1 ]; then
1874	if [ X${Pack} = Xtrue ] ; then
1875	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1876	else
1877	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1878	fi
1879	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1880	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1881	fi
1882	SaveOnArchive=false
1883	fi
1884	fi
1885	#
1886	if [ ${SaveOnArchive} = true ] ; then
1887	#
1888	# Rebuild has been done online or it was not needed
1889	#
1890	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1891	#
1892	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1893	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1894	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1895	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1896	#
1897	if [ $DRYRUN -le 1 ]; then
1898	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1899	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1900	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1901	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1902	done
1903	#
1904	if [ X${Pack} = Xtrue ] ; then
1905	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1906	else
1907	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1908	fi
1909	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1910	#
1911	fi
1912	else
1913	#
1914	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1915	#
1916	if [ X${Pack} = Xtrue ] ; then
1917	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1918	else
1919	IGCM_sys_Put_Out ${file_in} ${file_out}
1920	fi
1921	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1922	if [ ${nb_rebuild_file} -gt 1 ] ; then
1923	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1924	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1925	done
1926	fi
1927	fi
1928	fi
1929	(( i=i+3 ))
1930	done
1931	fi
1932	echo
1933	done
1934	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1935	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1936	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1937	i=0
1938	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1939	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1940	(( i=i+1 ))
1941	done
1942	fi
1943	IGCM_debug_PopStack "IGCM_comp_Finalize"
1944	}

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