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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1438

Last change on this file since 1438 was 1431, checked in by sdipsl, 6 years ago
CMIP6 files go in CCCWORKDIR and alike.
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: 79.2 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" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
707	eval config_${comp}_Restart="y"
708	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
709	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
710	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
711	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
712	eval CompOldName=${comp}
713	else
714	# Read component Restarts parameters
715	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
716	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
717
718	if [ "${do_start}" = "y" ] ; then
719	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
720	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
721	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
722	else
723	eval config_${comp}_RestartDate=-1
724	eval config_${comp}_RestartJobName=${NULL_STR}
725	eval config_${comp}_RestartPath=${NULL_STR}
726	fi
727
728	eval CompOldName=\${config_${comp}_OldName}
729	if [ X${CompOldName} = X ] ; then
730	eval CompOldName=${comp}
731	fi
732
733	# Reinitialize IsMatching to allow searching for a different tar file for each component.
734	IsMatching=""
735	TarFileFound=""
736	fi
737
738	if [ "${do_start}" = "y" ] ; then
739
740	# Restore Restarts files
741	#-----------------------
742	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
743	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
744
745	(( i=1 ))
746	until [ $i -gt $NbFiles ]; do
747	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
748	eval file_in=${file_in_}
749	(( i_ = i+1 ))
750	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
751	eval file_out=${file_out_}
752
753	eval Date_tmp=\${config_${comp}_RestartDate}
754	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
755	# will be re-use
756	eval RestartPath=\${config_${comp}_RestartPath}
757	eval RestartJobName=\${config_${comp}_RestartJobName}
758	#
759	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
760	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
761
762	extension_in=$( echo ${file_in_Name##*.} )
763	extension_out=$( echo ${file_out##*.} )
764
765	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
766	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
767
768	Path_OUT=${Path_r}/${generic_restart_file_name_in}
769
770	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
771	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
772	Buffered=true
773	Archived=false
774	Tared=false
775	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
776	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
777	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
778	Buffered=false
779	Archived=true
780	Tared=false
781	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
782	else
783	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
784	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
785	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
786	Buffered=false
787	Archived=false
788	Tared=true
789	# Look after the tar file we want if we did not found it already
790	if [ X${IsMatching} = X ] ; then
791	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
792	if [ $? ] ; then
793	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
794	IsMatching=$( echo ${PotentialTarFile##*/} \| \
795	sed "s:_restart::" \| \
796	sed "s:^${RestartJobName}_::" \| \
797	sed "s:\.tar$::" \| \
798	gawk -F_ -v restartdate=${Date_r} \
799	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
800	if [ ! X${IsMatching} = X ] ; then
801	TarFileFound=${PotentialTarFile}
802	break
803	fi
804	done
805	fi
806	# Stop here if nothing has been found
807	if [ X${TarFileFound} = X ] ; then
808	IGCM_debug_Print 3 "Restart files were not found!"
809	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
810	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
811	IGCM_debug_Exit "Please double check restart settings in config.card"
812	IGCM_debug_Verif_Exit
813	fi
814	fi
815	IGCM_sys_PrepareTaredRestart ${TarFileFound}
816	TarFileLocation=$( basename ${TarFileFound} )
817	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
818	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
819	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
820	fi
821
822	if [ ${nb_restart_file} -gt 1 ] ; then
823	j=0 # BASH LINE NOT NEEDED
824	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
825	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
826	j4=${j} # BASH LINE NOT NEEDED
827	if [ X${Buffered} = Xtrue ] ; then
828	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
829	elif [ X${Archived} = Xtrue ] ; then
830	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
831	elif [ X${Tared} = Xtrue ] ; then
832	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
833	fi
834	(( j=j+1 )) #BASH LINE NOT NEEDED
835	done
836
837	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
838	if [ X${OCE_PROC_MPI} != X ] ; then
839	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
840	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
841	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
842	fi
843	fi
844	else
845	if [ X${Buffered} = Xtrue ] ; then
846	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
847	elif [ X${Archived} = Xtrue ] ; then
848	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
849	elif [ X${Tared} = Xtrue ] ; then
850	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
851	fi
852	fi
853	(( i=i+3 ))
854	done
855	else
856	if [ X${FileName0} != XNONE ] ; then
857	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
858	else
859	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
860	fi
861	fi
862	fi
863	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
864	# if not FirstInitialize and first loop of this job
865
866	# Restore Restarts files
867	#-----------------------
868	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
869	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
870
871	(( i=1 ))
872	until [ $i -gt $NbFiles ]; do
873	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
874	eval file_in=${file_in_}
875	(( i_ = i+1 ))
876	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
877	eval file_out=${file_out_}
878
879	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
880
881	extension_in=$( echo ${file_in_Name##*.} )
882	extension_out=$( echo ${file_out##*.} )
883
884	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
885	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
886
887	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
888	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
889
890	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
891	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
892	Buffered=true
893	Archived=false
894	Tared=false
895	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
896	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
897	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
898	Buffered=false
899	Archived=true
900	Tared=false
901	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
902	else
903	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
904	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
905	Buffered=false
906	Archived=false
907	Tared=true
908	# Look after the tar file we want if we did not found it already
909	if [ X${IsMatching} = X ] ; then
910	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
911	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
912	if [ ! X${IsMatching} = X ] ; then
913	TarFileFound=${PotentialTarFile}
914	break
915	fi
916	done
917	fi
918	# Stop here if nothing has been found
919	if [ X${TarFileFound} = X ] ; then
920	IGCM_debug_Print 3 "Restart files were not found!"
921	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
922	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
923	IGCM_debug_Exit "Please double check restart settings in config.card"
924	IGCM_debug_Verif_Exit
925	fi
926	IGCM_sys_PrepareTaredRestart ${TarFileFound}
927	TarFileLocation=$( basename ${TarFileFound} )
928	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
929	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
930	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
931	fi
932
933	if [ ${nb_restart_file} -gt 1 ] ; then
934	j=0 # BASH LINE NOT NEEDED
935	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
936	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
937	j4=${j} # BASH LINE NOT NEEDED
938	if [ X${Buffered} = Xtrue ] ; then
939	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
940	elif [ X${Archived} = Xtrue ] ; then
941	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
942	elif [ X${Tared} = Xtrue ] ; then
943	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
944	fi
945	(( j=j+1 )) # BASH LINE NOT NEEDED
946	done
947	else
948	if [ X${Buffered} = Xtrue ] ; then
949	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
950	elif [ X${Archived} = Xtrue ] ; then
951	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
952	elif [ X${Tared} = Xtrue ] ; then
953	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
954	fi
955	fi
956	(( i=i+3 ))
957	done
958	else
959	if [ X${FileName0} != XNONE ] ; then
960	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
961	else
962	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
963	fi
964	fi
965	fi
966	done
967
968	NbFiles=$( ls * 2> /dev/null \| wc -l )
969	if [ ${NbFiles} -gt 0 ] ; then
970	IGCM_sys_Chmod u+rw *
971	fi
972
973	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
974	}
975
976	#=======================================================================
977	function IGCM_comp_GetInputBinaryFiles
978	{
979	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
980
981	# Debug Print :
982	echo
983	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
984	echo
985
986	# Clean up previous pass
987	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
988
989	typeset comp ExeNameIn ExeNameOut byPass
990	typeset compilerNmbr compilerUnit compilerFull
991	byPass=false
992	for comp in ${config_ListOfComponents[*]} ; do
993	# Define component
994
995	# Copy executable for this component
996	eval ExeNameIn=\${config_Executable_${comp}[0]}
997	eval ExeNameOut=\${config_Executable_${comp}[1]}
998
999	# If missing executable and DRYRUN is set to 0 or 1 then stop!
1000	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1001	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1002	fi
1003
1004	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1005	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1006	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1007	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1008	fi
1009	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1010	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1011	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1012	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1013	fi
1014	fi
1015
1016	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1017	# Get the compiler version
1018	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1019	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1020	# Save it
1021	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1022	[ X${compilerFull} = X ] && byPass=true
1023	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1024	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1025	fi
1026	done
1027
1028	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1029	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1030
1031	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1032	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1033	fi
1034
1035	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
1036	IGCM_debug_Exit "IPSLCM6.0.13, IPSLCM6.0.14, IPSLCM6.0.15 and IPSLCM6.1 must be compiled with intel 2017 compiler"
1037	fi
1038
1039	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1040	}
1041
1042	#=======================================================================
1043	function IGCM_comp_PeriodStart
1044	{
1045	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1046
1047	# Debug Print :
1048	echo
1049	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1050	echo
1051
1052	typeset ExeNameIn ExeNameOut
1053	typeset comp compname comptagname
1054	for comp in ${config_ListOfComponents[*]} ; do
1055	# Define component
1056	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1057	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1058
1059	# Copy executable for this component
1060	eval ExeNameIn=\${config_Executable_${comp}[0]}
1061	eval ExeNameOut=\${config_Executable_${comp}[1]}
1062
1063	# Debug Print
1064	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1065	# UPDATE component
1066	${comp}_PeriodStart 2> /dev/null
1067
1068	done
1069
1070	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1071	}
1072
1073
1074
1075	#=======================================================================
1076	function IGCM_comp_modifyFile
1077	{
1078	#
1079	# syntax: IGCM_comp_modifyFile filein key [value]
1080	#
1081	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1082	#
1083	# This function is used to replace a pattern in a file for a specific variable.
1084	#
1085	# Arguments:
1086	# - filein : the file in run directory in which the variable should be set
1087	# - key : the variable to modify
1088	# - value : the value to set the key equal to
1089	#
1090	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1091
1092	typeset filein key value pattern
1093
1094	# Set local variables and test the arguments
1095	if [ $# = 3 ] ; then
1096	# Normal case with 3 arguments
1097	filein=$1 ; key=$2 ; value=$3
1098	else
1099	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1100	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1101	return
1102	fi
1103	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1104
1105	# Test if the file exist
1106	if [ ! -f ${filein} ] ; then
1107	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1108	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1109	return
1110	fi
1111
1112	# Read the line with key in the file without the comments
1113	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1114
1115	# Verify the existance of the pattern
1116	if [ X"${pattern}" = X ] ; then
1117	# Variable key is not set in filein, stop.
1118	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1119	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1120	return
1121	fi
1122
1123	# Now change key in filein
1124	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1125	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1126	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1127	\mv ${filein}.tmp ${filein}
1128
1129	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1130	}
1131
1132	#=======================================================================
1133	function IGCM_comp_modifyDefFile
1134	{
1135	#
1136	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1137	#
1138	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1139	#
1140	# This function is used to modify a parameter file for a specific variable.
1141	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1142	# This function can be used in the comp.driver files for the components.
1143	#
1144	# Arguments:
1145	# - type : first argument must be blocker, nonblocker or force
1146	# For "blocker" case, the variable must be attributed the keyworld AUTO
1147	# otherwise this function will exit.
1148	# For "nonblocker" case, the user can remove or modify the variable. For
1149	# this case, as long as AUTO is not set, no modification will be done.
1150	# For "force" case, the variable will be modified even if it is not set to AUTO
1151	# - filein : the file in run directory of .def type in which the variable should be set
1152	# - key : the variable to modify
1153	# - value : the value to set the key equal to, optional. If value is not set or if
1154	# value=DEFAULT, then a default value must be given in filein using syntax :
1155	# key= AUTO : DEFAULT=def_value
1156	#
1157	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1158
1159	typeset type filein key value
1160	typeset filelist nb_occ modify
1161
1162	# Set local variables and test the arguments
1163	if [ $# = 4 ] ; then
1164	# Normal case with 4 arguments
1165	type=$1 ; filein=$2 ; key=$3 ; value=$4
1166	elif [ $# = 3 ] ; then
1167	# Normal case with 3 arguments
1168	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1169	else
1170	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1171	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1172	return
1173	fi
1174	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1175
1176	# Test if first argument is correct
1177	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1178	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1179	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1180	return
1181	fi
1182
1183	# Test if the file exist.
1184	# Exit with error if the file does not exist for the case blocker or force.
1185	# Only return for the case nonblocker.
1186	if [ ! -f ${filein} ] ; then
1187	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1188	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1189	else
1190	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1191	fi
1192	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1193	return
1194	fi
1195
1196	# Define list of files to test using all files with suffix .def (except used*.def)
1197	filelist=$( ls *def \| grep -v used )
1198
1199	# Count number of occurances for the key in all files
1200	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1201
1202	# Test if key is set several times
1203	if [ ${nb_occ} -gt 1 ] ; then
1204	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1205	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1206	return
1207	fi
1208
1209	# Treatement according to different cases
1210	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1211	# Stop if the key is never set and the function is blocker
1212	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1213	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1214	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1215	# The key is not set but it is a nonblocker call so nothing is done.
1216	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1217	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1218	modify=no
1219	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1220	# Variable key is not set in filein, stop.
1221	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1222	fi
1223
1224	# Check if AUTO is set in the filein on the same line as the key variable
1225	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1226	# Modification will be done for all cases
1227	modify=yes
1228	else
1229	# The variable was not set to AUTO
1230	if [ ${type} = blocker ] ; then
1231	# Exit because this is a blocker call
1232	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1233	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1234	return
1235	elif [ ${type} = nonblocker ] ; then
1236	# Do nothing. Suppose that the user did set the variable correct
1237	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1238	modify=no
1239	elif [ ${type} = force ] ; then
1240	# Force modification
1241	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1242	modify=yes
1243	fi
1244	fi
1245
1246	# Do the modifcation now
1247	if [ ${modify} = yes ] ; then
1248
1249	# For option DEFAULT, read default value from file.
1250	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1251	# Case to set DEFAULT value
1252	# Read default value from filein
1253	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1254
1255	if [ X"${value}" = X ] ; then
1256	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1257	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1258	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1259	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1260	return
1261	fi
1262	fi
1263
1264	# Now change key in filein
1265	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1266	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1267	\mv ${filein}.tmp ${filein}
1268	fi
1269	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1270	}
1271
1272	#=======================================================================
1273	function IGCM_comp_modifyNamelist
1274	{
1275	#
1276	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1277	#
1278	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1279	#
1280	# This function is used to modify a parameter file for a specific variable.
1281	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1282	# This function can be used in the comp.driver files for the components.
1283	#
1284	# Arguments:
1285	# - type : first argument must be blocker, nonblocker or force
1286	# For "blocker" case, the variable must be attributed the keyworld AUTO
1287	# otherwise this function will exit.
1288	# For "nonblocker" case, the user can remove or modify the variable. For
1289	# this case, as long as AUTO is not set, no modification will be done.
1290	# For "force" case, the variable will be modified even if it is not set to AUTO
1291	# - filein : the file in run directory of .def type in which the variable should be set
1292	# - key : the variable to modify
1293	# - value : the value to set the key equal to, optional. If value is not set or if
1294	# value=DEFAULT, then a default value must be given in filein using syntax :
1295	# key= AUTO : DEFAULT=def_value
1296	#
1297	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1298
1299	typeset type filein key value pattern modify
1300
1301	# Set local variables and test the arguments
1302	if [ $# = 4 ] ; then
1303	# Normal case with 4 arguments
1304	type=$1 ; filein=$2 ; key=$3 ; value=$4
1305	elif [ $# = 3 ] ; then
1306	# Normal case with 3 arguments
1307	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1308	else
1309	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1310	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1311	return
1312	fi
1313	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1314
1315	# Test if first argument is correct
1316	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1317	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1318	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1319	return
1320	fi
1321
1322	# Test if the file exist.
1323	# Exit with error if the file does not exist for the case blocker or force.
1324	# Only return for the case nonblocker.
1325	if [ ! -f ${filein} ] ; then
1326	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1327	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1328	else
1329	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1330	fi
1331	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1332	return
1333	fi
1334
1335	# Read the line with key in the file without the comments
1336	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1337
1338	# Verify the existance of the pattern
1339	if [ X"$pattern" = X ] ; then
1340	# Variable key is not set in filein, stop.
1341	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1342	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1343	return
1344	fi
1345
1346	# Check if the variable is set to AUTO in the filein
1347	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1348	# Modification will be done for all cases
1349	modify=yes
1350	else
1351	# The variable was not set to AUTO
1352	if [ ${type} = blocker ] ; then
1353	# Exit because this is a blocker call
1354	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1355	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1356	return
1357	elif [ ${type} = nonblocker ] ; then
1358	# Do nothing. Suppose that the user did set the variable correct
1359	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1360	modify=no
1361	elif [ ${type} = force ] ; then
1362	# Force modification
1363	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1364	modify=yes
1365	fi
1366	fi
1367
1368	# Do the modifcation now
1369	if [ ${modify} = yes ] ; then
1370
1371	# For option DEFAULT, read default value from file.
1372	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1373	# Case to set DEFAULT value
1374	# Read default value from filein
1375	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1376
1377	if [ X"${value}" = X ] ; then
1378	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1379	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1380	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1381	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1382	return
1383	fi
1384	fi
1385
1386	# Now change key in filein
1387	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1388	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1389	\mv ${filein}.tmp ${filein}
1390	fi
1391	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1392	}
1393
1394	#=======================================================================
1395	function IGCM_comp_modifyXmlFile
1396	{
1397	#
1398	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1399	#
1400	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1401	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1402	#
1403	# This function is used to modify the value for a specific attribute and variable id.
1404	# The file must be a valid xml file.
1405	# This function can be used in the comp.driver files for the components.
1406	#
1407	# Arguments:
1408	# - type : first argument must be blocker, nonblocker or force.
1409	# For "blocker" case, the variable must be attributed the keyworld AUTO
1410	# otherwise this function will exit.
1411	# For "nonblocker" case, the user can remove or modify the variable. For
1412	# this case, as long as AUTO is not set, no modification will be done.
1413	# For "force" case, the variable will be modified even if it is not set to AUTO
1414	# - filein : the file in run directory of .xml type in which the variable should be set
1415	# - keyid : the variable to modify
1416	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1417	# - value : the value to set in the filein
1418	#
1419	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1420
1421	typeset type filein keyid keyattrib value modify
1422
1423	# Set local variables and test the arguments
1424	if [ $# = 5 ] ; then
1425	# Normal case with 4 arguments
1426	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1427	else
1428	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1429	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1430	return
1431	fi
1432	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1433
1434	# Test if first argument is correct
1435	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1436	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1437	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1438	return
1439	fi
1440
1441	# Test if the file exist.
1442	# Exit with error if the file does not exist for the case blocker or force.
1443	# Only return for the case nonblocker.
1444	if [ ! -f ${filein} ] ; then
1445	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1446	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1447	else
1448	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1449	fi
1450	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1451	return
1452	fi
1453
1454	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1455	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1456	if [ ${type} = nonblocker ] ; then
1457	# This is a nonblocker case, print warning but do nothing else
1458	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1459	else
1460	# This is a blocker or force case : stop now
1461	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1462	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1463	return
1464	fi
1465	fi
1466
1467	# Check if AUTO is set on the same line as keyid and keyattrib
1468	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1469	# Modification will be done
1470	modify=yes
1471	else
1472	if [ ${type} = blocker ] ; then
1473	# Exit, the variable must be set to AUTO
1474	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1475	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1476	return
1477	elif [ ${type} = nonblocker ] ; then
1478	# Nothing will be done
1479	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1480	modify=no
1481	elif [ ${type} = force ] ; then
1482	# Force modification
1483	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1484	modify=yes
1485	fi
1486	fi
1487
1488	# Do the modifcation now
1489	if [ ${modify} = yes ] ; then
1490	if [ ${keyattrib} = NONE ] ; then
1491	# Case to modify the variable itself
1492	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1493	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1494	else
1495	# Check if keyattrib is set on the same line as keyid
1496	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1497	# Case to modify the attribute value
1498	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1499	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1500	else
1501	# Case to add the attribute and its value
1502	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1503	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1504	fi
1505	fi
1506	\mv ${filein}.tmp ${filein}
1507	fi
1508	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1509	}
1510
1511	#=======================================================================
1512	function IGCM_comp_Update
1513	{
1514	IGCM_debug_PushStack "IGCM_comp_Update"
1515
1516	# Debug Print :
1517	echo
1518	IGCM_debug_Print 1 "IGCM_comp_Update"
1519	echo
1520
1521	typeset comp compname comptagname
1522	for comp in ${config_ListOfComponents[*]} ; do
1523	# Define component
1524	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1525	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1526
1527	# Debug Print
1528	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1529	# UPDATE component
1530	${comp}_Update
1531
1532	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1533	if [ -f timeseries_def_${compname}.xml ]; then
1534	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1535	for line in $( cat ts.temp.${compname}.txt ); do
1536	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1537	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1538	case ${output_freq} in
1539	Y\|y)
1540	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1541	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1542	;;
1543	MO\|mo)
1544	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1545	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1546	;;
1547	D\|d)
1548	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1549	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1550	;;
1551	S\|s)
1552	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1553	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1554	;;
1555	esac
1556	done
1557	fi
1558
1559	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1560	if [ -f dr2xml_${compname}.xml ]; then
1561	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1562	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1563
1564	# Modify path from dr2xml_{compname}.xml
1565	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1566
1567	# Overwrite the original file
1568	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1569	fi
1570	done
1571
1572	IGCM_debug_PopStack "IGCM_comp_Update"
1573	}
1574
1575	#=======================================================================
1576	function IGCM_comp_Finalize
1577	{
1578	IGCM_debug_PushStack "IGCM_comp_Finalize"
1579
1580	# Debug Print :
1581	echo
1582	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1583	echo
1584
1585	typeset ListTextName TextName0
1586	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1587	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1588	typeset -Z4 j4 #BASH declare j4
1589	typeset list_file nlist_file
1590	typeset compactoutputs
1591
1592	# Initialize array hosting list of rebuilded files to copy
1593	unset rebuildedActionsList
1594
1595	# Text compacting options
1596	compactoutputs=false
1597	if [ X${JobType} != XRUN ] ; then
1598	compactoutputs=true
1599	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1600	compactoutputs=true
1601	fi
1602
1603	# Prepare headers for the shell dedicated to offline rebuild
1604	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1605	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1606	if [ ${DRYRUN} -le 1 ] ; then
1607	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1608	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1609	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1610	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1611	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1612	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1613	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1614	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1615	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1616	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1617	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1618	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1619	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1620	fi
1621	fi
1622
1623	for comp in ${config_ListOfComponents[*]} ; do
1624	# Define component
1625	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1626	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1627
1628	# Debug Print
1629	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1630	# FINALIZE component
1631	${comp}_Finalize
1632
1633	card=${SUBMIT_DIR}/COMP/${compname}.card
1634
1635	# Save Output Text files of models
1636	#---------------------------------
1637	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1638	IGCM_card_DefineArrayFromOption ${card} OutputText List
1639	ListTextName=${compname}_OutputText_List
1640
1641	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1642	if [ X${TextName0} != X${NULL_STR} ] ; then
1643	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1644
1645	(( i=0 ))
1646	until [ $i -eq $NbFiles ]; do
1647	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1648	eval file_out=${PREFIX}_${file_in}
1649
1650	(( i=i+1 ))
1651
1652	unset list_file
1653	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1654	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1655	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 )
1656	nlist_file=${#list_file[@]}
1657	if [ ${nlist_file} -gt 1 ] ; then
1658	if ( ${compactoutputs} ) ; then
1659	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1660	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1661	echo ${list_file[*]} > ${file_out}
1662	echo "" >> ${file_out}
1663
1664	(( i_ = 0 ))
1665	for file in ${list_file[@]} ; do
1666	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1667	echo "\| " ${i_} " " ${file} >> ${file_out}
1668	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1669	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1670	echo "" >> ${file_out}
1671	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1672	(( i_ = i_ + 1 ))
1673	done
1674	if ( ${ExecutionFail} ) ; then
1675	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1676	fi
1677
1678	if [ X${Pack} = Xtrue ] ; then
1679	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1680	else
1681	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1682	fi
1683
1684	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1685	else
1686	for file in ${list_file[@]} ; do
1687	if ( ${ExecutionFail} ) ; then
1688	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1689	fi
1690
1691	if [ X${Pack} = Xtrue ] ; then
1692	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1693	else
1694	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1695	fi
1696
1697	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1698	done
1699	fi
1700	else
1701	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1702	eval IGCM_sys_Mv ${file_in}* ${file_in}
1703	fi
1704
1705	if ( ${ExecutionFail} ) ; then
1706	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1707	fi
1708
1709	if [ X${Pack} = Xtrue ] ; then
1710	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1711	else
1712	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1713	fi
1714	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1715	fi
1716	done
1717	fi
1718
1719	# Save Restarts files
1720	#--------------------
1721	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1722	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1723	ListFilesName=${compname}_RestartFiles_List
1724	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1725
1726	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1727	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1728
1729	(( i=0 ))
1730	until [ $i -ge $NbFiles ]; do
1731	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1732	eval file_in=${file_in_}
1733
1734	(( i_ = i+1 ))
1735	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1736	eval file_out=${file_out_}
1737
1738	(( i_ = i+2 ))
1739	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1740	eval file_outin=${file_outin_}
1741
1742	generic_restart_file_name_in=$( basename ${file_in} .nc )
1743	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1744	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1745
1746	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1747	if [ ${nb_restart_file} -gt 1 ] ; then
1748	j=0 # BASH LINE NOT NEEDED
1749	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1750	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1751	j4=${j} # BASH LINE NOT NEEDED
1752	if [ X${Pack} = Xtrue ] ; then
1753	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1754	else
1755	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1756	fi
1757	if [ ! ${file_in} = ${file_outin} ] ; then
1758	if ( ${ExitFlag} ) ; then
1759	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1760	else
1761	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1762	fi
1763	fi
1764	(( j=j+1 )) # BASH LINE NOT NEEDED
1765	done
1766	else
1767	if [ X${Pack} = Xtrue ] ; then
1768	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1769	else
1770	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1771	fi
1772	if [ ! ${file_in} = ${file_outin} ] ; then
1773	if ( ${ExitFlag} ) ; then
1774	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1775	else
1776	IGCM_sys_Mv ${file_in} ${file_outin}
1777	fi
1778	fi
1779	fi
1780
1781	(( i=i+3 ))
1782	done
1783	else
1784	if [ X${FileName0} != XNONE ] ; then
1785	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1786	else
1787	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1788	fi
1789	fi
1790
1791	# Save Output files
1792	#------------------
1793	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1794	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1795	ListFilesName=${compname}_OutputFiles_List
1796	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1797
1798	if [ X${FileName0} != X${NULL_STR} ] ; then
1799	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1800
1801	(( i=0 ))
1802	until [ $i -ge $NbFiles ]; do
1803	SaveOnArchive=true
1804	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1805	eval file_in=${file_in_}
1806	(( i_ = i+1 ))
1807	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1808	eval file_out=${file_out_}
1809	#
1810	# Override file_out path remplacing R_SAVE by R_BUFR
1811	#
1812	if [ X${Pack} = Xtrue ] ; then
1813	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1814	fi
1815	#
1816	# Not necessarily the best option. /!\ Potential side effects /!\
1817	#
1818	(( i_ = i+2 ))
1819	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1820	#
1821	generic_file_name=$( basename ${file_in} .nc )
1822	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1823	#
1824	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1825	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1826	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1827	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1828	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1829	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1830	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1831	#
1832	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
1833	if [ ${file_in} = output.abort.nc ] ; then
1834	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
1835	else
1836	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
1837	fi
1838	else
1839	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1840	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1841
1842	# Prepare the shell dedicated to offline rebuild
1843	if [ $DRYRUN -le 1 ]; then
1844	if [ ${file_in} = histstn.nc ] ; then
1845	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1846	else
1847	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1848	fi
1849	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1850	fi
1851	#
1852	# Load Patch we need to apply and apply
1853	if [ $DRYRUN -le 1 ]; then
1854	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1855	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1856	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1857	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1858	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1859	done
1860	fi
1861	fi
1862	#
1863	if [ $DRYRUN -le 1 ]; then
1864	if [ X${Pack} = Xtrue ] ; then
1865	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1866	else
1867	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1868	fi
1869	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1870	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1871	fi
1872	SaveOnArchive=false
1873	fi
1874	fi
1875	#
1876	if [ ${SaveOnArchive} = true ] ; then
1877	#
1878	# Rebuild has been done online or it was not needed
1879	#
1880	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1881	#
1882	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1883	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1884	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1885	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1886	#
1887	if [ $DRYRUN -le 1 ]; then
1888	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1889	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1890	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1891	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1892	done
1893	#
1894	if [ X${Pack} = Xtrue ] ; then
1895	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1896	else
1897	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1898	fi
1899	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1900	#
1901	fi
1902	else
1903	#
1904	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1905	#
1906	if [ X${Pack} = Xtrue ] ; then
1907	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1908	else
1909	IGCM_sys_Put_Out ${file_in} ${file_out}
1910	fi
1911	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1912	if [ ${nb_rebuild_file} -gt 1 ] ; then
1913	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1914	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1915	done
1916	fi
1917	fi
1918	fi
1919	(( i=i+3 ))
1920	done
1921	fi
1922	echo
1923	done
1924	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1925	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1926	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1927	i=0
1928	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1929	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1930	(( i=i+1 ))
1931	done
1932	fi
1933	IGCM_debug_PopStack "IGCM_comp_Finalize"
1934	}

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