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libIGCM_comp.ksh @ 1628

Last change on this file since 1628 was 1628, checked in by aclsce, 3 months ago
Modified to add the functionality to run many instances in concurrent mode. Only available on Irene SKL with slurm.
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: 85.9 KB

Line
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 +1))
248	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
249	eval Testvar=${Testvar_}
250	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
251	((i = i+4))
252	else
253	(( i=i+3 ))
254	fi
255	done
256	fi
257	# Debug Print
258	IGCM_debug_Print 3 "Initialize ${compname} with driver."
259	# INIT component
260	${comp}_Initialize
261	echo
262	done
263
264	IGCM_debug_PopStack "IGCM_comp_Initialize"
265	}
266
267	#=======================================================================
268	function IGCM_comp_PrepareDeletedFiles
269	{
270	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
271
272	if [ X${2} != X. ] ; then
273	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
274	else
275	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
276	fi
277
278	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
279	}
280
281	#=======================================================================
282	function IGCM_comp_PrepareXiosFiles
283	{
284	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
285
286	typeset file
287	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
288
289	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
290	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
291	fi
292	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
293	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
294	fi
295	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
296	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
297	fi
298
299	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
300	}
301
302	#=======================================================================
303	function IGCM_comp_GetInputInitialStateFiles
304	{
305	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
306
307	# Debug Print :
308	echo
309	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
310	echo
311
312	# Only the first time step need InitialStateFiles
313	# otherwise it's BoundaryConditions
314	if ( ${FirstInitialize} ) ; then
315	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
316	typeset file_in_ file_in file_out_ file_out do_init
317	for comp in ${config_ListOfComponents[*]} ; do
318	number_rundir=$(echo ${comp} \| sed 's/[^0-9]*//g')
319	if [ X${number_rundir} != X ] ; then
320	[ ! -d RUNDIR_${number_rundir} ] && mkdir RUNDIR_${number_rundir}
321	cd RUNDIR_${number_rundir} ;
322	fi
323	# Initialize
324	do_init="y"
325	# Do we need to bring initial state file for this component
326	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
327	eval do_init="n"
328	else
329	# Read component Restarts parameters
330	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
331	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
332	if [ "${do_start}" = "y" ] ; then
333	do_init="n"
334	else
335	do_init="y"
336	fi
337	fi
338
339	if [ "${do_init}" = "y" ] ; then
340	# Define component
341	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
342	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
343
344	# Debug Print :
345	IGCM_debug_Print 3 "Initialisation files ${compname}"
346
347	card=${SUBMIT_DIR}/COMP/${compname}.card
348
349	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
350	ListFilesName=${compname}_InitialStateFiles_List
351
352	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
353	if [ X${FileName0} != X${NULL_STR} ] ; then
354	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
355	(( i=0 ))
356	until [ $i -ge $NbFiles ]; do
357	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
358	eval file_in=${file_in_}
359	(( i_ = i+1 ))
360	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
361	eval file_out=${file_out_}
362
363	IGCM_sys_IsFileArchived ${file_in}
364	if [ $? = 0 ] ; then
365	IGCM_sys_Get ${file_in} ${file_out}
366	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
367	else
368	IGCM_sys_Cp ${file_in} ${file_out}
369	fi
370	(( i=i+2 ))
371	done
372	fi
373	fi
374	if [ X${number_rundir} != X ] ; then
375	cd $RUN_DIR
376	fi
377	done
378	fi
379	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
380	}
381
382	#=======================================================================
383	# Definition of Smooth modulo function
384	# usage :
385	# IGCM_SmoothModulo StringModulo value
386	#
387	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
388	# [min]:[modulo:][max]
389	# where :
390	# [] value are optionnals;
391	# empty min equal 1
392	# empty max equal infinity
393	# modulo not given or empty equal 1
394	# empty string or just ':' equal always.
395	#
396	# value : the value to test with the definition
397	#
398	# return : true(1)/false(0)
399	function IGCM_SmoothModulo
400	{
401	IGCM_debug_PushStack "IGCM_SmoothModulo"
402	typeset defVector ModValue
403
404	eval set +A defVector -- $( echo "${1}" \| \
405	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
406
407	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
408	arr[1]=${defVector[0]}
409	arr[2]=${defVector[2]}
410
411	# Test limits :
412	# ${defVector[0]} <= ${2} <= ${defVector[2]}
413	# or ${defVector[2]} == -1
414	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
415	# Test modulo
416	ModValue=$( expr $ ${2} - ${defVector[0]} $ % ${defVector[1]} )
417	if [ ${ModValue} -eq 0 ] ; then
418	arr[3]=true
419	echo ${arr[@]}
420	IGCM_debug_PopStack "IGCM_SmoothModulo"
421	return 1
422	else
423	arr[3]=false
424	echo ${arr[@]}
425	IGCM_debug_PopStack "IGCM_SmoothModulo"
426	return 0
427	fi
428	else
429	arr[3]=false
430	echo ${arr[@]}
431	IGCM_debug_PopStack "IGCM_SmoothModulo"
432	return 0
433	fi
434	}
435
436	#=======================================================================
437	function IGCM_comp_GetInputSmoothFiles
438	{
439	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
440
441	# Debug Print :
442	echo
443	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
444	echo
445
446	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
447	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
448
449	for comp in ${config_ListOfComponents[*]} ; do
450	number_rundir=$(echo ${comp} \| sed 's/[^0-9]*//g')
451	if [ X${number_rundir} != X ] ; then
452	[ ! -d RUNDIR_${number_rundir} ] && mkdir RUNDIR_${number_rundir}
453	cd RUNDIR_${number_rundir} ;
454	fi
455	# Define component
456	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
457	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
458
459	# Debug Print :
460	IGCM_debug_Print 3 "Smooth files ${compname}"
461
462	card=${SUBMIT_DIR}/COMP/${compname}.card
463
464	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
465	ListFilesName=${compname}_SmoothFiles_List
466	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
467
468	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
469	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
470
471	(( i=0 ))
472	until [ $i -ge $NbFiles ]; do
473	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
474	eval file_in=${file_in_}
475	(( i_ = i+1 ))
476	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
477	eval file_out=${file_out_}
478
479	# define CumulPeriod definition for this file
480	(( i__ = i+2 ))
481	eval SmoothDef=\${${ListFilesName}[$i__]}
482	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
483	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
484	j=1
485	for val in ${aux} ; do
486	[ ${j} -eq 1 ] && SmoothMin=${val}
487	[ ${j} -eq 2 ] && SmoothMax=${val}
488	[ ${j} -eq 3 ] && ret=${val}
489	(( j=j+1 ))
490	done
491	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
492	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
493
494	IGCM_sys_IsFileArchived ${file_in}
495	if [ $? = 0 ] ; then
496	IGCM_sys_Get ${file_in} ${file_out}
497	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
498	else
499	IGCM_sys_Cp ${file_in} ${file_out}
500	fi
501	fi
502	(( i=i+3 ))
503	done
504	fi
505	if [ X${number_rundir} != X ] ; then
506	cd $RUN_DIR
507	fi
508	done
509
510	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
511	}
512
513	#=======================================================================
514	function IGCM_comp_GetInputBoundaryFiles
515	{
516	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
517
518	# Debug Print :
519	echo
520	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
521	echo
522
523	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
524	typeset file_in_ file_in file_out_ file_out
525
526	if [ ${Period} = 1 ]; then
527	ListFixBoundary=" "
528	fi
529
530	for comp in ${config_ListOfComponents[*]} ; do
531	number_rundir=$(echo ${comp} \| sed 's/[^0-9]*//g')
532	if [ X${number_rundir} != X ] ; then
533	[ ! -d RUNDIR_${number_rundir} ] && mkdir RUNDIR_${number_rundir}
534	cd RUNDIR_${number_rundir} ;
535	fi
536
537	# Define component
538	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
539	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
540
541	# Debug Print :
542	IGCM_debug_Print 3 "Boundary files ${compname}"
543
544	card=${SUBMIT_DIR}/COMP/${compname}.card
545
546	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
547	ListFilesName=${compname}_BoundaryFiles_List
548	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
549
550	if [ X${FileName0} != X${NULL_STR} ] ; then
551	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
552
553	(( i=0 ))
554	until [ $i -ge $NbFiles ]; do
555	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
556	eval file_in=${file_in_}
557	(( i_ = i+1 ))
558	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
559	eval file_out=${file_out_}
560
561	IGCM_sys_IsFileArchived ${file_in}
562	if [ $? = 0 ] ; then
563	IGCM_sys_Get ${file_in} ${file_out}
564	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
565	else
566	IGCM_sys_Cp ${file_in} ${file_out}
567	fi
568
569	(( i=i+2 ))
570	done
571	fi
572
573	# Get non deleted files
574	if [ ${Period} = 1 ]; then
575
576	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
577	ListFilesName=${compname}_BoundaryFiles_ListNonDel
578	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
579
580	if [ X${FileName0} != X${NULL_STR} ] ; then
581	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
582
583	(( i=0 ))
584	until [ $i -ge $NbFiles ]; do
585	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
586	eval file_in=${file_in_}
587	(( i_ = i+1 ))
588	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
589	eval file_out=${file_out_}
590
591	IGCM_sys_IsFileArchived ${file_in}
592	if [ $? = 0 ] ; then
593	IGCM_sys_Get ${file_in} ${file_out}
594	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
595	else
596	IGCM_sys_Cp ${file_in} ${file_out}
597	fi
598
599	if [ X${file_out} != X. ] ; then
600	ListFixBoundary=${ListFixBoundary}" "${file_out}
601	else
602	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
603	fi
604
605	(( i=i+2 ))
606	done
607	fi
608	fi
609	if [ X${number_rundir} != X ] ; then
610	cd $RUN_DIR
611	fi
612	done
613
614	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
615	}
616
617	#=======================================================================
618	function IGCM_comp_DelFixeBoundaryFiles
619	{
620	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
621
622	# Debug Print :
623	echo
624	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
625	echo
626
627	ls -l ${ListFixBoundary}
628	rm -f ${ListFixBoundary}
629
630	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
631	}
632
633	#=======================================================================
634	function IGCM_comp_GetInputParametersFiles
635	{
636	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
637
638	# Debug Print :
639	echo
640	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
641	echo
642
643	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
644	for comp in ${config_ListOfComponents[*]} ; do
645	number_rundir=$(echo ${comp} \| sed 's/[^0-9]*//g')
646	if [ X${number_rundir} != X ] ; then
647	[ ! -d RUNDIR_${number_rundir} ] && mkdir RUNDIR_${number_rundir}
648	cd RUNDIR_${number_rundir} ;
649	fi
650	# Define component
651	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
652	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
653
654	# Initialize array hosting file_def and field_def files to check and/or modify
655	unset FieldDef
656	unset FileDef
657
658	# Debug Print :
659	IGCM_debug_Print 3 "Parameters ${compname}"
660
661	card=${SUBMIT_DIR}/COMP/${compname}.card
662
663	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
664	ListFilesName=${compname}_ParametersFiles_List
665	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
666
667	if [ X${FileName0} != X${NULL_STR} ] ; then
668	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
669
670	(( i=0 ))
671	until [ $i -ge $NbFiles ]; do
672	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
673	eval file_in=${file_in_}
674	(( i_ = i+1 ))
675	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
676	eval file_out=${file_out_}
677
678	IGCM_sys_Cp ${file_in} ${file_out}
679	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
680	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
681
682	(( i=i+2 ))
683	done
684	fi
685	if [ X${number_rundir} != X ] ; then
686	cd $RUN_DIR
687	fi
688
689	done
690
691	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
692	}
693
694	#=======================================================================
695	function IGCM_comp_GetInputRestartFiles
696	{
697	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
698
699	# Debug Print :
700	echo
701	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
702	echo
703
704	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
705	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
706	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
707	typeset file_in file_out file_in_ file_out_ file_in_Name
708	typeset -Z4 j4
709	#BASH declare j4
710
711	IsMatching=""
712
713	for comp in ${config_ListOfComponents[*]} ; do
714	number_rundir=$(echo ${comp} \| sed 's/[^0-9]*//g')
715	if [ X${number_rundir} != X ] ; then
716	[ ! -d RUNDIR_${number_rundir} ] && mkdir RUNDIR_${number_rundir}
717	cd RUNDIR_${number_rundir} ;
718	fi
719
720	# Define component
721	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
722	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
723	#
724	card=${SUBMIT_DIR}/COMP/${compname}.card
725	#
726	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
727	ListFilesName=${compname}_RestartFiles_List
728	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
729
730	# Debug Print :
731	IGCM_debug_Print 3 "restart ${compname}"
732
733	if ( ${FirstInitialize} ) ; then
734
735	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
736	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
737	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
738	CompOldName=IOS
739	config_IOS_Restart="n"
740	do_start="n"
741	config_IOS_RestartDate=-1
742	config_IOS_RestartJobName=${NULL_STR}
743	config_IOS_RestartPath=${NULL_STR}
744	else
745	eval config_${comp}_Restart="y"
746	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
747	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
748	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
749	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
750	eval CompOldName=${comp}
751	fi
752	else
753	# Read component Restarts parameters
754	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
755	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
756
757	if [ "${do_start}" = "y" ] ; then
758	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
759	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
760	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
761	else
762	eval config_${comp}_RestartDate=-1
763	eval config_${comp}_RestartJobName=${NULL_STR}
764	eval config_${comp}_RestartPath=${NULL_STR}
765	fi
766
767	eval CompOldName=\${config_${comp}_OldName}
768	if [ X${CompOldName} = X ] ; then
769	eval CompOldName=${comp}
770	fi
771
772	# Reinitialize IsMatching to allow searching for a different tar file for each component.
773	IsMatching=""
774	TarFileFound=""
775	fi
776
777	if [ "${do_start}" = "y" ] ; then
778
779	# Restore Restarts files
780	#-----------------------
781	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
782	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
783
784	(( i=1 ))
785	until [ $i -gt $NbFiles ]; do
786	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
787	eval file_in=${file_in_}
788	(( i_ = i+1 ))
789	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
790	eval file_out=${file_out_}
791
792	(( i_ = i+2 ))
793	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
794	if [ X${is_opt} = XOPTIONAL ] ; then
795	echo ${file_in} is optional
796	(( i=i+4 ))
797	else
798	is_opt="MANDATORY"
799	echo ${file_in} is mandatory
800	(( i=i+3 ))
801	fi
802	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=y)"
803
804	eval Date_tmp=\${config_${comp}_RestartDate}
805	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
806	# will be re-use
807	eval RestartPath=\${config_${comp}_RestartPath}
808	eval RestartJobName=\${config_${comp}_RestartJobName}
809	#
810	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
811	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
812
813	extension_in=$( echo ${file_in_Name##*.} )
814	extension_out=$( echo ${file_out##*.} )
815
816	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
817	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
818
819	Path_OUT=${Path_r}/${generic_restart_file_name_in}
820
821	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
822	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
823	Buffered=true
824	Archived=false
825	Tared=false
826	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
827	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
828	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
829	Buffered=false
830	Archived=true
831	Tared=false
832	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
833	else
834	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
835	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
836	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
837	Buffered=false
838	Archived=false
839	Tared=true
840	# Look after the tar file we want if we did not found it already
841	if [ X${IsMatching} = X ] ; then
842	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
843	if [ $? ] ; then
844	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
845	IsMatching=$( echo ${PotentialTarFile##*/} \| \
846	sed "s:_restart::" \| \
847	sed "s:^${RestartJobName}_::" \| \
848	sed "s:\.tar$::" \| \
849	gawk -F_ -v restartdate=${Date_r} \
850	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
851	if [ ! X${IsMatching} = X ] ; then
852	TarFileFound=${PotentialTarFile}
853	break
854	fi
855	done
856	fi
857	# Stop here if nothing has been found
858	if [ X${TarFileFound} = X ] ; then
859	IGCM_debug_Print 3 "Restart files were not found!"
860	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
861	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
862	if [ ${is_opt} = 'OPTIONAL' ] ; then
863	IGCM_debug_Print 3 "The restart file is optional. Now continue."
864	nb_restart_file=0
865	Tared=false
866	else
867	IGCM_debug_Exit "Please double check restart settings in config.card"
868	IGCM_debug_Verif_Exit
869	fi
870	fi
871	fi
872
873	if [ X${Tared} = Xtrue ] ; then
874	# The tar file exist but not sure all files are inside
875	IGCM_sys_PrepareTaredRestart ${TarFileFound}
876	TarFileLocation=$( basename ${TarFileFound} )
877	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in}*.${extension_in} \| wc -l )
878	if [ ${nb_files} -gt 0 ] ; then
879	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
880	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
881	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
882	else
883	# No file was found
884	if [ ${is_opt} = 'OPTIONAL' ] ; then
885	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
886	nb_restart_file=0
887	Tared=false
888	else
889	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
890	IGCM_debug_Exit "Please double check restart settings in config.card"
891	IGCM_debug_Verif_Exit
892	fi
893	fi
894	fi
895	fi
896
897	if [ ${nb_restart_file} -gt 1 ] ; then
898	j=0 # BASH LINE NOT NEEDED
899	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
900	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
901	j4=${j} # BASH LINE NOT NEEDED
902	if [ X${Buffered} = Xtrue ] ; then
903	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
904	elif [ X${Archived} = Xtrue ] ; then
905	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
906	elif [ X${Tared} = Xtrue ] ; then
907	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
908	fi
909	(( j=j+1 )) #BASH LINE NOT NEEDED
910	done
911
912	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
913	if [ X${OCE_PROC_MPI} != X ] ; then
914	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
915	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
916	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
917	fi
918	fi
919	else
920	if [ X${Buffered} = Xtrue ] ; then
921	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
922	elif [ X${Archived} = Xtrue ] ; then
923	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
924	elif [ X${Tared} = Xtrue ] ; then
925	if [ -f ${comp}_${file_in_Name} ] ; then
926	# The file exixt
927	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
928	elif [ ${is_opt} = 'OPTIONAL' ] ; then
929	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
930	else
931	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
932	IGCM_debug_Exit "Please double check restart settings in config.card"
933	IGCM_debug_Verif_Exit
934	fi
935	fi
936	fi
937	done
938	else
939	if [ X${FileName0} != XNONE ] ; then
940	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
941	else
942	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
943	fi
944	fi
945	fi
946	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
947	# if not FirstInitialize and first loop of this job
948
949	# Restore Restarts files
950	#-----------------------
951	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
952	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
953
954	(( i=1 ))
955	until [ $i -gt $NbFiles ]; do
956	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
957	eval file_in=${file_in_}
958
959	(( i_ = i+1 ))
960	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
961	eval file_out=${file_out_}
962
963	(( i_ = i+2 ))
964	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
965	if [ X${is_opt} = XOPTIONAL ] ; then
966	# Read a forth argument
967	echo ${file_in} is optional
968	(( i=i+4 ))
969	else
970	is_opt="MANDATORY"
971	echo ${file_in} is mandatory
972	(( i=i+3 ))
973	fi
974
975	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=n)"
976
977	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
978
979	extension_in=$( echo ${file_in_Name##*.} )
980	extension_out=$( echo ${file_out##*.} )
981
982	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
983	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
984
985	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
986	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
987
988	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
989	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
990	Buffered=true
991	Archived=false
992	Tared=false
993	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
994	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
995	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
996	Buffered=false
997	Archived=true
998	Tared=false
999	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
1000	else
1001	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
1002	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
1003	Buffered=false
1004	Archived=false
1005	Tared=true
1006	# Look after the tar file we want if we did not found it already
1007	if [ X${IsMatching} = X ] ; then
1008	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
1009	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
1010	if [ ! X${IsMatching} = X ] ; then
1011	TarFileFound=${PotentialTarFile}
1012	break
1013	fi
1014	done
1015	fi
1016	# Stop here if nothing has been found
1017	if [ X${TarFileFound} = X ] ; then
1018	IGCM_debug_Print 3 "Restart files were not found!"
1019	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
1020	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
1021	if [ ${is_opt} = 'OPTIONAL' ] ; then
1022	IGCM_debug_Print 3 "The restart file is optional. Now continue."
1023	nb_restart_file=0
1024	Tared=false
1025	else
1026	IGCM_debug_Print 3 "The restart file is mandatory."
1027	IGCM_debug_Exit "Please double check restart settings in config.card"
1028	IGCM_debug_Verif_Exit
1029	fi
1030	else
1031	# The tar file exist but not sure all files are inside
1032	IGCM_sys_PrepareTaredRestart ${TarFileFound}
1033	TarFileLocation=$( basename ${TarFileFound} )
1034	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in}*.${extension_in} \| wc -l )
1035	if [ ${nb_files} -gt 0 ] ; then
1036	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
1037	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
1038	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
1039	else
1040	# No file was found
1041	if [ ${is_opt} = 'OPTIONAL' ] ; then
1042	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
1043	nb_restart_file=0
1044	Tared=false
1045	else
1046	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
1047	IGCM_debug_Exit "Please double check restart settings in config.card"
1048	IGCM_debug_Verif_Exit
1049	fi
1050	fi
1051
1052	fi
1053	fi
1054
1055	if [ ${nb_restart_file} -gt 1 ] ; then
1056	j=0 # BASH LINE NOT NEEDED
1057	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1058	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1059	j4=${j} # BASH LINE NOT NEEDED
1060	if [ X${Buffered} = Xtrue ] ; then
1061	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1062	elif [ X${Archived} = Xtrue ] ; then
1063	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1064	elif [ X${Tared} = Xtrue ] ; then
1065	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1066	fi
1067	(( j=j+1 )) # BASH LINE NOT NEEDED
1068	done
1069	else
1070	if [ X${Buffered} = Xtrue ] ; then
1071	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
1072	elif [ X${Archived} = Xtrue ] ; then
1073	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
1074	elif [ X${Tared} = Xtrue ] ; then
1075	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
1076	fi
1077	fi
1078	done
1079	else
1080	if [ X${FileName0} != XNONE ] ; then
1081	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
1082	else
1083	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
1084	fi
1085	fi
1086	fi
1087	if [ X${number_rundir} != X ] ; then
1088	cd $RUN_DIR
1089	fi
1090	done
1091
1092	NbFiles=$( ls * 2> /dev/null \| wc -l )
1093	if [ ${NbFiles} -gt 0 ] ; then
1094	IGCM_sys_Chmod u+rw *
1095	fi
1096
1097	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
1098	}
1099
1100	#=======================================================================
1101	function IGCM_comp_GetInputBinaryFiles
1102	{
1103	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
1104
1105	# Debug Print :
1106	echo
1107	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
1108	echo
1109
1110	# Clean up previous pass
1111	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
1112
1113	typeset comp ExeNameIn ExeNameOut byPass
1114	typeset compilerNmbr compilerUnit compilerFull
1115	byPass=false
1116	for comp in ${config_ListOfComponents[*]} ; do
1117	number_rundir=$(echo ${comp} \| sed 's/[^0-9]*//g')
1118	if [ X${number_rundir} != X ] ; then
1119	[ ! -d RUNDIR_${number_rundir} ] && mkdir RUNDIR_${number_rundir}
1120	cd RUNDIR_${number_rundir} ;
1121	fi
1122
1123	# Define component
1124
1125	# Copy executable for this component
1126	eval ExeNameIn=\${config_Executable_${comp}[0]}
1127	eval ExeNameOut=\${config_Executable_${comp}[1]}
1128	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
1129	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
1130	# The executable is set in config.card and is different from ""
1131	# Use eval to expand ExeNameIn if variables are used in the name
1132	eval ExeNameIn=${ExeNameIn}
1133	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1134	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1135	fi
1136	fi
1137
1138	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1139	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1140	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1141	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1142	fi
1143	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1144	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1145	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1146	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1147	fi
1148	fi
1149
1150	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1151	# Get the compiler version
1152	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1153	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1154	# Save it
1155	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1156	[ X${compilerFull} = X ] && byPass=true
1157	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1158	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1159	fi
1160	if [ X${number_rundir} != X ] ; then
1161	cd $RUN_DIR
1162	fi
1163
1164	done
1165
1166	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1167	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1168
1169	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1170	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1171	fi
1172
1173
1174	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1175	}
1176
1177	#=======================================================================
1178	function IGCM_comp_PeriodStart
1179	{
1180	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1181
1182	# Debug Print :
1183	echo
1184	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1185	echo
1186
1187	typeset ExeNameIn ExeNameOut
1188	typeset comp compname comptagname
1189	for comp in ${config_ListOfComponents[*]} ; do
1190	# Define component
1191	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1192	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1193
1194	# Copy executable for this component
1195	eval ExeNameIn=\${config_Executable_${comp}[0]}
1196	eval ExeNameIn=${ExeNameIn}
1197	eval ExeNameOut=\${config_Executable_${comp}[1]}
1198
1199	# Debug Print
1200	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1201	# UPDATE component
1202	${comp}_PeriodStart 2> /dev/null
1203
1204	done
1205
1206	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1207	}
1208
1209
1210
1211	#=======================================================================
1212	function IGCM_comp_modifyFile
1213	{
1214	#
1215	# syntax: IGCM_comp_modifyFile filein key [value]
1216	#
1217	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1218	#
1219	# This function is used to replace a pattern in a file for a specific variable.
1220	#
1221	# Arguments:
1222	# - filein : the file in run directory in which the variable should be set
1223	# - key : the variable to modify
1224	# - value : the value to set the key equal to
1225	#
1226	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1227
1228	typeset filein key value pattern
1229
1230	# Set local variables and test the arguments
1231	if [ $# = 3 ] ; then
1232	# Normal case with 3 arguments
1233	filein=$1 ; key=$2 ; value=$3
1234	else
1235	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1236	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1237	return
1238	fi
1239	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1240
1241	# Test if the file exist
1242	if [ ! -f ${filein} ] ; then
1243	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1244	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1245	return
1246	fi
1247
1248	# Read the line with key in the file without the comments
1249	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1250
1251	# Verify the existance of the pattern
1252	if [ X"${pattern}" = X ] ; then
1253	# Variable key is not set in filein, stop.
1254	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1255	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1256	return
1257	fi
1258
1259	# Now change key in filein
1260	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1261	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1262	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1263	\mv ${filein}.tmp ${filein}
1264
1265	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1266	}
1267
1268	#=======================================================================
1269	function IGCM_comp_modifyDefFile
1270	{
1271	#
1272	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1273	#
1274	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1275	#
1276	# This function is used to modify a parameter file for a specific variable.
1277	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1278	# This function can be used in the comp.driver files for the components.
1279	#
1280	# Arguments:
1281	# - type : first argument must be blocker, nonblocker or force
1282	# For "blocker" case, the variable must be attributed the keyworld AUTO
1283	# otherwise this function will exit.
1284	# For "nonblocker" case, the user can remove or modify the variable. For
1285	# this case, as long as AUTO is not set, no modification will be done.
1286	# For "force" case, the variable will be modified even if it is not set to AUTO
1287	# - filein : the file in run directory of .def type in which the variable should be set
1288	# - key : the variable to modify
1289	# - value : the value to set the key equal to, optional. If value is not set or if
1290	# value=DEFAULT, then a default value must be given in filein using syntax :
1291	# key= AUTO : DEFAULT=def_value
1292	#
1293	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1294
1295	typeset type filein key value
1296	typeset filelist nb_occ modify
1297
1298	# Set local variables and test the arguments
1299	if [ $# = 4 ] ; then
1300	# Normal case with 4 arguments
1301	type=$1 ; filein=$2 ; key=$3 ; value=$4
1302	elif [ $# = 3 ] ; then
1303	# Normal case with 3 arguments
1304	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1305	else
1306	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1307	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1308	return
1309	fi
1310	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1311
1312	# Test if first argument is correct
1313	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1314	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1315	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1316	return
1317	fi
1318
1319	# Test if the file exist.
1320	# Exit with error if the file does not exist for the case blocker or force.
1321	# Only return for the case nonblocker.
1322	if [ ! -f ${filein} ] ; then
1323	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1324	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1325	else
1326	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1327	fi
1328	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1329	return
1330	fi
1331
1332	# Define list of files to test using all files with suffix .def (except used*.def)
1333	filelist=$( ls *def \| grep -v used )
1334
1335	# Count number of occurances for the key in all files
1336	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1337
1338	# Test if key is set several times
1339	if [ ${nb_occ} -gt 1 ] ; then
1340	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1341	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1342	return
1343	fi
1344
1345	# Treatement according to different cases
1346	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1347	# Stop if the key is never set and the function is blocker
1348	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1349	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1350	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1351	# The key is not set but it is a nonblocker call so nothing is done.
1352	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1353	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1354	modify=no
1355	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1356	# Variable key is not set in filein, stop.
1357	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1358	fi
1359
1360	# Check if AUTO is set in the filein on the same line as the key variable
1361	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1362	# Modification will be done for all cases
1363	modify=yes
1364	else
1365	# The variable was not set to AUTO
1366	if [ ${type} = blocker ] ; then
1367	# Exit because this is a blocker call
1368	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1369	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1370	return
1371	elif [ ${type} = nonblocker ] ; then
1372	# Do nothing. Suppose that the user did set the variable correct
1373	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1374	modify=no
1375	elif [ ${type} = force ] ; then
1376	# Force modification
1377	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1378	modify=yes
1379	fi
1380	fi
1381
1382	# Do the modifcation now
1383	if [ ${modify} = yes ] ; then
1384
1385	# For option DEFAULT, read default value from file.
1386	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1387	# Case to set DEFAULT value
1388	# Read default value from filein
1389	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1390
1391	if [ X"${value}" = X ] ; then
1392	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1393	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1394	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1395	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1396	return
1397	fi
1398	fi
1399
1400	# Now change key in filein
1401	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1402	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1403	\mv ${filein}.tmp ${filein}
1404	fi
1405	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1406	}
1407
1408	#=======================================================================
1409	function IGCM_comp_modifyNamelist
1410	{
1411	#
1412	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1413	#
1414	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1415	#
1416	# This function is used to modify a parameter file for a specific variable.
1417	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1418	# This function can be used in the comp.driver files for the components.
1419	#
1420	# Arguments:
1421	# - type : first argument must be blocker, nonblocker or force
1422	# For "blocker" case, the variable must be attributed the keyworld AUTO
1423	# otherwise this function will exit.
1424	# For "nonblocker" case, the user can remove or modify the variable. For
1425	# this case, as long as AUTO is not set, no modification will be done.
1426	# For "force" case, the variable will be modified even if it is not set to AUTO
1427	# - filein : the file in run directory of .def type in which the variable should be set
1428	# - key : the variable to modify
1429	# - value : the value to set the key equal to, optional. If value is not set or if
1430	# value=DEFAULT, then a default value must be given in filein using syntax :
1431	# key= AUTO : DEFAULT=def_value
1432	#
1433	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1434
1435	typeset type filein key value pattern modify
1436
1437	# Set local variables and test the arguments
1438	if [ $# = 4 ] ; then
1439	# Normal case with 4 arguments
1440	type=$1 ; filein=$2 ; key=$3 ; value=$4
1441	elif [ $# = 3 ] ; then
1442	# Normal case with 3 arguments
1443	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1444	else
1445	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1446	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1447	return
1448	fi
1449	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1450
1451	# Test if first argument is correct
1452	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1453	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1454	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1455	return
1456	fi
1457
1458	# Test if the file exist.
1459	# Exit with error if the file does not exist for the case blocker or force.
1460	# Only return for the case nonblocker.
1461	if [ ! -f ${filein} ] ; then
1462	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1463	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1464	else
1465	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1466	fi
1467	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1468	return
1469	fi
1470
1471	# Read the line with key in the file without the comments
1472	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1473
1474	# Verify the existance of the pattern
1475	if [ X"$pattern" = X ] ; then
1476	# Variable key is not set in filein, stop.
1477	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1478	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1479	return
1480	fi
1481
1482	# Check if the variable is set to AUTO in the filein
1483	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1484	# Modification will be done for all cases
1485	modify=yes
1486	else
1487	# The variable was not set to AUTO
1488	if [ ${type} = blocker ] ; then
1489	# Exit because this is a blocker call
1490	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1491	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1492	return
1493	elif [ ${type} = nonblocker ] ; then
1494	# Do nothing. Suppose that the user did set the variable correct
1495	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1496	modify=no
1497	elif [ ${type} = force ] ; then
1498	# Force modification
1499	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1500	modify=yes
1501	fi
1502	fi
1503
1504	# Do the modifcation now
1505	if [ ${modify} = yes ] ; then
1506
1507	# For option DEFAULT, read default value from file.
1508	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1509	# Case to set DEFAULT value
1510	# Read default value from filein
1511	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1512
1513	if [ X"${value}" = X ] ; then
1514	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1515	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1516	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1517	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1518	return
1519	fi
1520	fi
1521
1522	# Now change key in filein
1523	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1524	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1525	\mv ${filein}.tmp ${filein}
1526	fi
1527	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1528	}
1529
1530	#=======================================================================
1531	function IGCM_comp_modifyXmlFile
1532	{
1533	#
1534	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1535	#
1536	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1537	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1538	#
1539	# This function is used to modify the value for a specific attribute and variable id.
1540	# The file must be a valid xml file.
1541	# This function can be used in the comp.driver files for the components.
1542	#
1543	# Arguments:
1544	# - type : first argument must be blocker, nonblocker or force.
1545	# For "blocker" case, the variable must be attributed the keyworld AUTO
1546	# otherwise this function will exit.
1547	# For "nonblocker" case, the user can remove or modify the variable. For
1548	# this case, as long as AUTO is not set, no modification will be done.
1549	# For "force" case, the variable will be modified even if it is not set to AUTO
1550	# - filein : the file in run directory of .xml type in which the variable should be set
1551	# - keyid : the variable to modify
1552	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1553	# - value : the value to set in the filein
1554	#
1555	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1556
1557	typeset type filein keyid keyattrib value modify
1558
1559	# Set local variables and test the arguments
1560	if [ $# = 5 ] ; then
1561	# Normal case with 4 arguments
1562	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1563	else
1564	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1565	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1566	return
1567	fi
1568	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1569
1570	# Test if first argument is correct
1571	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1572	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1573	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1574	return
1575	fi
1576
1577	# Test if the file exist.
1578	# Exit with error if the file does not exist for the case blocker or force.
1579	# Only return for the case nonblocker.
1580	if [ ! -f ${filein} ] ; then
1581	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1582	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1583	else
1584	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1585	fi
1586	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1587	return
1588	fi
1589
1590	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1591	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1592	if [ ${type} = nonblocker ] ; then
1593	# This is a nonblocker case, print warning but do nothing else
1594	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1595	else
1596	# This is a blocker or force case : stop now
1597	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1598	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1599	return
1600	fi
1601	fi
1602
1603	# Check if AUTO is set on the same line as keyid and keyattrib
1604	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1605	# Modification will be done
1606	modify=yes
1607	else
1608	if [ ${type} = blocker ] ; then
1609	# Exit, the variable must be set to AUTO
1610	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1611	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1612	return
1613	elif [ ${type} = nonblocker ] ; then
1614	# Nothing will be done
1615	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1616	modify=no
1617	elif [ ${type} = force ] ; then
1618	# Force modification
1619	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1620	modify=yes
1621	fi
1622	fi
1623
1624	# Do the modifcation now
1625	if [ ${modify} = yes ] ; then
1626	if [ ${keyattrib} = NONE ] ; then
1627	# Case to modify the variable itself
1628	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1629	sed -e "s/$<[^\"]\"${keyid}\".>$$[^<]$$<[^>]$/\1${value}\3/" ${filein} > ${filein}.tmp
1630	else
1631	# Check if keyattrib is set on the same line as keyid
1632	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1633	# Case to modify the attribute value
1634	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1635	sed -e "/id=\"${keyid}\"/s/$${keyattrib}=\"$[^\"]*$\"$/\1${value}\2/" ${filein} > ${filein}.tmp
1636	else
1637	# Case to add the attribute and its value
1638	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1639	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1640	fi
1641	fi
1642	\mv ${filein}.tmp ${filein}
1643	fi
1644	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1645	}
1646
1647	#=======================================================================
1648	function IGCM_comp_Update
1649	{
1650	IGCM_debug_PushStack "IGCM_comp_Update"
1651
1652	# Debug Print :
1653	echo
1654	IGCM_debug_Print 1 "IGCM_comp_Update"
1655	echo
1656
1657	typeset comp compname comptagname
1658	for comp in ${config_ListOfComponents[*]} ; do
1659	number_rundir=$(echo ${comp} \| sed 's/[^0-9]*//g')
1660	if [ X${number_rundir} != X ] ; then
1661	[ ! -d RUNDIR_${number_rundir} ] && mkdir RUNDIR_${number_rundir}
1662	cd RUNDIR_${number_rundir} ;
1663	fi
1664	# Define component
1665	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1666	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1667
1668	# Debug Print
1669	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1670	# UPDATE component
1671	${comp}_Update
1672
1673	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1674	if [ -f timeseries_def_${compname}.xml ]; then
1675	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1676	for line in $( cat ts.temp.${compname}.txt ); do
1677	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1678	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1679	case ${output_freq} in
1680	Y\|y)
1681	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1682	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1683	;;
1684	MO\|mo)
1685	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1686	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1687	;;
1688	D\|d)
1689	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1690	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1691	;;
1692	S\|s)
1693	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1694	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1695	;;
1696	esac
1697	done
1698	fi
1699
1700	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1701	if [ -f dr2xml_${compname}.xml ]; then
1702	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
1703	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1704	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1705	# Modify path from dr2xml_{compname}.xml
1706	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
1707	${libIGCM}/libIGCM_post/xios_parser.py -v modifydr2xmlIPSL --newPath ${CMIP6_DIR} --splitLastDate ${EndYear_p1} --JobName ${config_UserChoices_JobName} --ModelName ${config_UserChoices_ModelName} --ModelVersion ${config_UserChoices_LongName} --ExperimentName ${config_UserChoices_ExperimentName} --file dr2xml_${compname}.xml
1708	else
1709	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1710	fi
1711	# Overwrite the original file
1712	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1713	fi
1714	fi
1715	if [ X${number_rundir} != X ] ; then
1716	cd $RUN_DIR
1717	fi
1718	done
1719
1720	IGCM_debug_PopStack "IGCM_comp_Update"
1721	}
1722
1723	#=======================================================================
1724	function IGCM_comp_Finalize
1725	{
1726	IGCM_debug_PushStack "IGCM_comp_Finalize"
1727
1728	# Debug Print :
1729	echo
1730	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1731	echo
1732
1733	typeset ListTextName TextName0
1734	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1735	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1736	typeset -Z4 j4 #BASH declare j4
1737	typeset list_file nlist_file
1738	typeset compactoutputs
1739
1740	# Initialize array hosting list of rebuilded files to copy
1741	unset rebuildedActionsList
1742
1743	# Text compacting options
1744	compactoutputs=false
1745	if [ X${JobType} != XRUN ] ; then
1746	compactoutputs=true
1747	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1748	compactoutputs=true
1749	fi
1750
1751	# Prepare headers for the shell dedicated to offline rebuild
1752	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1753	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1754	if [ ${DRYRUN} -le 1 ] ; then
1755	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1756	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1757	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1758	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1759	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1760	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1761	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1762	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1763	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1764	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1765	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1766	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1767	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1768	fi
1769	fi
1770	for comp in ${config_ListOfComponents[*]} ; do
1771	number_rundir=$(echo ${comp} \| sed 's/[^0-9]*//g')
1772	if [ X${number_rundir} != X ] ; then
1773	[ ! -d RUNDIR_${number_rundir} ] && mkdir RUNDIR_${number_rundir}
1774	cd RUNDIR_${number_rundir} ;
1775	fi
1776
1777	# Define component
1778	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1779	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1780
1781	# Debug Print
1782	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1783	# FINALIZE component
1784	${comp}_Finalize
1785
1786	card=${SUBMIT_DIR}/COMP/${compname}.card
1787
1788	# Save Output Text files of models
1789	#---------------------------------
1790	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1791	IGCM_card_DefineArrayFromOption ${card} OutputText List
1792	ListTextName=${compname}_OutputText_List
1793
1794	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1795	if [ X${TextName0} != X${NULL_STR} ] ; then
1796	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1797
1798	(( i=0 ))
1799	until [ $i -eq $NbFiles ]; do
1800	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1801	eval file_out=${PREFIX}_${file_in}
1802
1803	(( i=i+1 ))
1804
1805	unset list_file
1806	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1807	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1808	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 )
1809	nlist_file=${#list_file[@]}
1810	if [ ${nlist_file} -gt 1 ] ; then
1811	if ( ${compactoutputs} ) ; then
1812	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1813	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1814	echo ${list_file[*]} > ${file_out}
1815	echo "" >> ${file_out}
1816
1817	(( i_ = 0 ))
1818	for file in ${list_file[@]} ; do
1819	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1820	echo "\| " ${i_} " " ${file} >> ${file_out}
1821	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1822	cat ${file} \| sed "s/$.*$/${i_}\1/" >> ${file_out}
1823	echo "" >> ${file_out}
1824	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1825	(( i_ = i_ + 1 ))
1826	done
1827	if ( ${ExecutionFail} ) ; then
1828	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1829	fi
1830
1831	if [ X${Pack} = Xtrue ] ; then
1832	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1833	else
1834	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1835	fi
1836
1837	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1838	else
1839	for file in ${list_file[@]} ; do
1840	if ( ${ExecutionFail} ) ; then
1841	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1842	fi
1843
1844	if [ X${Pack} = Xtrue ] ; then
1845	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1846	else
1847	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1848	fi
1849
1850	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1851	done
1852	fi
1853	else
1854	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1855	eval IGCM_sys_Mv ${file_in}* ${file_in}
1856	fi
1857
1858	if ( ${ExecutionFail} ) ; then
1859	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1860	fi
1861
1862	if [ X${Pack} = Xtrue ] ; then
1863	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1864	else
1865	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1866	fi
1867	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1868	fi
1869	done
1870	fi
1871
1872	# Save Restarts files
1873	#--------------------
1874	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1875	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1876	ListFilesName=${compname}_RestartFiles_List
1877	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1878
1879	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1880	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1881	(( i=0 ))
1882	until [ $i -ge $NbFiles ]; do
1883	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1884	eval file_in=${file_in_}
1885
1886	(( i_ = i+1 ))
1887	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1888	eval file_out=${file_out_}
1889
1890	(( i_ = i+2 ))
1891	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1892	eval file_outin=${file_outin_}
1893
1894	(( i_ = i+3 ))
1895	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1896	if [ X${is_opt} = XOPTIONAL ] ; then
1897	echo ${file_in} is optional
1898	(( i=i+4 ))
1899	else
1900	is_opt=""
1901	echo ${file_in} is mandatory
1902	(( i=i+3 ))
1903	fi
1904
1905	generic_restart_file_name_in=$( basename ${file_in} .nc )
1906	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1907	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1908
1909	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1910	if [ ${nb_restart_file} -gt 1 ] ; then
1911	j=0 # BASH LINE NOT NEEDED
1912	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1913	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1914	j4=${j} # BASH LINE NOT NEEDED
1915	if [ X${Pack} = Xtrue ] ; then
1916	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc ${is_opt}
1917	else
1918	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc ${is_opt}
1919	fi
1920
1921	if [ -f ${generic_restart_file_name_in}_${j4}.nc ] ; then
1922	if [ ! ${file_in} = ${file_outin} ] ; then
1923	if ( ${ExitFlag} ) ; then
1924	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1925	else
1926	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1927	fi
1928	fi
1929	else
1930	# This is the case where the restart file no not exist.
1931	# It has already been checked if the model should stop for this case.
1932	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${generic_restart_file_name_in}_${j4}.nc"
1933	fi
1934	(( j=j+1 )) # BASH LINE NOT NEEDED
1935	done
1936	else
1937	if [ X${Pack} = Xtrue ] ; then
1938	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1939	else
1940	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1941	fi
1942
1943	if [ -f ${file_in} ] ; then
1944	if [ ! ${file_in} = ${file_outin} ] ; then
1945	if ( ${ExitFlag} ) ; then
1946	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1947	else
1948	IGCM_sys_Mv ${file_in} ${file_outin}
1949	fi
1950	fi
1951	else
1952	# This is the case where the restart file no not exist.
1953	# It has already been checked if the model should stop for this case.
1954	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${file_in}"
1955	fi
1956	fi
1957
1958	done
1959	else
1960	if [ X${FileName0} != XNONE ] ; then
1961	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1962	else
1963	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1964	fi
1965	fi
1966
1967	# Save Output files
1968	#------------------
1969	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1970	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1971	ListFilesName=${compname}_OutputFiles_List
1972	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1973
1974	if [ X${FileName0} != X${NULL_STR} ] ; then
1975	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1976
1977	(( i=0 ))
1978	until [ $i -ge $NbFiles ]; do
1979	SaveOnArchive=true
1980	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1981	eval file_in=${file_in_}
1982	(( i_ = i+1 ))
1983	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1984	eval file_out=${file_out_}
1985	#
1986	# Override file_out path remplacing R_SAVE by R_BUFR
1987	#
1988	if [ X${Pack} = Xtrue ] ; then
1989	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1990	fi
1991	#
1992	# Not necessarily the best option. /!\ Potential side effects /!\
1993	#
1994	(( i_ = i+2 ))
1995	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1996	#
1997	generic_file_name=$( basename ${file_in} .nc )
1998	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1999	#
2000	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
2001	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
2002	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
2003	elif [ ${nb_rebuild_file} -gt 1 ] ; then
2004	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
2005	if [ X${AsynchronousRebuild} = Xfalse ] ; then
2006	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
2007	#
2008	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
2009	if [ ${file_in} = output.abort.nc ] ; then
2010	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
2011	else
2012	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
2013	fi
2014	else
2015	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
2016	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
2017
2018	# Prepare the shell dedicated to offline rebuild
2019	if [ $DRYRUN -le 1 ]; then
2020	if [ ${file_in} = histstn.nc ] ; then
2021	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2022	else
2023	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2024	fi
2025	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2026	fi
2027	#
2028	# Load Patch we need to apply and apply
2029	if [ $DRYRUN -le 1 ]; then
2030	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
2031	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2032	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2033	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2034	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2035	done
2036	fi
2037	fi
2038	#
2039	if [ $DRYRUN -le 1 ]; then
2040	if [ X${Pack} = Xtrue ] ; then
2041	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
2042	else
2043	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
2044	fi
2045	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
2046	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
2047	fi
2048	SaveOnArchive=false
2049	fi
2050	fi
2051	#
2052	if [ ${SaveOnArchive} = true ] ; then
2053	#
2054	# Rebuild has been done online or it was not needed
2055	#
2056	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
2057	#
2058	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
2059	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
2060	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
2061	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
2062	#
2063	if [ $DRYRUN -le 1 ]; then
2064	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2065	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2066	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2067	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2068	done
2069	#
2070	if [ X${Pack} = Xtrue ] ; then
2071	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2072	else
2073	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2074	fi
2075	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2076	#
2077	fi
2078	else
2079	#
2080	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
2081	#
2082	if [ X${Pack} = Xtrue ] ; then
2083	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
2084	else
2085	IGCM_sys_Put_Out ${file_in} ${file_out}
2086	fi
2087	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
2088	if [ ${nb_rebuild_file} -gt 1 ] ; then
2089	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
2090	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
2091	done
2092	fi
2093	fi
2094	fi
2095	((i_ = i_ +1))
2096	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
2097	eval Testvar=${Testvar_}
2098	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
2099	((i = i+4))
2100	else
2101	(( i=i+3 ))
2102	fi
2103	done
2104	fi
2105	echo
2106	if [ X${number_rundir} != X ] ; then
2107	cd $RUN_DIR
2108	fi
2109	done
2110	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
2111	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
2112	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2113	i=0
2114	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
2115	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2116	(( i=i+1 ))
2117	done
2118	fi
2119	IGCM_debug_PopStack "IGCM_comp_Finalize"
2120	}

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source: branches/libIGCM_concurrent/libIGCM_comp/libIGCM_comp.ksh @ 1628

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