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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1649

Last change on this file since 1649 was 1649, checked in by aclsce, 2 months ago
Fixed bug in case of RESTART tar file is targeted.
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: 87.9 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
77	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
78
79	eval R_OUT_${comp}_A=\${R_OUT_${comp}}/Analyse
80
81	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
82	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
83
84	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
86
87	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
88	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
89	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
90	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
91
92	eval R_OUT_${comp}_A_H=\${R_OUT_${comp}_A}/TS_HF
93	eval R_OUT_${comp}_A_D=\${R_OUT_${comp}_A}/TS_DA
94	eval R_OUT_${comp}_A_M=\${R_OUT_${comp}_A}/TS_MO
95	eval R_OUT_${comp}_A_Y=\${R_OUT_${comp}_A}/TS_YE
96
97	# Define BUFFERED Dirs
98	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
99	eval R_BUF_${comp}=${R_BUFR}/${comp}
100	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
101
102	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
103	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
104
105	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
107
108	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
110
111	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
112	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
113
114	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
115	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
116	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
117	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
118
119	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
120	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
121	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
122	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
123
124	# Define CMIP6 Dirs
125	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
126	fi
127
128	# Read UserChoices section of component card
129	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
130	IGCM_card_DefineArrayFromSection ${card} UserChoices
131	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
132
133	# If section is not empty we define corresponding variables
134	if [ X${first_option} != X"Error:" ] ; then
135	if [ X${card_UserChoices[0]} != X ] ; then
136	unset card_UserChoices
137	fi
138	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
139	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
140	for option in ${card_UserChoices[*]} ; do
141	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
142	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
143	done
144	fi
145
146	# Read and Build Output File stuff
147	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
148	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
149	ListFilesName=${compname}_OutputFiles_List
150	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
151	#
152	if [ X${FileName0} != X${NULL_STR} ] ; then
153	#
154	#IGCM_debug_Print 1 "Component : ${compname}"
155	#
156	# INITIALISATION
157	#
158	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
159	#
160	i=2
161	#
162	until [ $i -ge $NbFiles ]; do
163	#
164	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
165	#
166	if [ X${flag_post} != XNONE ] ; then
167	#
168	# First of all
169	#
170	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
171	# This section is mandatory
172	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
173	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
174	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
175	IGCM_debug_Verif_Exit
176	fi
177	#
178	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
179	#
180	# variable option allready typeset above
181	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
182	if [ ${option} = Seasonal ] ; then
183	FoundSeasonal=true
184	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
185	fi
186	done
187	#
188	if [ ! X${FoundSeasonal} = Xtrue ] ; then
189	eval ${compname}_${flag_post}_Seasonal=ON
190	fi
191	#
192	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
193	Seasonal=true
194	fi
195
196	# Dimension = vide si vieille card.
197	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
198	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
199	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
200	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
201	ListDimension[0]=2D
202	ListDimension[1]=3D
203	TimeSeries=false
204	iLoop=${#ListDimension[*]}
205	j=0
206	until [ $j -ge ${iLoop} ]; do
207	Dimension=${ListDimension[${j}]}
208	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
209	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
210	#
211	# Time series WITHOUT chunk
212	#
213	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
214	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
215	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
216	eval TimeSeries${Dimension}=true
217	fi
218	fi
219	#
220	# Time series WITH chunk
221	#
222	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
223	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
224	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
225	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
226	eval TimeSeriesChunck${Dimension}=true
227	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
228	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
229	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
230	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
231	fi
232	fi
233	(( j=j+1 ))
234	done
235	else
236	ListDimension[0]=""
237	TimeSeries=true
238	TimeSeries2D=false
239	TimeSeries3D=false
240	TimeSeriesChunck2D=false
241	TimeSeriesChunck3D=false
242	fi
243	fi
244	((i_ = i +1))
245	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
246	eval Testvar=${Testvar_}
247	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
248	((i = i+4))
249	else
250	(( i=i+3 ))
251	fi
252	done
253	fi
254	# Debug Print
255	IGCM_debug_Print 3 "Initialize ${compname} with driver."
256	# INIT component
257	${comp}_Initialize
258	echo
259	done
260
261	IGCM_debug_PopStack "IGCM_comp_Initialize"
262	}
263
264	#=======================================================================
265	function IGCM_comp_PrepareDeletedFiles
266	{
267	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
268
269	if [ X${2} != X. ] ; then
270	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
271	else
272	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
273	fi
274
275	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
276	}
277
278	#=======================================================================
279	function IGCM_comp_PrepareXiosFiles
280	{
281	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
282
283	typeset file
284	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
285
286	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
287	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
288	fi
289	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
290	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
291	fi
292	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
293	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
294	fi
295
296	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
297	}
298
299	#=======================================================================
300	function IGCM_comp_GetInputInitialStateFiles
301	{
302	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
303
304	# Debug Print :
305	echo
306	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
307	echo
308
309	# Only the first time step need InitialStateFiles
310	# otherwise it's BoundaryConditions
311	if ( ${FirstInitialize} ) ; then
312	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
313	typeset file_in_ file_in file_out_ file_out do_init
314	for comp in ${config_ListOfComponents[*]} ; do
315	# Initialize
316	do_init="y"
317	# Do we need to bring initial state file for this component
318	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
319	eval do_init="n"
320	else
321	# Read component Restarts parameters
322	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
323	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
324	if [ "${do_start}" = "y" ] ; then
325	do_init="n"
326	else
327	do_init="y"
328	fi
329	fi
330
331	if [ "${do_init}" = "y" ] ; then
332	# Define component
333	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
334	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
335
336	# Debug Print :
337	IGCM_debug_Print 3 "Initialisation files ${compname}"
338
339	card=${SUBMIT_DIR}/COMP/${compname}.card
340
341	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
342	ListFilesName=${compname}_InitialStateFiles_List
343
344	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
345	if [ X${FileName0} != X${NULL_STR} ] ; then
346	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
347	(( i=0 ))
348	until [ $i -ge $NbFiles ]; do
349	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
350	eval file_in=${file_in_}
351	(( i_ = i+1 ))
352	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
353	eval file_out=${file_out_}
354
355	IGCM_sys_IsFileArchived ${file_in}
356	if [ $? = 0 ] ; then
357	IGCM_sys_Get ${file_in} ${file_out}
358	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
359	else
360	IGCM_sys_Cp ${file_in} ${file_out}
361	fi
362	(( i=i+2 ))
363	done
364	fi
365	fi
366	done
367	fi
368	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
369	}
370
371	#=======================================================================
372	# Definition of Smooth modulo function
373	# usage :
374	# IGCM_SmoothModulo StringModulo value
375	#
376	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
377	# [min]:[modulo:][max]
378	# where :
379	# [] value are optionnals;
380	# empty min equal 1
381	# empty max equal infinity
382	# modulo not given or empty equal 1
383	# empty string or just ':' equal always.
384	#
385	# value : the value to test with the definition
386	#
387	# return : true(1)/false(0)
388	function IGCM_SmoothModulo
389	{
390	IGCM_debug_PushStack "IGCM_SmoothModulo"
391	typeset defVector ModValue
392
393	eval set +A defVector -- $( echo "${1}" \| \
394	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
395
396	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
397	arr[1]=${defVector[0]}
398	arr[2]=${defVector[2]}
399
400	# Test limits :
401	# ${defVector[0]} <= ${2} <= ${defVector[2]}
402	# or ${defVector[2]} == -1
403	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
404	# Test modulo
405	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
406	if [ ${ModValue} -eq 0 ] ; then
407	arr[3]=true
408	echo ${arr[@]}
409	IGCM_debug_PopStack "IGCM_SmoothModulo"
410	return 1
411	else
412	arr[3]=false
413	echo ${arr[@]}
414	IGCM_debug_PopStack "IGCM_SmoothModulo"
415	return 0
416	fi
417	else
418	arr[3]=false
419	echo ${arr[@]}
420	IGCM_debug_PopStack "IGCM_SmoothModulo"
421	return 0
422	fi
423	}
424
425	#=======================================================================
426	function IGCM_comp_GetInputSmoothFiles
427	{
428	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
429
430	# Debug Print :
431	echo
432	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
433	echo
434
435	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
436	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
437
438	for comp in ${config_ListOfComponents[*]} ; do
439	# Define component
440	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
441	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
442
443	# Debug Print :
444	IGCM_debug_Print 3 "Smooth files ${compname}"
445
446	card=${SUBMIT_DIR}/COMP/${compname}.card
447
448	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
449	ListFilesName=${compname}_SmoothFiles_List
450	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
451
452	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
453	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
454
455	(( i=0 ))
456	until [ $i -ge $NbFiles ]; do
457	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
458	eval file_in=${file_in_}
459	(( i_ = i+1 ))
460	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
461	eval file_out=${file_out_}
462
463	# define CumulPeriod definition for this file
464	(( i__ = i+2 ))
465	eval SmoothDef=\${${ListFilesName}[$i__]}
466	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
467	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
468	j=1
469	for val in ${aux} ; do
470	[ ${j} -eq 1 ] && SmoothMin=${val}
471	[ ${j} -eq 2 ] && SmoothMax=${val}
472	[ ${j} -eq 3 ] && ret=${val}
473	(( j=j+1 ))
474	done
475	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
476	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
477
478	IGCM_sys_IsFileArchived ${file_in}
479	if [ $? = 0 ] ; then
480	IGCM_sys_Get ${file_in} ${file_out}
481	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
482	else
483	IGCM_sys_Cp ${file_in} ${file_out}
484	fi
485	fi
486	(( i=i+3 ))
487	done
488	fi
489	done
490
491	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
492	}
493
494	#=======================================================================
495	function IGCM_comp_GetInputBoundaryFiles
496	{
497	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
498
499	# Debug Print :
500	echo
501	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
502	echo
503
504	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
505	typeset file_in_ file_in file_out_ file_out
506
507	if [ ${Period} = 1 ]; then
508	ListFixBoundary=" "
509	fi
510
511	for comp in ${config_ListOfComponents[*]} ; do
512
513	# Define component
514	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
515	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
516
517	# Debug Print :
518	IGCM_debug_Print 3 "Boundary files ${compname}"
519
520	card=${SUBMIT_DIR}/COMP/${compname}.card
521
522	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
523	ListFilesName=${compname}_BoundaryFiles_List
524	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
525
526	if [ X${FileName0} != X${NULL_STR} ] ; then
527	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
528
529	(( i=0 ))
530	until [ $i -ge $NbFiles ]; do
531	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
532	eval file_in=${file_in_}
533	(( i_ = i+1 ))
534	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
535	eval file_out=${file_out_}
536
537	IGCM_sys_IsFileArchived ${file_in}
538	if [ $? = 0 ] ; then
539	IGCM_sys_Get ${file_in} ${file_out}
540	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
541	else
542	IGCM_sys_Cp ${file_in} ${file_out}
543	fi
544
545	(( i=i+2 ))
546	done
547	fi
548
549	# Get non deleted files
550	if [ ${Period} = 1 ]; then
551
552	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
553	ListFilesName=${compname}_BoundaryFiles_ListNonDel
554	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
555
556	if [ X${FileName0} != X${NULL_STR} ] ; then
557	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
558
559	(( i=0 ))
560	until [ $i -ge $NbFiles ]; do
561	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
562	eval file_in=${file_in_}
563	(( i_ = i+1 ))
564	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
565	eval file_out=${file_out_}
566
567	IGCM_sys_IsFileArchived ${file_in}
568	if [ $? = 0 ] ; then
569	IGCM_sys_Get ${file_in} ${file_out}
570	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
571	else
572	IGCM_sys_Cp ${file_in} ${file_out}
573	fi
574
575	if [ X${file_out} != X. ] ; then
576	ListFixBoundary=${ListFixBoundary}" "${file_out}
577	else
578	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
579	fi
580
581	(( i=i+2 ))
582	done
583	fi
584	fi
585	done
586
587	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
588	}
589
590	#=======================================================================
591	function IGCM_comp_DelFixeBoundaryFiles
592	{
593	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
594
595	# Debug Print :
596	echo
597	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
598	echo
599
600	ls -l ${ListFixBoundary}
601	rm -f ${ListFixBoundary}
602
603	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
604	}
605
606	#=======================================================================
607	function IGCM_comp_GetInputParametersFiles
608	{
609	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
610
611	# Debug Print :
612	echo
613	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
614	echo
615
616	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
617	for comp in ${config_ListOfComponents[*]} ; do
618	# Define component
619	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
620	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
621
622	# Initialize array hosting file_def and field_def files to check and/or modify
623	unset FieldDef
624	unset FileDef
625
626	# Debug Print :
627	IGCM_debug_Print 3 "Parameters ${compname}"
628
629	card=${SUBMIT_DIR}/COMP/${compname}.card
630
631	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
632	ListFilesName=${compname}_ParametersFiles_List
633	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
634
635	if [ X${FileName0} != X${NULL_STR} ] ; then
636	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
637
638	(( i=0 ))
639	until [ $i -ge $NbFiles ]; do
640	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
641	eval file_in=${file_in_}
642	(( i_ = i+1 ))
643	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
644	eval file_out=${file_out_}
645
646	IGCM_sys_Cp ${file_in} ${file_out}
647	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
648	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
649
650	(( i=i+2 ))
651	done
652	fi
653
654	done
655
656	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
657	}
658
659	#=======================================================================
660	function IGCM_comp_GetInputRestartFiles
661	{
662	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
663
664	# Debug Print :
665	echo
666	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
667	echo
668
669	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
670	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
671	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
672	typeset file_in file_out file_in_ file_out_ file_in_Name
673	typeset -Z4 j4
674	#BASH declare j4
675
676	IsMatching=""
677
678	for comp in ${config_ListOfComponents[*]} ; do
679	# Define component
680	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
681	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
682	#
683	card=${SUBMIT_DIR}/COMP/${compname}.card
684	#
685	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
686	ListFilesName=${compname}_RestartFiles_List
687	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
688
689	# Debug Print :
690	IGCM_debug_Print 3 "restart ${compname}"
691
692	if ( ${FirstInitialize} ) ; then
693
694	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
695	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
696	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
697	CompOldName=IOS
698	config_IOS_Restart="n"
699	do_start="n"
700	config_IOS_RestartDate=-1
701	config_IOS_RestartJobName=${NULL_STR}
702	config_IOS_RestartPath=${NULL_STR}
703	else
704	eval config_${comp}_Restart="y"
705	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
706	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
707	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
708	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
709	eval CompOldName=${comp}
710	fi
711	else
712	# Read component Restarts parameters
713	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
714	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
715
716	if [ "${do_start}" = "y" ] ; then
717	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
718	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
719	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
720	else
721	eval config_${comp}_RestartDate=-1
722	eval config_${comp}_RestartJobName=${NULL_STR}
723	eval config_${comp}_RestartPath=${NULL_STR}
724	fi
725
726	eval CompOldName=\${config_${comp}_OldName}
727	if [ X${CompOldName} = X ] ; then
728	eval CompOldName=${comp}
729	fi
730
731	# Reinitialize IsMatching to allow searching for a different tar file for each component.
732	IsMatching=""
733	TarFileFound=""
734	fi
735
736	if [ "${do_start}" = "y" ] ; then
737
738	# Restore Restarts files
739	#-----------------------
740	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
741	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
742
743	(( i=1 ))
744	until [ $i -gt $NbFiles ]; do
745	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
746	eval file_in=${file_in_}
747	(( i_ = i+1 ))
748	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
749	eval file_out=${file_out_}
750
751	(( i_ = i+2 ))
752	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
753	if [ X${is_opt} = XOPTIONAL ] ; then
754	echo ${file_in} is optional
755	(( i=i+4 ))
756	else
757	is_opt="MANDATORY"
758	echo ${file_in} is mandatory
759	(( i=i+3 ))
760	fi
761	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=y)"
762
763	eval Date_tmp=\${config_${comp}_RestartDate}
764	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
765	# will be re-use
766	eval RestartPath=\${config_${comp}_RestartPath}
767	eval RestartJobName=\${config_${comp}_RestartJobName}
768	#
769	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
770	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
771
772	extension_in=$( echo ${file_in_Name##*.} )
773	extension_out=$( echo ${file_out##*.} )
774
775	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
776	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
777
778	Path_OUT=${Path_r}/${generic_restart_file_name_in}
779
780	if [ ! X${OLDARCHIVE} = X ]; then
781	IsSTOREFlag=$( [ X$( echo ${Path_OUT} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
782	if [ ${IsSTOREFlag} = 0 ] ; then
783	Path_OLDOUT=$( echo ${Path_OUT} \| sed "s%/lustre/fsstor/projects%/gpfsstore%" )
784	else
785	Path_OLDOUT="null"
786	fi
787	else
788	Path_OLDOUT="null"
789	fi
790
791	if [ ! X${TMPARCHIVE} = X ]; then
792	IsSTOREFlag=$( [ X$( echo ${Path_OUT} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
793	if [ ${IsSTOREFlag} = 0 ] ; then
794	Path_TMPOUT=$( echo ${Path_OUT} \| sed "s%/lustre/fsstor/projects%/lustre/fsnomig/ipsl/tmpstore%" )
795	else
796	Path_TMPOUT="null"
797	fi
798	else
799	Path_TMPOUT="null"
800	fi
801
802	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
803	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
804	Buffered=true
805	Archived=false
806	Tared=false
807	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
808	elif [ $( IGCM_sys_TestFileArchive ${Path_OLDOUT}*.${extension_in} ; echo $? ) = 0 ] ; then
809	IGCM_debug_Print 3 "Archived restart ${Path_OLDOUT}*.${extension_in}"
810	Buffered=false
811	Archived=true
812	Tared=false
813	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OLDOUT}_????.${extension_in})
814	Path_OUT=${Path_OLDOUT}
815	elif [ $( IGCM_sys_TestFileArchive ${Path_TMPOUT}*.${extension_in} ; echo $? ) = 0 ] ; then
816	IGCM_debug_Print 3 "Archived restart ${Path_TMPOUT}*.${extension_in}"
817	Buffered=false
818	Archived=true
819	Tared=false
820	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_TMPOUT}_????.${extension_in})
821	Path_OUT=${Path_TMPOUT}
822	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
823	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
824	Buffered=false
825	Archived=true
826	Tared=false
827	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
828	else
829	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
830	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
831	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
832	Buffered=false
833	Archived=false
834	Tared=true
835	# Look after the tar file we want if we did not found it already
836	if [ X${IsMatching} = X ] ; then
837	if ( [ ! X${OLDARCHIVE} = X ] && [ ! X${TMPARCHIVE} = X ] ) ; then
838	IsSTOREFlag=$( [ X$( echo ${RestartPath} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
839	if [ ${IsSTOREFlag} = 0 ] ; then
840	OLDRestartPath=$( echo ${RestartPath} \| sed "s%/lustre/fsstor/projects%/gpfsstore%" )
841	TMPRestartPath=$( echo ${RestartPath} \| sed "s%/lustre/fsstor/projects%/lustre/fsnomig/ipsl/tmpstore%" )
842	else
843	OLDRestartPath="null"
844	TMPRestartPath="null"
845	fi
846	IGCM_sys_TestDirArchive ${OLDRestartPath}/${RestartJobName}/RESTART
847	if [ $? = 0 ] ; then
848	RestartPath=${OLDRestartPath}
849	else
850	IGCM_sys_TestDirArchive ${TMPRestartPath}/${RestartJobName}/RESTART
851	if [ $? = 0 ] ; then
852	RestartPath=${TMPRestartPath}
853	fi
854	fi
855	fi
856	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
857	if [ $? ] ; then
858	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
859	IsMatching=$( echo ${PotentialTarFile##*/} \| \
860	sed "s:_restart::" \| \
861	sed "s:^${RestartJobName}_::" \| \
862	sed "s:\.tar$::" \| \
863	gawk -F_ -v restartdate=${Date_r} \
864	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
865	if [ ! X${IsMatching} = X ] ; then
866	TarFileFound=${PotentialTarFile}
867	break
868	fi
869	done
870	fi
871
872	# Stop here if nothing has been found
873	if [ X${TarFileFound} = X ] ; then
874	IGCM_debug_Print 3 "Restart files were not found!"
875	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
876	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
877	if [ ${is_opt} = 'OPTIONAL' ] ; then
878	IGCM_debug_Print 3 "The restart file is optional. Now continue."
879	nb_restart_file=0
880	Tared=false
881	else
882	IGCM_debug_Exit "Please double check restart settings in config.card"
883	IGCM_debug_Verif_Exit
884	fi
885	fi
886	fi
887
888	if [ X${Tared} = Xtrue ] ; then
889	# The tar file exist but not sure all files are inside
890	IGCM_sys_PrepareTaredRestart ${TarFileFound}
891	TarFileLocation=$( basename ${TarFileFound} )
892	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in} \| wc -l )
893	if [ ${nb_files} -gt 0 ] ; then
894	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
895	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
896	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
897	else
898	# No file was found
899	if [ ${is_opt} = 'OPTIONAL' ] ; then
900	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
901	nb_restart_file=0
902	Tared=false
903	else
904	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
905	IGCM_debug_Exit "Please double check restart settings in config.card"
906	IGCM_debug_Verif_Exit
907	fi
908	fi
909	fi
910	fi
911
912	if [ ${nb_restart_file} -gt 1 ] ; then
913	j=0 # BASH LINE NOT NEEDED
914	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
915	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
916	j4=${j} # BASH LINE NOT NEEDED
917	if [ X${Buffered} = Xtrue ] ; then
918	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
919	elif [ X${Archived} = Xtrue ] ; then
920	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
921	elif [ X${Tared} = Xtrue ] ; then
922	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
923	fi
924	(( j=j+1 )) #BASH LINE NOT NEEDED
925	done
926
927	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
928	if [ X${OCE_PROC_MPI} != X ] ; then
929	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
930	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
931	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
932	fi
933	fi
934	else
935	if [ X${Buffered} = Xtrue ] ; then
936	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
937	elif [ X${Archived} = Xtrue ] ; then
938	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
939	elif [ X${Tared} = Xtrue ] ; then
940	if [ -f ${comp}_${file_in_Name} ] ; then
941	# The file exixt
942	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
943	elif [ ${is_opt} = 'OPTIONAL' ] ; then
944	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
945	else
946	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
947	IGCM_debug_Exit "Please double check restart settings in config.card"
948	IGCM_debug_Verif_Exit
949	fi
950	fi
951	fi
952	done
953	else
954	if [ X${FileName0} != XNONE ] ; then
955	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
956	else
957	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
958	fi
959	fi
960	fi
961	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
962	# if not FirstInitialize and first loop of this job
963
964	# Restore Restarts files
965	#-----------------------
966	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
967	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
968
969	(( i=1 ))
970	until [ $i -gt $NbFiles ]; do
971	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
972	eval file_in=${file_in_}
973
974	(( i_ = i+1 ))
975	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
976	eval file_out=${file_out_}
977
978	(( i_ = i+2 ))
979	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
980	if [ X${is_opt} = XOPTIONAL ] ; then
981	# Read a forth argument
982	echo ${file_in} is optional
983	(( i=i+4 ))
984	else
985	is_opt="MANDATORY"
986	echo ${file_in} is mandatory
987	(( i=i+3 ))
988	fi
989
990	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=n)"
991
992	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
993
994	extension_in=$( echo ${file_in_Name##*.} )
995	extension_out=$( echo ${file_out##*.} )
996
997	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
998	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
999
1000	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
1001	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
1002
1003	if [ ! X${OLDARCHIVE} = X ]; then
1004	IsSTOREFlag=$( [ X$( echo ${Path_OUT} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
1005	if [ ${IsSTOREFlag} = 0 ] ; then
1006	Path_OLDOUT=$( echo ${Path_OUT} \| sed "s%/lustre/fsstor/projects%/gpfsstore%" )
1007	else
1008	Path_OLDOUT="null"
1009	fi
1010	fi
1011
1012	if [ ! X${TMPARCHIVE} = X ]; then
1013	IsSTOREFlag=$( [ X$( echo ${Path_OUT} \| grep fsstor ) != X ] && echo 0 \|\| echo 1 )
1014	if [ ${IsSTOREFlag} = 0 ] ; then
1015	Path_TMPOUT=$( echo ${Path_OUT} \| sed "s%/lustre/fsstor/projects%/lustre/fsnomig/ipsl/tmpstore%" )
1016	else
1017	Path_TMPOUT="null"
1018	fi
1019	fi
1020	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
1021	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
1022	Buffered=true
1023	Archived=false
1024	Tared=false
1025	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
1026	elif [ $( IGCM_sys_TestFileArchive ${Path_OLDOUT}*.${extension_in} ; echo $? ) = 0 ] ; then
1027	IGCM_debug_Print 3 "Archived restart ${Path_OLDOUT}*.${extension_in}"
1028	Buffered=false
1029	Archived=true
1030	Tared=false
1031	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OLDOUT}_????.${extension_in})
1032	Path_OUT=${Path_OLDOUT}
1033	elif [ $( IGCM_sys_TestFileArchive ${Path_TMPOUT}*.${extension_in} ; echo $? ) = 0 ] ; then
1034	IGCM_debug_Print 3 "Archived restart ${Path_TMPOUT}*.${extension_in}"
1035	Buffered=false
1036	Archived=true
1037	Tared=false
1038	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_TMPOUT}_????.${extension_in})
1039	Path_OUT=${Path_TMPOUT}
1040	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
1041	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
1042	Buffered=false
1043	Archived=true
1044	Tared=false
1045	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
1046	else
1047	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
1048	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
1049	Buffered=false
1050	Archived=false
1051	Tared=true
1052	# Look after the tar file we want if we did not found it already
1053	if [ X${IsMatching} = X ] ; then
1054	if ( [ ! X${OLDARCHIVE} = X ] && [ ! X${TMPARCHIVE} = X ] ) ; then
1055	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_OLDSAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
1056	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
1057	if [ ! X${IsMatching} = X ] ; then
1058	TarFileFound=${PotentialTarFile}
1059	break
1060	else
1061	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_TMPSAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
1062	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
1063	if [ ! X${IsMatching} = X ] ; then
1064	TarFileFound=${PotentialTarFile}
1065	break
1066	else
1067	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
1068	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
1069	if [ ! X${IsMatching} = X ] ; then
1070	TarFileFound=${PotentialTarFile}
1071	break
1072	fi
1073	done
1074	fi
1075	done
1076	fi
1077	done
1078	else
1079	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
1080	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
1081	if [ ! X${IsMatching} = X ] ; then
1082	TarFileFound=${PotentialTarFile}
1083	break
1084	fi
1085	done
1086	fi
1087	fi
1088
1089	# Stop here if nothing has been found
1090	if [ X${TarFileFound} = X ] ; then
1091	IGCM_debug_Print 3 "Restart files were not found!"
1092	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
1093	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
1094	if [ ${is_opt} = 'OPTIONAL' ] ; then
1095	IGCM_debug_Print 3 "The restart file is optional. Now continue."
1096	nb_restart_file=0
1097	Tared=false
1098	else
1099	IGCM_debug_Print 3 "The restart file is mandatory."
1100	IGCM_debug_Exit "Please double check restart settings in config.card"
1101	IGCM_debug_Verif_Exit
1102	fi
1103	else
1104	# The tar file exist but not sure all files are inside
1105	IGCM_sys_PrepareTaredRestart ${TarFileFound}
1106	TarFileLocation=$( basename ${TarFileFound} )
1107	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in} \| wc -l )
1108	if [ ${nb_files} -gt 0 ] ; then
1109	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
1110	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
1111	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
1112	else
1113	# No file was found
1114	if [ ${is_opt} = 'OPTIONAL' ] ; then
1115	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
1116	nb_restart_file=0
1117	Tared=false
1118	else
1119	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
1120	IGCM_debug_Exit "Please double check restart settings in config.card"
1121	IGCM_debug_Verif_Exit
1122	fi
1123	fi
1124
1125	fi
1126	fi
1127
1128	if [ ${nb_restart_file} -gt 1 ] ; then
1129	j=0 # BASH LINE NOT NEEDED
1130	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1131	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1132	j4=${j} # BASH LINE NOT NEEDED
1133	if [ X${Buffered} = Xtrue ] ; then
1134	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1135	elif [ X${Archived} = Xtrue ] ; then
1136	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1137	elif [ X${Tared} = Xtrue ] ; then
1138	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1139	fi
1140	(( j=j+1 )) # BASH LINE NOT NEEDED
1141	done
1142	else
1143	if [ X${Buffered} = Xtrue ] ; then
1144	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
1145	elif [ X${Archived} = Xtrue ] ; then
1146	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
1147	elif [ X${Tared} = Xtrue ] ; then
1148	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
1149	fi
1150	fi
1151	done
1152	else
1153	if [ X${FileName0} != XNONE ] ; then
1154	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
1155	else
1156	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
1157	fi
1158	fi
1159	fi
1160	done
1161
1162	NbFiles=$( ls * 2> /dev/null \| wc -l )
1163	if [ ${NbFiles} -gt 0 ] ; then
1164	IGCM_sys_Chmod u+rw *
1165	fi
1166
1167	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
1168	}
1169
1170	#=======================================================================
1171	function IGCM_comp_GetInputBinaryFiles
1172	{
1173	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
1174
1175	# Debug Print :
1176	echo
1177	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
1178	echo
1179
1180	# Clean up previous pass
1181	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
1182
1183	typeset comp ExeNameIn ExeNameOut byPass
1184	typeset compilerNmbr compilerUnit compilerFull
1185	byPass=false
1186	for comp in ${config_ListOfComponents[*]} ; do
1187	# Define component
1188
1189	# Copy executable for this component
1190	eval ExeNameIn=\${config_Executable_${comp}[0]}
1191	eval ExeNameOut=\${config_Executable_${comp}[1]}
1192	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
1193	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
1194	# The executable is set in config.card and is different from ""
1195	# Use eval to expand ExeNameIn if variables are used in the name
1196	eval ExeNameIn=${ExeNameIn}
1197	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1198	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1199	fi
1200	fi
1201
1202	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1203	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1204	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1205	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1206	fi
1207	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1208	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1209	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1210	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1211	fi
1212	fi
1213
1214	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1215	# Get the compiler version
1216	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1217	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1218	# Save it
1219	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1220	[ X${compilerFull} = X ] && byPass=true
1221	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1222	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1223	fi
1224	done
1225
1226	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1227	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1228
1229	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1230	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1231	fi
1232
1233
1234	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1235	}
1236
1237	#=======================================================================
1238	function IGCM_comp_PeriodStart
1239	{
1240	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1241
1242	# Debug Print :
1243	echo
1244	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1245	echo
1246
1247	typeset ExeNameIn ExeNameOut
1248	typeset comp compname comptagname
1249	for comp in ${config_ListOfComponents[*]} ; do
1250	# Define component
1251	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1252	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1253
1254	# Copy executable for this component
1255	eval ExeNameIn=\${config_Executable_${comp}[0]}
1256	eval ExeNameIn=${ExeNameIn}
1257	eval ExeNameOut=\${config_Executable_${comp}[1]}
1258
1259	# Debug Print
1260	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1261	# UPDATE component
1262	${comp}_PeriodStart 2> /dev/null
1263
1264	done
1265
1266	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1267	}
1268
1269
1270
1271	#=======================================================================
1272	function IGCM_comp_modifyFile
1273	{
1274	#
1275	# syntax: IGCM_comp_modifyFile filein key [value]
1276	#
1277	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1278	#
1279	# This function is used to replace a pattern in a file for a specific variable.
1280	#
1281	# Arguments:
1282	# - filein : the file in run directory in which the variable should be set
1283	# - key : the variable to modify
1284	# - value : the value to set the key equal to
1285	#
1286	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1287
1288	typeset filein key value pattern
1289
1290	# Set local variables and test the arguments
1291	if [ $# = 3 ] ; then
1292	# Normal case with 3 arguments
1293	filein=$1 ; key=$2 ; value=$3
1294	else
1295	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1296	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1297	return
1298	fi
1299	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1300
1301	# Test if the file exist
1302	if [ ! -f ${filein} ] ; then
1303	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1304	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1305	return
1306	fi
1307
1308	# Read the line with key in the file without the comments
1309	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1310
1311	# Verify the existance of the pattern
1312	if [ X"${pattern}" = X ] ; then
1313	# Variable key is not set in filein, stop.
1314	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1315	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1316	return
1317	fi
1318
1319	# Now change key in filein
1320	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1321	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1322	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1323	\mv ${filein}.tmp ${filein}
1324
1325	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1326	}
1327
1328	#=======================================================================
1329	function IGCM_comp_modifyDefFile
1330	{
1331	#
1332	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1333	#
1334	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1335	#
1336	# This function is used to modify a parameter file for a specific variable.
1337	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1338	# This function can be used in the comp.driver files for the components.
1339	#
1340	# Arguments:
1341	# - type : first argument must be blocker, nonblocker or force
1342	# For "blocker" case, the variable must be attributed the keyworld AUTO
1343	# otherwise this function will exit.
1344	# For "nonblocker" case, the user can remove or modify the variable. For
1345	# this case, as long as AUTO is not set, no modification will be done.
1346	# For "force" case, the variable will be modified even if it is not set to AUTO
1347	# - filein : the file in run directory of .def type in which the variable should be set
1348	# - key : the variable to modify
1349	# - value : the value to set the key equal to, optional. If value is not set or if
1350	# value=DEFAULT, then a default value must be given in filein using syntax :
1351	# key= AUTO : DEFAULT=def_value
1352	#
1353	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1354
1355	typeset type filein key value
1356	typeset filelist nb_occ modify
1357
1358	# Set local variables and test the arguments
1359	if [ $# = 4 ] ; then
1360	# Normal case with 4 arguments
1361	type=$1 ; filein=$2 ; key=$3 ; value=$4
1362	elif [ $# = 3 ] ; then
1363	# Normal case with 3 arguments
1364	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1365	else
1366	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1367	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1368	return
1369	fi
1370	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1371
1372	# Test if first argument is correct
1373	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1374	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1375	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1376	return
1377	fi
1378
1379	# Test if the file exist.
1380	# Exit with error if the file does not exist for the case blocker or force.
1381	# Only return for the case nonblocker.
1382	if [ ! -f ${filein} ] ; then
1383	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1384	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1385	else
1386	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1387	fi
1388	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1389	return
1390	fi
1391
1392	# Define list of files to test using all files with suffix .def (except used*.def)
1393	filelist=$( ls *def \| grep -v used )
1394
1395	# Count number of occurances for the key in all files
1396	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1397
1398	# Test if key is set several times
1399	if [ ${nb_occ} -gt 1 ] ; then
1400	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1401	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1402	return
1403	fi
1404
1405	# Treatement according to different cases
1406	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1407	# Stop if the key is never set and the function is blocker
1408	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1409	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1410	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1411	# The key is not set but it is a nonblocker call so nothing is done.
1412	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1413	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1414	modify=no
1415	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1416	# Variable key is not set in filein, stop.
1417	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1418	fi
1419
1420	# Check if AUTO is set in the filein on the same line as the key variable
1421	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1422	# Modification will be done for all cases
1423	modify=yes
1424	else
1425	# The variable was not set to AUTO
1426	if [ ${type} = blocker ] ; then
1427	# Exit because this is a blocker call
1428	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1429	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1430	return
1431	elif [ ${type} = nonblocker ] ; then
1432	# Do nothing. Suppose that the user did set the variable correct
1433	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1434	modify=no
1435	elif [ ${type} = force ] ; then
1436	# Force modification
1437	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1438	modify=yes
1439	fi
1440	fi
1441
1442	# Do the modifcation now
1443	if [ ${modify} = yes ] ; then
1444
1445	# For option DEFAULT, read default value from file.
1446	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1447	# Case to set DEFAULT value
1448	# Read default value from filein
1449	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1450
1451	if [ X"${value}" = X ] ; then
1452	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1453	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1454	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1455	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1456	return
1457	fi
1458	fi
1459
1460	# Now change key in filein
1461	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1462	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1463	\mv ${filein}.tmp ${filein}
1464	fi
1465	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1466	}
1467
1468	#=======================================================================
1469	function IGCM_comp_modifyNamelist
1470	{
1471	#
1472	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1473	#
1474	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1475	#
1476	# This function is used to modify a parameter file for a specific variable.
1477	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1478	# This function can be used in the comp.driver files for the components.
1479	#
1480	# Arguments:
1481	# - type : first argument must be blocker, nonblocker or force
1482	# For "blocker" case, the variable must be attributed the keyworld AUTO
1483	# otherwise this function will exit.
1484	# For "nonblocker" case, the user can remove or modify the variable. For
1485	# this case, as long as AUTO is not set, no modification will be done.
1486	# For "force" case, the variable will be modified even if it is not set to AUTO
1487	# - filein : the file in run directory of .def type in which the variable should be set
1488	# - key : the variable to modify
1489	# - value : the value to set the key equal to, optional. If value is not set or if
1490	# value=DEFAULT, then a default value must be given in filein using syntax :
1491	# key= AUTO : DEFAULT=def_value
1492	#
1493	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1494
1495	typeset type filein key value pattern modify
1496
1497	# Set local variables and test the arguments
1498	if [ $# = 4 ] ; then
1499	# Normal case with 4 arguments
1500	type=$1 ; filein=$2 ; key=$3 ; value=$4
1501	elif [ $# = 3 ] ; then
1502	# Normal case with 3 arguments
1503	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1504	else
1505	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1506	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1507	return
1508	fi
1509	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1510
1511	# Test if first argument is correct
1512	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1513	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1514	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1515	return
1516	fi
1517
1518	# Test if the file exist.
1519	# Exit with error if the file does not exist for the case blocker or force.
1520	# Only return for the case nonblocker.
1521	if [ ! -f ${filein} ] ; then
1522	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1523	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1524	else
1525	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1526	fi
1527	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1528	return
1529	fi
1530
1531	# Read the line with key in the file without the comments
1532	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1533
1534	# Verify the existance of the pattern
1535	if [ X"$pattern" = X ] ; then
1536	# Variable key is not set in filein, stop.
1537	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1538	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1539	return
1540	fi
1541
1542	# Check if the variable is set to AUTO in the filein
1543	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1544	# Modification will be done for all cases
1545	modify=yes
1546	else
1547	# The variable was not set to AUTO
1548	if [ ${type} = blocker ] ; then
1549	# Exit because this is a blocker call
1550	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1551	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1552	return
1553	elif [ ${type} = nonblocker ] ; then
1554	# Do nothing. Suppose that the user did set the variable correct
1555	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1556	modify=no
1557	elif [ ${type} = force ] ; then
1558	# Force modification
1559	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1560	modify=yes
1561	fi
1562	fi
1563
1564	# Do the modifcation now
1565	if [ ${modify} = yes ] ; then
1566
1567	# For option DEFAULT, read default value from file.
1568	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1569	# Case to set DEFAULT value
1570	# Read default value from filein
1571	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1572
1573	if [ X"${value}" = X ] ; then
1574	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1575	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1576	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1577	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1578	return
1579	fi
1580	fi
1581
1582	# Now change key in filein
1583	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1584	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1585	\mv ${filein}.tmp ${filein}
1586	fi
1587	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1588	}
1589
1590	#=======================================================================
1591	function IGCM_comp_modifyXmlFile
1592	{
1593	#
1594	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1595	#
1596	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1597	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1598	#
1599	# This function is used to modify the value for a specific attribute and variable id.
1600	# The file must be a valid xml file.
1601	# This function can be used in the comp.driver files for the components.
1602	#
1603	# Arguments:
1604	# - type : first argument must be blocker, nonblocker or force.
1605	# For "blocker" case, the variable must be attributed the keyworld AUTO
1606	# otherwise this function will exit.
1607	# For "nonblocker" case, the user can remove or modify the variable. For
1608	# this case, as long as AUTO is not set, no modification will be done.
1609	# For "force" case, the variable will be modified even if it is not set to AUTO
1610	# - filein : the file in run directory of .xml type in which the variable should be set
1611	# - keyid : the variable to modify
1612	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1613	# - value : the value to set in the filein
1614	#
1615	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1616
1617	typeset type filein keyid keyattrib value modify
1618
1619	# Set local variables and test the arguments
1620	if [ $# = 5 ] ; then
1621	# Normal case with 4 arguments
1622	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1623	else
1624	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1625	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1626	return
1627	fi
1628	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1629
1630	# Test if first argument is correct
1631	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1632	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1633	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1634	return
1635	fi
1636
1637	# Test if the file exist.
1638	# Exit with error if the file does not exist for the case blocker or force.
1639	# Only return for the case nonblocker.
1640	if [ ! -f ${filein} ] ; then
1641	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1642	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1643	else
1644	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1645	fi
1646	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1647	return
1648	fi
1649
1650	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1651	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1652	if [ ${type} = nonblocker ] ; then
1653	# This is a nonblocker case, print warning but do nothing else
1654	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1655	else
1656	# This is a blocker or force case : stop now
1657	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1658	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1659	return
1660	fi
1661	fi
1662
1663	# Check if AUTO is set on the same line as keyid and keyattrib
1664	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1665	# Modification will be done
1666	modify=yes
1667	else
1668	if [ ${type} = blocker ] ; then
1669	# Exit, the variable must be set to AUTO
1670	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1671	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1672	return
1673	elif [ ${type} = nonblocker ] ; then
1674	# Nothing will be done
1675	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1676	modify=no
1677	elif [ ${type} = force ] ; then
1678	# Force modification
1679	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1680	modify=yes
1681	fi
1682	fi
1683
1684	# Do the modifcation now
1685	if [ ${modify} = yes ] ; then
1686	if [ ${keyattrib} = NONE ] ; then
1687	# Case to modify the variable itself
1688	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1689	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1690	else
1691	# Check if keyattrib is set on the same line as keyid
1692	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1693	# Case to modify the attribute value
1694	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1695	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1696	else
1697	# Case to add the attribute and its value
1698	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1699	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1700	fi
1701	fi
1702	\mv ${filein}.tmp ${filein}
1703	fi
1704	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1705	}
1706
1707	#=======================================================================
1708	function IGCM_comp_Update
1709	{
1710	IGCM_debug_PushStack "IGCM_comp_Update"
1711
1712	# Debug Print :
1713	echo
1714	IGCM_debug_Print 1 "IGCM_comp_Update"
1715	echo
1716
1717	typeset comp compname comptagname
1718	for comp in ${config_ListOfComponents[*]} ; do
1719	# Define component
1720	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1721	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1722
1723	# Debug Print
1724	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1725	# UPDATE component
1726	${comp}_Update
1727
1728	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1729	if [ -f timeseries_def_${compname}.xml ]; then
1730	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1731	for line in $( cat ts.temp.${compname}.txt ); do
1732	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1733	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1734	case ${output_freq} in
1735	Y\|y)
1736	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1737	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1738	;;
1739	MO\|mo)
1740	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1741	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1742	;;
1743	D\|d)
1744	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1745	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1746	;;
1747	S\|s)
1748	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1749	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1750	;;
1751	esac
1752	done
1753	fi
1754
1755	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1756	if [ -f dr2xml_${compname}.xml ]; then
1757	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
1758	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1759	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1760	# Modify path from dr2xml_{compname}.xml
1761	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
1762	${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
1763	else
1764	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1765	fi
1766	# Overwrite the original file
1767	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1768	fi
1769	fi
1770	done
1771
1772	IGCM_debug_PopStack "IGCM_comp_Update"
1773	}
1774
1775	#=======================================================================
1776	function IGCM_comp_Finalize
1777	{
1778	IGCM_debug_PushStack "IGCM_comp_Finalize"
1779
1780	# Debug Print :
1781	echo
1782	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1783	echo
1784
1785	typeset ListTextName TextName0
1786	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1787	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1788	typeset -Z4 j4 #BASH declare j4
1789	typeset list_file nlist_file
1790	typeset compactoutputs
1791
1792	# Initialize array hosting list of rebuilded files to copy
1793	unset rebuildedActionsList
1794
1795	# Text compacting options
1796	compactoutputs=false
1797	if [ X${JobType} != XRUN ] ; then
1798	compactoutputs=true
1799	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1800	compactoutputs=true
1801	fi
1802
1803	# Prepare headers for the shell dedicated to offline rebuild
1804	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1805	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1806	if [ ${DRYRUN} -le 1 ] ; then
1807	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1808	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1809	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1810	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1811	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1812	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1813	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1814	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1815	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1816	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1817	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1818	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1819	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1820	fi
1821	fi
1822
1823	for comp in ${config_ListOfComponents[*]} ; do
1824	# Define component
1825	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1826	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1827
1828	# Debug Print
1829	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1830	# FINALIZE component
1831	${comp}_Finalize
1832
1833	card=${SUBMIT_DIR}/COMP/${compname}.card
1834
1835	# Save Output Text files of models
1836	#---------------------------------
1837	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1838	IGCM_card_DefineArrayFromOption ${card} OutputText List
1839	ListTextName=${compname}_OutputText_List
1840
1841	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1842	if [ X${TextName0} != X${NULL_STR} ] ; then
1843	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1844
1845	(( i=0 ))
1846	until [ $i -eq $NbFiles ]; do
1847	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1848	eval file_out=${PREFIX}_${file_in}
1849
1850	(( i=i+1 ))
1851
1852	unset list_file
1853	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1854	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1855	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 )
1856	nlist_file=${#list_file[@]}
1857	if [ ${nlist_file} -gt 1 ] ; then
1858	if ( ${compactoutputs} ) ; then
1859	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1860	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1861	echo ${list_file[*]} > ${file_out}
1862	echo "" >> ${file_out}
1863
1864	(( i_ = 0 ))
1865	for file in ${list_file[@]} ; do
1866	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1867	echo "\| " ${i_} " " ${file} >> ${file_out}
1868	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1869	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1870	echo "" >> ${file_out}
1871	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1872	(( i_ = i_ + 1 ))
1873	done
1874	if ( ${ExecutionFail} ) ; then
1875	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1876	fi
1877
1878	if [ X${Pack} = Xtrue ] ; then
1879	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1880	else
1881	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1882	fi
1883
1884	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1885	else
1886	for file in ${list_file[@]} ; do
1887	if ( ${ExecutionFail} ) ; then
1888	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1889	fi
1890
1891	if [ X${Pack} = Xtrue ] ; then
1892	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1893	else
1894	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1895	fi
1896
1897	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1898	done
1899	fi
1900	else
1901	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1902	eval IGCM_sys_Mv ${file_in}* ${file_in}
1903	fi
1904
1905	if ( ${ExecutionFail} ) ; then
1906	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1907	fi
1908
1909	if [ X${Pack} = Xtrue ] ; then
1910	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1911	else
1912	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1913	fi
1914	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1915	fi
1916	done
1917	fi
1918
1919	# Save Restarts files
1920	#--------------------
1921	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1922	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1923	ListFilesName=${compname}_RestartFiles_List
1924	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1925
1926	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1927	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1928	(( i=0 ))
1929	until [ $i -ge $NbFiles ]; do
1930	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1931	eval file_in=${file_in_}
1932
1933	(( i_ = i+1 ))
1934	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1935	eval file_out=${file_out_}
1936
1937	(( i_ = i+2 ))
1938	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1939	eval file_outin=${file_outin_}
1940
1941	(( i_ = i+3 ))
1942	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1943	if [ X${is_opt} = XOPTIONAL ] ; then
1944	echo ${file_in} is optional
1945	(( i=i+4 ))
1946	else
1947	is_opt=""
1948	echo ${file_in} is mandatory
1949	(( i=i+3 ))
1950	fi
1951
1952	generic_restart_file_name_in=$( basename ${file_in} .nc )
1953	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1954	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1955
1956	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1957	if [ ${nb_restart_file} -gt 1 ] ; then
1958	IGCM_sys_rebuild_nemo ${generic_restart_file_name_in} ${nb_restart_file}
1959	IGCM_sys_Rm ${generic_restart_file_name_in}_????.nc
1960	if [ X${Pack} = Xtrue ] ; then
1961	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1962	else
1963	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1964	fi
1965	if [ -f ${file_in} ] ; then
1966	if [ ! ${file_in} = ${file_outin} ] ; then
1967	if ( ${ExitFlag} ) ; then
1968	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1969	else
1970	IGCM_sys_Mv ${file_in} ${file_outin}
1971	fi
1972	fi
1973	else
1974	# This is the case where the restart file no not exist.
1975	# It has already been checked if the model should stop for this case.
1976	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${file_in}"
1977	fi
1978	else
1979	if [ X${Pack} = Xtrue ] ; then
1980	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1981	else
1982	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1983	fi
1984
1985	if [ -f ${file_in} ] ; then
1986	if [ ! ${file_in} = ${file_outin} ] ; then
1987	if ( ${ExitFlag} ) ; then
1988	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1989	else
1990	IGCM_sys_Mv ${file_in} ${file_outin}
1991	fi
1992	fi
1993	else
1994	# This is the case where the restart file no not exist.
1995	# It has already been checked if the model should stop for this case.
1996	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${file_in}"
1997	fi
1998	fi
1999
2000	done
2001	else
2002	if [ X${FileName0} != XNONE ] ; then
2003	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
2004	else
2005	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
2006	fi
2007	fi
2008
2009	# Save Output files
2010	#------------------
2011	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
2012	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
2013	ListFilesName=${compname}_OutputFiles_List
2014	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
2015
2016	if [ X${FileName0} != X${NULL_STR} ] ; then
2017	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
2018
2019	(( i=0 ))
2020	until [ $i -ge $NbFiles ]; do
2021	SaveOnArchive=true
2022	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
2023	eval file_in=${file_in_}
2024	(( i_ = i+1 ))
2025	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
2026	eval file_out=${file_out_}
2027	#
2028	# Override file_out path remplacing R_SAVE by R_BUFR
2029	#
2030	if [ X${Pack} = Xtrue ] ; then
2031	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
2032	fi
2033	#
2034	# Not necessarily the best option. /!\ Potential side effects /!\
2035	#
2036	(( i_ = i+2 ))
2037	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
2038	#
2039	generic_file_name=$( basename ${file_in} .nc )
2040	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
2041	#
2042	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
2043	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
2044	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
2045	elif [ ${nb_rebuild_file} -gt 1 ] ; then
2046	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
2047	if [ X${AsynchronousRebuild} = Xfalse ] ; then
2048	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
2049	#
2050	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
2051	if [ ${file_in} = output.abort.nc ] ; then
2052	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
2053	else
2054	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
2055	fi
2056	else
2057	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
2058	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
2059
2060	# Prepare the shell dedicated to offline rebuild
2061	if [ $DRYRUN -le 1 ]; then
2062	if [ ${file_in} = histstn.nc ] ; then
2063	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2064	else
2065	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2066	fi
2067	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2068	fi
2069	#
2070	# Load Patch we need to apply and apply
2071	if [ $DRYRUN -le 1 ]; then
2072	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
2073	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2074	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2075	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2076	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2077	done
2078	fi
2079	fi
2080	#
2081	if [ $DRYRUN -le 1 ]; then
2082	if [ X${Pack} = Xtrue ] ; then
2083	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
2084	else
2085	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
2086	fi
2087	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
2088	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
2089	fi
2090	SaveOnArchive=false
2091	fi
2092	fi
2093	#
2094	if [ ${SaveOnArchive} = true ] ; then
2095	#
2096	# Rebuild has been done online or it was not needed
2097	#
2098	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
2099	#
2100	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
2101	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
2102	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
2103	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
2104	#
2105	if [ $DRYRUN -le 1 ]; then
2106	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2107	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2108	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2109	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2110	done
2111	#
2112	if [ X${Pack} = Xtrue ] ; then
2113	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2114	else
2115	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2116	fi
2117	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2118	#
2119	fi
2120	else
2121	#
2122	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
2123	#
2124	if [ X${Pack} = Xtrue ] ; then
2125	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
2126	else
2127	IGCM_sys_Put_Out ${file_in} ${file_out}
2128	fi
2129	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
2130	if [ ${nb_rebuild_file} -gt 1 ] ; then
2131	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
2132	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
2133	done
2134	fi
2135	fi
2136	fi
2137	((i_ = i_ +1))
2138	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
2139	eval Testvar=${Testvar_}
2140	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
2141	((i = i+4))
2142	else
2143	(( i=i+3 ))
2144	fi
2145	done
2146	fi
2147	echo
2148	done
2149	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
2150	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
2151	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2152	i=0
2153	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
2154	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2155	(( i=i+1 ))
2156	done
2157	fi
2158	IGCM_debug_PopStack "IGCM_comp_Finalize"
2159	}

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