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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1572

Last change on this file since 1572 was 1552, checked in by aclsce, 2 years ago
Modified to use CMIP6 workflow for non CMIP6 runs.
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
File size: 79.8 KB

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1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
6	# $Revision:: $ Revision of last commit
7	# $Author:: $ Author of last commit
8	# $Date:: $ Date of last commit
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	#
12	#**************************************************************
13
14	#========================================================================
15	function IGCM_comp_Initialize
16	{
17	IGCM_debug_PushStack "IGCM_comp_Initialize"
18
19	# Debug Print :
20	echo
21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
22	echo
23
24	typeset comp compname comptagname auxprint card_UserChoices first_option option i j
25	for comp in ${config_ListOfComponents[*]} ; do
26
27	# Define component
28	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
29	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
30	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
31
32	# Debug Print
33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
34
35	# ${compname}.card PATH
36	card=${SUBMIT_DIR}/COMP/${compname}.card
37
38	# Manage component executable
39	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
40
41	# Define all options in section [comp]
42	IGCM_debug_Print 3 " DefineArrayFromSection : ${comp}"
43	IGCM_card_DefineArrayFromSection ${SUBMIT_DIR}/config.card ${comp}
44	eval config_comp=\${config_${comp}[*]} > /dev/null 2>&1
45	for option in ${config_comp[*]} ; do
46	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
47	done
48	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
49
50	# Debug Print :
51	eval auxprint=\${config_${comp}_WriteFrequency}
52	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
53	#2> /dev/null
54
55	# Debug Print :
56	IGCM_debug_Print 2 "Initialize following component library"
57
58	# Source drivers in directory DRIVER if it exist
59	# else source them from directory COMP
60	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
61	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
62	# Source component library
63	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
64	else
65	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
66	# Source component library
67	. ${SUBMIT_DIR}/COMP/${compname}.driver
68	fi
69	IGCM_debug_Print 3 "With tag : ${comptagname}"
70
71	# Debug Print
72	IGCM_debug_Print 3 "Initialize ${comp} output directory."
73
74	# Define ARCHIVED Dirs
75	eval R_OUT_${comp}=${R_SAVE}/${comp}
76	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
77
78	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
79	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
80
81	eval R_OUT_${comp}_A=\${R_OUT_${comp}}/Analyse
82	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_A}
83
84	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
86
87	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
88	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
89
90	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
91	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
92	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
93	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
94
95	eval R_OUT_${comp}_A_H=\${R_OUT_${comp}_A}/TS_HF
96	eval R_OUT_${comp}_A_D=\${R_OUT_${comp}_A}/TS_DA
97	eval R_OUT_${comp}_A_M=\${R_OUT_${comp}_A}/TS_MO
98	eval R_OUT_${comp}_A_Y=\${R_OUT_${comp}_A}/TS_YE
99
100	# Define BUFFERED Dirs
101	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
102	eval R_BUF_${comp}=${R_BUFR}/${comp}
103	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
104
105	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
107
108	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
110
111	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
112	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
113
114	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
115	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
116
117	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
118	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
119	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
120	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
121
122	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
123	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
124	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
125	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
126
127	# Define CMIP6 Dirs
128	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
129	fi
130
131	# Read UserChoices section of component card
132	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
133	IGCM_card_DefineArrayFromSection ${card} UserChoices
134	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
135
136	# If section is not empty we define corresponding variables
137	if [ X${first_option} != X"Error:" ] ; then
138	if [ X${card_UserChoices[0]} != X ] ; then
139	unset card_UserChoices
140	fi
141	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
142	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
143	for option in ${card_UserChoices[*]} ; do
144	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
145	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
146	done
147	fi
148
149	# Read and Build Output File stuff
150	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
151	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
152	ListFilesName=${compname}_OutputFiles_List
153	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
154	#
155	if [ X${FileName0} != X${NULL_STR} ] ; then
156	#
157	#IGCM_debug_Print 1 "Component : ${compname}"
158	#
159	# INITIALISATION
160	#
161	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
162	#
163	i=2
164	#
165	until [ $i -ge $NbFiles ]; do
166	#
167	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
168	#
169	if [ X${flag_post} != XNONE ] ; then
170	#
171	# First of all
172	#
173	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
174	# This section is mandatory
175	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
176	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
177	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
178	IGCM_debug_Verif_Exit
179	fi
180	#
181	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
182	#
183	# variable option allready typeset above
184	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
185	if [ ${option} = Seasonal ] ; then
186	FoundSeasonal=true
187	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
188	fi
189	done
190	#
191	if [ ! X${FoundSeasonal} = Xtrue ] ; then
192	eval ${compname}_${flag_post}_Seasonal=ON
193	fi
194	#
195	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
196	Seasonal=true
197	fi
198
199	# Dimension = vide si vieille card.
200	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
201	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
202	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
203	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
204	ListDimension[0]=2D
205	ListDimension[1]=3D
206	TimeSeries=false
207	iLoop=${#ListDimension[*]}
208	j=0
209	until [ $j -ge ${iLoop} ]; do
210	Dimension=${ListDimension[${j}]}
211	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
212	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
213	#
214	# Time series WITHOUT chunk
215	#
216	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
217	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
218	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
219	eval TimeSeries${Dimension}=true
220	fi
221	fi
222	#
223	# Time series WITH chunk
224	#
225	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
226	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
227	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
228	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
229	eval TimeSeriesChunck${Dimension}=true
230	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
231	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
232	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
233	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
234	fi
235	fi
236	(( j=j+1 ))
237	done
238	else
239	ListDimension[0]=""
240	TimeSeries=true
241	TimeSeries2D=false
242	TimeSeries3D=false
243	TimeSeriesChunck2D=false
244	TimeSeriesChunck3D=false
245	fi
246	fi
247	(( i=i+3 ))
248	done
249	fi
250	# Debug Print
251	IGCM_debug_Print 3 "Initialize ${compname} with driver."
252	# INIT component
253	${comp}_Initialize
254	echo
255	done
256
257	IGCM_debug_PopStack "IGCM_comp_Initialize"
258	}
259
260	#=======================================================================
261	function IGCM_comp_PrepareDeletedFiles
262	{
263	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
264
265	if [ X${2} != X. ] ; then
266	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
267	else
268	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
269	fi
270
271	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
272	}
273
274	#=======================================================================
275	function IGCM_comp_PrepareXiosFiles
276	{
277	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
278
279	typeset file
280	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
281
282	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
283	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
284	fi
285	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
286	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
287	fi
288	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
289	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
290	fi
291
292	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
293	}
294
295	#=======================================================================
296	function IGCM_comp_GetInputInitialStateFiles
297	{
298	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
299
300	# Debug Print :
301	echo
302	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
303	echo
304
305	# Only the first time step need InitialStateFiles
306	# otherwise it's BoundaryConditions
307	if ( ${FirstInitialize} ) ; then
308	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
309	typeset file_in_ file_in file_out_ file_out do_init
310	for comp in ${config_ListOfComponents[*]} ; do
311	# Initialize
312	do_init="y"
313	# Do we need to bring initial state file for this component
314	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
315	eval do_init="n"
316	else
317	# Read component Restarts parameters
318	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
319	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
320	if [ "${do_start}" = "y" ] ; then
321	do_init="n"
322	else
323	do_init="y"
324	fi
325	fi
326
327	if [ "${do_init}" = "y" ] ; then
328	# Define component
329	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
330	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
331
332	# Debug Print :
333	IGCM_debug_Print 3 "Initialisation files ${compname}"
334
335	card=${SUBMIT_DIR}/COMP/${compname}.card
336
337	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
338	ListFilesName=${compname}_InitialStateFiles_List
339
340	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
341	if [ X${FileName0} != X${NULL_STR} ] ; then
342	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
343	(( i=0 ))
344	until [ $i -ge $NbFiles ]; do
345	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
346	eval file_in=${file_in_}
347	(( i_ = i+1 ))
348	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
349	eval file_out=${file_out_}
350
351	IGCM_sys_IsFileArchived ${file_in}
352	if [ $? = 0 ] ; then
353	IGCM_sys_Get ${file_in} ${file_out}
354	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
355	else
356	IGCM_sys_Cp ${file_in} ${file_out}
357	fi
358	(( i=i+2 ))
359	done
360	fi
361	fi
362	done
363	fi
364	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
365	}
366
367	#=======================================================================
368	# Definition of Smooth modulo function
369	# usage :
370	# IGCM_SmoothModulo StringModulo value
371	#
372	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
373	# [min]:[modulo:][max]
374	# where :
375	# [] value are optionnals;
376	# empty min equal 1
377	# empty max equal infinity
378	# modulo not given or empty equal 1
379	# empty string or just ':' equal always.
380	#
381	# value : the value to test with the definition
382	#
383	# return : true(1)/false(0)
384	function IGCM_SmoothModulo
385	{
386	IGCM_debug_PushStack "IGCM_SmoothModulo"
387	typeset defVector ModValue
388
389	eval set +A defVector -- $( echo "${1}" \| \
390	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
391
392	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
393	arr[1]=${defVector[0]}
394	arr[2]=${defVector[2]}
395
396	# Test limits :
397	# ${defVector[0]} <= ${2} <= ${defVector[2]}
398	# or ${defVector[2]} == -1
399	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
400	# Test modulo
401	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
402	if [ ${ModValue} -eq 0 ] ; then
403	arr[3]=true
404	echo ${arr[@]}
405	IGCM_debug_PopStack "IGCM_SmoothModulo"
406	return 1
407	else
408	arr[3]=false
409	echo ${arr[@]}
410	IGCM_debug_PopStack "IGCM_SmoothModulo"
411	return 0
412	fi
413	else
414	arr[3]=false
415	echo ${arr[@]}
416	IGCM_debug_PopStack "IGCM_SmoothModulo"
417	return 0
418	fi
419	}
420
421	#=======================================================================
422	function IGCM_comp_GetInputSmoothFiles
423	{
424	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
425
426	# Debug Print :
427	echo
428	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
429	echo
430
431	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
432	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
433
434	for comp in ${config_ListOfComponents[*]} ; do
435	# Define component
436	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
437	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
438
439	# Debug Print :
440	IGCM_debug_Print 3 "Smooth files ${compname}"
441
442	card=${SUBMIT_DIR}/COMP/${compname}.card
443
444	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
445	ListFilesName=${compname}_SmoothFiles_List
446	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
447
448	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
449	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
450
451	(( i=0 ))
452	until [ $i -ge $NbFiles ]; do
453	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
454	eval file_in=${file_in_}
455	(( i_ = i+1 ))
456	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
457	eval file_out=${file_out_}
458
459	# define CumulPeriod definition for this file
460	(( i__ = i+2 ))
461	eval SmoothDef=\${${ListFilesName}[$i__]}
462	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
463	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
464	j=1
465	for val in ${aux} ; do
466	[ ${j} -eq 1 ] && SmoothMin=${val}
467	[ ${j} -eq 2 ] && SmoothMax=${val}
468	[ ${j} -eq 3 ] && ret=${val}
469	(( j=j+1 ))
470	done
471	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
472	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
473
474	IGCM_sys_IsFileArchived ${file_in}
475	if [ $? = 0 ] ; then
476	IGCM_sys_Get ${file_in} ${file_out}
477	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
478	else
479	IGCM_sys_Cp ${file_in} ${file_out}
480	fi
481	fi
482	(( i=i+3 ))
483	done
484	fi
485	done
486
487	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
488	}
489
490	#=======================================================================
491	function IGCM_comp_GetInputBoundaryFiles
492	{
493	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
494
495	# Debug Print :
496	echo
497	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
498	echo
499
500	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
501	typeset file_in_ file_in file_out_ file_out
502
503	if [ ${Period} = 1 ]; then
504	ListFixBoundary=" "
505	fi
506
507	for comp in ${config_ListOfComponents[*]} ; do
508
509	# Define component
510	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
511	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
512
513	# Debug Print :
514	IGCM_debug_Print 3 "Boundary files ${compname}"
515
516	card=${SUBMIT_DIR}/COMP/${compname}.card
517
518	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
519	ListFilesName=${compname}_BoundaryFiles_List
520	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
521
522	if [ X${FileName0} != X${NULL_STR} ] ; then
523	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
524
525	(( i=0 ))
526	until [ $i -ge $NbFiles ]; do
527	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
528	eval file_in=${file_in_}
529	(( i_ = i+1 ))
530	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
531	eval file_out=${file_out_}
532
533	IGCM_sys_IsFileArchived ${file_in}
534	if [ $? = 0 ] ; then
535	IGCM_sys_Get ${file_in} ${file_out}
536	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
537	else
538	IGCM_sys_Cp ${file_in} ${file_out}
539	fi
540
541	(( i=i+2 ))
542	done
543	fi
544
545	# Get non deleted files
546	if [ ${Period} = 1 ]; then
547
548	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
549	ListFilesName=${compname}_BoundaryFiles_ListNonDel
550	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
551
552	if [ X${FileName0} != X${NULL_STR} ] ; then
553	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
554
555	(( i=0 ))
556	until [ $i -ge $NbFiles ]; do
557	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
558	eval file_in=${file_in_}
559	(( i_ = i+1 ))
560	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
561	eval file_out=${file_out_}
562
563	IGCM_sys_IsFileArchived ${file_in}
564	if [ $? = 0 ] ; then
565	IGCM_sys_Get ${file_in} ${file_out}
566	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
567	else
568	IGCM_sys_Cp ${file_in} ${file_out}
569	fi
570
571	if [ X${file_out} != X. ] ; then
572	ListFixBoundary=${ListFixBoundary}" "${file_out}
573	else
574	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
575	fi
576
577	(( i=i+2 ))
578	done
579	fi
580	fi
581	done
582
583	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
584	}
585
586	#=======================================================================
587	function IGCM_comp_DelFixeBoundaryFiles
588	{
589	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
590
591	# Debug Print :
592	echo
593	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
594	echo
595
596	ls -l ${ListFixBoundary}
597	rm -f ${ListFixBoundary}
598
599	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
600	}
601
602	#=======================================================================
603	function IGCM_comp_GetInputParametersFiles
604	{
605	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
606
607	# Debug Print :
608	echo
609	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
610	echo
611
612	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
613	for comp in ${config_ListOfComponents[*]} ; do
614	# Define component
615	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
616	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
617
618	# Initialize array hosting file_def and field_def files to check and/or modify
619	unset FieldDef
620	unset FileDef
621
622	# Debug Print :
623	IGCM_debug_Print 3 "Parameters ${compname}"
624
625	card=${SUBMIT_DIR}/COMP/${compname}.card
626
627	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
628	ListFilesName=${compname}_ParametersFiles_List
629	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
630
631	if [ X${FileName0} != X${NULL_STR} ] ; then
632	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
633
634	(( i=0 ))
635	until [ $i -ge $NbFiles ]; do
636	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
637	eval file_in=${file_in_}
638	(( i_ = i+1 ))
639	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
640	eval file_out=${file_out_}
641
642	IGCM_sys_Cp ${file_in} ${file_out}
643	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
644	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
645
646	(( i=i+2 ))
647	done
648	fi
649
650	done
651
652	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
653	}
654
655	#=======================================================================
656	function IGCM_comp_GetInputRestartFiles
657	{
658	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
659
660	# Debug Print :
661	echo
662	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
663	echo
664
665	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
666	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
667	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
668	typeset file_in file_out file_in_ file_out_ file_in_Name
669	typeset -Z4 j4
670	#BASH declare j4
671
672	IsMatching=""
673
674	for comp in ${config_ListOfComponents[*]} ; do
675	# Define component
676	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
677	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
678	#
679	card=${SUBMIT_DIR}/COMP/${compname}.card
680	#
681	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
682	ListFilesName=${compname}_RestartFiles_List
683	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
684
685	# Debug Print :
686	IGCM_debug_Print 3 "restart ${compname}"
687
688	if ( ${FirstInitialize} ) ; then
689
690	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
691	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
692	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
693	CompOldName=IOS
694	config_IOS_Restart="n"
695	do_start="n"
696	config_IOS_RestartDate=-1
697	config_IOS_RestartJobName=${NULL_STR}
698	config_IOS_RestartPath=${NULL_STR}
699	else
700	eval config_${comp}_Restart="y"
701	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
702	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
703	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
704	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
705	eval CompOldName=${comp}
706	fi
707	else
708	# Read component Restarts parameters
709	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
710	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
711
712	if [ "${do_start}" = "y" ] ; then
713	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
714	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
715	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
716	else
717	eval config_${comp}_RestartDate=-1
718	eval config_${comp}_RestartJobName=${NULL_STR}
719	eval config_${comp}_RestartPath=${NULL_STR}
720	fi
721
722	eval CompOldName=\${config_${comp}_OldName}
723	if [ X${CompOldName} = X ] ; then
724	eval CompOldName=${comp}
725	fi
726
727	# Reinitialize IsMatching to allow searching for a different tar file for each component.
728	IsMatching=""
729	TarFileFound=""
730	fi
731
732	if [ "${do_start}" = "y" ] ; then
733
734	# Restore Restarts files
735	#-----------------------
736	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
737	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
738
739	(( i=1 ))
740	until [ $i -gt $NbFiles ]; do
741	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
742	eval file_in=${file_in_}
743	(( i_ = i+1 ))
744	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
745	eval file_out=${file_out_}
746
747	eval Date_tmp=\${config_${comp}_RestartDate}
748	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
749	# will be re-use
750	eval RestartPath=\${config_${comp}_RestartPath}
751	eval RestartJobName=\${config_${comp}_RestartJobName}
752	#
753	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
754	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
755
756	extension_in=$( echo ${file_in_Name##*.} )
757	extension_out=$( echo ${file_out##*.} )
758
759	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
760	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
761
762	Path_OUT=${Path_r}/${generic_restart_file_name_in}
763
764	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
765	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
766	Buffered=true
767	Archived=false
768	Tared=false
769	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
770	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
771	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
772	Buffered=false
773	Archived=true
774	Tared=false
775	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
776	else
777	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
778	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
779	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
780	Buffered=false
781	Archived=false
782	Tared=true
783	# Look after the tar file we want if we did not found it already
784	if [ X${IsMatching} = X ] ; then
785	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
786	if [ $? ] ; then
787	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
788	IsMatching=$( echo ${PotentialTarFile##*/} \| \
789	sed "s:_restart::" \| \
790	sed "s:^${RestartJobName}_::" \| \
791	sed "s:\.tar$::" \| \
792	gawk -F_ -v restartdate=${Date_r} \
793	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
794	if [ ! X${IsMatching} = X ] ; then
795	TarFileFound=${PotentialTarFile}
796	break
797	fi
798	done
799	fi
800	# Stop here if nothing has been found
801	if [ X${TarFileFound} = X ] ; then
802	IGCM_debug_Print 3 "Restart files were not found!"
803	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
804	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
805	IGCM_debug_Exit "Please double check restart settings in config.card"
806	IGCM_debug_Verif_Exit
807	fi
808	fi
809	IGCM_sys_PrepareTaredRestart ${TarFileFound}
810	TarFileLocation=$( basename ${TarFileFound} )
811	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
812	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
813	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
814	fi
815
816	if [ ${nb_restart_file} -gt 1 ] ; then
817	j=0 # BASH LINE NOT NEEDED
818	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
819	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
820	j4=${j} # BASH LINE NOT NEEDED
821	if [ X${Buffered} = Xtrue ] ; then
822	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
823	elif [ X${Archived} = Xtrue ] ; then
824	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
825	elif [ X${Tared} = Xtrue ] ; then
826	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
827	fi
828	(( j=j+1 )) #BASH LINE NOT NEEDED
829	done
830
831	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
832	if [ X${OCE_PROC_MPI} != X ] ; then
833	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
834	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
835	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
836	fi
837	fi
838	else
839	if [ X${Buffered} = Xtrue ] ; then
840	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
841	elif [ X${Archived} = Xtrue ] ; then
842	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
843	elif [ X${Tared} = Xtrue ] ; then
844	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
845	fi
846	fi
847	(( i=i+3 ))
848	done
849	else
850	if [ X${FileName0} != XNONE ] ; then
851	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
852	else
853	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
854	fi
855	fi
856	fi
857	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
858	# if not FirstInitialize and first loop of this job
859
860	# Restore Restarts files
861	#-----------------------
862	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
863	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
864
865	(( i=1 ))
866	until [ $i -gt $NbFiles ]; do
867	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
868	eval file_in=${file_in_}
869	(( i_ = i+1 ))
870	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
871	eval file_out=${file_out_}
872
873	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
874
875	extension_in=$( echo ${file_in_Name##*.} )
876	extension_out=$( echo ${file_out##*.} )
877
878	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
879	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
880
881	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
882	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
883
884	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
885	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
886	Buffered=true
887	Archived=false
888	Tared=false
889	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
890	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
891	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
892	Buffered=false
893	Archived=true
894	Tared=false
895	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
896	else
897	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
898	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
899	Buffered=false
900	Archived=false
901	Tared=true
902	# Look after the tar file we want if we did not found it already
903	if [ X${IsMatching} = X ] ; then
904	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
905	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
906	if [ ! X${IsMatching} = X ] ; then
907	TarFileFound=${PotentialTarFile}
908	break
909	fi
910	done
911	fi
912	# Stop here if nothing has been found
913	if [ X${TarFileFound} = X ] ; then
914	IGCM_debug_Print 3 "Restart files were not found!"
915	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
916	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
917	IGCM_debug_Exit "Please double check restart settings in config.card"
918	IGCM_debug_Verif_Exit
919	fi
920	IGCM_sys_PrepareTaredRestart ${TarFileFound}
921	TarFileLocation=$( basename ${TarFileFound} )
922	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
923	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
924	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
925	fi
926
927	if [ ${nb_restart_file} -gt 1 ] ; then
928	j=0 # BASH LINE NOT NEEDED
929	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
930	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
931	j4=${j} # BASH LINE NOT NEEDED
932	if [ X${Buffered} = Xtrue ] ; then
933	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
934	elif [ X${Archived} = Xtrue ] ; then
935	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
936	elif [ X${Tared} = Xtrue ] ; then
937	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
938	fi
939	(( j=j+1 )) # BASH LINE NOT NEEDED
940	done
941	else
942	if [ X${Buffered} = Xtrue ] ; then
943	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
944	elif [ X${Archived} = Xtrue ] ; then
945	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
946	elif [ X${Tared} = Xtrue ] ; then
947	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
948	fi
949	fi
950	(( i=i+3 ))
951	done
952	else
953	if [ X${FileName0} != XNONE ] ; then
954	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
955	else
956	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
957	fi
958	fi
959	fi
960	done
961
962	NbFiles=$( ls * 2> /dev/null \| wc -l )
963	if [ ${NbFiles} -gt 0 ] ; then
964	IGCM_sys_Chmod u+rw *
965	fi
966
967	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
968	}
969
970	#=======================================================================
971	function IGCM_comp_GetInputBinaryFiles
972	{
973	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
974
975	# Debug Print :
976	echo
977	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
978	echo
979
980	# Clean up previous pass
981	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
982
983	typeset comp ExeNameIn ExeNameOut byPass
984	typeset compilerNmbr compilerUnit compilerFull
985	byPass=false
986	for comp in ${config_ListOfComponents[*]} ; do
987	# Define component
988
989	# Copy executable for this component
990	eval ExeNameIn=\${config_Executable_${comp}[0]}
991	eval ExeNameOut=\${config_Executable_${comp}[1]}
992	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
993	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
994	# The executable is set in config.card and is different from ""
995	# Use eval to expand ExeNameIn if variables are used in the name
996	eval ExeNameIn=${ExeNameIn}
997	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
998	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
999	fi
1000	fi
1001
1002	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1003	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1004	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1005	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1006	fi
1007	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1008	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1009	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1010	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1011	fi
1012	fi
1013
1014	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1015	# Get the compiler version
1016	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1017	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1018	# Save it
1019	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1020	[ X${compilerFull} = X ] && byPass=true
1021	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1022	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1023	fi
1024	done
1025
1026	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1027	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1028
1029	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1030	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1031	fi
1032
1033	# Test on compiler version for IPSLCM6* configuration on irene (only for CMIP6 production)
1034	if [ ${SYSTEM} = irene ]; then
1035	if ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.13 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.14 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.15 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.1 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM5A2.1 )" != "X" ] && [ X${compilerFull} != XV17 ] ) ; then
1036	IGCM_debug_Exit "IPSLCM6.0.13, IPSLCM6.0.14, IPSLCM6.0.15, IPSLCM6.1 and IPSLCM5A2.1 must be compiled with intel 2017 compiler"
1037	fi
1038	fi
1039
1040	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1041	}
1042
1043	#=======================================================================
1044	function IGCM_comp_PeriodStart
1045	{
1046	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1047
1048	# Debug Print :
1049	echo
1050	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1051	echo
1052
1053	typeset ExeNameIn ExeNameOut
1054	typeset comp compname comptagname
1055	for comp in ${config_ListOfComponents[*]} ; do
1056	# Define component
1057	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1058	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1059
1060	# Copy executable for this component
1061	eval ExeNameIn=\${config_Executable_${comp}[0]}
1062	eval ExeNameIn=${ExeNameIn}
1063	eval ExeNameOut=\${config_Executable_${comp}[1]}
1064
1065	# Debug Print
1066	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1067	# UPDATE component
1068	${comp}_PeriodStart 2> /dev/null
1069
1070	done
1071
1072	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1073	}
1074
1075
1076
1077	#=======================================================================
1078	function IGCM_comp_modifyFile
1079	{
1080	#
1081	# syntax: IGCM_comp_modifyFile filein key [value]
1082	#
1083	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1084	#
1085	# This function is used to replace a pattern in a file for a specific variable.
1086	#
1087	# Arguments:
1088	# - filein : the file in run directory in which the variable should be set
1089	# - key : the variable to modify
1090	# - value : the value to set the key equal to
1091	#
1092	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1093
1094	typeset filein key value pattern
1095
1096	# Set local variables and test the arguments
1097	if [ $# = 3 ] ; then
1098	# Normal case with 3 arguments
1099	filein=$1 ; key=$2 ; value=$3
1100	else
1101	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1102	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1103	return
1104	fi
1105	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1106
1107	# Test if the file exist
1108	if [ ! -f ${filein} ] ; then
1109	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1110	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1111	return
1112	fi
1113
1114	# Read the line with key in the file without the comments
1115	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1116
1117	# Verify the existance of the pattern
1118	if [ X"${pattern}" = X ] ; then
1119	# Variable key is not set in filein, stop.
1120	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1121	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1122	return
1123	fi
1124
1125	# Now change key in filein
1126	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1127	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1128	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1129	\mv ${filein}.tmp ${filein}
1130
1131	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1132	}
1133
1134	#=======================================================================
1135	function IGCM_comp_modifyDefFile
1136	{
1137	#
1138	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1139	#
1140	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1141	#
1142	# This function is used to modify a parameter file for a specific variable.
1143	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1144	# This function can be used in the comp.driver files for the components.
1145	#
1146	# Arguments:
1147	# - type : first argument must be blocker, nonblocker or force
1148	# For "blocker" case, the variable must be attributed the keyworld AUTO
1149	# otherwise this function will exit.
1150	# For "nonblocker" case, the user can remove or modify the variable. For
1151	# this case, as long as AUTO is not set, no modification will be done.
1152	# For "force" case, the variable will be modified even if it is not set to AUTO
1153	# - filein : the file in run directory of .def type in which the variable should be set
1154	# - key : the variable to modify
1155	# - value : the value to set the key equal to, optional. If value is not set or if
1156	# value=DEFAULT, then a default value must be given in filein using syntax :
1157	# key= AUTO : DEFAULT=def_value
1158	#
1159	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1160
1161	typeset type filein key value
1162	typeset filelist nb_occ modify
1163
1164	# Set local variables and test the arguments
1165	if [ $# = 4 ] ; then
1166	# Normal case with 4 arguments
1167	type=$1 ; filein=$2 ; key=$3 ; value=$4
1168	elif [ $# = 3 ] ; then
1169	# Normal case with 3 arguments
1170	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1171	else
1172	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1173	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1174	return
1175	fi
1176	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1177
1178	# Test if first argument is correct
1179	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1180	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1181	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1182	return
1183	fi
1184
1185	# Test if the file exist.
1186	# Exit with error if the file does not exist for the case blocker or force.
1187	# Only return for the case nonblocker.
1188	if [ ! -f ${filein} ] ; then
1189	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1190	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1191	else
1192	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1193	fi
1194	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1195	return
1196	fi
1197
1198	# Define list of files to test using all files with suffix .def (except used*.def)
1199	filelist=$( ls *def \| grep -v used )
1200
1201	# Count number of occurances for the key in all files
1202	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1203
1204	# Test if key is set several times
1205	if [ ${nb_occ} -gt 1 ] ; then
1206	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1207	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1208	return
1209	fi
1210
1211	# Treatement according to different cases
1212	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1213	# Stop if the key is never set and the function is blocker
1214	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1215	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1216	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1217	# The key is not set but it is a nonblocker call so nothing is done.
1218	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1219	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1220	modify=no
1221	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1222	# Variable key is not set in filein, stop.
1223	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1224	fi
1225
1226	# Check if AUTO is set in the filein on the same line as the key variable
1227	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1228	# Modification will be done for all cases
1229	modify=yes
1230	else
1231	# The variable was not set to AUTO
1232	if [ ${type} = blocker ] ; then
1233	# Exit because this is a blocker call
1234	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1235	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1236	return
1237	elif [ ${type} = nonblocker ] ; then
1238	# Do nothing. Suppose that the user did set the variable correct
1239	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1240	modify=no
1241	elif [ ${type} = force ] ; then
1242	# Force modification
1243	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1244	modify=yes
1245	fi
1246	fi
1247
1248	# Do the modifcation now
1249	if [ ${modify} = yes ] ; then
1250
1251	# For option DEFAULT, read default value from file.
1252	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1253	# Case to set DEFAULT value
1254	# Read default value from filein
1255	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1256
1257	if [ X"${value}" = X ] ; then
1258	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1259	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1260	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1261	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1262	return
1263	fi
1264	fi
1265
1266	# Now change key in filein
1267	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1268	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1269	\mv ${filein}.tmp ${filein}
1270	fi
1271	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1272	}
1273
1274	#=======================================================================
1275	function IGCM_comp_modifyNamelist
1276	{
1277	#
1278	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1279	#
1280	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1281	#
1282	# This function is used to modify a parameter file for a specific variable.
1283	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1284	# This function can be used in the comp.driver files for the components.
1285	#
1286	# Arguments:
1287	# - type : first argument must be blocker, nonblocker or force
1288	# For "blocker" case, the variable must be attributed the keyworld AUTO
1289	# otherwise this function will exit.
1290	# For "nonblocker" case, the user can remove or modify the variable. For
1291	# this case, as long as AUTO is not set, no modification will be done.
1292	# For "force" case, the variable will be modified even if it is not set to AUTO
1293	# - filein : the file in run directory of .def type in which the variable should be set
1294	# - key : the variable to modify
1295	# - value : the value to set the key equal to, optional. If value is not set or if
1296	# value=DEFAULT, then a default value must be given in filein using syntax :
1297	# key= AUTO : DEFAULT=def_value
1298	#
1299	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1300
1301	typeset type filein key value pattern modify
1302
1303	# Set local variables and test the arguments
1304	if [ $# = 4 ] ; then
1305	# Normal case with 4 arguments
1306	type=$1 ; filein=$2 ; key=$3 ; value=$4
1307	elif [ $# = 3 ] ; then
1308	# Normal case with 3 arguments
1309	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1310	else
1311	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1312	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1313	return
1314	fi
1315	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1316
1317	# Test if first argument is correct
1318	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1319	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1320	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1321	return
1322	fi
1323
1324	# Test if the file exist.
1325	# Exit with error if the file does not exist for the case blocker or force.
1326	# Only return for the case nonblocker.
1327	if [ ! -f ${filein} ] ; then
1328	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1329	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1330	else
1331	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1332	fi
1333	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1334	return
1335	fi
1336
1337	# Read the line with key in the file without the comments
1338	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1339
1340	# Verify the existance of the pattern
1341	if [ X"$pattern" = X ] ; then
1342	# Variable key is not set in filein, stop.
1343	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1344	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1345	return
1346	fi
1347
1348	# Check if the variable is set to AUTO in the filein
1349	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1350	# Modification will be done for all cases
1351	modify=yes
1352	else
1353	# The variable was not set to AUTO
1354	if [ ${type} = blocker ] ; then
1355	# Exit because this is a blocker call
1356	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1357	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1358	return
1359	elif [ ${type} = nonblocker ] ; then
1360	# Do nothing. Suppose that the user did set the variable correct
1361	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1362	modify=no
1363	elif [ ${type} = force ] ; then
1364	# Force modification
1365	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1366	modify=yes
1367	fi
1368	fi
1369
1370	# Do the modifcation now
1371	if [ ${modify} = yes ] ; then
1372
1373	# For option DEFAULT, read default value from file.
1374	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1375	# Case to set DEFAULT value
1376	# Read default value from filein
1377	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1378
1379	if [ X"${value}" = X ] ; then
1380	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1381	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1382	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1383	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1384	return
1385	fi
1386	fi
1387
1388	# Now change key in filein
1389	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1390	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1391	\mv ${filein}.tmp ${filein}
1392	fi
1393	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1394	}
1395
1396	#=======================================================================
1397	function IGCM_comp_modifyXmlFile
1398	{
1399	#
1400	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1401	#
1402	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1403	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1404	#
1405	# This function is used to modify the value for a specific attribute and variable id.
1406	# The file must be a valid xml file.
1407	# This function can be used in the comp.driver files for the components.
1408	#
1409	# Arguments:
1410	# - type : first argument must be blocker, nonblocker or force.
1411	# For "blocker" case, the variable must be attributed the keyworld AUTO
1412	# otherwise this function will exit.
1413	# For "nonblocker" case, the user can remove or modify the variable. For
1414	# this case, as long as AUTO is not set, no modification will be done.
1415	# For "force" case, the variable will be modified even if it is not set to AUTO
1416	# - filein : the file in run directory of .xml type in which the variable should be set
1417	# - keyid : the variable to modify
1418	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1419	# - value : the value to set in the filein
1420	#
1421	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1422
1423	typeset type filein keyid keyattrib value modify
1424
1425	# Set local variables and test the arguments
1426	if [ $# = 5 ] ; then
1427	# Normal case with 4 arguments
1428	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1429	else
1430	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1431	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1432	return
1433	fi
1434	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1435
1436	# Test if first argument is correct
1437	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1438	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1439	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1440	return
1441	fi
1442
1443	# Test if the file exist.
1444	# Exit with error if the file does not exist for the case blocker or force.
1445	# Only return for the case nonblocker.
1446	if [ ! -f ${filein} ] ; then
1447	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1448	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1449	else
1450	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1451	fi
1452	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1453	return
1454	fi
1455
1456	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1457	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1458	if [ ${type} = nonblocker ] ; then
1459	# This is a nonblocker case, print warning but do nothing else
1460	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1461	else
1462	# This is a blocker or force case : stop now
1463	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1464	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1465	return
1466	fi
1467	fi
1468
1469	# Check if AUTO is set on the same line as keyid and keyattrib
1470	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1471	# Modification will be done
1472	modify=yes
1473	else
1474	if [ ${type} = blocker ] ; then
1475	# Exit, the variable must be set to AUTO
1476	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1477	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1478	return
1479	elif [ ${type} = nonblocker ] ; then
1480	# Nothing will be done
1481	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1482	modify=no
1483	elif [ ${type} = force ] ; then
1484	# Force modification
1485	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1486	modify=yes
1487	fi
1488	fi
1489
1490	# Do the modifcation now
1491	if [ ${modify} = yes ] ; then
1492	if [ ${keyattrib} = NONE ] ; then
1493	# Case to modify the variable itself
1494	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1495	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1496	else
1497	# Check if keyattrib is set on the same line as keyid
1498	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1499	# Case to modify the attribute value
1500	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1501	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1502	else
1503	# Case to add the attribute and its value
1504	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1505	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1506	fi
1507	fi
1508	\mv ${filein}.tmp ${filein}
1509	fi
1510	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1511	}
1512
1513	#=======================================================================
1514	function IGCM_comp_Update
1515	{
1516	IGCM_debug_PushStack "IGCM_comp_Update"
1517
1518	# Debug Print :
1519	echo
1520	IGCM_debug_Print 1 "IGCM_comp_Update"
1521	echo
1522
1523	typeset comp compname comptagname
1524	for comp in ${config_ListOfComponents[*]} ; do
1525	# Define component
1526	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1527	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1528
1529	# Debug Print
1530	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1531	# UPDATE component
1532	${comp}_Update
1533
1534	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1535	if [ -f timeseries_def_${compname}.xml ]; then
1536	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1537	for line in $( cat ts.temp.${compname}.txt ); do
1538	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1539	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1540	case ${output_freq} in
1541	Y\|y)
1542	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1543	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1544	;;
1545	MO\|mo)
1546	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1547	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1548	;;
1549	D\|d)
1550	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1551	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1552	;;
1553	S\|s)
1554	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1555	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1556	;;
1557	esac
1558	done
1559	fi
1560
1561	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1562	if [ -f dr2xml_${compname}.xml ]; then
1563	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
1564	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1565	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1566	# Modify path from dr2xml_{compname}.xml
1567	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
1568	${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
1569	else
1570	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1571	fi
1572	# Overwrite the original file
1573	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1574	fi
1575	fi
1576	done
1577
1578	IGCM_debug_PopStack "IGCM_comp_Update"
1579	}
1580
1581	#=======================================================================
1582	function IGCM_comp_Finalize
1583	{
1584	IGCM_debug_PushStack "IGCM_comp_Finalize"
1585
1586	# Debug Print :
1587	echo
1588	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1589	echo
1590
1591	typeset ListTextName TextName0
1592	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1593	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1594	typeset -Z4 j4 #BASH declare j4
1595	typeset list_file nlist_file
1596	typeset compactoutputs
1597
1598	# Initialize array hosting list of rebuilded files to copy
1599	unset rebuildedActionsList
1600
1601	# Text compacting options
1602	compactoutputs=false
1603	if [ X${JobType} != XRUN ] ; then
1604	compactoutputs=true
1605	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1606	compactoutputs=true
1607	fi
1608
1609	# Prepare headers for the shell dedicated to offline rebuild
1610	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1611	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1612	if [ ${DRYRUN} -le 1 ] ; then
1613	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1614	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1615	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1616	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1617	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1618	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1619	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1620	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1621	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1622	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1623	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1624	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1625	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1626	fi
1627	fi
1628
1629	for comp in ${config_ListOfComponents[*]} ; do
1630	# Define component
1631	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1632	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1633
1634	# Debug Print
1635	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1636	# FINALIZE component
1637	${comp}_Finalize
1638
1639	card=${SUBMIT_DIR}/COMP/${compname}.card
1640
1641	# Save Output Text files of models
1642	#---------------------------------
1643	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1644	IGCM_card_DefineArrayFromOption ${card} OutputText List
1645	ListTextName=${compname}_OutputText_List
1646
1647	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1648	if [ X${TextName0} != X${NULL_STR} ] ; then
1649	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1650
1651	(( i=0 ))
1652	until [ $i -eq $NbFiles ]; do
1653	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1654	eval file_out=${PREFIX}_${file_in}
1655
1656	(( i=i+1 ))
1657
1658	unset list_file
1659	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1660	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1661	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 )
1662	nlist_file=${#list_file[@]}
1663	if [ ${nlist_file} -gt 1 ] ; then
1664	if ( ${compactoutputs} ) ; then
1665	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1666	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1667	echo ${list_file[*]} > ${file_out}
1668	echo "" >> ${file_out}
1669
1670	(( i_ = 0 ))
1671	for file in ${list_file[@]} ; do
1672	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1673	echo "\| " ${i_} " " ${file} >> ${file_out}
1674	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1675	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1676	echo "" >> ${file_out}
1677	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1678	(( i_ = i_ + 1 ))
1679	done
1680	if ( ${ExecutionFail} ) ; then
1681	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1682	fi
1683
1684	if [ X${Pack} = Xtrue ] ; then
1685	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1686	else
1687	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1688	fi
1689
1690	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1691	else
1692	for file in ${list_file[@]} ; do
1693	if ( ${ExecutionFail} ) ; then
1694	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1695	fi
1696
1697	if [ X${Pack} = Xtrue ] ; then
1698	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1699	else
1700	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1701	fi
1702
1703	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1704	done
1705	fi
1706	else
1707	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1708	eval IGCM_sys_Mv ${file_in}* ${file_in}
1709	fi
1710
1711	if ( ${ExecutionFail} ) ; then
1712	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1713	fi
1714
1715	if [ X${Pack} = Xtrue ] ; then
1716	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1717	else
1718	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1719	fi
1720	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1721	fi
1722	done
1723	fi
1724
1725	# Save Restarts files
1726	#--------------------
1727	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1728	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1729	ListFilesName=${compname}_RestartFiles_List
1730	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1731
1732	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1733	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1734
1735	(( i=0 ))
1736	until [ $i -ge $NbFiles ]; do
1737	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1738	eval file_in=${file_in_}
1739
1740	(( i_ = i+1 ))
1741	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1742	eval file_out=${file_out_}
1743
1744	(( i_ = i+2 ))
1745	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1746	eval file_outin=${file_outin_}
1747
1748	generic_restart_file_name_in=$( basename ${file_in} .nc )
1749	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1750	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1751
1752	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1753	if [ ${nb_restart_file} -gt 1 ] ; then
1754	j=0 # BASH LINE NOT NEEDED
1755	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1756	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1757	j4=${j} # BASH LINE NOT NEEDED
1758	if [ X${Pack} = Xtrue ] ; then
1759	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1760	else
1761	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1762	fi
1763	if [ ! ${file_in} = ${file_outin} ] ; then
1764	if ( ${ExitFlag} ) ; then
1765	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1766	else
1767	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1768	fi
1769	fi
1770	(( j=j+1 )) # BASH LINE NOT NEEDED
1771	done
1772	else
1773	if [ X${Pack} = Xtrue ] ; then
1774	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1775	else
1776	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1777	fi
1778	if [ ! ${file_in} = ${file_outin} ] ; then
1779	if ( ${ExitFlag} ) ; then
1780	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1781	else
1782	IGCM_sys_Mv ${file_in} ${file_outin}
1783	fi
1784	fi
1785	fi
1786
1787	(( i=i+3 ))
1788	done
1789	else
1790	if [ X${FileName0} != XNONE ] ; then
1791	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1792	else
1793	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1794	fi
1795	fi
1796
1797	# Save Output files
1798	#------------------
1799	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1800	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1801	ListFilesName=${compname}_OutputFiles_List
1802	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1803
1804	if [ X${FileName0} != X${NULL_STR} ] ; then
1805	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1806
1807	(( i=0 ))
1808	until [ $i -ge $NbFiles ]; do
1809	SaveOnArchive=true
1810	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1811	eval file_in=${file_in_}
1812	(( i_ = i+1 ))
1813	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1814	eval file_out=${file_out_}
1815	#
1816	# Override file_out path remplacing R_SAVE by R_BUFR
1817	#
1818	if [ X${Pack} = Xtrue ] ; then
1819	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1820	fi
1821	#
1822	# Not necessarily the best option. /!\ Potential side effects /!\
1823	#
1824	(( i_ = i+2 ))
1825	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1826	#
1827	generic_file_name=$( basename ${file_in} .nc )
1828	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1829	#
1830	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1831	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1832	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1833	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1834	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1835	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1836	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1837	#
1838	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
1839	if [ ${file_in} = output.abort.nc ] ; then
1840	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
1841	else
1842	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
1843	fi
1844	else
1845	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1846	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1847
1848	# Prepare the shell dedicated to offline rebuild
1849	if [ $DRYRUN -le 1 ]; then
1850	if [ ${file_in} = histstn.nc ] ; then
1851	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1852	else
1853	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1854	fi
1855	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1856	fi
1857	#
1858	# Load Patch we need to apply and apply
1859	if [ $DRYRUN -le 1 ]; then
1860	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1861	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1862	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1863	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1864	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1865	done
1866	fi
1867	fi
1868	#
1869	if [ $DRYRUN -le 1 ]; then
1870	if [ X${Pack} = Xtrue ] ; then
1871	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1872	else
1873	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1874	fi
1875	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1876	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1877	fi
1878	SaveOnArchive=false
1879	fi
1880	fi
1881	#
1882	if [ ${SaveOnArchive} = true ] ; then
1883	#
1884	# Rebuild has been done online or it was not needed
1885	#
1886	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1887	#
1888	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1889	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1890	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1891	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1892	#
1893	if [ $DRYRUN -le 1 ]; then
1894	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1895	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1896	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1897	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1898	done
1899	#
1900	if [ X${Pack} = Xtrue ] ; then
1901	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1902	else
1903	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1904	fi
1905	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1906	#
1907	fi
1908	else
1909	#
1910	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1911	#
1912	if [ X${Pack} = Xtrue ] ; then
1913	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1914	else
1915	IGCM_sys_Put_Out ${file_in} ${file_out}
1916	fi
1917	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1918	if [ ${nb_rebuild_file} -gt 1 ] ; then
1919	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1920	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1921	done
1922	fi
1923	fi
1924	fi
1925	(( i=i+3 ))
1926	done
1927	fi
1928	echo
1929	done
1930	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1931	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1932	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1933	i=0
1934	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1935	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1936	(( i=i+1 ))
1937	done
1938	fi
1939	IGCM_debug_PopStack "IGCM_comp_Finalize"
1940	}

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