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libIGCM_comp.ksh @ 1624

Last change on this file since 1624 was 1624, checked in by jgipsl, 4 months ago

Added possibility to declare a restart file as optional which means that libIGCM want stop if the file is not found. Only a warning will be written.

For example, in the following case, if the routing_restart file is not available when starting the model or if it is not produced, libIGCM will not stop. But if the file sechiba_rest is not available, libIGCM will stop as usual.

[RestartFiles]
List=   (sechiba_rest_out.nc, sechiba_rest.nc, sechiba_rest_in.nc) ,\
        (routing_restart.nc, routing_restart.nc, routing_start.nc, OPTIONAL)

Read optional argument OPTIONAL on the line where the restart file is declared.
Each time when a restart file is not found for coping in or out, if the argument OPTIONAL is set, then just continue. If not set, the file is considered as MANDATORY and libIGCM will exist if it is missing as before.
on irene-amd and jean-zay, corrected a bug for the case in config.card DataProject?=DEFAULT

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: 83.8 KB

Line
1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
6	# $Revision:: $ Revision of last commit
7	# $Author:: $ Author of last commit
8	# $Date:: $ Date of last commit
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	#
12	#**************************************************************
13
14	#========================================================================
15	function IGCM_comp_Initialize
16	{
17	IGCM_debug_PushStack "IGCM_comp_Initialize"
18
19	# Debug Print :
20	echo
21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
22	echo
23
24	typeset comp compname comptagname auxprint card_UserChoices first_option option i j
25	for comp in ${config_ListOfComponents[*]} ; do
26
27	# Define component
28	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
29	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
30	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
31
32	# Debug Print
33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
34
35	# ${compname}.card PATH
36	card=${SUBMIT_DIR}/COMP/${compname}.card
37
38	# Manage component executable
39	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
40
41	# Define all options in section [comp]
42	IGCM_debug_Print 3 " DefineArrayFromSection : ${comp}"
43	IGCM_card_DefineArrayFromSection ${SUBMIT_DIR}/config.card ${comp}
44	eval config_comp=\${config_${comp}[*]} > /dev/null 2>&1
45	for option in ${config_comp[*]} ; do
46	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
47	done
48	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
49
50	# Debug Print :
51	eval auxprint=\${config_${comp}_WriteFrequency}
52	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
53	#2> /dev/null
54
55	# Debug Print :
56	IGCM_debug_Print 2 "Initialize following component library"
57
58	# Source drivers in directory DRIVER if it exist
59	# else source them from directory COMP
60	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
61	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
62	# Source component library
63	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
64	else
65	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
66	# Source component library
67	. ${SUBMIT_DIR}/COMP/${compname}.driver
68	fi
69	IGCM_debug_Print 3 "With tag : ${comptagname}"
70
71	# Debug Print
72	IGCM_debug_Print 3 "Initialize ${comp} output directory."
73
74	# Define ARCHIVED Dirs
75	eval R_OUT_${comp}=${R_SAVE}/${comp}
76	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
77
78	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
79	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
80
81	eval R_OUT_${comp}_A=\${R_OUT_${comp}}/Analyse
82	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_A}
83
84	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
86
87	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
88	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
89
90	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
91	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
92	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
93	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
94
95	eval R_OUT_${comp}_A_H=\${R_OUT_${comp}_A}/TS_HF
96	eval R_OUT_${comp}_A_D=\${R_OUT_${comp}_A}/TS_DA
97	eval R_OUT_${comp}_A_M=\${R_OUT_${comp}_A}/TS_MO
98	eval R_OUT_${comp}_A_Y=\${R_OUT_${comp}_A}/TS_YE
99
100	# Define BUFFERED Dirs
101	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
102	eval R_BUF_${comp}=${R_BUFR}/${comp}
103	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
104
105	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
107
108	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
110
111	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
112	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
113
114	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
115	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
116
117	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
118	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
119	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
120	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
121
122	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
123	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
124	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
125	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
126
127	# Define CMIP6 Dirs
128	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
129	fi
130
131	# Read UserChoices section of component card
132	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
133	IGCM_card_DefineArrayFromSection ${card} UserChoices
134	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
135
136	# If section is not empty we define corresponding variables
137	if [ X${first_option} != X"Error:" ] ; then
138	if [ X${card_UserChoices[0]} != X ] ; then
139	unset card_UserChoices
140	fi
141	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
142	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
143	for option in ${card_UserChoices[*]} ; do
144	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
145	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
146	done
147	fi
148
149	# Read and Build Output File stuff
150	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
151	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
152	ListFilesName=${compname}_OutputFiles_List
153	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
154	#
155	if [ X${FileName0} != X${NULL_STR} ] ; then
156	#
157	#IGCM_debug_Print 1 "Component : ${compname}"
158	#
159	# INITIALISATION
160	#
161	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
162	#
163	i=2
164	#
165	until [ $i -ge $NbFiles ]; do
166	#
167	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
168	#
169	if [ X${flag_post} != XNONE ] ; then
170	#
171	# First of all
172	#
173	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
174	# This section is mandatory
175	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
176	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
177	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
178	IGCM_debug_Verif_Exit
179	fi
180	#
181	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
182	#
183	# variable option allready typeset above
184	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
185	if [ ${option} = Seasonal ] ; then
186	FoundSeasonal=true
187	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
188	fi
189	done
190	#
191	if [ ! X${FoundSeasonal} = Xtrue ] ; then
192	eval ${compname}_${flag_post}_Seasonal=ON
193	fi
194	#
195	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
196	Seasonal=true
197	fi
198
199	# Dimension = vide si vieille card.
200	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
201	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
202	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
203	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
204	ListDimension[0]=2D
205	ListDimension[1]=3D
206	TimeSeries=false
207	iLoop=${#ListDimension[*]}
208	j=0
209	until [ $j -ge ${iLoop} ]; do
210	Dimension=${ListDimension[${j}]}
211	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
212	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
213	#
214	# Time series WITHOUT chunk
215	#
216	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
217	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
218	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
219	eval TimeSeries${Dimension}=true
220	fi
221	fi
222	#
223	# Time series WITH chunk
224	#
225	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
226	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
227	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
228	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
229	eval TimeSeriesChunck${Dimension}=true
230	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
231	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
232	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
233	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
234	fi
235	fi
236	(( j=j+1 ))
237	done
238	else
239	ListDimension[0]=""
240	TimeSeries=true
241	TimeSeries2D=false
242	TimeSeries3D=false
243	TimeSeriesChunck2D=false
244	TimeSeriesChunck3D=false
245	fi
246	fi
247	((i_ = i +1))
248	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
249	eval Testvar=${Testvar_}
250	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
251	((i = i+4))
252	else
253	(( i=i+3 ))
254	fi
255	done
256	fi
257	# Debug Print
258	IGCM_debug_Print 3 "Initialize ${compname} with driver."
259	# INIT component
260	${comp}_Initialize
261	echo
262	done
263
264	IGCM_debug_PopStack "IGCM_comp_Initialize"
265	}
266
267	#=======================================================================
268	function IGCM_comp_PrepareDeletedFiles
269	{
270	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
271
272	if [ X${2} != X. ] ; then
273	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
274	else
275	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
276	fi
277
278	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
279	}
280
281	#=======================================================================
282	function IGCM_comp_PrepareXiosFiles
283	{
284	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
285
286	typeset file
287	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
288
289	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
290	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
291	fi
292	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
293	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
294	fi
295	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
296	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
297	fi
298
299	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
300	}
301
302	#=======================================================================
303	function IGCM_comp_GetInputInitialStateFiles
304	{
305	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
306
307	# Debug Print :
308	echo
309	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
310	echo
311
312	# Only the first time step need InitialStateFiles
313	# otherwise it's BoundaryConditions
314	if ( ${FirstInitialize} ) ; then
315	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
316	typeset file_in_ file_in file_out_ file_out do_init
317	for comp in ${config_ListOfComponents[*]} ; do
318	# Initialize
319	do_init="y"
320	# Do we need to bring initial state file for this component
321	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
322	eval do_init="n"
323	else
324	# Read component Restarts parameters
325	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
326	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
327	if [ "${do_start}" = "y" ] ; then
328	do_init="n"
329	else
330	do_init="y"
331	fi
332	fi
333
334	if [ "${do_init}" = "y" ] ; then
335	# Define component
336	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
337	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
338
339	# Debug Print :
340	IGCM_debug_Print 3 "Initialisation files ${compname}"
341
342	card=${SUBMIT_DIR}/COMP/${compname}.card
343
344	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
345	ListFilesName=${compname}_InitialStateFiles_List
346
347	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
348	if [ X${FileName0} != X${NULL_STR} ] ; then
349	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
350	(( i=0 ))
351	until [ $i -ge $NbFiles ]; do
352	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
353	eval file_in=${file_in_}
354	(( i_ = i+1 ))
355	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
356	eval file_out=${file_out_}
357
358	IGCM_sys_IsFileArchived ${file_in}
359	if [ $? = 0 ] ; then
360	IGCM_sys_Get ${file_in} ${file_out}
361	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
362	else
363	IGCM_sys_Cp ${file_in} ${file_out}
364	fi
365	(( i=i+2 ))
366	done
367	fi
368	fi
369	done
370	fi
371	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
372	}
373
374	#=======================================================================
375	# Definition of Smooth modulo function
376	# usage :
377	# IGCM_SmoothModulo StringModulo value
378	#
379	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
380	# [min]:[modulo:][max]
381	# where :
382	# [] value are optionnals;
383	# empty min equal 1
384	# empty max equal infinity
385	# modulo not given or empty equal 1
386	# empty string or just ':' equal always.
387	#
388	# value : the value to test with the definition
389	#
390	# return : true(1)/false(0)
391	function IGCM_SmoothModulo
392	{
393	IGCM_debug_PushStack "IGCM_SmoothModulo"
394	typeset defVector ModValue
395
396	eval set +A defVector -- $( echo "${1}" \| \
397	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
398
399	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
400	arr[1]=${defVector[0]}
401	arr[2]=${defVector[2]}
402
403	# Test limits :
404	# ${defVector[0]} <= ${2} <= ${defVector[2]}
405	# or ${defVector[2]} == -1
406	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
407	# Test modulo
408	ModValue=$( expr $ ${2} - ${defVector[0]} $ % ${defVector[1]} )
409	if [ ${ModValue} -eq 0 ] ; then
410	arr[3]=true
411	echo ${arr[@]}
412	IGCM_debug_PopStack "IGCM_SmoothModulo"
413	return 1
414	else
415	arr[3]=false
416	echo ${arr[@]}
417	IGCM_debug_PopStack "IGCM_SmoothModulo"
418	return 0
419	fi
420	else
421	arr[3]=false
422	echo ${arr[@]}
423	IGCM_debug_PopStack "IGCM_SmoothModulo"
424	return 0
425	fi
426	}
427
428	#=======================================================================
429	function IGCM_comp_GetInputSmoothFiles
430	{
431	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
432
433	# Debug Print :
434	echo
435	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
436	echo
437
438	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
439	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
440
441	for comp in ${config_ListOfComponents[*]} ; do
442	# Define component
443	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
444	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
445
446	# Debug Print :
447	IGCM_debug_Print 3 "Smooth files ${compname}"
448
449	card=${SUBMIT_DIR}/COMP/${compname}.card
450
451	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
452	ListFilesName=${compname}_SmoothFiles_List
453	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
454
455	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
456	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
457
458	(( i=0 ))
459	until [ $i -ge $NbFiles ]; do
460	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
461	eval file_in=${file_in_}
462	(( i_ = i+1 ))
463	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
464	eval file_out=${file_out_}
465
466	# define CumulPeriod definition for this file
467	(( i__ = i+2 ))
468	eval SmoothDef=\${${ListFilesName}[$i__]}
469	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
470	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
471	j=1
472	for val in ${aux} ; do
473	[ ${j} -eq 1 ] && SmoothMin=${val}
474	[ ${j} -eq 2 ] && SmoothMax=${val}
475	[ ${j} -eq 3 ] && ret=${val}
476	(( j=j+1 ))
477	done
478	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
479	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
480
481	IGCM_sys_IsFileArchived ${file_in}
482	if [ $? = 0 ] ; then
483	IGCM_sys_Get ${file_in} ${file_out}
484	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
485	else
486	IGCM_sys_Cp ${file_in} ${file_out}
487	fi
488	fi
489	(( i=i+3 ))
490	done
491	fi
492	done
493
494	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
495	}
496
497	#=======================================================================
498	function IGCM_comp_GetInputBoundaryFiles
499	{
500	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
501
502	# Debug Print :
503	echo
504	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
505	echo
506
507	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
508	typeset file_in_ file_in file_out_ file_out
509
510	if [ ${Period} = 1 ]; then
511	ListFixBoundary=" "
512	fi
513
514	for comp in ${config_ListOfComponents[*]} ; do
515
516	# Define component
517	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
518	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
519
520	# Debug Print :
521	IGCM_debug_Print 3 "Boundary files ${compname}"
522
523	card=${SUBMIT_DIR}/COMP/${compname}.card
524
525	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
526	ListFilesName=${compname}_BoundaryFiles_List
527	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
528
529	if [ X${FileName0} != X${NULL_STR} ] ; then
530	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
531
532	(( i=0 ))
533	until [ $i -ge $NbFiles ]; do
534	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
535	eval file_in=${file_in_}
536	(( i_ = i+1 ))
537	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
538	eval file_out=${file_out_}
539
540	IGCM_sys_IsFileArchived ${file_in}
541	if [ $? = 0 ] ; then
542	IGCM_sys_Get ${file_in} ${file_out}
543	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
544	else
545	IGCM_sys_Cp ${file_in} ${file_out}
546	fi
547
548	(( i=i+2 ))
549	done
550	fi
551
552	# Get non deleted files
553	if [ ${Period} = 1 ]; then
554
555	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
556	ListFilesName=${compname}_BoundaryFiles_ListNonDel
557	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
558
559	if [ X${FileName0} != X${NULL_STR} ] ; then
560	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
561
562	(( i=0 ))
563	until [ $i -ge $NbFiles ]; do
564	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
565	eval file_in=${file_in_}
566	(( i_ = i+1 ))
567	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
568	eval file_out=${file_out_}
569
570	IGCM_sys_IsFileArchived ${file_in}
571	if [ $? = 0 ] ; then
572	IGCM_sys_Get ${file_in} ${file_out}
573	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
574	else
575	IGCM_sys_Cp ${file_in} ${file_out}
576	fi
577
578	if [ X${file_out} != X. ] ; then
579	ListFixBoundary=${ListFixBoundary}" "${file_out}
580	else
581	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
582	fi
583
584	(( i=i+2 ))
585	done
586	fi
587	fi
588	done
589
590	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
591	}
592
593	#=======================================================================
594	function IGCM_comp_DelFixeBoundaryFiles
595	{
596	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
597
598	# Debug Print :
599	echo
600	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
601	echo
602
603	ls -l ${ListFixBoundary}
604	rm -f ${ListFixBoundary}
605
606	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
607	}
608
609	#=======================================================================
610	function IGCM_comp_GetInputParametersFiles
611	{
612	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
613
614	# Debug Print :
615	echo
616	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
617	echo
618
619	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
620	for comp in ${config_ListOfComponents[*]} ; do
621	# Define component
622	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
623	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
624
625	# Initialize array hosting file_def and field_def files to check and/or modify
626	unset FieldDef
627	unset FileDef
628
629	# Debug Print :
630	IGCM_debug_Print 3 "Parameters ${compname}"
631
632	card=${SUBMIT_DIR}/COMP/${compname}.card
633
634	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
635	ListFilesName=${compname}_ParametersFiles_List
636	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
637
638	if [ X${FileName0} != X${NULL_STR} ] ; then
639	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
640
641	(( i=0 ))
642	until [ $i -ge $NbFiles ]; do
643	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
644	eval file_in=${file_in_}
645	(( i_ = i+1 ))
646	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
647	eval file_out=${file_out_}
648
649	IGCM_sys_Cp ${file_in} ${file_out}
650	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
651	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
652
653	(( i=i+2 ))
654	done
655	fi
656
657	done
658
659	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
660	}
661
662	#=======================================================================
663	function IGCM_comp_GetInputRestartFiles
664	{
665	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
666
667	# Debug Print :
668	echo
669	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
670	echo
671
672	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
673	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
674	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
675	typeset file_in file_out file_in_ file_out_ file_in_Name
676	typeset -Z4 j4
677	#BASH declare j4
678
679	IsMatching=""
680
681	for comp in ${config_ListOfComponents[*]} ; do
682	# Define component
683	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
684	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
685	#
686	card=${SUBMIT_DIR}/COMP/${compname}.card
687	#
688	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
689	ListFilesName=${compname}_RestartFiles_List
690	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
691
692	# Debug Print :
693	IGCM_debug_Print 3 "restart ${compname}"
694
695	if ( ${FirstInitialize} ) ; then
696
697	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
698	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
699	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
700	CompOldName=IOS
701	config_IOS_Restart="n"
702	do_start="n"
703	config_IOS_RestartDate=-1
704	config_IOS_RestartJobName=${NULL_STR}
705	config_IOS_RestartPath=${NULL_STR}
706	else
707	eval config_${comp}_Restart="y"
708	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
709	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
710	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
711	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
712	eval CompOldName=${comp}
713	fi
714	else
715	# Read component Restarts parameters
716	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
717	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
718
719	if [ "${do_start}" = "y" ] ; then
720	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
721	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
722	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
723	else
724	eval config_${comp}_RestartDate=-1
725	eval config_${comp}_RestartJobName=${NULL_STR}
726	eval config_${comp}_RestartPath=${NULL_STR}
727	fi
728
729	eval CompOldName=\${config_${comp}_OldName}
730	if [ X${CompOldName} = X ] ; then
731	eval CompOldName=${comp}
732	fi
733
734	# Reinitialize IsMatching to allow searching for a different tar file for each component.
735	IsMatching=""
736	TarFileFound=""
737	fi
738
739	if [ "${do_start}" = "y" ] ; then
740
741	# Restore Restarts files
742	#-----------------------
743	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
744	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
745
746	(( i=1 ))
747	until [ $i -gt $NbFiles ]; do
748	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
749	eval file_in=${file_in_}
750	(( i_ = i+1 ))
751	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
752	eval file_out=${file_out_}
753
754	(( i_ = i+2 ))
755	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
756	if [ X${is_opt} = XOPTIONAL ] ; then
757	echo ${file_in} is optional
758	(( i=i+4 ))
759	else
760	is_opt="MANDATORY"
761	echo ${file_in} is mandatory
762	(( i=i+3 ))
763	fi
764	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=y)"
765
766	eval Date_tmp=\${config_${comp}_RestartDate}
767	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
768	# will be re-use
769	eval RestartPath=\${config_${comp}_RestartPath}
770	eval RestartJobName=\${config_${comp}_RestartJobName}
771	#
772	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
773	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
774
775	extension_in=$( echo ${file_in_Name##*.} )
776	extension_out=$( echo ${file_out##*.} )
777
778	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
779	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
780
781	Path_OUT=${Path_r}/${generic_restart_file_name_in}
782
783	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
784	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
785	Buffered=true
786	Archived=false
787	Tared=false
788	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
789	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
790	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
791	Buffered=false
792	Archived=true
793	Tared=false
794	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
795	else
796	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
797	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
798	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
799	Buffered=false
800	Archived=false
801	Tared=true
802	# Look after the tar file we want if we did not found it already
803	if [ X${IsMatching} = X ] ; then
804	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
805	if [ $? ] ; then
806	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
807	IsMatching=$( echo ${PotentialTarFile##*/} \| \
808	sed "s:_restart::" \| \
809	sed "s:^${RestartJobName}_::" \| \
810	sed "s:\.tar$::" \| \
811	gawk -F_ -v restartdate=${Date_r} \
812	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
813	if [ ! X${IsMatching} = X ] ; then
814	TarFileFound=${PotentialTarFile}
815	break
816	fi
817	done
818	fi
819	# Stop here if nothing has been found
820	if [ X${TarFileFound} = X ] ; then
821	IGCM_debug_Print 3 "Restart files were not found!"
822	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
823	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
824	if [ ${is_opt} = 'OPTIONAL' ] ; then
825	IGCM_debug_Print 3 "The restart file is optional. Now continue."
826	nb_restart_file=0
827	Tared=false
828	else
829	IGCM_debug_Exit "Please double check restart settings in config.card"
830	IGCM_debug_Verif_Exit
831	fi
832	fi
833	fi
834
835	if [ X${Tared} = Xtrue ] ; then
836	# The tar file exist but not sure all files are inside
837	IGCM_sys_PrepareTaredRestart ${TarFileFound}
838	TarFileLocation=$( basename ${TarFileFound} )
839	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in}*.${extension_in} \| wc -l )
840	if [ ${nb_files} -gt 0 ] ; then
841	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
842	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
843	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
844	else
845	# No file was found
846	if [ ${is_opt} = 'OPTIONAL' ] ; then
847	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
848	nb_restart_file=0
849	Tared=false
850	else
851	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
852	IGCM_debug_Exit "Please double check restart settings in config.card"
853	IGCM_debug_Verif_Exit
854	fi
855	fi
856	fi
857	fi
858
859	if [ ${nb_restart_file} -gt 1 ] ; then
860	j=0 # BASH LINE NOT NEEDED
861	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
862	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
863	j4=${j} # BASH LINE NOT NEEDED
864	if [ X${Buffered} = Xtrue ] ; then
865	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
866	elif [ X${Archived} = Xtrue ] ; then
867	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
868	elif [ X${Tared} = Xtrue ] ; then
869	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
870	fi
871	(( j=j+1 )) #BASH LINE NOT NEEDED
872	done
873
874	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
875	if [ X${OCE_PROC_MPI} != X ] ; then
876	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
877	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
878	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
879	fi
880	fi
881	else
882	if [ X${Buffered} = Xtrue ] ; then
883	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
884	elif [ X${Archived} = Xtrue ] ; then
885	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
886	elif [ X${Tared} = Xtrue ] ; then
887	if [ -f ${comp}_${file_in_Name} ] ; then
888	# The file exixt
889	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
890	elif [ ${is_opt} = 'OPTIONAL' ] ; then
891	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
892	else
893	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
894	IGCM_debug_Exit "Please double check restart settings in config.card"
895	IGCM_debug_Verif_Exit
896	fi
897	fi
898	fi
899	done
900	else
901	if [ X${FileName0} != XNONE ] ; then
902	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
903	else
904	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
905	fi
906	fi
907	fi
908	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
909	# if not FirstInitialize and first loop of this job
910
911	# Restore Restarts files
912	#-----------------------
913	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
914	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
915
916	(( i=1 ))
917	until [ $i -gt $NbFiles ]; do
918	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
919	eval file_in=${file_in_}
920
921	(( i_ = i+1 ))
922	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
923	eval file_out=${file_out_}
924
925	(( i_ = i+2 ))
926	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
927	if [ X${is_opt} = XOPTIONAL ] ; then
928	# Read a forth argument
929	echo ${file_in} is optional
930	(( i=i+4 ))
931	else
932	is_opt="MANDATORY"
933	echo ${file_in} is mandatory
934	(( i=i+3 ))
935	fi
936
937	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=n)"
938
939	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
940
941	extension_in=$( echo ${file_in_Name##*.} )
942	extension_out=$( echo ${file_out##*.} )
943
944	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
945	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
946
947	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
948	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
949
950	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
951	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
952	Buffered=true
953	Archived=false
954	Tared=false
955	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
956	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
957	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
958	Buffered=false
959	Archived=true
960	Tared=false
961	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
962	else
963	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
964	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
965	Buffered=false
966	Archived=false
967	Tared=true
968	# Look after the tar file we want if we did not found it already
969	if [ X${IsMatching} = X ] ; then
970	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
971	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
972	if [ ! X${IsMatching} = X ] ; then
973	TarFileFound=${PotentialTarFile}
974	break
975	fi
976	done
977	fi
978	# Stop here if nothing has been found
979	if [ X${TarFileFound} = X ] ; then
980	IGCM_debug_Print 3 "Restart files were not found!"
981	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
982	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
983	if [ ${is_opt} = 'OPTIONAL' ] ; then
984	IGCM_debug_Print 3 "The restart file is optional. Now continue."
985	nb_restart_file=0
986	Tared=false
987	else
988	IGCM_debug_Print 3 "The restart file is mandatory."
989	IGCM_debug_Exit "Please double check restart settings in config.card"
990	IGCM_debug_Verif_Exit
991	fi
992	else
993	# The tar file exist but not sure all files are inside
994	IGCM_sys_PrepareTaredRestart ${TarFileFound}
995	TarFileLocation=$( basename ${TarFileFound} )
996	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in}*.${extension_in} \| wc -l )
997	if [ ${nb_files} -gt 0 ] ; then
998	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
999	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
1000	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
1001	else
1002	# No file was found
1003	if [ ${is_opt} = 'OPTIONAL' ] ; then
1004	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
1005	nb_restart_file=0
1006	Tared=false
1007	else
1008	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
1009	IGCM_debug_Exit "Please double check restart settings in config.card"
1010	IGCM_debug_Verif_Exit
1011	fi
1012	fi
1013
1014	fi
1015	fi
1016
1017	if [ ${nb_restart_file} -gt 1 ] ; then
1018	j=0 # BASH LINE NOT NEEDED
1019	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1020	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1021	j4=${j} # BASH LINE NOT NEEDED
1022	if [ X${Buffered} = Xtrue ] ; then
1023	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1024	elif [ X${Archived} = Xtrue ] ; then
1025	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1026	elif [ X${Tared} = Xtrue ] ; then
1027	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
1028	fi
1029	(( j=j+1 )) # BASH LINE NOT NEEDED
1030	done
1031	else
1032	if [ X${Buffered} = Xtrue ] ; then
1033	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
1034	elif [ X${Archived} = Xtrue ] ; then
1035	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
1036	elif [ X${Tared} = Xtrue ] ; then
1037	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
1038	fi
1039	fi
1040	done
1041	else
1042	if [ X${FileName0} != XNONE ] ; then
1043	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
1044	else
1045	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
1046	fi
1047	fi
1048	fi
1049	done
1050
1051	NbFiles=$( ls * 2> /dev/null \| wc -l )
1052	if [ ${NbFiles} -gt 0 ] ; then
1053	IGCM_sys_Chmod u+rw *
1054	fi
1055
1056	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
1057	}
1058
1059	#=======================================================================
1060	function IGCM_comp_GetInputBinaryFiles
1061	{
1062	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
1063
1064	# Debug Print :
1065	echo
1066	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
1067	echo
1068
1069	# Clean up previous pass
1070	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
1071
1072	typeset comp ExeNameIn ExeNameOut byPass
1073	typeset compilerNmbr compilerUnit compilerFull
1074	byPass=false
1075	for comp in ${config_ListOfComponents[*]} ; do
1076	# Define component
1077
1078	# Copy executable for this component
1079	eval ExeNameIn=\${config_Executable_${comp}[0]}
1080	eval ExeNameOut=\${config_Executable_${comp}[1]}
1081	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
1082	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
1083	# The executable is set in config.card and is different from ""
1084	# Use eval to expand ExeNameIn if variables are used in the name
1085	eval ExeNameIn=${ExeNameIn}
1086	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1087	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1088	fi
1089	fi
1090
1091	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1092	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1093	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1094	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1095	fi
1096	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1097	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1098	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1099	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1100	fi
1101	fi
1102
1103	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1104	# Get the compiler version
1105	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1106	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1107	# Save it
1108	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1109	[ X${compilerFull} = X ] && byPass=true
1110	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1111	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1112	fi
1113	done
1114
1115	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1116	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1117
1118	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1119	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1120	fi
1121
1122
1123	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1124	}
1125
1126	#=======================================================================
1127	function IGCM_comp_PeriodStart
1128	{
1129	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1130
1131	# Debug Print :
1132	echo
1133	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1134	echo
1135
1136	typeset ExeNameIn ExeNameOut
1137	typeset comp compname comptagname
1138	for comp in ${config_ListOfComponents[*]} ; do
1139	# Define component
1140	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1141	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1142
1143	# Copy executable for this component
1144	eval ExeNameIn=\${config_Executable_${comp}[0]}
1145	eval ExeNameIn=${ExeNameIn}
1146	eval ExeNameOut=\${config_Executable_${comp}[1]}
1147
1148	# Debug Print
1149	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1150	# UPDATE component
1151	${comp}_PeriodStart 2> /dev/null
1152
1153	done
1154
1155	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1156	}
1157
1158
1159
1160	#=======================================================================
1161	function IGCM_comp_modifyFile
1162	{
1163	#
1164	# syntax: IGCM_comp_modifyFile filein key [value]
1165	#
1166	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1167	#
1168	# This function is used to replace a pattern in a file for a specific variable.
1169	#
1170	# Arguments:
1171	# - filein : the file in run directory in which the variable should be set
1172	# - key : the variable to modify
1173	# - value : the value to set the key equal to
1174	#
1175	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1176
1177	typeset filein key value pattern
1178
1179	# Set local variables and test the arguments
1180	if [ $# = 3 ] ; then
1181	# Normal case with 3 arguments
1182	filein=$1 ; key=$2 ; value=$3
1183	else
1184	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1185	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1186	return
1187	fi
1188	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1189
1190	# Test if the file exist
1191	if [ ! -f ${filein} ] ; then
1192	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1193	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1194	return
1195	fi
1196
1197	# Read the line with key in the file without the comments
1198	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1199
1200	# Verify the existance of the pattern
1201	if [ X"${pattern}" = X ] ; then
1202	# Variable key is not set in filein, stop.
1203	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1204	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1205	return
1206	fi
1207
1208	# Now change key in filein
1209	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1210	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1211	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1212	\mv ${filein}.tmp ${filein}
1213
1214	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1215	}
1216
1217	#=======================================================================
1218	function IGCM_comp_modifyDefFile
1219	{
1220	#
1221	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1222	#
1223	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1224	#
1225	# This function is used to modify a parameter file for a specific variable.
1226	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1227	# This function can be used in the comp.driver files for the components.
1228	#
1229	# Arguments:
1230	# - type : first argument must be blocker, nonblocker or force
1231	# For "blocker" case, the variable must be attributed the keyworld AUTO
1232	# otherwise this function will exit.
1233	# For "nonblocker" case, the user can remove or modify the variable. For
1234	# this case, as long as AUTO is not set, no modification will be done.
1235	# For "force" case, the variable will be modified even if it is not set to AUTO
1236	# - filein : the file in run directory of .def type in which the variable should be set
1237	# - key : the variable to modify
1238	# - value : the value to set the key equal to, optional. If value is not set or if
1239	# value=DEFAULT, then a default value must be given in filein using syntax :
1240	# key= AUTO : DEFAULT=def_value
1241	#
1242	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1243
1244	typeset type filein key value
1245	typeset filelist nb_occ modify
1246
1247	# Set local variables and test the arguments
1248	if [ $# = 4 ] ; then
1249	# Normal case with 4 arguments
1250	type=$1 ; filein=$2 ; key=$3 ; value=$4
1251	elif [ $# = 3 ] ; then
1252	# Normal case with 3 arguments
1253	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1254	else
1255	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1256	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1257	return
1258	fi
1259	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1260
1261	# Test if first argument is correct
1262	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1263	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1264	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1265	return
1266	fi
1267
1268	# Test if the file exist.
1269	# Exit with error if the file does not exist for the case blocker or force.
1270	# Only return for the case nonblocker.
1271	if [ ! -f ${filein} ] ; then
1272	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1273	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1274	else
1275	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1276	fi
1277	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1278	return
1279	fi
1280
1281	# Define list of files to test using all files with suffix .def (except used*.def)
1282	filelist=$( ls *def \| grep -v used )
1283
1284	# Count number of occurances for the key in all files
1285	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1286
1287	# Test if key is set several times
1288	if [ ${nb_occ} -gt 1 ] ; then
1289	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1290	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1291	return
1292	fi
1293
1294	# Treatement according to different cases
1295	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1296	# Stop if the key is never set and the function is blocker
1297	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1298	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1299	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1300	# The key is not set but it is a nonblocker call so nothing is done.
1301	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1302	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1303	modify=no
1304	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1305	# Variable key is not set in filein, stop.
1306	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1307	fi
1308
1309	# Check if AUTO is set in the filein on the same line as the key variable
1310	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1311	# Modification will be done for all cases
1312	modify=yes
1313	else
1314	# The variable was not set to AUTO
1315	if [ ${type} = blocker ] ; then
1316	# Exit because this is a blocker call
1317	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1318	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1319	return
1320	elif [ ${type} = nonblocker ] ; then
1321	# Do nothing. Suppose that the user did set the variable correct
1322	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1323	modify=no
1324	elif [ ${type} = force ] ; then
1325	# Force modification
1326	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1327	modify=yes
1328	fi
1329	fi
1330
1331	# Do the modifcation now
1332	if [ ${modify} = yes ] ; then
1333
1334	# For option DEFAULT, read default value from file.
1335	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1336	# Case to set DEFAULT value
1337	# Read default value from filein
1338	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1339
1340	if [ X"${value}" = X ] ; then
1341	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1342	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1343	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1344	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1345	return
1346	fi
1347	fi
1348
1349	# Now change key in filein
1350	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1351	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1352	\mv ${filein}.tmp ${filein}
1353	fi
1354	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1355	}
1356
1357	#=======================================================================
1358	function IGCM_comp_modifyNamelist
1359	{
1360	#
1361	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1362	#
1363	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1364	#
1365	# This function is used to modify a parameter file for a specific variable.
1366	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1367	# This function can be used in the comp.driver files for the components.
1368	#
1369	# Arguments:
1370	# - type : first argument must be blocker, nonblocker or force
1371	# For "blocker" case, the variable must be attributed the keyworld AUTO
1372	# otherwise this function will exit.
1373	# For "nonblocker" case, the user can remove or modify the variable. For
1374	# this case, as long as AUTO is not set, no modification will be done.
1375	# For "force" case, the variable will be modified even if it is not set to AUTO
1376	# - filein : the file in run directory of .def type in which the variable should be set
1377	# - key : the variable to modify
1378	# - value : the value to set the key equal to, optional. If value is not set or if
1379	# value=DEFAULT, then a default value must be given in filein using syntax :
1380	# key= AUTO : DEFAULT=def_value
1381	#
1382	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1383
1384	typeset type filein key value pattern modify
1385
1386	# Set local variables and test the arguments
1387	if [ $# = 4 ] ; then
1388	# Normal case with 4 arguments
1389	type=$1 ; filein=$2 ; key=$3 ; value=$4
1390	elif [ $# = 3 ] ; then
1391	# Normal case with 3 arguments
1392	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1393	else
1394	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1395	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1396	return
1397	fi
1398	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1399
1400	# Test if first argument is correct
1401	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1402	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1403	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1404	return
1405	fi
1406
1407	# Test if the file exist.
1408	# Exit with error if the file does not exist for the case blocker or force.
1409	# Only return for the case nonblocker.
1410	if [ ! -f ${filein} ] ; then
1411	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1412	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1413	else
1414	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1415	fi
1416	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1417	return
1418	fi
1419
1420	# Read the line with key in the file without the comments
1421	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1422
1423	# Verify the existance of the pattern
1424	if [ X"$pattern" = X ] ; then
1425	# Variable key is not set in filein, stop.
1426	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1427	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1428	return
1429	fi
1430
1431	# Check if the variable is set to AUTO in the filein
1432	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1433	# Modification will be done for all cases
1434	modify=yes
1435	else
1436	# The variable was not set to AUTO
1437	if [ ${type} = blocker ] ; then
1438	# Exit because this is a blocker call
1439	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1440	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1441	return
1442	elif [ ${type} = nonblocker ] ; then
1443	# Do nothing. Suppose that the user did set the variable correct
1444	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1445	modify=no
1446	elif [ ${type} = force ] ; then
1447	# Force modification
1448	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1449	modify=yes
1450	fi
1451	fi
1452
1453	# Do the modifcation now
1454	if [ ${modify} = yes ] ; then
1455
1456	# For option DEFAULT, read default value from file.
1457	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1458	# Case to set DEFAULT value
1459	# Read default value from filein
1460	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1461
1462	if [ X"${value}" = X ] ; then
1463	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1464	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1465	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1466	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1467	return
1468	fi
1469	fi
1470
1471	# Now change key in filein
1472	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1473	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1474	\mv ${filein}.tmp ${filein}
1475	fi
1476	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1477	}
1478
1479	#=======================================================================
1480	function IGCM_comp_modifyXmlFile
1481	{
1482	#
1483	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1484	#
1485	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1486	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1487	#
1488	# This function is used to modify the value for a specific attribute and variable id.
1489	# The file must be a valid xml file.
1490	# This function can be used in the comp.driver files for the components.
1491	#
1492	# Arguments:
1493	# - type : first argument must be blocker, nonblocker or force.
1494	# For "blocker" case, the variable must be attributed the keyworld AUTO
1495	# otherwise this function will exit.
1496	# For "nonblocker" case, the user can remove or modify the variable. For
1497	# this case, as long as AUTO is not set, no modification will be done.
1498	# For "force" case, the variable will be modified even if it is not set to AUTO
1499	# - filein : the file in run directory of .xml type in which the variable should be set
1500	# - keyid : the variable to modify
1501	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1502	# - value : the value to set in the filein
1503	#
1504	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1505
1506	typeset type filein keyid keyattrib value modify
1507
1508	# Set local variables and test the arguments
1509	if [ $# = 5 ] ; then
1510	# Normal case with 4 arguments
1511	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1512	else
1513	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1514	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1515	return
1516	fi
1517	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1518
1519	# Test if first argument is correct
1520	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1521	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1522	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1523	return
1524	fi
1525
1526	# Test if the file exist.
1527	# Exit with error if the file does not exist for the case blocker or force.
1528	# Only return for the case nonblocker.
1529	if [ ! -f ${filein} ] ; then
1530	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1531	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1532	else
1533	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1534	fi
1535	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1536	return
1537	fi
1538
1539	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1540	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1541	if [ ${type} = nonblocker ] ; then
1542	# This is a nonblocker case, print warning but do nothing else
1543	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1544	else
1545	# This is a blocker or force case : stop now
1546	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1547	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1548	return
1549	fi
1550	fi
1551
1552	# Check if AUTO is set on the same line as keyid and keyattrib
1553	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1554	# Modification will be done
1555	modify=yes
1556	else
1557	if [ ${type} = blocker ] ; then
1558	# Exit, the variable must be set to AUTO
1559	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1560	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1561	return
1562	elif [ ${type} = nonblocker ] ; then
1563	# Nothing will be done
1564	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1565	modify=no
1566	elif [ ${type} = force ] ; then
1567	# Force modification
1568	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1569	modify=yes
1570	fi
1571	fi
1572
1573	# Do the modifcation now
1574	if [ ${modify} = yes ] ; then
1575	if [ ${keyattrib} = NONE ] ; then
1576	# Case to modify the variable itself
1577	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1578	sed -e "s/$<[^\"]\"${keyid}\".>$$[^<]$$<[^>]$/\1${value}\3/" ${filein} > ${filein}.tmp
1579	else
1580	# Check if keyattrib is set on the same line as keyid
1581	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1582	# Case to modify the attribute value
1583	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1584	sed -e "/id=\"${keyid}\"/s/$${keyattrib}=\"$[^\"]*$\"$/\1${value}\2/" ${filein} > ${filein}.tmp
1585	else
1586	# Case to add the attribute and its value
1587	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1588	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1589	fi
1590	fi
1591	\mv ${filein}.tmp ${filein}
1592	fi
1593	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1594	}
1595
1596	#=======================================================================
1597	function IGCM_comp_Update
1598	{
1599	IGCM_debug_PushStack "IGCM_comp_Update"
1600
1601	# Debug Print :
1602	echo
1603	IGCM_debug_Print 1 "IGCM_comp_Update"
1604	echo
1605
1606	typeset comp compname comptagname
1607	for comp in ${config_ListOfComponents[*]} ; do
1608	# Define component
1609	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1610	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1611
1612	# Debug Print
1613	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1614	# UPDATE component
1615	${comp}_Update
1616
1617	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1618	if [ -f timeseries_def_${compname}.xml ]; then
1619	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1620	for line in $( cat ts.temp.${compname}.txt ); do
1621	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1622	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1623	case ${output_freq} in
1624	Y\|y)
1625	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1626	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1627	;;
1628	MO\|mo)
1629	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1630	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1631	;;
1632	D\|d)
1633	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1634	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1635	;;
1636	S\|s)
1637	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1638	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1639	;;
1640	esac
1641	done
1642	fi
1643
1644	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1645	if [ -f dr2xml_${compname}.xml ]; then
1646	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
1647	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1648	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1649	# Modify path from dr2xml_{compname}.xml
1650	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
1651	${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
1652	else
1653	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1654	fi
1655	# Overwrite the original file
1656	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1657	fi
1658	fi
1659	done
1660
1661	IGCM_debug_PopStack "IGCM_comp_Update"
1662	}
1663
1664	#=======================================================================
1665	function IGCM_comp_Finalize
1666	{
1667	IGCM_debug_PushStack "IGCM_comp_Finalize"
1668
1669	# Debug Print :
1670	echo
1671	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1672	echo
1673
1674	typeset ListTextName TextName0
1675	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1676	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1677	typeset -Z4 j4 #BASH declare j4
1678	typeset list_file nlist_file
1679	typeset compactoutputs
1680
1681	# Initialize array hosting list of rebuilded files to copy
1682	unset rebuildedActionsList
1683
1684	# Text compacting options
1685	compactoutputs=false
1686	if [ X${JobType} != XRUN ] ; then
1687	compactoutputs=true
1688	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1689	compactoutputs=true
1690	fi
1691
1692	# Prepare headers for the shell dedicated to offline rebuild
1693	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1694	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1695	if [ ${DRYRUN} -le 1 ] ; then
1696	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1697	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1698	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1699	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1700	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1701	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1702	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1703	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1704	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1705	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1706	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1707	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1708	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1709	fi
1710	fi
1711
1712	for comp in ${config_ListOfComponents[*]} ; do
1713	# Define component
1714	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1715	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1716
1717	# Debug Print
1718	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1719	# FINALIZE component
1720	${comp}_Finalize
1721
1722	card=${SUBMIT_DIR}/COMP/${compname}.card
1723
1724	# Save Output Text files of models
1725	#---------------------------------
1726	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1727	IGCM_card_DefineArrayFromOption ${card} OutputText List
1728	ListTextName=${compname}_OutputText_List
1729
1730	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1731	if [ X${TextName0} != X${NULL_STR} ] ; then
1732	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1733
1734	(( i=0 ))
1735	until [ $i -eq $NbFiles ]; do
1736	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1737	eval file_out=${PREFIX}_${file_in}
1738
1739	(( i=i+1 ))
1740
1741	unset list_file
1742	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1743	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1744	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 )
1745	nlist_file=${#list_file[@]}
1746	if [ ${nlist_file} -gt 1 ] ; then
1747	if ( ${compactoutputs} ) ; then
1748	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1749	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1750	echo ${list_file[*]} > ${file_out}
1751	echo "" >> ${file_out}
1752
1753	(( i_ = 0 ))
1754	for file in ${list_file[@]} ; do
1755	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1756	echo "\| " ${i_} " " ${file} >> ${file_out}
1757	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1758	cat ${file} \| sed "s/$.*$/${i_}\1/" >> ${file_out}
1759	echo "" >> ${file_out}
1760	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1761	(( i_ = i_ + 1 ))
1762	done
1763	if ( ${ExecutionFail} ) ; then
1764	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1765	fi
1766
1767	if [ X${Pack} = Xtrue ] ; then
1768	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1769	else
1770	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1771	fi
1772
1773	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1774	else
1775	for file in ${list_file[@]} ; do
1776	if ( ${ExecutionFail} ) ; then
1777	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1778	fi
1779
1780	if [ X${Pack} = Xtrue ] ; then
1781	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1782	else
1783	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1784	fi
1785
1786	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1787	done
1788	fi
1789	else
1790	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1791	eval IGCM_sys_Mv ${file_in}* ${file_in}
1792	fi
1793
1794	if ( ${ExecutionFail} ) ; then
1795	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1796	fi
1797
1798	if [ X${Pack} = Xtrue ] ; then
1799	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1800	else
1801	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1802	fi
1803	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1804	fi
1805	done
1806	fi
1807
1808	# Save Restarts files
1809	#--------------------
1810	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1811	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1812	ListFilesName=${compname}_RestartFiles_List
1813	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1814
1815	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1816	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1817	(( i=0 ))
1818	until [ $i -ge $NbFiles ]; do
1819	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1820	eval file_in=${file_in_}
1821
1822	(( i_ = i+1 ))
1823	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1824	eval file_out=${file_out_}
1825
1826	(( i_ = i+2 ))
1827	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1828	eval file_outin=${file_outin_}
1829
1830	(( i_ = i+3 ))
1831	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1832	if [ X${is_opt} = XOPTIONAL ] ; then
1833	echo ${file_in} is optional
1834	(( i=i+4 ))
1835	else
1836	is_opt=""
1837	echo ${file_in} is mandatory
1838	(( i=i+3 ))
1839	fi
1840
1841	generic_restart_file_name_in=$( basename ${file_in} .nc )
1842	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1843	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1844
1845	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1846	if [ ${nb_restart_file} -gt 1 ] ; then
1847	j=0 # BASH LINE NOT NEEDED
1848	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1849	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1850	j4=${j} # BASH LINE NOT NEEDED
1851	if [ X${Pack} = Xtrue ] ; then
1852	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc ${is_opt}
1853	else
1854	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc ${is_opt}
1855	fi
1856
1857	if [ -f ${generic_restart_file_name_in}_${j4}.nc ] ; then
1858	if [ ! ${file_in} = ${file_outin} ] ; then
1859	if ( ${ExitFlag} ) ; then
1860	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1861	else
1862	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1863	fi
1864	fi
1865	else
1866	# This is the case where the restart file no not exist.
1867	# It has already been checked if the model should stop for this case.
1868	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${generic_restart_file_name_in}_${j4}.nc"
1869	fi
1870	(( j=j+1 )) # BASH LINE NOT NEEDED
1871	done
1872	else
1873	if [ X${Pack} = Xtrue ] ; then
1874	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1875	else
1876	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
1877	fi
1878
1879	if [ -f ${file_in} ] ; then
1880	if [ ! ${file_in} = ${file_outin} ] ; then
1881	if ( ${ExitFlag} ) ; then
1882	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1883	else
1884	IGCM_sys_Mv ${file_in} ${file_outin}
1885	fi
1886	fi
1887	else
1888	# This is the case where the restart file no not exist.
1889	# It has already been checked if the model should stop for this case.
1890	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${file_in}"
1891	fi
1892	fi
1893
1894	done
1895	else
1896	if [ X${FileName0} != XNONE ] ; then
1897	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1898	else
1899	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1900	fi
1901	fi
1902
1903	# Save Output files
1904	#------------------
1905	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1906	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1907	ListFilesName=${compname}_OutputFiles_List
1908	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1909
1910	if [ X${FileName0} != X${NULL_STR} ] ; then
1911	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1912
1913	(( i=0 ))
1914	until [ $i -ge $NbFiles ]; do
1915	SaveOnArchive=true
1916	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1917	eval file_in=${file_in_}
1918	(( i_ = i+1 ))
1919	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1920	eval file_out=${file_out_}
1921	#
1922	# Override file_out path remplacing R_SAVE by R_BUFR
1923	#
1924	if [ X${Pack} = Xtrue ] ; then
1925	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1926	fi
1927	#
1928	# Not necessarily the best option. /!\ Potential side effects /!\
1929	#
1930	(( i_ = i+2 ))
1931	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1932	#
1933	generic_file_name=$( basename ${file_in} .nc )
1934	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1935	#
1936	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1937	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1938	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1939	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1940	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1941	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1942	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1943	#
1944	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
1945	if [ ${file_in} = output.abort.nc ] ; then
1946	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
1947	else
1948	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
1949	fi
1950	else
1951	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1952	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1953
1954	# Prepare the shell dedicated to offline rebuild
1955	if [ $DRYRUN -le 1 ]; then
1956	if [ ${file_in} = histstn.nc ] ; then
1957	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1958	else
1959	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1960	fi
1961	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1962	fi
1963	#
1964	# Load Patch we need to apply and apply
1965	if [ $DRYRUN -le 1 ]; then
1966	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1967	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1968	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1969	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1970	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1971	done
1972	fi
1973	fi
1974	#
1975	if [ $DRYRUN -le 1 ]; then
1976	if [ X${Pack} = Xtrue ] ; then
1977	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1978	else
1979	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1980	fi
1981	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1982	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1983	fi
1984	SaveOnArchive=false
1985	fi
1986	fi
1987	#
1988	if [ ${SaveOnArchive} = true ] ; then
1989	#
1990	# Rebuild has been done online or it was not needed
1991	#
1992	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1993	#
1994	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1995	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1996	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1997	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1998	#
1999	if [ $DRYRUN -le 1 ]; then
2000	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
2001	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2002	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2003	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2004	done
2005	#
2006	if [ X${Pack} = Xtrue ] ; then
2007	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2008	else
2009	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2010	fi
2011	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2012	#
2013	fi
2014	else
2015	#
2016	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
2017	#
2018	if [ X${Pack} = Xtrue ] ; then
2019	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
2020	else
2021	IGCM_sys_Put_Out ${file_in} ${file_out}
2022	fi
2023	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
2024	if [ ${nb_rebuild_file} -gt 1 ] ; then
2025	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
2026	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
2027	done
2028	fi
2029	fi
2030	fi
2031	((i_ = i_ +1))
2032	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
2033	eval Testvar=${Testvar_}
2034	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
2035	((i = i+4))
2036	else
2037	(( i=i+3 ))
2038	fi
2039	done
2040	fi
2041	echo
2042	done
2043	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
2044	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
2045	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2046	i=0
2047	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
2048	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
2049	(( i=i+1 ))
2050	done
2051	fi
2052	IGCM_debug_PopStack "IGCM_comp_Finalize"
2053	}

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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1624

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