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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1156

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

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