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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1338

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

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