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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 884

Last change on this file since 884 was 884, checked in by mafoipsl, 11 years ago
add treatment to recognize RESTART file with this pattern : _20781231_20781231_.tar. Correction of #152.
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 [ ! ${config_Post_PackFrequency} = NONE ] ; then
101	eval R_BUF_${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	#
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_GetInputInitialStateFiles
259	{
260	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
261
262	# Debug Print :
263	echo
264	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
265	echo
266
267	# Only the first time step need InitialStateFiles
268	# otherwise it's BoundaryConditions
269	if ( ${FirstInitialize} ) ; then
270	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
271	typeset file_in_ file_in file_out_ file_out do_init
272	for comp in ${config_ListOfComponents[*]} ; do
273	# Initialize
274	do_init="y"
275	# Do we need to bring initial state file for this component
276	if [ "${config_Restarts_OverRule}" = "y" ] ; then
277	eval do_init="n"
278	else
279	# Read component Restarts parameters
280	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
281	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
282	if [ "${do_start}" = "y" ] ; then
283	do_init="n"
284	else
285	do_init="y"
286	fi
287	fi
288
289	if [ "${do_init}" = "y" ] ; then
290	# Define component
291	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
292	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
293
294	# Debug Print :
295	IGCM_debug_Print 3 "Initialisation files ${compname}"
296
297	card=${SUBMIT_DIR}/COMP/${compname}.card
298
299	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
300	ListFilesName=${compname}_InitialStateFiles_List
301
302	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
303	if [ X${FileName0} != X${NULL_STR} ] ; then
304	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
305	(( i=0 ))
306	until [ $i -ge $NbFiles ]; do
307	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
308	eval file_in=${file_in_}
309	(( i_ = i+1 ))
310	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
311	eval file_out=${file_out_}
312
313	IGCM_sys_IsFileArchived ${file_in}
314	if [ $? = 0 ] ; then
315	IGCM_sys_Get ${file_in} ${file_out}
316	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
317	else
318	IGCM_sys_Cp ${file_in} ${file_out}
319	fi
320	(( i=i+2 ))
321	done
322	fi
323	fi
324	done
325	fi
326	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
327	}
328
329	#=======================================================================
330	# Definition of Smooth modulo function
331	# usage :
332	# IGCM_SmoothModulo StringModulo value
333	#
334	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
335	# [min]:[modulo:][max]
336	# where :
337	# [] value are optionnals;
338	# empty min equal 1
339	# empty max equal infinity
340	# modulo not given or empty equal 1
341	# empty string or just ':' equal always.
342	#
343	# value : the value to test with the definition
344	#
345	# return : true(1)/false(0)
346	function IGCM_SmoothModulo
347	{
348	IGCM_debug_PushStack "IGCM_SmoothModulo"
349	typeset defVector ModValue
350
351	eval set +A defVector -- $( echo "${1}" \| \
352	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
353
354	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
355	arr[1]=${defVector[0]}
356	arr[2]=${defVector[2]}
357
358	# Test limits :
359	# ${defVector[0]} <= ${2} <= ${defVector[2]}
360	# or ${defVector[2]} == -1
361	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
362	# Test modulo
363	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
364	if [ ${ModValue} -eq 0 ] ; then
365	arr[3]=true
366	echo ${arr[@]}
367	IGCM_debug_PopStack "IGCM_SmoothModulo"
368	return 1
369	else
370	arr[3]=false
371	echo ${arr[@]}
372	IGCM_debug_PopStack "IGCM_SmoothModulo"
373	return 0
374	fi
375	else
376	arr[3]=false
377	echo ${arr[@]}
378	IGCM_debug_PopStack "IGCM_SmoothModulo"
379	return 0
380	fi
381	}
382
383	#=======================================================================
384	function IGCM_comp_GetInputSmoothFiles
385	{
386	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
387
388	# Debug Print :
389	echo
390	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
391	echo
392
393	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
394	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
395
396	for comp in ${config_ListOfComponents[*]} ; do
397	# Define component
398	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
399	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
400
401	# Debug Print :
402	IGCM_debug_Print 3 "Smooth files ${compname}"
403
404	card=${SUBMIT_DIR}/COMP/${compname}.card
405
406	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
407	ListFilesName=${compname}_SmoothFiles_List
408	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
409
410	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
411	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
412
413	(( i=0 ))
414	until [ $i -ge $NbFiles ]; do
415	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
416	eval file_in=${file_in_}
417	(( i_ = i+1 ))
418	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
419	eval file_out=${file_out_}
420
421	# define CumulPeriod definition for this file
422	(( i__ = i+2 ))
423	eval SmoothDef=\${${ListFilesName}[$i__]}
424	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
425	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
426	j=1
427	for val in ${aux} ; do
428	[ ${j} -eq 1 ] && SmoothMin=${val}
429	[ ${j} -eq 2 ] && SmoothMax=${val}
430	[ ${j} -eq 3 ] && ret=${val}
431	(( j=j+1 ))
432	done
433	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
434	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
435
436	IGCM_sys_IsFileArchived ${file_in}
437	if [ $? = 0 ] ; then
438	IGCM_sys_Get ${file_in} ${file_out}
439	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
440	else
441	IGCM_sys_Cp ${file_in} ${file_out}
442	fi
443	fi
444	(( i=i+3 ))
445	done
446	fi
447	done
448
449	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
450	}
451
452	#=======================================================================
453	function IGCM_comp_GetInputBoundaryFiles
454	{
455	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
456
457	# Debug Print :
458	echo
459	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
460	echo
461
462	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
463	typeset file_in_ file_in file_out_ file_out
464
465	if [ ${Period} = 1 ]; then
466	ListFixBoundary=" "
467	fi
468
469	for comp in ${config_ListOfComponents[*]} ; do
470
471	# Define component
472	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
473	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
474
475	# Debug Print :
476	IGCM_debug_Print 3 "Boundary files ${compname}"
477
478	card=${SUBMIT_DIR}/COMP/${compname}.card
479
480	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
481	ListFilesName=${compname}_BoundaryFiles_List
482	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
483
484	if [ X${FileName0} != X${NULL_STR} ] ; then
485	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
486
487	(( i=0 ))
488	until [ $i -ge $NbFiles ]; do
489	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
490	eval file_in=${file_in_}
491	(( i_ = i+1 ))
492	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
493	eval file_out=${file_out_}
494
495	IGCM_sys_IsFileArchived ${file_in}
496	if [ $? = 0 ] ; then
497	IGCM_sys_Get ${file_in} ${file_out}
498	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
499	else
500	IGCM_sys_Cp ${file_in} ${file_out}
501	fi
502
503	(( i=i+2 ))
504	done
505	fi
506
507	# Get non deleted files
508	if [ ${Period} = 1 ]; then
509
510	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
511	ListFilesName=${compname}_BoundaryFiles_ListNonDel
512	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
513
514	if [ X${FileName0} != X${NULL_STR} ] ; then
515	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
516
517	(( i=0 ))
518	until [ $i -ge $NbFiles ]; do
519	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
520	eval file_in=${file_in_}
521	(( i_ = i+1 ))
522	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
523	eval file_out=${file_out_}
524
525	IGCM_sys_IsFileArchived ${file_in}
526	if [ $? = 0 ] ; then
527	IGCM_sys_Get ${file_in} ${file_out}
528	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
529	else
530	IGCM_sys_Cp ${file_in} ${file_out}
531	fi
532
533	if [ X${file_out} != X. ] ; then
534	ListFixBoundary=${ListFixBoundary}" "${file_out}
535	else
536	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
537	fi
538
539	(( i=i+2 ))
540	done
541	fi
542	fi
543	done
544
545	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
546	}
547
548	#=======================================================================
549	function IGCM_comp_DelFixeBoundaryFiles
550	{
551	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
552
553	# Debug Print :
554	echo
555	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
556	echo
557
558	ls -l ${ListFixBoundary}
559	rm -f ${ListFixBoundary}
560
561	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
562	}
563
564	#=======================================================================
565	function IGCM_comp_GetInputParametersFiles
566	{
567	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
568
569	# Debug Print :
570	echo
571	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
572	echo
573
574	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
575	for comp in ${config_ListOfComponents[*]} ; do
576	# Define component
577	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
578	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
579
580	# Debug Print :
581	IGCM_debug_Print 3 "Parameters ${compname}"
582
583	card=${SUBMIT_DIR}/COMP/${compname}.card
584
585	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
586	ListFilesName=${compname}_ParametersFiles_List
587	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
588
589	if [ X${FileName0} != X${NULL_STR} ] ; then
590	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
591
592	(( i=0 ))
593	until [ $i -ge $NbFiles ]; do
594	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
595	eval file_in=${file_in_}
596	(( i_ = i+1 ))
597	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
598	eval file_out=${file_out_}
599
600	IGCM_sys_Cp ${file_in} ${file_out}
601	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
602
603	(( i=i+2 ))
604	done
605	fi
606	done
607
608	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
609	}
610
611	#=======================================================================
612	function IGCM_comp_GetInputRestartFiles
613	{
614	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
615
616	# Debug Print :
617	echo
618	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
619	echo
620
621	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
622	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
623	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
624	typeset file_in file_out file_in_ file_out_ file_in_Name
625	typeset -Z4 j4
626	#BASH declare j4
627
628	IsMatching=""
629
630	for comp in ${config_ListOfComponents[*]} ; do
631	# Define component
632	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
633	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
634	#
635	card=${SUBMIT_DIR}/COMP/${compname}.card
636	#
637	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
638	ListFilesName=${compname}_RestartFiles_List
639	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
640
641	# Debug Print :
642	IGCM_debug_Print 3 "restart ${compname}"
643
644	if ( ${FirstInitialize} ) ; then
645
646	if [ "${config_Restarts_OverRule}" = "y" ] ; then
647	eval config_${comp}_Restart="y"
648	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
649	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
650	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
651	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
652	eval CompOldName=${comp}
653	else
654	# Read component Restarts parameters
655	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
656	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
657
658	if [ "${do_start}" = "y" ] ; then
659	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
660	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
661	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
662	else
663	eval config_${comp}_RestartDate=-1
664	eval config_${comp}_RestartJobName=${NULL_STR}
665	eval config_${comp}_RestartPath=${NULL_STR}
666	fi
667
668	eval CompOldName=\${config_${comp}_OldName}
669	if [ X${CompOldName} = X ] ; then
670	eval CompOldName=${comp}
671	fi
672
673	# Reinitialize IsMatching to allow searching for a different tar file for each component.
674	IsMatching=""
675	TarFileFound=""
676	fi
677
678	if [ "${do_start}" = "y" ] ; then
679
680	# Restore Restarts files
681	#-----------------------
682	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
683	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
684
685	(( i=1 ))
686	until [ $i -gt $NbFiles ]; do
687	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
688	eval file_in=${file_in_}
689	(( i_ = i+1 ))
690	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
691	eval file_out=${file_out_}
692
693	eval Date_tmp=\${config_${comp}_RestartDate}
694	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
695	# will be re-use
696	eval RestartPath=\${config_${comp}_RestartPath}
697	eval RestartJobName=\${config_${comp}_RestartJobName}
698	#
699	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
700	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
701
702	extension_in=$( echo ${file_in_Name##*.} )
703	extension_out=$( echo ${file_out##*.} )
704
705	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
706	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
707
708	Path_OUT=${Path_r}/${generic_restart_file_name_in}
709
710	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
711	IGCM_debug_Print 3 "Buffered restart"
712	Buffered=true
713	Archived=false
714	Tared=false
715	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
716	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
717	IGCM_debug_Print 3 "Archived restart"
718	Buffered=false
719	Archived=true
720	Tared=false
721	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
722	else
723	IGCM_debug_Print 3 "Tared restart"
724	Buffered=false
725	Archived=false
726	Tared=true
727	# Look after the tar file we want if we did not found it already
728	if [ X${IsMatching} = X ] ; then
729	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_*_restart.tar" -print" ) ; do
730	IsMatching=$( echo ${PotentialTarFile##*/} \| \
731	sed "s:^${RestartJobName}_::" \| \
732	sed "s:\.restart\.tar$::" \| \
733	gawk -F_ -v restartdate=${Date_r} \
734	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
735	if [ ! X${IsMatching} = X ] ; then
736	TarFileFound=${PotentialTarFile}
737	break
738	fi
739	done
740	fi
741	TarFileLocation=$( IGCM_sys_PrepareTaredRestart ${TarFileFound} )
742	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
743	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
744	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
745	fi
746
747	if [ ${nb_restart_file} -gt 1 ] ; then
748	j=0 # BASH LINE NOT NEEDED
749	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
750	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
751	j4=${j} # BASH LINE NOT NEEDED
752	if [ X${Buffered} = Xtrue ] ; then
753	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
754	elif [ X${Archived} = Xtrue ] ; then
755	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
756	elif [ X${Tared} = Xtrue ] ; then
757	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
758	fi
759	(( j=j+1 )) #BASH LINE NOT NEEDED
760	done
761
762	if [ X${NUM_PROC_OCE} != X ] ; then
763	if [ ${NUM_PROC_OCE} -ne ${nb_restart_file} ] ; then
764	IGCM_sys_rebuild ${generic_restart_file_name_out}.${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
765	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
766	fi
767	fi
768	else
769	if [ X${Buffered} = Xtrue ] ; then
770	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
771	elif [ X${Archived} = Xtrue ] ; then
772	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
773	elif [ X${Tared} = Xtrue ] ; then
774	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
775	fi
776	fi
777	(( i=i+3 ))
778	done
779
780	else
781	if [ X${FileName0} != XNONE ] ; then
782	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
783	else
784	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
785	fi
786	fi
787	fi
788	elif [ ${Period} -eq 1 ] ; then
789	# if not FirstInitialize and first loop of this job
790
791	# Restore Restarts files
792	#-----------------------
793	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
794	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
795
796	(( i=1 ))
797	until [ $i -gt $NbFiles ]; do
798	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
799	eval file_in=${file_in_}
800	(( i_ = i+1 ))
801	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
802	eval file_out=${file_out_}
803
804	file_in_Name=${run_Configuration_OldPrefix}_${file_in}
805
806	extension_in=$( echo ${file_in_Name##*.} )
807	extension_out=$( echo ${file_out##*.} )
808
809	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
810	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
811
812	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
813	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
814
815	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
816	IGCM_debug_Print 3 "Buffered restart"
817	Buffered=true
818	Archived=false
819	Tared=false
820	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
821	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
822	IGCM_debug_Print 3 "Archived restart"
823	Buffered=false
824	Archived=true
825	Tared=false
826	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
827	else
828	IGCM_debug_Print 3 "Tared restart"
829	Buffered=false
830	Archived=false
831	Tared=true
832	# Look after the tar file we want if we did not found it already
833	if [ X${IsMatching} = X ] ; then
834	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
835	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
836	if [ ! X${IsMatching} = X ] ; then
837	TarFileFound=${PotentialTarFile}
838	break
839	fi
840	done
841	fi
842	TarFileLocation=$( IGCM_sys_PrepareTaredRestart ${TarFileFound} )
843	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
844	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
845	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
846	fi
847
848	if [ ${nb_restart_file} -gt 1 ] ; then
849	j=0 # BASH LINE NOT NEEDED
850	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
851	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
852	j4=${j} # BASH LINE NOT NEEDED
853	if [ X${Buffered} = Xtrue ] ; then
854	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
855	elif [ X${Archived} = Xtrue ] ; then
856	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
857	elif [ X${Tared} = Xtrue ] ; then
858	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
859	fi
860	(( j=j+1 )) # BASH LINE NOT NEEDED
861	done
862	else
863	if [ X${Buffered} = Xtrue ] ; then
864	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
865	elif [ X${Archived} = Xtrue ] ; then
866	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
867	elif [ X${Tared} = Xtrue ] ; then
868	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
869	fi
870	fi
871	(( i=i+3 ))
872	done
873	else
874	if [ X${FileName0} != XNONE ] ; then
875	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
876	else
877	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
878	fi
879	fi
880	fi
881	done
882
883	NbFiles=$( ls * 2> /dev/null \| wc -l )
884	if [ ${NbFiles} -gt 0 ] ; then
885	IGCM_sys_Chmod u+rw *
886	fi
887
888	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
889	}
890
891	#=======================================================================
892	function IGCM_comp_PeriodStart
893	{
894	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
895
896	# Debug Print :
897	echo
898	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
899	echo
900
901	typeset ExeNameIn ExeNameOut
902	typeset comp compname comptagname
903	for comp in ${config_ListOfComponents[*]} ; do
904	# Define component
905	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
906	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
907
908	# Copy executable for this component
909	eval ExeNameIn=\${config_Executable_${comp}[0]}
910	eval ExeNameOut=\${config_Executable_${comp}[1]}
911
912	# Debug Print
913	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
914	# UPDATE component
915	${comp}_PeriodStart 2> /dev/null
916
917	done
918
919	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
920	}
921
922	#=======================================================================
923	function IGCM_comp_Update
924	{
925	IGCM_debug_PushStack "IGCM_comp_Update"
926
927	# Debug Print :
928	echo
929	IGCM_debug_Print 1 "IGCM_comp_Update"
930	echo
931
932	typeset ExeNameIn ExeNameOut
933	typeset comp compname comptagname
934	for comp in ${config_ListOfComponents[*]} ; do
935	# Define component
936	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
937	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
938
939	# Copy executable for this component
940	eval ExeNameIn=\${config_Executable_${comp}[0]}
941	eval ExeNameOut=\${config_Executable_${comp}[1]}
942
943	# If missing executable and DRYRUN is set to 0 or 1 then stop!
944	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
945	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
946	fi
947
948	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
949	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
950	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
951	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
952	fi
953	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
954	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
955	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
956	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
957	fi
958	fi
959
960	# Debug Print
961	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
962	# UPDATE component
963	${comp}_Update
964
965	done
966
967	IGCM_debug_PopStack "IGCM_comp_Update"
968	}
969
970	#=======================================================================
971	function IGCM_comp_Finalize
972	{
973	IGCM_debug_PushStack "IGCM_comp_Finalize"
974
975	# Debug Print :
976	echo
977	IGCM_debug_Print 1 "IGCM_comp_Finalize"
978	echo
979
980	typeset ListTextName TextName0
981	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
982	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
983	typeset -Z4 j4
984	#BASH declare j4
985	typeset list_file nlist_file
986	typeset compactoutputs
987
988	compactoutputs=false
989	if [ X${JobType} != XRUN ] ; then
990	compactoutputs=true
991	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
992	compactoutputs=true
993	fi
994
995	for comp in ${config_ListOfComponents[*]} ; do
996	# Define component
997	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
998	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
999
1000	# Debug Print
1001	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1002	# FINALIZE component
1003	${comp}_Finalize
1004
1005	card=${SUBMIT_DIR}/COMP/${compname}.card
1006
1007	# Save Output Text files of models
1008	#---------------------------------
1009	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1010	IGCM_card_DefineArrayFromOption ${card} OutputText List
1011	ListTextName=${compname}_OutputText_List
1012
1013	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1014	if [ X${TextName0} != X${NULL_STR} ] ; then
1015	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1016
1017	(( i=0 ))
1018	until [ $i -eq $NbFiles ]; do
1019	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1020	eval file_out=${PREFIX}_${file_in}
1021
1022	(( i=i+1 ))
1023
1024	unset list_file
1025	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1026	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1027	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 )
1028	nlist_file=${#list_file[@]}
1029	if [ ${nlist_file} -gt 1 ] ; then
1030	if ( ${compactoutputs} ) ; then
1031	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1032	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1033	echo ${list_file[*]} > ${file_out}
1034	echo "" >> ${file_out}
1035
1036	(( i_ = 0 ))
1037	for file in ${list_file[@]}
1038	do
1039	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1040	echo "\| " ${i_} " " ${file} >> ${file_out}
1041	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1042	cat ${file} \| sed "s/\(.*\)/${i_}\1/" ${file} >> ${file_out}
1043	echo "" >> ${file_out}
1044	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1045	(( i_ = i_ + 1 ))
1046	done
1047	if [ X${Pack} = Xtrue ] ; then
1048	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1049	else
1050	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1051	fi
1052	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1053
1054	if ( ${ExecutionFail} ) ; then
1055	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1056	fi
1057	else
1058	for file in ${list_file[@]}
1059	do
1060	if [ X${Pack} = Xtrue ] ; then
1061	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1062	else
1063	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1064	fi
1065	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1066
1067	if ( ${ExecutionFail} ) ; then
1068	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1069	fi
1070	done
1071	fi
1072	else
1073	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1074	eval IGCM_sys_Mv ${file_in}* ${file_in}
1075	fi
1076	if [ X${Pack} = Xtrue ] ; then
1077	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1078	else
1079	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1080	fi
1081	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1082
1083	if ( ${ExecutionFail} ) ; then
1084	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1085	fi
1086	fi
1087	done
1088	fi
1089
1090	# Save Restarts files
1091	#--------------------
1092	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1093	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1094	ListFilesName=${compname}_RestartFiles_List
1095	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1096
1097	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1098	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1099
1100	(( i=0 ))
1101	until [ $i -ge $NbFiles ]; do
1102	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1103	eval file_in=${file_in_}
1104
1105	(( i_ = i+1 ))
1106	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1107	eval file_out=${file_out_}
1108
1109	(( i_ = i+2 ))
1110	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1111	eval file_outin=${file_outin_}
1112
1113	generic_restart_file_name_in=$( basename ${file_in} .nc )
1114	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1115	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1116
1117	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1118	if [ ${nb_restart_file} -gt 1 ] ; then
1119	j=0 # BASH LINE NOT NEEDED
1120	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1121	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1122	j4=${j} # BASH LINE NOT NEEDED
1123	if [ X${Pack} = Xtrue ] ; then
1124	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1125	else
1126	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1127	fi
1128	if [ ! ${file_in} = ${file_outin} ] ; then
1129	if ( ${ExitFlag} ) ; then
1130	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1131	else
1132	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1133	fi
1134	fi
1135	(( j=j+1 )) # BASH LINE NOT NEEDED
1136	done
1137	else
1138	if [ X${Pack} = Xtrue ] ; then
1139	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1140	else
1141	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1142	fi
1143	if [ ! ${file_in} = ${file_outin} ] ; then
1144	if ( ${ExitFlag} ) ; then
1145	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1146	else
1147	IGCM_sys_Mv ${file_in} ${file_outin}
1148	fi
1149	fi
1150	fi
1151
1152	(( i=i+3 ))
1153	done
1154	else
1155	if [ X${FileName0} != XNONE ] ; then
1156	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1157	else
1158	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1159	fi
1160	fi
1161
1162	# Save Output files
1163	#------------------
1164	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1165	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1166	ListFilesName=${compname}_OutputFiles_List
1167	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1168
1169	if [ X${FileName0} != X${NULL_STR} ] ; then
1170	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1171
1172	(( i=0 ))
1173	until [ $i -ge $NbFiles ]; do
1174	SaveOnArchive=true
1175	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1176	eval file_in=${file_in_}
1177	(( i_ = i+1 ))
1178	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1179	eval file_out=${file_out_}
1180	#
1181	# Override file_out path remplacing R_SAVE by R_BUFR
1182	#
1183	if [ X${Pack} = Xtrue ] ; then
1184	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1185	fi
1186	#
1187	# Not necessarily the best option. /!\ Potential side effects /!\
1188	#
1189	(( i_ = i+2 ))
1190	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1191	#
1192	generic_file_name=$( basename ${file_in} .nc )
1193	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1194	#
1195	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1196	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1197	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1198	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1199	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1200	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1201	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1202	IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc
1203	else
1204	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1205	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1206	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1207
1208	# Prepare headers for the shell dedicated to offline rebuild
1209	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1210	if [ $DRYRUN -le 1 ]; then
1211	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1212	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1213	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1214	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1215	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1216	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1217	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1218	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1219	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1220	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1221	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1222	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1223	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1224	fi
1225	fi
1226	# Prepare the shell dedicated to offline rebuild
1227	if [ $DRYRUN -le 1 ]; then
1228	if [ ${file_in} = histstn.nc ] ; then
1229	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1230	else
1231	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1232	fi
1233	echo "IGCM_debug_Verif_Exit_Post" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1234	fi
1235	#
1236	# Load Patch we need to apply and apply
1237	if [ $DRYRUN -le 1 ]; then
1238	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1239	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1240	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1241	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1242	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1243	done
1244	fi
1245	fi
1246	#
1247	if [ $DRYRUN -le 1 ]; then
1248	if [ X${Pack} = Xtrue ] ; then
1249	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1250	else
1251	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1252	fi
1253	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1254	echo "IGCM_sys_Rm ${generic_file_name}_*.nc " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1255	fi
1256	SaveOnArchive=false
1257	fi
1258	fi
1259	#
1260	if [ ${SaveOnArchive} = true ] ; then
1261	#
1262	# Rebuild has been done online or it was not needed
1263	#
1264	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1265	#
1266	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1267	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1268	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1269	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1270	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1271	#
1272	if [ $DRYRUN -le 1 ]; then
1273	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1274	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1275	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1276	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1277	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1278	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1279	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1280	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1281	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1282	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1283	fi
1284	#
1285	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1286	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1287	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1288	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1289	done
1290	#
1291	if [ X${Pack} = Xtrue ] ; then
1292	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1293	else
1294	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1295	fi
1296	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1297	#
1298	fi
1299	else
1300	#
1301	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1302	#
1303	if [ X${Pack} = Xtrue ] ; then
1304	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1305	else
1306	IGCM_sys_Put_Out ${file_in} ${file_out}
1307	fi
1308	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1309	if [ ${nb_rebuild_file} -gt 1 ] ; then
1310	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1311	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1312	done
1313	fi
1314	fi
1315	fi
1316	(( i=i+3 ))
1317	done
1318	fi
1319	echo
1320	done
1321	IGCM_debug_PopStack "IGCM_comp_Finalize"
1322	}

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