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source: tags/libIGCM_v2.0_beta3/libIGCM_comp/libIGCM_comp.ksh @ 1137

Last change on this file since 1137 was 672, checked in by sdipsl, 12 years ago
Can restart from "tared" restarts. overule=y/n lot of code duplication. needs refactoring some time soon
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
File size: 46.3 KB

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1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
6	# $Revision:: $ Revision of last commit
7	# $Author:: $ Author of last commit
8	# $Date:: $ Date of last commit
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	#
12	#**************************************************************
13
14	#========================================================================
15	function IGCM_comp_Initialize
16	{
17	IGCM_debug_PushStack "IGCM_comp_Initialize"
18
19	# Debug Print :
20	echo
21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
22	echo
23
24	typeset comp compname comptagname 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	# Read component Write Frequency in config.card
48	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} WriteFrequency
49	# Debug Print :
50	eval auxprint=\${config_${comp}_WriteFrequency}
51	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
52	#2> /dev/null
53
54	# Debug Print :
55	IGCM_debug_Print 2 "Initialize following component library"
56
57	# Source drivers in directory DRIVER if it exist
58	# else source them from directory COMP
59	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
60	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
61	# Source component library
62	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
63	else
64	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
65	# Source component library
66	. ${SUBMIT_DIR}/COMP/${compname}.driver
67	fi
68	IGCM_debug_Print 3 "With tag : ${comptagname}"
69
70	# Debug Print
71	IGCM_debug_Print 3 "Initialize ${comp} output directory."
72
73	# Define ARCHIVED Dirs
74	eval R_OUT_${comp}=${R_SAVE}/${comp}
75	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
76
77	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
78	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
79
80	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
81	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
82
83	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
84	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
85
86	eval R_OUT_${comp}_O_I=\${R_OUT_${comp}_O}/INS
87	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
88	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
89	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
90	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
91
92	# Define BUFFERED Dirs
93	eval R_BUF_${comp}=${R_BUFR}/${comp}
94	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
95
96	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
97	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
98
99	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
100	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
101
102	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
103	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
104
105	eval R_BUF_${comp}_O_I=\${R_BUF_${comp}_O}/INS
106	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
107	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
108	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
109	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
110
111	# Read UserChoices section of component card
112	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
113	IGCM_card_DefineArrayFromSection ${card} UserChoices
114	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
115	# If section is not empty we define corresponding variables
116	if [ X${first_option} != X"Error:" ] ; then
117	if [ X${card_UserChoices[0]} != X ] ; then
118	unset card_UserChoices
119	fi
120	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
121	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
122	for option in ${card_UserChoices[*]} ; do
123	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
124	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
125	done
126	fi
127
128	# Read and Build Output File stuff
129	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
130	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
131	ListFilesName=${compname}_OutputFiles_List
132	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
133	#
134	if [ X${FileName0} != X${NULL_STR} ] ; then
135	#
136	#IGCM_debug_Print 1 "Component : ${compname}"
137	#
138	# INITIALISATION
139	#
140	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
141	#
142	i=2
143	#
144	until [ $i -ge $NbFiles ]; do
145	#
146	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
147	#
148	if [ X${flag_post} != XNONE ] ; then
149	#
150	# First of all
151	#
152	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
153	#
154	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
155	#
156	# variable option allready typeset above
157	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
158	if [ ${option} = Seasonal ] ; then
159	FoundSeasonal=true
160	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
161	fi
162	done
163	#
164	if [ ! X${FoundSeasonal} = Xtrue ] ; then
165	eval ${compname}_${flag_post}_Seasonal=ON
166	fi
167	#
168	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
169	Seasonal=true
170	fi
171
172	# Dimension = vide si vieille card.
173	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
174	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
175	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
176	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
177	ListDimension[0]=2D
178	ListDimension[1]=3D
179	TimeSeries=false
180	iLoop=${#ListDimension[*]}
181	j=0
182	until [ $j -ge ${iLoop} ]; do
183	Dimension=${ListDimension[${j}]}
184	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
185	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
186	#
187	# Time series WITHOUT chunk
188	#
189	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
190	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
191	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
192	eval TimeSeries${Dimension}=true
193	fi
194	fi
195	#
196	# Time series WITH chunk
197	#
198	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
199	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
200	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
201	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
202	eval TimeSeriesChunck${Dimension}=true
203	eval set +A CHUNCK${Dimension}_COMP \${CHUNCK${Dimension}_COMP[*]} ${comp}
204	eval set +A CHUNCK${Dimension}_FLAG \${CHUNCK${Dimension}_FLAG[*]} ${i}
205	eval set +A CHUNCK${Dimension}_NAME \${CHUNCK${Dimension}_NAME[*]} ${flag_post}
206	eval set +A CHUNCK${Dimension}_SIZE \${CHUNCK${Dimension}_SIZE[*]} ${chunck_size}
207	fi
208	fi
209	(( j=j+1 ))
210	done
211	else
212	ListDimension[0]=""
213	TimeSeries=true
214	TimeSeries2D=false
215	TimeSeries3D=false
216	TimeSeriesChunck2D=false
217	TimeSeriesChunck3D=false
218	fi
219	fi
220	(( i=i+3 ))
221	done
222	fi
223	# Debug Print
224	IGCM_debug_Print 3 "Initialize ${compname} with driver."
225	# INIT component
226	${comp}_Initialize
227	echo
228	done
229
230	IGCM_debug_PopStack "IGCM_comp_Initialize"
231	}
232
233	#=======================================================================
234	function IGCM_comp_PrepareDeletedFiles
235	{
236	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
237
238	if [ X${2} != X. ] ; then
239	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
240	else
241	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
242	fi
243
244	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
245	}
246
247	#=======================================================================
248	function IGCM_comp_GetInputInitialStateFiles
249	{
250	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
251
252	# Debug Print :
253	echo
254	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
255	echo
256
257	# Only the first time step need InitialStateFiles
258	# otherwise it's BoundaryConditions
259	if ( ${FirstInitialize} ) ; then
260	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
261	typeset file_in_ file_in file_out_ file_out do_init
262	for comp in ${config_ListOfComponents[*]} ; do
263	# Initialize
264	do_init="y"
265	# Do we need to bring initial state file for this component
266	if [ "${config_Restarts_OverRule}" = "y" ] ; then
267	eval do_init="n"
268	else
269	# Read component Restarts parameters
270	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
271	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
272	if [ "${do_start}" = "y" ] ; then
273	do_init="n"
274	else
275	do_init="y"
276	fi
277	fi
278
279	if [ "${do_init}" = "y" ] ; then
280	# Define component
281	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
282	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
283
284	# Debug Print :
285	IGCM_debug_Print 3 "Initialisation files ${compname}"
286
287	card=${SUBMIT_DIR}/COMP/${compname}.card
288
289	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
290	ListFilesName=${compname}_InitialStateFiles_List
291
292	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
293	if [ X${FileName0} != X${NULL_STR} ] ; then
294	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
295	(( i=0 ))
296	until [ $i -ge $NbFiles ]; do
297	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
298	eval file_in=${file_in_}
299	(( i_ = i+1 ))
300	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
301	eval file_out=${file_out_}
302
303	IGCM_sys_IsFileArchived ${file_in}
304	if [ $? = 0 ] ; then
305	IGCM_sys_Get ${file_in} ${file_out}
306	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
307	else
308	IGCM_sys_Cp ${file_in} ${file_out}
309	fi
310	(( i=i+2 ))
311	done
312	fi
313	fi
314	done
315	fi
316	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
317	}
318
319	#=======================================================================
320	# Definition of Smooth modulo function
321	# usage :
322	# IGCM_SmoothModulo StringModulo value
323	#
324	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
325	# [min]:[modulo:][max]
326	# where :
327	# [] value are optionnals;
328	# empty min equal 1
329	# empty max equal infinity
330	# modulo not given or empty equal 1
331	# empty string or just ':' equal always.
332	#
333	# value : the value to test with the definition
334	#
335	# return : true(1)/false(0)
336	function IGCM_SmoothModulo
337	{
338	IGCM_debug_PushStack "IGCM_SmoothModulo"
339	typeset defVector ModValue
340
341	eval set +A defVector -- $( echo "${1}" \| \
342	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
343
344	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
345	arr[1]=${defVector[0]}
346	arr[2]=${defVector[2]}
347
348	# Test limits :
349	# ${defVector[0]} <= ${2} <= ${defVector[2]}
350	# or ${defVector[2]} == -1
351	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
352	# Test modulo
353	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
354	if [ ${ModValue} -eq 0 ] ; then
355	arr[3]=true
356	echo ${arr[@]}
357	IGCM_debug_PopStack "IGCM_SmoothModulo"
358	return 1
359	else
360	arr[3]=false
361	echo ${arr[@]}
362	IGCM_debug_PopStack "IGCM_SmoothModulo"
363	return 0
364	fi
365	else
366	arr[3]=false
367	echo ${arr[@]}
368	IGCM_debug_PopStack "IGCM_SmoothModulo"
369	return 0
370	fi
371	}
372
373	#=======================================================================
374	function IGCM_comp_GetInputSmoothFiles
375	{
376	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
377
378	# Debug Print :
379	echo
380	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
381	echo
382
383	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
384	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
385
386	for comp in ${config_ListOfComponents[*]} ; do
387	# Define component
388	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
389	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
390
391	# Debug Print :
392	IGCM_debug_Print 3 "Smooth files ${compname}"
393
394	card=${SUBMIT_DIR}/COMP/${compname}.card
395
396	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
397	ListFilesName=${compname}_SmoothFiles_List
398	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
399
400	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
401	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
402
403	(( i=0 ))
404	until [ $i -ge $NbFiles ]; do
405	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
406	eval file_in=${file_in_}
407	(( i_ = i+1 ))
408	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
409	eval file_out=${file_out_}
410
411	# define CumulPeriod definition for this file
412	(( i__ = i+2 ))
413	eval SmoothDef=\${${ListFilesName}[$i__]}
414	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
415	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
416	j=1
417	for val in ${aux} ; do
418	[ ${j} -eq 1 ] && SmoothMin=${val}
419	[ ${j} -eq 2 ] && SmoothMax=${val}
420	[ ${j} -eq 3 ] && ret=${val}
421	(( j=j+1 ))
422	done
423	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
424	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
425
426	IGCM_sys_IsFileArchived ${file_in}
427	if [ $? = 0 ] ; then
428	IGCM_sys_Get ${file_in} ${file_out}
429	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
430	else
431	IGCM_sys_Cp ${file_in} ${file_out}
432	fi
433	fi
434	(( i=i+3 ))
435	done
436	fi
437	done
438
439	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
440	}
441
442	#=======================================================================
443	function IGCM_comp_GetInputBoundaryFiles
444	{
445	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
446
447	# Debug Print :
448	echo
449	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
450	echo
451
452	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
453	typeset file_in_ file_in file_out_ file_out
454
455	if [ ${Period} = 1 ]; then
456	ListFixBoundary=" "
457	fi
458
459	for comp in ${config_ListOfComponents[*]} ; do
460
461	# Define component
462	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
463	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
464
465	# Debug Print :
466	IGCM_debug_Print 3 "Boundary files ${compname}"
467
468	card=${SUBMIT_DIR}/COMP/${compname}.card
469
470	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
471	ListFilesName=${compname}_BoundaryFiles_List
472	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
473
474	if [ X${FileName0} != X${NULL_STR} ] ; then
475	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
476
477	(( i=0 ))
478	until [ $i -ge $NbFiles ]; do
479	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
480	eval file_in=${file_in_}
481	(( i_ = i+1 ))
482	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
483	eval file_out=${file_out_}
484
485	IGCM_sys_IsFileArchived ${file_in}
486	if [ $? = 0 ] ; then
487	IGCM_sys_Get ${file_in} ${file_out}
488	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
489	else
490	IGCM_sys_Cp ${file_in} ${file_out}
491	fi
492
493	(( i=i+2 ))
494	done
495	fi
496
497	# Get non deleted files
498	if [ ${Period} = 1 ]; then
499
500	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
501	ListFilesName=${compname}_BoundaryFiles_ListNonDel
502	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
503
504	if [ X${FileName0} != X${NULL_STR} ] ; then
505	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
506
507	(( i=0 ))
508	until [ $i -ge $NbFiles ]; do
509	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
510	eval file_in=${file_in_}
511	(( i_ = i+1 ))
512	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
513	eval file_out=${file_out_}
514
515	IGCM_sys_IsFileArchived ${file_in}
516	if [ $? = 0 ] ; then
517	IGCM_sys_Get ${file_in} ${file_out}
518	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
519	else
520	IGCM_sys_Cp ${file_in} ${file_out}
521	fi
522
523	if [ X${file_out} != X. ] ; then
524	ListFixBoundary=${ListFixBoundary}" "${file_out}
525	else
526	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
527	fi
528
529	(( i=i+2 ))
530	done
531	fi
532	fi
533	done
534
535	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
536	}
537
538	#=======================================================================
539	function IGCM_comp_DelFixeBoundaryFiles
540	{
541	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
542
543	# Debug Print :
544	echo
545	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
546	echo
547
548	ls -l ${ListFixBoundary}
549	rm -f ${ListFixBoundary}
550
551	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
552	}
553
554	#=======================================================================
555	function IGCM_comp_GetInputParametersFiles
556	{
557	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
558
559	# Debug Print :
560	echo
561	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
562	echo
563
564	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
565	for comp in ${config_ListOfComponents[*]} ; do
566	# Define component
567	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
568	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
569
570	# Debug Print :
571	IGCM_debug_Print 3 "Parameters ${compname}"
572
573	card=${SUBMIT_DIR}/COMP/${compname}.card
574
575	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
576	ListFilesName=${compname}_ParametersFiles_List
577	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
578
579	if [ X${FileName0} != X${NULL_STR} ] ; then
580	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
581
582	(( i=0 ))
583	until [ $i -ge $NbFiles ]; do
584	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
585	eval file_in=${file_in_}
586	(( i_ = i+1 ))
587	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
588	eval file_out=${file_out_}
589
590	IGCM_sys_Cp ${file_in} ${file_out}
591	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
592
593	(( i=i+2 ))
594	done
595	fi
596	done
597
598	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
599	}
600
601	#=======================================================================
602	function IGCM_comp_GetInputRestartFiles
603	{
604	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
605
606	# Debug Print :
607	echo
608	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
609	echo
610
611	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
612	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
613	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
614	typeset file_in file_out file_in_ file_out_ file_in_Name
615	typeset -Z4 j4
616
617	for comp in ${config_ListOfComponents[*]} ; do
618	# Define component
619	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
620	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
621	#
622	card=${SUBMIT_DIR}/COMP/${compname}.card
623	#
624	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
625	ListFilesName=${compname}_RestartFiles_List
626	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
627
628	# Debug Print :
629	IGCM_debug_Print 3 "restart ${compname}"
630
631	if ( ${FirstInitialize} ) ; then
632
633	if [ "${config_Restarts_OverRule}" = "y" ] ; then
634	eval config_${comp}_Restart="y"
635	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
636	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
637	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
638	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
639	eval CompOldName=${comp}
640	else
641	# Read component Restarts parameters
642	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
643	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
644
645	if [ "${do_start}" = "y" ] ; then
646	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
647	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
648	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
649	else
650	eval config_${comp}_RestartDate=-1
651	eval config_${comp}_RestartJobName=${NULL_STR}
652	eval config_${comp}_RestartPath=${NULL_STR}
653	fi
654	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} OldName
655	eval CompOldName=\${config_${comp}_OldName}
656	if [ X${CompOldName} = X ] ; then
657	eval CompOldName=${comp}
658	fi
659	fi
660
661	if [ "${do_start}" = "y" ] ; then
662
663	# Restore Restarts files
664	#-----------------------
665	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
666	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
667
668	(( i=1 ))
669	until [ $i -gt $NbFiles ]; do
670	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
671	eval file_in=${file_in_}
672	(( i_ = i+1 ))
673	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
674	eval file_out=${file_out_}
675
676	eval Date_tmp=\${config_${comp}_RestartDate}
677	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
678	# will be re-use
679	eval RestartPath=\${config_${comp}_RestartPath}
680	eval RestartJobName=\${config_${comp}_RestartJobName}
681	#
682	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
683	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
684
685	extension_in=$( echo ${file_in_Name##*.} )
686	extension_out=$( echo ${file_out##*.} )
687
688	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
689	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
690
691	Path_OUT=${Path_r}/${generic_restart_file_name_in}
692
693	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
694	IGCM_debug_Print 3 "Buffered restart"
695	Buffered=true
696	Archived=false
697	Tared=false
698	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
699	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
700	IGCM_debug_Print 3 "Archived restart"
701	Buffered=false
702	Archived=true
703	Tared=false
704	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
705	else
706	IGCM_debug_Print 3 "Tared restart"
707	Buffered=false
708	Archived=false
709	Tared=true
710	# Look after the tar file we want if we did not found it already
711	if [ X${IsMatching} = X ] ; then
712	for PotentialTarFile in $( find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_*_restart.tar" -print ) ; do
713	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${RestartJobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${Date_r} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
714	if [ ! X${IsMatching} = X ] ; then
715	TarFileFound=${PotentialTarFile}
716	break
717	fi
718	done
719	fi
720	IGCM_debug_Print 1 "tar xvf ${TarFileFound} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
721	tar xvf ${TarFileFound} ${comp}_${generic_restart_file_name_in}*.${extension_in}
722	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
723	fi
724
725	if [ ${nb_restart_file} -gt 1 ] ; then
726	j=0
727	until [ $j -ge $nb_restart_file ]; do
728	j4=${j}
729	if [ X${Buffered} = Xtrue ] ; then
730	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
731	elif [ X${Archived} = Xtrue ] ; then
732	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
733	elif [ X${Tared} = Xtrue ] ; then
734	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
735	fi
736	(( j=j+1 ))
737	done
738	else
739	if [ X${Buffered} = Xtrue ] ; then
740	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
741	elif [ X${Archived} = Xtrue ] ; then
742	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
743	elif [ X${Tared} = Xtrue ] ; then
744	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
745	fi
746	fi
747	(( i=i+3 ))
748	done
749
750	else
751	if [ X${FileName0} != XNONE ] ; then
752	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
753	else
754	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
755	fi
756	fi
757	fi
758	elif [ ${Period} -eq 1 ] ; then
759	# if not FirstInitialize and first loop of this job
760
761	# Restore Restarts files
762	#-----------------------
763	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
764	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
765
766	(( i=1 ))
767	until [ $i -gt $NbFiles ]; do
768	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
769	eval file_in=${file_in_}
770	(( i_ = i+1 ))
771	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
772	eval file_out=${file_out_}
773
774	file_in_Name=${run_Configuration_OldPrefix}_${file_in}
775
776	extension_in=$( echo ${file_in_Name##*.} )
777	extension_out=$( echo ${file_out##*.} )
778
779	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
780	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
781
782	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
783	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
784
785	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
786	IGCM_debug_Print 3 "Buffered restart"
787	Buffered=true
788	Archived=false
789	Tared=false
790	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
791	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
792	IGCM_debug_Print 3 "Archived restart"
793	Buffered=false
794	Archived=true
795	Tared=false
796	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
797	else
798	IGCM_debug_Print 3 "Tared restart"
799	Buffered=false
800	Archived=false
801	Tared=true
802	# Look after the tar file we want if we did not found it already
803	if [ X${IsMatching} = X ] ; then
804	for PotentialTarFile in $( find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print ) ; do
805	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
806	if [ ! X${IsMatching} = X ] ; then
807	TarFileFound=${PotentialTarFile}
808	break
809	fi
810	done
811	fi
812	tar xvf ${TarFileFound} ${comp}_${generic_restart_file_name_in}*.${extension_in}
813	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
814	fi
815
816	if [ ${nb_restart_file} -gt 1 ] ; then
817	j=0
818	until [ $j -ge $nb_restart_file ]; do
819	j4=${j}
820	if [ X${Buffered} = Xtrue ] ; then
821	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
822	elif [ X${Archived} = Xtrue ] ; then
823	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
824	elif [ X${Tared} = Xtrue ] ; then
825	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
826	fi
827	(( j=j+1 ))
828	done
829	else
830	if [ X${Buffered} = Xtrue ] ; then
831	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
832	elif [ X${Archived} = Xtrue ] ; then
833	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
834	elif [ X${Tared} = Xtrue ] ; then
835	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
836	fi
837	fi
838	(( i=i+3 ))
839	done
840	else
841	if [ X${FileName0} != XNONE ] ; then
842	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
843	else
844	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
845	fi
846	fi
847	fi
848	done
849
850	NbFiles=$( ls * 2> /dev/null \| wc -l )
851	if [ ${NbFiles} -gt 0 ] ; then
852	IGCM_sys_Chmod u+rw *
853	fi
854
855	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
856	}
857
858	#=======================================================================
859	function IGCM_comp_PeriodStart
860	{
861	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
862
863	# Debug Print :
864	echo
865	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
866	echo
867
868	typeset ExeNameIn ExeNameOut
869	typeset comp compname comptagname
870	for comp in ${config_ListOfComponents[*]} ; do
871	# Define component
872	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
873	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
874
875	# Copy executable for this component
876	eval ExeNameIn=\${config_Executable_${comp}[0]}
877	eval ExeNameOut=\${config_Executable_${comp}[1]}
878
879	# Debug Print
880	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
881	# UPDATE component
882	${comp}_PeriodStart 2> /dev/null
883
884	done
885
886	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
887	}
888
889	#=======================================================================
890	function IGCM_comp_Update
891	{
892	IGCM_debug_PushStack "IGCM_comp_Update"
893
894	# Debug Print :
895	echo
896	IGCM_debug_Print 1 "IGCM_comp_Update"
897	echo
898
899	typeset ExeNameIn ExeNameOut
900	typeset comp compname comptagname
901	for comp in ${config_ListOfComponents[*]} ; do
902	# Define component
903	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
904	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
905
906	# Copy executable for this component
907	eval ExeNameIn=\${config_Executable_${comp}[0]}
908	eval ExeNameOut=\${config_Executable_${comp}[1]}
909
910	# If missing executable and DRYRUN is set to 0 or 1 then stop!
911	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
912	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
913	fi
914
915	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
916	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
917	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
918	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
919	fi
920	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
921	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
922	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
923	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
924	fi
925	fi
926
927	# Debug Print
928	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
929	# UPDATE component
930	${comp}_Update
931
932	done
933
934	IGCM_debug_PopStack "IGCM_comp_Update"
935	}
936
937	#=======================================================================
938	function IGCM_comp_Finalize
939	{
940	IGCM_debug_PushStack "IGCM_comp_Finalize"
941
942	# Debug Print :
943	echo
944	IGCM_debug_Print 1 "IGCM_comp_Finalize"
945	echo
946
947	typeset ListTextName TextName0
948	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
949	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
950	typeset -Z4 j4
951	typeset list_file nlist_file
952	typeset compactoutputs
953
954	compactoutputs=false
955	if [ X${JobType} != XRUN ] ; then
956	compactoutputs=true
957	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
958	compactoutputs=true
959	fi
960
961	for comp in ${config_ListOfComponents[*]} ; do
962	# Define component
963	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
964	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
965
966	# Debug Print
967	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
968	# FINALIZE component
969	${comp}_Finalize
970
971	card=${SUBMIT_DIR}/COMP/${compname}.card
972
973	# Save Restarts files
974	#--------------------
975	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
976	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
977	ListFilesName=${compname}_RestartFiles_List
978	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
979
980	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
981	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
982
983	(( i=0 ))
984	until [ $i -ge $NbFiles ]; do
985	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
986	eval file_in=${file_in_}
987
988	(( i_ = i+1 ))
989	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
990	eval file_out=${file_out_}
991
992	(( i_ = i+2 ))
993	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
994	eval file_outin=${file_outin_}
995
996	generic_restart_file_name_in=$( basename ${file_in} .nc )
997	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
998	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
999
1000	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1001	if [ ${nb_restart_file} -gt 1 ] ; then
1002	j=0
1003	until [ $j -ge $nb_restart_file ]; do
1004	j4=${j}
1005	if [ X${Pack} = Xtrue ] ; then
1006	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1007	else
1008	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1009	fi
1010	if [ ! ${file_in} = ${file_outin} ] ; then
1011	if ( ${ExitFlag} ) ; then
1012	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1013	else
1014	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1015	fi
1016	fi
1017	(( j=j+1 ))
1018	done
1019	else
1020	if [ X${Pack} = Xtrue ] ; then
1021	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1022	else
1023	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1024	fi
1025	if [ ! ${file_in} = ${file_outin} ] ; then
1026	if ( ${ExitFlag} ) ; then
1027	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1028	else
1029	IGCM_sys_Mv ${file_in} ${file_outin}
1030	fi
1031	fi
1032	fi
1033
1034	(( i=i+3 ))
1035	done
1036	else
1037	if [ X${FileName0} != XNONE ] ; then
1038	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1039	else
1040	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1041	fi
1042	fi
1043
1044	# Save Output files
1045	#------------------
1046	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1047	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1048	ListFilesName=${compname}_OutputFiles_List
1049	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1050
1051	if [ X${FileName0} != X${NULL_STR} ] ; then
1052	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1053
1054	(( i=0 ))
1055	until [ $i -ge $NbFiles ]; do
1056	SaveOnArchive=true
1057	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1058	eval file_in=${file_in_}
1059	(( i_ = i+1 ))
1060	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1061	eval file_out=${file_out_}
1062	#
1063	# Override file_out path remplacing R_SAVE by R_BUFR
1064	#
1065	if [ X${Pack} = Xtrue ] ; then
1066	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1067	fi
1068	#
1069	# Not necessarily the best option. /!\ Potential side effects /!\
1070	#
1071	(( i_ = i+2 ))
1072	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1073	#
1074	generic_file_name=$( basename ${file_in} .nc )
1075	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1076	#
1077	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1078	IGCM_debug_Print 2 "Parallelism with 1 process. Rebuilding ${file_in} not needed"
1079	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1080	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1081	IGCM_debug_Print 2 "Parallelism detected rebuilding ${file_in} is needed"
1082	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1083	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1084	IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc
1085	else
1086	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1087	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1088	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1089
1090	# Prepare headers for the shell dedicated to offline rebuild
1091	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1092	if [ $DRYRUN -le 1 ]; then
1093	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1094	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1095	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1096	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1097	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1098	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1099	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1100	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1101	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1102	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1103	fi
1104	fi
1105	# Prepare the shell dedicated to offline rebuild
1106	if [ $DRYRUN -le 1 ]; then
1107	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1108	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1109	fi
1110	#
1111	# Load Patch we need to apply and apply
1112	if [ $DRYRUN -le 1 ]; then
1113	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1114	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1115	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1116	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1117	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1118	done
1119	fi
1120	fi
1121	#
1122	if [ $DRYRUN -le 1 ]; then
1123	if [ X${Pack} = Xtrue ] ; then
1124	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1125	else
1126	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1127	fi
1128	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1129	echo "IGCM_sys_Rm ${generic_file_name}_*.nc " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1130	fi
1131	SaveOnArchive=false
1132	fi
1133	fi
1134	#
1135	if [ ${SaveOnArchive} = true ] ; then
1136	#
1137	# Rebuild has been done online or it was not needed
1138	#
1139	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1140	#
1141	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1142	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1143	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1144	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1145	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1146	#
1147	if [ $DRYRUN -le 1 ]; then
1148	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1149	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1150	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1151	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1152	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1153	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1154	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1155	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1156	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1157	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1158	fi
1159	#
1160	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1161	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1162	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1163	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1164	done
1165	#
1166	if [ X${Pack} = Xtrue ] ; then
1167	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1168	else
1169	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1170	fi
1171	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1172	#
1173	fi
1174	else
1175	#
1176	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1177	#
1178	if [ X${Pack} = Xtrue ] ; then
1179	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1180	else
1181	IGCM_sys_Put_Out ${file_in} ${file_out}
1182	fi
1183	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1184	if [ ${nb_rebuild_file} -gt 1 ] ; then
1185	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1186	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1187	done
1188	fi
1189	fi
1190	fi
1191	(( i=i+3 ))
1192	done
1193	fi
1194
1195	# Save Output Text files of models
1196	#---------------------------------
1197	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1198	IGCM_card_DefineArrayFromOption ${card} OutputText List
1199	ListTextName=${compname}_OutputText_List
1200
1201	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1202	if [ X${TextName0} != X${NULL_STR} ] ; then
1203	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1204
1205	(( i=0 ))
1206	until [ $i -eq $NbFiles ]; do
1207	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1208	eval file_out=${PREFIX}_${file_in}
1209
1210	(( i=i+1 ))
1211
1212	unset list_file
1213	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1214	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1215	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 )
1216	nlist_file=${#list_file[@]}
1217	if [ ${nlist_file} -gt 1 ] ; then
1218	if ( ${compactoutputs} ) ; then
1219	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1220	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1221	echo ${list_file[*]} > ${file_out}
1222	echo "" >> ${file_out}
1223
1224	(( i_ = 0 ))
1225	for file in ${list_file[@]}
1226	do
1227	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1228	echo "\| " ${i_} " " ${file} >> ${file_out}
1229	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1230	cat ${file} \| sed "s/\(.*\)/${i_}\1/" ${file} >> ${file_out}
1231	echo "" >> ${file_out}
1232	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1233	(( i_ = i_ + 1 ))
1234	done
1235	if [ X${Pack} = Xtrue ] ; then
1236	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1237	else
1238	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1239	fi
1240	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1241
1242	if ( ${ExecutionFail} ) ; then
1243	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1244	fi
1245	else
1246	for file in ${list_file[@]}
1247	do
1248	if [ X${Pack} = Xtrue ] ; then
1249	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1250	else
1251	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1252	fi
1253	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1254
1255	if ( ${ExecutionFail} ) ; then
1256	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1257	fi
1258	done
1259	fi
1260	else
1261	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1262	eval IGCM_sys_Mv ${file_in}* ${file_in}
1263	fi
1264	if [ X${Pack} = Xtrue ] ; then
1265	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1266	else
1267	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1268	fi
1269	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1270
1271	if ( ${ExecutionFail} ) ; then
1272	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1273	fi
1274	fi
1275	done
1276	fi
1277	echo
1278	done
1279	IGCM_debug_PopStack "IGCM_comp_Finalize"
1280	}

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