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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 778

Last change on this file since 778 was 778, checked in by labetoulle, 11 years ago
Bugfix in GetInputRestartFiles? when Restarts_OverRule=n (see #101).
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: 52.0 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	IsMatching=""
618
619	for comp in ${config_ListOfComponents[*]} ; do
620	# Define component
621	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
622	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
623	#
624	card=${SUBMIT_DIR}/COMP/${compname}.card
625	#
626	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
627	ListFilesName=${compname}_RestartFiles_List
628	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
629
630	# Debug Print :
631	IGCM_debug_Print 3 "restart ${compname}"
632
633	if ( ${FirstInitialize} ) ; then
634
635	if [ "${config_Restarts_OverRule}" = "y" ] ; then
636	eval config_${comp}_Restart="y"
637	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
638	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
639	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
640	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
641	eval CompOldName=${comp}
642	else
643	# Read component Restarts parameters
644	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
645	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
646
647	if [ "${do_start}" = "y" ] ; then
648	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
649	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
650	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
651	else
652	eval config_${comp}_RestartDate=-1
653	eval config_${comp}_RestartJobName=${NULL_STR}
654	eval config_${comp}_RestartPath=${NULL_STR}
655	fi
656	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} OldName
657	eval CompOldName=\${config_${comp}_OldName}
658	if [ X${CompOldName} = X ] ; then
659	eval CompOldName=${comp}
660	fi
661
662	# Reinitialize IsMatching to allow searching for a different tar file for each component.
663	IsMatching=""
664	TarFileFound=""
665	fi
666
667	if [ "${do_start}" = "y" ] ; then
668
669	# Restore Restarts files
670	#-----------------------
671	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
672	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
673
674	(( i=1 ))
675	until [ $i -gt $NbFiles ]; do
676	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
677	eval file_in=${file_in_}
678	(( i_ = i+1 ))
679	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
680	eval file_out=${file_out_}
681
682	eval Date_tmp=\${config_${comp}_RestartDate}
683	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
684	# will be re-use
685	eval RestartPath=\${config_${comp}_RestartPath}
686	eval RestartJobName=\${config_${comp}_RestartJobName}
687	#
688	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
689	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
690
691	extension_in=$( echo ${file_in_Name##*.} )
692	extension_out=$( echo ${file_out##*.} )
693
694	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
695	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
696
697	Path_OUT=${Path_r}/${generic_restart_file_name_in}
698
699	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
700	IGCM_debug_Print 3 "Buffered restart"
701	Buffered=true
702	Archived=false
703	Tared=false
704	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
705	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
706	IGCM_debug_Print 3 "Archived restart"
707	Buffered=false
708	Archived=true
709	Tared=false
710	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
711	else
712	IGCM_debug_Print 3 "Tared restart"
713	Buffered=false
714	Archived=false
715	Tared=true
716	# Look after the tar file we want if we did not found it already
717	if [ X${IsMatching} = X ] ; then
718	for PotentialTarFile in $( find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_*_restart.tar" -print ) ; do
719	IsMatching=$( echo ${PotentialTarFile##*/} \| \
720	sed "s:^${RestartJobName}_::" \| \
721	sed "s:\.restart\.tar$::" \| \
722	gawk -F_ -v restartdate=${Date_r} \
723	'{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
724	if [ ! X${IsMatching} = X ] ; then
725	TarFileFound=${PotentialTarFile}
726	break
727	fi
728	done
729	fi
730	IGCM_debug_Print 1 "tar xvf ${TarFileFound} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
731	tar xvf ${TarFileFound} ${comp}_${generic_restart_file_name_in}*.${extension_in}
732	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
733	fi
734
735	if [ ${nb_restart_file} -gt 1 ] ; then
736	j=0
737	until [ $j -ge ${nb_restart_file} ]; do
738	j4=${j}
739	if [ X${Buffered} = Xtrue ] ; then
740	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
741	elif [ X${Archived} = Xtrue ] ; then
742	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
743	elif [ X${Tared} = Xtrue ] ; then
744	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
745	fi
746	(( j=j+1 ))
747	done
748
749	if [ X${NUM_PROC_OCE} != X ] ; then
750	if [ ${NUM_PROC_OCE} -ne ${nb_restart_file} ] ; then
751	IGCM_sys_rebuild ${generic_restart_file_name_out}.${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
752	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
753	fi
754	fi
755	else
756	if [ X${Buffered} = Xtrue ] ; then
757	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
758	elif [ X${Archived} = Xtrue ] ; then
759	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
760	elif [ X${Tared} = Xtrue ] ; then
761	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
762	fi
763	fi
764	(( i=i+3 ))
765	done
766
767	else
768	if [ X${FileName0} != XNONE ] ; then
769	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
770	else
771	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
772	fi
773	fi
774	fi
775	elif [ ${Period} -eq 1 ] ; then
776	# if not FirstInitialize and first loop of this job
777
778	# Restore Restarts files
779	#-----------------------
780	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
781	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
782
783	(( i=1 ))
784	until [ $i -gt $NbFiles ]; do
785	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
786	eval file_in=${file_in_}
787	(( i_ = i+1 ))
788	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
789	eval file_out=${file_out_}
790
791	file_in_Name=${run_Configuration_OldPrefix}_${file_in}
792
793	extension_in=$( echo ${file_in_Name##*.} )
794	extension_out=$( echo ${file_out##*.} )
795
796	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
797	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
798
799	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
800	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
801
802	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
803	IGCM_debug_Print 3 "Buffered restart"
804	Buffered=true
805	Archived=false
806	Tared=false
807	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
808	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
809	IGCM_debug_Print 3 "Archived restart"
810	Buffered=false
811	Archived=true
812	Tared=false
813	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
814	else
815	IGCM_debug_Print 3 "Tared restart"
816	Buffered=false
817	Archived=false
818	Tared=true
819	# Look after the tar file we want if we did not found it already
820	if [ X${IsMatching} = X ] ; then
821	for PotentialTarFile in $( find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print ) ; do
822	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
823	if [ ! X${IsMatching} = X ] ; then
824	TarFileFound=${PotentialTarFile}
825	break
826	fi
827	done
828	fi
829	tar xvf ${TarFileFound} ${comp}_${generic_restart_file_name_in}*.${extension_in}
830	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
831	fi
832
833	if [ ${nb_restart_file} -gt 1 ] ; then
834	j=0
835	until [ $j -ge ${nb_restart_file} ]; do
836	j4=${j}
837	if [ X${Buffered} = Xtrue ] ; then
838	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
839	elif [ X${Archived} = Xtrue ] ; then
840	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
841	elif [ X${Tared} = Xtrue ] ; then
842	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
843	fi
844	(( j=j+1 ))
845	done
846	else
847	if [ X${Buffered} = Xtrue ] ; then
848	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
849	elif [ X${Archived} = Xtrue ] ; then
850	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
851	elif [ X${Tared} = Xtrue ] ; then
852	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
853	fi
854	fi
855	(( i=i+3 ))
856	done
857	else
858	if [ X${FileName0} != XNONE ] ; then
859	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
860	else
861	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
862	fi
863	fi
864	fi
865	done
866
867	NbFiles=$( ls * 2> /dev/null \| wc -l )
868	if [ ${NbFiles} -gt 0 ] ; then
869	IGCM_sys_Chmod u+rw *
870	fi
871
872	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
873	}
874
875	#=======================================================================
876	function IGCM_comp_PeriodStart
877	{
878	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
879
880	# Debug Print :
881	echo
882	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
883	echo
884
885	typeset ExeNameIn ExeNameOut
886	typeset comp compname comptagname
887	for comp in ${config_ListOfComponents[*]} ; do
888	# Define component
889	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
890	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
891
892	# Copy executable for this component
893	eval ExeNameIn=\${config_Executable_${comp}[0]}
894	eval ExeNameOut=\${config_Executable_${comp}[1]}
895
896	# Debug Print
897	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
898	# UPDATE component
899	${comp}_PeriodStart 2> /dev/null
900
901	done
902
903	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
904	}
905
906	#=======================================================================
907	function IGCM_comp_Update
908	{
909	IGCM_debug_PushStack "IGCM_comp_Update"
910
911	# Debug Print :
912	echo
913	IGCM_debug_Print 1 "IGCM_comp_Update"
914	echo
915
916	typeset ExeNameIn ExeNameOut
917	typeset comp compname comptagname
918	for comp in ${config_ListOfComponents[*]} ; do
919	# Define component
920	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
921	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
922
923	# Copy executable for this component
924	eval ExeNameIn=\${config_Executable_${comp}[0]}
925	eval ExeNameOut=\${config_Executable_${comp}[1]}
926
927	# If missing executable and DRYRUN is set to 0 or 1 then stop!
928	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
929	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
930	fi
931
932	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
933	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
934	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
935	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
936	fi
937	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
938	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
939	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
940	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
941	fi
942	fi
943
944	# Debug Print
945	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
946	# UPDATE component
947	${comp}_Update
948
949	done
950
951	IGCM_debug_PopStack "IGCM_comp_Update"
952	}
953
954	#=======================================================================
955	function IGCM_comp_Finalize
956	{
957	IGCM_debug_PushStack "IGCM_comp_Finalize"
958
959	# Debug Print :
960	echo
961	IGCM_debug_Print 1 "IGCM_comp_Finalize"
962	echo
963
964	typeset ListTextName TextName0
965	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
966	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
967	typeset -Z4 j4
968	typeset list_file nlist_file
969	typeset compactoutputs
970
971	compactoutputs=false
972	if [ X${JobType} != XRUN ] ; then
973	compactoutputs=true
974	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
975	compactoutputs=true
976	fi
977
978	for comp in ${config_ListOfComponents[*]} ; do
979	# Define component
980	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
981	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
982
983	# Debug Print
984	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
985	# FINALIZE component
986	${comp}_Finalize
987
988	card=${SUBMIT_DIR}/COMP/${compname}.card
989
990	# Save Restarts files
991	#--------------------
992	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
993	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
994	ListFilesName=${compname}_RestartFiles_List
995	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
996
997	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
998	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
999
1000	(( i=0 ))
1001	until [ $i -ge $NbFiles ]; do
1002	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1003	eval file_in=${file_in_}
1004
1005	(( i_ = i+1 ))
1006	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1007	eval file_out=${file_out_}
1008
1009	(( i_ = i+2 ))
1010	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1011	eval file_outin=${file_outin_}
1012
1013	generic_restart_file_name_in=$( basename ${file_in} .nc )
1014	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1015	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1016
1017	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1018	if [ ${nb_restart_file} -gt 1 ] ; then
1019	j=0
1020	until [ $j -ge ${nb_restart_file} ]; do
1021	j4=${j}
1022	if [ X${Pack} = Xtrue ] ; then
1023	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1024	else
1025	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1026	fi
1027	if [ ! ${file_in} = ${file_outin} ] ; then
1028	if ( ${ExitFlag} ) ; then
1029	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1030	else
1031	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1032	fi
1033	fi
1034	(( j=j+1 ))
1035	done
1036	else
1037	if [ X${Pack} = Xtrue ] ; then
1038	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1039	else
1040	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1041	fi
1042	if [ ! ${file_in} = ${file_outin} ] ; then
1043	if ( ${ExitFlag} ) ; then
1044	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1045	else
1046	IGCM_sys_Mv ${file_in} ${file_outin}
1047	fi
1048	fi
1049	fi
1050
1051	(( i=i+3 ))
1052	done
1053	else
1054	if [ X${FileName0} != XNONE ] ; then
1055	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1056	else
1057	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1058	fi
1059	fi
1060
1061	# Save Output files
1062	#------------------
1063	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1064	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1065	ListFilesName=${compname}_OutputFiles_List
1066	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1067
1068	if [ X${FileName0} != X${NULL_STR} ] ; then
1069	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1070
1071	(( i=0 ))
1072	until [ $i -ge $NbFiles ]; do
1073	SaveOnArchive=true
1074	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1075	eval file_in=${file_in_}
1076	(( i_ = i+1 ))
1077	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1078	eval file_out=${file_out_}
1079	#
1080	# Override file_out path remplacing R_SAVE by R_BUFR
1081	#
1082	if [ X${Pack} = Xtrue ] ; then
1083	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1084	fi
1085	#
1086	# Not necessarily the best option. /!\ Potential side effects /!\
1087	#
1088	(( i_ = i+2 ))
1089	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1090	#
1091	generic_file_name=$( basename ${file_in} .nc )
1092	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1093	#
1094	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1095	IGCM_debug_Print 2 "Parallelism with 1 process. Rebuilding ${file_in} not needed"
1096	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1097	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1098	IGCM_debug_Print 2 "Parallelism detected rebuilding ${file_in} is needed"
1099	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1100	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1101	IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc
1102	else
1103	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1104	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1105	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1106
1107	# Prepare headers for the shell dedicated to offline rebuild
1108	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1109	if [ $DRYRUN -le 1 ]; then
1110	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1111	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1112	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1113	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1114	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1115	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1116	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1117	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1118	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1119	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1120	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1121	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1122	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1123	fi
1124	fi
1125	# Prepare the shell dedicated to offline rebuild
1126	if [ $DRYRUN -le 1 ]; then
1127	if [ ${file_in} = histstn.nc ] ; then
1128	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1129	else
1130	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1131	fi
1132	echo "IGCM_debug_Verif_Exit_Post" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1133	fi
1134	#
1135	# Load Patch we need to apply and apply
1136	if [ $DRYRUN -le 1 ]; then
1137	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1138	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1139	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1140	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1141	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1142	done
1143	fi
1144	fi
1145	#
1146	if [ $DRYRUN -le 1 ]; then
1147	if [ X${Pack} = Xtrue ] ; then
1148	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1149	else
1150	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1151	fi
1152	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1153	echo "IGCM_sys_Rm ${generic_file_name}_*.nc " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1154	fi
1155	SaveOnArchive=false
1156	fi
1157	fi
1158	#
1159	if [ ${SaveOnArchive} = true ] ; then
1160	#
1161	# Rebuild has been done online or it was not needed
1162	#
1163	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1164	#
1165	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1166	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1167	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1168	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1169	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1170	#
1171	if [ $DRYRUN -le 1 ]; then
1172	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1173	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1174	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1175	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1176	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1177	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1178	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1179	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1180	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1181	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1182	fi
1183	#
1184	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1185	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1186	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1187	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1188	done
1189	#
1190	if [ X${Pack} = Xtrue ] ; then
1191	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1192	else
1193	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1194	fi
1195	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1196	#
1197	fi
1198	else
1199	#
1200	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1201	#
1202	if [ X${Pack} = Xtrue ] ; then
1203	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1204	else
1205	IGCM_sys_Put_Out ${file_in} ${file_out}
1206	fi
1207	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1208	if [ ${nb_rebuild_file} -gt 1 ] ; then
1209	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1210	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1211	done
1212	fi
1213	fi
1214	fi
1215	(( i=i+3 ))
1216	done
1217	fi
1218
1219	# Save Output Text files of models
1220	#---------------------------------
1221	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1222	IGCM_card_DefineArrayFromOption ${card} OutputText List
1223	ListTextName=${compname}_OutputText_List
1224
1225	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1226	if [ X${TextName0} != X${NULL_STR} ] ; then
1227	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1228
1229	(( i=0 ))
1230	until [ $i -eq $NbFiles ]; do
1231	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1232	eval file_out=${PREFIX}_${file_in}
1233
1234	(( i=i+1 ))
1235
1236	unset list_file
1237	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1238	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1239	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 )
1240	nlist_file=${#list_file[@]}
1241	if [ ${nlist_file} -gt 1 ] ; then
1242	if ( ${compactoutputs} ) ; then
1243	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1244	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1245	echo ${list_file[*]} > ${file_out}
1246	echo "" >> ${file_out}
1247
1248	(( i_ = 0 ))
1249	for file in ${list_file[@]}
1250	do
1251	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1252	echo "\| " ${i_} " " ${file} >> ${file_out}
1253	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1254	cat ${file} \| sed "s/\(.*\)/${i_}\1/" ${file} >> ${file_out}
1255	echo "" >> ${file_out}
1256	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1257	(( i_ = i_ + 1 ))
1258	done
1259	if [ X${Pack} = Xtrue ] ; then
1260	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1261	else
1262	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1263	fi
1264	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1265
1266	if ( ${ExecutionFail} ) ; then
1267	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1268	fi
1269	else
1270	for file in ${list_file[@]}
1271	do
1272	if [ X${Pack} = Xtrue ] ; then
1273	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1274	else
1275	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1276	fi
1277	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1278
1279	if ( ${ExecutionFail} ) ; then
1280	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1281	fi
1282	done
1283	fi
1284	else
1285	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1286	eval IGCM_sys_Mv ${file_in}* ${file_in}
1287	fi
1288	if [ X${Pack} = Xtrue ] ; then
1289	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1290	else
1291	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1292	fi
1293	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1294
1295	if ( ${ExecutionFail} ) ; then
1296	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1297	fi
1298	fi
1299	done
1300	fi
1301	echo
1302	done
1303	IGCM_debug_PopStack "IGCM_comp_Finalize"
1304	}

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