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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 740

Last change on this file since 740 was 740, checked in by sdipsl, 12 years ago
when restarting from a simulation having run on different number of cores that the current one we have to rebuild restarts
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
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1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
6	# $Revision:: $ Revision of last commit
7	# $Author:: $ Author of last commit
8	# $Date:: $ Date of last commit
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	#
12	#**************************************************************
13
14	#========================================================================
15	function IGCM_comp_Initialize
16	{
17	IGCM_debug_PushStack "IGCM_comp_Initialize"
18
19	# Debug Print :
20	echo
21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
22	echo
23
24	typeset comp compname comptagname CompatibilityTag auxprint card_UserChoices first_option option i j
25	for comp in ${config_ListOfComponents[*]} ; do
26
27	# Define component
28	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
29	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
30	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
31
32	# Debug Print
33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
34
35	# Read libIGCM compatibility version in ${compname}.card
36	card=${SUBMIT_DIR}/COMP/${compname}.card
37	IGCM_card_DefineVariableFromOption ${card} Compatibility libIGCM
38
39	eval CompatibilityTag=\${${compname}_Compatibility_libIGCM} > /dev/null 2>&1
40	if [ ! "${CompatibilityTag}" = "${libIGCM_CurrentTag}" ] ; then
41	IGCM_debug_Exit "${compname}.card is not compatible with libIGCM version ${libIGCM_CurrentTag} see libIGCM FAQ http://wiki.ipsl.jussieu.fr/wiki_ipsl/IGCMG/libIGCM/DocUtilisateur/FAQ ."
42	fi
43
44	# Manage component executable
45	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
46
47	# 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}.${extension_out}
735	fi
736	(( j=j+1 ))
737	done
738
739	if [ X${NUM_PROC_OCE} != X ] ; then
740	if [ ${NUM_PROC_OCE} -ne ${nb_restart_file} ] ; then
741	IGCM_sys_rebuild ${generic_restart_file_name_out}.${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
742	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
743	fi
744	fi
745	else
746	if [ X${Buffered} = Xtrue ] ; then
747	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
748	elif [ X${Archived} = Xtrue ] ; then
749	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
750	elif [ X${Tared} = Xtrue ] ; then
751	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
752	fi
753	fi
754	(( i=i+3 ))
755	done
756
757	else
758	if [ X${FileName0} != XNONE ] ; then
759	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
760	else
761	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
762	fi
763	fi
764	fi
765	elif [ ${Period} -eq 1 ] ; then
766	# if not FirstInitialize and first loop of this job
767
768	# Restore Restarts files
769	#-----------------------
770	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
771	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
772
773	(( i=1 ))
774	until [ $i -gt $NbFiles ]; do
775	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
776	eval file_in=${file_in_}
777	(( i_ = i+1 ))
778	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
779	eval file_out=${file_out_}
780
781	file_in_Name=${run_Configuration_OldPrefix}_${file_in}
782
783	extension_in=$( echo ${file_in_Name##*.} )
784	extension_out=$( echo ${file_out##*.} )
785
786	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
787	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
788
789	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
790	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
791
792	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
793	IGCM_debug_Print 3 "Buffered restart"
794	Buffered=true
795	Archived=false
796	Tared=false
797	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
798	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
799	IGCM_debug_Print 3 "Archived restart"
800	Buffered=false
801	Archived=true
802	Tared=false
803	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
804	else
805	IGCM_debug_Print 3 "Tared restart"
806	Buffered=false
807	Archived=false
808	Tared=true
809	# Look after the tar file we want if we did not found it already
810	if [ X${IsMatching} = X ] ; then
811	for PotentialTarFile in $( find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print ) ; do
812	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
813	if [ ! X${IsMatching} = X ] ; then
814	TarFileFound=${PotentialTarFile}
815	break
816	fi
817	done
818	fi
819	tar xvf ${TarFileFound} ${comp}_${generic_restart_file_name_in}*.${extension_in}
820	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
821	fi
822
823	if [ ${nb_restart_file} -gt 1 ] ; then
824	j=0
825	until [ $j -ge ${nb_restart_file} ]; do
826	j4=${j}
827	if [ X${Buffered} = Xtrue ] ; then
828	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
829	elif [ X${Archived} = Xtrue ] ; then
830	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
831	elif [ X${Tared} = Xtrue ] ; then
832	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
833	fi
834	(( j=j+1 ))
835	done
836	else
837	if [ X${Buffered} = Xtrue ] ; then
838	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
839	elif [ X${Archived} = Xtrue ] ; then
840	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
841	elif [ X${Tared} = Xtrue ] ; then
842	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
843	fi
844	fi
845	(( i=i+3 ))
846	done
847	else
848	if [ X${FileName0} != XNONE ] ; then
849	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
850	else
851	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
852	fi
853	fi
854	fi
855	done
856
857	NbFiles=$( ls * 2> /dev/null \| wc -l )
858	if [ ${NbFiles} -gt 0 ] ; then
859	IGCM_sys_Chmod u+rw *
860	fi
861
862	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
863	}
864
865	#=======================================================================
866	function IGCM_comp_PeriodStart
867	{
868	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
869
870	# Debug Print :
871	echo
872	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
873	echo
874
875	typeset ExeNameIn ExeNameOut
876	typeset comp compname comptagname
877	for comp in ${config_ListOfComponents[*]} ; do
878	# Define component
879	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
880	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
881
882	# Copy executable for this component
883	eval ExeNameIn=\${config_Executable_${comp}[0]}
884	eval ExeNameOut=\${config_Executable_${comp}[1]}
885
886	# Debug Print
887	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
888	# UPDATE component
889	${comp}_PeriodStart 2> /dev/null
890
891	done
892
893	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
894	}
895
896	#=======================================================================
897	function IGCM_comp_Update
898	{
899	IGCM_debug_PushStack "IGCM_comp_Update"
900
901	# Debug Print :
902	echo
903	IGCM_debug_Print 1 "IGCM_comp_Update"
904	echo
905
906	typeset ExeNameIn ExeNameOut
907	typeset comp compname comptagname
908	for comp in ${config_ListOfComponents[*]} ; do
909	# Define component
910	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
911	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
912
913	# Copy executable for this component
914	eval ExeNameIn=\${config_Executable_${comp}[0]}
915	eval ExeNameOut=\${config_Executable_${comp}[1]}
916
917	# If missing executable and DRYRUN is set to 0 or 1 then stop!
918	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
919	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
920	fi
921
922	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
923	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
924	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
925	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
926	fi
927	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
928	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
929	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
930	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
931	fi
932	fi
933
934	# Debug Print
935	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
936	# UPDATE component
937	${comp}_Update
938
939	done
940
941	IGCM_debug_PopStack "IGCM_comp_Update"
942	}
943
944	#=======================================================================
945	function IGCM_comp_Finalize
946	{
947	IGCM_debug_PushStack "IGCM_comp_Finalize"
948
949	# Debug Print :
950	echo
951	IGCM_debug_Print 1 "IGCM_comp_Finalize"
952	echo
953
954	typeset ListTextName TextName0
955	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
956	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
957	typeset -Z4 j4
958	typeset list_file nlist_file
959	typeset compactoutputs
960
961	compactoutputs=false
962	if [ X${JobType} != XRUN ] ; then
963	compactoutputs=true
964	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
965	compactoutputs=true
966	fi
967
968	for comp in ${config_ListOfComponents[*]} ; do
969	# Define component
970	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
971	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
972
973	# Debug Print
974	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
975	# FINALIZE component
976	${comp}_Finalize
977
978	card=${SUBMIT_DIR}/COMP/${compname}.card
979
980	# Save Restarts files
981	#--------------------
982	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
983	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
984	ListFilesName=${compname}_RestartFiles_List
985	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
986
987	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
988	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
989
990	(( i=0 ))
991	until [ $i -ge $NbFiles ]; do
992	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
993	eval file_in=${file_in_}
994
995	(( i_ = i+1 ))
996	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
997	eval file_out=${file_out_}
998
999	(( i_ = i+2 ))
1000	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1001	eval file_outin=${file_outin_}
1002
1003	generic_restart_file_name_in=$( basename ${file_in} .nc )
1004	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1005	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1006
1007	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1008	if [ ${nb_restart_file} -gt 1 ] ; then
1009	j=0
1010	until [ $j -ge ${nb_restart_file} ]; do
1011	j4=${j}
1012	if [ X${Pack} = Xtrue ] ; then
1013	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1014	else
1015	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1016	fi
1017	if [ ! ${file_in} = ${file_outin} ] ; then
1018	if ( ${ExitFlag} ) ; then
1019	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1020	else
1021	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1022	fi
1023	fi
1024	(( j=j+1 ))
1025	done
1026	else
1027	if [ X${Pack} = Xtrue ] ; then
1028	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1029	else
1030	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1031	fi
1032	if [ ! ${file_in} = ${file_outin} ] ; then
1033	if ( ${ExitFlag} ) ; then
1034	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1035	else
1036	IGCM_sys_Mv ${file_in} ${file_outin}
1037	fi
1038	fi
1039	fi
1040
1041	(( i=i+3 ))
1042	done
1043	else
1044	if [ X${FileName0} != XNONE ] ; then
1045	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1046	else
1047	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1048	fi
1049	fi
1050
1051	# Save Output files
1052	#------------------
1053	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1054	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1055	ListFilesName=${compname}_OutputFiles_List
1056	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1057
1058	if [ X${FileName0} != X${NULL_STR} ] ; then
1059	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1060
1061	(( i=0 ))
1062	until [ $i -ge $NbFiles ]; do
1063	SaveOnArchive=true
1064	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1065	eval file_in=${file_in_}
1066	(( i_ = i+1 ))
1067	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1068	eval file_out=${file_out_}
1069	#
1070	# Override file_out path remplacing R_SAVE by R_BUFR
1071	#
1072	if [ X${Pack} = Xtrue ] ; then
1073	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1074	fi
1075	#
1076	# Not necessarily the best option. /!\ Potential side effects /!\
1077	#
1078	(( i_ = i+2 ))
1079	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1080	#
1081	generic_file_name=$( basename ${file_in} .nc )
1082	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1083	#
1084	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1085	IGCM_debug_Print 2 "Parallelism with 1 process. Rebuilding ${file_in} not needed"
1086	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1087	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1088	IGCM_debug_Print 2 "Parallelism detected rebuilding ${file_in} is needed"
1089	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1090	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1091	IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc
1092	else
1093	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1094	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1095	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1096
1097	# Prepare headers for the shell dedicated to offline rebuild
1098	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1099	if [ $DRYRUN -le 1 ]; then
1100	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1101	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1102	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1103	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1104	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1105	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1106	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1107	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1108	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1109	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1110	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1111	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1112	fi
1113	fi
1114	# Prepare the shell dedicated to offline rebuild
1115	if [ $DRYRUN -le 1 ]; then
1116	if [ ${file_in} = histstn.nc ] ; then
1117	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1118	else
1119	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1120	fi
1121	echo "IGCM_debug_Verif_Exit_Post" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1122	fi
1123	#
1124	# Load Patch we need to apply and apply
1125	if [ $DRYRUN -le 1 ]; then
1126	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1127	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1128	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1129	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1130	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1131	done
1132	fi
1133	fi
1134	#
1135	if [ $DRYRUN -le 1 ]; then
1136	if [ X${Pack} = Xtrue ] ; then
1137	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1138	else
1139	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1140	fi
1141	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1142	echo "IGCM_sys_Rm ${generic_file_name}_*.nc " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1143	fi
1144	SaveOnArchive=false
1145	fi
1146	fi
1147	#
1148	if [ ${SaveOnArchive} = true ] ; then
1149	#
1150	# Rebuild has been done online or it was not needed
1151	#
1152	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1153	#
1154	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1155	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1156	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1157	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1158	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1159	#
1160	if [ $DRYRUN -le 1 ]; then
1161	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1162	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1163	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1164	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1165	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1166	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1167	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1168	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1169	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1170	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1171	fi
1172	#
1173	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1174	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1175	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1176	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1177	done
1178	#
1179	if [ X${Pack} = Xtrue ] ; then
1180	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1181	else
1182	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1183	fi
1184	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1185	#
1186	fi
1187	else
1188	#
1189	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1190	#
1191	if [ X${Pack} = Xtrue ] ; then
1192	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1193	else
1194	IGCM_sys_Put_Out ${file_in} ${file_out}
1195	fi
1196	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1197	if [ ${nb_rebuild_file} -gt 1 ] ; then
1198	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1199	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1200	done
1201	fi
1202	fi
1203	fi
1204	(( i=i+3 ))
1205	done
1206	fi
1207
1208	# Save Output Text files of models
1209	#---------------------------------
1210	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1211	IGCM_card_DefineArrayFromOption ${card} OutputText List
1212	ListTextName=${compname}_OutputText_List
1213
1214	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1215	if [ X${TextName0} != X${NULL_STR} ] ; then
1216	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1217
1218	(( i=0 ))
1219	until [ $i -eq $NbFiles ]; do
1220	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1221	eval file_out=${PREFIX}_${file_in}
1222
1223	(( i=i+1 ))
1224
1225	unset list_file
1226	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1227	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1228	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 )
1229	nlist_file=${#list_file[@]}
1230	if [ ${nlist_file} -gt 1 ] ; then
1231	if ( ${compactoutputs} ) ; then
1232	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1233	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1234	echo ${list_file[*]} > ${file_out}
1235	echo "" >> ${file_out}
1236
1237	(( i_ = 0 ))
1238	for file in ${list_file[@]}
1239	do
1240	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1241	echo "\| " ${i_} " " ${file} >> ${file_out}
1242	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1243	cat ${file} \| sed "s/\(.*\)/${i_}\1/" ${file} >> ${file_out}
1244	echo "" >> ${file_out}
1245	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1246	(( i_ = i_ + 1 ))
1247	done
1248	if [ X${Pack} = Xtrue ] ; then
1249	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1250	else
1251	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1252	fi
1253	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1254
1255	if ( ${ExecutionFail} ) ; then
1256	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1257	fi
1258	else
1259	for file in ${list_file[@]}
1260	do
1261	if [ X${Pack} = Xtrue ] ; then
1262	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1263	else
1264	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1265	fi
1266	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1267
1268	if ( ${ExecutionFail} ) ; then
1269	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1270	fi
1271	done
1272	fi
1273	else
1274	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1275	eval IGCM_sys_Mv ${file_in}* ${file_in}
1276	fi
1277	if [ X${Pack} = Xtrue ] ; then
1278	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1279	else
1280	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1281	fi
1282	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1283
1284	if ( ${ExecutionFail} ) ; then
1285	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1286	fi
1287	fi
1288	done
1289	fi
1290	echo
1291	done
1292	IGCM_debug_PopStack "IGCM_comp_Finalize"
1293	}

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