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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 809

Last change on this file since 809 was 809, checked in by sdipsl, 11 years ago
Activate IGCM_sys_Chmod from DRYRUN=3 and add BoundaryFiles? list in FileToBeDeleted list at each Period. Whitespace cleanup (from emacs macro) on libIGCM_sys_iitm.ksh see #105
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: 52.5 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	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
82
83	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
84	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${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	if [ ! ${config_Post_PackFrequency} = NONE ] ; then
94	eval R_BUF_${comp}=${R_BUFR}/${comp}
95	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
96
97	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
98	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
99
100	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
101	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
102
103	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
104	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
105
106	eval R_BUF_${comp}_O_I=\${R_BUF_${comp}_O}/INS
107	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
108	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
109	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
110	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
111	fi
112
113	# Read UserChoices section of component card
114	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
115	IGCM_card_DefineArrayFromSection ${card} UserChoices
116	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
117
118	# If section is not empty we define corresponding variables
119	if [ X${first_option} != X"Error:" ] ; then
120	if [ X${card_UserChoices[0]} != X ] ; then
121	unset card_UserChoices
122	fi
123	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
124	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
125	for option in ${card_UserChoices[*]} ; do
126	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
127	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
128	done
129	fi
130
131	# Read and Build Output File stuff
132	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
133	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
134	ListFilesName=${compname}_OutputFiles_List
135	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
136	#
137	if [ X${FileName0} != X${NULL_STR} ] ; then
138	#
139	#IGCM_debug_Print 1 "Component : ${compname}"
140	#
141	# INITIALISATION
142	#
143	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
144	#
145	i=2
146	#
147	until [ $i -ge $NbFiles ]; do
148	#
149	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
150	#
151	if [ X${flag_post} != XNONE ] ; then
152	#
153	# First of all
154	#
155	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
156	#
157	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
158	#
159	# variable option allready typeset above
160	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
161	if [ ${option} = Seasonal ] ; then
162	FoundSeasonal=true
163	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
164	fi
165	done
166	#
167	if [ ! X${FoundSeasonal} = Xtrue ] ; then
168	eval ${compname}_${flag_post}_Seasonal=ON
169	fi
170	#
171	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
172	Seasonal=true
173	fi
174
175	# Dimension = vide si vieille card.
176	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
177	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
178	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
179	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
180	ListDimension[0]=2D
181	ListDimension[1]=3D
182	TimeSeries=false
183	iLoop=${#ListDimension[*]}
184	j=0
185	until [ $j -ge ${iLoop} ]; do
186	Dimension=${ListDimension[${j}]}
187	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
188	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
189	#
190	# Time series WITHOUT chunk
191	#
192	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
193	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
194	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
195	eval TimeSeries${Dimension}=true
196	fi
197	fi
198	#
199	# Time series WITH chunk
200	#
201	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
202	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
203	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
204	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
205	eval TimeSeriesChunck${Dimension}=true
206	eval set +A CHUNCK${Dimension}_COMP \${CHUNCK${Dimension}_COMP[*]} ${comp}
207	eval set +A CHUNCK${Dimension}_FLAG \${CHUNCK${Dimension}_FLAG[*]} ${i}
208	eval set +A CHUNCK${Dimension}_NAME \${CHUNCK${Dimension}_NAME[*]} ${flag_post}
209	eval set +A CHUNCK${Dimension}_SIZE \${CHUNCK${Dimension}_SIZE[*]} ${chunck_size}
210	fi
211	fi
212	(( j=j+1 ))
213	done
214	else
215	ListDimension[0]=""
216	TimeSeries=true
217	TimeSeries2D=false
218	TimeSeries3D=false
219	TimeSeriesChunck2D=false
220	TimeSeriesChunck3D=false
221	fi
222	fi
223	(( i=i+3 ))
224	done
225	fi
226	# Debug Print
227	IGCM_debug_Print 3 "Initialize ${compname} with driver."
228	# INIT component
229	${comp}_Initialize
230	echo
231	done
232
233	IGCM_debug_PopStack "IGCM_comp_Initialize"
234	}
235
236	#=======================================================================
237	function IGCM_comp_PrepareDeletedFiles
238	{
239	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
240
241	if [ X${2} != X. ] ; then
242	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
243	else
244	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
245	fi
246
247	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
248	}
249
250	#=======================================================================
251	function IGCM_comp_GetInputInitialStateFiles
252	{
253	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
254
255	# Debug Print :
256	echo
257	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
258	echo
259
260	# Only the first time step need InitialStateFiles
261	# otherwise it's BoundaryConditions
262	if ( ${FirstInitialize} ) ; then
263	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
264	typeset file_in_ file_in file_out_ file_out do_init
265	for comp in ${config_ListOfComponents[*]} ; do
266	# Initialize
267	do_init="y"
268	# Do we need to bring initial state file for this component
269	if [ "${config_Restarts_OverRule}" = "y" ] ; then
270	eval do_init="n"
271	else
272	# Read component Restarts parameters
273	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
274	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
275	if [ "${do_start}" = "y" ] ; then
276	do_init="n"
277	else
278	do_init="y"
279	fi
280	fi
281
282	if [ "${do_init}" = "y" ] ; then
283	# Define component
284	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
285	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
286
287	# Debug Print :
288	IGCM_debug_Print 3 "Initialisation files ${compname}"
289
290	card=${SUBMIT_DIR}/COMP/${compname}.card
291
292	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
293	ListFilesName=${compname}_InitialStateFiles_List
294
295	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
296	if [ X${FileName0} != X${NULL_STR} ] ; then
297	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
298	(( i=0 ))
299	until [ $i -ge $NbFiles ]; do
300	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
301	eval file_in=${file_in_}
302	(( i_ = i+1 ))
303	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
304	eval file_out=${file_out_}
305
306	IGCM_sys_IsFileArchived ${file_in}
307	if [ $? = 0 ] ; then
308	IGCM_sys_Get ${file_in} ${file_out}
309	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
310	else
311	IGCM_sys_Cp ${file_in} ${file_out}
312	fi
313	(( i=i+2 ))
314	done
315	fi
316	fi
317	done
318	fi
319	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
320	}
321
322	#=======================================================================
323	# Definition of Smooth modulo function
324	# usage :
325	# IGCM_SmoothModulo StringModulo value
326	#
327	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
328	# [min]:[modulo:][max]
329	# where :
330	# [] value are optionnals;
331	# empty min equal 1
332	# empty max equal infinity
333	# modulo not given or empty equal 1
334	# empty string or just ':' equal always.
335	#
336	# value : the value to test with the definition
337	#
338	# return : true(1)/false(0)
339	function IGCM_SmoothModulo
340	{
341	IGCM_debug_PushStack "IGCM_SmoothModulo"
342	typeset defVector ModValue
343
344	eval set +A defVector -- $( echo "${1}" \| \
345	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
346
347	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
348	arr[1]=${defVector[0]}
349	arr[2]=${defVector[2]}
350
351	# Test limits :
352	# ${defVector[0]} <= ${2} <= ${defVector[2]}
353	# or ${defVector[2]} == -1
354	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
355	# Test modulo
356	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
357	if [ ${ModValue} -eq 0 ] ; then
358	arr[3]=true
359	echo ${arr[@]}
360	IGCM_debug_PopStack "IGCM_SmoothModulo"
361	return 1
362	else
363	arr[3]=false
364	echo ${arr[@]}
365	IGCM_debug_PopStack "IGCM_SmoothModulo"
366	return 0
367	fi
368	else
369	arr[3]=false
370	echo ${arr[@]}
371	IGCM_debug_PopStack "IGCM_SmoothModulo"
372	return 0
373	fi
374	}
375
376	#=======================================================================
377	function IGCM_comp_GetInputSmoothFiles
378	{
379	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
380
381	# Debug Print :
382	echo
383	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
384	echo
385
386	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
387	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
388
389	for comp in ${config_ListOfComponents[*]} ; do
390	# Define component
391	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
392	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
393
394	# Debug Print :
395	IGCM_debug_Print 3 "Smooth files ${compname}"
396
397	card=${SUBMIT_DIR}/COMP/${compname}.card
398
399	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
400	ListFilesName=${compname}_SmoothFiles_List
401	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
402
403	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
404	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
405
406	(( i=0 ))
407	until [ $i -ge $NbFiles ]; do
408	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
409	eval file_in=${file_in_}
410	(( i_ = i+1 ))
411	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
412	eval file_out=${file_out_}
413
414	# define CumulPeriod definition for this file
415	(( i__ = i+2 ))
416	eval SmoothDef=\${${ListFilesName}[$i__]}
417	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
418	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
419	j=1
420	for val in ${aux} ; do
421	[ ${j} -eq 1 ] && SmoothMin=${val}
422	[ ${j} -eq 2 ] && SmoothMax=${val}
423	[ ${j} -eq 3 ] && ret=${val}
424	(( j=j+1 ))
425	done
426	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
427	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
428
429	IGCM_sys_IsFileArchived ${file_in}
430	if [ $? = 0 ] ; then
431	IGCM_sys_Get ${file_in} ${file_out}
432	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
433	else
434	IGCM_sys_Cp ${file_in} ${file_out}
435	fi
436	fi
437	(( i=i+3 ))
438	done
439	fi
440	done
441
442	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
443	}
444
445	#=======================================================================
446	function IGCM_comp_GetInputBoundaryFiles
447	{
448	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
449
450	# Debug Print :
451	echo
452	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
453	echo
454
455	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
456	typeset file_in_ file_in file_out_ file_out
457
458	if [ ${Period} = 1 ]; then
459	ListFixBoundary=" "
460	fi
461
462	for comp in ${config_ListOfComponents[*]} ; do
463
464	# Define component
465	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
466	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
467
468	# Debug Print :
469	IGCM_debug_Print 3 "Boundary files ${compname}"
470
471	card=${SUBMIT_DIR}/COMP/${compname}.card
472
473	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
474	ListFilesName=${compname}_BoundaryFiles_List
475	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
476
477	if [ X${FileName0} != X${NULL_STR} ] ; then
478	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
479
480	(( i=0 ))
481	until [ $i -ge $NbFiles ]; do
482	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
483	eval file_in=${file_in_}
484	(( i_ = i+1 ))
485	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
486	eval file_out=${file_out_}
487
488	IGCM_sys_IsFileArchived ${file_in}
489	if [ $? = 0 ] ; then
490	IGCM_sys_Get ${file_in} ${file_out}
491	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
492	else
493	IGCM_sys_Cp ${file_in} ${file_out}
494	fi
495
496	(( i=i+2 ))
497	done
498	fi
499
500	# Get non deleted files
501	if [ ${Period} = 1 ]; then
502
503	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
504	ListFilesName=${compname}_BoundaryFiles_ListNonDel
505	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
506
507	if [ X${FileName0} != X${NULL_STR} ] ; then
508	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
509
510	(( i=0 ))
511	until [ $i -ge $NbFiles ]; do
512	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
513	eval file_in=${file_in_}
514	(( i_ = i+1 ))
515	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
516	eval file_out=${file_out_}
517
518	IGCM_sys_IsFileArchived ${file_in}
519	if [ $? = 0 ] ; then
520	IGCM_sys_Get ${file_in} ${file_out}
521	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
522	else
523	IGCM_sys_Cp ${file_in} ${file_out}
524	fi
525
526	if [ X${file_out} != X. ] ; then
527	ListFixBoundary=${ListFixBoundary}" "${file_out}
528	else
529	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
530	fi
531
532	(( i=i+2 ))
533	done
534	fi
535	fi
536	done
537
538	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
539	}
540
541	#=======================================================================
542	function IGCM_comp_DelFixeBoundaryFiles
543	{
544	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
545
546	# Debug Print :
547	echo
548	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
549	echo
550
551	ls -l ${ListFixBoundary}
552	rm -f ${ListFixBoundary}
553
554	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
555	}
556
557	#=======================================================================
558	function IGCM_comp_GetInputParametersFiles
559	{
560	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
561
562	# Debug Print :
563	echo
564	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
565	echo
566
567	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
568	for comp in ${config_ListOfComponents[*]} ; do
569	# Define component
570	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
571	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
572
573	# Debug Print :
574	IGCM_debug_Print 3 "Parameters ${compname}"
575
576	card=${SUBMIT_DIR}/COMP/${compname}.card
577
578	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
579	ListFilesName=${compname}_ParametersFiles_List
580	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
581
582	if [ X${FileName0} != X${NULL_STR} ] ; then
583	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
584
585	(( i=0 ))
586	until [ $i -ge $NbFiles ]; do
587	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
588	eval file_in=${file_in_}
589	(( i_ = i+1 ))
590	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
591	eval file_out=${file_out_}
592
593	IGCM_sys_Cp ${file_in} ${file_out}
594	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
595
596	(( i=i+2 ))
597	done
598	fi
599	done
600
601	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
602	}
603
604	#=======================================================================
605	function IGCM_comp_GetInputRestartFiles
606	{
607	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
608
609	# Debug Print :
610	echo
611	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
612	echo
613
614	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
615	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
616	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
617	typeset file_in file_out file_in_ file_out_ file_in_Name
618	typeset -Z4 j4
619
620	IsMatching=""
621
622	for comp in ${config_ListOfComponents[*]} ; do
623	# Define component
624	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
625	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
626	#
627	card=${SUBMIT_DIR}/COMP/${compname}.card
628	#
629	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
630	ListFilesName=${compname}_RestartFiles_List
631	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
632
633	# Debug Print :
634	IGCM_debug_Print 3 "restart ${compname}"
635
636	if ( ${FirstInitialize} ) ; then
637
638	if [ "${config_Restarts_OverRule}" = "y" ] ; then
639	eval config_${comp}_Restart="y"
640	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
641	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
642	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
643	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
644	eval CompOldName=${comp}
645	else
646	# Read component Restarts parameters
647	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
648	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
649
650	if [ "${do_start}" = "y" ] ; then
651	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
652	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
653	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
654	else
655	eval config_${comp}_RestartDate=-1
656	eval config_${comp}_RestartJobName=${NULL_STR}
657	eval config_${comp}_RestartPath=${NULL_STR}
658	fi
659	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} OldName
660	eval CompOldName=\${config_${comp}_OldName}
661	if [ X${CompOldName} = X ] ; then
662	eval CompOldName=${comp}
663	fi
664
665	# Reinitialize IsMatching to allow searching for a different tar file for each component.
666	IsMatching=""
667	TarFileFound=""
668	fi
669
670	if [ "${do_start}" = "y" ] ; then
671
672	# Restore Restarts files
673	#-----------------------
674	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
675	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
676
677	(( i=1 ))
678	until [ $i -gt $NbFiles ]; do
679	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
680	eval file_in=${file_in_}
681	(( i_ = i+1 ))
682	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
683	eval file_out=${file_out_}
684
685	eval Date_tmp=\${config_${comp}_RestartDate}
686	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
687	# will be re-use
688	eval RestartPath=\${config_${comp}_RestartPath}
689	eval RestartJobName=\${config_${comp}_RestartJobName}
690	#
691	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
692	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
693
694	extension_in=$( echo ${file_in_Name##*.} )
695	extension_out=$( echo ${file_out##*.} )
696
697	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
698	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
699
700	Path_OUT=${Path_r}/${generic_restart_file_name_in}
701
702	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
703	IGCM_debug_Print 3 "Buffered restart"
704	Buffered=true
705	Archived=false
706	Tared=false
707	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
708	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
709	IGCM_debug_Print 3 "Archived restart"
710	Buffered=false
711	Archived=true
712	Tared=false
713	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
714	else
715	IGCM_debug_Print 3 "Tared restart"
716	Buffered=false
717	Archived=false
718	Tared=true
719	# Look after the tar file we want if we did not found it already
720	if [ X${IsMatching} = X ] ; then
721	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_*_restart.tar" -print" ) ; do
722	IsMatching=$( echo ${PotentialTarFile##*/} \| \
723	sed "s:^${RestartJobName}_::" \| \
724	sed "s:\.restart\.tar$::" \| \
725	gawk -F_ -v restartdate=${Date_r} \
726	'{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
727	if [ ! X${IsMatching} = X ] ; then
728	TarFileFound=${PotentialTarFile}
729	break
730	fi
731	done
732	fi
733	TarFileLocation=$( IGCM_sys_PrepareTaredRestart ${TarFileFound} )
734	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
735	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
736	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
737	fi
738
739	if [ ${nb_restart_file} -gt 1 ] ; then
740	j=0
741	until [ $j -ge ${nb_restart_file} ]; do
742	j4=${j}
743	if [ X${Buffered} = Xtrue ] ; then
744	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
745	elif [ X${Archived} = Xtrue ] ; then
746	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
747	elif [ X${Tared} = Xtrue ] ; then
748	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
749	fi
750	(( j=j+1 ))
751	done
752
753	if [ X${NUM_PROC_OCE} != X ] ; then
754	if [ ${NUM_PROC_OCE} -ne ${nb_restart_file} ] ; then
755	IGCM_sys_rebuild ${generic_restart_file_name_out}.${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
756	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
757	fi
758	fi
759	else
760	if [ X${Buffered} = Xtrue ] ; then
761	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
762	elif [ X${Archived} = Xtrue ] ; then
763	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
764	elif [ X${Tared} = Xtrue ] ; then
765	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
766	fi
767	fi
768	(( i=i+3 ))
769	done
770
771	else
772	if [ X${FileName0} != XNONE ] ; then
773	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
774	else
775	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
776	fi
777	fi
778	fi
779	elif [ ${Period} -eq 1 ] ; then
780	# if not FirstInitialize and first loop of this job
781
782	# Restore Restarts files
783	#-----------------------
784	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
785	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
786
787	(( i=1 ))
788	until [ $i -gt $NbFiles ]; do
789	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
790	eval file_in=${file_in_}
791	(( i_ = i+1 ))
792	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
793	eval file_out=${file_out_}
794
795	file_in_Name=${run_Configuration_OldPrefix}_${file_in}
796
797	extension_in=$( echo ${file_in_Name##*.} )
798	extension_out=$( echo ${file_out##*.} )
799
800	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
801	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
802
803	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
804	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
805
806	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
807	IGCM_debug_Print 3 "Buffered restart"
808	Buffered=true
809	Archived=false
810	Tared=false
811	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
812	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
813	IGCM_debug_Print 3 "Archived restart"
814	Buffered=false
815	Archived=true
816	Tared=false
817	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
818	else
819	IGCM_debug_Print 3 "Tared restart"
820	Buffered=false
821	Archived=false
822	Tared=true
823	# Look after the tar file we want if we did not found it already
824	if [ X${IsMatching} = X ] ; then
825	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
826	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
827	if [ ! X${IsMatching} = X ] ; then
828	TarFileFound=${PotentialTarFile}
829	break
830	fi
831	done
832	fi
833	TarFileLocation=$( IGCM_sys_PrepareTaredRestart ${TarFileFound} )
834	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
835	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
836	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
837	fi
838
839	if [ ${nb_restart_file} -gt 1 ] ; then
840	j=0
841	until [ $j -ge ${nb_restart_file} ]; do
842	j4=${j}
843	if [ X${Buffered} = Xtrue ] ; then
844	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
845	elif [ X${Archived} = Xtrue ] ; then
846	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
847	elif [ X${Tared} = Xtrue ] ; then
848	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
849	fi
850	(( j=j+1 ))
851	done
852	else
853	if [ X${Buffered} = Xtrue ] ; then
854	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
855	elif [ X${Archived} = Xtrue ] ; then
856	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
857	elif [ X${Tared} = Xtrue ] ; then
858	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
859	fi
860	fi
861	(( i=i+3 ))
862	done
863	else
864	if [ X${FileName0} != XNONE ] ; then
865	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
866	else
867	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
868	fi
869	fi
870	fi
871	done
872
873	NbFiles=$( ls * 2> /dev/null \| wc -l )
874	if [ ${NbFiles} -gt 0 ] ; then
875	IGCM_sys_Chmod u+rw *
876	fi
877
878	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
879	}
880
881	#=======================================================================
882	function IGCM_comp_PeriodStart
883	{
884	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
885
886	# Debug Print :
887	echo
888	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
889	echo
890
891	typeset ExeNameIn ExeNameOut
892	typeset comp compname comptagname
893	for comp in ${config_ListOfComponents[*]} ; do
894	# Define component
895	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
896	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
897
898	# Copy executable for this component
899	eval ExeNameIn=\${config_Executable_${comp}[0]}
900	eval ExeNameOut=\${config_Executable_${comp}[1]}
901
902	# Debug Print
903	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
904	# UPDATE component
905	${comp}_PeriodStart 2> /dev/null
906
907	done
908
909	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
910	}
911
912	#=======================================================================
913	function IGCM_comp_Update
914	{
915	IGCM_debug_PushStack "IGCM_comp_Update"
916
917	# Debug Print :
918	echo
919	IGCM_debug_Print 1 "IGCM_comp_Update"
920	echo
921
922	typeset ExeNameIn ExeNameOut
923	typeset comp compname comptagname
924	for comp in ${config_ListOfComponents[*]} ; do
925	# Define component
926	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
927	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
928
929	# Copy executable for this component
930	eval ExeNameIn=\${config_Executable_${comp}[0]}
931	eval ExeNameOut=\${config_Executable_${comp}[1]}
932
933	# If missing executable and DRYRUN is set to 0 or 1 then stop!
934	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
935	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
936	fi
937
938	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
939	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
940	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
941	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
942	fi
943	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
944	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
945	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
946	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
947	fi
948	fi
949
950	# Debug Print
951	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
952	# UPDATE component
953	${comp}_Update
954
955	done
956
957	IGCM_debug_PopStack "IGCM_comp_Update"
958	}
959
960	#=======================================================================
961	function IGCM_comp_Finalize
962	{
963	IGCM_debug_PushStack "IGCM_comp_Finalize"
964
965	# Debug Print :
966	echo
967	IGCM_debug_Print 1 "IGCM_comp_Finalize"
968	echo
969
970	typeset ListTextName TextName0
971	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
972	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
973	typeset -Z4 j4
974	typeset list_file nlist_file
975	typeset compactoutputs
976
977	compactoutputs=false
978	if [ X${JobType} != XRUN ] ; then
979	compactoutputs=true
980	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
981	compactoutputs=true
982	fi
983
984	for comp in ${config_ListOfComponents[*]} ; do
985	# Define component
986	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
987	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
988
989	# Debug Print
990	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
991	# FINALIZE component
992	${comp}_Finalize
993
994	card=${SUBMIT_DIR}/COMP/${compname}.card
995
996	# Save Output Text files of models
997	#---------------------------------
998	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
999	IGCM_card_DefineArrayFromOption ${card} OutputText List
1000	ListTextName=${compname}_OutputText_List
1001
1002	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1003	if [ X${TextName0} != X${NULL_STR} ] ; then
1004	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1005
1006	(( i=0 ))
1007	until [ $i -eq $NbFiles ]; do
1008	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1009	eval file_out=${PREFIX}_${file_in}
1010
1011	(( i=i+1 ))
1012
1013	unset list_file
1014	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1015	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1016	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 )
1017	nlist_file=${#list_file[@]}
1018	if [ ${nlist_file} -gt 1 ] ; then
1019	if ( ${compactoutputs} ) ; then
1020	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1021	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1022	echo ${list_file[*]} > ${file_out}
1023	echo "" >> ${file_out}
1024
1025	(( i_ = 0 ))
1026	for file in ${list_file[@]}
1027	do
1028	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1029	echo "\| " ${i_} " " ${file} >> ${file_out}
1030	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1031	cat ${file} \| sed "s/\(.*\)/${i_}\1/" ${file} >> ${file_out}
1032	echo "" >> ${file_out}
1033	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1034	(( i_ = i_ + 1 ))
1035	done
1036	if [ X${Pack} = Xtrue ] ; then
1037	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1038	else
1039	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1040	fi
1041	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1042
1043	if ( ${ExecutionFail} ) ; then
1044	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1045	fi
1046	else
1047	for file in ${list_file[@]}
1048	do
1049	if [ X${Pack} = Xtrue ] ; then
1050	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1051	else
1052	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1053	fi
1054	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1055
1056	if ( ${ExecutionFail} ) ; then
1057	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1058	fi
1059	done
1060	fi
1061	else
1062	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1063	eval IGCM_sys_Mv ${file_in}* ${file_in}
1064	fi
1065	if [ X${Pack} = Xtrue ] ; then
1066	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1067	else
1068	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1069	fi
1070	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1071
1072	if ( ${ExecutionFail} ) ; then
1073	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1074	fi
1075	fi
1076	done
1077	fi
1078
1079	# Save Restarts files
1080	#--------------------
1081	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1082	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1083	ListFilesName=${compname}_RestartFiles_List
1084	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1085
1086	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1087	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1088
1089	(( i=0 ))
1090	until [ $i -ge $NbFiles ]; do
1091	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1092	eval file_in=${file_in_}
1093
1094	(( i_ = i+1 ))
1095	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1096	eval file_out=${file_out_}
1097
1098	(( i_ = i+2 ))
1099	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1100	eval file_outin=${file_outin_}
1101
1102	generic_restart_file_name_in=$( basename ${file_in} .nc )
1103	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1104	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1105
1106	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1107	if [ ${nb_restart_file} -gt 1 ] ; then
1108	j=0
1109	until [ $j -ge ${nb_restart_file} ]; do
1110	j4=${j}
1111	if [ X${Pack} = Xtrue ] ; then
1112	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1113	else
1114	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1115	fi
1116	if [ ! ${file_in} = ${file_outin} ] ; then
1117	if ( ${ExitFlag} ) ; then
1118	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1119	else
1120	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1121	fi
1122	fi
1123	(( j=j+1 ))
1124	done
1125	else
1126	if [ X${Pack} = Xtrue ] ; then
1127	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1128	else
1129	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1130	fi
1131	if [ ! ${file_in} = ${file_outin} ] ; then
1132	if ( ${ExitFlag} ) ; then
1133	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1134	else
1135	IGCM_sys_Mv ${file_in} ${file_outin}
1136	fi
1137	fi
1138	fi
1139
1140	(( i=i+3 ))
1141	done
1142	else
1143	if [ X${FileName0} != XNONE ] ; then
1144	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1145	else
1146	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1147	fi
1148	fi
1149
1150	# Save Output files
1151	#------------------
1152	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1153	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1154	ListFilesName=${compname}_OutputFiles_List
1155	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1156
1157	if [ X${FileName0} != X${NULL_STR} ] ; then
1158	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1159
1160	(( i=0 ))
1161	until [ $i -ge $NbFiles ]; do
1162	SaveOnArchive=true
1163	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1164	eval file_in=${file_in_}
1165	(( i_ = i+1 ))
1166	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1167	eval file_out=${file_out_}
1168	#
1169	# Override file_out path remplacing R_SAVE by R_BUFR
1170	#
1171	if [ X${Pack} = Xtrue ] ; then
1172	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1173	fi
1174	#
1175	# Not necessarily the best option. /!\ Potential side effects /!\
1176	#
1177	(( i_ = i+2 ))
1178	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1179	#
1180	generic_file_name=$( basename ${file_in} .nc )
1181	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1182	#
1183	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1184	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1185	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1186	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1187	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1188	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1189	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1190	IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc
1191	else
1192	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1193	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1194	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1195
1196	# Prepare headers for the shell dedicated to offline rebuild
1197	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1198	if [ $DRYRUN -le 1 ]; then
1199	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1200	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1201	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1202	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1203	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1204	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1205	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1206	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1207	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1208	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1209	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1210	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1211	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1212	fi
1213	fi
1214	# Prepare the shell dedicated to offline rebuild
1215	if [ $DRYRUN -le 1 ]; then
1216	if [ ${file_in} = histstn.nc ] ; then
1217	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1218	else
1219	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1220	fi
1221	echo "IGCM_debug_Verif_Exit_Post" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1222	fi
1223	#
1224	# Load Patch we need to apply and apply
1225	if [ $DRYRUN -le 1 ]; then
1226	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1227	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1228	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1229	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1230	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1231	done
1232	fi
1233	fi
1234	#
1235	if [ $DRYRUN -le 1 ]; then
1236	if [ X${Pack} = Xtrue ] ; then
1237	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1238	else
1239	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1240	fi
1241	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1242	echo "IGCM_sys_Rm ${generic_file_name}_*.nc " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1243	fi
1244	SaveOnArchive=false
1245	fi
1246	fi
1247	#
1248	if [ ${SaveOnArchive} = true ] ; then
1249	#
1250	# Rebuild has been done online or it was not needed
1251	#
1252	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1253	#
1254	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1255	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1256	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1257	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1258	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1259	#
1260	if [ $DRYRUN -le 1 ]; then
1261	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1262	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1263	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1264	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1265	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1266	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1267	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1268	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1269	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1270	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1271	fi
1272	#
1273	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1274	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1275	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1276	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1277	done
1278	#
1279	if [ X${Pack} = Xtrue ] ; then
1280	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1281	else
1282	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1283	fi
1284	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1285	#
1286	fi
1287	else
1288	#
1289	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1290	#
1291	if [ X${Pack} = Xtrue ] ; then
1292	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1293	else
1294	IGCM_sys_Put_Out ${file_in} ${file_out}
1295	fi
1296	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1297	if [ ${nb_rebuild_file} -gt 1 ] ; then
1298	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1299	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1300	done
1301	fi
1302	fi
1303	fi
1304	(( i=i+3 ))
1305	done
1306	fi
1307	echo
1308	done
1309	IGCM_debug_PopStack "IGCM_comp_Finalize"
1310	}

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