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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1224

Last change on this file since 1224 was 1215, checked in by jgipsl, 9 years ago
Ticket #263 Only return for the case nonblocker if the file do not exist.
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: 72.4 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	# Define all options in section [comp]
48	IGCM_debug_Print 3 " DefineArrayFromSection : ${comp}"
49	IGCM_card_DefineArrayFromSection ${SUBMIT_DIR}/config.card ${comp}
50	eval config_comp=\${config_${comp}[*]} > /dev/null 2>&1
51	for option in ${config_comp[*]} ; do
52	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
53	done
54	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
55
56	# Debug Print :
57	eval auxprint=\${config_${comp}_WriteFrequency}
58	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
59	#2> /dev/null
60
61	# Debug Print :
62	IGCM_debug_Print 2 "Initialize following component library"
63
64	# Source drivers in directory DRIVER if it exist
65	# else source them from directory COMP
66	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
67	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
68	# Source component library
69	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
70	else
71	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
72	# Source component library
73	. ${SUBMIT_DIR}/COMP/${compname}.driver
74	fi
75	IGCM_debug_Print 3 "With tag : ${comptagname}"
76
77	# Debug Print
78	IGCM_debug_Print 3 "Initialize ${comp} output directory."
79
80	# Define ARCHIVED Dirs
81	eval R_OUT_${comp}=${R_SAVE}/${comp}
82	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
83
84	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
85	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
86
87	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
88	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
89
90	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
91	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
92
93	eval R_OUT_${comp}_O_I=\${R_OUT_${comp}_O}/INS
94	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
95	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
96	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
97	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
98
99	# Define BUFFERED Dirs
100	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
101	eval R_BUF_${comp}=${R_BUFR}/${comp}
102	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
103
104	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
105	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
106
107	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
108	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
109
110	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
111	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
112
113	eval R_BUF_${comp}_O_I=\${R_BUF_${comp}_O}/INS
114	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
115	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
116	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
117	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
118	fi
119
120	# Read UserChoices section of component card
121	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
122	IGCM_card_DefineArrayFromSection ${card} UserChoices
123	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
124
125	# If section is not empty we define corresponding variables
126	if [ X${first_option} != X"Error:" ] ; then
127	if [ X${card_UserChoices[0]} != X ] ; then
128	unset card_UserChoices
129	fi
130	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
131	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
132	for option in ${card_UserChoices[*]} ; do
133	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
134	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
135	done
136	fi
137
138	# Read and Build Output File stuff
139	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
140	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
141	ListFilesName=${compname}_OutputFiles_List
142	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
143	#
144	if [ X${FileName0} != X${NULL_STR} ] ; then
145	#
146	#IGCM_debug_Print 1 "Component : ${compname}"
147	#
148	# INITIALISATION
149	#
150	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
151	#
152	i=2
153	#
154	until [ $i -ge $NbFiles ]; do
155	#
156	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
157	#
158	if [ X${flag_post} != XNONE ] ; then
159	#
160	# First of all
161	#
162	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
163	# This section is mandatory
164	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
165	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
166	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
167	IGCM_debug_Verif_Exit
168	fi
169	#
170	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
171	#
172	# variable option allready typeset above
173	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
174	if [ ${option} = Seasonal ] ; then
175	FoundSeasonal=true
176	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
177	fi
178	done
179	#
180	if [ ! X${FoundSeasonal} = Xtrue ] ; then
181	eval ${compname}_${flag_post}_Seasonal=ON
182	fi
183	#
184	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
185	Seasonal=true
186	fi
187
188	# Dimension = vide si vieille card.
189	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
190	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
191	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
192	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
193	ListDimension[0]=2D
194	ListDimension[1]=3D
195	TimeSeries=false
196	iLoop=${#ListDimension[*]}
197	j=0
198	until [ $j -ge ${iLoop} ]; do
199	Dimension=${ListDimension[${j}]}
200	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
201	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
202	#
203	# Time series WITHOUT chunk
204	#
205	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
206	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
207	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
208	eval TimeSeries${Dimension}=true
209	fi
210	fi
211	#
212	# Time series WITH chunk
213	#
214	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
215	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
216	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
217	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
218	eval TimeSeriesChunck${Dimension}=true
219	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
220	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
221	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
222	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
223	fi
224	fi
225	(( j=j+1 ))
226	done
227	else
228	ListDimension[0]=""
229	TimeSeries=true
230	TimeSeries2D=false
231	TimeSeries3D=false
232	TimeSeriesChunck2D=false
233	TimeSeriesChunck3D=false
234	fi
235	fi
236	(( i=i+3 ))
237	done
238	fi
239	# Debug Print
240	IGCM_debug_Print 3 "Initialize ${compname} with driver."
241	# INIT component
242	${comp}_Initialize
243	echo
244	done
245
246	IGCM_debug_PopStack "IGCM_comp_Initialize"
247	}
248
249	#=======================================================================
250	function IGCM_comp_PrepareDeletedFiles
251	{
252	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
253
254	if [ X${2} != X. ] ; then
255	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
256	else
257	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
258	fi
259
260	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
261	}
262
263	#=======================================================================
264	function IGCM_comp_GetInputInitialStateFiles
265	{
266	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
267
268	# Debug Print :
269	echo
270	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
271	echo
272
273	# Only the first time step need InitialStateFiles
274	# otherwise it's BoundaryConditions
275	if ( ${FirstInitialize} ) ; then
276	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
277	typeset file_in_ file_in file_out_ file_out do_init
278	for comp in ${config_ListOfComponents[*]} ; do
279	# Initialize
280	do_init="y"
281	# Do we need to bring initial state file for this component
282	if [ "${config_Restarts_OverRule}" = "y" ] ; then
283	eval do_init="n"
284	else
285	# Read component Restarts parameters
286	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
287	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
288	if [ "${do_start}" = "y" ] ; then
289	do_init="n"
290	else
291	do_init="y"
292	fi
293	fi
294
295	if [ "${do_init}" = "y" ] ; then
296	# Define component
297	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
298	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
299
300	# Debug Print :
301	IGCM_debug_Print 3 "Initialisation files ${compname}"
302
303	card=${SUBMIT_DIR}/COMP/${compname}.card
304
305	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
306	ListFilesName=${compname}_InitialStateFiles_List
307
308	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
309	if [ X${FileName0} != X${NULL_STR} ] ; then
310	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
311	(( i=0 ))
312	until [ $i -ge $NbFiles ]; do
313	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
314	eval file_in=${file_in_}
315	(( i_ = i+1 ))
316	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
317	eval file_out=${file_out_}
318
319	IGCM_sys_IsFileArchived ${file_in}
320	if [ $? = 0 ] ; then
321	IGCM_sys_Get ${file_in} ${file_out}
322	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
323	else
324	IGCM_sys_Cp ${file_in} ${file_out}
325	fi
326	(( i=i+2 ))
327	done
328	fi
329	fi
330	done
331	fi
332	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
333	}
334
335	#=======================================================================
336	# Definition of Smooth modulo function
337	# usage :
338	# IGCM_SmoothModulo StringModulo value
339	#
340	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
341	# [min]:[modulo:][max]
342	# where :
343	# [] value are optionnals;
344	# empty min equal 1
345	# empty max equal infinity
346	# modulo not given or empty equal 1
347	# empty string or just ':' equal always.
348	#
349	# value : the value to test with the definition
350	#
351	# return : true(1)/false(0)
352	function IGCM_SmoothModulo
353	{
354	IGCM_debug_PushStack "IGCM_SmoothModulo"
355	typeset defVector ModValue
356
357	eval set +A defVector -- $( echo "${1}" \| \
358	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
359
360	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
361	arr[1]=${defVector[0]}
362	arr[2]=${defVector[2]}
363
364	# Test limits :
365	# ${defVector[0]} <= ${2} <= ${defVector[2]}
366	# or ${defVector[2]} == -1
367	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
368	# Test modulo
369	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
370	if [ ${ModValue} -eq 0 ] ; then
371	arr[3]=true
372	echo ${arr[@]}
373	IGCM_debug_PopStack "IGCM_SmoothModulo"
374	return 1
375	else
376	arr[3]=false
377	echo ${arr[@]}
378	IGCM_debug_PopStack "IGCM_SmoothModulo"
379	return 0
380	fi
381	else
382	arr[3]=false
383	echo ${arr[@]}
384	IGCM_debug_PopStack "IGCM_SmoothModulo"
385	return 0
386	fi
387	}
388
389	#=======================================================================
390	function IGCM_comp_GetInputSmoothFiles
391	{
392	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
393
394	# Debug Print :
395	echo
396	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
397	echo
398
399	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
400	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
401
402	for comp in ${config_ListOfComponents[*]} ; do
403	# Define component
404	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
405	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
406
407	# Debug Print :
408	IGCM_debug_Print 3 "Smooth files ${compname}"
409
410	card=${SUBMIT_DIR}/COMP/${compname}.card
411
412	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
413	ListFilesName=${compname}_SmoothFiles_List
414	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
415
416	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
417	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
418
419	(( i=0 ))
420	until [ $i -ge $NbFiles ]; do
421	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
422	eval file_in=${file_in_}
423	(( i_ = i+1 ))
424	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
425	eval file_out=${file_out_}
426
427	# define CumulPeriod definition for this file
428	(( i__ = i+2 ))
429	eval SmoothDef=\${${ListFilesName}[$i__]}
430	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
431	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
432	j=1
433	for val in ${aux} ; do
434	[ ${j} -eq 1 ] && SmoothMin=${val}
435	[ ${j} -eq 2 ] && SmoothMax=${val}
436	[ ${j} -eq 3 ] && ret=${val}
437	(( j=j+1 ))
438	done
439	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
440	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
441
442	IGCM_sys_IsFileArchived ${file_in}
443	if [ $? = 0 ] ; then
444	IGCM_sys_Get ${file_in} ${file_out}
445	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
446	else
447	IGCM_sys_Cp ${file_in} ${file_out}
448	fi
449	fi
450	(( i=i+3 ))
451	done
452	fi
453	done
454
455	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
456	}
457
458	#=======================================================================
459	function IGCM_comp_GetInputBoundaryFiles
460	{
461	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
462
463	# Debug Print :
464	echo
465	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
466	echo
467
468	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
469	typeset file_in_ file_in file_out_ file_out
470
471	if [ ${Period} = 1 ]; then
472	ListFixBoundary=" "
473	fi
474
475	for comp in ${config_ListOfComponents[*]} ; do
476
477	# Define component
478	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
479	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
480
481	# Debug Print :
482	IGCM_debug_Print 3 "Boundary files ${compname}"
483
484	card=${SUBMIT_DIR}/COMP/${compname}.card
485
486	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
487	ListFilesName=${compname}_BoundaryFiles_List
488	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
489
490	if [ X${FileName0} != X${NULL_STR} ] ; then
491	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
492
493	(( i=0 ))
494	until [ $i -ge $NbFiles ]; do
495	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
496	eval file_in=${file_in_}
497	(( i_ = i+1 ))
498	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
499	eval file_out=${file_out_}
500
501	IGCM_sys_IsFileArchived ${file_in}
502	if [ $? = 0 ] ; then
503	IGCM_sys_Get ${file_in} ${file_out}
504	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
505	else
506	IGCM_sys_Cp ${file_in} ${file_out}
507	fi
508
509	(( i=i+2 ))
510	done
511	fi
512
513	# Get non deleted files
514	if [ ${Period} = 1 ]; then
515
516	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
517	ListFilesName=${compname}_BoundaryFiles_ListNonDel
518	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
519
520	if [ X${FileName0} != X${NULL_STR} ] ; then
521	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
522
523	(( i=0 ))
524	until [ $i -ge $NbFiles ]; do
525	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
526	eval file_in=${file_in_}
527	(( i_ = i+1 ))
528	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
529	eval file_out=${file_out_}
530
531	IGCM_sys_IsFileArchived ${file_in}
532	if [ $? = 0 ] ; then
533	IGCM_sys_Get ${file_in} ${file_out}
534	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
535	else
536	IGCM_sys_Cp ${file_in} ${file_out}
537	fi
538
539	if [ X${file_out} != X. ] ; then
540	ListFixBoundary=${ListFixBoundary}" "${file_out}
541	else
542	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
543	fi
544
545	(( i=i+2 ))
546	done
547	fi
548	fi
549	done
550
551	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
552	}
553
554	#=======================================================================
555	function IGCM_comp_DelFixeBoundaryFiles
556	{
557	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
558
559	# Debug Print :
560	echo
561	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
562	echo
563
564	ls -l ${ListFixBoundary}
565	rm -f ${ListFixBoundary}
566
567	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
568	}
569
570	#=======================================================================
571	function IGCM_comp_GetInputParametersFiles
572	{
573	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
574
575	# Debug Print :
576	echo
577	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
578	echo
579
580	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
581	for comp in ${config_ListOfComponents[*]} ; do
582	# Define component
583	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
584	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
585
586	# Debug Print :
587	IGCM_debug_Print 3 "Parameters ${compname}"
588
589	card=${SUBMIT_DIR}/COMP/${compname}.card
590
591	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
592	ListFilesName=${compname}_ParametersFiles_List
593	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
594
595	if [ X${FileName0} != X${NULL_STR} ] ; then
596	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
597
598	(( i=0 ))
599	until [ $i -ge $NbFiles ]; do
600	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
601	eval file_in=${file_in_}
602	(( i_ = i+1 ))
603	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
604	eval file_out=${file_out_}
605
606	IGCM_sys_Cp ${file_in} ${file_out}
607	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
608
609	(( i=i+2 ))
610	done
611	fi
612	done
613
614	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
615	}
616
617	#=======================================================================
618	function IGCM_comp_GetInputRestartFiles
619	{
620	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
621
622	# Debug Print :
623	echo
624	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
625	echo
626
627	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
628	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
629	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
630	typeset file_in file_out file_in_ file_out_ file_in_Name
631	typeset -Z4 j4
632	#BASH declare j4
633
634	IsMatching=""
635
636	for comp in ${config_ListOfComponents[*]} ; do
637	# Define component
638	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
639	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
640	#
641	card=${SUBMIT_DIR}/COMP/${compname}.card
642	#
643	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
644	ListFilesName=${compname}_RestartFiles_List
645	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
646
647	# Debug Print :
648	IGCM_debug_Print 3 "restart ${compname}"
649
650	if ( ${FirstInitialize} ) ; then
651
652	if [ "${config_Restarts_OverRule}" = "y" ] ; then
653	eval config_${comp}_Restart="y"
654	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
655	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
656	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
657	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
658	eval CompOldName=${comp}
659	else
660	# Read component Restarts parameters
661	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
662	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
663
664	if [ "${do_start}" = "y" ] ; then
665	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
666	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
667	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
668	else
669	eval config_${comp}_RestartDate=-1
670	eval config_${comp}_RestartJobName=${NULL_STR}
671	eval config_${comp}_RestartPath=${NULL_STR}
672	fi
673
674	eval CompOldName=\${config_${comp}_OldName}
675	if [ X${CompOldName} = X ] ; then
676	eval CompOldName=${comp}
677	fi
678
679	# Reinitialize IsMatching to allow searching for a different tar file for each component.
680	IsMatching=""
681	TarFileFound=""
682	fi
683
684	if [ "${do_start}" = "y" ] ; then
685
686	# Restore Restarts files
687	#-----------------------
688	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
689	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
690
691	(( i=1 ))
692	until [ $i -gt $NbFiles ]; do
693	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
694	eval file_in=${file_in_}
695	(( i_ = i+1 ))
696	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
697	eval file_out=${file_out_}
698
699	eval Date_tmp=\${config_${comp}_RestartDate}
700	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
701	# will be re-use
702	eval RestartPath=\${config_${comp}_RestartPath}
703	eval RestartJobName=\${config_${comp}_RestartJobName}
704	#
705	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
706	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
707
708	extension_in=$( echo ${file_in_Name##*.} )
709	extension_out=$( echo ${file_out##*.} )
710
711	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
712	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
713
714	Path_OUT=${Path_r}/${generic_restart_file_name_in}
715
716	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
717	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
718	Buffered=true
719	Archived=false
720	Tared=false
721	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
722	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
723	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
724	Buffered=false
725	Archived=true
726	Tared=false
727	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
728	else
729	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
730	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
731	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
732	Buffered=false
733	Archived=false
734	Tared=true
735	# Look after the tar file we want if we did not found it already
736	if [ X${IsMatching} = X ] ; then
737	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
738	if [ $? ] ; then
739	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
740	IsMatching=$( echo ${PotentialTarFile##*/} \| \
741	sed "s:_restart::" \| \
742	sed "s:^${RestartJobName}_::" \| \
743	sed "s:\.tar$::" \| \
744	gawk -F_ -v restartdate=${Date_r} \
745	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
746	if [ ! X${IsMatching} = X ] ; then
747	TarFileFound=${PotentialTarFile}
748	break
749	fi
750	done
751	fi
752	# Stop here if nothing has been found
753	if [ X${TarFileFound} = X ] ; then
754	IGCM_debug_Print 3 "Restart files were not found!"
755	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
756	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
757	IGCM_debug_Exit "Please double check restart settings in config.card"
758	IGCM_debug_Verif_Exit
759	fi
760	fi
761	IGCM_sys_PrepareTaredRestart ${TarFileFound}
762	TarFileLocation=$( basename ${TarFileFound} )
763	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
764	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
765	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
766	fi
767
768	if [ ${nb_restart_file} -gt 1 ] ; then
769	j=0 # BASH LINE NOT NEEDED
770	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
771	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
772	j4=${j} # BASH LINE NOT NEEDED
773	if [ X${Buffered} = Xtrue ] ; then
774	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
775	elif [ X${Archived} = Xtrue ] ; then
776	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
777	elif [ X${Tared} = Xtrue ] ; then
778	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
779	fi
780	(( j=j+1 )) #BASH LINE NOT NEEDED
781	done
782
783	if [ X${NUM_PROC_OCE} != X ] ; then
784	if [ ${NUM_PROC_OCE} -ne ${nb_restart_file} ] ; then
785	IGCM_sys_rebuild ${generic_restart_file_name_out}.${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
786	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
787	fi
788	fi
789	else
790	if [ X${Buffered} = Xtrue ] ; then
791	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
792	elif [ X${Archived} = Xtrue ] ; then
793	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
794	elif [ X${Tared} = Xtrue ] ; then
795	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
796	fi
797	fi
798	(( i=i+3 ))
799	done
800	else
801	if [ X${FileName0} != XNONE ] ; then
802	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
803	else
804	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
805	fi
806	fi
807	fi
808	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
809	# if not FirstInitialize and first loop of this job
810
811	# Restore Restarts files
812	#-----------------------
813	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
814	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
815
816	(( i=1 ))
817	until [ $i -gt $NbFiles ]; do
818	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
819	eval file_in=${file_in_}
820	(( i_ = i+1 ))
821	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
822	eval file_out=${file_out_}
823
824	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
825
826	extension_in=$( echo ${file_in_Name##*.} )
827	extension_out=$( echo ${file_out##*.} )
828
829	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
830	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
831
832	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
833	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
834
835	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
836	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
837	Buffered=true
838	Archived=false
839	Tared=false
840	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
841	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
842	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
843	Buffered=false
844	Archived=true
845	Tared=false
846	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
847	else
848	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
849	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
850	Buffered=false
851	Archived=false
852	Tared=true
853	# Look after the tar file we want if we did not found it already
854	if [ X${IsMatching} = X ] ; then
855	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
856	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
857	if [ ! X${IsMatching} = X ] ; then
858	TarFileFound=${PotentialTarFile}
859	break
860	fi
861	done
862	fi
863	# Stop here if nothing has been found
864	if [ X${TarFileFound} = X ] ; then
865	IGCM_debug_Print 3 "Restart files were not found!"
866	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
867	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
868	IGCM_debug_Exit "Please double check restart settings in config.card"
869	IGCM_debug_Verif_Exit
870	fi
871	IGCM_sys_PrepareTaredRestart ${TarFileFound}
872	TarFileLocation=$( basename ${TarFileFound} )
873	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
874	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
875	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
876	fi
877
878	if [ ${nb_restart_file} -gt 1 ] ; then
879	j=0 # BASH LINE NOT NEEDED
880	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
881	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
882	j4=${j} # BASH LINE NOT NEEDED
883	if [ X${Buffered} = Xtrue ] ; then
884	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
885	elif [ X${Archived} = Xtrue ] ; then
886	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
887	elif [ X${Tared} = Xtrue ] ; then
888	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
889	fi
890	(( j=j+1 )) # BASH LINE NOT NEEDED
891	done
892	else
893	if [ X${Buffered} = Xtrue ] ; then
894	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
895	elif [ X${Archived} = Xtrue ] ; then
896	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
897	elif [ X${Tared} = Xtrue ] ; then
898	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
899	fi
900	fi
901	(( i=i+3 ))
902	done
903	else
904	if [ X${FileName0} != XNONE ] ; then
905	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
906	else
907	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
908	fi
909	fi
910	fi
911	done
912
913	NbFiles=$( ls * 2> /dev/null \| wc -l )
914	if [ ${NbFiles} -gt 0 ] ; then
915	IGCM_sys_Chmod u+rw *
916	fi
917
918	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
919	}
920
921	#=======================================================================
922	function IGCM_comp_PeriodStart
923	{
924	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
925
926	# Debug Print :
927	echo
928	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
929	echo
930
931	typeset ExeNameIn ExeNameOut
932	typeset comp compname comptagname
933	for comp in ${config_ListOfComponents[*]} ; do
934	# Define component
935	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
936	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
937
938	# Copy executable for this component
939	eval ExeNameIn=\${config_Executable_${comp}[0]}
940	eval ExeNameOut=\${config_Executable_${comp}[1]}
941
942	# Debug Print
943	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
944	# UPDATE component
945	${comp}_PeriodStart 2> /dev/null
946
947	done
948
949	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
950	}
951
952
953
954	#=======================================================================
955	function IGCM_comp_modifyFile
956	{
957	#
958	# syntax: IGCM_comp_modifyFile filein key [value]
959	#
960	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
961	#
962	# This function is used to replace a pattern in a file for a specific variable.
963	#
964	# Arguments:
965	# - filein : the file in run directory in which the variable should be set
966	# - key : the variable to modify
967	# - value : the value to set the key equal to
968	#
969	IGCM_debug_PushStack "IGCM_comp_modifyFile"
970
971	typeset filein key value pattern
972
973	# Set local variables and test the arguments
974	if [ $# = 3 ] ; then
975	# Normal case with 3 arguments
976	filein=$1 ; key=$2 ; value=$3
977	else
978	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
979	IGCM_debug_PopStack "IGCM_comp_modifyFile"
980	return
981	fi
982	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
983
984	# Test if the file exist
985	if [ ! -f ${filein} ] ; then
986	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
987	IGCM_debug_PopStack "IGCM_comp_modifyFile"
988	return
989	fi
990
991	# Read the line with key in the file without the comments
992	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
993
994	# Verify the existance of the pattern
995	if [ X"${pattern}" = X ] ; then
996	# Variable key is not set in filein, stop.
997	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
998	IGCM_debug_PopStack "IGCM_comp_modifyFile"
999	return
1000	fi
1001
1002	# Now change key in filein
1003	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1004	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1005	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1006	\mv ${filein}.tmp ${filein}
1007
1008	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1009	}
1010
1011	#=======================================================================
1012	function IGCM_comp_modifyDefFile
1013	{
1014	#
1015	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1016	#
1017	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1018	#
1019	# This function is used to modify a parameter file for a specific variable.
1020	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1021	# This function can be used in the comp.driver files for the components.
1022	#
1023	# Arguments:
1024	# - type : first argument must be blocker, nonblocker or force
1025	# For "blocker" case, the variable must be attributed the keyworld AUTO
1026	# otherwise this function will exit.
1027	# For "nonblocker" case, the user can remove or modify the variable. For
1028	# this case, as long as AUTO is not set, no modification will be done.
1029	# For "force" case, the variable will be modified even if it is not set to AUTO
1030	# - filein : the file in run directory of .def type in which the variable should be set
1031	# - key : the variable to modify
1032	# - value : the value to set the key equal to, optional. If value is not set or if
1033	# value=DEFAULT, then a default value must be given in filein using syntax :
1034	# key= AUTO : DEFAULT=def_value
1035	#
1036	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1037
1038	typeset type filein key value
1039	typeset filelist nb_occ modify
1040
1041	# Set local variables and test the arguments
1042	if [ $# = 4 ] ; then
1043	# Normal case with 4 arguments
1044	type=$1 ; filein=$2 ; key=$3 ; value=$4
1045	elif [ $# = 3 ] ; then
1046	# Normal case with 3 arguments
1047	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1048	else
1049	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1050	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1051	return
1052	fi
1053	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1054
1055	# Test if first argument is correct
1056	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1057	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1058	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1059	return
1060	fi
1061
1062	# Test if the file exist.
1063	# Exit with error if the file does not exist for the case blocker or force.
1064	# Only return for the case nonblocker.
1065	if [ ! -f ${filein} ] ; then
1066	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1067	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1068	else
1069	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1070	fi
1071	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1072	return
1073	fi
1074
1075	# Define list of files to test using all files with suffix .def (except used*.def)
1076	filelist=$( ls *def \| grep -v used )
1077
1078	# Count number of occurances for the key in all files
1079	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1080
1081	# Test if key is set several times
1082	if [ ${nb_occ} -gt 1 ] ; then
1083	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1084	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1085	return
1086	fi
1087
1088	# Treatement according to different cases
1089	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1090	# Stop if the key is never set and the function is blocker
1091	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1092	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1093	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1094	# The key is not set but it is a nonblocker call so nothing is done.
1095	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1096	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1097	modify=no
1098	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1099	# Variable key is not set in filein, stop.
1100	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1101	fi
1102
1103	# Check if AUTO is set in the filein on the same line as the key variable
1104	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1105	# Modification will be done for all cases
1106	modify=yes
1107	else
1108	# The variable was not set to AUTO
1109	if [ ${type} = blocker ] ; then
1110	# Exit because this is a blocker call
1111	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1112	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1113	return
1114	elif [ ${type} = nonblocker ] ; then
1115	# Do nothing. Suppose that the user did set the variable correct
1116	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1117	modify=no
1118	elif [ ${type} = force ] ; then
1119	# Force modification
1120	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1121	modify=yes
1122	fi
1123	fi
1124
1125	# Do the modifcation now
1126	if [ ${modify} = yes ] ; then
1127
1128	# For option DEFAULT, read default value from file.
1129	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1130	# Case to set DEFAULT value
1131	# Read default value from filein
1132	value=$( grep ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1133
1134	if [ X"${value}" = X ] ; then
1135	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1136	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1137	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1138	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1139	return
1140	fi
1141	fi
1142
1143	# Now change key in filein
1144	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1145	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1146	\mv ${filein}.tmp ${filein}
1147	fi
1148	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1149	}
1150
1151	#=======================================================================
1152	function IGCM_comp_modifyNamelist
1153	{
1154	#
1155	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1156	#
1157	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1158	#
1159	# This function is used to modify a parameter file for a specific variable.
1160	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1161	# This function can be used in the comp.driver files for the components.
1162	#
1163	# Arguments:
1164	# - type : first argument must be blocker, nonblocker or force
1165	# For "blocker" case, the variable must be attributed the keyworld AUTO
1166	# otherwise this function will exit.
1167	# For "nonblocker" case, the user can remove or modify the variable. For
1168	# this case, as long as AUTO is not set, no modification will be done.
1169	# For "force" case, the variable will be modified even if it is not set to AUTO
1170	# - filein : the file in run directory of .def type in which the variable should be set
1171	# - key : the variable to modify
1172	# - value : the value to set the key equal to, optional. If value is not set or if
1173	# value=DEFAULT, then a default value must be given in filein using syntax :
1174	# key= AUTO : DEFAULT=def_value
1175	#
1176	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1177
1178	typeset type filein key value pattern modify
1179
1180	# Set local variables and test the arguments
1181	if [ $# = 4 ] ; then
1182	# Normal case with 4 arguments
1183	type=$1 ; filein=$2 ; key=$3 ; value=$4
1184	elif [ $# = 3 ] ; then
1185	# Normal case with 3 arguments
1186	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1187	else
1188	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1189	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1190	return
1191	fi
1192	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1193
1194	# Test if first argument is correct
1195	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1196	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1197	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1198	return
1199	fi
1200
1201	# Test if the file exist.
1202	# Exit with error if the file does not exist for the case blocker or force.
1203	# Only return for the case nonblocker.
1204	if [ ! -f ${filein} ] ; then
1205	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1206	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1207	else
1208	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1209	fi
1210	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1211	return
1212	fi
1213
1214	# Read the line with key in the file without the comments
1215	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1216
1217	# Verify the existance of the pattern
1218	if [ X"$pattern" = X ] ; then
1219	# Variable key is not set in filein, stop.
1220	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1221	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1222	return
1223	fi
1224
1225	# Check if the variable is set to AUTO in the filein
1226	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1227	# Modification will be done for all cases
1228	modify=yes
1229	else
1230	# The variable was not set to AUTO
1231	if [ ${type} = blocker ] ; then
1232	# Exit because this is a blocker call
1233	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1234	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1235	return
1236	elif [ ${type} = nonblocker ] ; then
1237	# Do nothing. Suppose that the user did set the variable correct
1238	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1239	modify=no
1240	elif [ ${type} = force ] ; then
1241	# Force modification
1242	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1243	modify=yes
1244	fi
1245	fi
1246
1247	# Do the modifcation now
1248	if [ ${modify} = yes ] ; then
1249
1250	# For option DEFAULT, read default value from file.
1251	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1252	# Case to set DEFAULT value
1253	# Read default value from filein
1254	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1255
1256	if [ X"${value}" = X ] ; then
1257	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1258	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1259	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1260	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1261	return
1262	fi
1263	fi
1264
1265	# Now change key in filein
1266	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1267	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1268	\mv ${filein}.tmp ${filein}
1269	fi
1270	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1271	}
1272
1273	#=======================================================================
1274	function IGCM_comp_modifyXmlFile
1275	{
1276	#
1277	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1278	#
1279	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1280	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1281	#
1282	# This function is used to modify the value for a specific attribute and variable id.
1283	# The file must be a valid xml file.
1284	# This function can be used in the comp.driver files for the components.
1285	#
1286	# Arguments:
1287	# - type : first argument must be blocker, nonblocker or force.
1288	# For "blocker" case, the variable must be attributed the keyworld AUTO
1289	# otherwise this function will exit.
1290	# For "nonblocker" case, the user can remove or modify the variable. For
1291	# this case, as long as AUTO is not set, no modification will be done.
1292	# For "force" case, the variable will be modified even if it is not set to AUTO
1293	# - filein : the file in run directory of .xml type in which the variable should be set
1294	# - keyid : the variable to modify
1295	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1296	# - value : the value to set in the filein
1297	#
1298	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1299
1300	typeset type filein keyid keyattrib value modify
1301
1302	# Set local variables and test the arguments
1303	if [ $# = 5 ] ; then
1304	# Normal case with 4 arguments
1305	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1306	else
1307	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1308	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1309	return
1310	fi
1311	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1312
1313	# Test if first argument is correct
1314	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1315	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1316	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1317	return
1318	fi
1319
1320	# Test if the file exist.
1321	# Exit with error if the file does not exist for the case blocker or force.
1322	# Only return for the case nonblocker.
1323	if [ ! -f ${filein} ] ; then
1324	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1325	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1326	else
1327	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1328	fi
1329	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1330	return
1331	fi
1332
1333	# Test if keyid is set in filein, otherwise exit
1334	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1335	# Variable key is not set in filein, stop.
1336	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1337	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1338	return
1339	fi
1340
1341	# Check if AUTO is set on the same line as keyid and keyattrib
1342	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1343	# Modifification will be done
1344	modify=yes
1345	else
1346	if [ ${type} = blocker ] ; then
1347	# Exit, the variable must be set to AUTO
1348	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1349	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1350	return
1351	elif [ ${type} = nonblocker ] ; then
1352	# Nothing will be done
1353	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1354	modify=no
1355	elif [ ${type} = force ] ; then
1356	# Force modification
1357	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1358	modify=yes
1359	fi
1360	fi
1361
1362	# Do the modifcation now
1363	if [ ${modify} = yes ] ; then
1364	if [ ${keyattrib} = NONE ] ; then
1365	# Case to modify the variable itself
1366	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1367	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1368	else
1369	# Check if keyattrib is set on the same line as keyid
1370	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1371	# Case to modify the attribute value
1372	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1373	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1374	else
1375	# Case to add the attribute and its value
1376	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1377	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1378	fi
1379	fi
1380	\mv ${filein}.tmp ${filein}
1381	fi
1382	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1383	}
1384
1385	#=======================================================================
1386	function IGCM_comp_Update
1387	{
1388	IGCM_debug_PushStack "IGCM_comp_Update"
1389
1390	# Debug Print :
1391	echo
1392	IGCM_debug_Print 1 "IGCM_comp_Update"
1393	echo
1394
1395	typeset ExeNameIn ExeNameOut
1396	typeset comp compname comptagname
1397	for comp in ${config_ListOfComponents[*]} ; do
1398	# Define component
1399	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1400	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1401
1402	# Copy executable for this component
1403	eval ExeNameIn=\${config_Executable_${comp}[0]}
1404	eval ExeNameOut=\${config_Executable_${comp}[1]}
1405
1406	# If missing executable and DRYRUN is set to 0 or 1 then stop!
1407	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1408	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
1409	fi
1410
1411	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1412	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1413	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1414	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1415	fi
1416	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1417	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1418	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1419	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1420	fi
1421	fi
1422
1423	# Debug Print
1424	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1425	# UPDATE component
1426	${comp}_Update
1427
1428	done
1429
1430	IGCM_debug_PopStack "IGCM_comp_Update"
1431	}
1432
1433	#=======================================================================
1434	function IGCM_comp_Finalize
1435	{
1436	IGCM_debug_PushStack "IGCM_comp_Finalize"
1437
1438	# Debug Print :
1439	echo
1440	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1441	echo
1442
1443	typeset ListTextName TextName0
1444	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1445	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1446	typeset -Z4 j4 #BASH declare j4
1447	typeset list_file nlist_file
1448	typeset compactoutputs
1449
1450	# Initialize array hosting list of rebuilded files to copy
1451	unset rebuildedActionsList
1452
1453	# Text compacting options
1454	compactoutputs=false
1455	if [ X${JobType} != XRUN ] ; then
1456	compactoutputs=true
1457	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1458	compactoutputs=true
1459	fi
1460
1461	# Prepare headers for the shell dedicated to offline rebuild
1462	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1463	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1464	if [ ${DRYRUN} -le 1 ] ; then
1465	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1466	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1467	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1468	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1469	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1470	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1471	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1472	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1473	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1474	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1475	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1476	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1477	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1478	fi
1479	fi
1480
1481	for comp in ${config_ListOfComponents[*]} ; do
1482	# Define component
1483	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1484	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1485
1486	# Debug Print
1487	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1488	# FINALIZE component
1489	${comp}_Finalize
1490
1491	card=${SUBMIT_DIR}/COMP/${compname}.card
1492
1493	# Save Output Text files of models
1494	#---------------------------------
1495	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1496	IGCM_card_DefineArrayFromOption ${card} OutputText List
1497	ListTextName=${compname}_OutputText_List
1498
1499	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1500	if [ X${TextName0} != X${NULL_STR} ] ; then
1501	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1502
1503	(( i=0 ))
1504	until [ $i -eq $NbFiles ]; do
1505	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1506	eval file_out=${PREFIX}_${file_in}
1507
1508	(( i=i+1 ))
1509
1510	unset list_file
1511	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1512	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1513	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 )
1514	nlist_file=${#list_file[@]}
1515	if [ ${nlist_file} -gt 1 ] ; then
1516	if ( ${compactoutputs} ) ; then
1517	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1518	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1519	echo ${list_file[*]} > ${file_out}
1520	echo "" >> ${file_out}
1521
1522	(( i_ = 0 ))
1523	for file in ${list_file[@]} ; do
1524	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1525	echo "\| " ${i_} " " ${file} >> ${file_out}
1526	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1527	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1528	echo "" >> ${file_out}
1529	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1530	(( i_ = i_ + 1 ))
1531	done
1532	if ( ${ExecutionFail} ) ; then
1533	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1534	fi
1535
1536	if [ X${Pack} = Xtrue ] ; then
1537	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1538	else
1539	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1540	fi
1541
1542	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1543	else
1544	for file in ${list_file[@]} ; do
1545	if ( ${ExecutionFail} ) ; then
1546	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1547	fi
1548
1549	if [ X${Pack} = Xtrue ] ; then
1550	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1551	else
1552	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1553	fi
1554
1555	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1556	done
1557	fi
1558	else
1559	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1560	eval IGCM_sys_Mv ${file_in}* ${file_in}
1561	fi
1562
1563	if ( ${ExecutionFail} ) ; then
1564	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1565	fi
1566
1567	if [ X${Pack} = Xtrue ] ; then
1568	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1569	else
1570	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1571	fi
1572	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1573	fi
1574	done
1575	fi
1576
1577	# Save Restarts files
1578	#--------------------
1579	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1580	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1581	ListFilesName=${compname}_RestartFiles_List
1582	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1583
1584	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1585	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1586
1587	(( i=0 ))
1588	until [ $i -ge $NbFiles ]; do
1589	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1590	eval file_in=${file_in_}
1591
1592	(( i_ = i+1 ))
1593	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1594	eval file_out=${file_out_}
1595
1596	(( i_ = i+2 ))
1597	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1598	eval file_outin=${file_outin_}
1599
1600	generic_restart_file_name_in=$( basename ${file_in} .nc )
1601	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1602	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1603
1604	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1605	if [ ${nb_restart_file} -gt 1 ] ; then
1606	j=0 # BASH LINE NOT NEEDED
1607	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1608	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1609	j4=${j} # BASH LINE NOT NEEDED
1610	if [ X${Pack} = Xtrue ] ; then
1611	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1612	else
1613	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1614	fi
1615	if [ ! ${file_in} = ${file_outin} ] ; then
1616	if ( ${ExitFlag} ) ; then
1617	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1618	else
1619	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1620	fi
1621	fi
1622	(( j=j+1 )) # BASH LINE NOT NEEDED
1623	done
1624	else
1625	if [ X${Pack} = Xtrue ] ; then
1626	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1627	else
1628	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1629	fi
1630	if [ ! ${file_in} = ${file_outin} ] ; then
1631	if ( ${ExitFlag} ) ; then
1632	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1633	else
1634	IGCM_sys_Mv ${file_in} ${file_outin}
1635	fi
1636	fi
1637	fi
1638
1639	(( i=i+3 ))
1640	done
1641	else
1642	if [ X${FileName0} != XNONE ] ; then
1643	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1644	else
1645	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1646	fi
1647	fi
1648
1649	# Save Output files
1650	#------------------
1651	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1652	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1653	ListFilesName=${compname}_OutputFiles_List
1654	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1655
1656	if [ X${FileName0} != X${NULL_STR} ] ; then
1657	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1658
1659	(( i=0 ))
1660	until [ $i -ge $NbFiles ]; do
1661	SaveOnArchive=true
1662	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1663	eval file_in=${file_in_}
1664	(( i_ = i+1 ))
1665	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1666	eval file_out=${file_out_}
1667	#
1668	# Override file_out path remplacing R_SAVE by R_BUFR
1669	#
1670	if [ X${Pack} = Xtrue ] ; then
1671	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1672	fi
1673	#
1674	# Not necessarily the best option. /!\ Potential side effects /!\
1675	#
1676	(( i_ = i+2 ))
1677	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1678	#
1679	generic_file_name=$( basename ${file_in} .nc )
1680	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1681	#
1682	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1683	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1684	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1685	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1686	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1687	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1688	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1689	IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc
1690	else
1691	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1692	IGCM_sys_Mv ${generic_file_name}_[0-9]*.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1693
1694	# Prepare the shell dedicated to offline rebuild
1695	if [ $DRYRUN -le 1 ]; then
1696	if [ ${file_in} = histstn.nc ] ; then
1697	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1698	else
1699	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1700	fi
1701	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1702	fi
1703	#
1704	# Load Patch we need to apply and apply
1705	if [ $DRYRUN -le 1 ]; then
1706	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1707	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1708	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1709	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1710	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1711	done
1712	fi
1713	fi
1714	#
1715	if [ $DRYRUN -le 1 ]; then
1716	if [ X${Pack} = Xtrue ] ; then
1717	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1718	else
1719	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1720	fi
1721	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1722	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1723	fi
1724	SaveOnArchive=false
1725	fi
1726	fi
1727	#
1728	if [ ${SaveOnArchive} = true ] ; then
1729	#
1730	# Rebuild has been done online or it was not needed
1731	#
1732	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1733	#
1734	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1735	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1736	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1737	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1738	#
1739	if [ $DRYRUN -le 1 ]; then
1740	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1741	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1742	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1743	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1744	done
1745	#
1746	if [ X${Pack} = Xtrue ] ; then
1747	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1748	else
1749	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1750	fi
1751	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1752	#
1753	fi
1754	else
1755	#
1756	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1757	#
1758	if [ X${Pack} = Xtrue ] ; then
1759	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1760	else
1761	IGCM_sys_Put_Out ${file_in} ${file_out}
1762	fi
1763	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1764	if [ ${nb_rebuild_file} -gt 1 ] ; then
1765	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1766	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1767	done
1768	fi
1769	fi
1770	fi
1771	(( i=i+3 ))
1772	done
1773	fi
1774	echo
1775	done
1776	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1777	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1778	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1779	i=0
1780	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1781	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1782	(( i=i+1 ))
1783	done
1784	fi
1785	IGCM_debug_PopStack "IGCM_comp_Finalize"
1786	}

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