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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1151

Last change on this file since 1151 was 1151, checked in by sdipsl, 9 years ago
adressing #237
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
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1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
6	# $Revision:: $ Revision of last commit
7	# $Author:: $ Author of last commit
8	# $Date:: $ Date of last commit
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	#
12	#**************************************************************
13
14	#========================================================================
15	function IGCM_comp_Initialize
16	{
17	IGCM_debug_PushStack "IGCM_comp_Initialize"
18
19	# Debug Print :
20	echo
21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
22	echo
23
24	typeset comp compname comptagname CompatibilityTag auxprint card_UserChoices first_option option i j
25	for comp in ${config_ListOfComponents[*]} ; do
26
27	# Define component
28	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
29	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
30	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
31
32	# Debug Print
33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
34
35	# Read libIGCM compatibility version in ${compname}.card
36	card=${SUBMIT_DIR}/COMP/${compname}.card
37	IGCM_card_DefineVariableFromOption ${card} Compatibility libIGCM
38
39	eval CompatibilityTag=\${${compname}_Compatibility_libIGCM} > /dev/null 2>&1
40	if [ ! "${CompatibilityTag}" = "${libIGCM_CurrentTag}" ] ; then
41	IGCM_debug_Exit "${compname}.card is not compatible with libIGCM version ${libIGCM_CurrentTag} see libIGCM FAQ http://wiki.ipsl.jussieu.fr/wiki_ipsl/IGCMG/libIGCM/DocUtilisateur/FAQ ."
42	fi
43
44	# Manage component executable
45	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
46
47	# 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	function IGCM_comp_modifyDefFile
954	{
955	#
956	# syntax: IGCM_comp_modifyDefFile type filein key [value]
957	#
958	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
959	#
960	# This function is used to modify a parameter file for a specific variable.
961	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
962	# This function can be used in the comp.driver files for the components.
963	#
964	# Arguments:
965	# - type : first argument must be blocker, nonblocker or force
966	# For "blocker" case, the variable must be attributed the keyworld AUTO
967	# otherwise this function will exit.
968	# For "nonblocker" case, the user can remove or modify the variable. For
969	# this case, as long as AUTO is not set, no modification will be done.
970	# For "force" case, the variable will be modified even if it is not set to AUTO
971	# - filein : the file in run directory of .def type in which the variable should be set
972	# - key : the variable to modify
973	# - value : the value to set the key equal to, optional. If value is not set or if
974	# value=DEFAULT, then a default value must be given in filein using syntax :
975	# key= AUTO : DEFAULT=def_value
976	#
977	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
978
979	# Set local variables and test the arguments
980	if [ $# = 4 ] ; then
981	# Normal case with 4 arguments
982	type=$1 ; filein=$2 ; key=$3 ; value=$4
983	elif [ $# = 3 ] ; then
984	# Normal case with 3 arguments
985	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
986	else
987	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
988	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
989	return
990	fi
991	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: $type $filein $key $value"
992
993
994	# Test if first argument is correct
995	if [ $type != blocker ] && [ $type != nonblocker ] && [ $type != force ] ; then
996	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
997	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
998	return
999	fi
1000
1001	# Test if the file exist
1002	if [ ! -f ${filein} ] ; then
1003	IGCM_debug_Exit "IGCM_comp_modifyDefFile: $filein does not exist."
1004	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1005	return
1006	fi
1007
1008	# Define list of files to test using all files with suffix .def (except used*.def)
1009	filelist=$( ls *def \| grep -v used )
1010
1011	# Count number of occurances for the key in all files
1012	nb_occ=$( grep -w $key $filelist \|grep -v "#" \|wc -l )
1013
1014	# Test if key is set several times
1015	if [ $nb_occ -gt 1 ] ; then
1016	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in $filein: Variable=$key is set ${nb_occ} times"
1017	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1018	return
1019	fi
1020
1021	# Treatement according to different cases
1022	if [ $nb_occ -eq 0 ] && [ $type = blocker ] ; then
1023	# Stop if the key is never set and the function is blocker
1024	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in $filein: Variable=$key has been removed but this function is blocker. "
1025	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore $filein for variable $key."
1026	elif [ $nb_occ -eq 0 ] && [ $type = nonblocker ] ; then
1027	# The key is not set but it is a nonblocker call so nothing is done.
1028	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: $key is not set in $filein. This is a nonblocker call so nothing is done."
1029	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for $key from the model will be used."
1030	modify=no
1031	elif [ $( grep $key $filein \| grep -v "\#" \|wc -l ) = 0 ] ; then
1032	# Variable key is not set in filein, stop.
1033	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable $key is not set in correct file. It should be set in $filein."
1034	fi
1035
1036
1037	# Check if AUTO is set in the filein on the same line as the key variable
1038	if [ $( grep -w $key $filein \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1039	# Modification will be done for all cases
1040	modify=yes
1041	else
1042	# The variable was not set to AUTO
1043	if [ $type = blocker ] ; then
1044	# Exit because this is a blocker call
1045	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable $key cannot be modified. It should be set to AUTO."
1046	return
1047	elif [ $type = nonblocker ] ; then
1048	# Do nothing. Suppose that the user did set the variable correct
1049	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: $key is set by the user. Nothing done."
1050	modify=no
1051	elif [ $type = force ] ; then
1052	# Force modification
1053	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=$key was not set to AUTO. Modification will be forced."
1054	modify=yes
1055	fi
1056	fi
1057
1058	# Do the modifcation now
1059	if [ $modify = yes ] ; then
1060
1061	# For option DEFAULT, read default value from file.
1062	if [ X"$value" = XDEFAULT ] \|\| [ X"$value" = X ] ; then
1063	# Case to set DEFAULT value
1064	# Read default value from filein
1065	value=$( grep $key $filein \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1066
1067	if [ X"$value" = X ] ; then
1068	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable $key needs a DEFAULT value in $filein."
1069	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in $filein should be:"
1070	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: $key=_AUTO_:DEFAULT=def_value"
1071	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1072	return
1073	fi
1074	fi
1075
1076	# Now change key in filein
1077	sed -e "s/^${key}\ =./${key}= ${value}/" $filein > $filein.tmp
1078	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In $filein set $key=$value"
1079	\mv $filein.tmp $filein
1080	fi
1081	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1082	}
1083
1084
1085	#=======================================================================
1086	function IGCM_comp_modifyNamelist
1087	{
1088	#
1089	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1090	#
1091	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1092	#
1093	# This function is used to modify a parameter file for a specific variable.
1094	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1095	# This function can be used in the comp.driver files for the components.
1096	#
1097	# Arguments:
1098	# - type : first argument must be blocker, nonblocker or force
1099	# For "blocker" case, the variable must be attributed the keyworld AUTO
1100	# otherwise this function will exit.
1101	# For "nonblocker" case, the user can remove or modify the variable. For
1102	# this case, as long as AUTO is not set, no modification will be done.
1103	# For "force" case, the variable will be modified even if it is not set to AUTO
1104	# - filein : the file in run directory of .def type in which the variable should be set
1105	# - key : the variable to modify
1106	# - value : the value to set the key equal to, optional. If value is not set or if
1107	# value=DEFAULT, then a default value must be given in filein using syntax :
1108	# key= AUTO : DEFAULT=def_value
1109	#
1110	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1111
1112	# Set local variables and test the arguments
1113	if [ $# = 4 ] ; then
1114	# Normal case with 4 arguments
1115	type=$1 ; filein=$2 ; key=$3 ; value=$4
1116	elif [ $# = 3 ] ; then
1117	# Normal case with 3 arguments
1118	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1119	else
1120	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1121	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1122	return
1123	fi
1124	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: $type $filein $key $value"
1125
1126
1127	# Test if first argument is correct
1128	if [ $type != blocker ] && [ $type != nonblocker ] && [ $type != force ] ; then
1129	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1130	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1131	return
1132	fi
1133
1134	# Test if the file exist
1135	if [ ! -f ${filein} ] ; then
1136	IGCM_debug_Exit "IGCM_comp_modifyNamelist: $filein does not exist."
1137	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1138	return
1139	fi
1140
1141	# Read the line with key in the file without the comments
1142	pattern=$( grep "^ $key =" $filein \| sed -e "s% \!.%%" )
1143
1144	# Verify the existance of the pattern
1145	if [ X"$pattern" = X ] ; then
1146	# Variable key is not set in filein, stop.
1147	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable $key is not set in correct file. It should be set in $filein."
1148	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1149	return
1150	fi
1151
1152	# Check if the variable is set to AUTO in the filein
1153	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1154	# Modification will be done for all cases
1155	modify=yes
1156	else
1157	# The variable was not set to AUTO
1158	if [ $type = blocker ] ; then
1159	# Exit because this is a blocker call
1160	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable $key cannot be modified. It should be set to AUTO."
1161	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1162	return
1163	elif [ $type = nonblocker ] ; then
1164	# Do nothing. Suppose that the user did set the variable correct
1165	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: $key is set by the user. Nothing done."
1166	modify=no
1167	elif [ $type = force ] ; then
1168	# Force modification
1169	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=$key was not set to AUTO. Modification will be forced."
1170	modify=yes
1171	fi
1172	fi
1173
1174	# Do the modifcation now
1175	if [ $modify = yes ] ; then
1176
1177	# For option DEFAULT, read default value from file.
1178	if [ X"$value" = XDEFAULT ] \|\| [ X"$value" = X ] ; then
1179	# Case to set DEFAULT value
1180	# Read default value from filein
1181	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1182
1183	if [ X"$value" = X ] ; then
1184	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable $key needs a DEFAULT value in $filein."
1185	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in $filein should be:"
1186	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: $key=_AUTO_:DEFAULT=def_value"
1187	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1188	return
1189	fi
1190	fi
1191
1192	# Now change key in filein
1193	sed -e "s/${pattern}/ $key=${value}/" $filein > $filein.tmp
1194	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In $filein set $key=$value"
1195	\mv $filein.tmp $filein
1196	fi
1197	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1198	}
1199
1200	#=======================================================================
1201	function IGCM_comp_modifyXmlFile
1202	{
1203	#
1204	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1205	#
1206	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1207	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1208	#
1209	# This function is used to modify the value for a specific attribute and variable id.
1210	# The file must be a of xml syntax.
1211	# This function can be used in the comp.driver files for the components.
1212	#
1213	# Arguments:
1214	# - type : first argument must be blocker, nonblocker or force.
1215	# For "blocker" case, the variable must be attributed the keyworld AUTO
1216	# otherwise this function will exit.
1217	# For "nonblocker" case, the user can remove or modify the variable. For
1218	# this case, as long as AUTO is not set, no modification will be done.
1219	# For "force" case, the variable will be modified even if it is not set to AUTO
1220	# - filein : the file in run directory of .xml type in which the variable should be set
1221	# - keyid : the variable to modify
1222	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1223	# - value : the value to set in the filein
1224	#
1225	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1226
1227	# Set local variables and test the arguments
1228	if [ $# = 5 ] ; then
1229	# Normal case with 4 arguments
1230	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1231	else
1232	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1233	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1234	return
1235	fi
1236	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=$type file=$filein, id=$keyid attribute=$keyattrib, value=$value"
1237
1238	# Test if first argument is correct
1239	if [ $type != blocker ] && [ $type != nonblocker ] && [ $type != force ] ; then
1240	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1241	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1242	return
1243	fi
1244
1245	# Test if the file exist
1246	if [ ! -f ${filein} ] ; then
1247	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: $filein does not exist."
1248	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1249	return
1250	fi
1251
1252	# Test if keyid is set in filein, otherwise exit
1253	if [ $( grep -w $keyid $filein \| wc -l ) = 0 ] ; then
1254	# Variable key is not set in filein, stop.
1255	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : $keyid is not set in the file. Bad syntax of $filein file."
1256	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1257	return
1258	fi
1259
1260	# Check if AUTO is set on the same line as keyid and keyattrib
1261	if [ $( grep -w $keyid $filein \| grep AUTO \| wc -l ) = 1 ] ; then
1262	# Modifification will be done
1263	modify=yes
1264	else
1265	if [ $type = blocker ] ; then
1266	# Exit, the variable must be set to AUTO
1267	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The $keyattrib for $keyid must be set to AUTO in $filein."
1268	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1269	return
1270	elif [ $type = nonblocker ] ; then
1271	# Nothing will be done
1272	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1273	modify=no
1274	elif [ $type = force ] ; then
1275	# Force modification
1276	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=$keyattrib for id=$keyid was not set to AUTO. Modification will be forced."
1277	modify=yes
1278	fi
1279	fi
1280
1281	# Do the modifcation now
1282	if [ $modify = yes ] ; then
1283	if [ $keyattrib = NONE ] ; then
1284	# Case to modify the variable itself
1285	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1286	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" $filein > $filein.tmp
1287	else
1288	# Check if keyattrib is set on the same line as keyid
1289	if [ $( grep -w $keyid $filein \| grep $keyattrib \| wc -l ) = 1 ] ; then
1290	# Case to modify the attribute value
1291	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1292	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" $filein > $filein.tmp
1293	else
1294	# Case to add the attribute and its value
1295	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1296	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" $filein > $filein.tmp
1297	fi
1298	fi
1299	\mv $filein.tmp $filein
1300	fi
1301	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1302	}
1303
1304	#=======================================================================
1305	function IGCM_comp_Update
1306	{
1307	IGCM_debug_PushStack "IGCM_comp_Update"
1308
1309	# Debug Print :
1310	echo
1311	IGCM_debug_Print 1 "IGCM_comp_Update"
1312	echo
1313
1314	typeset ExeNameIn ExeNameOut
1315	typeset comp compname comptagname
1316	for comp in ${config_ListOfComponents[*]} ; do
1317	# Define component
1318	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1319	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1320
1321	# Copy executable for this component
1322	eval ExeNameIn=\${config_Executable_${comp}[0]}
1323	eval ExeNameOut=\${config_Executable_${comp}[1]}
1324
1325	# If missing executable and DRYRUN is set to 0 or 1 then stop!
1326	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1327	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
1328	fi
1329
1330	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1331	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1332	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1333	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1334	fi
1335	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1336	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1337	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1338	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1339	fi
1340	fi
1341
1342	# Debug Print
1343	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1344	# UPDATE component
1345	${comp}_Update
1346
1347	done
1348
1349	IGCM_debug_PopStack "IGCM_comp_Update"
1350	}
1351
1352	#=======================================================================
1353	function IGCM_comp_Finalize
1354	{
1355	IGCM_debug_PushStack "IGCM_comp_Finalize"
1356
1357	# Debug Print :
1358	echo
1359	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1360	echo
1361
1362	typeset ListTextName TextName0
1363	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1364	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1365	typeset -Z4 j4
1366	#BASH declare j4
1367	typeset list_file nlist_file
1368	typeset compactoutputs
1369
1370	compactoutputs=false
1371	if [ X${JobType} != XRUN ] ; then
1372	compactoutputs=true
1373	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1374	compactoutputs=true
1375	fi
1376
1377	# Prepare headers for the shell dedicated to offline rebuild
1378	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1379	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1380	if [ ${DRYRUN} -le 1 ] ; then
1381	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1382	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1383	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1384	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1385	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1386	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1387	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1388	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1389	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1390	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1391	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1392	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1393	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1394	fi
1395	fi
1396
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	# Debug Print
1403	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1404	# FINALIZE component
1405	${comp}_Finalize
1406
1407	card=${SUBMIT_DIR}/COMP/${compname}.card
1408
1409	# Save Output Text files of models
1410	#---------------------------------
1411	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1412	IGCM_card_DefineArrayFromOption ${card} OutputText List
1413	ListTextName=${compname}_OutputText_List
1414
1415	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1416	if [ X${TextName0} != X${NULL_STR} ] ; then
1417	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1418
1419	(( i=0 ))
1420	until [ $i -eq $NbFiles ]; do
1421	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1422	eval file_out=${PREFIX}_${file_in}
1423
1424	(( i=i+1 ))
1425
1426	unset list_file
1427	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1428	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1429	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 )
1430	nlist_file=${#list_file[@]}
1431	if [ ${nlist_file} -gt 1 ] ; then
1432	if ( ${compactoutputs} ) ; then
1433	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1434	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1435	echo ${list_file[*]} > ${file_out}
1436	echo "" >> ${file_out}
1437
1438	(( i_ = 0 ))
1439	for file in ${list_file[@]} ; do
1440	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1441	echo "\| " ${i_} " " ${file} >> ${file_out}
1442	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1443	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1444	echo "" >> ${file_out}
1445	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1446	(( i_ = i_ + 1 ))
1447	done
1448	if ( ${ExecutionFail} ) ; then
1449	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1450	fi
1451
1452	if [ X${Pack} = Xtrue ] ; then
1453	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1454	else
1455	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1456	fi
1457
1458	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1459	else
1460	for file in ${list_file[@]} ; do
1461	if ( ${ExecutionFail} ) ; then
1462	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1463	fi
1464
1465	if [ X${Pack} = Xtrue ] ; then
1466	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1467	else
1468	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1469	fi
1470
1471	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1472	done
1473	fi
1474	else
1475	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1476	eval IGCM_sys_Mv ${file_in}* ${file_in}
1477	fi
1478
1479	if ( ${ExecutionFail} ) ; then
1480	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1481	fi
1482
1483	if [ X${Pack} = Xtrue ] ; then
1484	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1485	else
1486	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1487	fi
1488	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1489	fi
1490	done
1491	fi
1492
1493	# Save Restarts files
1494	#--------------------
1495	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1496	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1497	ListFilesName=${compname}_RestartFiles_List
1498	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1499
1500	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1501	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1502
1503	(( i=0 ))
1504	until [ $i -ge $NbFiles ]; do
1505	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1506	eval file_in=${file_in_}
1507
1508	(( i_ = i+1 ))
1509	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1510	eval file_out=${file_out_}
1511
1512	(( i_ = i+2 ))
1513	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1514	eval file_outin=${file_outin_}
1515
1516	generic_restart_file_name_in=$( basename ${file_in} .nc )
1517	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1518	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1519
1520	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1521	if [ ${nb_restart_file} -gt 1 ] ; then
1522	j=0 # BASH LINE NOT NEEDED
1523	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1524	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1525	j4=${j} # BASH LINE NOT NEEDED
1526	if [ X${Pack} = Xtrue ] ; then
1527	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1528	else
1529	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1530	fi
1531	if [ ! ${file_in} = ${file_outin} ] ; then
1532	if ( ${ExitFlag} ) ; then
1533	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1534	else
1535	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1536	fi
1537	fi
1538	(( j=j+1 )) # BASH LINE NOT NEEDED
1539	done
1540	else
1541	if [ X${Pack} = Xtrue ] ; then
1542	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1543	else
1544	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1545	fi
1546	if [ ! ${file_in} = ${file_outin} ] ; then
1547	if ( ${ExitFlag} ) ; then
1548	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1549	else
1550	IGCM_sys_Mv ${file_in} ${file_outin}
1551	fi
1552	fi
1553	fi
1554
1555	(( i=i+3 ))
1556	done
1557	else
1558	if [ X${FileName0} != XNONE ] ; then
1559	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1560	else
1561	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1562	fi
1563	fi
1564
1565	# Save Output files
1566	#------------------
1567	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1568	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1569	ListFilesName=${compname}_OutputFiles_List
1570	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1571
1572	if [ X${FileName0} != X${NULL_STR} ] ; then
1573	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1574
1575	(( i=0 ))
1576	until [ $i -ge $NbFiles ]; do
1577	SaveOnArchive=true
1578	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1579	eval file_in=${file_in_}
1580	(( i_ = i+1 ))
1581	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1582	eval file_out=${file_out_}
1583	#
1584	# Override file_out path remplacing R_SAVE by R_BUFR
1585	#
1586	if [ X${Pack} = Xtrue ] ; then
1587	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1588	fi
1589	#
1590	# Not necessarily the best option. /!\ Potential side effects /!\
1591	#
1592	(( i_ = i+2 ))
1593	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1594	#
1595	generic_file_name=$( basename ${file_in} .nc )
1596	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1597	#
1598	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1599	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1600	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1601	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1602	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1603	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1604	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1605	IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc
1606	else
1607	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1608	IGCM_sys_Mv ${generic_file_name}_[0-9]*.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1609
1610	# Prepare the shell dedicated to offline rebuild
1611	if [ $DRYRUN -le 1 ]; then
1612	if [ ${file_in} = histstn.nc ] ; then
1613	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1614	else
1615	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1616	fi
1617	echo "IGCM_debug_Verif_Exit_Post" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1618	fi
1619	#
1620	# Load Patch we need to apply and apply
1621	if [ $DRYRUN -le 1 ]; then
1622	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1623	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1624	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1625	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1626	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1627	done
1628	fi
1629	fi
1630	#
1631	if [ $DRYRUN -le 1 ]; then
1632	if [ X${Pack} = Xtrue ] ; then
1633	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1634	else
1635	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1636	fi
1637	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1638	echo "IGCM_sys_Rm ${generic_file_name}_[0-9]*.nc " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1639	fi
1640	SaveOnArchive=false
1641	fi
1642	fi
1643	#
1644	if [ ${SaveOnArchive} = true ] ; then
1645	#
1646	# Rebuild has been done online or it was not needed
1647	#
1648	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1649	#
1650	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1651	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1652	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1653	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1654	#
1655	if [ $DRYRUN -le 1 ]; then
1656	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1657	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1658	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1659	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1660	done
1661	#
1662	if [ X${Pack} = Xtrue ] ; then
1663	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1664	else
1665	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1666	fi
1667	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1668	#
1669	fi
1670	else
1671	#
1672	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1673	#
1674	if [ X${Pack} = Xtrue ] ; then
1675	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1676	else
1677	IGCM_sys_Put_Out ${file_in} ${file_out}
1678	fi
1679	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1680	if [ ${nb_rebuild_file} -gt 1 ] ; then
1681	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1682	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1683	done
1684	fi
1685	fi
1686	fi
1687	(( i=i+3 ))
1688	done
1689	fi
1690	echo
1691	done
1692	IGCM_debug_PopStack "IGCM_comp_Finalize"
1693	}

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