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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1085

Last change on this file since 1085 was 1085, checked in by jgipsl, 10 years ago
Added function IGCM_comp_modifyNamelist See #222
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: 67.8 KB

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

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