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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1339

Last change on this file since 1339 was 1339, checked in by sdipsl, 8 years ago
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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 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	# ${compname}.card PATH
36	card=${SUBMIT_DIR}/COMP/${compname}.card
37
38	# Manage component executable
39	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
40
41	# Define all options in section [comp]
42	IGCM_debug_Print 3 " DefineArrayFromSection : ${comp}"
43	IGCM_card_DefineArrayFromSection ${SUBMIT_DIR}/config.card ${comp}
44	eval config_comp=\${config_${comp}[*]} > /dev/null 2>&1
45	for option in ${config_comp[*]} ; do
46	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
47	done
48	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
49
50	# Debug Print :
51	eval auxprint=\${config_${comp}_WriteFrequency}
52	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
53	#2> /dev/null
54
55	# Debug Print :
56	IGCM_debug_Print 2 "Initialize following component library"
57
58	# Source drivers in directory DRIVER if it exist
59	# else source them from directory COMP
60	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
61	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
62	# Source component library
63	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
64	else
65	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
66	# Source component library
67	. ${SUBMIT_DIR}/COMP/${compname}.driver
68	fi
69	IGCM_debug_Print 3 "With tag : ${comptagname}"
70
71	# Debug Print
72	IGCM_debug_Print 3 "Initialize ${comp} output directory."
73
74	# Define ARCHIVED Dirs
75	eval R_OUT_${comp}=${R_SAVE}/${comp}
76	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
77
78	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
79	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
80
81	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
82	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
83
84	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
86
87	eval R_OUT_${comp}_O_I=\${R_OUT_${comp}_O}/INS
88	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
89	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
90	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
91	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
92
93	# Define BUFFERED Dirs
94	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
95	eval R_BUF_${comp}=${R_BUFR}/${comp}
96	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
97
98	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
99	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
100
101	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
102	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
103
104	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
105	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
106
107	eval R_BUF_${comp}_O_I=\${R_BUF_${comp}_O}/INS
108	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
109	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
110	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
111	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
112	fi
113
114	# Read UserChoices section of component card
115	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
116	IGCM_card_DefineArrayFromSection ${card} UserChoices
117	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
118
119	# If section is not empty we define corresponding variables
120	if [ X${first_option} != X"Error:" ] ; then
121	if [ X${card_UserChoices[0]} != X ] ; then
122	unset card_UserChoices
123	fi
124	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
125	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
126	for option in ${card_UserChoices[*]} ; do
127	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
128	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
129	done
130	fi
131
132	# Read and Build Output File stuff
133	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
134	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
135	ListFilesName=${compname}_OutputFiles_List
136	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
137	#
138	if [ X${FileName0} != X${NULL_STR} ] ; then
139	#
140	#IGCM_debug_Print 1 "Component : ${compname}"
141	#
142	# INITIALISATION
143	#
144	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
145	#
146	i=2
147	#
148	until [ $i -ge $NbFiles ]; do
149	#
150	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
151	#
152	if [ X${flag_post} != XNONE ] ; then
153	#
154	# First of all
155	#
156	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
157	# This section is mandatory
158	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
159	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
160	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
161	IGCM_debug_Verif_Exit
162	fi
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_PrepareXiosFiles
259	{
260	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
261
262	typeset file
263	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
264
265	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
266	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
267	fi
268	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
269	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
270	fi
271
272	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
273	}
274
275	#=======================================================================
276	function IGCM_comp_GetInputInitialStateFiles
277	{
278	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
279
280	# Debug Print :
281	echo
282	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
283	echo
284
285	# Only the first time step need InitialStateFiles
286	# otherwise it's BoundaryConditions
287	if ( ${FirstInitialize} ) ; then
288	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
289	typeset file_in_ file_in file_out_ file_out do_init
290	for comp in ${config_ListOfComponents[*]} ; do
291	# Initialize
292	do_init="y"
293	# Do we need to bring initial state file for this component
294	if [ "${config_Restarts_OverRule}" = "y" ] ; then
295	eval do_init="n"
296	else
297	# Read component Restarts parameters
298	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
299	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
300	if [ "${do_start}" = "y" ] ; then
301	do_init="n"
302	else
303	do_init="y"
304	fi
305	fi
306
307	if [ "${do_init}" = "y" ] ; then
308	# Define component
309	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
310	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
311
312	# Debug Print :
313	IGCM_debug_Print 3 "Initialisation files ${compname}"
314
315	card=${SUBMIT_DIR}/COMP/${compname}.card
316
317	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
318	ListFilesName=${compname}_InitialStateFiles_List
319
320	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
321	if [ X${FileName0} != X${NULL_STR} ] ; then
322	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
323	(( i=0 ))
324	until [ $i -ge $NbFiles ]; do
325	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
326	eval file_in=${file_in_}
327	(( i_ = i+1 ))
328	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
329	eval file_out=${file_out_}
330
331	IGCM_sys_IsFileArchived ${file_in}
332	if [ $? = 0 ] ; then
333	IGCM_sys_Get ${file_in} ${file_out}
334	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
335	else
336	IGCM_sys_Cp ${file_in} ${file_out}
337	fi
338	(( i=i+2 ))
339	done
340	fi
341	fi
342	done
343	fi
344	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
345	}
346
347	#=======================================================================
348	# Definition of Smooth modulo function
349	# usage :
350	# IGCM_SmoothModulo StringModulo value
351	#
352	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
353	# [min]:[modulo:][max]
354	# where :
355	# [] value are optionnals;
356	# empty min equal 1
357	# empty max equal infinity
358	# modulo not given or empty equal 1
359	# empty string or just ':' equal always.
360	#
361	# value : the value to test with the definition
362	#
363	# return : true(1)/false(0)
364	function IGCM_SmoothModulo
365	{
366	IGCM_debug_PushStack "IGCM_SmoothModulo"
367	typeset defVector ModValue
368
369	eval set +A defVector -- $( echo "${1}" \| \
370	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
371
372	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
373	arr[1]=${defVector[0]}
374	arr[2]=${defVector[2]}
375
376	# Test limits :
377	# ${defVector[0]} <= ${2} <= ${defVector[2]}
378	# or ${defVector[2]} == -1
379	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
380	# Test modulo
381	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
382	if [ ${ModValue} -eq 0 ] ; then
383	arr[3]=true
384	echo ${arr[@]}
385	IGCM_debug_PopStack "IGCM_SmoothModulo"
386	return 1
387	else
388	arr[3]=false
389	echo ${arr[@]}
390	IGCM_debug_PopStack "IGCM_SmoothModulo"
391	return 0
392	fi
393	else
394	arr[3]=false
395	echo ${arr[@]}
396	IGCM_debug_PopStack "IGCM_SmoothModulo"
397	return 0
398	fi
399	}
400
401	#=======================================================================
402	function IGCM_comp_GetInputSmoothFiles
403	{
404	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
405
406	# Debug Print :
407	echo
408	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
409	echo
410
411	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
412	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
413
414	for comp in ${config_ListOfComponents[*]} ; do
415	# Define component
416	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
417	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
418
419	# Debug Print :
420	IGCM_debug_Print 3 "Smooth files ${compname}"
421
422	card=${SUBMIT_DIR}/COMP/${compname}.card
423
424	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
425	ListFilesName=${compname}_SmoothFiles_List
426	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
427
428	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
429	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
430
431	(( i=0 ))
432	until [ $i -ge $NbFiles ]; do
433	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
434	eval file_in=${file_in_}
435	(( i_ = i+1 ))
436	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
437	eval file_out=${file_out_}
438
439	# define CumulPeriod definition for this file
440	(( i__ = i+2 ))
441	eval SmoothDef=\${${ListFilesName}[$i__]}
442	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
443	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
444	j=1
445	for val in ${aux} ; do
446	[ ${j} -eq 1 ] && SmoothMin=${val}
447	[ ${j} -eq 2 ] && SmoothMax=${val}
448	[ ${j} -eq 3 ] && ret=${val}
449	(( j=j+1 ))
450	done
451	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
452	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
453
454	IGCM_sys_IsFileArchived ${file_in}
455	if [ $? = 0 ] ; then
456	IGCM_sys_Get ${file_in} ${file_out}
457	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
458	else
459	IGCM_sys_Cp ${file_in} ${file_out}
460	fi
461	fi
462	(( i=i+3 ))
463	done
464	fi
465	done
466
467	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
468	}
469
470	#=======================================================================
471	function IGCM_comp_GetInputBoundaryFiles
472	{
473	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
474
475	# Debug Print :
476	echo
477	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
478	echo
479
480	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
481	typeset file_in_ file_in file_out_ file_out
482
483	if [ ${Period} = 1 ]; then
484	ListFixBoundary=" "
485	fi
486
487	for comp in ${config_ListOfComponents[*]} ; do
488
489	# Define component
490	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
491	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
492
493	# Debug Print :
494	IGCM_debug_Print 3 "Boundary files ${compname}"
495
496	card=${SUBMIT_DIR}/COMP/${compname}.card
497
498	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
499	ListFilesName=${compname}_BoundaryFiles_List
500	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
501
502	if [ X${FileName0} != X${NULL_STR} ] ; then
503	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
504
505	(( i=0 ))
506	until [ $i -ge $NbFiles ]; do
507	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
508	eval file_in=${file_in_}
509	(( i_ = i+1 ))
510	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
511	eval file_out=${file_out_}
512
513	IGCM_sys_IsFileArchived ${file_in}
514	if [ $? = 0 ] ; then
515	IGCM_sys_Get ${file_in} ${file_out}
516	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
517	else
518	IGCM_sys_Cp ${file_in} ${file_out}
519	fi
520
521	(( i=i+2 ))
522	done
523	fi
524
525	# Get non deleted files
526	if [ ${Period} = 1 ]; then
527
528	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
529	ListFilesName=${compname}_BoundaryFiles_ListNonDel
530	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
531
532	if [ X${FileName0} != X${NULL_STR} ] ; then
533	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
534
535	(( i=0 ))
536	until [ $i -ge $NbFiles ]; do
537	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
538	eval file_in=${file_in_}
539	(( i_ = i+1 ))
540	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
541	eval file_out=${file_out_}
542
543	IGCM_sys_IsFileArchived ${file_in}
544	if [ $? = 0 ] ; then
545	IGCM_sys_Get ${file_in} ${file_out}
546	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
547	else
548	IGCM_sys_Cp ${file_in} ${file_out}
549	fi
550
551	if [ X${file_out} != X. ] ; then
552	ListFixBoundary=${ListFixBoundary}" "${file_out}
553	else
554	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
555	fi
556
557	(( i=i+2 ))
558	done
559	fi
560	fi
561	done
562
563	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
564	}
565
566	#=======================================================================
567	function IGCM_comp_DelFixeBoundaryFiles
568	{
569	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
570
571	# Debug Print :
572	echo
573	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
574	echo
575
576	ls -l ${ListFixBoundary}
577	rm -f ${ListFixBoundary}
578
579	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
580	}
581
582	#=======================================================================
583	function IGCM_comp_GetInputParametersFiles
584	{
585	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
586
587	# Debug Print :
588	echo
589	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
590	echo
591
592	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
593	for comp in ${config_ListOfComponents[*]} ; do
594	# Define component
595	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
596	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
597
598	# Initialize array hosting file_def and field_def files to check and/or modify
599	unset FieldDef
600	unset FileDef
601
602	# Debug Print :
603	IGCM_debug_Print 3 "Parameters ${compname}"
604
605	card=${SUBMIT_DIR}/COMP/${compname}.card
606
607	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
608	ListFilesName=${compname}_ParametersFiles_List
609	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
610
611	if [ X${FileName0} != X${NULL_STR} ] ; then
612	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
613
614	(( i=0 ))
615	until [ $i -ge $NbFiles ]; do
616	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
617	eval file_in=${file_in_}
618	(( i_ = i+1 ))
619	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
620	eval file_out=${file_out_}
621
622	IGCM_sys_Cp ${file_in} ${file_out}
623	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
624	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
625
626	(( i=i+2 ))
627	done
628	fi
629
630	if [ ${#FileDef[@]} -ne 0 ] ; then
631	# Check XMLs coherency now
632	IGCM_debug_Print 1 "${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}"
633	${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}
634	if [ $? = 0 ] ; then
635	IGCM_debug_Print 1 "${compname} XIOS XMLs are consistent"
636	else
637	IGCM_debug_Print 1 "${compname} XIOS XMLs ARE NOT consistent. Try to fix it:"
638	IGCM_debug_Print 3 "${libIGCM}/libIGCM_post/xios_parser.py -v modify --field ${FieldDef[]} --file ${FileDef[]}"
639	${libIGCM}/libIGCM_post/xios_parser.py -vv modify --field ${FieldDef[]} --file ${FileDef[]}
640	[ $? != 0 ] && IGCM_debug_Exit "Failed to fix XIOS xml files for ${compname}"
641	fi
642	fi
643	done
644
645	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
646	}
647
648	#=======================================================================
649	function IGCM_comp_GetInputRestartFiles
650	{
651	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
652
653	# Debug Print :
654	echo
655	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
656	echo
657
658	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
659	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
660	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
661	typeset file_in file_out file_in_ file_out_ file_in_Name
662	typeset -Z4 j4
663	#BASH declare j4
664
665	IsMatching=""
666
667	for comp in ${config_ListOfComponents[*]} ; do
668	# Define component
669	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
670	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
671	#
672	card=${SUBMIT_DIR}/COMP/${compname}.card
673	#
674	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
675	ListFilesName=${compname}_RestartFiles_List
676	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
677
678	# Debug Print :
679	IGCM_debug_Print 3 "restart ${compname}"
680
681	if ( ${FirstInitialize} ) ; then
682
683	if [ "${config_Restarts_OverRule}" = "y" ] ; then
684	eval config_${comp}_Restart="y"
685	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
686	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
687	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
688	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
689	eval CompOldName=${comp}
690	else
691	# Read component Restarts parameters
692	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
693	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
694
695	if [ "${do_start}" = "y" ] ; then
696	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
697	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
698	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
699	else
700	eval config_${comp}_RestartDate=-1
701	eval config_${comp}_RestartJobName=${NULL_STR}
702	eval config_${comp}_RestartPath=${NULL_STR}
703	fi
704
705	eval CompOldName=\${config_${comp}_OldName}
706	if [ X${CompOldName} = X ] ; then
707	eval CompOldName=${comp}
708	fi
709
710	# Reinitialize IsMatching to allow searching for a different tar file for each component.
711	IsMatching=""
712	TarFileFound=""
713	fi
714
715	if [ "${do_start}" = "y" ] ; then
716
717	# Restore Restarts files
718	#-----------------------
719	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
720	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
721
722	(( i=1 ))
723	until [ $i -gt $NbFiles ]; do
724	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
725	eval file_in=${file_in_}
726	(( i_ = i+1 ))
727	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
728	eval file_out=${file_out_}
729
730	eval Date_tmp=\${config_${comp}_RestartDate}
731	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
732	# will be re-use
733	eval RestartPath=\${config_${comp}_RestartPath}
734	eval RestartJobName=\${config_${comp}_RestartJobName}
735	#
736	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
737	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
738
739	extension_in=$( echo ${file_in_Name##*.} )
740	extension_out=$( echo ${file_out##*.} )
741
742	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
743	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
744
745	Path_OUT=${Path_r}/${generic_restart_file_name_in}
746
747	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
748	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
749	Buffered=true
750	Archived=false
751	Tared=false
752	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
753	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
754	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
755	Buffered=false
756	Archived=true
757	Tared=false
758	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
759	else
760	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
761	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
762	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
763	Buffered=false
764	Archived=false
765	Tared=true
766	# Look after the tar file we want if we did not found it already
767	if [ X${IsMatching} = X ] ; then
768	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
769	if [ $? ] ; then
770	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
771	IsMatching=$( echo ${PotentialTarFile##*/} \| \
772	sed "s:_restart::" \| \
773	sed "s:^${RestartJobName}_::" \| \
774	sed "s:\.tar$::" \| \
775	gawk -F_ -v restartdate=${Date_r} \
776	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
777	if [ ! X${IsMatching} = X ] ; then
778	TarFileFound=${PotentialTarFile}
779	break
780	fi
781	done
782	fi
783	# Stop here if nothing has been found
784	if [ X${TarFileFound} = X ] ; then
785	IGCM_debug_Print 3 "Restart files were not found!"
786	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
787	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
788	IGCM_debug_Exit "Please double check restart settings in config.card"
789	IGCM_debug_Verif_Exit
790	fi
791	fi
792	IGCM_sys_PrepareTaredRestart ${TarFileFound}
793	TarFileLocation=$( basename ${TarFileFound} )
794	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
795	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
796	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
797	fi
798
799	if [ ${nb_restart_file} -gt 1 ] ; then
800	j=0 # BASH LINE NOT NEEDED
801	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
802	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
803	j4=${j} # BASH LINE NOT NEEDED
804	if [ X${Buffered} = Xtrue ] ; then
805	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
806	elif [ X${Archived} = Xtrue ] ; then
807	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
808	elif [ X${Tared} = Xtrue ] ; then
809	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
810	fi
811	(( j=j+1 )) #BASH LINE NOT NEEDED
812	done
813
814	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
815	if [ X${OCE_PROC_MPI} != X ] ; then
816	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
817	IGCM_sys_rebuild ${generic_restart_file_name_out}.${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
818	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
819	fi
820	fi
821	else
822	if [ X${Buffered} = Xtrue ] ; then
823	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
824	elif [ X${Archived} = Xtrue ] ; then
825	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
826	elif [ X${Tared} = Xtrue ] ; then
827	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
828	fi
829	fi
830	(( i=i+3 ))
831	done
832	else
833	if [ X${FileName0} != XNONE ] ; then
834	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
835	else
836	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
837	fi
838	fi
839	fi
840	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
841	# if not FirstInitialize and first loop of this job
842
843	# Restore Restarts files
844	#-----------------------
845	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
846	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
847
848	(( i=1 ))
849	until [ $i -gt $NbFiles ]; do
850	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
851	eval file_in=${file_in_}
852	(( i_ = i+1 ))
853	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
854	eval file_out=${file_out_}
855
856	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
857
858	extension_in=$( echo ${file_in_Name##*.} )
859	extension_out=$( echo ${file_out##*.} )
860
861	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
862	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
863
864	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
865	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
866
867	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
868	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
869	Buffered=true
870	Archived=false
871	Tared=false
872	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
873	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
874	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
875	Buffered=false
876	Archived=true
877	Tared=false
878	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
879	else
880	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
881	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
882	Buffered=false
883	Archived=false
884	Tared=true
885	# Look after the tar file we want if we did not found it already
886	if [ X${IsMatching} = X ] ; then
887	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
888	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
889	if [ ! X${IsMatching} = X ] ; then
890	TarFileFound=${PotentialTarFile}
891	break
892	fi
893	done
894	fi
895	# Stop here if nothing has been found
896	if [ X${TarFileFound} = X ] ; then
897	IGCM_debug_Print 3 "Restart files were not found!"
898	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
899	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
900	IGCM_debug_Exit "Please double check restart settings in config.card"
901	IGCM_debug_Verif_Exit
902	fi
903	IGCM_sys_PrepareTaredRestart ${TarFileFound}
904	TarFileLocation=$( basename ${TarFileFound} )
905	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
906	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
907	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
908	fi
909
910	if [ ${nb_restart_file} -gt 1 ] ; then
911	j=0 # BASH LINE NOT NEEDED
912	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
913	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
914	j4=${j} # BASH LINE NOT NEEDED
915	if [ X${Buffered} = Xtrue ] ; then
916	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
917	elif [ X${Archived} = Xtrue ] ; then
918	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
919	elif [ X${Tared} = Xtrue ] ; then
920	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
921	fi
922	(( j=j+1 )) # BASH LINE NOT NEEDED
923	done
924	else
925	if [ X${Buffered} = Xtrue ] ; then
926	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
927	elif [ X${Archived} = Xtrue ] ; then
928	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
929	elif [ X${Tared} = Xtrue ] ; then
930	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
931	fi
932	fi
933	(( i=i+3 ))
934	done
935	else
936	if [ X${FileName0} != XNONE ] ; then
937	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
938	else
939	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
940	fi
941	fi
942	fi
943	done
944
945	NbFiles=$( ls * 2> /dev/null \| wc -l )
946	if [ ${NbFiles} -gt 0 ] ; then
947	IGCM_sys_Chmod u+rw *
948	fi
949
950	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
951	}
952
953	#=======================================================================
954	function IGCM_comp_PeriodStart
955	{
956	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
957
958	# Debug Print :
959	echo
960	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
961	echo
962
963	typeset ExeNameIn ExeNameOut
964	typeset comp compname comptagname
965	for comp in ${config_ListOfComponents[*]} ; do
966	# Define component
967	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
968	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
969
970	# Copy executable for this component
971	eval ExeNameIn=\${config_Executable_${comp}[0]}
972	eval ExeNameOut=\${config_Executable_${comp}[1]}
973
974	# Debug Print
975	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
976	# UPDATE component
977	${comp}_PeriodStart 2> /dev/null
978
979	done
980
981	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
982	}
983
984
985
986	#=======================================================================
987	function IGCM_comp_modifyFile
988	{
989	#
990	# syntax: IGCM_comp_modifyFile filein key [value]
991	#
992	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
993	#
994	# This function is used to replace a pattern in a file for a specific variable.
995	#
996	# Arguments:
997	# - filein : the file in run directory in which the variable should be set
998	# - key : the variable to modify
999	# - value : the value to set the key equal to
1000	#
1001	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1002
1003	typeset filein key value pattern
1004
1005	# Set local variables and test the arguments
1006	if [ $# = 3 ] ; then
1007	# Normal case with 3 arguments
1008	filein=$1 ; key=$2 ; value=$3
1009	else
1010	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1011	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1012	return
1013	fi
1014	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1015
1016	# Test if the file exist
1017	if [ ! -f ${filein} ] ; then
1018	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1019	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1020	return
1021	fi
1022
1023	# Read the line with key in the file without the comments
1024	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1025
1026	# Verify the existance of the pattern
1027	if [ X"${pattern}" = X ] ; then
1028	# Variable key is not set in filein, stop.
1029	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1030	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1031	return
1032	fi
1033
1034	# Now change key in filein
1035	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1036	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1037	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1038	\mv ${filein}.tmp ${filein}
1039
1040	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1041	}
1042
1043	#=======================================================================
1044	function IGCM_comp_modifyDefFile
1045	{
1046	#
1047	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1048	#
1049	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1050	#
1051	# This function is used to modify a parameter file for a specific variable.
1052	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1053	# This function can be used in the comp.driver files for the components.
1054	#
1055	# Arguments:
1056	# - type : first argument must be blocker, nonblocker or force
1057	# For "blocker" case, the variable must be attributed the keyworld AUTO
1058	# otherwise this function will exit.
1059	# For "nonblocker" case, the user can remove or modify the variable. For
1060	# this case, as long as AUTO is not set, no modification will be done.
1061	# For "force" case, the variable will be modified even if it is not set to AUTO
1062	# - filein : the file in run directory of .def type in which the variable should be set
1063	# - key : the variable to modify
1064	# - value : the value to set the key equal to, optional. If value is not set or if
1065	# value=DEFAULT, then a default value must be given in filein using syntax :
1066	# key= AUTO : DEFAULT=def_value
1067	#
1068	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1069
1070	typeset type filein key value
1071	typeset filelist nb_occ modify
1072
1073	# Set local variables and test the arguments
1074	if [ $# = 4 ] ; then
1075	# Normal case with 4 arguments
1076	type=$1 ; filein=$2 ; key=$3 ; value=$4
1077	elif [ $# = 3 ] ; then
1078	# Normal case with 3 arguments
1079	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1080	else
1081	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1082	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1083	return
1084	fi
1085	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1086
1087	# Test if first argument is correct
1088	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1089	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1090	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1091	return
1092	fi
1093
1094	# Test if the file exist.
1095	# Exit with error if the file does not exist for the case blocker or force.
1096	# Only return for the case nonblocker.
1097	if [ ! -f ${filein} ] ; then
1098	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1099	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1100	else
1101	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1102	fi
1103	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1104	return
1105	fi
1106
1107	# Define list of files to test using all files with suffix .def (except used*.def)
1108	filelist=$( ls *def \| grep -v used )
1109
1110	# Count number of occurances for the key in all files
1111	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1112
1113	# Test if key is set several times
1114	if [ ${nb_occ} -gt 1 ] ; then
1115	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1116	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1117	return
1118	fi
1119
1120	# Treatement according to different cases
1121	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1122	# Stop if the key is never set and the function is blocker
1123	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1124	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1125	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1126	# The key is not set but it is a nonblocker call so nothing is done.
1127	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1128	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1129	modify=no
1130	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1131	# Variable key is not set in filein, stop.
1132	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1133	fi
1134
1135	# Check if AUTO is set in the filein on the same line as the key variable
1136	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1137	# Modification will be done for all cases
1138	modify=yes
1139	else
1140	# The variable was not set to AUTO
1141	if [ ${type} = blocker ] ; then
1142	# Exit because this is a blocker call
1143	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1144	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1145	return
1146	elif [ ${type} = nonblocker ] ; then
1147	# Do nothing. Suppose that the user did set the variable correct
1148	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1149	modify=no
1150	elif [ ${type} = force ] ; then
1151	# Force modification
1152	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1153	modify=yes
1154	fi
1155	fi
1156
1157	# Do the modifcation now
1158	if [ ${modify} = yes ] ; then
1159
1160	# For option DEFAULT, read default value from file.
1161	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1162	# Case to set DEFAULT value
1163	# Read default value from filein
1164	value=$( grep ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1165
1166	if [ X"${value}" = X ] ; then
1167	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1168	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1169	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1170	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1171	return
1172	fi
1173	fi
1174
1175	# Now change key in filein
1176	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1177	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1178	\mv ${filein}.tmp ${filein}
1179	fi
1180	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1181	}
1182
1183	#=======================================================================
1184	function IGCM_comp_modifyNamelist
1185	{
1186	#
1187	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1188	#
1189	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1190	#
1191	# This function is used to modify a parameter file for a specific variable.
1192	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1193	# This function can be used in the comp.driver files for the components.
1194	#
1195	# Arguments:
1196	# - type : first argument must be blocker, nonblocker or force
1197	# For "blocker" case, the variable must be attributed the keyworld AUTO
1198	# otherwise this function will exit.
1199	# For "nonblocker" case, the user can remove or modify the variable. For
1200	# this case, as long as AUTO is not set, no modification will be done.
1201	# For "force" case, the variable will be modified even if it is not set to AUTO
1202	# - filein : the file in run directory of .def type in which the variable should be set
1203	# - key : the variable to modify
1204	# - value : the value to set the key equal to, optional. If value is not set or if
1205	# value=DEFAULT, then a default value must be given in filein using syntax :
1206	# key= AUTO : DEFAULT=def_value
1207	#
1208	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1209
1210	typeset type filein key value pattern modify
1211
1212	# Set local variables and test the arguments
1213	if [ $# = 4 ] ; then
1214	# Normal case with 4 arguments
1215	type=$1 ; filein=$2 ; key=$3 ; value=$4
1216	elif [ $# = 3 ] ; then
1217	# Normal case with 3 arguments
1218	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1219	else
1220	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1221	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1222	return
1223	fi
1224	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1225
1226	# Test if first argument is correct
1227	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1228	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1229	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1230	return
1231	fi
1232
1233	# Test if the file exist.
1234	# Exit with error if the file does not exist for the case blocker or force.
1235	# Only return for the case nonblocker.
1236	if [ ! -f ${filein} ] ; then
1237	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1238	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1239	else
1240	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1241	fi
1242	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1243	return
1244	fi
1245
1246	# Read the line with key in the file without the comments
1247	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1248
1249	# Verify the existance of the pattern
1250	if [ X"$pattern" = X ] ; then
1251	# Variable key is not set in filein, stop.
1252	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1253	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1254	return
1255	fi
1256
1257	# Check if the variable is set to AUTO in the filein
1258	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1259	# Modification will be done for all cases
1260	modify=yes
1261	else
1262	# The variable was not set to AUTO
1263	if [ ${type} = blocker ] ; then
1264	# Exit because this is a blocker call
1265	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1266	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1267	return
1268	elif [ ${type} = nonblocker ] ; then
1269	# Do nothing. Suppose that the user did set the variable correct
1270	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1271	modify=no
1272	elif [ ${type} = force ] ; then
1273	# Force modification
1274	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1275	modify=yes
1276	fi
1277	fi
1278
1279	# Do the modifcation now
1280	if [ ${modify} = yes ] ; then
1281
1282	# For option DEFAULT, read default value from file.
1283	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1284	# Case to set DEFAULT value
1285	# Read default value from filein
1286	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1287
1288	if [ X"${value}" = X ] ; then
1289	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1290	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1291	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1292	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1293	return
1294	fi
1295	fi
1296
1297	# Now change key in filein
1298	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1299	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1300	\mv ${filein}.tmp ${filein}
1301	fi
1302	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1303	}
1304
1305	#=======================================================================
1306	function IGCM_comp_modifyXmlFile
1307	{
1308	#
1309	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1310	#
1311	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1312	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1313	#
1314	# This function is used to modify the value for a specific attribute and variable id.
1315	# The file must be a valid xml file.
1316	# This function can be used in the comp.driver files for the components.
1317	#
1318	# Arguments:
1319	# - type : first argument must be blocker, nonblocker or force.
1320	# For "blocker" case, the variable must be attributed the keyworld AUTO
1321	# otherwise this function will exit.
1322	# For "nonblocker" case, the user can remove or modify the variable. For
1323	# this case, as long as AUTO is not set, no modification will be done.
1324	# For "force" case, the variable will be modified even if it is not set to AUTO
1325	# - filein : the file in run directory of .xml type in which the variable should be set
1326	# - keyid : the variable to modify
1327	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1328	# - value : the value to set in the filein
1329	#
1330	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1331
1332	typeset type filein keyid keyattrib value modify
1333
1334	# Set local variables and test the arguments
1335	if [ $# = 5 ] ; then
1336	# Normal case with 4 arguments
1337	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1338	else
1339	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1340	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1341	return
1342	fi
1343	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1344
1345	# Test if first argument is correct
1346	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1347	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1348	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1349	return
1350	fi
1351
1352	# Test if the file exist.
1353	# Exit with error if the file does not exist for the case blocker or force.
1354	# Only return for the case nonblocker.
1355	if [ ! -f ${filein} ] ; then
1356	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1357	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1358	else
1359	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1360	fi
1361	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1362	return
1363	fi
1364
1365	# Test if keyid is set in filein, otherwise exit
1366	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1367	# Variable key is not set in filein, stop.
1368	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1369	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1370	return
1371	fi
1372
1373	# Check if AUTO is set on the same line as keyid and keyattrib
1374	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1375	# Modifification will be done
1376	modify=yes
1377	else
1378	if [ ${type} = blocker ] ; then
1379	# Exit, the variable must be set to AUTO
1380	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1381	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1382	return
1383	elif [ ${type} = nonblocker ] ; then
1384	# Nothing will be done
1385	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1386	modify=no
1387	elif [ ${type} = force ] ; then
1388	# Force modification
1389	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1390	modify=yes
1391	fi
1392	fi
1393
1394	# Do the modifcation now
1395	if [ ${modify} = yes ] ; then
1396	if [ ${keyattrib} = NONE ] ; then
1397	# Case to modify the variable itself
1398	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1399	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1400	else
1401	# Check if keyattrib is set on the same line as keyid
1402	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1403	# Case to modify the attribute value
1404	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1405	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1406	else
1407	# Case to add the attribute and its value
1408	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1409	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1410	fi
1411	fi
1412	\mv ${filein}.tmp ${filein}
1413	fi
1414	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1415	}
1416
1417	#=======================================================================
1418	function IGCM_comp_Update
1419	{
1420	IGCM_debug_PushStack "IGCM_comp_Update"
1421
1422	# Debug Print :
1423	echo
1424	IGCM_debug_Print 1 "IGCM_comp_Update"
1425	echo
1426
1427	typeset ExeNameIn ExeNameOut
1428	typeset comp compname comptagname
1429	for comp in ${config_ListOfComponents[*]} ; do
1430	# Define component
1431	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1432	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1433
1434	# Copy executable for this component
1435	eval ExeNameIn=\${config_Executable_${comp}[0]}
1436	eval ExeNameOut=\${config_Executable_${comp}[1]}
1437
1438	# If missing executable and DRYRUN is set to 0 or 1 then stop!
1439	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1440	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
1441	fi
1442
1443	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1444	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1445	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1446	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1447	fi
1448	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1449	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1450	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1451	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1452	fi
1453	fi
1454
1455	# Debug Print
1456	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1457	# UPDATE component
1458	${comp}_Update
1459
1460	done
1461
1462	IGCM_debug_PopStack "IGCM_comp_Update"
1463	}
1464
1465	#=======================================================================
1466	function IGCM_comp_Finalize
1467	{
1468	IGCM_debug_PushStack "IGCM_comp_Finalize"
1469
1470	# Debug Print :
1471	echo
1472	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1473	echo
1474
1475	typeset ListTextName TextName0
1476	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1477	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1478	typeset -Z4 j4 #BASH declare j4
1479	typeset list_file nlist_file
1480	typeset compactoutputs
1481
1482	# Initialize array hosting list of rebuilded files to copy
1483	unset rebuildedActionsList
1484
1485	# Text compacting options
1486	compactoutputs=false
1487	if [ X${JobType} != XRUN ] ; then
1488	compactoutputs=true
1489	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1490	compactoutputs=true
1491	fi
1492
1493	# Prepare headers for the shell dedicated to offline rebuild
1494	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1495	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1496	if [ ${DRYRUN} -le 1 ] ; then
1497	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1498	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1499	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1500	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1501	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1502	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1503	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1504	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1505	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1506	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1507	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1508	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1509	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1510	fi
1511	fi
1512
1513	for comp in ${config_ListOfComponents[*]} ; do
1514	# Define component
1515	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1516	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1517
1518	# Debug Print
1519	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1520	# FINALIZE component
1521	${comp}_Finalize
1522
1523	card=${SUBMIT_DIR}/COMP/${compname}.card
1524
1525	# Save Output Text files of models
1526	#---------------------------------
1527	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1528	IGCM_card_DefineArrayFromOption ${card} OutputText List
1529	ListTextName=${compname}_OutputText_List
1530
1531	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1532	if [ X${TextName0} != X${NULL_STR} ] ; then
1533	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1534
1535	(( i=0 ))
1536	until [ $i -eq $NbFiles ]; do
1537	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1538	eval file_out=${PREFIX}_${file_in}
1539
1540	(( i=i+1 ))
1541
1542	unset list_file
1543	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1544	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1545	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 )
1546	nlist_file=${#list_file[@]}
1547	if [ ${nlist_file} -gt 1 ] ; then
1548	if ( ${compactoutputs} ) ; then
1549	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1550	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1551	echo ${list_file[*]} > ${file_out}
1552	echo "" >> ${file_out}
1553
1554	(( i_ = 0 ))
1555	for file in ${list_file[@]} ; do
1556	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1557	echo "\| " ${i_} " " ${file} >> ${file_out}
1558	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1559	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1560	echo "" >> ${file_out}
1561	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1562	(( i_ = i_ + 1 ))
1563	done
1564	if ( ${ExecutionFail} ) ; then
1565	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1566	fi
1567
1568	if [ X${Pack} = Xtrue ] ; then
1569	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1570	else
1571	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1572	fi
1573
1574	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1575	else
1576	for file in ${list_file[@]} ; do
1577	if ( ${ExecutionFail} ) ; then
1578	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1579	fi
1580
1581	if [ X${Pack} = Xtrue ] ; then
1582	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1583	else
1584	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1585	fi
1586
1587	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1588	done
1589	fi
1590	else
1591	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1592	eval IGCM_sys_Mv ${file_in}* ${file_in}
1593	fi
1594
1595	if ( ${ExecutionFail} ) ; then
1596	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1597	fi
1598
1599	if [ X${Pack} = Xtrue ] ; then
1600	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1601	else
1602	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1603	fi
1604	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1605	fi
1606	done
1607	fi
1608
1609	# Save Restarts files
1610	#--------------------
1611	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1612	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1613	ListFilesName=${compname}_RestartFiles_List
1614	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1615
1616	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1617	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1618
1619	(( i=0 ))
1620	until [ $i -ge $NbFiles ]; do
1621	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1622	eval file_in=${file_in_}
1623
1624	(( i_ = i+1 ))
1625	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1626	eval file_out=${file_out_}
1627
1628	(( i_ = i+2 ))
1629	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1630	eval file_outin=${file_outin_}
1631
1632	generic_restart_file_name_in=$( basename ${file_in} .nc )
1633	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1634	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1635
1636	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1637	if [ ${nb_restart_file} -gt 1 ] ; then
1638	j=0 # BASH LINE NOT NEEDED
1639	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1640	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1641	j4=${j} # BASH LINE NOT NEEDED
1642	if [ X${Pack} = Xtrue ] ; then
1643	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1644	else
1645	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1646	fi
1647	if [ ! ${file_in} = ${file_outin} ] ; then
1648	if ( ${ExitFlag} ) ; then
1649	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1650	else
1651	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1652	fi
1653	fi
1654	(( j=j+1 )) # BASH LINE NOT NEEDED
1655	done
1656	else
1657	if [ X${Pack} = Xtrue ] ; then
1658	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1659	else
1660	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1661	fi
1662	if [ ! ${file_in} = ${file_outin} ] ; then
1663	if ( ${ExitFlag} ) ; then
1664	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1665	else
1666	IGCM_sys_Mv ${file_in} ${file_outin}
1667	fi
1668	fi
1669	fi
1670
1671	(( i=i+3 ))
1672	done
1673	else
1674	if [ X${FileName0} != XNONE ] ; then
1675	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1676	else
1677	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1678	fi
1679	fi
1680
1681	# Save Output files
1682	#------------------
1683	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1684	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1685	ListFilesName=${compname}_OutputFiles_List
1686	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1687
1688	if [ X${FileName0} != X${NULL_STR} ] ; then
1689	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1690
1691	(( i=0 ))
1692	until [ $i -ge $NbFiles ]; do
1693	SaveOnArchive=true
1694	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1695	eval file_in=${file_in_}
1696	(( i_ = i+1 ))
1697	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1698	eval file_out=${file_out_}
1699	#
1700	# Override file_out path remplacing R_SAVE by R_BUFR
1701	#
1702	if [ X${Pack} = Xtrue ] ; then
1703	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1704	fi
1705	#
1706	# Not necessarily the best option. /!\ Potential side effects /!\
1707	#
1708	(( i_ = i+2 ))
1709	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1710	#
1711	generic_file_name=$( basename ${file_in} .nc )
1712	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1713	#
1714	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1715	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1716	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1717	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1718	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1719	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1720	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1721	IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc
1722	else
1723	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1724	IGCM_sys_Mv ${generic_file_name}_[0-9]*.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1725
1726	# Prepare the shell dedicated to offline rebuild
1727	if [ $DRYRUN -le 1 ]; then
1728	if [ ${file_in} = histstn.nc ] ; then
1729	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1730	else
1731	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1732	fi
1733	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1734	fi
1735	#
1736	# Load Patch we need to apply and apply
1737	if [ $DRYRUN -le 1 ]; then
1738	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1739	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1740	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1741	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1742	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1743	done
1744	fi
1745	fi
1746	#
1747	if [ $DRYRUN -le 1 ]; then
1748	if [ X${Pack} = Xtrue ] ; then
1749	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1750	else
1751	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1752	fi
1753	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1754	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1755	fi
1756	SaveOnArchive=false
1757	fi
1758	fi
1759	#
1760	if [ ${SaveOnArchive} = true ] ; then
1761	#
1762	# Rebuild has been done online or it was not needed
1763	#
1764	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1765	#
1766	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1767	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1768	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1769	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1770	#
1771	if [ $DRYRUN -le 1 ]; then
1772	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1773	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1774	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1775	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1776	done
1777	#
1778	if [ X${Pack} = Xtrue ] ; then
1779	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1780	else
1781	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1782	fi
1783	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1784	#
1785	fi
1786	else
1787	#
1788	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1789	#
1790	if [ X${Pack} = Xtrue ] ; then
1791	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1792	else
1793	IGCM_sys_Put_Out ${file_in} ${file_out}
1794	fi
1795	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1796	if [ ${nb_rebuild_file} -gt 1 ] ; then
1797	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1798	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1799	done
1800	fi
1801	fi
1802	fi
1803	(( i=i+3 ))
1804	done
1805	fi
1806	echo
1807	done
1808	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1809	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1810	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1811	i=0
1812	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1813	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1814	(( i=i+1 ))
1815	done
1816	fi
1817	IGCM_debug_PopStack "IGCM_comp_Finalize"
1818	}

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