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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1411

Last change on this file since 1411 was 1411, checked in by sdipsl, 7 years ago
Bypass cases where compiler version cant be identified. Usefull at IDRIS. Will need a fix shortly.
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: 75.8 KB

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1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
6	# $Revision:: $ Revision of last commit
7	# $Author:: $ Author of last commit
8	# $Date:: $ Date of last commit
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	#
12	#**************************************************************
13
14	#========================================================================
15	function IGCM_comp_Initialize
16	{
17	IGCM_debug_PushStack "IGCM_comp_Initialize"
18
19	# Debug Print :
20	echo
21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
22	echo
23
24	typeset comp compname comptagname 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" ] \|\| [ "${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 "${compname} XIOS XMLs ARE NOT consistent"
638	if [ X${config_Post_ParserXIOS} = XTRUE ] ; then
639	IGCM_debug_Print 1 "Try to fix it:"
640	IGCM_debug_Print 3 "${libIGCM}/libIGCM_post/xios_parser.py -v modify --field ${FieldDef[]} --file ${FileDef[]}"
641	${libIGCM}/libIGCM_post/xios_parser.py -vv modify --field ${FieldDef[]} --file ${FileDef[]}
642	[ $? != 0 ] && IGCM_debug_Exit "Failed to fix XIOS xml files for ${compname}"
643	fi
644	fi
645	fi
646	done
647
648	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
649	}
650
651	#=======================================================================
652	function IGCM_comp_GetInputRestartFiles
653	{
654	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
655
656	# Debug Print :
657	echo
658	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
659	echo
660
661	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
662	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
663	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
664	typeset file_in file_out file_in_ file_out_ file_in_Name
665	typeset -Z4 j4
666	#BASH declare j4
667
668	IsMatching=""
669
670	for comp in ${config_ListOfComponents[*]} ; do
671	# Define component
672	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
673	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
674	#
675	card=${SUBMIT_DIR}/COMP/${compname}.card
676	#
677	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
678	ListFilesName=${compname}_RestartFiles_List
679	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
680
681	# Debug Print :
682	IGCM_debug_Print 3 "restart ${compname}"
683
684	if ( ${FirstInitialize} ) ; then
685
686	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
687	eval config_${comp}_Restart="y"
688	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
689	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
690	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
691	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
692	eval CompOldName=${comp}
693	else
694	# Read component Restarts parameters
695	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
696	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
697
698	if [ "${do_start}" = "y" ] ; then
699	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
700	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
701	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
702	else
703	eval config_${comp}_RestartDate=-1
704	eval config_${comp}_RestartJobName=${NULL_STR}
705	eval config_${comp}_RestartPath=${NULL_STR}
706	fi
707
708	eval CompOldName=\${config_${comp}_OldName}
709	if [ X${CompOldName} = X ] ; then
710	eval CompOldName=${comp}
711	fi
712
713	# Reinitialize IsMatching to allow searching for a different tar file for each component.
714	IsMatching=""
715	TarFileFound=""
716	fi
717
718	if [ "${do_start}" = "y" ] ; then
719
720	# Restore Restarts files
721	#-----------------------
722	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
723	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
724
725	(( i=1 ))
726	until [ $i -gt $NbFiles ]; do
727	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
728	eval file_in=${file_in_}
729	(( i_ = i+1 ))
730	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
731	eval file_out=${file_out_}
732
733	eval Date_tmp=\${config_${comp}_RestartDate}
734	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
735	# will be re-use
736	eval RestartPath=\${config_${comp}_RestartPath}
737	eval RestartJobName=\${config_${comp}_RestartJobName}
738	#
739	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
740	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
741
742	extension_in=$( echo ${file_in_Name##*.} )
743	extension_out=$( echo ${file_out##*.} )
744
745	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
746	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
747
748	Path_OUT=${Path_r}/${generic_restart_file_name_in}
749
750	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
751	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
752	Buffered=true
753	Archived=false
754	Tared=false
755	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
756	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
757	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
758	Buffered=false
759	Archived=true
760	Tared=false
761	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
762	else
763	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
764	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
765	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
766	Buffered=false
767	Archived=false
768	Tared=true
769	# Look after the tar file we want if we did not found it already
770	if [ X${IsMatching} = X ] ; then
771	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
772	if [ $? ] ; then
773	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
774	IsMatching=$( echo ${PotentialTarFile##*/} \| \
775	sed "s:_restart::" \| \
776	sed "s:^${RestartJobName}_::" \| \
777	sed "s:\.tar$::" \| \
778	gawk -F_ -v restartdate=${Date_r} \
779	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
780	if [ ! X${IsMatching} = X ] ; then
781	TarFileFound=${PotentialTarFile}
782	break
783	fi
784	done
785	fi
786	# Stop here if nothing has been found
787	if [ X${TarFileFound} = X ] ; then
788	IGCM_debug_Print 3 "Restart files were not found!"
789	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
790	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
791	IGCM_debug_Exit "Please double check restart settings in config.card"
792	IGCM_debug_Verif_Exit
793	fi
794	fi
795	IGCM_sys_PrepareTaredRestart ${TarFileFound}
796	TarFileLocation=$( basename ${TarFileFound} )
797	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
798	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
799	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
800	fi
801
802	if [ ${nb_restart_file} -gt 1 ] ; then
803	j=0 # BASH LINE NOT NEEDED
804	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
805	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
806	j4=${j} # BASH LINE NOT NEEDED
807	if [ X${Buffered} = Xtrue ] ; then
808	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
809	elif [ X${Archived} = Xtrue ] ; then
810	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
811	elif [ X${Tared} = Xtrue ] ; then
812	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
813	fi
814	(( j=j+1 )) #BASH LINE NOT NEEDED
815	done
816
817	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
818	if [ X${OCE_PROC_MPI} != X ] ; then
819	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
820	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
821	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
822	fi
823	fi
824	else
825	if [ X${Buffered} = Xtrue ] ; then
826	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
827	elif [ X${Archived} = Xtrue ] ; then
828	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
829	elif [ X${Tared} = Xtrue ] ; then
830	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
831	fi
832	fi
833	(( i=i+3 ))
834	done
835	else
836	if [ X${FileName0} != XNONE ] ; then
837	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
838	else
839	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
840	fi
841	fi
842	fi
843	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
844	# if not FirstInitialize and first loop of this job
845
846	# Restore Restarts files
847	#-----------------------
848	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
849	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
850
851	(( i=1 ))
852	until [ $i -gt $NbFiles ]; do
853	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
854	eval file_in=${file_in_}
855	(( i_ = i+1 ))
856	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
857	eval file_out=${file_out_}
858
859	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
860
861	extension_in=$( echo ${file_in_Name##*.} )
862	extension_out=$( echo ${file_out##*.} )
863
864	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
865	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
866
867	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
868	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
869
870	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
871	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
872	Buffered=true
873	Archived=false
874	Tared=false
875	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
876	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
877	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
878	Buffered=false
879	Archived=true
880	Tared=false
881	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
882	else
883	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
884	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
885	Buffered=false
886	Archived=false
887	Tared=true
888	# Look after the tar file we want if we did not found it already
889	if [ X${IsMatching} = X ] ; then
890	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
891	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
892	if [ ! X${IsMatching} = X ] ; then
893	TarFileFound=${PotentialTarFile}
894	break
895	fi
896	done
897	fi
898	# Stop here if nothing has been found
899	if [ X${TarFileFound} = X ] ; then
900	IGCM_debug_Print 3 "Restart files were not found!"
901	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
902	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
903	IGCM_debug_Exit "Please double check restart settings in config.card"
904	IGCM_debug_Verif_Exit
905	fi
906	IGCM_sys_PrepareTaredRestart ${TarFileFound}
907	TarFileLocation=$( basename ${TarFileFound} )
908	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
909	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
910	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
911	fi
912
913	if [ ${nb_restart_file} -gt 1 ] ; then
914	j=0 # BASH LINE NOT NEEDED
915	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
916	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
917	j4=${j} # BASH LINE NOT NEEDED
918	if [ X${Buffered} = Xtrue ] ; then
919	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
920	elif [ X${Archived} = Xtrue ] ; then
921	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
922	elif [ X${Tared} = Xtrue ] ; then
923	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
924	fi
925	(( j=j+1 )) # BASH LINE NOT NEEDED
926	done
927	else
928	if [ X${Buffered} = Xtrue ] ; then
929	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
930	elif [ X${Archived} = Xtrue ] ; then
931	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
932	elif [ X${Tared} = Xtrue ] ; then
933	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
934	fi
935	fi
936	(( i=i+3 ))
937	done
938	else
939	if [ X${FileName0} != XNONE ] ; then
940	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
941	else
942	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
943	fi
944	fi
945	fi
946	done
947
948	NbFiles=$( ls * 2> /dev/null \| wc -l )
949	if [ ${NbFiles} -gt 0 ] ; then
950	IGCM_sys_Chmod u+rw *
951	fi
952
953	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
954	}
955
956	#=======================================================================
957	function IGCM_comp_GetInputBinaryFiles
958	{
959	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
960
961	# Debug Print :
962	echo
963	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
964	echo
965
966	# Clean up previous pass
967	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
968
969	typeset comp ExeNameIn ExeNameOut byPass
970	typeset compilerNmbr compilerUnit compilerFull
971	byPass=false
972	for comp in ${config_ListOfComponents[*]} ; do
973	# Define component
974
975	# Copy executable for this component
976	eval ExeNameIn=\${config_Executable_${comp}[0]}
977	eval ExeNameOut=\${config_Executable_${comp}[1]}
978
979	# If missing executable and DRYRUN is set to 0 or 1 then stop!
980	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
981	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
982	fi
983
984	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
985	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
986	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
987	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
988	fi
989	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
990	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
991	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
992	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
993	fi
994	fi
995
996	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
997	# Get the compiler version
998	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
999	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1000	# Save it
1001	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1002	[ X${compilerFull} = X ] && byPass=true
1003	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1004	fi
1005	done
1006
1007	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1008	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1009
1010	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1011	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1012	fi
1013
1014	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1015	}
1016
1017	#=======================================================================
1018	function IGCM_comp_PeriodStart
1019	{
1020	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1021
1022	# Debug Print :
1023	echo
1024	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1025	echo
1026
1027	typeset ExeNameIn ExeNameOut
1028	typeset comp compname comptagname
1029	for comp in ${config_ListOfComponents[*]} ; do
1030	# Define component
1031	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1032	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1033
1034	# Copy executable for this component
1035	eval ExeNameIn=\${config_Executable_${comp}[0]}
1036	eval ExeNameOut=\${config_Executable_${comp}[1]}
1037
1038	# Debug Print
1039	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1040	# UPDATE component
1041	${comp}_PeriodStart 2> /dev/null
1042
1043	done
1044
1045	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1046	}
1047
1048
1049
1050	#=======================================================================
1051	function IGCM_comp_modifyFile
1052	{
1053	#
1054	# syntax: IGCM_comp_modifyFile filein key [value]
1055	#
1056	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1057	#
1058	# This function is used to replace a pattern in a file for a specific variable.
1059	#
1060	# Arguments:
1061	# - filein : the file in run directory in which the variable should be set
1062	# - key : the variable to modify
1063	# - value : the value to set the key equal to
1064	#
1065	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1066
1067	typeset filein key value pattern
1068
1069	# Set local variables and test the arguments
1070	if [ $# = 3 ] ; then
1071	# Normal case with 3 arguments
1072	filein=$1 ; key=$2 ; value=$3
1073	else
1074	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1075	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1076	return
1077	fi
1078	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1079
1080	# Test if the file exist
1081	if [ ! -f ${filein} ] ; then
1082	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1083	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1084	return
1085	fi
1086
1087	# Read the line with key in the file without the comments
1088	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1089
1090	# Verify the existance of the pattern
1091	if [ X"${pattern}" = X ] ; then
1092	# Variable key is not set in filein, stop.
1093	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1094	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1095	return
1096	fi
1097
1098	# Now change key in filein
1099	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1100	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1101	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1102	\mv ${filein}.tmp ${filein}
1103
1104	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1105	}
1106
1107	#=======================================================================
1108	function IGCM_comp_modifyDefFile
1109	{
1110	#
1111	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1112	#
1113	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1114	#
1115	# This function is used to modify a parameter file for a specific variable.
1116	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1117	# This function can be used in the comp.driver files for the components.
1118	#
1119	# Arguments:
1120	# - type : first argument must be blocker, nonblocker or force
1121	# For "blocker" case, the variable must be attributed the keyworld AUTO
1122	# otherwise this function will exit.
1123	# For "nonblocker" case, the user can remove or modify the variable. For
1124	# this case, as long as AUTO is not set, no modification will be done.
1125	# For "force" case, the variable will be modified even if it is not set to AUTO
1126	# - filein : the file in run directory of .def type in which the variable should be set
1127	# - key : the variable to modify
1128	# - value : the value to set the key equal to, optional. If value is not set or if
1129	# value=DEFAULT, then a default value must be given in filein using syntax :
1130	# key= AUTO : DEFAULT=def_value
1131	#
1132	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1133
1134	typeset type filein key value
1135	typeset filelist nb_occ modify
1136
1137	# Set local variables and test the arguments
1138	if [ $# = 4 ] ; then
1139	# Normal case with 4 arguments
1140	type=$1 ; filein=$2 ; key=$3 ; value=$4
1141	elif [ $# = 3 ] ; then
1142	# Normal case with 3 arguments
1143	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1144	else
1145	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1146	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1147	return
1148	fi
1149	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1150
1151	# Test if first argument is correct
1152	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1153	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1154	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1155	return
1156	fi
1157
1158	# Test if the file exist.
1159	# Exit with error if the file does not exist for the case blocker or force.
1160	# Only return for the case nonblocker.
1161	if [ ! -f ${filein} ] ; then
1162	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1163	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1164	else
1165	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1166	fi
1167	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1168	return
1169	fi
1170
1171	# Define list of files to test using all files with suffix .def (except used*.def)
1172	filelist=$( ls *def \| grep -v used )
1173
1174	# Count number of occurances for the key in all files
1175	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1176
1177	# Test if key is set several times
1178	if [ ${nb_occ} -gt 1 ] ; then
1179	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1180	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1181	return
1182	fi
1183
1184	# Treatement according to different cases
1185	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1186	# Stop if the key is never set and the function is blocker
1187	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1188	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1189	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1190	# The key is not set but it is a nonblocker call so nothing is done.
1191	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1192	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1193	modify=no
1194	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1195	# Variable key is not set in filein, stop.
1196	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1197	fi
1198
1199	# Check if AUTO is set in the filein on the same line as the key variable
1200	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1201	# Modification will be done for all cases
1202	modify=yes
1203	else
1204	# The variable was not set to AUTO
1205	if [ ${type} = blocker ] ; then
1206	# Exit because this is a blocker call
1207	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1208	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1209	return
1210	elif [ ${type} = nonblocker ] ; then
1211	# Do nothing. Suppose that the user did set the variable correct
1212	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1213	modify=no
1214	elif [ ${type} = force ] ; then
1215	# Force modification
1216	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1217	modify=yes
1218	fi
1219	fi
1220
1221	# Do the modifcation now
1222	if [ ${modify} = yes ] ; then
1223
1224	# For option DEFAULT, read default value from file.
1225	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1226	# Case to set DEFAULT value
1227	# Read default value from filein
1228	value=$( grep ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1229
1230	if [ X"${value}" = X ] ; then
1231	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1232	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1233	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1234	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1235	return
1236	fi
1237	fi
1238
1239	# Now change key in filein
1240	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1241	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1242	\mv ${filein}.tmp ${filein}
1243	fi
1244	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1245	}
1246
1247	#=======================================================================
1248	function IGCM_comp_modifyNamelist
1249	{
1250	#
1251	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1252	#
1253	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1254	#
1255	# This function is used to modify a parameter file for a specific variable.
1256	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1257	# This function can be used in the comp.driver files for the components.
1258	#
1259	# Arguments:
1260	# - type : first argument must be blocker, nonblocker or force
1261	# For "blocker" case, the variable must be attributed the keyworld AUTO
1262	# otherwise this function will exit.
1263	# For "nonblocker" case, the user can remove or modify the variable. For
1264	# this case, as long as AUTO is not set, no modification will be done.
1265	# For "force" case, the variable will be modified even if it is not set to AUTO
1266	# - filein : the file in run directory of .def type in which the variable should be set
1267	# - key : the variable to modify
1268	# - value : the value to set the key equal to, optional. If value is not set or if
1269	# value=DEFAULT, then a default value must be given in filein using syntax :
1270	# key= AUTO : DEFAULT=def_value
1271	#
1272	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1273
1274	typeset type filein key value pattern modify
1275
1276	# Set local variables and test the arguments
1277	if [ $# = 4 ] ; then
1278	# Normal case with 4 arguments
1279	type=$1 ; filein=$2 ; key=$3 ; value=$4
1280	elif [ $# = 3 ] ; then
1281	# Normal case with 3 arguments
1282	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1283	else
1284	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1285	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1286	return
1287	fi
1288	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1289
1290	# Test if first argument is correct
1291	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1292	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1293	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1294	return
1295	fi
1296
1297	# Test if the file exist.
1298	# Exit with error if the file does not exist for the case blocker or force.
1299	# Only return for the case nonblocker.
1300	if [ ! -f ${filein} ] ; then
1301	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1302	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1303	else
1304	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1305	fi
1306	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1307	return
1308	fi
1309
1310	# Read the line with key in the file without the comments
1311	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1312
1313	# Verify the existance of the pattern
1314	if [ X"$pattern" = X ] ; then
1315	# Variable key is not set in filein, stop.
1316	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1317	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1318	return
1319	fi
1320
1321	# Check if the variable is set to AUTO in the filein
1322	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1323	# Modification will be done for all cases
1324	modify=yes
1325	else
1326	# The variable was not set to AUTO
1327	if [ ${type} = blocker ] ; then
1328	# Exit because this is a blocker call
1329	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1330	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1331	return
1332	elif [ ${type} = nonblocker ] ; then
1333	# Do nothing. Suppose that the user did set the variable correct
1334	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1335	modify=no
1336	elif [ ${type} = force ] ; then
1337	# Force modification
1338	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1339	modify=yes
1340	fi
1341	fi
1342
1343	# Do the modifcation now
1344	if [ ${modify} = yes ] ; then
1345
1346	# For option DEFAULT, read default value from file.
1347	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1348	# Case to set DEFAULT value
1349	# Read default value from filein
1350	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1351
1352	if [ X"${value}" = X ] ; then
1353	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1354	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1355	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1356	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1357	return
1358	fi
1359	fi
1360
1361	# Now change key in filein
1362	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1363	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1364	\mv ${filein}.tmp ${filein}
1365	fi
1366	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1367	}
1368
1369	#=======================================================================
1370	function IGCM_comp_modifyXmlFile
1371	{
1372	#
1373	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1374	#
1375	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1376	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1377	#
1378	# This function is used to modify the value for a specific attribute and variable id.
1379	# The file must be a valid xml file.
1380	# This function can be used in the comp.driver files for the components.
1381	#
1382	# Arguments:
1383	# - type : first argument must be blocker, nonblocker or force.
1384	# For "blocker" case, the variable must be attributed the keyworld AUTO
1385	# otherwise this function will exit.
1386	# For "nonblocker" case, the user can remove or modify the variable. For
1387	# this case, as long as AUTO is not set, no modification will be done.
1388	# For "force" case, the variable will be modified even if it is not set to AUTO
1389	# - filein : the file in run directory of .xml type in which the variable should be set
1390	# - keyid : the variable to modify
1391	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1392	# - value : the value to set in the filein
1393	#
1394	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1395
1396	typeset type filein keyid keyattrib value modify
1397
1398	# Set local variables and test the arguments
1399	if [ $# = 5 ] ; then
1400	# Normal case with 4 arguments
1401	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1402	else
1403	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1404	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1405	return
1406	fi
1407	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1408
1409	# Test if first argument is correct
1410	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1411	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1412	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1413	return
1414	fi
1415
1416	# Test if the file exist.
1417	# Exit with error if the file does not exist for the case blocker or force.
1418	# Only return for the case nonblocker.
1419	if [ ! -f ${filein} ] ; then
1420	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1421	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1422	else
1423	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1424	fi
1425	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1426	return
1427	fi
1428
1429	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1430	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1431	if [ ${type} = nonblocker ] ; then
1432	# This is a nonblocker case, print warning but do nothing else
1433	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1434	else
1435	# This is a blocker or force case : stop now
1436	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1437	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1438	return
1439	fi
1440	fi
1441
1442	# Check if AUTO is set on the same line as keyid and keyattrib
1443	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1444	# Modification will be done
1445	modify=yes
1446	else
1447	if [ ${type} = blocker ] ; then
1448	# Exit, the variable must be set to AUTO
1449	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1450	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1451	return
1452	elif [ ${type} = nonblocker ] ; then
1453	# Nothing will be done
1454	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1455	modify=no
1456	elif [ ${type} = force ] ; then
1457	# Force modification
1458	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1459	modify=yes
1460	fi
1461	fi
1462
1463	# Do the modifcation now
1464	if [ ${modify} = yes ] ; then
1465	if [ ${keyattrib} = NONE ] ; then
1466	# Case to modify the variable itself
1467	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1468	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1469	else
1470	# Check if keyattrib is set on the same line as keyid
1471	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1472	# Case to modify the attribute value
1473	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1474	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1475	else
1476	# Case to add the attribute and its value
1477	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1478	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1479	fi
1480	fi
1481	\mv ${filein}.tmp ${filein}
1482	fi
1483	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1484	}
1485
1486	#=======================================================================
1487	function IGCM_comp_Update
1488	{
1489	IGCM_debug_PushStack "IGCM_comp_Update"
1490
1491	# Debug Print :
1492	echo
1493	IGCM_debug_Print 1 "IGCM_comp_Update"
1494	echo
1495
1496	typeset comp compname comptagname
1497	for comp in ${config_ListOfComponents[*]} ; do
1498	# Define component
1499	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1500	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1501
1502	# Debug Print
1503	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1504	# UPDATE component
1505	${comp}_Update
1506
1507	done
1508
1509	IGCM_debug_PopStack "IGCM_comp_Update"
1510	}
1511
1512	#=======================================================================
1513	function IGCM_comp_Finalize
1514	{
1515	IGCM_debug_PushStack "IGCM_comp_Finalize"
1516
1517	# Debug Print :
1518	echo
1519	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1520	echo
1521
1522	typeset ListTextName TextName0
1523	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1524	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1525	typeset -Z4 j4 #BASH declare j4
1526	typeset list_file nlist_file
1527	typeset compactoutputs
1528
1529	# Initialize array hosting list of rebuilded files to copy
1530	unset rebuildedActionsList
1531
1532	# Text compacting options
1533	compactoutputs=false
1534	if [ X${JobType} != XRUN ] ; then
1535	compactoutputs=true
1536	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1537	compactoutputs=true
1538	fi
1539
1540	# Prepare headers for the shell dedicated to offline rebuild
1541	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1542	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1543	if [ ${DRYRUN} -le 1 ] ; then
1544	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1545	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1546	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1547	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1548	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1549	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1550	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1551	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1552	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1553	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1554	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1555	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1556	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1557	fi
1558	fi
1559
1560	for comp in ${config_ListOfComponents[*]} ; do
1561	# Define component
1562	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1563	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1564
1565	# Debug Print
1566	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1567	# FINALIZE component
1568	${comp}_Finalize
1569
1570	card=${SUBMIT_DIR}/COMP/${compname}.card
1571
1572	# Save Output Text files of models
1573	#---------------------------------
1574	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1575	IGCM_card_DefineArrayFromOption ${card} OutputText List
1576	ListTextName=${compname}_OutputText_List
1577
1578	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1579	if [ X${TextName0} != X${NULL_STR} ] ; then
1580	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1581
1582	(( i=0 ))
1583	until [ $i -eq $NbFiles ]; do
1584	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1585	eval file_out=${PREFIX}_${file_in}
1586
1587	(( i=i+1 ))
1588
1589	unset list_file
1590	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1591	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1592	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 )
1593	nlist_file=${#list_file[@]}
1594	if [ ${nlist_file} -gt 1 ] ; then
1595	if ( ${compactoutputs} ) ; then
1596	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1597	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1598	echo ${list_file[*]} > ${file_out}
1599	echo "" >> ${file_out}
1600
1601	(( i_ = 0 ))
1602	for file in ${list_file[@]} ; do
1603	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1604	echo "\| " ${i_} " " ${file} >> ${file_out}
1605	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1606	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1607	echo "" >> ${file_out}
1608	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1609	(( i_ = i_ + 1 ))
1610	done
1611	if ( ${ExecutionFail} ) ; then
1612	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1613	fi
1614
1615	if [ X${Pack} = Xtrue ] ; then
1616	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1617	else
1618	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1619	fi
1620
1621	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1622	else
1623	for file in ${list_file[@]} ; do
1624	if ( ${ExecutionFail} ) ; then
1625	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1626	fi
1627
1628	if [ X${Pack} = Xtrue ] ; then
1629	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1630	else
1631	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1632	fi
1633
1634	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1635	done
1636	fi
1637	else
1638	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1639	eval IGCM_sys_Mv ${file_in}* ${file_in}
1640	fi
1641
1642	if ( ${ExecutionFail} ) ; then
1643	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1644	fi
1645
1646	if [ X${Pack} = Xtrue ] ; then
1647	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1648	else
1649	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1650	fi
1651	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1652	fi
1653	done
1654	fi
1655
1656	# Save Restarts files
1657	#--------------------
1658	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1659	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1660	ListFilesName=${compname}_RestartFiles_List
1661	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1662
1663	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1664	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1665
1666	(( i=0 ))
1667	until [ $i -ge $NbFiles ]; do
1668	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1669	eval file_in=${file_in_}
1670
1671	(( i_ = i+1 ))
1672	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1673	eval file_out=${file_out_}
1674
1675	(( i_ = i+2 ))
1676	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1677	eval file_outin=${file_outin_}
1678
1679	generic_restart_file_name_in=$( basename ${file_in} .nc )
1680	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1681	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1682
1683	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1684	if [ ${nb_restart_file} -gt 1 ] ; then
1685	j=0 # BASH LINE NOT NEEDED
1686	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1687	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1688	j4=${j} # BASH LINE NOT NEEDED
1689	if [ X${Pack} = Xtrue ] ; then
1690	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1691	else
1692	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1693	fi
1694	if [ ! ${file_in} = ${file_outin} ] ; then
1695	if ( ${ExitFlag} ) ; then
1696	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1697	else
1698	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1699	fi
1700	fi
1701	(( j=j+1 )) # BASH LINE NOT NEEDED
1702	done
1703	else
1704	if [ X${Pack} = Xtrue ] ; then
1705	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1706	else
1707	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1708	fi
1709	if [ ! ${file_in} = ${file_outin} ] ; then
1710	if ( ${ExitFlag} ) ; then
1711	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1712	else
1713	IGCM_sys_Mv ${file_in} ${file_outin}
1714	fi
1715	fi
1716	fi
1717
1718	(( i=i+3 ))
1719	done
1720	else
1721	if [ X${FileName0} != XNONE ] ; then
1722	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1723	else
1724	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1725	fi
1726	fi
1727
1728	# Save Output files
1729	#------------------
1730	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1731	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1732	ListFilesName=${compname}_OutputFiles_List
1733	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1734
1735	if [ X${FileName0} != X${NULL_STR} ] ; then
1736	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1737
1738	(( i=0 ))
1739	until [ $i -ge $NbFiles ]; do
1740	SaveOnArchive=true
1741	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1742	eval file_in=${file_in_}
1743	(( i_ = i+1 ))
1744	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1745	eval file_out=${file_out_}
1746	#
1747	# Override file_out path remplacing R_SAVE by R_BUFR
1748	#
1749	if [ X${Pack} = Xtrue ] ; then
1750	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1751	fi
1752	#
1753	# Not necessarily the best option. /!\ Potential side effects /!\
1754	#
1755	(( i_ = i+2 ))
1756	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1757	#
1758	generic_file_name=$( basename ${file_in} .nc )
1759	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1760	#
1761	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1762	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1763	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1764	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1765	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1766	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1767	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1768	#
1769	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
1770	if [ ${file_in} = output.abort.nc ] ; then
1771	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
1772	else
1773	IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc
1774	fi
1775	else
1776	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1777	IGCM_sys_Mv ${generic_file_name}_[0-9]*.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1778
1779	# Prepare the shell dedicated to offline rebuild
1780	if [ $DRYRUN -le 1 ]; then
1781	if [ ${file_in} = histstn.nc ] ; then
1782	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1783	else
1784	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1785	fi
1786	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1787	fi
1788	#
1789	# Load Patch we need to apply and apply
1790	if [ $DRYRUN -le 1 ]; then
1791	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1792	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1793	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1794	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1795	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1796	done
1797	fi
1798	fi
1799	#
1800	if [ $DRYRUN -le 1 ]; then
1801	if [ X${Pack} = Xtrue ] ; then
1802	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1803	else
1804	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1805	fi
1806	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1807	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1808	fi
1809	SaveOnArchive=false
1810	fi
1811	fi
1812	#
1813	if [ ${SaveOnArchive} = true ] ; then
1814	#
1815	# Rebuild has been done online or it was not needed
1816	#
1817	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1818	#
1819	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1820	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1821	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1822	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1823	#
1824	if [ $DRYRUN -le 1 ]; then
1825	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1826	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1827	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1828	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1829	done
1830	#
1831	if [ X${Pack} = Xtrue ] ; then
1832	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1833	else
1834	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1835	fi
1836	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1837	#
1838	fi
1839	else
1840	#
1841	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1842	#
1843	if [ X${Pack} = Xtrue ] ; then
1844	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1845	else
1846	IGCM_sys_Put_Out ${file_in} ${file_out}
1847	fi
1848	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1849	if [ ${nb_rebuild_file} -gt 1 ] ; then
1850	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1851	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1852	done
1853	fi
1854	fi
1855	fi
1856	(( i=i+3 ))
1857	done
1858	fi
1859	echo
1860	done
1861	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1862	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1863	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1864	i=0
1865	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1866	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1867	(( i=i+1 ))
1868	done
1869	fi
1870	IGCM_debug_PopStack "IGCM_comp_Finalize"
1871	}

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