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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1248

Last change on this file since 1248 was 1248, checked in by sdipsl, 9 years ago
Fix an issue impacting opa9.driver
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
File size: 72.1 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_GetInputInitialStateFiles
259	{
260	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
261
262	# Debug Print :
263	echo
264	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
265	echo
266
267	# Only the first time step need InitialStateFiles
268	# otherwise it's BoundaryConditions
269	if ( ${FirstInitialize} ) ; then
270	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
271	typeset file_in_ file_in file_out_ file_out do_init
272	for comp in ${config_ListOfComponents[*]} ; do
273	# Initialize
274	do_init="y"
275	# Do we need to bring initial state file for this component
276	if [ "${config_Restarts_OverRule}" = "y" ] ; then
277	eval do_init="n"
278	else
279	# Read component Restarts parameters
280	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
281	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
282	if [ "${do_start}" = "y" ] ; then
283	do_init="n"
284	else
285	do_init="y"
286	fi
287	fi
288
289	if [ "${do_init}" = "y" ] ; then
290	# Define component
291	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
292	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
293
294	# Debug Print :
295	IGCM_debug_Print 3 "Initialisation files ${compname}"
296
297	card=${SUBMIT_DIR}/COMP/${compname}.card
298
299	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
300	ListFilesName=${compname}_InitialStateFiles_List
301
302	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
303	if [ X${FileName0} != X${NULL_STR} ] ; then
304	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
305	(( i=0 ))
306	until [ $i -ge $NbFiles ]; do
307	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
308	eval file_in=${file_in_}
309	(( i_ = i+1 ))
310	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
311	eval file_out=${file_out_}
312
313	IGCM_sys_IsFileArchived ${file_in}
314	if [ $? = 0 ] ; then
315	IGCM_sys_Get ${file_in} ${file_out}
316	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
317	else
318	IGCM_sys_Cp ${file_in} ${file_out}
319	fi
320	(( i=i+2 ))
321	done
322	fi
323	fi
324	done
325	fi
326	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
327	}
328
329	#=======================================================================
330	# Definition of Smooth modulo function
331	# usage :
332	# IGCM_SmoothModulo StringModulo value
333	#
334	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
335	# [min]:[modulo:][max]
336	# where :
337	# [] value are optionnals;
338	# empty min equal 1
339	# empty max equal infinity
340	# modulo not given or empty equal 1
341	# empty string or just ':' equal always.
342	#
343	# value : the value to test with the definition
344	#
345	# return : true(1)/false(0)
346	function IGCM_SmoothModulo
347	{
348	IGCM_debug_PushStack "IGCM_SmoothModulo"
349	typeset defVector ModValue
350
351	eval set +A defVector -- $( echo "${1}" \| \
352	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
353
354	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
355	arr[1]=${defVector[0]}
356	arr[2]=${defVector[2]}
357
358	# Test limits :
359	# ${defVector[0]} <= ${2} <= ${defVector[2]}
360	# or ${defVector[2]} == -1
361	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
362	# Test modulo
363	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
364	if [ ${ModValue} -eq 0 ] ; then
365	arr[3]=true
366	echo ${arr[@]}
367	IGCM_debug_PopStack "IGCM_SmoothModulo"
368	return 1
369	else
370	arr[3]=false
371	echo ${arr[@]}
372	IGCM_debug_PopStack "IGCM_SmoothModulo"
373	return 0
374	fi
375	else
376	arr[3]=false
377	echo ${arr[@]}
378	IGCM_debug_PopStack "IGCM_SmoothModulo"
379	return 0
380	fi
381	}
382
383	#=======================================================================
384	function IGCM_comp_GetInputSmoothFiles
385	{
386	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
387
388	# Debug Print :
389	echo
390	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
391	echo
392
393	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
394	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
395
396	for comp in ${config_ListOfComponents[*]} ; do
397	# Define component
398	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
399	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
400
401	# Debug Print :
402	IGCM_debug_Print 3 "Smooth files ${compname}"
403
404	card=${SUBMIT_DIR}/COMP/${compname}.card
405
406	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
407	ListFilesName=${compname}_SmoothFiles_List
408	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
409
410	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
411	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
412
413	(( i=0 ))
414	until [ $i -ge $NbFiles ]; do
415	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
416	eval file_in=${file_in_}
417	(( i_ = i+1 ))
418	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
419	eval file_out=${file_out_}
420
421	# define CumulPeriod definition for this file
422	(( i__ = i+2 ))
423	eval SmoothDef=\${${ListFilesName}[$i__]}
424	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
425	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
426	j=1
427	for val in ${aux} ; do
428	[ ${j} -eq 1 ] && SmoothMin=${val}
429	[ ${j} -eq 2 ] && SmoothMax=${val}
430	[ ${j} -eq 3 ] && ret=${val}
431	(( j=j+1 ))
432	done
433	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
434	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
435
436	IGCM_sys_IsFileArchived ${file_in}
437	if [ $? = 0 ] ; then
438	IGCM_sys_Get ${file_in} ${file_out}
439	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
440	else
441	IGCM_sys_Cp ${file_in} ${file_out}
442	fi
443	fi
444	(( i=i+3 ))
445	done
446	fi
447	done
448
449	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
450	}
451
452	#=======================================================================
453	function IGCM_comp_GetInputBoundaryFiles
454	{
455	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
456
457	# Debug Print :
458	echo
459	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
460	echo
461
462	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
463	typeset file_in_ file_in file_out_ file_out
464
465	if [ ${Period} = 1 ]; then
466	ListFixBoundary=" "
467	fi
468
469	for comp in ${config_ListOfComponents[*]} ; do
470
471	# Define component
472	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
473	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
474
475	# Debug Print :
476	IGCM_debug_Print 3 "Boundary files ${compname}"
477
478	card=${SUBMIT_DIR}/COMP/${compname}.card
479
480	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
481	ListFilesName=${compname}_BoundaryFiles_List
482	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
483
484	if [ X${FileName0} != X${NULL_STR} ] ; then
485	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
486
487	(( i=0 ))
488	until [ $i -ge $NbFiles ]; do
489	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
490	eval file_in=${file_in_}
491	(( i_ = i+1 ))
492	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
493	eval file_out=${file_out_}
494
495	IGCM_sys_IsFileArchived ${file_in}
496	if [ $? = 0 ] ; then
497	IGCM_sys_Get ${file_in} ${file_out}
498	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
499	else
500	IGCM_sys_Cp ${file_in} ${file_out}
501	fi
502
503	(( i=i+2 ))
504	done
505	fi
506
507	# Get non deleted files
508	if [ ${Period} = 1 ]; then
509
510	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
511	ListFilesName=${compname}_BoundaryFiles_ListNonDel
512	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
513
514	if [ X${FileName0} != X${NULL_STR} ] ; then
515	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
516
517	(( i=0 ))
518	until [ $i -ge $NbFiles ]; do
519	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
520	eval file_in=${file_in_}
521	(( i_ = i+1 ))
522	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
523	eval file_out=${file_out_}
524
525	IGCM_sys_IsFileArchived ${file_in}
526	if [ $? = 0 ] ; then
527	IGCM_sys_Get ${file_in} ${file_out}
528	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
529	else
530	IGCM_sys_Cp ${file_in} ${file_out}
531	fi
532
533	if [ X${file_out} != X. ] ; then
534	ListFixBoundary=${ListFixBoundary}" "${file_out}
535	else
536	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
537	fi
538
539	(( i=i+2 ))
540	done
541	fi
542	fi
543	done
544
545	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
546	}
547
548	#=======================================================================
549	function IGCM_comp_DelFixeBoundaryFiles
550	{
551	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
552
553	# Debug Print :
554	echo
555	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
556	echo
557
558	ls -l ${ListFixBoundary}
559	rm -f ${ListFixBoundary}
560
561	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
562	}
563
564	#=======================================================================
565	function IGCM_comp_GetInputParametersFiles
566	{
567	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
568
569	# Debug Print :
570	echo
571	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
572	echo
573
574	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
575	for comp in ${config_ListOfComponents[*]} ; do
576	# Define component
577	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
578	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
579
580	# Debug Print :
581	IGCM_debug_Print 3 "Parameters ${compname}"
582
583	card=${SUBMIT_DIR}/COMP/${compname}.card
584
585	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
586	ListFilesName=${compname}_ParametersFiles_List
587	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
588
589	if [ X${FileName0} != X${NULL_STR} ] ; then
590	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
591
592	(( i=0 ))
593	until [ $i -ge $NbFiles ]; do
594	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
595	eval file_in=${file_in_}
596	(( i_ = i+1 ))
597	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
598	eval file_out=${file_out_}
599
600	IGCM_sys_Cp ${file_in} ${file_out}
601	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
602
603	(( i=i+2 ))
604	done
605	fi
606	done
607
608	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
609	}
610
611	#=======================================================================
612	function IGCM_comp_GetInputRestartFiles
613	{
614	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
615
616	# Debug Print :
617	echo
618	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
619	echo
620
621	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
622	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
623	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
624	typeset file_in file_out file_in_ file_out_ file_in_Name
625	typeset -Z4 j4
626	#BASH declare j4
627
628	IsMatching=""
629
630	for comp in ${config_ListOfComponents[*]} ; do
631	# Define component
632	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
633	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
634	#
635	card=${SUBMIT_DIR}/COMP/${compname}.card
636	#
637	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
638	ListFilesName=${compname}_RestartFiles_List
639	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
640
641	# Debug Print :
642	IGCM_debug_Print 3 "restart ${compname}"
643
644	if ( ${FirstInitialize} ) ; then
645
646	if [ "${config_Restarts_OverRule}" = "y" ] ; then
647	eval config_${comp}_Restart="y"
648	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
649	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
650	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
651	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
652	eval CompOldName=${comp}
653	else
654	# Read component Restarts parameters
655	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
656	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
657
658	if [ "${do_start}" = "y" ] ; then
659	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
660	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
661	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
662	else
663	eval config_${comp}_RestartDate=-1
664	eval config_${comp}_RestartJobName=${NULL_STR}
665	eval config_${comp}_RestartPath=${NULL_STR}
666	fi
667
668	eval CompOldName=\${config_${comp}_OldName}
669	if [ X${CompOldName} = X ] ; then
670	eval CompOldName=${comp}
671	fi
672
673	# Reinitialize IsMatching to allow searching for a different tar file for each component.
674	IsMatching=""
675	TarFileFound=""
676	fi
677
678	if [ "${do_start}" = "y" ] ; then
679
680	# Restore Restarts files
681	#-----------------------
682	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
683	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
684
685	(( i=1 ))
686	until [ $i -gt $NbFiles ]; do
687	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
688	eval file_in=${file_in_}
689	(( i_ = i+1 ))
690	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
691	eval file_out=${file_out_}
692
693	eval Date_tmp=\${config_${comp}_RestartDate}
694	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
695	# will be re-use
696	eval RestartPath=\${config_${comp}_RestartPath}
697	eval RestartJobName=\${config_${comp}_RestartJobName}
698	#
699	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
700	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
701
702	extension_in=$( echo ${file_in_Name##*.} )
703	extension_out=$( echo ${file_out##*.} )
704
705	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
706	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
707
708	Path_OUT=${Path_r}/${generic_restart_file_name_in}
709
710	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
711	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
712	Buffered=true
713	Archived=false
714	Tared=false
715	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
716	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
717	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
718	Buffered=false
719	Archived=true
720	Tared=false
721	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
722	else
723	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
724	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
725	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
726	Buffered=false
727	Archived=false
728	Tared=true
729	# Look after the tar file we want if we did not found it already
730	if [ X${IsMatching} = X ] ; then
731	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
732	if [ $? ] ; then
733	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
734	IsMatching=$( echo ${PotentialTarFile##*/} \| \
735	sed "s:_restart::" \| \
736	sed "s:^${RestartJobName}_::" \| \
737	sed "s:\.tar$::" \| \
738	gawk -F_ -v restartdate=${Date_r} \
739	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
740	if [ ! X${IsMatching} = X ] ; then
741	TarFileFound=${PotentialTarFile}
742	break
743	fi
744	done
745	fi
746	# Stop here if nothing has been found
747	if [ X${TarFileFound} = X ] ; then
748	IGCM_debug_Print 3 "Restart files were not found!"
749	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
750	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
751	IGCM_debug_Exit "Please double check restart settings in config.card"
752	IGCM_debug_Verif_Exit
753	fi
754	fi
755	IGCM_sys_PrepareTaredRestart ${TarFileFound}
756	TarFileLocation=$( basename ${TarFileFound} )
757	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
758	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
759	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
760	fi
761
762	if [ ${nb_restart_file} -gt 1 ] ; then
763	j=0 # BASH LINE NOT NEEDED
764	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
765	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
766	j4=${j} # BASH LINE NOT NEEDED
767	if [ X${Buffered} = Xtrue ] ; then
768	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
769	elif [ X${Archived} = Xtrue ] ; then
770	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
771	elif [ X${Tared} = Xtrue ] ; then
772	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
773	fi
774	(( j=j+1 )) #BASH LINE NOT NEEDED
775	done
776
777	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
778	if [ X${OCE_PROC_MPI} != X ] ; then
779	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
780	IGCM_sys_rebuild ${generic_restart_file_name_out}.${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
781	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
782	fi
783	fi
784	else
785	if [ X${Buffered} = Xtrue ] ; then
786	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
787	elif [ X${Archived} = Xtrue ] ; then
788	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
789	elif [ X${Tared} = Xtrue ] ; then
790	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
791	fi
792	fi
793	(( i=i+3 ))
794	done
795	else
796	if [ X${FileName0} != XNONE ] ; then
797	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
798	else
799	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
800	fi
801	fi
802	fi
803	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
804	# if not FirstInitialize and first loop of this job
805
806	# Restore Restarts files
807	#-----------------------
808	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
809	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
810
811	(( i=1 ))
812	until [ $i -gt $NbFiles ]; do
813	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
814	eval file_in=${file_in_}
815	(( i_ = i+1 ))
816	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
817	eval file_out=${file_out_}
818
819	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
820
821	extension_in=$( echo ${file_in_Name##*.} )
822	extension_out=$( echo ${file_out##*.} )
823
824	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
825	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
826
827	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
828	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
829
830	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
831	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
832	Buffered=true
833	Archived=false
834	Tared=false
835	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
836	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
837	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
838	Buffered=false
839	Archived=true
840	Tared=false
841	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
842	else
843	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
844	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
845	Buffered=false
846	Archived=false
847	Tared=true
848	# Look after the tar file we want if we did not found it already
849	if [ X${IsMatching} = X ] ; then
850	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
851	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
852	if [ ! X${IsMatching} = X ] ; then
853	TarFileFound=${PotentialTarFile}
854	break
855	fi
856	done
857	fi
858	# Stop here if nothing has been found
859	if [ X${TarFileFound} = X ] ; then
860	IGCM_debug_Print 3 "Restart files were not found!"
861	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
862	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
863	IGCM_debug_Exit "Please double check restart settings in config.card"
864	IGCM_debug_Verif_Exit
865	fi
866	IGCM_sys_PrepareTaredRestart ${TarFileFound}
867	TarFileLocation=$( basename ${TarFileFound} )
868	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
869	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
870	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
871	fi
872
873	if [ ${nb_restart_file} -gt 1 ] ; then
874	j=0 # BASH LINE NOT NEEDED
875	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
876	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
877	j4=${j} # BASH LINE NOT NEEDED
878	if [ X${Buffered} = Xtrue ] ; then
879	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
880	elif [ X${Archived} = Xtrue ] ; then
881	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
882	elif [ X${Tared} = Xtrue ] ; then
883	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
884	fi
885	(( j=j+1 )) # BASH LINE NOT NEEDED
886	done
887	else
888	if [ X${Buffered} = Xtrue ] ; then
889	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
890	elif [ X${Archived} = Xtrue ] ; then
891	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
892	elif [ X${Tared} = Xtrue ] ; then
893	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
894	fi
895	fi
896	(( i=i+3 ))
897	done
898	else
899	if [ X${FileName0} != XNONE ] ; then
900	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
901	else
902	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
903	fi
904	fi
905	fi
906	done
907
908	NbFiles=$( ls * 2> /dev/null \| wc -l )
909	if [ ${NbFiles} -gt 0 ] ; then
910	IGCM_sys_Chmod u+rw *
911	fi
912
913	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
914	}
915
916	#=======================================================================
917	function IGCM_comp_PeriodStart
918	{
919	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
920
921	# Debug Print :
922	echo
923	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
924	echo
925
926	typeset ExeNameIn ExeNameOut
927	typeset comp compname comptagname
928	for comp in ${config_ListOfComponents[*]} ; do
929	# Define component
930	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
931	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
932
933	# Copy executable for this component
934	eval ExeNameIn=\${config_Executable_${comp}[0]}
935	eval ExeNameOut=\${config_Executable_${comp}[1]}
936
937	# Debug Print
938	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
939	# UPDATE component
940	${comp}_PeriodStart 2> /dev/null
941
942	done
943
944	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
945	}
946
947
948
949	#=======================================================================
950	function IGCM_comp_modifyFile
951	{
952	#
953	# syntax: IGCM_comp_modifyFile filein key [value]
954	#
955	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
956	#
957	# This function is used to replace a pattern in a file for a specific variable.
958	#
959	# Arguments:
960	# - filein : the file in run directory in which the variable should be set
961	# - key : the variable to modify
962	# - value : the value to set the key equal to
963	#
964	IGCM_debug_PushStack "IGCM_comp_modifyFile"
965
966	typeset filein key value pattern
967
968	# Set local variables and test the arguments
969	if [ $# = 3 ] ; then
970	# Normal case with 3 arguments
971	filein=$1 ; key=$2 ; value=$3
972	else
973	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
974	IGCM_debug_PopStack "IGCM_comp_modifyFile"
975	return
976	fi
977	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
978
979	# Test if the file exist
980	if [ ! -f ${filein} ] ; then
981	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
982	IGCM_debug_PopStack "IGCM_comp_modifyFile"
983	return
984	fi
985
986	# Read the line with key in the file without the comments
987	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
988
989	# Verify the existance of the pattern
990	if [ X"${pattern}" = X ] ; then
991	# Variable key is not set in filein, stop.
992	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
993	IGCM_debug_PopStack "IGCM_comp_modifyFile"
994	return
995	fi
996
997	# Now change key in filein
998	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
999	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1000	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1001	\mv ${filein}.tmp ${filein}
1002
1003	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1004	}
1005
1006	#=======================================================================
1007	function IGCM_comp_modifyDefFile
1008	{
1009	#
1010	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1011	#
1012	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1013	#
1014	# This function is used to modify a parameter file for a specific variable.
1015	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1016	# This function can be used in the comp.driver files for the components.
1017	#
1018	# Arguments:
1019	# - type : first argument must be blocker, nonblocker or force
1020	# For "blocker" case, the variable must be attributed the keyworld AUTO
1021	# otherwise this function will exit.
1022	# For "nonblocker" case, the user can remove or modify the variable. For
1023	# this case, as long as AUTO is not set, no modification will be done.
1024	# For "force" case, the variable will be modified even if it is not set to AUTO
1025	# - filein : the file in run directory of .def type in which the variable should be set
1026	# - key : the variable to modify
1027	# - value : the value to set the key equal to, optional. If value is not set or if
1028	# value=DEFAULT, then a default value must be given in filein using syntax :
1029	# key= AUTO : DEFAULT=def_value
1030	#
1031	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1032
1033	typeset type filein key value
1034	typeset filelist nb_occ modify
1035
1036	# Set local variables and test the arguments
1037	if [ $# = 4 ] ; then
1038	# Normal case with 4 arguments
1039	type=$1 ; filein=$2 ; key=$3 ; value=$4
1040	elif [ $# = 3 ] ; then
1041	# Normal case with 3 arguments
1042	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1043	else
1044	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1045	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1046	return
1047	fi
1048	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1049
1050	# Test if first argument is correct
1051	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1052	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1053	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1054	return
1055	fi
1056
1057	# Test if the file exist.
1058	# Exit with error if the file does not exist for the case blocker or force.
1059	# Only return for the case nonblocker.
1060	if [ ! -f ${filein} ] ; then
1061	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1062	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1063	else
1064	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1065	fi
1066	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1067	return
1068	fi
1069
1070	# Define list of files to test using all files with suffix .def (except used*.def)
1071	filelist=$( ls *def \| grep -v used )
1072
1073	# Count number of occurances for the key in all files
1074	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1075
1076	# Test if key is set several times
1077	if [ ${nb_occ} -gt 1 ] ; then
1078	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1079	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1080	return
1081	fi
1082
1083	# Treatement according to different cases
1084	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1085	# Stop if the key is never set and the function is blocker
1086	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1087	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1088	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1089	# The key is not set but it is a nonblocker call so nothing is done.
1090	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1091	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1092	modify=no
1093	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1094	# Variable key is not set in filein, stop.
1095	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1096	fi
1097
1098	# Check if AUTO is set in the filein on the same line as the key variable
1099	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1100	# Modification will be done for all cases
1101	modify=yes
1102	else
1103	# The variable was not set to AUTO
1104	if [ ${type} = blocker ] ; then
1105	# Exit because this is a blocker call
1106	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1107	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1108	return
1109	elif [ ${type} = nonblocker ] ; then
1110	# Do nothing. Suppose that the user did set the variable correct
1111	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1112	modify=no
1113	elif [ ${type} = force ] ; then
1114	# Force modification
1115	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1116	modify=yes
1117	fi
1118	fi
1119
1120	# Do the modifcation now
1121	if [ ${modify} = yes ] ; then
1122
1123	# For option DEFAULT, read default value from file.
1124	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1125	# Case to set DEFAULT value
1126	# Read default value from filein
1127	value=$( grep ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1128
1129	if [ X"${value}" = X ] ; then
1130	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1131	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1132	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1133	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1134	return
1135	fi
1136	fi
1137
1138	# Now change key in filein
1139	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1140	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1141	\mv ${filein}.tmp ${filein}
1142	fi
1143	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1144	}
1145
1146	#=======================================================================
1147	function IGCM_comp_modifyNamelist
1148	{
1149	#
1150	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1151	#
1152	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1153	#
1154	# This function is used to modify a parameter file for a specific variable.
1155	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1156	# This function can be used in the comp.driver files for the components.
1157	#
1158	# Arguments:
1159	# - type : first argument must be blocker, nonblocker or force
1160	# For "blocker" case, the variable must be attributed the keyworld AUTO
1161	# otherwise this function will exit.
1162	# For "nonblocker" case, the user can remove or modify the variable. For
1163	# this case, as long as AUTO is not set, no modification will be done.
1164	# For "force" case, the variable will be modified even if it is not set to AUTO
1165	# - filein : the file in run directory of .def type in which the variable should be set
1166	# - key : the variable to modify
1167	# - value : the value to set the key equal to, optional. If value is not set or if
1168	# value=DEFAULT, then a default value must be given in filein using syntax :
1169	# key= AUTO : DEFAULT=def_value
1170	#
1171	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1172
1173	typeset type filein key value pattern modify
1174
1175	# Set local variables and test the arguments
1176	if [ $# = 4 ] ; then
1177	# Normal case with 4 arguments
1178	type=$1 ; filein=$2 ; key=$3 ; value=$4
1179	elif [ $# = 3 ] ; then
1180	# Normal case with 3 arguments
1181	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1182	else
1183	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1184	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1185	return
1186	fi
1187	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1188
1189	# Test if first argument is correct
1190	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1191	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1192	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1193	return
1194	fi
1195
1196	# Test if the file exist.
1197	# Exit with error if the file does not exist for the case blocker or force.
1198	# Only return for the case nonblocker.
1199	if [ ! -f ${filein} ] ; then
1200	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1201	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1202	else
1203	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1204	fi
1205	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1206	return
1207	fi
1208
1209	# Read the line with key in the file without the comments
1210	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1211
1212	# Verify the existance of the pattern
1213	if [ X"$pattern" = X ] ; then
1214	# Variable key is not set in filein, stop.
1215	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1216	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1217	return
1218	fi
1219
1220	# Check if the variable is set to AUTO in the filein
1221	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1222	# Modification will be done for all cases
1223	modify=yes
1224	else
1225	# The variable was not set to AUTO
1226	if [ ${type} = blocker ] ; then
1227	# Exit because this is a blocker call
1228	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1229	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1230	return
1231	elif [ ${type} = nonblocker ] ; then
1232	# Do nothing. Suppose that the user did set the variable correct
1233	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1234	modify=no
1235	elif [ ${type} = force ] ; then
1236	# Force modification
1237	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1238	modify=yes
1239	fi
1240	fi
1241
1242	# Do the modifcation now
1243	if [ ${modify} = yes ] ; then
1244
1245	# For option DEFAULT, read default value from file.
1246	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1247	# Case to set DEFAULT value
1248	# Read default value from filein
1249	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1250
1251	if [ X"${value}" = X ] ; then
1252	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1253	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1254	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1255	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1256	return
1257	fi
1258	fi
1259
1260	# Now change key in filein
1261	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1262	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1263	\mv ${filein}.tmp ${filein}
1264	fi
1265	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1266	}
1267
1268	#=======================================================================
1269	function IGCM_comp_modifyXmlFile
1270	{
1271	#
1272	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1273	#
1274	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1275	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1276	#
1277	# This function is used to modify the value for a specific attribute and variable id.
1278	# The file must be a valid xml file.
1279	# This function can be used in the comp.driver files for the components.
1280	#
1281	# Arguments:
1282	# - type : first argument must be blocker, nonblocker or force.
1283	# For "blocker" case, the variable must be attributed the keyworld AUTO
1284	# otherwise this function will exit.
1285	# For "nonblocker" case, the user can remove or modify the variable. For
1286	# this case, as long as AUTO is not set, no modification will be done.
1287	# For "force" case, the variable will be modified even if it is not set to AUTO
1288	# - filein : the file in run directory of .xml type in which the variable should be set
1289	# - keyid : the variable to modify
1290	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1291	# - value : the value to set in the filein
1292	#
1293	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1294
1295	typeset type filein keyid keyattrib value modify
1296
1297	# Set local variables and test the arguments
1298	if [ $# = 5 ] ; then
1299	# Normal case with 4 arguments
1300	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1301	else
1302	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1303	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1304	return
1305	fi
1306	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1307
1308	# Test if first argument is correct
1309	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1310	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1311	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1312	return
1313	fi
1314
1315	# Test if the file exist.
1316	# Exit with error if the file does not exist for the case blocker or force.
1317	# Only return for the case nonblocker.
1318	if [ ! -f ${filein} ] ; then
1319	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1320	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1321	else
1322	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1323	fi
1324	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1325	return
1326	fi
1327
1328	# Test if keyid is set in filein, otherwise exit
1329	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1330	# Variable key is not set in filein, stop.
1331	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1332	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1333	return
1334	fi
1335
1336	# Check if AUTO is set on the same line as keyid and keyattrib
1337	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1338	# Modifification will be done
1339	modify=yes
1340	else
1341	if [ ${type} = blocker ] ; then
1342	# Exit, the variable must be set to AUTO
1343	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1344	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1345	return
1346	elif [ ${type} = nonblocker ] ; then
1347	# Nothing will be done
1348	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1349	modify=no
1350	elif [ ${type} = force ] ; then
1351	# Force modification
1352	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1353	modify=yes
1354	fi
1355	fi
1356
1357	# Do the modifcation now
1358	if [ ${modify} = yes ] ; then
1359	if [ ${keyattrib} = NONE ] ; then
1360	# Case to modify the variable itself
1361	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1362	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
1363	else
1364	# Check if keyattrib is set on the same line as keyid
1365	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1366	# Case to modify the attribute value
1367	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1368	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
1369	else
1370	# Case to add the attribute and its value
1371	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1372	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1373	fi
1374	fi
1375	\mv ${filein}.tmp ${filein}
1376	fi
1377	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1378	}
1379
1380	#=======================================================================
1381	function IGCM_comp_Update
1382	{
1383	IGCM_debug_PushStack "IGCM_comp_Update"
1384
1385	# Debug Print :
1386	echo
1387	IGCM_debug_Print 1 "IGCM_comp_Update"
1388	echo
1389
1390	typeset ExeNameIn ExeNameOut
1391	typeset comp compname comptagname
1392	for comp in ${config_ListOfComponents[*]} ; do
1393	# Define component
1394	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1395	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1396
1397	# Copy executable for this component
1398	eval ExeNameIn=\${config_Executable_${comp}[0]}
1399	eval ExeNameOut=\${config_Executable_${comp}[1]}
1400
1401	# If missing executable and DRYRUN is set to 0 or 1 then stop!
1402	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1403	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
1404	fi
1405
1406	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1407	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1408	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1409	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1410	fi
1411	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1412	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1413	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1414	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1415	fi
1416	fi
1417
1418	# Debug Print
1419	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1420	# UPDATE component
1421	${comp}_Update
1422
1423	done
1424
1425	IGCM_debug_PopStack "IGCM_comp_Update"
1426	}
1427
1428	#=======================================================================
1429	function IGCM_comp_Finalize
1430	{
1431	IGCM_debug_PushStack "IGCM_comp_Finalize"
1432
1433	# Debug Print :
1434	echo
1435	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1436	echo
1437
1438	typeset ListTextName TextName0
1439	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1440	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1441	typeset -Z4 j4 #BASH declare j4
1442	typeset list_file nlist_file
1443	typeset compactoutputs
1444
1445	# Initialize array hosting list of rebuilded files to copy
1446	unset rebuildedActionsList
1447
1448	# Text compacting options
1449	compactoutputs=false
1450	if [ X${JobType} != XRUN ] ; then
1451	compactoutputs=true
1452	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1453	compactoutputs=true
1454	fi
1455
1456	# Prepare headers for the shell dedicated to offline rebuild
1457	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1458	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1459	if [ ${DRYRUN} -le 1 ] ; then
1460	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1461	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1462	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1463	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1464	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1465	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1466	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1467	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1468	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1469	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1470	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1471	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1472	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1473	fi
1474	fi
1475
1476	for comp in ${config_ListOfComponents[*]} ; do
1477	# Define component
1478	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1479	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1480
1481	# Debug Print
1482	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1483	# FINALIZE component
1484	${comp}_Finalize
1485
1486	card=${SUBMIT_DIR}/COMP/${compname}.card
1487
1488	# Save Output Text files of models
1489	#---------------------------------
1490	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1491	IGCM_card_DefineArrayFromOption ${card} OutputText List
1492	ListTextName=${compname}_OutputText_List
1493
1494	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1495	if [ X${TextName0} != X${NULL_STR} ] ; then
1496	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1497
1498	(( i=0 ))
1499	until [ $i -eq $NbFiles ]; do
1500	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1501	eval file_out=${PREFIX}_${file_in}
1502
1503	(( i=i+1 ))
1504
1505	unset list_file
1506	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1507	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1508	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 )
1509	nlist_file=${#list_file[@]}
1510	if [ ${nlist_file} -gt 1 ] ; then
1511	if ( ${compactoutputs} ) ; then
1512	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1513	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1514	echo ${list_file[*]} > ${file_out}
1515	echo "" >> ${file_out}
1516
1517	(( i_ = 0 ))
1518	for file in ${list_file[@]} ; do
1519	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1520	echo "\| " ${i_} " " ${file} >> ${file_out}
1521	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1522	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1523	echo "" >> ${file_out}
1524	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1525	(( i_ = i_ + 1 ))
1526	done
1527	if ( ${ExecutionFail} ) ; then
1528	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1529	fi
1530
1531	if [ X${Pack} = Xtrue ] ; then
1532	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1533	else
1534	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1535	fi
1536
1537	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1538	else
1539	for file in ${list_file[@]} ; do
1540	if ( ${ExecutionFail} ) ; then
1541	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1542	fi
1543
1544	if [ X${Pack} = Xtrue ] ; then
1545	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1546	else
1547	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1548	fi
1549
1550	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1551	done
1552	fi
1553	else
1554	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1555	eval IGCM_sys_Mv ${file_in}* ${file_in}
1556	fi
1557
1558	if ( ${ExecutionFail} ) ; then
1559	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1560	fi
1561
1562	if [ X${Pack} = Xtrue ] ; then
1563	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1564	else
1565	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1566	fi
1567	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1568	fi
1569	done
1570	fi
1571
1572	# Save Restarts files
1573	#--------------------
1574	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1575	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1576	ListFilesName=${compname}_RestartFiles_List
1577	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1578
1579	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1580	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1581
1582	(( i=0 ))
1583	until [ $i -ge $NbFiles ]; do
1584	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1585	eval file_in=${file_in_}
1586
1587	(( i_ = i+1 ))
1588	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1589	eval file_out=${file_out_}
1590
1591	(( i_ = i+2 ))
1592	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1593	eval file_outin=${file_outin_}
1594
1595	generic_restart_file_name_in=$( basename ${file_in} .nc )
1596	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1597	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1598
1599	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1600	if [ ${nb_restart_file} -gt 1 ] ; then
1601	j=0 # BASH LINE NOT NEEDED
1602	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1603	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1604	j4=${j} # BASH LINE NOT NEEDED
1605	if [ X${Pack} = Xtrue ] ; then
1606	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1607	else
1608	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1609	fi
1610	if [ ! ${file_in} = ${file_outin} ] ; then
1611	if ( ${ExitFlag} ) ; then
1612	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1613	else
1614	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1615	fi
1616	fi
1617	(( j=j+1 )) # BASH LINE NOT NEEDED
1618	done
1619	else
1620	if [ X${Pack} = Xtrue ] ; then
1621	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1622	else
1623	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1624	fi
1625	if [ ! ${file_in} = ${file_outin} ] ; then
1626	if ( ${ExitFlag} ) ; then
1627	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1628	else
1629	IGCM_sys_Mv ${file_in} ${file_outin}
1630	fi
1631	fi
1632	fi
1633
1634	(( i=i+3 ))
1635	done
1636	else
1637	if [ X${FileName0} != XNONE ] ; then
1638	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1639	else
1640	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1641	fi
1642	fi
1643
1644	# Save Output files
1645	#------------------
1646	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1647	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1648	ListFilesName=${compname}_OutputFiles_List
1649	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1650
1651	if [ X${FileName0} != X${NULL_STR} ] ; then
1652	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1653
1654	(( i=0 ))
1655	until [ $i -ge $NbFiles ]; do
1656	SaveOnArchive=true
1657	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1658	eval file_in=${file_in_}
1659	(( i_ = i+1 ))
1660	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1661	eval file_out=${file_out_}
1662	#
1663	# Override file_out path remplacing R_SAVE by R_BUFR
1664	#
1665	if [ X${Pack} = Xtrue ] ; then
1666	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1667	fi
1668	#
1669	# Not necessarily the best option. /!\ Potential side effects /!\
1670	#
1671	(( i_ = i+2 ))
1672	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1673	#
1674	generic_file_name=$( basename ${file_in} .nc )
1675	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1676	#
1677	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1678	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1679	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1680	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1681	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1682	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1683	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1684	IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc
1685	else
1686	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1687	IGCM_sys_Mv ${generic_file_name}_[0-9]*.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1688
1689	# Prepare the shell dedicated to offline rebuild
1690	if [ $DRYRUN -le 1 ]; then
1691	if [ ${file_in} = histstn.nc ] ; then
1692	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1693	else
1694	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1695	fi
1696	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1697	fi
1698	#
1699	# Load Patch we need to apply and apply
1700	if [ $DRYRUN -le 1 ]; then
1701	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1702	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1703	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1704	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1705	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1706	done
1707	fi
1708	fi
1709	#
1710	if [ $DRYRUN -le 1 ]; then
1711	if [ X${Pack} = Xtrue ] ; then
1712	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1713	else
1714	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1715	fi
1716	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1717	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1718	fi
1719	SaveOnArchive=false
1720	fi
1721	fi
1722	#
1723	if [ ${SaveOnArchive} = true ] ; then
1724	#
1725	# Rebuild has been done online or it was not needed
1726	#
1727	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1728	#
1729	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1730	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1731	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1732	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1733	#
1734	if [ $DRYRUN -le 1 ]; then
1735	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1736	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1737	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1738	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1739	done
1740	#
1741	if [ X${Pack} = Xtrue ] ; then
1742	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1743	else
1744	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1745	fi
1746	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1747	#
1748	fi
1749	else
1750	#
1751	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1752	#
1753	if [ X${Pack} = Xtrue ] ; then
1754	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1755	else
1756	IGCM_sys_Put_Out ${file_in} ${file_out}
1757	fi
1758	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1759	if [ ${nb_rebuild_file} -gt 1 ] ; then
1760	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1761	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1762	done
1763	fi
1764	fi
1765	fi
1766	(( i=i+3 ))
1767	done
1768	fi
1769	echo
1770	done
1771	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1772	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1773	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1774	i=0
1775	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1776	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1777	(( i=i+1 ))
1778	done
1779	fi
1780	IGCM_debug_PopStack "IGCM_comp_Finalize"
1781	}

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