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libIGCM_comp.ksh @ 1603

Last change on this file since 1603 was 1603, checked in by aclsce, 7 months ago

Changed libIGCM behaviour in case of pb in pack_output.job : now, we exit from the job if there is any problem, whatever we are in PROD, DEVT, TEST mode.
Specification of pack frequency per file :

In order to reduce the number of inodes, it is possible to specify by file the frequency of packing. The syntax to do that is in the 4th column of OutputFiles? section of the component.card, for example as follows in lmdz.card :
[OutputFiles?]
List= (histmth.nc, ${R_OUT_ATM_O_M}/${PREFIX}_1M_histmth.nc, Post_1M_histmth, 100Y), \

(histday.nc, ${R_OUT_ATM_O_D}/${PREFIX}_1D_histday.nc, Post_1D_histday, 10Y), \

...

In this example, histmth files will be packed every 100 years and histday files will be packed every 10 years.
The pack frequency you defined in config.card is the frequency of pack by default, that means if a specific frequency of pack is specified for a file in a component.card, this file will be packed at the specific frequency whereas all other files will be packed at global pack frequency (specified in config.card) and in this case, the frequency pack (from the config.card) is the frequency the pack_output job will be launched at.
There is a constraint to use this fonctionality : the Packfrequency you defined in config.card must be greater or equal to the pack frequencies you specified for each type of file in component.card, otherwise the computing job will be stopped (with an explicit error message).
Surpack mode :
A surpack mode functionality is available through the use of pack_output.job. To enable this functionality, you have to put "surpack_mode=y" (default value is n). The way to use is similar to restart post-processing pack_output jobs, as indicated here : http://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/CheckDebug#RestartPack_output. You can either use a global pack frequency in config.card or specific pack frequency per file, as explained above.

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: 79.3 KB

Line
1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
6	# $Revision:: $ Revision of last commit
7	# $Author:: $ Author of last commit
8	# $Date:: $ Date of last commit
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	#
12	#**************************************************************
13
14	#========================================================================
15	function IGCM_comp_Initialize
16	{
17	IGCM_debug_PushStack "IGCM_comp_Initialize"
18
19	# Debug Print :
20	echo
21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
22	echo
23
24	typeset comp compname comptagname 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_${comp}_A=\${R_OUT_${comp}}/Analyse
82	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_A}
83
84	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
86
87	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
88	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
89
90	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
91	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
92	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
93	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
94
95	eval R_OUT_${comp}_A_H=\${R_OUT_${comp}_A}/TS_HF
96	eval R_OUT_${comp}_A_D=\${R_OUT_${comp}_A}/TS_DA
97	eval R_OUT_${comp}_A_M=\${R_OUT_${comp}_A}/TS_MO
98	eval R_OUT_${comp}_A_Y=\${R_OUT_${comp}_A}/TS_YE
99
100	# Define BUFFERED Dirs
101	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
102	eval R_BUF_${comp}=${R_BUFR}/${comp}
103	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
104
105	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
107
108	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
110
111	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
112	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
113
114	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
115	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
116
117	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
118	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
119	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
120	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
121
122	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
123	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
124	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
125	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
126
127	# Define CMIP6 Dirs
128	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
129	fi
130
131	# Read UserChoices section of component card
132	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
133	IGCM_card_DefineArrayFromSection ${card} UserChoices
134	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
135
136	# If section is not empty we define corresponding variables
137	if [ X${first_option} != X"Error:" ] ; then
138	if [ X${card_UserChoices[0]} != X ] ; then
139	unset card_UserChoices
140	fi
141	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
142	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
143	for option in ${card_UserChoices[*]} ; do
144	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
145	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
146	done
147	fi
148
149	# Read and Build Output File stuff
150	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
151	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
152	ListFilesName=${compname}_OutputFiles_List
153	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
154	#
155	if [ X${FileName0} != X${NULL_STR} ] ; then
156	#
157	#IGCM_debug_Print 1 "Component : ${compname}"
158	#
159	# INITIALISATION
160	#
161	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
162	#
163	i=2
164	#
165	until [ $i -ge $NbFiles ]; do
166	#
167	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
168	#
169	if [ X${flag_post} != XNONE ] ; then
170	#
171	# First of all
172	#
173	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
174	# This section is mandatory
175	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
176	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
177	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
178	IGCM_debug_Verif_Exit
179	fi
180	#
181	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
182	#
183	# variable option allready typeset above
184	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
185	if [ ${option} = Seasonal ] ; then
186	FoundSeasonal=true
187	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
188	fi
189	done
190	#
191	if [ ! X${FoundSeasonal} = Xtrue ] ; then
192	eval ${compname}_${flag_post}_Seasonal=ON
193	fi
194	#
195	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
196	Seasonal=true
197	fi
198
199	# Dimension = vide si vieille card.
200	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
201	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
202	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
203	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
204	ListDimension[0]=2D
205	ListDimension[1]=3D
206	TimeSeries=false
207	iLoop=${#ListDimension[*]}
208	j=0
209	until [ $j -ge ${iLoop} ]; do
210	Dimension=${ListDimension[${j}]}
211	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
212	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
213	#
214	# Time series WITHOUT chunk
215	#
216	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
217	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
218	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
219	eval TimeSeries${Dimension}=true
220	fi
221	fi
222	#
223	# Time series WITH chunk
224	#
225	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
226	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
227	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
228	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
229	eval TimeSeriesChunck${Dimension}=true
230	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
231	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
232	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
233	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
234	fi
235	fi
236	(( j=j+1 ))
237	done
238	else
239	ListDimension[0]=""
240	TimeSeries=true
241	TimeSeries2D=false
242	TimeSeries3D=false
243	TimeSeriesChunck2D=false
244	TimeSeriesChunck3D=false
245	fi
246	fi
247	((i_ = i +1))
248	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
249	eval Testvar=${Testvar_}
250	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
251	((i = i+4))
252	else
253	(( i=i+3 ))
254	fi
255	done
256	fi
257	# Debug Print
258	IGCM_debug_Print 3 "Initialize ${compname} with driver."
259	# INIT component
260	${comp}_Initialize
261	echo
262	done
263
264	IGCM_debug_PopStack "IGCM_comp_Initialize"
265	}
266
267	#=======================================================================
268	function IGCM_comp_PrepareDeletedFiles
269	{
270	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
271
272	if [ X${2} != X. ] ; then
273	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
274	else
275	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
276	fi
277
278	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
279	}
280
281	#=======================================================================
282	function IGCM_comp_PrepareXiosFiles
283	{
284	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
285
286	typeset file
287	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
288
289	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
290	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
291	fi
292	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
293	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
294	fi
295	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
296	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
297	fi
298
299	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
300	}
301
302	#=======================================================================
303	function IGCM_comp_GetInputInitialStateFiles
304	{
305	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
306
307	# Debug Print :
308	echo
309	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
310	echo
311
312	# Only the first time step need InitialStateFiles
313	# otherwise it's BoundaryConditions
314	if ( ${FirstInitialize} ) ; then
315	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
316	typeset file_in_ file_in file_out_ file_out do_init
317	for comp in ${config_ListOfComponents[*]} ; do
318	# Initialize
319	do_init="y"
320	# Do we need to bring initial state file for this component
321	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
322	eval do_init="n"
323	else
324	# Read component Restarts parameters
325	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
326	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
327	if [ "${do_start}" = "y" ] ; then
328	do_init="n"
329	else
330	do_init="y"
331	fi
332	fi
333
334	if [ "${do_init}" = "y" ] ; then
335	# Define component
336	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
337	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
338
339	# Debug Print :
340	IGCM_debug_Print 3 "Initialisation files ${compname}"
341
342	card=${SUBMIT_DIR}/COMP/${compname}.card
343
344	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
345	ListFilesName=${compname}_InitialStateFiles_List
346
347	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
348	if [ X${FileName0} != X${NULL_STR} ] ; then
349	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
350	(( i=0 ))
351	until [ $i -ge $NbFiles ]; do
352	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
353	eval file_in=${file_in_}
354	(( i_ = i+1 ))
355	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
356	eval file_out=${file_out_}
357
358	IGCM_sys_IsFileArchived ${file_in}
359	if [ $? = 0 ] ; then
360	IGCM_sys_Get ${file_in} ${file_out}
361	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
362	else
363	IGCM_sys_Cp ${file_in} ${file_out}
364	fi
365	(( i=i+2 ))
366	done
367	fi
368	fi
369	done
370	fi
371	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
372	}
373
374	#=======================================================================
375	# Definition of Smooth modulo function
376	# usage :
377	# IGCM_SmoothModulo StringModulo value
378	#
379	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
380	# [min]:[modulo:][max]
381	# where :
382	# [] value are optionnals;
383	# empty min equal 1
384	# empty max equal infinity
385	# modulo not given or empty equal 1
386	# empty string or just ':' equal always.
387	#
388	# value : the value to test with the definition
389	#
390	# return : true(1)/false(0)
391	function IGCM_SmoothModulo
392	{
393	IGCM_debug_PushStack "IGCM_SmoothModulo"
394	typeset defVector ModValue
395
396	eval set +A defVector -- $( echo "${1}" \| \
397	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
398
399	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
400	arr[1]=${defVector[0]}
401	arr[2]=${defVector[2]}
402
403	# Test limits :
404	# ${defVector[0]} <= ${2} <= ${defVector[2]}
405	# or ${defVector[2]} == -1
406	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
407	# Test modulo
408	ModValue=$( expr $ ${2} - ${defVector[0]} $ % ${defVector[1]} )
409	if [ ${ModValue} -eq 0 ] ; then
410	arr[3]=true
411	echo ${arr[@]}
412	IGCM_debug_PopStack "IGCM_SmoothModulo"
413	return 1
414	else
415	arr[3]=false
416	echo ${arr[@]}
417	IGCM_debug_PopStack "IGCM_SmoothModulo"
418	return 0
419	fi
420	else
421	arr[3]=false
422	echo ${arr[@]}
423	IGCM_debug_PopStack "IGCM_SmoothModulo"
424	return 0
425	fi
426	}
427
428	#=======================================================================
429	function IGCM_comp_GetInputSmoothFiles
430	{
431	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
432
433	# Debug Print :
434	echo
435	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
436	echo
437
438	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
439	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
440
441	for comp in ${config_ListOfComponents[*]} ; do
442	# Define component
443	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
444	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
445
446	# Debug Print :
447	IGCM_debug_Print 3 "Smooth files ${compname}"
448
449	card=${SUBMIT_DIR}/COMP/${compname}.card
450
451	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
452	ListFilesName=${compname}_SmoothFiles_List
453	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
454
455	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
456	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
457
458	(( i=0 ))
459	until [ $i -ge $NbFiles ]; do
460	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
461	eval file_in=${file_in_}
462	(( i_ = i+1 ))
463	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
464	eval file_out=${file_out_}
465
466	# define CumulPeriod definition for this file
467	(( i__ = i+2 ))
468	eval SmoothDef=\${${ListFilesName}[$i__]}
469	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
470	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
471	j=1
472	for val in ${aux} ; do
473	[ ${j} -eq 1 ] && SmoothMin=${val}
474	[ ${j} -eq 2 ] && SmoothMax=${val}
475	[ ${j} -eq 3 ] && ret=${val}
476	(( j=j+1 ))
477	done
478	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
479	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
480
481	IGCM_sys_IsFileArchived ${file_in}
482	if [ $? = 0 ] ; then
483	IGCM_sys_Get ${file_in} ${file_out}
484	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
485	else
486	IGCM_sys_Cp ${file_in} ${file_out}
487	fi
488	fi
489	(( i=i+3 ))
490	done
491	fi
492	done
493
494	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
495	}
496
497	#=======================================================================
498	function IGCM_comp_GetInputBoundaryFiles
499	{
500	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
501
502	# Debug Print :
503	echo
504	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
505	echo
506
507	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
508	typeset file_in_ file_in file_out_ file_out
509
510	if [ ${Period} = 1 ]; then
511	ListFixBoundary=" "
512	fi
513
514	for comp in ${config_ListOfComponents[*]} ; do
515
516	# Define component
517	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
518	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
519
520	# Debug Print :
521	IGCM_debug_Print 3 "Boundary files ${compname}"
522
523	card=${SUBMIT_DIR}/COMP/${compname}.card
524
525	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
526	ListFilesName=${compname}_BoundaryFiles_List
527	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
528
529	if [ X${FileName0} != X${NULL_STR} ] ; then
530	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
531
532	(( i=0 ))
533	until [ $i -ge $NbFiles ]; do
534	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
535	eval file_in=${file_in_}
536	(( i_ = i+1 ))
537	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
538	eval file_out=${file_out_}
539
540	IGCM_sys_IsFileArchived ${file_in}
541	if [ $? = 0 ] ; then
542	IGCM_sys_Get ${file_in} ${file_out}
543	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
544	else
545	IGCM_sys_Cp ${file_in} ${file_out}
546	fi
547
548	(( i=i+2 ))
549	done
550	fi
551
552	# Get non deleted files
553	if [ ${Period} = 1 ]; then
554
555	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
556	ListFilesName=${compname}_BoundaryFiles_ListNonDel
557	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
558
559	if [ X${FileName0} != X${NULL_STR} ] ; then
560	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
561
562	(( i=0 ))
563	until [ $i -ge $NbFiles ]; do
564	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
565	eval file_in=${file_in_}
566	(( i_ = i+1 ))
567	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
568	eval file_out=${file_out_}
569
570	IGCM_sys_IsFileArchived ${file_in}
571	if [ $? = 0 ] ; then
572	IGCM_sys_Get ${file_in} ${file_out}
573	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
574	else
575	IGCM_sys_Cp ${file_in} ${file_out}
576	fi
577
578	if [ X${file_out} != X. ] ; then
579	ListFixBoundary=${ListFixBoundary}" "${file_out}
580	else
581	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
582	fi
583
584	(( i=i+2 ))
585	done
586	fi
587	fi
588	done
589
590	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
591	}
592
593	#=======================================================================
594	function IGCM_comp_DelFixeBoundaryFiles
595	{
596	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
597
598	# Debug Print :
599	echo
600	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
601	echo
602
603	ls -l ${ListFixBoundary}
604	rm -f ${ListFixBoundary}
605
606	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
607	}
608
609	#=======================================================================
610	function IGCM_comp_GetInputParametersFiles
611	{
612	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
613
614	# Debug Print :
615	echo
616	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
617	echo
618
619	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
620	for comp in ${config_ListOfComponents[*]} ; do
621	# Define component
622	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
623	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
624
625	# Initialize array hosting file_def and field_def files to check and/or modify
626	unset FieldDef
627	unset FileDef
628
629	# Debug Print :
630	IGCM_debug_Print 3 "Parameters ${compname}"
631
632	card=${SUBMIT_DIR}/COMP/${compname}.card
633
634	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
635	ListFilesName=${compname}_ParametersFiles_List
636	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
637
638	if [ X${FileName0} != X${NULL_STR} ] ; then
639	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
640
641	(( i=0 ))
642	until [ $i -ge $NbFiles ]; do
643	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
644	eval file_in=${file_in_}
645	(( i_ = i+1 ))
646	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
647	eval file_out=${file_out_}
648
649	IGCM_sys_Cp ${file_in} ${file_out}
650	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
651	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
652
653	(( i=i+2 ))
654	done
655	fi
656
657	done
658
659	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
660	}
661
662	#=======================================================================
663	function IGCM_comp_GetInputRestartFiles
664	{
665	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
666
667	# Debug Print :
668	echo
669	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
670	echo
671
672	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
673	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
674	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
675	typeset file_in file_out file_in_ file_out_ file_in_Name
676	typeset -Z4 j4
677	#BASH declare j4
678
679	IsMatching=""
680
681	for comp in ${config_ListOfComponents[*]} ; do
682	# Define component
683	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
684	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
685	#
686	card=${SUBMIT_DIR}/COMP/${compname}.card
687	#
688	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
689	ListFilesName=${compname}_RestartFiles_List
690	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
691
692	# Debug Print :
693	IGCM_debug_Print 3 "restart ${compname}"
694
695	if ( ${FirstInitialize} ) ; then
696
697	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
698	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
699	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
700	CompOldName=IOS
701	config_IOS_Restart="n"
702	do_start="n"
703	config_IOS_RestartDate=-1
704	config_IOS_RestartJobName=${NULL_STR}
705	config_IOS_RestartPath=${NULL_STR}
706	else
707	eval config_${comp}_Restart="y"
708	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
709	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
710	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
711	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
712	eval CompOldName=${comp}
713	fi
714	else
715	# Read component Restarts parameters
716	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
717	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
718
719	if [ "${do_start}" = "y" ] ; then
720	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
721	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
722	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
723	else
724	eval config_${comp}_RestartDate=-1
725	eval config_${comp}_RestartJobName=${NULL_STR}
726	eval config_${comp}_RestartPath=${NULL_STR}
727	fi
728
729	eval CompOldName=\${config_${comp}_OldName}
730	if [ X${CompOldName} = X ] ; then
731	eval CompOldName=${comp}
732	fi
733
734	# Reinitialize IsMatching to allow searching for a different tar file for each component.
735	IsMatching=""
736	TarFileFound=""
737	fi
738
739	if [ "${do_start}" = "y" ] ; then
740
741	# Restore Restarts files
742	#-----------------------
743	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
744	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
745
746	(( i=1 ))
747	until [ $i -gt $NbFiles ]; do
748	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
749	eval file_in=${file_in_}
750	(( i_ = i+1 ))
751	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
752	eval file_out=${file_out_}
753
754	eval Date_tmp=\${config_${comp}_RestartDate}
755	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
756	# will be re-use
757	eval RestartPath=\${config_${comp}_RestartPath}
758	eval RestartJobName=\${config_${comp}_RestartJobName}
759	#
760	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
761	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
762
763	extension_in=$( echo ${file_in_Name##*.} )
764	extension_out=$( echo ${file_out##*.} )
765
766	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
767	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
768
769	Path_OUT=${Path_r}/${generic_restart_file_name_in}
770
771	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
772	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
773	Buffered=true
774	Archived=false
775	Tared=false
776	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
777	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
778	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
779	Buffered=false
780	Archived=true
781	Tared=false
782	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
783	else
784	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
785	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
786	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
787	Buffered=false
788	Archived=false
789	Tared=true
790	# Look after the tar file we want if we did not found it already
791	if [ X${IsMatching} = X ] ; then
792	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
793	if [ $? ] ; then
794	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
795	IsMatching=$( echo ${PotentialTarFile##*/} \| \
796	sed "s:_restart::" \| \
797	sed "s:^${RestartJobName}_::" \| \
798	sed "s:\.tar$::" \| \
799	gawk -F_ -v restartdate=${Date_r} \
800	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
801	if [ ! X${IsMatching} = X ] ; then
802	TarFileFound=${PotentialTarFile}
803	break
804	fi
805	done
806	fi
807	# Stop here if nothing has been found
808	if [ X${TarFileFound} = X ] ; then
809	IGCM_debug_Print 3 "Restart files were not found!"
810	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
811	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
812	IGCM_debug_Exit "Please double check restart settings in config.card"
813	IGCM_debug_Verif_Exit
814	fi
815	fi
816	IGCM_sys_PrepareTaredRestart ${TarFileFound}
817	TarFileLocation=$( basename ${TarFileFound} )
818	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
819	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
820	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
821	fi
822
823	if [ ${nb_restart_file} -gt 1 ] ; then
824	j=0 # BASH LINE NOT NEEDED
825	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
826	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
827	j4=${j} # BASH LINE NOT NEEDED
828	if [ X${Buffered} = Xtrue ] ; then
829	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
830	elif [ X${Archived} = Xtrue ] ; then
831	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
832	elif [ X${Tared} = Xtrue ] ; then
833	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
834	fi
835	(( j=j+1 )) #BASH LINE NOT NEEDED
836	done
837
838	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
839	if [ X${OCE_PROC_MPI} != X ] ; then
840	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
841	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
842	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
843	fi
844	fi
845	else
846	if [ X${Buffered} = Xtrue ] ; then
847	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
848	elif [ X${Archived} = Xtrue ] ; then
849	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
850	elif [ X${Tared} = Xtrue ] ; then
851	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
852	fi
853	fi
854	(( i=i+3 ))
855	done
856	else
857	if [ X${FileName0} != XNONE ] ; then
858	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
859	else
860	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
861	fi
862	fi
863	fi
864	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
865	# if not FirstInitialize and first loop of this job
866
867	# Restore Restarts files
868	#-----------------------
869	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
870	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
871
872	(( i=1 ))
873	until [ $i -gt $NbFiles ]; do
874	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
875	eval file_in=${file_in_}
876	(( i_ = i+1 ))
877	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
878	eval file_out=${file_out_}
879
880	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
881
882	extension_in=$( echo ${file_in_Name##*.} )
883	extension_out=$( echo ${file_out##*.} )
884
885	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
886	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
887
888	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
889	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
890
891	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
892	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
893	Buffered=true
894	Archived=false
895	Tared=false
896	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
897	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
898	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
899	Buffered=false
900	Archived=true
901	Tared=false
902	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
903	else
904	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
905	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
906	Buffered=false
907	Archived=false
908	Tared=true
909	# Look after the tar file we want if we did not found it already
910	if [ X${IsMatching} = X ] ; then
911	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
912	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
913	if [ ! X${IsMatching} = X ] ; then
914	TarFileFound=${PotentialTarFile}
915	break
916	fi
917	done
918	fi
919	# Stop here if nothing has been found
920	if [ X${TarFileFound} = X ] ; then
921	IGCM_debug_Print 3 "Restart files were not found!"
922	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
923	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
924	IGCM_debug_Exit "Please double check restart settings in config.card"
925	IGCM_debug_Verif_Exit
926	fi
927	IGCM_sys_PrepareTaredRestart ${TarFileFound}
928	TarFileLocation=$( basename ${TarFileFound} )
929	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
930	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
931	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
932	fi
933
934	if [ ${nb_restart_file} -gt 1 ] ; then
935	j=0 # BASH LINE NOT NEEDED
936	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
937	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
938	j4=${j} # BASH LINE NOT NEEDED
939	if [ X${Buffered} = Xtrue ] ; then
940	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
941	elif [ X${Archived} = Xtrue ] ; then
942	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
943	elif [ X${Tared} = Xtrue ] ; then
944	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
945	fi
946	(( j=j+1 )) # BASH LINE NOT NEEDED
947	done
948	else
949	if [ X${Buffered} = Xtrue ] ; then
950	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
951	elif [ X${Archived} = Xtrue ] ; then
952	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
953	elif [ X${Tared} = Xtrue ] ; then
954	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
955	fi
956	fi
957	(( i=i+3 ))
958	done
959	else
960	if [ X${FileName0} != XNONE ] ; then
961	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
962	else
963	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
964	fi
965	fi
966	fi
967	done
968
969	NbFiles=$( ls * 2> /dev/null \| wc -l )
970	if [ ${NbFiles} -gt 0 ] ; then
971	IGCM_sys_Chmod u+rw *
972	fi
973
974	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
975	}
976
977	#=======================================================================
978	function IGCM_comp_GetInputBinaryFiles
979	{
980	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
981
982	# Debug Print :
983	echo
984	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
985	echo
986
987	# Clean up previous pass
988	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
989
990	typeset comp ExeNameIn ExeNameOut byPass
991	typeset compilerNmbr compilerUnit compilerFull
992	byPass=false
993	for comp in ${config_ListOfComponents[*]} ; do
994	# Define component
995
996	# Copy executable for this component
997	eval ExeNameIn=\${config_Executable_${comp}[0]}
998	eval ExeNameOut=\${config_Executable_${comp}[1]}
999	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
1000	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
1001	# The executable is set in config.card and is different from ""
1002	# Use eval to expand ExeNameIn if variables are used in the name
1003	eval ExeNameIn=${ExeNameIn}
1004	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1005	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
1006	fi
1007	fi
1008
1009	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1010	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1011	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1012	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1013	fi
1014	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1015	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1016	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1017	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1018	fi
1019	fi
1020
1021	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1022	# Get the compiler version
1023	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1024	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
1025	# Save it
1026	echo $compilerFull >> ${RUN_DIR}/compiler.txt
1027	[ X${compilerFull} = X ] && byPass=true
1028	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
1029	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
1030	fi
1031	done
1032
1033	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
1034	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
1035
1036	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
1037	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
1038	fi
1039
1040
1041	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
1042	}
1043
1044	#=======================================================================
1045	function IGCM_comp_PeriodStart
1046	{
1047	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
1048
1049	# Debug Print :
1050	echo
1051	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
1052	echo
1053
1054	typeset ExeNameIn ExeNameOut
1055	typeset comp compname comptagname
1056	for comp in ${config_ListOfComponents[*]} ; do
1057	# Define component
1058	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1059	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1060
1061	# Copy executable for this component
1062	eval ExeNameIn=\${config_Executable_${comp}[0]}
1063	eval ExeNameIn=${ExeNameIn}
1064	eval ExeNameOut=\${config_Executable_${comp}[1]}
1065
1066	# Debug Print
1067	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
1068	# UPDATE component
1069	${comp}_PeriodStart 2> /dev/null
1070
1071	done
1072
1073	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
1074	}
1075
1076
1077
1078	#=======================================================================
1079	function IGCM_comp_modifyFile
1080	{
1081	#
1082	# syntax: IGCM_comp_modifyFile filein key [value]
1083	#
1084	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
1085	#
1086	# This function is used to replace a pattern in a file for a specific variable.
1087	#
1088	# Arguments:
1089	# - filein : the file in run directory in which the variable should be set
1090	# - key : the variable to modify
1091	# - value : the value to set the key equal to
1092	#
1093	IGCM_debug_PushStack "IGCM_comp_modifyFile"
1094
1095	typeset filein key value pattern
1096
1097	# Set local variables and test the arguments
1098	if [ $# = 3 ] ; then
1099	# Normal case with 3 arguments
1100	filein=$1 ; key=$2 ; value=$3
1101	else
1102	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
1103	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1104	return
1105	fi
1106	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
1107
1108	# Test if the file exist
1109	if [ ! -f ${filein} ] ; then
1110	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
1111	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1112	return
1113	fi
1114
1115	# Read the line with key in the file without the comments
1116	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1117
1118	# Verify the existance of the pattern
1119	if [ X"${pattern}" = X ] ; then
1120	# Variable key is not set in filein, stop.
1121	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1122	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1123	return
1124	fi
1125
1126	# Now change key in filein
1127	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
1128	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1129	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1130	\mv ${filein}.tmp ${filein}
1131
1132	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1133	}
1134
1135	#=======================================================================
1136	function IGCM_comp_modifyDefFile
1137	{
1138	#
1139	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1140	#
1141	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1142	#
1143	# This function is used to modify a parameter file for a specific variable.
1144	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1145	# This function can be used in the comp.driver files for the components.
1146	#
1147	# Arguments:
1148	# - type : first argument must be blocker, nonblocker or force
1149	# For "blocker" case, the variable must be attributed the keyworld AUTO
1150	# otherwise this function will exit.
1151	# For "nonblocker" case, the user can remove or modify the variable. For
1152	# this case, as long as AUTO is not set, no modification will be done.
1153	# For "force" case, the variable will be modified even if it is not set to AUTO
1154	# - filein : the file in run directory of .def type in which the variable should be set
1155	# - key : the variable to modify
1156	# - value : the value to set the key equal to, optional. If value is not set or if
1157	# value=DEFAULT, then a default value must be given in filein using syntax :
1158	# key= AUTO : DEFAULT=def_value
1159	#
1160	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1161
1162	typeset type filein key value
1163	typeset filelist nb_occ modify
1164
1165	# Set local variables and test the arguments
1166	if [ $# = 4 ] ; then
1167	# Normal case with 4 arguments
1168	type=$1 ; filein=$2 ; key=$3 ; value=$4
1169	elif [ $# = 3 ] ; then
1170	# Normal case with 3 arguments
1171	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1172	else
1173	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1174	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1175	return
1176	fi
1177	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1178
1179	# Test if first argument is correct
1180	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1181	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1182	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1183	return
1184	fi
1185
1186	# Test if the file exist.
1187	# Exit with error if the file does not exist for the case blocker or force.
1188	# Only return for the case nonblocker.
1189	if [ ! -f ${filein} ] ; then
1190	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1191	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1192	else
1193	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1194	fi
1195	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1196	return
1197	fi
1198
1199	# Define list of files to test using all files with suffix .def (except used*.def)
1200	filelist=$( ls *def \| grep -v used )
1201
1202	# Count number of occurances for the key in all files
1203	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1204
1205	# Test if key is set several times
1206	if [ ${nb_occ} -gt 1 ] ; then
1207	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1208	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1209	return
1210	fi
1211
1212	# Treatement according to different cases
1213	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1214	# Stop if the key is never set and the function is blocker
1215	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1216	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1217	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1218	# The key is not set but it is a nonblocker call so nothing is done.
1219	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1220	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1221	modify=no
1222	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1223	# Variable key is not set in filein, stop.
1224	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1225	fi
1226
1227	# Check if AUTO is set in the filein on the same line as the key variable
1228	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1229	# Modification will be done for all cases
1230	modify=yes
1231	else
1232	# The variable was not set to AUTO
1233	if [ ${type} = blocker ] ; then
1234	# Exit because this is a blocker call
1235	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1236	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1237	return
1238	elif [ ${type} = nonblocker ] ; then
1239	# Do nothing. Suppose that the user did set the variable correct
1240	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1241	modify=no
1242	elif [ ${type} = force ] ; then
1243	# Force modification
1244	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1245	modify=yes
1246	fi
1247	fi
1248
1249	# Do the modifcation now
1250	if [ ${modify} = yes ] ; then
1251
1252	# For option DEFAULT, read default value from file.
1253	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1254	# Case to set DEFAULT value
1255	# Read default value from filein
1256	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1257
1258	if [ X"${value}" = X ] ; then
1259	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1260	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1261	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1262	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1263	return
1264	fi
1265	fi
1266
1267	# Now change key in filein
1268	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1269	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1270	\mv ${filein}.tmp ${filein}
1271	fi
1272	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1273	}
1274
1275	#=======================================================================
1276	function IGCM_comp_modifyNamelist
1277	{
1278	#
1279	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1280	#
1281	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1282	#
1283	# This function is used to modify a parameter file for a specific variable.
1284	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1285	# This function can be used in the comp.driver files for the components.
1286	#
1287	# Arguments:
1288	# - type : first argument must be blocker, nonblocker or force
1289	# For "blocker" case, the variable must be attributed the keyworld AUTO
1290	# otherwise this function will exit.
1291	# For "nonblocker" case, the user can remove or modify the variable. For
1292	# this case, as long as AUTO is not set, no modification will be done.
1293	# For "force" case, the variable will be modified even if it is not set to AUTO
1294	# - filein : the file in run directory of .def type in which the variable should be set
1295	# - key : the variable to modify
1296	# - value : the value to set the key equal to, optional. If value is not set or if
1297	# value=DEFAULT, then a default value must be given in filein using syntax :
1298	# key= AUTO : DEFAULT=def_value
1299	#
1300	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1301
1302	typeset type filein key value pattern modify
1303
1304	# Set local variables and test the arguments
1305	if [ $# = 4 ] ; then
1306	# Normal case with 4 arguments
1307	type=$1 ; filein=$2 ; key=$3 ; value=$4
1308	elif [ $# = 3 ] ; then
1309	# Normal case with 3 arguments
1310	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1311	else
1312	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1313	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1314	return
1315	fi
1316	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1317
1318	# Test if first argument is correct
1319	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1320	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1321	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1322	return
1323	fi
1324
1325	# Test if the file exist.
1326	# Exit with error if the file does not exist for the case blocker or force.
1327	# Only return for the case nonblocker.
1328	if [ ! -f ${filein} ] ; then
1329	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1330	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1331	else
1332	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1333	fi
1334	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1335	return
1336	fi
1337
1338	# Read the line with key in the file without the comments
1339	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1340
1341	# Verify the existance of the pattern
1342	if [ X"$pattern" = X ] ; then
1343	# Variable key is not set in filein, stop.
1344	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1345	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1346	return
1347	fi
1348
1349	# Check if the variable is set to AUTO in the filein
1350	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1351	# Modification will be done for all cases
1352	modify=yes
1353	else
1354	# The variable was not set to AUTO
1355	if [ ${type} = blocker ] ; then
1356	# Exit because this is a blocker call
1357	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1358	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1359	return
1360	elif [ ${type} = nonblocker ] ; then
1361	# Do nothing. Suppose that the user did set the variable correct
1362	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1363	modify=no
1364	elif [ ${type} = force ] ; then
1365	# Force modification
1366	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1367	modify=yes
1368	fi
1369	fi
1370
1371	# Do the modifcation now
1372	if [ ${modify} = yes ] ; then
1373
1374	# For option DEFAULT, read default value from file.
1375	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1376	# Case to set DEFAULT value
1377	# Read default value from filein
1378	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1379
1380	if [ X"${value}" = X ] ; then
1381	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1382	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1383	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1384	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1385	return
1386	fi
1387	fi
1388
1389	# Now change key in filein
1390	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1391	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1392	\mv ${filein}.tmp ${filein}
1393	fi
1394	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1395	}
1396
1397	#=======================================================================
1398	function IGCM_comp_modifyXmlFile
1399	{
1400	#
1401	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1402	#
1403	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1404	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1405	#
1406	# This function is used to modify the value for a specific attribute and variable id.
1407	# The file must be a valid xml file.
1408	# This function can be used in the comp.driver files for the components.
1409	#
1410	# Arguments:
1411	# - type : first argument must be blocker, nonblocker or force.
1412	# For "blocker" case, the variable must be attributed the keyworld AUTO
1413	# otherwise this function will exit.
1414	# For "nonblocker" case, the user can remove or modify the variable. For
1415	# this case, as long as AUTO is not set, no modification will be done.
1416	# For "force" case, the variable will be modified even if it is not set to AUTO
1417	# - filein : the file in run directory of .xml type in which the variable should be set
1418	# - keyid : the variable to modify
1419	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1420	# - value : the value to set in the filein
1421	#
1422	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1423
1424	typeset type filein keyid keyattrib value modify
1425
1426	# Set local variables and test the arguments
1427	if [ $# = 5 ] ; then
1428	# Normal case with 4 arguments
1429	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1430	else
1431	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1432	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1433	return
1434	fi
1435	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1436
1437	# Test if first argument is correct
1438	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1439	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1440	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1441	return
1442	fi
1443
1444	# Test if the file exist.
1445	# Exit with error if the file does not exist for the case blocker or force.
1446	# Only return for the case nonblocker.
1447	if [ ! -f ${filein} ] ; then
1448	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1449	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1450	else
1451	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1452	fi
1453	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1454	return
1455	fi
1456
1457	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
1458	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1459	if [ ${type} = nonblocker ] ; then
1460	# This is a nonblocker case, print warning but do nothing else
1461	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
1462	else
1463	# This is a blocker or force case : stop now
1464	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1465	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1466	return
1467	fi
1468	fi
1469
1470	# Check if AUTO is set on the same line as keyid and keyattrib
1471	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1472	# Modification will be done
1473	modify=yes
1474	else
1475	if [ ${type} = blocker ] ; then
1476	# Exit, the variable must be set to AUTO
1477	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1478	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1479	return
1480	elif [ ${type} = nonblocker ] ; then
1481	# Nothing will be done
1482	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1483	modify=no
1484	elif [ ${type} = force ] ; then
1485	# Force modification
1486	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1487	modify=yes
1488	fi
1489	fi
1490
1491	# Do the modifcation now
1492	if [ ${modify} = yes ] ; then
1493	if [ ${keyattrib} = NONE ] ; then
1494	# Case to modify the variable itself
1495	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1496	sed -e "s/$<[^\"]\"${keyid}\".>$$[^<]$$<[^>]$/\1${value}\3/" ${filein} > ${filein}.tmp
1497	else
1498	# Check if keyattrib is set on the same line as keyid
1499	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1500	# Case to modify the attribute value
1501	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1502	sed -e "/id=\"${keyid}\"/s/$${keyattrib}=\"$[^\"]*$\"$/\1${value}\2/" ${filein} > ${filein}.tmp
1503	else
1504	# Case to add the attribute and its value
1505	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1506	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
1507	fi
1508	fi
1509	\mv ${filein}.tmp ${filein}
1510	fi
1511	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1512	}
1513
1514	#=======================================================================
1515	function IGCM_comp_Update
1516	{
1517	IGCM_debug_PushStack "IGCM_comp_Update"
1518
1519	# Debug Print :
1520	echo
1521	IGCM_debug_Print 1 "IGCM_comp_Update"
1522	echo
1523
1524	typeset comp compname comptagname
1525	for comp in ${config_ListOfComponents[*]} ; do
1526	# Define component
1527	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1528	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1529
1530	# Debug Print
1531	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1532	# UPDATE component
1533	${comp}_Update
1534
1535	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1536	if [ -f timeseries_def_${compname}.xml ]; then
1537	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1538	for line in $( cat ts.temp.${compname}.txt ); do
1539	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1540	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1541	case ${output_freq} in
1542	Y\|y)
1543	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1544	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1545	;;
1546	MO\|mo)
1547	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1548	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1549	;;
1550	D\|d)
1551	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1552	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1553	;;
1554	S\|s)
1555	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1556	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1557	;;
1558	esac
1559	done
1560	fi
1561
1562	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
1563	if [ -f dr2xml_${compname}.xml ]; then
1564	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
1565	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
1566	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
1567	# Modify path from dr2xml_{compname}.xml
1568	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
1569	${libIGCM}/libIGCM_post/xios_parser.py -v modifydr2xmlIPSL --newPath ${CMIP6_DIR} --splitLastDate ${EndYear_p1} --JobName ${config_UserChoices_JobName} --ModelName ${config_UserChoices_ModelName} --ModelVersion ${config_UserChoices_LongName} --ExperimentName ${config_UserChoices_ExperimentName} --file dr2xml_${compname}.xml
1570	else
1571	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
1572	fi
1573	# Overwrite the original file
1574	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
1575	fi
1576	fi
1577	done
1578
1579	IGCM_debug_PopStack "IGCM_comp_Update"
1580	}
1581
1582	#=======================================================================
1583	function IGCM_comp_Finalize
1584	{
1585	IGCM_debug_PushStack "IGCM_comp_Finalize"
1586
1587	# Debug Print :
1588	echo
1589	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1590	echo
1591
1592	typeset ListTextName TextName0
1593	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1594	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1595	typeset -Z4 j4 #BASH declare j4
1596	typeset list_file nlist_file
1597	typeset compactoutputs
1598
1599	# Initialize array hosting list of rebuilded files to copy
1600	unset rebuildedActionsList
1601
1602	# Text compacting options
1603	compactoutputs=false
1604	if [ X${JobType} != XRUN ] ; then
1605	compactoutputs=true
1606	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1607	compactoutputs=true
1608	fi
1609
1610	# Prepare headers for the shell dedicated to offline rebuild
1611	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1612	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1613	if [ ${DRYRUN} -le 1 ] ; then
1614	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1615	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1616	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1617	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1618	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1619	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1620	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1621	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1622	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1623	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1624	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1625	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1626	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1627	fi
1628	fi
1629
1630	for comp in ${config_ListOfComponents[*]} ; do
1631	# Define component
1632	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1633	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1634
1635	# Debug Print
1636	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1637	# FINALIZE component
1638	${comp}_Finalize
1639
1640	card=${SUBMIT_DIR}/COMP/${compname}.card
1641
1642	# Save Output Text files of models
1643	#---------------------------------
1644	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1645	IGCM_card_DefineArrayFromOption ${card} OutputText List
1646	ListTextName=${compname}_OutputText_List
1647
1648	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1649	if [ X${TextName0} != X${NULL_STR} ] ; then
1650	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1651
1652	(( i=0 ))
1653	until [ $i -eq $NbFiles ]; do
1654	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1655	eval file_out=${PREFIX}_${file_in}
1656
1657	(( i=i+1 ))
1658
1659	unset list_file
1660	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1661	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1662	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 )
1663	nlist_file=${#list_file[@]}
1664	if [ ${nlist_file} -gt 1 ] ; then
1665	if ( ${compactoutputs} ) ; then
1666	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1667	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1668	echo ${list_file[*]} > ${file_out}
1669	echo "" >> ${file_out}
1670
1671	(( i_ = 0 ))
1672	for file in ${list_file[@]} ; do
1673	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1674	echo "\| " ${i_} " " ${file} >> ${file_out}
1675	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1676	cat ${file} \| sed "s/$.*$/${i_}\1/" >> ${file_out}
1677	echo "" >> ${file_out}
1678	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1679	(( i_ = i_ + 1 ))
1680	done
1681	if ( ${ExecutionFail} ) ; then
1682	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1683	fi
1684
1685	if [ X${Pack} = Xtrue ] ; then
1686	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1687	else
1688	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1689	fi
1690
1691	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1692	else
1693	for file in ${list_file[@]} ; do
1694	if ( ${ExecutionFail} ) ; then
1695	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1696	fi
1697
1698	if [ X${Pack} = Xtrue ] ; then
1699	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1700	else
1701	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1702	fi
1703
1704	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1705	done
1706	fi
1707	else
1708	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1709	eval IGCM_sys_Mv ${file_in}* ${file_in}
1710	fi
1711
1712	if ( ${ExecutionFail} ) ; then
1713	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1714	fi
1715
1716	if [ X${Pack} = Xtrue ] ; then
1717	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1718	else
1719	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1720	fi
1721	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1722	fi
1723	done
1724	fi
1725
1726	# Save Restarts files
1727	#--------------------
1728	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1729	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1730	ListFilesName=${compname}_RestartFiles_List
1731	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1732
1733	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1734	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1735
1736	(( i=0 ))
1737	until [ $i -ge $NbFiles ]; do
1738	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1739	eval file_in=${file_in_}
1740
1741	(( i_ = i+1 ))
1742	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1743	eval file_out=${file_out_}
1744
1745	(( i_ = i+2 ))
1746	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1747	eval file_outin=${file_outin_}
1748
1749	generic_restart_file_name_in=$( basename ${file_in} .nc )
1750	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1751	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1752
1753	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1754	if [ ${nb_restart_file} -gt 1 ] ; then
1755	j=0 # BASH LINE NOT NEEDED
1756	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1757	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1758	j4=${j} # BASH LINE NOT NEEDED
1759	if [ X${Pack} = Xtrue ] ; then
1760	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1761	else
1762	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1763	fi
1764	if [ ! ${file_in} = ${file_outin} ] ; then
1765	if ( ${ExitFlag} ) ; then
1766	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1767	else
1768	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1769	fi
1770	fi
1771	(( j=j+1 )) # BASH LINE NOT NEEDED
1772	done
1773	else
1774	if [ X${Pack} = Xtrue ] ; then
1775	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1776	else
1777	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1778	fi
1779	if [ ! ${file_in} = ${file_outin} ] ; then
1780	if ( ${ExitFlag} ) ; then
1781	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1782	else
1783	IGCM_sys_Mv ${file_in} ${file_outin}
1784	fi
1785	fi
1786	fi
1787
1788	(( i=i+3 ))
1789	done
1790	else
1791	if [ X${FileName0} != XNONE ] ; then
1792	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1793	else
1794	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1795	fi
1796	fi
1797
1798	# Save Output files
1799	#------------------
1800	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1801	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1802	ListFilesName=${compname}_OutputFiles_List
1803	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1804
1805	if [ X${FileName0} != X${NULL_STR} ] ; then
1806	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1807
1808	(( i=0 ))
1809	until [ $i -ge $NbFiles ]; do
1810	SaveOnArchive=true
1811	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1812	eval file_in=${file_in_}
1813	(( i_ = i+1 ))
1814	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1815	eval file_out=${file_out_}
1816	#
1817	# Override file_out path remplacing R_SAVE by R_BUFR
1818	#
1819	if [ X${Pack} = Xtrue ] ; then
1820	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1821	fi
1822	#
1823	# Not necessarily the best option. /!\ Potential side effects /!\
1824	#
1825	(( i_ = i+2 ))
1826	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1827	#
1828	generic_file_name=$( basename ${file_in} .nc )
1829	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1830	#
1831	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1832	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1833	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1834	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1835	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1836	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1837	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1838	#
1839	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
1840	if [ ${file_in} = output.abort.nc ] ; then
1841	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
1842	else
1843	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
1844	fi
1845	else
1846	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1847	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1848
1849	# Prepare the shell dedicated to offline rebuild
1850	if [ $DRYRUN -le 1 ]; then
1851	if [ ${file_in} = histstn.nc ] ; then
1852	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1853	else
1854	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1855	fi
1856	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1857	fi
1858	#
1859	# Load Patch we need to apply and apply
1860	if [ $DRYRUN -le 1 ]; then
1861	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1862	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1863	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1864	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1865	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1866	done
1867	fi
1868	fi
1869	#
1870	if [ $DRYRUN -le 1 ]; then
1871	if [ X${Pack} = Xtrue ] ; then
1872	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1873	else
1874	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1875	fi
1876	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1877	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1878	fi
1879	SaveOnArchive=false
1880	fi
1881	fi
1882	#
1883	if [ ${SaveOnArchive} = true ] ; then
1884	#
1885	# Rebuild has been done online or it was not needed
1886	#
1887	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1888	#
1889	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1890	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1891	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1892	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1893	#
1894	if [ $DRYRUN -le 1 ]; then
1895	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1896	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1897	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1898	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1899	done
1900	#
1901	if [ X${Pack} = Xtrue ] ; then
1902	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1903	else
1904	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1905	fi
1906	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1907	#
1908	fi
1909	else
1910	#
1911	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1912	#
1913	if [ X${Pack} = Xtrue ] ; then
1914	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1915	else
1916	IGCM_sys_Put_Out ${file_in} ${file_out}
1917	fi
1918	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1919	if [ ${nb_rebuild_file} -gt 1 ] ; then
1920	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1921	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1922	done
1923	fi
1924	fi
1925	fi
1926	((i_ = i_ +1))
1927	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1928	eval Testvar=${Testvar_}
1929	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
1930	((i = i+4))
1931	else
1932	(( i=i+3 ))
1933	fi
1934	done
1935	fi
1936	echo
1937	done
1938	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1939	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1940	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1941	i=0
1942	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1943	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1944	(( i=i+1 ))
1945	done
1946	fi
1947	IGCM_debug_PopStack "IGCM_comp_Finalize"
1948	}

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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1603

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