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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1394

Last change on this file since 1394 was 1394, checked in by sdipsl, 7 years ago
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Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
File size: 74.3 KB

Rev	Line
[2]	1	#!/bin/ksh
	2
	3	#**************************************************************
	4	# Author: Sebastien Denvil, Martial Mancip
[373]	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
[2]	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	{
[544]	17	IGCM_debug_PushStack "IGCM_comp_Initialize"
[2]	18
[778]	19	# Debug Print :
[544]	20	echo
	21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
	22	echo
[2]	23
[1244]	24	typeset comp compname comptagname auxprint card_UserChoices first_option option i j
[544]	25	for comp in ${config_ListOfComponents[*]} ; do
[2]	26
[902]	27	# Define component
[544]	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
[457]	31
[615]	32	# Debug Print
	33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
	34
[1244]	35	# ${compname}.card PATH
[544]	36	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	37
[544]	38	# Manage component executable
	39	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
[2]	40
[849]	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
[902]	46	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
[849]	47	done
	48	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
	49
[544]	50	# Debug Print :
	51	eval auxprint=\${config_${comp}_WriteFrequency}
	52	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
	53	#2> /dev/null
[2]	54
[544]	55	# Debug Print :
	56	IGCM_debug_Print 2 "Initialize following component library"
[522]	57
[544]	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}"
[2]	70
[544]	71	# Debug Print
	72	IGCM_debug_Print 3 "Initialize ${comp} output directory."
[2]	73
[544]	74	# Define ARCHIVED Dirs
	75	eval R_OUT_${comp}=${R_SAVE}/${comp}
	76	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
[2]	77
[544]	78	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
	79	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
[2]	80
[544]	81	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
[804]	82	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
[2]	83
[544]	84	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
[804]	85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
[2]	86
[544]	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
[1022]	94	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
[804]	95	eval R_BUF_${comp}=${R_BUFR}/${comp}
	96	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
[544]	97
[804]	98	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
	99	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
[544]	100
[804]	101	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
	102	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
[544]	103
[804]	104	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
	105	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
[544]	106
[804]	107	eval R_BUF_${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
[544]	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
[804]	118
[544]	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
[778]	122	unset card_UserChoices
[544]	123	fi
[833]	124	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
[544]	125	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
	126	for option in ${card_UserChoices[*]} ; do
[778]	127	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
	128	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
[544]	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 $NbFiles ]; do
[778]	149	#
	150	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
	151	#
	152	if [ X${flag_post} != XNONE ] ; then
	153	#
[544]	154	# First of all
	155	#
[778]	156	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
[1151]	157	# This section is mandatory
	158	if [ "X$( 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
[778]	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}
[544]	196	#
[778]	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
[829]	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}
[778]	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 ))
[544]	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
[2]	239
[544]	240	IGCM_debug_PopStack "IGCM_comp_Initialize"
[2]	241	}
	242
	243	#=======================================================================
	244	function IGCM_comp_PrepareDeletedFiles
	245	{
[544]	246	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
[778]	247
[544]	248	if [ X${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
[2]	253
[544]	254	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
[2]	255	}
	256
	257	#=======================================================================
[1338]	258	function IGCM_comp_PrepareXiosFiles
	259	{
	260	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
	261
	262	typeset file
	263	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
	264
	265	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
	266	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
	267	fi
	268	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
	269	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
	270	fi
	271
	272	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
	273	}
	274
	275	#=======================================================================
[2]	276	function IGCM_comp_GetInputInitialStateFiles
	277	{
[544]	278	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
[2]	279
[544]	280	# Debug Print :
	281	echo
	282	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
	283	echo
[2]	284
[902]	285	# Only the first time step need InitialStateFiles
[544]	286	# otherwise it's BoundaryConditions
	287	if ( ${FirstInitialize} ) ; then
[902]	288	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	289	typeset file_in_ file_in file_out_ file_out do_init
[544]	290	for comp in ${config_ListOfComponents[*]} ; do
	291	# Initialize
	292	do_init="y"
	293	# Do we need to bring initial state file for this component
	294	if [ "${config_Restarts_OverRule}" = "y" ] ; then
[778]	295	eval do_init="n"
[544]	296	else
[778]	297	# Read component Restarts parameters
	298	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	299	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
	300	if [ "${do_start}" = "y" ] ; then
	301	do_init="n"
	302	else
	303	do_init="y"
	304	fi
[544]	305	fi
[2]	306
[544]	307	if [ "${do_init}" = "y" ] ; then
[902]	308	# Define component
[778]	309	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	310	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	311
[778]	312	# Debug Print :
	313	IGCM_debug_Print 3 "Initialisation files ${compname}"
[2]	314
[778]	315	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	316
[778]	317	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
	318	ListFilesName=${compname}_InitialStateFiles_List
[2]	319
[778]	320	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
	321	if [ X${FileName0} != X${NULL_STR} ] ; then
	322	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
	323	(( i=0 ))
	324	until [ $i -ge $NbFiles ]; do
	325	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	326	eval file_in=${file_in_}
	327	(( i_ = i+1 ))
	328	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	329	eval file_out=${file_out_}
[2]	330
[778]	331	IGCM_sys_IsFileArchived ${file_in}
	332	if [ $? = 0 ] ; then
	333	IGCM_sys_Get ${file_in} ${file_out}
	334	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	335	else
	336	IGCM_sys_Cp ${file_in} ${file_out}
	337	fi
	338	(( i=i+2 ))
	339	done
	340	fi
[544]	341	fi
	342	done
	343	fi
	344	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
[2]	345	}
	346
	347	#=======================================================================
[247]	348	# Definition of Smooth modulo function
[902]	349	# usage :
[247]	350	# IGCM_SmoothModulo StringModulo value
	351	#
	352	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
	353	# [min]:[modulo:][max]
	354	# where :
[902]	355	# [] value are optionnals;
[247]	356	# empty min equal 1
	357	# empty max equal infinity
	358	# modulo not given or empty equal 1
	359	# empty string or just ':' equal always.
	360	#
	361	# value : the value to test with the definition
	362	#
[902]	363	# return : true(1)/false(0)
[247]	364	function IGCM_SmoothModulo
	365	{
[544]	366	IGCM_debug_PushStack "IGCM_SmoothModulo"
	367	typeset defVector ModValue
[247]	368
[544]	369	eval set +A defVector -- $( echo "${1}" \| \
	370	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
[247]	371
[544]	372	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
	373	arr[1]=${defVector[0]}
	374	arr[2]=${defVector[2]}
[412]	375
[902]	376	# Test limits :
	377	# ${defVector[0]} <= ${2} <= ${defVector[2]}
[544]	378	# or ${defVector[2]} == -1
	379	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
	380	# Test modulo
	381	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
	382	if [ ${ModValue} -eq 0 ] ; then
	383	arr[3]=true
	384	echo ${arr[@]}
	385	IGCM_debug_PopStack "IGCM_SmoothModulo"
	386	return 1
[247]	387	else
[544]	388	arr[3]=false
	389	echo ${arr[@]}
	390	IGCM_debug_PopStack "IGCM_SmoothModulo"
	391	return 0
[247]	392	fi
[544]	393	else
	394	arr[3]=false
	395	echo ${arr[@]}
	396	IGCM_debug_PopStack "IGCM_SmoothModulo"
	397	return 0
	398	fi
[247]	399	}
	400
	401	#=======================================================================
	402	function IGCM_comp_GetInputSmoothFiles
	403	{
[544]	404	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
[247]	405
[544]	406	# Debug Print :
	407	echo
	408	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
	409	echo
[247]	410
[544]	411	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
	412	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
[247]	413
[544]	414	for comp in ${config_ListOfComponents[*]} ; do
	415	# Define component
	416	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	417	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[247]	418
[544]	419	# Debug Print :
	420	IGCM_debug_Print 3 "Smooth files ${compname}"
[247]	421
[544]	422	card=${SUBMIT_DIR}/COMP/${compname}.card
[247]	423
[544]	424	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
	425	ListFilesName=${compname}_SmoothFiles_List
	426	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[247]	427
[544]	428	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
	429	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[247]	430
[544]	431	(( i=0 ))
	432	until [ $i -ge $NbFiles ]; do
[778]	433	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	434	eval file_in=${file_in_}
	435	(( i_ = i+1 ))
	436	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	437	eval file_out=${file_out_}
[247]	438
[778]	439	# define CumulPeriod definition for this file
	440	(( i__ = i+2 ))
	441	eval SmoothDef=\${${ListFilesName}[$i__]}
	442	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
	443	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
	444	j=1
	445	for val in ${aux} ; do
	446	[ ${j} -eq 1 ] && SmoothMin=${val}
	447	[ ${j} -eq 2 ] && SmoothMax=${val}
	448	[ ${j} -eq 3 ] && ret=${val}
	449	(( j=j+1 ))
	450	done
	451	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
	452	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
[548]	453
[778]	454	IGCM_sys_IsFileArchived ${file_in}
	455	if [ $? = 0 ] ; then
	456	IGCM_sys_Get ${file_in} ${file_out}
	457	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	458	else
	459	IGCM_sys_Cp ${file_in} ${file_out}
	460	fi
	461	fi
	462	(( i=i+3 ))
[544]	463	done
	464	fi
	465	done
[778]	466
[544]	467	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
[247]	468	}
	469
	470	#=======================================================================
[2]	471	function IGCM_comp_GetInputBoundaryFiles
	472	{
[544]	473	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
[2]	474
[544]	475	# Debug Print :
	476	echo
	477	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
	478	echo
[2]	479
[902]	480	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	481	typeset file_in_ file_in file_out_ file_out
[2]	482
[544]	483	if [ ${Period} = 1 ]; then
	484	ListFixBoundary=" "
	485	fi
[2]	486
[544]	487	for comp in ${config_ListOfComponents[*]} ; do
[2]	488
[544]	489	# Define component
	490	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	491	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	492
[544]	493	# Debug Print :
	494	IGCM_debug_Print 3 "Boundary files ${compname}"
[2]	495
[544]	496	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	497
[544]	498	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
	499	ListFilesName=${compname}_BoundaryFiles_List
	500	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	501
[544]	502	if [ X${FileName0} != X${NULL_STR} ] ; then
	503	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	504
[544]	505	(( i=0 ))
	506	until [ $i -ge $NbFiles ]; do
[778]	507	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	508	eval file_in=${file_in_}
	509	(( i_ = i+1 ))
	510	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	511	eval file_out=${file_out_}
[2]	512
[778]	513	IGCM_sys_IsFileArchived ${file_in}
	514	if [ $? = 0 ] ; then
	515	IGCM_sys_Get ${file_in} ${file_out}
[809]	516	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[778]	517	else
	518	IGCM_sys_Cp ${file_in} ${file_out}
	519	fi
[2]	520
[778]	521	(( i=i+2 ))
[544]	522	done
	523	fi
[2]	524
[544]	525	# Get non deleted files
	526	if [ ${Period} = 1 ]; then
[2]	527
[544]	528	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
	529	ListFilesName=${compname}_BoundaryFiles_ListNonDel
	530	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	531
[544]	532	if [ X${FileName0} != X${NULL_STR} ] ; then
[778]	533	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	534
[778]	535	(( i=0 ))
	536	until [ $i -ge $NbFiles ]; do
	537	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	538	eval file_in=${file_in_}
	539	(( i_ = i+1 ))
	540	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	541	eval file_out=${file_out_}
[2]	542
[778]	543	IGCM_sys_IsFileArchived ${file_in}
	544	if [ $? = 0 ] ; then
	545	IGCM_sys_Get ${file_in} ${file_out}
	546	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	547	else
	548	IGCM_sys_Cp ${file_in} ${file_out}
	549	fi
[2]	550
[778]	551	if [ X${file_out} != X. ] ; then
	552	ListFixBoundary=${ListFixBoundary}" "${file_out}
	553	else
	554	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
	555	fi
	556
	557	(( i=i+2 ))
	558	done
[544]	559	fi
	560	fi
	561	done
[778]	562
[544]	563	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
[2]	564	}
	565
	566	#=======================================================================
	567	function IGCM_comp_DelFixeBoundaryFiles
	568	{
[544]	569	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	570
[544]	571	# Debug Print :
	572	echo
	573	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
	574	echo
[2]	575
[544]	576	ls -l ${ListFixBoundary}
	577	rm -f ${ListFixBoundary}
[2]	578
[544]	579	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	580	}
	581
	582	#=======================================================================
	583	function IGCM_comp_GetInputParametersFiles
	584	{
[544]	585	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
[2]	586
[544]	587	# Debug Print :
	588	echo
	589	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
	590	echo
[2]	591
[544]	592	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
	593	for comp in ${config_ListOfComponents[*]} ; do
[902]	594	# Define component
[544]	595	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	596	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	597
[1338]	598	# Initialize array hosting file_def and field_def files to check and/or modify
	599	unset FieldDef
	600	unset FileDef
	601
[544]	602	# Debug Print :
	603	IGCM_debug_Print 3 "Parameters ${compname}"
[2]	604
[778]	605	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	606
[544]	607	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
	608	ListFilesName=${compname}_ParametersFiles_List
	609	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	610
[544]	611	if [ X${FileName0} != X${NULL_STR} ] ; then
	612	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	613
[544]	614	(( i=0 ))
	615	until [ $i -ge $NbFiles ]; do
[778]	616	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	617	eval file_in=${file_in_}
	618	(( i_ = i+1 ))
	619	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
[902]	620	eval file_out=${file_out_}
[2]	621
[902]	622	IGCM_sys_Cp ${file_in} ${file_out}
[778]	623	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[1338]	624	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
[2]	625
[778]	626	(( i=i+2 ))
[544]	627	done
	628	fi
[1338]	629
	630	if [ ${#FileDef[@]} -ne 0 ] ; then
	631	# Check XMLs coherency now
[1339]	632	IGCM_debug_Print 1 "${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}"
	633	${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}
[1338]	634	if [ $? = 0 ] ; then
[1339]	635	IGCM_debug_Print 1 "${compname} XIOS XMLs are consistent"
[1338]	636	else
[1373]	637	IGCM_debug_Print 1 "${compname} XIOS XMLs ARE NOT consistent"
	638	if [ X${config_Post_ParserXIOS} = XTRUE ] ; then
	639	IGCM_debug_Print 1 "Try to fix it:"
	640	IGCM_debug_Print 3 "${libIGCM}/libIGCM_post/xios_parser.py -v modify --field ${FieldDef[]} --file ${FileDef[]}"
	641	${libIGCM}/libIGCM_post/xios_parser.py -vv modify --field ${FieldDef[]} --file ${FileDef[]}
	642	[ $? != 0 ] && IGCM_debug_Exit "Failed to fix XIOS xml files for ${compname}"
	643	fi
[1338]	644	fi
	645	fi
[544]	646	done
[2]	647
[544]	648	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
[2]	649	}
	650
	651	#=======================================================================
	652	function IGCM_comp_GetInputRestartFiles
	653	{
[544]	654	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
[2]	655
[544]	656	# Debug Print :
	657	echo
	658	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
	659	echo
[2]	660
[590]	661	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
	662	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
[902]	663	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
[544]	664	typeset file_in file_out file_in_ file_out_ file_in_Name
	665	typeset -Z4 j4
[821]	666	#BASH declare j4
[2]	667
[778]	668	IsMatching=""
	669
[544]	670	for comp in ${config_ListOfComponents[*]} ; do
[902]	671	# Define component
[544]	672	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	673	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
	674	#
	675	card=${SUBMIT_DIR}/COMP/${compname}.card
	676	#
	677	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	678	ListFilesName=${compname}_RestartFiles_List
	679	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	680
[544]	681	# Debug Print :
	682	IGCM_debug_Print 3 "restart ${compname}"
[2]	683
[544]	684	if ( ${FirstInitialize} ) ; then
[2]	685
[544]	686	if [ "${config_Restarts_OverRule}" = "y" ] ; then
[778]	687	eval config_${comp}_Restart="y"
	688	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
	689	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
	690	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
	691	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
	692	eval CompOldName=${comp}
[544]	693	else
[778]	694	# Read component Restarts parameters
	695	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	696	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
[2]	697
[778]	698	if [ "${do_start}" = "y" ] ; then
	699	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
	700	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
	701	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
	702	else
	703	eval config_${comp}_RestartDate=-1
	704	eval config_${comp}_RestartJobName=${NULL_STR}
	705	eval config_${comp}_RestartPath=${NULL_STR}
	706	fi
[849]	707
[778]	708	eval CompOldName=\${config_${comp}_OldName}
	709	if [ X${CompOldName} = X ] ; then
	710	eval CompOldName=${comp}
	711	fi
	712
	713	# Reinitialize IsMatching to allow searching for a different tar file for each component.
	714	IsMatching=""
	715	TarFileFound=""
[544]	716	fi
[2]	717
[544]	718	if [ "${do_start}" = "y" ] ; then
[2]	719
[672]	720	# Restore Restarts files
	721	#-----------------------
[778]	722	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	723	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	724
[778]	725	(( i=1 ))
	726	until [ $i -gt $NbFiles ]; do
	727	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	728	eval file_in=${file_in_}
	729	(( i_ = i+1 ))
	730	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	731	eval file_out=${file_out_}
	732
	733	eval Date_tmp=\${config_${comp}_RestartDate}
	734	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
[672]	735	# will be re-use
	736	eval RestartPath=\${config_${comp}_RestartPath}
	737	eval RestartJobName=\${config_${comp}_RestartJobName}
	738	#
[778]	739	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
	740	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
[2]	741
[778]	742	extension_in=$( echo ${file_in_Name##*.} )
	743	extension_out=$( echo ${file_out##*.} )
[672]	744
[778]	745	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	746	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
[2]	747
[778]	748	Path_OUT=${Path_r}/${generic_restart_file_name_in}
	749
[672]	750	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	751	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
[778]	752	Buffered=true
	753	Archived=false
	754	Tared=false
	755	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
[672]	756	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	757	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	758	Buffered=false
	759	Archived=true
	760	Tared=false
	761	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
[672]	762	else
[897]	763	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
	764	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
[902]	765	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
[778]	766	Buffered=false
	767	Archived=false
	768	Tared=true
[672]	769	# Look after the tar file we want if we did not found it already
[778]	770	if [ X${IsMatching} = X ] ; then
[947]	771	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
	772	if [ $? ] ; then
[897]	773	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
	774	IsMatching=$( echo ${PotentialTarFile##*/} \| \
	775	sed "s:_restart::" \| \
	776	sed "s:^${RestartJobName}_::" \| \
	777	sed "s:\.tar$::" \| \
	778	gawk -F_ -v restartdate=${Date_r} \
	779	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	780	if [ ! X${IsMatching} = X ] ; then
	781	TarFileFound=${PotentialTarFile}
	782	break
	783	fi
	784	done
[1017]	785	fi
	786	# Stop here if nothing has been found
	787	if [ X${TarFileFound} = X ] ; then
[902]	788	IGCM_debug_Print 3 "Restart files were not found!"
	789	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	790	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
[897]	791	IGCM_debug_Exit "Please double check restart settings in config.card"
	792	IGCM_debug_Verif_Exit
	793	fi
[778]	794	fi
[918]	795	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	796	TarFileLocation=$( basename ${TarFileFound} )
[801]	797	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	798	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	799	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	800	fi
[672]	801
	802	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	803	j=0 # BASH LINE NOT NEEDED
	804	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	805	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	806	j4=${j} # BASH LINE NOT NEEDED
[778]	807	if [ X${Buffered} = Xtrue ] ; then
	808	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	809	elif [ X${Archived} = Xtrue ] ; then
	810	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	811	elif [ X${Tared} = Xtrue ] ; then
	812	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	813	fi
[821]	814	(( j=j+1 )) #BASH LINE NOT NEEDED
[778]	815	done
[740]	816
[1248]	817	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
	818	if [ X${OCE_PROC_MPI} != X ] ; then
	819	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
[1380]	820	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
[740]	821	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
	822	fi
	823	fi
[778]	824	else
	825	if [ X${Buffered} = Xtrue ] ; then
	826	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
	827	elif [ X${Archived} = Xtrue ] ; then
	828	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
	829	elif [ X${Tared} = Xtrue ] ; then
	830	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	831	fi
	832	fi
	833	(( i=i+3 ))
	834	done
	835	else
	836	if [ X${FileName0} != XNONE ] ; then
	837	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	838	else
	839	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	840	fi
	841	fi
[544]	842	fi
[893]	843	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
[544]	844	# if not FirstInitialize and first loop of this job
[2]	845
[544]	846	# Restore Restarts files
	847	#-----------------------
	848	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
[778]	849	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	850
[778]	851	(( i=1 ))
	852	until [ $i -gt $NbFiles ]; do
	853	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	854	eval file_in=${file_in_}
	855	(( i_ = i+1 ))
	856	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	857	eval file_out=${file_out_}
[2]	858
[1028]	859	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
[662]	860
[778]	861	extension_in=$( echo ${file_in_Name##*.} )
	862	extension_out=$( echo ${file_out##*.} )
[67]	863
[778]	864	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	865	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
	866
	867	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
	868	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
	869
[662]	870	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	871	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
[778]	872	Buffered=true
	873	Archived=false
	874	Tared=false
	875	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
[672]	876	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	877	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	878	Buffered=false
	879	Archived=true
	880	Tared=false
	881	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
	882	else
[897]	883	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
[902]	884	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
[778]	885	Buffered=false
	886	Archived=false
	887	Tared=true
	888	# Look after the tar file we want if we did not found it already
	889	if [ X${IsMatching} = X ] ; then
[801]	890	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
[778]	891	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	892	if [ ! X${IsMatching} = X ] ; then
	893	TarFileFound=${PotentialTarFile}
	894	break
	895	fi
	896	done
	897	fi
[1017]	898	# Stop here if nothing has been found
	899	if [ X${TarFileFound} = X ] ; then
	900	IGCM_debug_Print 3 "Restart files were not found!"
	901	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	902	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
	903	IGCM_debug_Exit "Please double check restart settings in config.card"
	904	IGCM_debug_Verif_Exit
	905	fi
[918]	906	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	907	TarFileLocation=$( basename ${TarFileFound} )
[801]	908	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	909	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	910	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	911	fi
[41]	912
[778]	913	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	914	j=0 # BASH LINE NOT NEEDED
	915	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	916	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	917	j4=${j} # BASH LINE NOT NEEDED
[778]	918	if [ X${Buffered} = Xtrue ] ; then
	919	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	920	elif [ X${Archived} = Xtrue ] ; then
	921	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	922	elif [ X${Tared} = Xtrue ] ; then
	923	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	924	fi
[821]	925	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	926	done
	927	else
	928	if [ X${Buffered} = Xtrue ] ; then
	929	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
	930	elif [ X${Archived} = Xtrue ] ; then
	931	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
	932	elif [ X${Tared} = Xtrue ] ; then
	933	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	934	fi
	935	fi
	936	(( i=i+3 ))
	937	done
[544]	938	else
[778]	939	if [ X${FileName0} != XNONE ] ; then
	940	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	941	else
	942	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	943	fi
[544]	944	fi
[420]	945	fi
[544]	946	done
[420]	947
[544]	948	NbFiles=$( ls * 2> /dev/null \| wc -l )
	949	if [ ${NbFiles} -gt 0 ] ; then
	950	IGCM_sys_Chmod u+rw *
	951	fi
	952
	953	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
[2]	954	}
	955
	956	#=======================================================================
[269]	957	function IGCM_comp_PeriodStart
	958	{
[544]	959	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
[269]	960
[544]	961	# Debug Print :
	962	echo
	963	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
	964	echo
[269]	965
[902]	966	typeset ExeNameIn ExeNameOut
[544]	967	typeset comp compname comptagname
	968	for comp in ${config_ListOfComponents[*]} ; do
[902]	969	# Define component
[544]	970	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	971	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[269]	972
[544]	973	# Copy executable for this component
	974	eval ExeNameIn=\${config_Executable_${comp}[0]}
	975	eval ExeNameOut=\${config_Executable_${comp}[1]}
[269]	976
[544]	977	# Debug Print
	978	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
	979	# UPDATE component
	980	${comp}_PeriodStart 2> /dev/null
[269]	981
[544]	982	done
[269]	983
[544]	984	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
[269]	985	}
	986
[1166]	987
	988
[269]	989	#=======================================================================
[1166]	990	function IGCM_comp_modifyFile
	991	{
	992	#
	993	# syntax: IGCM_comp_modifyFile filein key [value]
	994	#
	995	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
	996	#
	997	# This function is used to replace a pattern in a file for a specific variable.
	998	#
	999	# Arguments:
	1000	# - filein : the file in run directory in which the variable should be set
	1001	# - key : the variable to modify
	1002	# - value : the value to set the key equal to
	1003	#
	1004	IGCM_debug_PushStack "IGCM_comp_modifyFile"
	1005
	1006	typeset filein key value pattern
	1007
	1008	# Set local variables and test the arguments
	1009	if [ $# = 3 ] ; then
	1010	# Normal case with 3 arguments
	1011	filein=$1 ; key=$2 ; value=$3
	1012	else
	1013	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
	1014	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1015	return
	1016	fi
	1017	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
	1018
	1019	# Test if the file exist
	1020	if [ ! -f ${filein} ] ; then
	1021	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
	1022	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1023	return
	1024	fi
	1025
	1026	# Read the line with key in the file without the comments
	1027	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
	1028
	1029	# Verify the existance of the pattern
	1030	if [ X"${pattern}" = X ] ; then
	1031	# Variable key is not set in filein, stop.
	1032	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
	1033	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1034	return
	1035	fi
	1036
	1037	# Now change key in filein
[1176]	1038	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
	1039	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
[1166]	1040	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
	1041	\mv ${filein}.tmp ${filein}
	1042
	1043	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1044	}
	1045
	1046	#=======================================================================
[1069]	1047	function IGCM_comp_modifyDefFile
	1048	{
	1049	#
	1050	# syntax: IGCM_comp_modifyDefFile type filein key [value]
	1051	#
	1052	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
	1053	#
	1054	# This function is used to modify a parameter file for a specific variable.
[1075]	1055	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
	1056	# This function can be used in the comp.driver files for the components.
[1069]	1057	#
[1075]	1058	# Arguments:
[1081]	1059	# - type : first argument must be blocker, nonblocker or force
[1075]	1060	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1069]	1061	# otherwise this function will exit.
[1075]	1062	# For "nonblocker" case, the user can remove or modify the variable. For
	1063	# this case, as long as AUTO is not set, no modification will be done.
[1081]	1064	# For "force" case, the variable will be modified even if it is not set to AUTO
[1069]	1065	# - filein : the file in run directory of .def type in which the variable should be set
	1066	# - key : the variable to modify
[1075]	1067	# - value : the value to set the key equal to, optional. If value is not set or if
[1069]	1068	# value=DEFAULT, then a default value must be given in filein using syntax :
	1069	# key= AUTO : DEFAULT=def_value
	1070	#
[1075]	1071	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
[1069]	1072
[1166]	1073	typeset type filein key value
	1074	typeset filelist nb_occ modify
	1075
[1075]	1076	# Set local variables and test the arguments
	1077	if [ $# = 4 ] ; then
	1078	# Normal case with 4 arguments
	1079	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1080	elif [ $# = 3 ] ; then
	1081	# Normal case with 3 arguments
	1082	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1083	else
	1084	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
[1079]	1085	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1086	return
	1087	fi
[1166]	1088	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
[1069]	1089
[1075]	1090	# Test if first argument is correct
[1166]	1091	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1081]	1092	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
[1079]	1093	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1094	return
	1095	fi
[1069]	1096
[1215]	1097	# Test if the file exist.
	1098	# Exit with error if the file does not exist for the case blocker or force.
	1099	# Only return for the case nonblocker.
[1075]	1100	if [ ! -f ${filein} ] ; then
[1215]	1101	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1102	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
	1103	else
	1104	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
	1105	fi
[1079]	1106	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1107	return
	1108	fi
[1069]	1109
[1102]	1110	# Define list of files to test using all files with suffix .def (except used*.def)
	1111	filelist=$( ls *def \| grep -v used )
[1069]	1112
[1075]	1113	# Count number of occurances for the key in all files
[1166]	1114	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
[1069]	1115
[1075]	1116	# Test if key is set several times
[1166]	1117	if [ ${nb_occ} -gt 1 ] ; then
	1118	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
[1079]	1119	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1120	return
	1121	fi
	1122
	1123	# Treatement according to different cases
[1166]	1124	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
[1075]	1125	# Stop if the key is never set and the function is blocker
[1166]	1126	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
	1127	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
	1128	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
[1075]	1129	# The key is not set but it is a nonblocker call so nothing is done.
[1166]	1130	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1131	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
[1081]	1132	modify=no
[1166]	1133	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
[1075]	1134	# Variable key is not set in filein, stop.
[1166]	1135	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1081]	1136	fi
	1137
	1138	# Check if AUTO is set in the filein on the same line as the key variable
[1166]	1139	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1140	# Modification will be done for all cases
	1141	modify=yes
	1142	else
	1143	# The variable was not set to AUTO
[1166]	1144	if [ ${type} = blocker ] ; then
[1156]	1145	# Exit because this is a blocker call
[1166]	1146	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
[1190]	1147	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1156]	1148	return
[1166]	1149	elif [ ${type} = nonblocker ] ; then
[1156]	1150	# Do nothing. Suppose that the user did set the variable correct
[1166]	1151	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
[1156]	1152	modify=no
[1166]	1153	elif [ ${type} = force ] ; then
[1156]	1154	# Force modification
[1166]	1155	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
[1081]	1156	modify=yes
[1156]	1157	fi
[1081]	1158	fi
[1069]	1159
[1081]	1160	# Do the modifcation now
[1166]	1161	if [ ${modify} = yes ] ; then
[1081]	1162
[1156]	1163	# For option DEFAULT, read default value from file.
[1166]	1164	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1165	# Case to set DEFAULT value
	1166	# Read default value from filein
[1166]	1167	value=$( grep ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
[1069]	1168
[1166]	1169	if [ X"${value}" = X ] ; then
	1170	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
	1171	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
	1172	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1173	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
	1174	return
[1075]	1175	fi
[1156]	1176	fi
[1069]	1177
[1156]	1178	# Now change key in filein
[1166]	1179	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
	1180	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
	1181	\mv ${filein}.tmp ${filein}
[1075]	1182	fi
[1079]	1183	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1069]	1184	}
	1185
	1186	#=======================================================================
[1085]	1187	function IGCM_comp_modifyNamelist
	1188	{
	1189	#
	1190	# syntax: IGCM_comp_modifyNamelist type filein key [value]
	1191	#
	1192	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
	1193	#
	1194	# This function is used to modify a parameter file for a specific variable.
[1155]	1195	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
[1085]	1196	# This function can be used in the comp.driver files for the components.
	1197	#
	1198	# Arguments:
	1199	# - type : first argument must be blocker, nonblocker or force
	1200	# For "blocker" case, the variable must be attributed the keyworld AUTO
	1201	# otherwise this function will exit.
	1202	# For "nonblocker" case, the user can remove or modify the variable. For
	1203	# this case, as long as AUTO is not set, no modification will be done.
	1204	# For "force" case, the variable will be modified even if it is not set to AUTO
	1205	# - filein : the file in run directory of .def type in which the variable should be set
	1206	# - key : the variable to modify
	1207	# - value : the value to set the key equal to, optional. If value is not set or if
	1208	# value=DEFAULT, then a default value must be given in filein using syntax :
	1209	# key= AUTO : DEFAULT=def_value
	1210	#
	1211	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
	1212
[1166]	1213	typeset type filein key value pattern modify
	1214
[1085]	1215	# Set local variables and test the arguments
	1216	if [ $# = 4 ] ; then
	1217	# Normal case with 4 arguments
	1218	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1219	elif [ $# = 3 ] ; then
	1220	# Normal case with 3 arguments
	1221	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1222	else
	1223	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
	1224	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1225	return
	1226	fi
[1166]	1227	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
[1085]	1228
	1229	# Test if first argument is correct
[1166]	1230	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1085]	1231	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
	1232	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1233	return
	1234	fi
	1235
[1215]	1236	# Test if the file exist.
	1237	# Exit with error if the file does not exist for the case blocker or force.
	1238	# Only return for the case nonblocker.
[1085]	1239	if [ ! -f ${filein} ] ; then
[1215]	1240	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1241	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
	1242	else
	1243	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
	1244	fi
[1085]	1245	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1246	return
	1247	fi
	1248
	1249	# Read the line with key in the file without the comments
[1166]	1250	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
[1155]	1251
[1085]	1252	# Verify the existance of the pattern
	1253	if [ X"$pattern" = X ] ; then
[1156]	1254	# Variable key is not set in filein, stop.
[1166]	1255	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1156]	1256	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1257	return
[1085]	1258	fi
[1155]	1259
[1085]	1260	# Check if the variable is set to AUTO in the filein
	1261	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1262	# Modification will be done for all cases
	1263	modify=yes
	1264	else
	1265	# The variable was not set to AUTO
[1166]	1266	if [ ${type} = blocker ] ; then
[1156]	1267	# Exit because this is a blocker call
[1166]	1268	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
[1156]	1269	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1270	return
[1166]	1271	elif [ ${type} = nonblocker ] ; then
[1156]	1272	# Do nothing. Suppose that the user did set the variable correct
[1166]	1273	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
[1156]	1274	modify=no
[1166]	1275	elif [ ${type} = force ] ; then
[1156]	1276	# Force modification
[1166]	1277	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
[1085]	1278	modify=yes
[1156]	1279	fi
[1085]	1280	fi
	1281
	1282	# Do the modifcation now
[1166]	1283	if [ ${modify} = yes ] ; then
[1085]	1284
[1156]	1285	# For option DEFAULT, read default value from file.
[1166]	1286	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1287	# Case to set DEFAULT value
	1288	# Read default value from filein
	1289	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
[1085]	1290
[1166]	1291	if [ X"${value}" = X ] ; then
	1292	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
	1293	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
	1294	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1295	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1296	return
[1085]	1297	fi
[1156]	1298	fi
[1085]	1299
[1156]	1300	# Now change key in filein
[1166]	1301	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
	1302	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
	1303	\mv ${filein}.tmp ${filein}
[1085]	1304	fi
	1305	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1306	}
	1307
	1308	#=======================================================================
[1074]	1309	function IGCM_comp_modifyXmlFile
	1310	{
	1311	#
	1312	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
	1313	#
	1314	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
	1315	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
	1316	#
	1317	# This function is used to modify the value for a specific attribute and variable id.
[1155]	1318	# The file must be a valid xml file.
[1075]	1319	# This function can be used in the comp.driver files for the components.
[1074]	1320	#
[1075]	1321	# Arguments:
	1322	# - type : first argument must be blocker, nonblocker or force.
	1323	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1074]	1324	# otherwise this function will exit.
[1075]	1325	# For "nonblocker" case, the user can remove or modify the variable. For
[1074]	1326	# this case, as long as AUTO is not set, no modification will be done.
[1075]	1327	# For "force" case, the variable will be modified even if it is not set to AUTO
[1074]	1328	# - filein : the file in run directory of .xml type in which the variable should be set
	1329	# - keyid : the variable to modify
	1330	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
	1331	# - value : the value to set in the filein
	1332	#
[1075]	1333	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
[1074]	1334
[1166]	1335	typeset type filein keyid keyattrib value modify
	1336
[1075]	1337	# Set local variables and test the arguments
	1338	if [ $# = 5 ] ; then
	1339	# Normal case with 4 arguments
	1340	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
	1341	else
	1342	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
[1089]	1343	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1344	return
	1345	fi
[1166]	1346	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
[1074]	1347
[1075]	1348	# Test if first argument is correct
[1166]	1349	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1075]	1350	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
[1089]	1351	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1352	return
	1353	fi
[1074]	1354
[1215]	1355	# Test if the file exist.
	1356	# Exit with error if the file does not exist for the case blocker or force.
	1357	# Only return for the case nonblocker.
[1075]	1358	if [ ! -f ${filein} ] ; then
[1215]	1359	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1360	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
	1361	else
	1362	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
	1363	fi
[1089]	1364	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1365	return
	1366	fi
	1367
[1386]	1368	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
[1166]	1369	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
[1386]	1370	if [ ${type} = nonblocker ] ; then
	1371	# This is a nonblocker case, print warning but do nothing else
	1372	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1373	else
	1374	# This is a blocker or force case : stop now
	1375	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
	1376	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
	1377	return
	1378	fi
[1075]	1379	fi
	1380
	1381	# Check if AUTO is set on the same line as keyid and keyattrib
[1166]	1382	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
[1394]	1383	# Modification will be done
[1075]	1384	modify=yes
	1385	else
[1166]	1386	if [ ${type} = blocker ] ; then
[1075]	1387	# Exit, the variable must be set to AUTO
[1166]	1388	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
[1089]	1389	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1390	return
[1166]	1391	elif [ ${type} = nonblocker ] ; then
[1075]	1392	# Nothing will be done
	1393	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
	1394	modify=no
[1166]	1395	elif [ ${type} = force ] ; then
[1075]	1396	# Force modification
[1166]	1397	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
[1075]	1398	modify=yes
[1074]	1399	fi
[1075]	1400	fi
[1074]	1401
[1075]	1402	# Do the modifcation now
[1166]	1403	if [ ${modify} = yes ] ; then
	1404	if [ ${keyattrib} = NONE ] ; then
[1075]	1405	# Case to modify the variable itself
	1406	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
[1166]	1407	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
[1074]	1408	else
[1156]	1409	# Check if keyattrib is set on the same line as keyid
[1166]	1410	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
[1156]	1411	# Case to modify the attribute value
	1412	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
[1166]	1413	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
[1156]	1414	else
	1415	# Case to add the attribute and its value
	1416	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
[1166]	1417	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
[1156]	1418	fi
[1074]	1419	fi
[1166]	1420	\mv ${filein}.tmp ${filein}
[1075]	1421	fi
	1422	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1074]	1423	}
	1424
	1425	#=======================================================================
[2]	1426	function IGCM_comp_Update
	1427	{
[544]	1428	IGCM_debug_PushStack "IGCM_comp_Update"
[2]	1429
	1430	# Debug Print :
[544]	1431	echo
	1432	IGCM_debug_Print 1 "IGCM_comp_Update"
	1433	echo
[2]	1434
[902]	1435	typeset ExeNameIn ExeNameOut
[544]	1436	typeset comp compname comptagname
	1437	for comp in ${config_ListOfComponents[*]} ; do
[902]	1438	# Define component
[544]	1439	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1440	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1441
[544]	1442	# Copy executable for this component
	1443	eval ExeNameIn=\${config_Executable_${comp}[0]}
	1444	eval ExeNameOut=\${config_Executable_${comp}[1]}
[151]	1445
[622]	1446	# If missing executable and DRYRUN is set to 0 or 1 then stop!
	1447	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
	1448	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
[778]	1449	fi
[236]	1450
[544]	1451	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
	1452	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1453	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1454	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1455	fi
	1456	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1457	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1458	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1459	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1460	fi
	1461	fi
[2]	1462
[544]	1463	# Debug Print
	1464	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
	1465	# UPDATE component
	1466	${comp}_Update
[2]	1467
[544]	1468	done
[2]	1469
[544]	1470	IGCM_debug_PopStack "IGCM_comp_Update"
[2]	1471	}
	1472
	1473	#=======================================================================
	1474	function IGCM_comp_Finalize
	1475	{
[544]	1476	IGCM_debug_PushStack "IGCM_comp_Finalize"
[2]	1477
[544]	1478	# Debug Print :
	1479	echo
	1480	IGCM_debug_Print 1 "IGCM_comp_Finalize"
	1481	echo
[2]	1482
[544]	1483	typeset ListTextName TextName0
	1484	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
	1485	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
[1165]	1486	typeset -Z4 j4 #BASH declare j4
[544]	1487	typeset list_file nlist_file
	1488	typeset compactoutputs
[429]	1489
[1165]	1490	# Initialize array hosting list of rebuilded files to copy
	1491	unset rebuildedActionsList
	1492
	1493	# Text compacting options
[544]	1494	compactoutputs=false
	1495	if [ X${JobType} != XRUN ] ; then
	1496	compactoutputs=true
	1497	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
	1498	compactoutputs=true
	1499	fi
[433]	1500
[1043]	1501	# Prepare headers for the shell dedicated to offline rebuild
	1502	if [ X${AsynchronousRebuild} = Xtrue ] ; then
	1503	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1504	if [ ${DRYRUN} -le 1 ] ; then
	1505	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1506	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1507	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1508	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1509	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1510	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1511	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1512	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1513	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1514	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1515	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1516	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1517	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1518	fi
	1519	fi
	1520
[544]	1521	for comp in ${config_ListOfComponents[*]} ; do
[902]	1522	# Define component
[544]	1523	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1524	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1525
[544]	1526	# Debug Print
	1527	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
	1528	# FINALIZE component
	1529	${comp}_Finalize
[2]	1530
[778]	1531	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	1532
[804]	1533	# Save Output Text files of models
	1534	#---------------------------------
	1535	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
	1536	IGCM_card_DefineArrayFromOption ${card} OutputText List
	1537	ListTextName=${compname}_OutputText_List
	1538
	1539	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
	1540	if [ X${TextName0} != X${NULL_STR} ] ; then
	1541	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
	1542
	1543	(( i=0 ))
	1544	until [ $i -eq $NbFiles ]; do
	1545	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
	1546	eval file_out=${PREFIX}_${file_in}
	1547
	1548	(( i=i+1 ))
	1549
	1550	unset list_file
	1551	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
	1552	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
	1553	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 )
	1554	nlist_file=${#list_file[@]}
	1555	if [ ${nlist_file} -gt 1 ] ; then
	1556	if ( ${compactoutputs} ) ; then
	1557	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
	1558	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
	1559	echo ${list_file[*]} > ${file_out}
	1560	echo "" >> ${file_out}
	1561
	1562	(( i_ = 0 ))
[1080]	1563	for file in ${list_file[@]} ; do
[804]	1564	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
	1565	echo "\| " ${i_} " " ${file} >> ${file_out}
	1566	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
[999]	1567	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
[804]	1568	echo "" >> ${file_out}
	1569	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1570	(( i_ = i_ + 1 ))
	1571	done
[1080]	1572	if ( ${ExecutionFail} ) ; then
	1573	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
	1574	fi
	1575
[804]	1576	if [ X${Pack} = Xtrue ] ; then
	1577	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
	1578	else
	1579	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
	1580	fi
[1080]	1581
[804]	1582	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
[1080]	1583	else
	1584	for file in ${list_file[@]} ; do
	1585	if ( ${ExecutionFail} ) ; then
	1586	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
	1587	fi
[804]	1588
	1589	if [ X${Pack} = Xtrue ] ; then
	1590	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
	1591	else
	1592	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
	1593	fi
[1080]	1594
[804]	1595	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1596	done
	1597	fi
	1598	else
	1599	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
	1600	eval IGCM_sys_Mv ${file_in}* ${file_in}
	1601	fi
[1080]	1602
	1603	if ( ${ExecutionFail} ) ; then
	1604	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
	1605	fi
	1606
[804]	1607	if [ X${Pack} = Xtrue ] ; then
	1608	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
	1609	else
	1610	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
	1611	fi
	1612	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1613	fi
	1614	done
	1615	fi
	1616
[544]	1617	# Save Restarts files
	1618	#--------------------
	1619	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
	1620	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	1621	ListFilesName=${compname}_RestartFiles_List
	1622	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	1623
[544]	1624	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	1625	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[778]	1626
[544]	1627	(( i=0 ))
	1628	until [ $i -ge $NbFiles ]; do
[778]	1629	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1630	eval file_in=${file_in_}
[2]	1631
[778]	1632	(( i_ = i+1 ))
	1633	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1634	eval file_out=${file_out_}
[151]	1635
[778]	1636	(( i_ = i+2 ))
	1637	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1638	eval file_outin=${file_outin_}
[151]	1639
[778]	1640	generic_restart_file_name_in=$( basename ${file_in} .nc )
	1641	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
	1642	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
[2]	1643
[902]	1644	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
[778]	1645	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	1646	j=0 # BASH LINE NOT NEEDED
	1647	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	1648	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	1649	j4=${j} # BASH LINE NOT NEEDED
[778]	1650	if [ X${Pack} = Xtrue ] ; then
	1651	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1652	else
	1653	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1654	fi
	1655	if [ ! ${file_in} = ${file_outin} ] ; then
	1656	if ( ${ExitFlag} ) ; then
	1657	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
	1658	else
	1659	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
	1660	fi
	1661	fi
[821]	1662	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	1663	done
	1664	else
	1665	if [ X${Pack} = Xtrue ] ; then
	1666	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1667	else
	1668	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1669	fi
	1670	if [ ! ${file_in} = ${file_outin} ] ; then
	1671	if ( ${ExitFlag} ) ; then
	1672	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
	1673	else
	1674	IGCM_sys_Mv ${file_in} ${file_outin}
	1675	fi
	1676	fi
	1677	fi
	1678
	1679	(( i=i+3 ))
[544]	1680	done
	1681	else
	1682	if [ X${FileName0} != XNONE ] ; then
[778]	1683	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
[544]	1684	else
[778]	1685	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
[544]	1686	fi
	1687	fi
[2]	1688
[544]	1689	# Save Output files
	1690	#------------------
	1691	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
	1692	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	1693	ListFilesName=${compname}_OutputFiles_List
	1694	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	1695
[544]	1696	if [ X${FileName0} != X${NULL_STR} ] ; then
	1697	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[149]	1698
[544]	1699	(( i=0 ))
	1700	until [ $i -ge $NbFiles ]; do
[778]	1701	SaveOnArchive=true
	1702	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1703	eval file_in=${file_in_}
	1704	(( i_ = i+1 ))
	1705	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1706	eval file_out=${file_out_}
	1707	#
	1708	# Override file_out path remplacing R_SAVE by R_BUFR
	1709	#
	1710	if [ X${Pack} = Xtrue ] ; then
	1711	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
	1712	fi
	1713	#
	1714	# Not necessarily the best option. /!\ Potential side effects /!\
	1715	#
	1716	(( i_ = i+2 ))
	1717	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1718	#
	1719	generic_file_name=$( basename ${file_in} .nc )
	1720	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
	1721	#
	1722	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
[804]	1723	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
[778]	1724	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
	1725	elif [ ${nb_rebuild_file} -gt 1 ] ; then
[804]	1726	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
[778]	1727	if [ X${AsynchronousRebuild} = Xfalse ] ; then
	1728	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
[1388]	1729	#
	1730	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
	1731	if [ ${file_in} = output.abort.nc ] ; then
	1732	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
	1733	else
	1734	IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc
	1735	fi
[778]	1736	else
	1737	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
[980]	1738	IGCM_sys_Mv ${generic_file_name}_[0-9]*.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
[544]	1739
[778]	1740	# Prepare the shell dedicated to offline rebuild
	1741	if [ $DRYRUN -le 1 ]; then
[694]	1742	if [ ${file_in} = histstn.nc ] ; then
	1743	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1744	else
[980]	1745	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[694]	1746	fi
[1206]	1747	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1748	fi
	1749	#
	1750	# Load Patch we need to apply and apply
	1751	if [ $DRYRUN -le 1 ]; then
	1752	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
[1080]	1753	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1754	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1755	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1756	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1757	done
	1758	fi
	1759	fi
	1760	#
	1761	if [ $DRYRUN -le 1 ]; then
	1762	if [ X${Pack} = Xtrue ] ; then
[1165]	1763	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
[778]	1764	else
[1165]	1765	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
[778]	1766	fi
[1206]	1767	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
[1165]	1768	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
[778]	1769	fi
	1770	SaveOnArchive=false
	1771	fi
	1772	fi
	1773	#
	1774	if [ ${SaveOnArchive} = true ] ; then
	1775	#
	1776	# Rebuild has been done online or it was not needed
	1777	#
	1778	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
	1779	#
	1780	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
[1289]	1781	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
[778]	1782	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1783	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
	1784	#
	1785	if [ $DRYRUN -le 1 ]; then
[1080]	1786	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1787	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1788	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1789	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1790	done
	1791	#
	1792	if [ X${Pack} = Xtrue ] ; then
	1793	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1794	else
	1795	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1796	fi
[1206]	1797	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1798	#
	1799	fi
	1800	else
	1801	#
	1802	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
	1803	#
	1804	if [ X${Pack} = Xtrue ] ; then
	1805	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
	1806	else
	1807	IGCM_sys_Put_Out ${file_in} ${file_out}
	1808	fi
	1809	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1810	if [ ${nb_rebuild_file} -gt 1 ] ; then
	1811	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
	1812	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
	1813	done
	1814	fi
	1815	fi
	1816	fi
	1817	(( i=i+3 ))
[544]	1818	done
	1819	fi
	1820	echo
	1821	done
[1165]	1822	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
	1823	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
[1166]	1824	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1165]	1825	i=0
	1826	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
	1827	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1828	(( i=i+1 ))
	1829	done
	1830	fi
[544]	1831	IGCM_debug_PopStack "IGCM_comp_Finalize"
[2]	1832	}

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