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libIGCM_comp.ksh

Last change on this file was 1637, checked in by aclsce, 2 weeks ago
Fixed bug in case of many restart files to untar (ex with NEMO)
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: 83.8 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
[1413]	81	eval R_OUT_${comp}_A=\${R_OUT_${comp}}/Analyse
	82	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_A}
	83
[544]	84	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
[804]	85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
[2]	86
[544]	87	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
[804]	88	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
[2]	89
[544]	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
[1413]	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
[544]	100	# Define BUFFERED Dirs
[1022]	101	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
[804]	102	eval R_BUF_${comp}=${R_BUFR}/${comp}
	103	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
[544]	104
[804]	105	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
	106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
[544]	107
[1413]	108	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
	109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
	110
[804]	111	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
	112	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
[544]	113
[804]	114	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
	115	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
[544]	116
[804]	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
[1413]	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
[1431]	128	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
[804]	129	fi
[544]	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
[804]	135
[544]	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
[778]	139	unset card_UserChoices
[544]	140	fi
[833]	141	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
[544]	142	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
	143	for option in ${card_UserChoices[*]} ; do
[778]	144	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
	145	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
[544]	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 $NbFiles ]; do
[778]	166	#
	167	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
	168	#
	169	if [ X${flag_post} != XNONE ] ; then
	170	#
[544]	171	# First of all
	172	#
[778]	173	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
[1151]	174	# This section is mandatory
	175	if [ "X$( 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
[778]	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}
[544]	213	#
[778]	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
[829]	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}
[778]	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
[1603]	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
[778]	253	(( i=i+3 ))
[1603]	254	fi
[544]	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
[2]	263
[544]	264	IGCM_debug_PopStack "IGCM_comp_Initialize"
[2]	265	}
	266
	267	#=======================================================================
	268	function IGCM_comp_PrepareDeletedFiles
	269	{
[544]	270	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
[778]	271
[544]	272	if [ X${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
[2]	277
[544]	278	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
[2]	279	}
	280
	281	#=======================================================================
[1338]	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
[1413]	295	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
	296	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
	297	fi
[1338]	298
	299	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
	300	}
	301
	302	#=======================================================================
[2]	303	function IGCM_comp_GetInputInitialStateFiles
	304	{
[544]	305	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
[2]	306
[544]	307	# Debug Print :
	308	echo
	309	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
	310	echo
[2]	311
[902]	312	# Only the first time step need InitialStateFiles
[544]	313	# otherwise it's BoundaryConditions
	314	if ( ${FirstInitialize} ) ; then
[902]	315	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	316	typeset file_in_ file_in file_out_ file_out do_init
[544]	317	for comp in ${config_ListOfComponents[*]} ; do
	318	# Initialize
	319	do_init="y"
	320	# Do we need to bring initial state file for this component
[1401]	321	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[778]	322	eval do_init="n"
[544]	323	else
[778]	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 [ "${do_start}" = "y" ] ; then
	328	do_init="n"
	329	else
	330	do_init="y"
	331	fi
[544]	332	fi
[2]	333
[544]	334	if [ "${do_init}" = "y" ] ; then
[902]	335	# Define component
[778]	336	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	337	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	338
[778]	339	# Debug Print :
	340	IGCM_debug_Print 3 "Initialisation files ${compname}"
[2]	341
[778]	342	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	343
[778]	344	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
	345	ListFilesName=${compname}_InitialStateFiles_List
[2]	346
[778]	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_}
[2]	357
[778]	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
[544]	368	fi
	369	done
	370	fi
	371	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
[2]	372	}
	373
	374	#=======================================================================
[247]	375	# Definition of Smooth modulo function
[902]	376	# usage :
[247]	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 :
[902]	382	# [] value are optionnals;
[247]	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	#
[902]	390	# return : true(1)/false(0)
[247]	391	function IGCM_SmoothModulo
	392	{
[544]	393	IGCM_debug_PushStack "IGCM_SmoothModulo"
	394	typeset defVector ModValue
[247]	395
[544]	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 : $2))}' )
[247]	398
[544]	399	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
	400	arr[1]=${defVector[0]}
	401	arr[2]=${defVector[2]}
[412]	402
[902]	403	# Test limits :
	404	# ${defVector[0]} <= ${2} <= ${defVector[2]}
[544]	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
[247]	414	else
[544]	415	arr[3]=false
	416	echo ${arr[@]}
	417	IGCM_debug_PopStack "IGCM_SmoothModulo"
	418	return 0
[247]	419	fi
[544]	420	else
	421	arr[3]=false
	422	echo ${arr[@]}
	423	IGCM_debug_PopStack "IGCM_SmoothModulo"
	424	return 0
	425	fi
[247]	426	}
	427
	428	#=======================================================================
	429	function IGCM_comp_GetInputSmoothFiles
	430	{
[544]	431	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
[247]	432
[544]	433	# Debug Print :
	434	echo
	435	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
	436	echo
[247]	437
[544]	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
[247]	440
[544]	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
[247]	445
[544]	446	# Debug Print :
	447	IGCM_debug_Print 3 "Smooth files ${compname}"
[247]	448
[544]	449	card=${SUBMIT_DIR}/COMP/${compname}.card
[247]	450
[544]	451	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
	452	ListFilesName=${compname}_SmoothFiles_List
	453	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[247]	454
[544]	455	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
	456	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[247]	457
[544]	458	(( i=0 ))
	459	until [ $i -ge $NbFiles ]; do
[778]	460	eval file_in_=\${${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=${file_out_}
[247]	465
[778]	466	# define CumulPeriod definition for this file
	467	(( i__ = i+2 ))
	468	eval SmoothDef=\${${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
[548]	480
[778]	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 ))
[544]	490	done
	491	fi
	492	done
[778]	493
[544]	494	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
[247]	495	}
	496
	497	#=======================================================================
[2]	498	function IGCM_comp_GetInputBoundaryFiles
	499	{
[544]	500	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
[2]	501
[544]	502	# Debug Print :
	503	echo
	504	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
	505	echo
[2]	506
[902]	507	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	508	typeset file_in_ file_in file_out_ file_out
[2]	509
[544]	510	if [ ${Period} = 1 ]; then
	511	ListFixBoundary=" "
	512	fi
[2]	513
[544]	514	for comp in ${config_ListOfComponents[*]} ; do
[2]	515
[544]	516	# Define component
	517	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	518	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	519
[544]	520	# Debug Print :
	521	IGCM_debug_Print 3 "Boundary files ${compname}"
[2]	522
[544]	523	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	524
[544]	525	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
	526	ListFilesName=${compname}_BoundaryFiles_List
	527	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	528
[544]	529	if [ X${FileName0} != X${NULL_STR} ] ; then
	530	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	531
[544]	532	(( i=0 ))
	533	until [ $i -ge $NbFiles ]; do
[778]	534	eval file_in_=\${${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_}
[2]	539
[778]	540	IGCM_sys_IsFileArchived ${file_in}
	541	if [ $? = 0 ] ; then
	542	IGCM_sys_Get ${file_in} ${file_out}
[809]	543	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[778]	544	else
	545	IGCM_sys_Cp ${file_in} ${file_out}
	546	fi
[2]	547
[778]	548	(( i=i+2 ))
[544]	549	done
	550	fi
[2]	551
[544]	552	# Get non deleted files
	553	if [ ${Period} = 1 ]; then
[2]	554
[544]	555	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
	556	ListFilesName=${compname}_BoundaryFiles_ListNonDel
	557	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	558
[544]	559	if [ X${FileName0} != X${NULL_STR} ] ; then
[778]	560	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	561
[778]	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_}
[2]	569
[778]	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} ${file_out}
	576	fi
[2]	577
[778]	578	if [ X${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
[544]	586	fi
	587	fi
	588	done
[778]	589
[544]	590	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
[2]	591	}
	592
	593	#=======================================================================
	594	function IGCM_comp_DelFixeBoundaryFiles
	595	{
[544]	596	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	597
[544]	598	# Debug Print :
	599	echo
	600	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
	601	echo
[2]	602
[544]	603	ls -l ${ListFixBoundary}
	604	rm -f ${ListFixBoundary}
[2]	605
[544]	606	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	607	}
	608
	609	#=======================================================================
	610	function IGCM_comp_GetInputParametersFiles
	611	{
[544]	612	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
[2]	613
[544]	614	# Debug Print :
	615	echo
	616	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
	617	echo
[2]	618
[544]	619	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
	620	for comp in ${config_ListOfComponents[*]} ; do
[902]	621	# Define component
[544]	622	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	623	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	624
[1338]	625	# Initialize array hosting file_def and field_def files to check and/or modify
	626	unset FieldDef
	627	unset FileDef
	628
[544]	629	# Debug Print :
	630	IGCM_debug_Print 3 "Parameters ${compname}"
[2]	631
[778]	632	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	633
[544]	634	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
	635	ListFilesName=${compname}_ParametersFiles_List
	636	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	637
[544]	638	if [ X${FileName0} != X${NULL_STR} ] ; then
	639	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	640
[544]	641	(( i=0 ))
	642	until [ $i -ge $NbFiles ]; do
[778]	643	eval file_in_=\${${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
[902]	647	eval file_out=${file_out_}
[2]	648
[902]	649	IGCM_sys_Cp ${file_in} ${file_out}
[778]	650	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[1338]	651	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
[2]	652
[778]	653	(( i=i+2 ))
[544]	654	done
	655	fi
[1338]	656
[544]	657	done
[2]	658
[544]	659	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
[2]	660	}
	661
	662	#=======================================================================
	663	function IGCM_comp_GetInputRestartFiles
	664	{
[544]	665	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
[2]	666
[544]	667	# Debug Print :
	668	echo
	669	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
	670	echo
[2]	671
[590]	672	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
	673	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
[902]	674	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
[544]	675	typeset file_in file_out file_in_ file_out_ file_in_Name
	676	typeset -Z4 j4
[821]	677	#BASH declare j4
[2]	678
[778]	679	IsMatching=""
	680
[544]	681	for comp in ${config_ListOfComponents[*]} ; do
[902]	682	# Define component
[544]	683	eval compname=\${config_ListOfComponents_${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
[2]	691
[544]	692	# Debug Print :
	693	IGCM_debug_Print 3 "restart ${compname}"
[2]	694
[544]	695	if ( ${FirstInitialize} ) ; then
[2]	696
[1401]	697	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[1446]	698	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
[1538]	699	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
[1447]	700	CompOldName=IOS
	701	config_IOS_Restart="n"
	702	do_start="n"
[1449]	703	config_IOS_RestartDate=-1
	704	config_IOS_RestartJobName=${NULL_STR}
	705	config_IOS_RestartPath=${NULL_STR}
[1447]	706	else
[1446]	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
[544]	714	else
[778]	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
[2]	718
[778]	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
[849]	728
[778]	729	eval CompOldName=\${config_${comp}_OldName}
	730	if [ X${CompOldName} = X ] ; then
	731	eval CompOldName=${comp}
	732	fi
	733
	734	# Reinitialize IsMatching to allow searching for a different tar file for each component.
	735	IsMatching=""
	736	TarFileFound=""
[544]	737	fi
[2]	738
[544]	739	if [ "${do_start}" = "y" ] ; then
[2]	740
[672]	741	# Restore Restarts files
	742	#-----------------------
[778]	743	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	744	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	745
[778]	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=${file_out_}
	753
[1624]	754	(( i_ = i+2 ))
	755	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	756	if [ X${is_opt} = XOPTIONAL ] ; then
	757	echo ${file_in} is optional
	758	(( i=i+4 ))
	759	else
	760	is_opt="MANDATORY"
	761	echo ${file_in} is mandatory
	762	(( i=i+3 ))
	763	fi
	764	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=y)"
	765
[778]	766	eval Date_tmp=\${config_${comp}_RestartDate}
	767	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
[672]	768	# will be re-use
	769	eval RestartPath=\${config_${comp}_RestartPath}
	770	eval RestartJobName=\${config_${comp}_RestartJobName}
	771	#
[778]	772	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
	773	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
[2]	774
[778]	775	extension_in=$( echo ${file_in_Name##*.} )
	776	extension_out=$( echo ${file_out##*.} )
[672]	777
[778]	778	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	779	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
[2]	780
[778]	781	Path_OUT=${Path_r}/${generic_restart_file_name_in}
	782
[672]	783	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	784	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
[778]	785	Buffered=true
	786	Archived=false
	787	Tared=false
	788	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
[672]	789	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	790	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	791	Buffered=false
	792	Archived=true
	793	Tared=false
	794	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
[672]	795	else
[897]	796	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
	797	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
[902]	798	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
[778]	799	Buffered=false
	800	Archived=false
	801	Tared=true
[672]	802	# Look after the tar file we want if we did not found it already
[778]	803	if [ X${IsMatching} = X ] ; then
[947]	804	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
	805	if [ $? ] ; then
[897]	806	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
	807	IsMatching=$( echo ${PotentialTarFile##*/} \| \
	808	sed "s:_restart::" \| \
	809	sed "s:^${RestartJobName}_::" \| \
	810	sed "s:\.tar$::" \| \
	811	gawk -F_ -v restartdate=${Date_r} \
	812	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	813	if [ ! X${IsMatching} = X ] ; then
	814	TarFileFound=${PotentialTarFile}
	815	break
	816	fi
	817	done
[1017]	818	fi
	819	# Stop here if nothing has been found
	820	if [ X${TarFileFound} = X ] ; then
[902]	821	IGCM_debug_Print 3 "Restart files were not found!"
	822	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	823	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
[1624]	824	if [ ${is_opt} = 'OPTIONAL' ] ; then
	825	IGCM_debug_Print 3 "The restart file is optional. Now continue."
	826	nb_restart_file=0
	827	Tared=false
	828	else
	829	IGCM_debug_Exit "Please double check restart settings in config.card"
	830	IGCM_debug_Verif_Exit
	831	fi
	832	fi
	833	fi
	834
	835	if [ X${Tared} = Xtrue ] ; then
	836	# The tar file exist but not sure all files are inside
	837	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	838	TarFileLocation=$( basename ${TarFileFound} )
[1637]	839	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in} \| wc -l )
[1624]	840	if [ ${nb_files} -gt 0 ] ; then
	841	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	842	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
	843	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	844	else
	845	# No file was found
	846	if [ ${is_opt} = 'OPTIONAL' ] ; then
	847	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
	848	nb_restart_file=0
	849	Tared=false
	850	else
	851	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
	852	IGCM_debug_Exit "Please double check restart settings in config.card"
	853	IGCM_debug_Verif_Exit
	854	fi
[897]	855	fi
[1624]	856	fi
[778]	857	fi
[1624]	858
[672]	859	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	860	j=0 # BASH LINE NOT NEEDED
	861	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	862	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	863	j4=${j} # BASH LINE NOT NEEDED
[778]	864	if [ X${Buffered} = Xtrue ] ; then
	865	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	866	elif [ X${Archived} = Xtrue ] ; then
	867	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	868	elif [ X${Tared} = Xtrue ] ; then
	869	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	870	fi
[821]	871	(( j=j+1 )) #BASH LINE NOT NEEDED
[778]	872	done
[740]	873
[1248]	874	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
	875	if [ X${OCE_PROC_MPI} != X ] ; then
	876	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
[1380]	877	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
[740]	878	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
	879	fi
	880	fi
[778]	881	else
	882	if [ X${Buffered} = Xtrue ] ; then
	883	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
	884	elif [ X${Archived} = Xtrue ] ; then
	885	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
	886	elif [ X${Tared} = Xtrue ] ; then
[1624]	887	if [ -f ${comp}_${file_in_Name} ] ; then
	888	# The file exixt
	889	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	890	elif [ ${is_opt} = 'OPTIONAL' ] ; then
	891	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
	892	else
	893	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
	894	IGCM_debug_Exit "Please double check restart settings in config.card"
	895	IGCM_debug_Verif_Exit
	896	fi
[778]	897	fi
	898	fi
	899	done
	900	else
	901	if [ X${FileName0} != XNONE ] ; then
	902	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	903	else
	904	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	905	fi
	906	fi
[544]	907	fi
[893]	908	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
[544]	909	# if not FirstInitialize and first loop of this job
[2]	910
[544]	911	# Restore Restarts files
	912	#-----------------------
	913	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
[778]	914	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	915
[778]	916	(( i=1 ))
	917	until [ $i -gt $NbFiles ]; do
	918	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	919	eval file_in=${file_in_}
[1624]	920
[778]	921	(( i_ = i+1 ))
	922	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	923	eval file_out=${file_out_}
[2]	924
[1624]	925	(( i_ = i+2 ))
	926	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	927	if [ X${is_opt} = XOPTIONAL ] ; then
	928	# Read a forth argument
	929	echo ${file_in} is optional
	930	(( i=i+4 ))
	931	else
	932	is_opt="MANDATORY"
	933	echo ${file_in} is mandatory
	934	(( i=i+3 ))
	935	fi
	936
	937	IGCM_debug_Print 3 "Now search for restart file ${file_in} which is ${is_opt} (in section do_start=n)"
	938
[1028]	939	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
[662]	940
[778]	941	extension_in=$( echo ${file_in_Name##*.} )
	942	extension_out=$( echo ${file_out##*.} )
[67]	943
[778]	944	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	945	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
	946
	947	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
	948	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
	949
[662]	950	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	951	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
[778]	952	Buffered=true
	953	Archived=false
	954	Tared=false
	955	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
[672]	956	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	957	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	958	Buffered=false
	959	Archived=true
	960	Tared=false
	961	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
	962	else
[897]	963	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
[902]	964	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
[778]	965	Buffered=false
	966	Archived=false
	967	Tared=true
	968	# Look after the tar file we want if we did not found it already
	969	if [ X${IsMatching} = X ] ; then
[801]	970	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
[778]	971	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	972	if [ ! X${IsMatching} = X ] ; then
	973	TarFileFound=${PotentialTarFile}
	974	break
	975	fi
	976	done
	977	fi
[1017]	978	# Stop here if nothing has been found
	979	if [ X${TarFileFound} = X ] ; then
	980	IGCM_debug_Print 3 "Restart files were not found!"
	981	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	982	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
[1624]	983	if [ ${is_opt} = 'OPTIONAL' ] ; then
	984	IGCM_debug_Print 3 "The restart file is optional. Now continue."
	985	nb_restart_file=0
	986	Tared=false
	987	else
	988	IGCM_debug_Print 3 "The restart file is mandatory."
	989	IGCM_debug_Exit "Please double check restart settings in config.card"
	990	IGCM_debug_Verif_Exit
	991	fi
	992	else
	993	# The tar file exist but not sure all files are inside
	994	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	995	TarFileLocation=$( basename ${TarFileFound} )
[1637]	996	nb_files=$( tar tvf ${TarFileLocation} \| grep ${comp}_${generic_restart_file_name_in} \| wc -l )
[1624]	997	if [ ${nb_files} -gt 0 ] ; then
	998	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	999	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
	1000	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	1001	else
	1002	# No file was found
	1003	if [ ${is_opt} = 'OPTIONAL' ] ; then
	1004	IGCM_debug_Print 3 "The restart file is not found in the tar file but it is optional. Now continue."
	1005	nb_restart_file=0
	1006	Tared=false
	1007	else
	1008	IGCM_debug_Print 3 "The restart file was not found in the tar file but it is mandatory."
	1009	IGCM_debug_Exit "Please double check restart settings in config.card"
	1010	IGCM_debug_Verif_Exit
	1011	fi
	1012	fi
	1013
[1017]	1014	fi
[778]	1015	fi
[41]	1016
[778]	1017	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	1018	j=0 # BASH LINE NOT NEEDED
	1019	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	1020	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	1021	j4=${j} # BASH LINE NOT NEEDED
[778]	1022	if [ X${Buffered} = Xtrue ] ; then
	1023	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	1024	elif [ X${Archived} = Xtrue ] ; then
	1025	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	1026	elif [ X${Tared} = Xtrue ] ; then
	1027	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	1028	fi
[821]	1029	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	1030	done
	1031	else
	1032	if [ X${Buffered} = Xtrue ] ; then
	1033	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
	1034	elif [ X${Archived} = Xtrue ] ; then
	1035	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
	1036	elif [ X${Tared} = Xtrue ] ; then
	1037	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	1038	fi
	1039	fi
	1040	done
[544]	1041	else
[778]	1042	if [ X${FileName0} != XNONE ] ; then
	1043	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	1044	else
	1045	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	1046	fi
[544]	1047	fi
[420]	1048	fi
[544]	1049	done
[420]	1050
[544]	1051	NbFiles=$( ls * 2> /dev/null \| wc -l )
	1052	if [ ${NbFiles} -gt 0 ] ; then
	1053	IGCM_sys_Chmod u+rw *
	1054	fi
	1055
	1056	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
[2]	1057	}
	1058
	1059	#=======================================================================
[1409]	1060	function IGCM_comp_GetInputBinaryFiles
	1061	{
	1062	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
	1063
	1064	# Debug Print :
	1065	echo
	1066	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
	1067	echo
	1068
	1069	# Clean up previous pass
	1070	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
	1071
[1411]	1072	typeset comp ExeNameIn ExeNameOut byPass
[1409]	1073	typeset compilerNmbr compilerUnit compilerFull
[1411]	1074	byPass=false
[1409]	1075	for comp in ${config_ListOfComponents[*]} ; do
	1076	# Define component
	1077
	1078	# Copy executable for this component
	1079	eval ExeNameIn=\${config_Executable_${comp}[0]}
	1080	eval ExeNameOut=\${config_Executable_${comp}[1]}
[1486]	1081	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
	1082	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
	1083	# The executable is set in config.card and is different from ""
	1084	# Use eval to expand ExeNameIn if variables are used in the name
	1085	eval ExeNameIn=${ExeNameIn}
	1086	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
	1087	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
	1088	fi
[1409]	1089	fi
	1090
	1091	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
	1092	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1093	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1094	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1095	fi
	1096	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1097	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1098	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1099	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1100	fi
	1101	fi
	1102
	1103	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1104	# Get the compiler version
	1105	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1106	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1107	# Save it
	1108	echo $compilerFull >> ${RUN_DIR}/compiler.txt
[1411]	1109	[ X${compilerFull} = X ] && byPass=true
[1409]	1110	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
[1413]	1111	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
[1409]	1112	fi
	1113	done
	1114
	1115	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
	1116	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
	1117
[1411]	1118	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
[1409]	1119	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
	1120	fi
	1121
[1415]	1122
[1409]	1123	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
	1124	}
	1125
	1126	#=======================================================================
[269]	1127	function IGCM_comp_PeriodStart
	1128	{
[544]	1129	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
[269]	1130
[544]	1131	# Debug Print :
	1132	echo
	1133	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
	1134	echo
[269]	1135
[902]	1136	typeset ExeNameIn ExeNameOut
[544]	1137	typeset comp compname comptagname
	1138	for comp in ${config_ListOfComponents[*]} ; do
[902]	1139	# Define component
[544]	1140	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1141	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[269]	1142
[544]	1143	# Copy executable for this component
	1144	eval ExeNameIn=\${config_Executable_${comp}[0]}
[1486]	1145	eval ExeNameIn=${ExeNameIn}
[544]	1146	eval ExeNameOut=\${config_Executable_${comp}[1]}
[269]	1147
[544]	1148	# Debug Print
	1149	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
	1150	# UPDATE component
	1151	${comp}_PeriodStart 2> /dev/null
[269]	1152
[544]	1153	done
[269]	1154
[544]	1155	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
[269]	1156	}
	1157
[1166]	1158
	1159
[269]	1160	#=======================================================================
[1166]	1161	function IGCM_comp_modifyFile
	1162	{
	1163	#
	1164	# syntax: IGCM_comp_modifyFile filein key [value]
	1165	#
	1166	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
	1167	#
	1168	# This function is used to replace a pattern in a file for a specific variable.
	1169	#
	1170	# Arguments:
	1171	# - filein : the file in run directory in which the variable should be set
	1172	# - key : the variable to modify
	1173	# - value : the value to set the key equal to
	1174	#
	1175	IGCM_debug_PushStack "IGCM_comp_modifyFile"
	1176
	1177	typeset filein key value pattern
	1178
	1179	# Set local variables and test the arguments
	1180	if [ $# = 3 ] ; then
	1181	# Normal case with 3 arguments
	1182	filein=$1 ; key=$2 ; value=$3
	1183	else
	1184	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
	1185	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1186	return
	1187	fi
	1188	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
	1189
	1190	# Test if the file exist
	1191	if [ ! -f ${filein} ] ; then
	1192	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
	1193	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1194	return
	1195	fi
	1196
	1197	# Read the line with key in the file without the comments
	1198	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
	1199
	1200	# Verify the existance of the pattern
	1201	if [ X"${pattern}" = X ] ; then
	1202	# Variable key is not set in filein, stop.
	1203	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
	1204	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1205	return
	1206	fi
	1207
	1208	# Now change key in filein
[1176]	1209	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
	1210	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
[1166]	1211	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
	1212	\mv ${filein}.tmp ${filein}
	1213
	1214	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1215	}
	1216
	1217	#=======================================================================
[1069]	1218	function IGCM_comp_modifyDefFile
	1219	{
	1220	#
	1221	# syntax: IGCM_comp_modifyDefFile type filein key [value]
	1222	#
	1223	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
	1224	#
	1225	# This function is used to modify a parameter file for a specific variable.
[1075]	1226	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
	1227	# This function can be used in the comp.driver files for the components.
[1069]	1228	#
[1075]	1229	# Arguments:
[1081]	1230	# - type : first argument must be blocker, nonblocker or force
[1075]	1231	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1069]	1232	# otherwise this function will exit.
[1075]	1233	# For "nonblocker" case, the user can remove or modify the variable. For
	1234	# this case, as long as AUTO is not set, no modification will be done.
[1081]	1235	# For "force" case, the variable will be modified even if it is not set to AUTO
[1069]	1236	# - filein : the file in run directory of .def type in which the variable should be set
	1237	# - key : the variable to modify
[1075]	1238	# - value : the value to set the key equal to, optional. If value is not set or if
[1069]	1239	# value=DEFAULT, then a default value must be given in filein using syntax :
	1240	# key= AUTO : DEFAULT=def_value
	1241	#
[1075]	1242	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
[1069]	1243
[1166]	1244	typeset type filein key value
	1245	typeset filelist nb_occ modify
	1246
[1075]	1247	# Set local variables and test the arguments
	1248	if [ $# = 4 ] ; then
	1249	# Normal case with 4 arguments
	1250	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1251	elif [ $# = 3 ] ; then
	1252	# Normal case with 3 arguments
	1253	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1254	else
	1255	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
[1079]	1256	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1257	return
	1258	fi
[1166]	1259	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
[1069]	1260
[1075]	1261	# Test if first argument is correct
[1166]	1262	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1081]	1263	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
[1079]	1264	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1265	return
	1266	fi
[1069]	1267
[1215]	1268	# Test if the file exist.
	1269	# Exit with error if the file does not exist for the case blocker or force.
	1270	# Only return for the case nonblocker.
[1075]	1271	if [ ! -f ${filein} ] ; then
[1215]	1272	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1273	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
	1274	else
	1275	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
	1276	fi
[1079]	1277	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1278	return
	1279	fi
[1069]	1280
[1102]	1281	# Define list of files to test using all files with suffix .def (except used*.def)
	1282	filelist=$( ls *def \| grep -v used )
[1069]	1283
[1075]	1284	# Count number of occurances for the key in all files
[1166]	1285	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
[1069]	1286
[1075]	1287	# Test if key is set several times
[1166]	1288	if [ ${nb_occ} -gt 1 ] ; then
	1289	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
[1079]	1290	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1291	return
	1292	fi
	1293
	1294	# Treatement according to different cases
[1166]	1295	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
[1075]	1296	# Stop if the key is never set and the function is blocker
[1166]	1297	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
	1298	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
	1299	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
[1075]	1300	# The key is not set but it is a nonblocker call so nothing is done.
[1166]	1301	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1302	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
[1081]	1303	modify=no
[1166]	1304	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
[1075]	1305	# Variable key is not set in filein, stop.
[1166]	1306	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1081]	1307	fi
	1308
	1309	# Check if AUTO is set in the filein on the same line as the key variable
[1166]	1310	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1311	# Modification will be done for all cases
	1312	modify=yes
	1313	else
	1314	# The variable was not set to AUTO
[1166]	1315	if [ ${type} = blocker ] ; then
[1156]	1316	# Exit because this is a blocker call
[1166]	1317	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
[1190]	1318	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1156]	1319	return
[1166]	1320	elif [ ${type} = nonblocker ] ; then
[1156]	1321	# Do nothing. Suppose that the user did set the variable correct
[1166]	1322	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
[1156]	1323	modify=no
[1166]	1324	elif [ ${type} = force ] ; then
[1156]	1325	# Force modification
[1166]	1326	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
[1081]	1327	modify=yes
[1156]	1328	fi
[1081]	1329	fi
[1069]	1330
[1081]	1331	# Do the modifcation now
[1166]	1332	if [ ${modify} = yes ] ; then
[1081]	1333
[1156]	1334	# For option DEFAULT, read default value from file.
[1166]	1335	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1336	# Case to set DEFAULT value
	1337	# Read default value from filein
[1423]	1338	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
[1069]	1339
[1166]	1340	if [ X"${value}" = X ] ; then
	1341	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
	1342	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
	1343	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1344	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
	1345	return
[1075]	1346	fi
[1156]	1347	fi
[1069]	1348
[1156]	1349	# Now change key in filein
[1166]	1350	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
	1351	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
	1352	\mv ${filein}.tmp ${filein}
[1075]	1353	fi
[1079]	1354	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1069]	1355	}
	1356
	1357	#=======================================================================
[1085]	1358	function IGCM_comp_modifyNamelist
	1359	{
	1360	#
	1361	# syntax: IGCM_comp_modifyNamelist type filein key [value]
	1362	#
	1363	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
	1364	#
	1365	# This function is used to modify a parameter file for a specific variable.
[1155]	1366	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
[1085]	1367	# This function can be used in the comp.driver files for the components.
	1368	#
	1369	# Arguments:
	1370	# - type : first argument must be blocker, nonblocker or force
	1371	# For "blocker" case, the variable must be attributed the keyworld AUTO
	1372	# otherwise this function will exit.
	1373	# For "nonblocker" case, the user can remove or modify the variable. For
	1374	# this case, as long as AUTO is not set, no modification will be done.
	1375	# For "force" case, the variable will be modified even if it is not set to AUTO
	1376	# - filein : the file in run directory of .def type in which the variable should be set
	1377	# - key : the variable to modify
	1378	# - value : the value to set the key equal to, optional. If value is not set or if
	1379	# value=DEFAULT, then a default value must be given in filein using syntax :
	1380	# key= AUTO : DEFAULT=def_value
	1381	#
	1382	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
	1383
[1166]	1384	typeset type filein key value pattern modify
	1385
[1085]	1386	# Set local variables and test the arguments
	1387	if [ $# = 4 ] ; then
	1388	# Normal case with 4 arguments
	1389	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1390	elif [ $# = 3 ] ; then
	1391	# Normal case with 3 arguments
	1392	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1393	else
	1394	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
	1395	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1396	return
	1397	fi
[1166]	1398	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
[1085]	1399
	1400	# Test if first argument is correct
[1166]	1401	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1085]	1402	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
	1403	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1404	return
	1405	fi
	1406
[1215]	1407	# Test if the file exist.
	1408	# Exit with error if the file does not exist for the case blocker or force.
	1409	# Only return for the case nonblocker.
[1085]	1410	if [ ! -f ${filein} ] ; then
[1215]	1411	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1412	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
	1413	else
	1414	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
	1415	fi
[1085]	1416	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1417	return
	1418	fi
	1419
	1420	# Read the line with key in the file without the comments
[1166]	1421	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
[1155]	1422
[1085]	1423	# Verify the existance of the pattern
	1424	if [ X"$pattern" = X ] ; then
[1156]	1425	# Variable key is not set in filein, stop.
[1166]	1426	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1156]	1427	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1428	return
[1085]	1429	fi
[1155]	1430
[1085]	1431	# Check if the variable is set to AUTO in the filein
	1432	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1433	# Modification will be done for all cases
	1434	modify=yes
	1435	else
	1436	# The variable was not set to AUTO
[1166]	1437	if [ ${type} = blocker ] ; then
[1156]	1438	# Exit because this is a blocker call
[1166]	1439	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
[1156]	1440	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1441	return
[1166]	1442	elif [ ${type} = nonblocker ] ; then
[1156]	1443	# Do nothing. Suppose that the user did set the variable correct
[1166]	1444	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
[1156]	1445	modify=no
[1166]	1446	elif [ ${type} = force ] ; then
[1156]	1447	# Force modification
[1166]	1448	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
[1085]	1449	modify=yes
[1156]	1450	fi
[1085]	1451	fi
	1452
	1453	# Do the modifcation now
[1166]	1454	if [ ${modify} = yes ] ; then
[1085]	1455
[1156]	1456	# For option DEFAULT, read default value from file.
[1166]	1457	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1458	# Case to set DEFAULT value
	1459	# Read default value from filein
	1460	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
[1085]	1461
[1166]	1462	if [ X"${value}" = X ] ; then
	1463	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
	1464	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
	1465	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1466	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1467	return
[1085]	1468	fi
[1156]	1469	fi
[1085]	1470
[1156]	1471	# Now change key in filein
[1166]	1472	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
	1473	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
	1474	\mv ${filein}.tmp ${filein}
[1085]	1475	fi
	1476	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1477	}
	1478
	1479	#=======================================================================
[1074]	1480	function IGCM_comp_modifyXmlFile
	1481	{
	1482	#
	1483	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
	1484	#
	1485	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
	1486	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
	1487	#
	1488	# This function is used to modify the value for a specific attribute and variable id.
[1155]	1489	# The file must be a valid xml file.
[1075]	1490	# This function can be used in the comp.driver files for the components.
[1074]	1491	#
[1075]	1492	# Arguments:
	1493	# - type : first argument must be blocker, nonblocker or force.
	1494	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1074]	1495	# otherwise this function will exit.
[1075]	1496	# For "nonblocker" case, the user can remove or modify the variable. For
[1074]	1497	# this case, as long as AUTO is not set, no modification will be done.
[1075]	1498	# For "force" case, the variable will be modified even if it is not set to AUTO
[1074]	1499	# - filein : the file in run directory of .xml type in which the variable should be set
	1500	# - keyid : the variable to modify
	1501	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
	1502	# - value : the value to set in the filein
	1503	#
[1075]	1504	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
[1074]	1505
[1166]	1506	typeset type filein keyid keyattrib value modify
	1507
[1075]	1508	# Set local variables and test the arguments
	1509	if [ $# = 5 ] ; then
	1510	# Normal case with 4 arguments
	1511	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
	1512	else
	1513	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
[1089]	1514	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1515	return
	1516	fi
[1166]	1517	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
[1074]	1518
[1075]	1519	# Test if first argument is correct
[1166]	1520	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1075]	1521	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
[1089]	1522	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1523	return
	1524	fi
[1074]	1525
[1215]	1526	# Test if the file exist.
	1527	# Exit with error if the file does not exist for the case blocker or force.
	1528	# Only return for the case nonblocker.
[1075]	1529	if [ ! -f ${filein} ] ; then
[1215]	1530	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1531	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
	1532	else
	1533	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
	1534	fi
[1089]	1535	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1536	return
	1537	fi
	1538
[1386]	1539	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
[1166]	1540	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
[1386]	1541	if [ ${type} = nonblocker ] ; then
	1542	# This is a nonblocker case, print warning but do nothing else
	1543	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1544	else
	1545	# This is a blocker or force case : stop now
	1546	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
	1547	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
	1548	return
	1549	fi
[1075]	1550	fi
	1551
	1552	# Check if AUTO is set on the same line as keyid and keyattrib
[1166]	1553	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
[1394]	1554	# Modification will be done
[1075]	1555	modify=yes
	1556	else
[1166]	1557	if [ ${type} = blocker ] ; then
[1075]	1558	# Exit, the variable must be set to AUTO
[1166]	1559	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
[1089]	1560	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1561	return
[1166]	1562	elif [ ${type} = nonblocker ] ; then
[1075]	1563	# Nothing will be done
	1564	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
	1565	modify=no
[1166]	1566	elif [ ${type} = force ] ; then
[1075]	1567	# Force modification
[1166]	1568	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
[1075]	1569	modify=yes
[1074]	1570	fi
[1075]	1571	fi
[1074]	1572
[1075]	1573	# Do the modifcation now
[1166]	1574	if [ ${modify} = yes ] ; then
	1575	if [ ${keyattrib} = NONE ] ; then
[1075]	1576	# Case to modify the variable itself
	1577	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
[1166]	1578	sed -e "s/$<[^\"]\"${keyid}\".>$$[^<]$$<[^>]$/\1${value}\3/" ${filein} > ${filein}.tmp
[1074]	1579	else
[1156]	1580	# Check if keyattrib is set on the same line as keyid
[1166]	1581	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
[1156]	1582	# Case to modify the attribute value
	1583	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
[1166]	1584	sed -e "/id=\"${keyid}\"/s/$${keyattrib}=\"$[^\"]*$\"$/\1${value}\2/" ${filein} > ${filein}.tmp
[1156]	1585	else
	1586	# Case to add the attribute and its value
	1587	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
[1166]	1588	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
[1156]	1589	fi
[1074]	1590	fi
[1166]	1591	\mv ${filein}.tmp ${filein}
[1075]	1592	fi
	1593	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1074]	1594	}
	1595
	1596	#=======================================================================
[2]	1597	function IGCM_comp_Update
	1598	{
[544]	1599	IGCM_debug_PushStack "IGCM_comp_Update"
[2]	1600
[1409]	1601	# Debug Print :
[544]	1602	echo
	1603	IGCM_debug_Print 1 "IGCM_comp_Update"
	1604	echo
[2]	1605
[544]	1606	typeset comp compname comptagname
	1607	for comp in ${config_ListOfComponents[*]} ; do
[902]	1608	# Define component
[544]	1609	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1610	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1611
[544]	1612	# Debug Print
	1613	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
	1614	# UPDATE component
	1615	${comp}_Update
[2]	1616
[1413]	1617	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
	1618	if [ -f timeseries_def_${compname}.xml ]; then
	1619	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
	1620	for line in $( cat ts.temp.${compname}.txt ); do
	1621	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
	1622	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
	1623	case ${output_freq} in
	1624	Y\|y)
	1625	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
	1626	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
	1627	;;
	1628	MO\|mo)
	1629	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
	1630	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
	1631	;;
	1632	D\|d)
	1633	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
	1634	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
	1635	;;
	1636	S\|s)
	1637	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
	1638	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
	1639	;;
	1640	esac
	1641	done
	1642	fi
	1643
	1644	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
	1645	if [ -f dr2xml_${compname}.xml ]; then
[1535]	1646	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
	1647	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
	1648	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
	1649	# Modify path from dr2xml_{compname}.xml
	1650	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
[1552]	1651	${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
[1535]	1652	else
	1653	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
	1654	fi
	1655	# Overwrite the original file
	1656	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
[1467]	1657	fi
[1422]	1658	fi
[544]	1659	done
[2]	1660
[544]	1661	IGCM_debug_PopStack "IGCM_comp_Update"
[2]	1662	}
	1663
	1664	#=======================================================================
	1665	function IGCM_comp_Finalize
	1666	{
[544]	1667	IGCM_debug_PushStack "IGCM_comp_Finalize"
[2]	1668
[544]	1669	# Debug Print :
	1670	echo
	1671	IGCM_debug_Print 1 "IGCM_comp_Finalize"
	1672	echo
[2]	1673
[544]	1674	typeset ListTextName TextName0
	1675	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
	1676	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
[1165]	1677	typeset -Z4 j4 #BASH declare j4
[544]	1678	typeset list_file nlist_file
	1679	typeset compactoutputs
[429]	1680
[1165]	1681	# Initialize array hosting list of rebuilded files to copy
	1682	unset rebuildedActionsList
	1683
	1684	# Text compacting options
[544]	1685	compactoutputs=false
	1686	if [ X${JobType} != XRUN ] ; then
	1687	compactoutputs=true
	1688	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
	1689	compactoutputs=true
	1690	fi
[433]	1691
[1043]	1692	# Prepare headers for the shell dedicated to offline rebuild
	1693	if [ X${AsynchronousRebuild} = Xtrue ] ; then
	1694	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1695	if [ ${DRYRUN} -le 1 ] ; then
	1696	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1697	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1698	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1699	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1700	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1701	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1702	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1703	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1704	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1705	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1706	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1707	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1708	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1709	fi
	1710	fi
	1711
[544]	1712	for comp in ${config_ListOfComponents[*]} ; do
[902]	1713	# Define component
[544]	1714	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1715	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1716
[544]	1717	# Debug Print
	1718	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
	1719	# FINALIZE component
	1720	${comp}_Finalize
[2]	1721
[778]	1722	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	1723
[804]	1724	# Save Output Text files of models
	1725	#---------------------------------
	1726	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
	1727	IGCM_card_DefineArrayFromOption ${card} OutputText List
	1728	ListTextName=${compname}_OutputText_List
	1729
	1730	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
	1731	if [ X${TextName0} != X${NULL_STR} ] ; then
	1732	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
	1733
	1734	(( i=0 ))
	1735	until [ $i -eq $NbFiles ]; do
	1736	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
	1737	eval file_out=${PREFIX}_${file_in}
	1738
	1739	(( i=i+1 ))
	1740
	1741	unset list_file
	1742	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
	1743	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
	1744	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 )
	1745	nlist_file=${#list_file[@]}
	1746	if [ ${nlist_file} -gt 1 ] ; then
	1747	if ( ${compactoutputs} ) ; then
	1748	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
	1749	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
	1750	echo ${list_file[*]} > ${file_out}
	1751	echo "" >> ${file_out}
	1752
	1753	(( i_ = 0 ))
[1080]	1754	for file in ${list_file[@]} ; do
[804]	1755	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
	1756	echo "\| " ${i_} " " ${file} >> ${file_out}
	1757	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
[999]	1758	cat ${file} \| sed "s/$.*$/${i_}\1/" >> ${file_out}
[804]	1759	echo "" >> ${file_out}
	1760	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1761	(( i_ = i_ + 1 ))
	1762	done
[1080]	1763	if ( ${ExecutionFail} ) ; then
	1764	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
	1765	fi
	1766
[804]	1767	if [ X${Pack} = Xtrue ] ; then
	1768	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
	1769	else
	1770	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
	1771	fi
[1080]	1772
[804]	1773	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
[1080]	1774	else
	1775	for file in ${list_file[@]} ; do
	1776	if ( ${ExecutionFail} ) ; then
	1777	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
	1778	fi
[804]	1779
	1780	if [ X${Pack} = Xtrue ] ; then
	1781	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
	1782	else
	1783	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
	1784	fi
[1080]	1785
[804]	1786	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1787	done
	1788	fi
	1789	else
	1790	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
	1791	eval IGCM_sys_Mv ${file_in}* ${file_in}
	1792	fi
[1080]	1793
	1794	if ( ${ExecutionFail} ) ; then
	1795	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
	1796	fi
	1797
[804]	1798	if [ X${Pack} = Xtrue ] ; then
	1799	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
	1800	else
	1801	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
	1802	fi
	1803	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1804	fi
	1805	done
	1806	fi
	1807
[544]	1808	# Save Restarts files
	1809	#--------------------
	1810	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
	1811	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	1812	ListFilesName=${compname}_RestartFiles_List
	1813	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[1624]	1814
[544]	1815	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	1816	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
	1817	(( i=0 ))
	1818	until [ $i -ge $NbFiles ]; do
[778]	1819	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1820	eval file_in=${file_in_}
[2]	1821
[778]	1822	(( i_ = i+1 ))
	1823	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1824	eval file_out=${file_out_}
[151]	1825
[778]	1826	(( i_ = i+2 ))
	1827	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1828	eval file_outin=${file_outin_}
[151]	1829
[1624]	1830	(( i_ = i+3 ))
	1831	eval is_opt=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1832	if [ X${is_opt} = XOPTIONAL ] ; then
	1833	echo ${file_in} is optional
	1834	(( i=i+4 ))
	1835	else
	1836	is_opt=""
	1837	echo ${file_in} is mandatory
	1838	(( i=i+3 ))
	1839	fi
	1840
[778]	1841	generic_restart_file_name_in=$( basename ${file_in} .nc )
	1842	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
	1843	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
[2]	1844
[902]	1845	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
[778]	1846	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	1847	j=0 # BASH LINE NOT NEEDED
	1848	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	1849	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	1850	j4=${j} # BASH LINE NOT NEEDED
[778]	1851	if [ X${Pack} = Xtrue ] ; then
[1624]	1852	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc ${is_opt}
[778]	1853	else
[1624]	1854	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc ${is_opt}
[778]	1855	fi
[1624]	1856
	1857	if [ -f ${generic_restart_file_name_in}_${j4}.nc ] ; then
	1858	if [ ! ${file_in} = ${file_outin} ] ; then
	1859	if ( ${ExitFlag} ) ; then
	1860	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
	1861	else
	1862	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
	1863	fi
	1864	fi
	1865	else
	1866	# This is the case where the restart file no not exist.
	1867	# It has already been checked if the model should stop for this case.
	1868	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${generic_restart_file_name_in}_${j4}.nc"
	1869	fi
[821]	1870	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	1871	done
	1872	else
	1873	if [ X${Pack} = Xtrue ] ; then
[1624]	1874	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
[778]	1875	else
[1624]	1876	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} ${is_opt}
[778]	1877	fi
[1624]	1878
	1879	if [ -f ${file_in} ] ; then
	1880	if [ ! ${file_in} = ${file_outin} ] ; then
	1881	if ( ${ExitFlag} ) ; then
	1882	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
	1883	else
	1884	IGCM_sys_Mv ${file_in} ${file_outin}
	1885	fi
	1886	fi
	1887	else
	1888	# This is the case where the restart file no not exist.
	1889	# It has already been checked if the model should stop for this case.
	1890	IGCM_debug_Print 1 "Restart file does not exist, no move in RUN_DIR done : ${file_in}"
	1891	fi
[778]	1892	fi
	1893
[544]	1894	done
	1895	else
	1896	if [ X${FileName0} != XNONE ] ; then
[778]	1897	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
[544]	1898	else
[778]	1899	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
[544]	1900	fi
	1901	fi
[2]	1902
[544]	1903	# Save Output files
	1904	#------------------
	1905	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
	1906	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	1907	ListFilesName=${compname}_OutputFiles_List
	1908	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	1909
[544]	1910	if [ X${FileName0} != X${NULL_STR} ] ; then
	1911	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[149]	1912
[544]	1913	(( i=0 ))
	1914	until [ $i -ge $NbFiles ]; do
[778]	1915	SaveOnArchive=true
	1916	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1917	eval file_in=${file_in_}
	1918	(( i_ = i+1 ))
	1919	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1920	eval file_out=${file_out_}
	1921	#
	1922	# Override file_out path remplacing R_SAVE by R_BUFR
	1923	#
	1924	if [ X${Pack} = Xtrue ] ; then
	1925	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
	1926	fi
	1927	#
	1928	# Not necessarily the best option. /!\ Potential side effects /!\
	1929	#
	1930	(( i_ = i+2 ))
	1931	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1932	#
	1933	generic_file_name=$( basename ${file_in} .nc )
	1934	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
	1935	#
	1936	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
[804]	1937	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
[778]	1938	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
	1939	elif [ ${nb_rebuild_file} -gt 1 ] ; then
[804]	1940	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
[778]	1941	if [ X${AsynchronousRebuild} = Xfalse ] ; then
	1942	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
[1388]	1943	#
	1944	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
	1945	if [ ${file_in} = output.abort.nc ] ; then
	1946	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
	1947	else
[1429]	1948	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
[1388]	1949	fi
[778]	1950	else
	1951	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
[1429]	1952	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
[544]	1953
[778]	1954	# Prepare the shell dedicated to offline rebuild
	1955	if [ $DRYRUN -le 1 ]; then
[694]	1956	if [ ${file_in} = histstn.nc ] ; then
	1957	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1958	else
[980]	1959	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[694]	1960	fi
[1206]	1961	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1962	fi
	1963	#
	1964	# Load Patch we need to apply and apply
	1965	if [ $DRYRUN -le 1 ]; then
	1966	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
[1080]	1967	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1968	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1969	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1970	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1971	done
	1972	fi
	1973	fi
	1974	#
	1975	if [ $DRYRUN -le 1 ]; then
	1976	if [ X${Pack} = Xtrue ] ; then
[1165]	1977	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
[778]	1978	else
[1165]	1979	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
[778]	1980	fi
[1206]	1981	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
[1165]	1982	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
[778]	1983	fi
	1984	SaveOnArchive=false
	1985	fi
	1986	fi
	1987	#
	1988	if [ ${SaveOnArchive} = true ] ; then
	1989	#
	1990	# Rebuild has been done online or it was not needed
	1991	#
	1992	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
	1993	#
	1994	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
[1289]	1995	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
[778]	1996	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1997	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
	1998	#
	1999	if [ $DRYRUN -le 1 ]; then
[1080]	2000	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	2001	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	2002	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	2003	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	2004	done
	2005	#
	2006	if [ X${Pack} = Xtrue ] ; then
	2007	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	2008	else
	2009	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	2010	fi
[1206]	2011	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	2012	#
	2013	fi
	2014	else
	2015	#
	2016	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
	2017	#
	2018	if [ X${Pack} = Xtrue ] ; then
	2019	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
	2020	else
	2021	IGCM_sys_Put_Out ${file_in} ${file_out}
	2022	fi
	2023	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	2024	if [ ${nb_rebuild_file} -gt 1 ] ; then
	2025	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
	2026	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
	2027	done
	2028	fi
	2029	fi
	2030	fi
[1603]	2031	((i_ = i_ +1))
	2032	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	2033	eval Testvar=${Testvar_}
	2034	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
	2035	((i = i+4))
	2036	else
[778]	2037	(( i=i+3 ))
[1603]	2038	fi
[544]	2039	done
	2040	fi
	2041	echo
	2042	done
[1165]	2043	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
	2044	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
[1166]	2045	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1165]	2046	i=0
	2047	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
	2048	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	2049	(( i=i+1 ))
	2050	done
	2051	fi
[544]	2052	IGCM_debug_PopStack "IGCM_comp_Finalize"
[2]	2053	}

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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh

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