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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1538

Last change on this file since 1538 was 1538, checked in by aclsce, 4 years ago
Modified to not use restart files for XIOS in case of dr2xmlIPSL=true
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: 80.6 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
	247	(( i=i+3 ))
[544]	248	done
	249	fi
	250	# Debug Print
	251	IGCM_debug_Print 3 "Initialize ${compname} with driver."
	252	# INIT component
	253	${comp}_Initialize
	254	echo
	255	done
[2]	256
[544]	257	IGCM_debug_PopStack "IGCM_comp_Initialize"
[2]	258	}
	259
	260	#=======================================================================
	261	function IGCM_comp_PrepareDeletedFiles
	262	{
[544]	263	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
[778]	264
[544]	265	if [ X${2} != X. ] ; then
	266	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
	267	else
	268	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
	269	fi
[2]	270
[544]	271	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
[2]	272	}
	273
	274	#=======================================================================
[1338]	275	function IGCM_comp_PrepareXiosFiles
	276	{
	277	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
	278
	279	typeset file
	280	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
	281
	282	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
	283	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
	284	fi
	285	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
	286	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
	287	fi
[1413]	288	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
	289	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
	290	fi
[1338]	291
	292	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
	293	}
	294
	295	#=======================================================================
[2]	296	function IGCM_comp_GetInputInitialStateFiles
	297	{
[544]	298	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
[2]	299
[544]	300	# Debug Print :
	301	echo
	302	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
	303	echo
[2]	304
[902]	305	# Only the first time step need InitialStateFiles
[544]	306	# otherwise it's BoundaryConditions
	307	if ( ${FirstInitialize} ) ; then
[902]	308	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	309	typeset file_in_ file_in file_out_ file_out do_init
[544]	310	for comp in ${config_ListOfComponents[*]} ; do
	311	# Initialize
	312	do_init="y"
	313	# Do we need to bring initial state file for this component
[1401]	314	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[778]	315	eval do_init="n"
[544]	316	else
[778]	317	# Read component Restarts parameters
	318	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	319	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
	320	if [ "${do_start}" = "y" ] ; then
	321	do_init="n"
	322	else
	323	do_init="y"
	324	fi
[544]	325	fi
[2]	326
[544]	327	if [ "${do_init}" = "y" ] ; then
[902]	328	# Define component
[778]	329	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	330	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	331
[778]	332	# Debug Print :
	333	IGCM_debug_Print 3 "Initialisation files ${compname}"
[2]	334
[778]	335	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	336
[778]	337	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
	338	ListFilesName=${compname}_InitialStateFiles_List
[2]	339
[778]	340	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
	341	if [ X${FileName0} != X${NULL_STR} ] ; then
	342	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
	343	(( i=0 ))
	344	until [ $i -ge $NbFiles ]; do
	345	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	346	eval file_in=${file_in_}
	347	(( i_ = i+1 ))
	348	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	349	eval file_out=${file_out_}
[2]	350
[778]	351	IGCM_sys_IsFileArchived ${file_in}
	352	if [ $? = 0 ] ; then
	353	IGCM_sys_Get ${file_in} ${file_out}
	354	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	355	else
	356	IGCM_sys_Cp ${file_in} ${file_out}
	357	fi
	358	(( i=i+2 ))
	359	done
	360	fi
[544]	361	fi
	362	done
	363	fi
	364	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
[2]	365	}
	366
	367	#=======================================================================
[247]	368	# Definition of Smooth modulo function
[902]	369	# usage :
[247]	370	# IGCM_SmoothModulo StringModulo value
	371	#
	372	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
	373	# [min]:[modulo:][max]
	374	# where :
[902]	375	# [] value are optionnals;
[247]	376	# empty min equal 1
	377	# empty max equal infinity
	378	# modulo not given or empty equal 1
	379	# empty string or just ':' equal always.
	380	#
	381	# value : the value to test with the definition
	382	#
[902]	383	# return : true(1)/false(0)
[247]	384	function IGCM_SmoothModulo
	385	{
[544]	386	IGCM_debug_PushStack "IGCM_SmoothModulo"
	387	typeset defVector ModValue
[247]	388
[544]	389	eval set +A defVector -- $( echo "${1}" \| \
	390	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
[247]	391
[544]	392	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
	393	arr[1]=${defVector[0]}
	394	arr[2]=${defVector[2]}
[412]	395
[902]	396	# Test limits :
	397	# ${defVector[0]} <= ${2} <= ${defVector[2]}
[544]	398	# or ${defVector[2]} == -1
	399	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
	400	# Test modulo
	401	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
	402	if [ ${ModValue} -eq 0 ] ; then
	403	arr[3]=true
	404	echo ${arr[@]}
	405	IGCM_debug_PopStack "IGCM_SmoothModulo"
	406	return 1
[247]	407	else
[544]	408	arr[3]=false
	409	echo ${arr[@]}
	410	IGCM_debug_PopStack "IGCM_SmoothModulo"
	411	return 0
[247]	412	fi
[544]	413	else
	414	arr[3]=false
	415	echo ${arr[@]}
	416	IGCM_debug_PopStack "IGCM_SmoothModulo"
	417	return 0
	418	fi
[247]	419	}
	420
	421	#=======================================================================
	422	function IGCM_comp_GetInputSmoothFiles
	423	{
[544]	424	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
[247]	425
[544]	426	# Debug Print :
	427	echo
	428	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
	429	echo
[247]	430
[544]	431	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
	432	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
[247]	433
[544]	434	for comp in ${config_ListOfComponents[*]} ; do
	435	# Define component
	436	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	437	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[247]	438
[544]	439	# Debug Print :
	440	IGCM_debug_Print 3 "Smooth files ${compname}"
[247]	441
[544]	442	card=${SUBMIT_DIR}/COMP/${compname}.card
[247]	443
[544]	444	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
	445	ListFilesName=${compname}_SmoothFiles_List
	446	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[247]	447
[544]	448	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
	449	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[247]	450
[544]	451	(( i=0 ))
	452	until [ $i -ge $NbFiles ]; do
[778]	453	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	454	eval file_in=${file_in_}
	455	(( i_ = i+1 ))
	456	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	457	eval file_out=${file_out_}
[247]	458
[778]	459	# define CumulPeriod definition for this file
	460	(( i__ = i+2 ))
	461	eval SmoothDef=\${${ListFilesName}[$i__]}
	462	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
	463	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
	464	j=1
	465	for val in ${aux} ; do
	466	[ ${j} -eq 1 ] && SmoothMin=${val}
	467	[ ${j} -eq 2 ] && SmoothMax=${val}
	468	[ ${j} -eq 3 ] && ret=${val}
	469	(( j=j+1 ))
	470	done
	471	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
	472	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
[548]	473
[778]	474	IGCM_sys_IsFileArchived ${file_in}
	475	if [ $? = 0 ] ; then
	476	IGCM_sys_Get ${file_in} ${file_out}
	477	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	478	else
	479	IGCM_sys_Cp ${file_in} ${file_out}
	480	fi
	481	fi
	482	(( i=i+3 ))
[544]	483	done
	484	fi
	485	done
[778]	486
[544]	487	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
[247]	488	}
	489
	490	#=======================================================================
[2]	491	function IGCM_comp_GetInputBoundaryFiles
	492	{
[544]	493	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
[2]	494
[544]	495	# Debug Print :
	496	echo
	497	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
	498	echo
[2]	499
[902]	500	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	501	typeset file_in_ file_in file_out_ file_out
[2]	502
[544]	503	if [ ${Period} = 1 ]; then
	504	ListFixBoundary=" "
	505	fi
[2]	506
[544]	507	for comp in ${config_ListOfComponents[*]} ; do
[2]	508
[544]	509	# Define component
	510	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	511	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	512
[544]	513	# Debug Print :
	514	IGCM_debug_Print 3 "Boundary files ${compname}"
[2]	515
[544]	516	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	517
[544]	518	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
	519	ListFilesName=${compname}_BoundaryFiles_List
	520	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	521
[544]	522	if [ X${FileName0} != X${NULL_STR} ] ; then
	523	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	524
[544]	525	(( i=0 ))
	526	until [ $i -ge $NbFiles ]; do
[778]	527	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	528	eval file_in=${file_in_}
	529	(( i_ = i+1 ))
	530	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	531	eval file_out=${file_out_}
[2]	532
[778]	533	IGCM_sys_IsFileArchived ${file_in}
	534	if [ $? = 0 ] ; then
	535	IGCM_sys_Get ${file_in} ${file_out}
[809]	536	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[778]	537	else
	538	IGCM_sys_Cp ${file_in} ${file_out}
	539	fi
[2]	540
[778]	541	(( i=i+2 ))
[544]	542	done
	543	fi
[2]	544
[544]	545	# Get non deleted files
	546	if [ ${Period} = 1 ]; then
[2]	547
[544]	548	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
	549	ListFilesName=${compname}_BoundaryFiles_ListNonDel
	550	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	551
[544]	552	if [ X${FileName0} != X${NULL_STR} ] ; then
[778]	553	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	554
[778]	555	(( i=0 ))
	556	until [ $i -ge $NbFiles ]; do
	557	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	558	eval file_in=${file_in_}
	559	(( i_ = i+1 ))
	560	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	561	eval file_out=${file_out_}
[2]	562
[778]	563	IGCM_sys_IsFileArchived ${file_in}
	564	if [ $? = 0 ] ; then
	565	IGCM_sys_Get ${file_in} ${file_out}
	566	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	567	else
	568	IGCM_sys_Cp ${file_in} ${file_out}
	569	fi
[2]	570
[778]	571	if [ X${file_out} != X. ] ; then
	572	ListFixBoundary=${ListFixBoundary}" "${file_out}
	573	else
	574	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
	575	fi
	576
	577	(( i=i+2 ))
	578	done
[544]	579	fi
	580	fi
	581	done
[778]	582
[544]	583	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
[2]	584	}
	585
	586	#=======================================================================
	587	function IGCM_comp_DelFixeBoundaryFiles
	588	{
[544]	589	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	590
[544]	591	# Debug Print :
	592	echo
	593	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
	594	echo
[2]	595
[544]	596	ls -l ${ListFixBoundary}
	597	rm -f ${ListFixBoundary}
[2]	598
[544]	599	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	600	}
	601
	602	#=======================================================================
	603	function IGCM_comp_GetInputParametersFiles
	604	{
[544]	605	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
[2]	606
[544]	607	# Debug Print :
	608	echo
	609	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
	610	echo
[2]	611
[544]	612	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
	613	for comp in ${config_ListOfComponents[*]} ; do
[902]	614	# Define component
[544]	615	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	616	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	617
[1338]	618	# Initialize array hosting file_def and field_def files to check and/or modify
	619	unset FieldDef
	620	unset FileDef
	621
[544]	622	# Debug Print :
	623	IGCM_debug_Print 3 "Parameters ${compname}"
[2]	624
[778]	625	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	626
[544]	627	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
	628	ListFilesName=${compname}_ParametersFiles_List
	629	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	630
[544]	631	if [ X${FileName0} != X${NULL_STR} ] ; then
	632	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	633
[544]	634	(( i=0 ))
	635	until [ $i -ge $NbFiles ]; do
[778]	636	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	637	eval file_in=${file_in_}
	638	(( i_ = i+1 ))
	639	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
[902]	640	eval file_out=${file_out_}
[2]	641
[902]	642	IGCM_sys_Cp ${file_in} ${file_out}
[778]	643	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[1338]	644	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
[2]	645
[778]	646	(( i=i+2 ))
[544]	647	done
	648	fi
[1338]	649
	650	if [ ${#FileDef[@]} -ne 0 ] ; then
	651	# Check XMLs coherency now
[1339]	652	IGCM_debug_Print 1 "${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}"
	653	${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}
[1338]	654	if [ $? = 0 ] ; then
[1339]	655	IGCM_debug_Print 1 "${compname} XIOS XMLs are consistent"
[1338]	656	else
[1373]	657	IGCM_debug_Print 1 "${compname} XIOS XMLs ARE NOT consistent"
	658	if [ X${config_Post_ParserXIOS} = XTRUE ] ; then
	659	IGCM_debug_Print 1 "Try to fix it:"
	660	IGCM_debug_Print 3 "${libIGCM}/libIGCM_post/xios_parser.py -v modify --field ${FieldDef[]} --file ${FileDef[]}"
	661	${libIGCM}/libIGCM_post/xios_parser.py -vv modify --field ${FieldDef[]} --file ${FileDef[]}
	662	[ $? != 0 ] && IGCM_debug_Exit "Failed to fix XIOS xml files for ${compname}"
	663	fi
[1338]	664	fi
	665	fi
[544]	666	done
[2]	667
[544]	668	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
[2]	669	}
	670
	671	#=======================================================================
	672	function IGCM_comp_GetInputRestartFiles
	673	{
[544]	674	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
[2]	675
[544]	676	# Debug Print :
	677	echo
	678	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
	679	echo
[2]	680
[590]	681	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
	682	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
[902]	683	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
[544]	684	typeset file_in file_out file_in_ file_out_ file_in_Name
	685	typeset -Z4 j4
[821]	686	#BASH declare j4
[2]	687
[778]	688	IsMatching=""
	689
[544]	690	for comp in ${config_ListOfComponents[*]} ; do
[902]	691	# Define component
[544]	692	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	693	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
	694	#
	695	card=${SUBMIT_DIR}/COMP/${compname}.card
	696	#
	697	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	698	ListFilesName=${compname}_RestartFiles_List
	699	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	700
[544]	701	# Debug Print :
	702	IGCM_debug_Print 3 "restart ${compname}"
[2]	703
[544]	704	if ( ${FirstInitialize} ) ; then
[2]	705
[1401]	706	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[1446]	707	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
[1538]	708	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
[1447]	709	CompOldName=IOS
	710	config_IOS_Restart="n"
	711	do_start="n"
[1449]	712	config_IOS_RestartDate=-1
	713	config_IOS_RestartJobName=${NULL_STR}
	714	config_IOS_RestartPath=${NULL_STR}
[1447]	715	else
[1446]	716	eval config_${comp}_Restart="y"
	717	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
	718	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
	719	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
	720	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
	721	eval CompOldName=${comp}
	722	fi
[544]	723	else
[778]	724	# Read component Restarts parameters
	725	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	726	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
[2]	727
[778]	728	if [ "${do_start}" = "y" ] ; then
	729	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
	730	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
	731	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
	732	else
	733	eval config_${comp}_RestartDate=-1
	734	eval config_${comp}_RestartJobName=${NULL_STR}
	735	eval config_${comp}_RestartPath=${NULL_STR}
	736	fi
[849]	737
[778]	738	eval CompOldName=\${config_${comp}_OldName}
	739	if [ X${CompOldName} = X ] ; then
	740	eval CompOldName=${comp}
	741	fi
	742
	743	# Reinitialize IsMatching to allow searching for a different tar file for each component.
	744	IsMatching=""
	745	TarFileFound=""
[544]	746	fi
[2]	747
[544]	748	if [ "${do_start}" = "y" ] ; then
[2]	749
[672]	750	# Restore Restarts files
	751	#-----------------------
[778]	752	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	753	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	754
[778]	755	(( i=1 ))
	756	until [ $i -gt $NbFiles ]; do
	757	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	758	eval file_in=${file_in_}
	759	(( i_ = i+1 ))
	760	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	761	eval file_out=${file_out_}
	762
	763	eval Date_tmp=\${config_${comp}_RestartDate}
	764	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
[672]	765	# will be re-use
	766	eval RestartPath=\${config_${comp}_RestartPath}
	767	eval RestartJobName=\${config_${comp}_RestartJobName}
	768	#
[778]	769	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
	770	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
[2]	771
[778]	772	extension_in=$( echo ${file_in_Name##*.} )
	773	extension_out=$( echo ${file_out##*.} )
[672]	774
[778]	775	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	776	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
[2]	777
[778]	778	Path_OUT=${Path_r}/${generic_restart_file_name_in}
	779
[672]	780	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	781	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
[778]	782	Buffered=true
	783	Archived=false
	784	Tared=false
	785	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
[672]	786	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	787	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	788	Buffered=false
	789	Archived=true
	790	Tared=false
	791	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
[672]	792	else
[897]	793	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
	794	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
[902]	795	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
[778]	796	Buffered=false
	797	Archived=false
	798	Tared=true
[672]	799	# Look after the tar file we want if we did not found it already
[778]	800	if [ X${IsMatching} = X ] ; then
[947]	801	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
	802	if [ $? ] ; then
[897]	803	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
	804	IsMatching=$( echo ${PotentialTarFile##*/} \| \
	805	sed "s:_restart::" \| \
	806	sed "s:^${RestartJobName}_::" \| \
	807	sed "s:\.tar$::" \| \
	808	gawk -F_ -v restartdate=${Date_r} \
	809	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	810	if [ ! X${IsMatching} = X ] ; then
	811	TarFileFound=${PotentialTarFile}
	812	break
	813	fi
	814	done
[1017]	815	fi
	816	# Stop here if nothing has been found
	817	if [ X${TarFileFound} = X ] ; then
[902]	818	IGCM_debug_Print 3 "Restart files were not found!"
	819	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	820	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
[897]	821	IGCM_debug_Exit "Please double check restart settings in config.card"
	822	IGCM_debug_Verif_Exit
	823	fi
[778]	824	fi
[918]	825	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	826	TarFileLocation=$( basename ${TarFileFound} )
[801]	827	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	828	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	829	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	830	fi
[672]	831
	832	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	833	j=0 # BASH LINE NOT NEEDED
	834	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	835	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	836	j4=${j} # BASH LINE NOT NEEDED
[778]	837	if [ X${Buffered} = Xtrue ] ; then
	838	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	839	elif [ X${Archived} = Xtrue ] ; then
	840	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	841	elif [ X${Tared} = Xtrue ] ; then
	842	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	843	fi
[821]	844	(( j=j+1 )) #BASH LINE NOT NEEDED
[778]	845	done
[740]	846
[1248]	847	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
	848	if [ X${OCE_PROC_MPI} != X ] ; then
	849	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
[1380]	850	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
[740]	851	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
	852	fi
	853	fi
[778]	854	else
	855	if [ X${Buffered} = Xtrue ] ; then
	856	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
	857	elif [ X${Archived} = Xtrue ] ; then
	858	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
	859	elif [ X${Tared} = Xtrue ] ; then
	860	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	861	fi
	862	fi
	863	(( i=i+3 ))
	864	done
	865	else
	866	if [ X${FileName0} != XNONE ] ; then
	867	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	868	else
	869	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	870	fi
	871	fi
[544]	872	fi
[893]	873	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
[544]	874	# if not FirstInitialize and first loop of this job
[2]	875
[544]	876	# Restore Restarts files
	877	#-----------------------
	878	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
[778]	879	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	880
[778]	881	(( i=1 ))
	882	until [ $i -gt $NbFiles ]; do
	883	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	884	eval file_in=${file_in_}
	885	(( i_ = i+1 ))
	886	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	887	eval file_out=${file_out_}
[2]	888
[1028]	889	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
[662]	890
[778]	891	extension_in=$( echo ${file_in_Name##*.} )
	892	extension_out=$( echo ${file_out##*.} )
[67]	893
[778]	894	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	895	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
	896
	897	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
	898	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
	899
[662]	900	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	901	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
[778]	902	Buffered=true
	903	Archived=false
	904	Tared=false
	905	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
[672]	906	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	907	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	908	Buffered=false
	909	Archived=true
	910	Tared=false
	911	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
	912	else
[897]	913	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
[902]	914	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
[778]	915	Buffered=false
	916	Archived=false
	917	Tared=true
	918	# Look after the tar file we want if we did not found it already
	919	if [ X${IsMatching} = X ] ; then
[801]	920	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
[778]	921	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	922	if [ ! X${IsMatching} = X ] ; then
	923	TarFileFound=${PotentialTarFile}
	924	break
	925	fi
	926	done
	927	fi
[1017]	928	# Stop here if nothing has been found
	929	if [ X${TarFileFound} = X ] ; then
	930	IGCM_debug_Print 3 "Restart files were not found!"
	931	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	932	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
	933	IGCM_debug_Exit "Please double check restart settings in config.card"
	934	IGCM_debug_Verif_Exit
	935	fi
[918]	936	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	937	TarFileLocation=$( basename ${TarFileFound} )
[801]	938	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	939	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	940	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	941	fi
[41]	942
[778]	943	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	944	j=0 # BASH LINE NOT NEEDED
	945	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	946	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	947	j4=${j} # BASH LINE NOT NEEDED
[778]	948	if [ X${Buffered} = Xtrue ] ; then
	949	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	950	elif [ X${Archived} = Xtrue ] ; then
	951	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	952	elif [ X${Tared} = Xtrue ] ; then
	953	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	954	fi
[821]	955	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	956	done
	957	else
	958	if [ X${Buffered} = Xtrue ] ; then
	959	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
	960	elif [ X${Archived} = Xtrue ] ; then
	961	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
	962	elif [ X${Tared} = Xtrue ] ; then
	963	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	964	fi
	965	fi
	966	(( i=i+3 ))
	967	done
[544]	968	else
[778]	969	if [ X${FileName0} != XNONE ] ; then
	970	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	971	else
	972	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	973	fi
[544]	974	fi
[420]	975	fi
[544]	976	done
[420]	977
[544]	978	NbFiles=$( ls * 2> /dev/null \| wc -l )
	979	if [ ${NbFiles} -gt 0 ] ; then
	980	IGCM_sys_Chmod u+rw *
	981	fi
	982
	983	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
[2]	984	}
	985
	986	#=======================================================================
[1409]	987	function IGCM_comp_GetInputBinaryFiles
	988	{
	989	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
	990
	991	# Debug Print :
	992	echo
	993	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
	994	echo
	995
	996	# Clean up previous pass
	997	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
	998
[1411]	999	typeset comp ExeNameIn ExeNameOut byPass
[1409]	1000	typeset compilerNmbr compilerUnit compilerFull
[1411]	1001	byPass=false
[1409]	1002	for comp in ${config_ListOfComponents[*]} ; do
	1003	# Define component
	1004
	1005	# Copy executable for this component
	1006	eval ExeNameIn=\${config_Executable_${comp}[0]}
	1007	eval ExeNameOut=\${config_Executable_${comp}[1]}
[1486]	1008	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
	1009	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
	1010	# The executable is set in config.card and is different from ""
	1011	# Use eval to expand ExeNameIn if variables are used in the name
	1012	eval ExeNameIn=${ExeNameIn}
	1013	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
	1014	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
	1015	fi
[1409]	1016	fi
	1017
	1018	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
	1019	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1020	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1021	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1022	fi
	1023	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1024	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1025	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1026	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1027	fi
	1028	fi
	1029
	1030	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1031	# Get the compiler version
	1032	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1033	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1034	# Save it
	1035	echo $compilerFull >> ${RUN_DIR}/compiler.txt
[1411]	1036	[ X${compilerFull} = X ] && byPass=true
[1409]	1037	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
[1413]	1038	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
[1409]	1039	fi
	1040	done
	1041
	1042	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
	1043	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
	1044
[1411]	1045	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
[1409]	1046	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
	1047	fi
	1048
[1504]	1049	# Test on compiler version for IPSLCM6* configuration on irene (only for CMIP6 production)
	1050	if [ ${SYSTEM} = irene ]; then
[1520]	1051	if ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.13 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.14 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.15 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.1 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM5A2.1 )" != "X" ] && [ X${compilerFull} != XV17 ] ) ; then
	1052	IGCM_debug_Exit "IPSLCM6.0.13, IPSLCM6.0.14, IPSLCM6.0.15, IPSLCM6.1 and IPSLCM5A2.1 must be compiled with intel 2017 compiler"
[1504]	1053	fi
[1415]	1054	fi
	1055
[1409]	1056	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
	1057	}
	1058
	1059	#=======================================================================
[269]	1060	function IGCM_comp_PeriodStart
	1061	{
[544]	1062	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
[269]	1063
[544]	1064	# Debug Print :
	1065	echo
	1066	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
	1067	echo
[269]	1068
[902]	1069	typeset ExeNameIn ExeNameOut
[544]	1070	typeset comp compname comptagname
	1071	for comp in ${config_ListOfComponents[*]} ; do
[902]	1072	# Define component
[544]	1073	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1074	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[269]	1075
[544]	1076	# Copy executable for this component
	1077	eval ExeNameIn=\${config_Executable_${comp}[0]}
[1486]	1078	eval ExeNameIn=${ExeNameIn}
[544]	1079	eval ExeNameOut=\${config_Executable_${comp}[1]}
[269]	1080
[544]	1081	# Debug Print
	1082	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
	1083	# UPDATE component
	1084	${comp}_PeriodStart 2> /dev/null
[269]	1085
[544]	1086	done
[269]	1087
[544]	1088	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
[269]	1089	}
	1090
[1166]	1091
	1092
[269]	1093	#=======================================================================
[1166]	1094	function IGCM_comp_modifyFile
	1095	{
	1096	#
	1097	# syntax: IGCM_comp_modifyFile filein key [value]
	1098	#
	1099	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
	1100	#
	1101	# This function is used to replace a pattern in a file for a specific variable.
	1102	#
	1103	# Arguments:
	1104	# - filein : the file in run directory in which the variable should be set
	1105	# - key : the variable to modify
	1106	# - value : the value to set the key equal to
	1107	#
	1108	IGCM_debug_PushStack "IGCM_comp_modifyFile"
	1109
	1110	typeset filein key value pattern
	1111
	1112	# Set local variables and test the arguments
	1113	if [ $# = 3 ] ; then
	1114	# Normal case with 3 arguments
	1115	filein=$1 ; key=$2 ; value=$3
	1116	else
	1117	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
	1118	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1119	return
	1120	fi
	1121	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
	1122
	1123	# Test if the file exist
	1124	if [ ! -f ${filein} ] ; then
	1125	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
	1126	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1127	return
	1128	fi
	1129
	1130	# Read the line with key in the file without the comments
	1131	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
	1132
	1133	# Verify the existance of the pattern
	1134	if [ X"${pattern}" = X ] ; then
	1135	# Variable key is not set in filein, stop.
	1136	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
	1137	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1138	return
	1139	fi
	1140
	1141	# Now change key in filein
[1176]	1142	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
	1143	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
[1166]	1144	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
	1145	\mv ${filein}.tmp ${filein}
	1146
	1147	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1148	}
	1149
	1150	#=======================================================================
[1069]	1151	function IGCM_comp_modifyDefFile
	1152	{
	1153	#
	1154	# syntax: IGCM_comp_modifyDefFile type filein key [value]
	1155	#
	1156	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
	1157	#
	1158	# This function is used to modify a parameter file for a specific variable.
[1075]	1159	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
	1160	# This function can be used in the comp.driver files for the components.
[1069]	1161	#
[1075]	1162	# Arguments:
[1081]	1163	# - type : first argument must be blocker, nonblocker or force
[1075]	1164	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1069]	1165	# otherwise this function will exit.
[1075]	1166	# For "nonblocker" case, the user can remove or modify the variable. For
	1167	# this case, as long as AUTO is not set, no modification will be done.
[1081]	1168	# For "force" case, the variable will be modified even if it is not set to AUTO
[1069]	1169	# - filein : the file in run directory of .def type in which the variable should be set
	1170	# - key : the variable to modify
[1075]	1171	# - value : the value to set the key equal to, optional. If value is not set or if
[1069]	1172	# value=DEFAULT, then a default value must be given in filein using syntax :
	1173	# key= AUTO : DEFAULT=def_value
	1174	#
[1075]	1175	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
[1069]	1176
[1166]	1177	typeset type filein key value
	1178	typeset filelist nb_occ modify
	1179
[1075]	1180	# Set local variables and test the arguments
	1181	if [ $# = 4 ] ; then
	1182	# Normal case with 4 arguments
	1183	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1184	elif [ $# = 3 ] ; then
	1185	# Normal case with 3 arguments
	1186	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1187	else
	1188	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
[1079]	1189	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1190	return
	1191	fi
[1166]	1192	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
[1069]	1193
[1075]	1194	# Test if first argument is correct
[1166]	1195	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1081]	1196	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
[1079]	1197	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1198	return
	1199	fi
[1069]	1200
[1215]	1201	# Test if the file exist.
	1202	# Exit with error if the file does not exist for the case blocker or force.
	1203	# Only return for the case nonblocker.
[1075]	1204	if [ ! -f ${filein} ] ; then
[1215]	1205	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1206	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
	1207	else
	1208	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
	1209	fi
[1079]	1210	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1211	return
	1212	fi
[1069]	1213
[1102]	1214	# Define list of files to test using all files with suffix .def (except used*.def)
	1215	filelist=$( ls *def \| grep -v used )
[1069]	1216
[1075]	1217	# Count number of occurances for the key in all files
[1166]	1218	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
[1069]	1219
[1075]	1220	# Test if key is set several times
[1166]	1221	if [ ${nb_occ} -gt 1 ] ; then
	1222	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
[1079]	1223	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1224	return
	1225	fi
	1226
	1227	# Treatement according to different cases
[1166]	1228	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
[1075]	1229	# Stop if the key is never set and the function is blocker
[1166]	1230	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
	1231	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
	1232	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
[1075]	1233	# The key is not set but it is a nonblocker call so nothing is done.
[1166]	1234	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1235	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
[1081]	1236	modify=no
[1166]	1237	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
[1075]	1238	# Variable key is not set in filein, stop.
[1166]	1239	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1081]	1240	fi
	1241
	1242	# Check if AUTO is set in the filein on the same line as the key variable
[1166]	1243	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1244	# Modification will be done for all cases
	1245	modify=yes
	1246	else
	1247	# The variable was not set to AUTO
[1166]	1248	if [ ${type} = blocker ] ; then
[1156]	1249	# Exit because this is a blocker call
[1166]	1250	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
[1190]	1251	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1156]	1252	return
[1166]	1253	elif [ ${type} = nonblocker ] ; then
[1156]	1254	# Do nothing. Suppose that the user did set the variable correct
[1166]	1255	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
[1156]	1256	modify=no
[1166]	1257	elif [ ${type} = force ] ; then
[1156]	1258	# Force modification
[1166]	1259	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
[1081]	1260	modify=yes
[1156]	1261	fi
[1081]	1262	fi
[1069]	1263
[1081]	1264	# Do the modifcation now
[1166]	1265	if [ ${modify} = yes ] ; then
[1081]	1266
[1156]	1267	# For option DEFAULT, read default value from file.
[1166]	1268	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1269	# Case to set DEFAULT value
	1270	# Read default value from filein
[1423]	1271	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
[1069]	1272
[1166]	1273	if [ X"${value}" = X ] ; then
	1274	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
	1275	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
	1276	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1277	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
	1278	return
[1075]	1279	fi
[1156]	1280	fi
[1069]	1281
[1156]	1282	# Now change key in filein
[1166]	1283	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
	1284	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
	1285	\mv ${filein}.tmp ${filein}
[1075]	1286	fi
[1079]	1287	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1069]	1288	}
	1289
	1290	#=======================================================================
[1085]	1291	function IGCM_comp_modifyNamelist
	1292	{
	1293	#
	1294	# syntax: IGCM_comp_modifyNamelist type filein key [value]
	1295	#
	1296	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
	1297	#
	1298	# This function is used to modify a parameter file for a specific variable.
[1155]	1299	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
[1085]	1300	# This function can be used in the comp.driver files for the components.
	1301	#
	1302	# Arguments:
	1303	# - type : first argument must be blocker, nonblocker or force
	1304	# For "blocker" case, the variable must be attributed the keyworld AUTO
	1305	# otherwise this function will exit.
	1306	# For "nonblocker" case, the user can remove or modify the variable. For
	1307	# this case, as long as AUTO is not set, no modification will be done.
	1308	# For "force" case, the variable will be modified even if it is not set to AUTO
	1309	# - filein : the file in run directory of .def type in which the variable should be set
	1310	# - key : the variable to modify
	1311	# - value : the value to set the key equal to, optional. If value is not set or if
	1312	# value=DEFAULT, then a default value must be given in filein using syntax :
	1313	# key= AUTO : DEFAULT=def_value
	1314	#
	1315	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
	1316
[1166]	1317	typeset type filein key value pattern modify
	1318
[1085]	1319	# Set local variables and test the arguments
	1320	if [ $# = 4 ] ; then
	1321	# Normal case with 4 arguments
	1322	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1323	elif [ $# = 3 ] ; then
	1324	# Normal case with 3 arguments
	1325	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1326	else
	1327	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
	1328	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1329	return
	1330	fi
[1166]	1331	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
[1085]	1332
	1333	# Test if first argument is correct
[1166]	1334	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1085]	1335	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
	1336	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1337	return
	1338	fi
	1339
[1215]	1340	# Test if the file exist.
	1341	# Exit with error if the file does not exist for the case blocker or force.
	1342	# Only return for the case nonblocker.
[1085]	1343	if [ ! -f ${filein} ] ; then
[1215]	1344	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1345	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
	1346	else
	1347	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
	1348	fi
[1085]	1349	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1350	return
	1351	fi
	1352
	1353	# Read the line with key in the file without the comments
[1166]	1354	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
[1155]	1355
[1085]	1356	# Verify the existance of the pattern
	1357	if [ X"$pattern" = X ] ; then
[1156]	1358	# Variable key is not set in filein, stop.
[1166]	1359	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1156]	1360	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1361	return
[1085]	1362	fi
[1155]	1363
[1085]	1364	# Check if the variable is set to AUTO in the filein
	1365	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1366	# Modification will be done for all cases
	1367	modify=yes
	1368	else
	1369	# The variable was not set to AUTO
[1166]	1370	if [ ${type} = blocker ] ; then
[1156]	1371	# Exit because this is a blocker call
[1166]	1372	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
[1156]	1373	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1374	return
[1166]	1375	elif [ ${type} = nonblocker ] ; then
[1156]	1376	# Do nothing. Suppose that the user did set the variable correct
[1166]	1377	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
[1156]	1378	modify=no
[1166]	1379	elif [ ${type} = force ] ; then
[1156]	1380	# Force modification
[1166]	1381	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
[1085]	1382	modify=yes
[1156]	1383	fi
[1085]	1384	fi
	1385
	1386	# Do the modifcation now
[1166]	1387	if [ ${modify} = yes ] ; then
[1085]	1388
[1156]	1389	# For option DEFAULT, read default value from file.
[1166]	1390	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1391	# Case to set DEFAULT value
	1392	# Read default value from filein
	1393	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
[1085]	1394
[1166]	1395	if [ X"${value}" = X ] ; then
	1396	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
	1397	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
	1398	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1399	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1400	return
[1085]	1401	fi
[1156]	1402	fi
[1085]	1403
[1156]	1404	# Now change key in filein
[1166]	1405	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
	1406	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
	1407	\mv ${filein}.tmp ${filein}
[1085]	1408	fi
	1409	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1410	}
	1411
	1412	#=======================================================================
[1074]	1413	function IGCM_comp_modifyXmlFile
	1414	{
	1415	#
	1416	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
	1417	#
	1418	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
	1419	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
	1420	#
	1421	# This function is used to modify the value for a specific attribute and variable id.
[1155]	1422	# The file must be a valid xml file.
[1075]	1423	# This function can be used in the comp.driver files for the components.
[1074]	1424	#
[1075]	1425	# Arguments:
	1426	# - type : first argument must be blocker, nonblocker or force.
	1427	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1074]	1428	# otherwise this function will exit.
[1075]	1429	# For "nonblocker" case, the user can remove or modify the variable. For
[1074]	1430	# this case, as long as AUTO is not set, no modification will be done.
[1075]	1431	# For "force" case, the variable will be modified even if it is not set to AUTO
[1074]	1432	# - filein : the file in run directory of .xml type in which the variable should be set
	1433	# - keyid : the variable to modify
	1434	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
	1435	# - value : the value to set in the filein
	1436	#
[1075]	1437	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
[1074]	1438
[1166]	1439	typeset type filein keyid keyattrib value modify
	1440
[1075]	1441	# Set local variables and test the arguments
	1442	if [ $# = 5 ] ; then
	1443	# Normal case with 4 arguments
	1444	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
	1445	else
	1446	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
[1089]	1447	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1448	return
	1449	fi
[1166]	1450	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
[1074]	1451
[1075]	1452	# Test if first argument is correct
[1166]	1453	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1075]	1454	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
[1089]	1455	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1456	return
	1457	fi
[1074]	1458
[1215]	1459	# Test if the file exist.
	1460	# Exit with error if the file does not exist for the case blocker or force.
	1461	# Only return for the case nonblocker.
[1075]	1462	if [ ! -f ${filein} ] ; then
[1215]	1463	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1464	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
	1465	else
	1466	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
	1467	fi
[1089]	1468	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1469	return
	1470	fi
	1471
[1386]	1472	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
[1166]	1473	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
[1386]	1474	if [ ${type} = nonblocker ] ; then
	1475	# This is a nonblocker case, print warning but do nothing else
	1476	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1477	else
	1478	# This is a blocker or force case : stop now
	1479	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
	1480	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
	1481	return
	1482	fi
[1075]	1483	fi
	1484
	1485	# Check if AUTO is set on the same line as keyid and keyattrib
[1166]	1486	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
[1394]	1487	# Modification will be done
[1075]	1488	modify=yes
	1489	else
[1166]	1490	if [ ${type} = blocker ] ; then
[1075]	1491	# Exit, the variable must be set to AUTO
[1166]	1492	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
[1089]	1493	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1494	return
[1166]	1495	elif [ ${type} = nonblocker ] ; then
[1075]	1496	# Nothing will be done
	1497	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
	1498	modify=no
[1166]	1499	elif [ ${type} = force ] ; then
[1075]	1500	# Force modification
[1166]	1501	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
[1075]	1502	modify=yes
[1074]	1503	fi
[1075]	1504	fi
[1074]	1505
[1075]	1506	# Do the modifcation now
[1166]	1507	if [ ${modify} = yes ] ; then
	1508	if [ ${keyattrib} = NONE ] ; then
[1075]	1509	# Case to modify the variable itself
	1510	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
[1166]	1511	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
[1074]	1512	else
[1156]	1513	# Check if keyattrib is set on the same line as keyid
[1166]	1514	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
[1156]	1515	# Case to modify the attribute value
	1516	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
[1166]	1517	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
[1156]	1518	else
	1519	# Case to add the attribute and its value
	1520	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
[1166]	1521	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
[1156]	1522	fi
[1074]	1523	fi
[1166]	1524	\mv ${filein}.tmp ${filein}
[1075]	1525	fi
	1526	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1074]	1527	}
	1528
	1529	#=======================================================================
[2]	1530	function IGCM_comp_Update
	1531	{
[544]	1532	IGCM_debug_PushStack "IGCM_comp_Update"
[2]	1533
[1409]	1534	# Debug Print :
[544]	1535	echo
	1536	IGCM_debug_Print 1 "IGCM_comp_Update"
	1537	echo
[2]	1538
[544]	1539	typeset comp compname comptagname
	1540	for comp in ${config_ListOfComponents[*]} ; do
[902]	1541	# Define component
[544]	1542	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1543	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1544
[544]	1545	# Debug Print
	1546	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
	1547	# UPDATE component
	1548	${comp}_Update
[2]	1549
[1413]	1550	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
	1551	if [ -f timeseries_def_${compname}.xml ]; then
	1552	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
	1553	for line in $( cat ts.temp.${compname}.txt ); do
	1554	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
	1555	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
	1556	case ${output_freq} in
	1557	Y\|y)
	1558	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
	1559	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
	1560	;;
	1561	MO\|mo)
	1562	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
	1563	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
	1564	;;
	1565	D\|d)
	1566	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
	1567	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
	1568	;;
	1569	S\|s)
	1570	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
	1571	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
	1572	;;
	1573	esac
	1574	done
	1575	fi
	1576
	1577	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
	1578	if [ -f dr2xml_${compname}.xml ]; then
[1535]	1579	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
	1580	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
	1581	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
	1582	# Modify path from dr2xml_{compname}.xml
	1583	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
	1584	${libIGCM}/libIGCM_post/xios_parser.py -v modifydr2xmlIPSL --newPath ${CMIP6_DIR} --splitLastDate ${config_UserChoices_DateEnd} --JobName ${config_UserChoices_JobName} --ModelName ${config_UserChoices_ModelName} --ModelVersion ${config_UserChoices_LongName} --file dr2xml_${compname}.xml
	1585	else
	1586	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
	1587	fi
	1588	# Overwrite the original file
	1589	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
[1467]	1590	fi
[1422]	1591	fi
[544]	1592	done
[2]	1593
[544]	1594	IGCM_debug_PopStack "IGCM_comp_Update"
[2]	1595	}
	1596
	1597	#=======================================================================
	1598	function IGCM_comp_Finalize
	1599	{
[544]	1600	IGCM_debug_PushStack "IGCM_comp_Finalize"
[2]	1601
[544]	1602	# Debug Print :
	1603	echo
	1604	IGCM_debug_Print 1 "IGCM_comp_Finalize"
	1605	echo
[2]	1606
[544]	1607	typeset ListTextName TextName0
	1608	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
	1609	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
[1165]	1610	typeset -Z4 j4 #BASH declare j4
[544]	1611	typeset list_file nlist_file
	1612	typeset compactoutputs
[429]	1613
[1165]	1614	# Initialize array hosting list of rebuilded files to copy
	1615	unset rebuildedActionsList
	1616
	1617	# Text compacting options
[544]	1618	compactoutputs=false
	1619	if [ X${JobType} != XRUN ] ; then
	1620	compactoutputs=true
	1621	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
	1622	compactoutputs=true
	1623	fi
[433]	1624
[1043]	1625	# Prepare headers for the shell dedicated to offline rebuild
	1626	if [ X${AsynchronousRebuild} = Xtrue ] ; then
	1627	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1628	if [ ${DRYRUN} -le 1 ] ; then
	1629	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1630	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1631	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1632	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1633	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1634	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1635	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1636	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1637	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1638	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1639	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1640	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1641	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1642	fi
	1643	fi
	1644
[544]	1645	for comp in ${config_ListOfComponents[*]} ; do
[902]	1646	# Define component
[544]	1647	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1648	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1649
[544]	1650	# Debug Print
	1651	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
	1652	# FINALIZE component
	1653	${comp}_Finalize
[2]	1654
[778]	1655	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	1656
[804]	1657	# Save Output Text files of models
	1658	#---------------------------------
	1659	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
	1660	IGCM_card_DefineArrayFromOption ${card} OutputText List
	1661	ListTextName=${compname}_OutputText_List
	1662
	1663	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
	1664	if [ X${TextName0} != X${NULL_STR} ] ; then
	1665	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
	1666
	1667	(( i=0 ))
	1668	until [ $i -eq $NbFiles ]; do
	1669	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
	1670	eval file_out=${PREFIX}_${file_in}
	1671
	1672	(( i=i+1 ))
	1673
	1674	unset list_file
	1675	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
	1676	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
	1677	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 )
	1678	nlist_file=${#list_file[@]}
	1679	if [ ${nlist_file} -gt 1 ] ; then
	1680	if ( ${compactoutputs} ) ; then
	1681	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
	1682	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
	1683	echo ${list_file[*]} > ${file_out}
	1684	echo "" >> ${file_out}
	1685
	1686	(( i_ = 0 ))
[1080]	1687	for file in ${list_file[@]} ; do
[804]	1688	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
	1689	echo "\| " ${i_} " " ${file} >> ${file_out}
	1690	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
[999]	1691	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
[804]	1692	echo "" >> ${file_out}
	1693	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1694	(( i_ = i_ + 1 ))
	1695	done
[1080]	1696	if ( ${ExecutionFail} ) ; then
	1697	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
	1698	fi
	1699
[804]	1700	if [ X${Pack} = Xtrue ] ; then
	1701	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
	1702	else
	1703	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
	1704	fi
[1080]	1705
[804]	1706	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
[1080]	1707	else
	1708	for file in ${list_file[@]} ; do
	1709	if ( ${ExecutionFail} ) ; then
	1710	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
	1711	fi
[804]	1712
	1713	if [ X${Pack} = Xtrue ] ; then
	1714	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
	1715	else
	1716	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
	1717	fi
[1080]	1718
[804]	1719	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1720	done
	1721	fi
	1722	else
	1723	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
	1724	eval IGCM_sys_Mv ${file_in}* ${file_in}
	1725	fi
[1080]	1726
	1727	if ( ${ExecutionFail} ) ; then
	1728	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
	1729	fi
	1730
[804]	1731	if [ X${Pack} = Xtrue ] ; then
	1732	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
	1733	else
	1734	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
	1735	fi
	1736	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1737	fi
	1738	done
	1739	fi
	1740
[544]	1741	# Save Restarts files
	1742	#--------------------
	1743	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
	1744	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	1745	ListFilesName=${compname}_RestartFiles_List
	1746	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	1747
[544]	1748	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	1749	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[778]	1750
[544]	1751	(( i=0 ))
	1752	until [ $i -ge $NbFiles ]; do
[778]	1753	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1754	eval file_in=${file_in_}
[2]	1755
[778]	1756	(( i_ = i+1 ))
	1757	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1758	eval file_out=${file_out_}
[151]	1759
[778]	1760	(( i_ = i+2 ))
	1761	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1762	eval file_outin=${file_outin_}
[151]	1763
[778]	1764	generic_restart_file_name_in=$( basename ${file_in} .nc )
	1765	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
	1766	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
[2]	1767
[902]	1768	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
[778]	1769	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	1770	j=0 # BASH LINE NOT NEEDED
	1771	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	1772	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	1773	j4=${j} # BASH LINE NOT NEEDED
[778]	1774	if [ X${Pack} = Xtrue ] ; then
	1775	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1776	else
	1777	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1778	fi
	1779	if [ ! ${file_in} = ${file_outin} ] ; then
	1780	if ( ${ExitFlag} ) ; then
	1781	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
	1782	else
	1783	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
	1784	fi
	1785	fi
[821]	1786	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	1787	done
	1788	else
	1789	if [ X${Pack} = Xtrue ] ; then
	1790	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1791	else
	1792	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1793	fi
	1794	if [ ! ${file_in} = ${file_outin} ] ; then
	1795	if ( ${ExitFlag} ) ; then
	1796	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
	1797	else
	1798	IGCM_sys_Mv ${file_in} ${file_outin}
	1799	fi
	1800	fi
	1801	fi
	1802
	1803	(( i=i+3 ))
[544]	1804	done
	1805	else
	1806	if [ X${FileName0} != XNONE ] ; then
[778]	1807	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
[544]	1808	else
[778]	1809	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
[544]	1810	fi
	1811	fi
[2]	1812
[544]	1813	# Save Output files
	1814	#------------------
	1815	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
	1816	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	1817	ListFilesName=${compname}_OutputFiles_List
	1818	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	1819
[544]	1820	if [ X${FileName0} != X${NULL_STR} ] ; then
	1821	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[149]	1822
[544]	1823	(( i=0 ))
	1824	until [ $i -ge $NbFiles ]; do
[778]	1825	SaveOnArchive=true
	1826	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1827	eval file_in=${file_in_}
	1828	(( i_ = i+1 ))
	1829	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1830	eval file_out=${file_out_}
	1831	#
	1832	# Override file_out path remplacing R_SAVE by R_BUFR
	1833	#
	1834	if [ X${Pack} = Xtrue ] ; then
	1835	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
	1836	fi
	1837	#
	1838	# Not necessarily the best option. /!\ Potential side effects /!\
	1839	#
	1840	(( i_ = i+2 ))
	1841	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1842	#
	1843	generic_file_name=$( basename ${file_in} .nc )
	1844	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
	1845	#
	1846	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
[804]	1847	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
[778]	1848	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
	1849	elif [ ${nb_rebuild_file} -gt 1 ] ; then
[804]	1850	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
[778]	1851	if [ X${AsynchronousRebuild} = Xfalse ] ; then
	1852	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
[1388]	1853	#
	1854	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
	1855	if [ ${file_in} = output.abort.nc ] ; then
	1856	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
	1857	else
[1429]	1858	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
[1388]	1859	fi
[778]	1860	else
	1861	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
[1429]	1862	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
[544]	1863
[778]	1864	# Prepare the shell dedicated to offline rebuild
	1865	if [ $DRYRUN -le 1 ]; then
[694]	1866	if [ ${file_in} = histstn.nc ] ; then
	1867	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1868	else
[980]	1869	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[694]	1870	fi
[1206]	1871	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1872	fi
	1873	#
	1874	# Load Patch we need to apply and apply
	1875	if [ $DRYRUN -le 1 ]; then
	1876	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
[1080]	1877	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1878	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1879	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1880	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1881	done
	1882	fi
	1883	fi
	1884	#
	1885	if [ $DRYRUN -le 1 ]; then
	1886	if [ X${Pack} = Xtrue ] ; then
[1165]	1887	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
[778]	1888	else
[1165]	1889	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
[778]	1890	fi
[1206]	1891	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
[1165]	1892	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
[778]	1893	fi
	1894	SaveOnArchive=false
	1895	fi
	1896	fi
	1897	#
	1898	if [ ${SaveOnArchive} = true ] ; then
	1899	#
	1900	# Rebuild has been done online or it was not needed
	1901	#
	1902	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
	1903	#
	1904	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
[1289]	1905	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
[778]	1906	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1907	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
	1908	#
	1909	if [ $DRYRUN -le 1 ]; then
[1080]	1910	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1911	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1912	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1913	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1914	done
	1915	#
	1916	if [ X${Pack} = Xtrue ] ; then
	1917	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1918	else
	1919	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1920	fi
[1206]	1921	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1922	#
	1923	fi
	1924	else
	1925	#
	1926	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
	1927	#
	1928	if [ X${Pack} = Xtrue ] ; then
	1929	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
	1930	else
	1931	IGCM_sys_Put_Out ${file_in} ${file_out}
	1932	fi
	1933	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1934	if [ ${nb_rebuild_file} -gt 1 ] ; then
	1935	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
	1936	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
	1937	done
	1938	fi
	1939	fi
	1940	fi
	1941	(( i=i+3 ))
[544]	1942	done
	1943	fi
	1944	echo
	1945	done
[1165]	1946	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
	1947	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
[1166]	1948	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1165]	1949	i=0
	1950	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
	1951	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1952	(( i=i+1 ))
	1953	done
	1954	fi
[544]	1955	IGCM_debug_PopStack "IGCM_comp_Finalize"
[2]	1956	}

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