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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1422

Last change on this file since 1422 was 1422, checked in by jgipsl, 6 years ago
Corrected bug. fi was missing since changset [1420].
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: 78.9 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
[1419]	128	eval CMIP6_BUF_${comp}=${R_SAVE}/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" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[778]	707	eval config_${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}
[544]	713	else
[778]	714	# Read component Restarts parameters
	715	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	716	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
[2]	717
[778]	718	if [ "${do_start}" = "y" ] ; then
	719	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
	720	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
	721	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
	722	else
	723	eval config_${comp}_RestartDate=-1
	724	eval config_${comp}_RestartJobName=${NULL_STR}
	725	eval config_${comp}_RestartPath=${NULL_STR}
	726	fi
[849]	727
[778]	728	eval CompOldName=\${config_${comp}_OldName}
	729	if [ X${CompOldName} = X ] ; then
	730	eval CompOldName=${comp}
	731	fi
	732
	733	# Reinitialize IsMatching to allow searching for a different tar file for each component.
	734	IsMatching=""
	735	TarFileFound=""
[544]	736	fi
[2]	737
[544]	738	if [ "${do_start}" = "y" ] ; then
[2]	739
[672]	740	# Restore Restarts files
	741	#-----------------------
[778]	742	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	743	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	744
[778]	745	(( i=1 ))
	746	until [ $i -gt $NbFiles ]; do
	747	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	748	eval file_in=${file_in_}
	749	(( i_ = i+1 ))
	750	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	751	eval file_out=${file_out_}
	752
	753	eval Date_tmp=\${config_${comp}_RestartDate}
	754	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
[672]	755	# will be re-use
	756	eval RestartPath=\${config_${comp}_RestartPath}
	757	eval RestartJobName=\${config_${comp}_RestartJobName}
	758	#
[778]	759	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
	760	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
[2]	761
[778]	762	extension_in=$( echo ${file_in_Name##*.} )
	763	extension_out=$( echo ${file_out##*.} )
[672]	764
[778]	765	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	766	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
[2]	767
[778]	768	Path_OUT=${Path_r}/${generic_restart_file_name_in}
	769
[672]	770	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	771	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
[778]	772	Buffered=true
	773	Archived=false
	774	Tared=false
	775	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
[672]	776	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	777	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	778	Buffered=false
	779	Archived=true
	780	Tared=false
	781	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
[672]	782	else
[897]	783	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
	784	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
[902]	785	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
[778]	786	Buffered=false
	787	Archived=false
	788	Tared=true
[672]	789	# Look after the tar file we want if we did not found it already
[778]	790	if [ X${IsMatching} = X ] ; then
[947]	791	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
	792	if [ $? ] ; then
[897]	793	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
	794	IsMatching=$( echo ${PotentialTarFile##*/} \| \
	795	sed "s:_restart::" \| \
	796	sed "s:^${RestartJobName}_::" \| \
	797	sed "s:\.tar$::" \| \
	798	gawk -F_ -v restartdate=${Date_r} \
	799	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	800	if [ ! X${IsMatching} = X ] ; then
	801	TarFileFound=${PotentialTarFile}
	802	break
	803	fi
	804	done
[1017]	805	fi
	806	# Stop here if nothing has been found
	807	if [ X${TarFileFound} = X ] ; then
[902]	808	IGCM_debug_Print 3 "Restart files were not found!"
	809	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	810	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
[897]	811	IGCM_debug_Exit "Please double check restart settings in config.card"
	812	IGCM_debug_Verif_Exit
	813	fi
[778]	814	fi
[918]	815	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	816	TarFileLocation=$( basename ${TarFileFound} )
[801]	817	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	818	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	819	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	820	fi
[672]	821
	822	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	823	j=0 # BASH LINE NOT NEEDED
	824	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	825	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	826	j4=${j} # BASH LINE NOT NEEDED
[778]	827	if [ X${Buffered} = Xtrue ] ; then
	828	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	829	elif [ X${Archived} = Xtrue ] ; then
	830	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	831	elif [ X${Tared} = Xtrue ] ; then
	832	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	833	fi
[821]	834	(( j=j+1 )) #BASH LINE NOT NEEDED
[778]	835	done
[740]	836
[1248]	837	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
	838	if [ X${OCE_PROC_MPI} != X ] ; then
	839	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
[1380]	840	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
[740]	841	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
	842	fi
	843	fi
[778]	844	else
	845	if [ X${Buffered} = Xtrue ] ; then
	846	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
	847	elif [ X${Archived} = Xtrue ] ; then
	848	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
	849	elif [ X${Tared} = Xtrue ] ; then
	850	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	851	fi
	852	fi
	853	(( i=i+3 ))
	854	done
	855	else
	856	if [ X${FileName0} != XNONE ] ; then
	857	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	858	else
	859	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	860	fi
	861	fi
[544]	862	fi
[893]	863	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
[544]	864	# if not FirstInitialize and first loop of this job
[2]	865
[544]	866	# Restore Restarts files
	867	#-----------------------
	868	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
[778]	869	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	870
[778]	871	(( i=1 ))
	872	until [ $i -gt $NbFiles ]; do
	873	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	874	eval file_in=${file_in_}
	875	(( i_ = i+1 ))
	876	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	877	eval file_out=${file_out_}
[2]	878
[1028]	879	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
[662]	880
[778]	881	extension_in=$( echo ${file_in_Name##*.} )
	882	extension_out=$( echo ${file_out##*.} )
[67]	883
[778]	884	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	885	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
	886
	887	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
	888	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
	889
[662]	890	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	891	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
[778]	892	Buffered=true
	893	Archived=false
	894	Tared=false
	895	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
[672]	896	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	897	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	898	Buffered=false
	899	Archived=true
	900	Tared=false
	901	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
	902	else
[897]	903	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
[902]	904	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
[778]	905	Buffered=false
	906	Archived=false
	907	Tared=true
	908	# Look after the tar file we want if we did not found it already
	909	if [ X${IsMatching} = X ] ; then
[801]	910	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
[778]	911	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	912	if [ ! X${IsMatching} = X ] ; then
	913	TarFileFound=${PotentialTarFile}
	914	break
	915	fi
	916	done
	917	fi
[1017]	918	# Stop here if nothing has been found
	919	if [ X${TarFileFound} = X ] ; then
	920	IGCM_debug_Print 3 "Restart files were not found!"
	921	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	922	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
	923	IGCM_debug_Exit "Please double check restart settings in config.card"
	924	IGCM_debug_Verif_Exit
	925	fi
[918]	926	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	927	TarFileLocation=$( basename ${TarFileFound} )
[801]	928	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	929	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	930	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	931	fi
[41]	932
[778]	933	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	934	j=0 # BASH LINE NOT NEEDED
	935	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	936	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	937	j4=${j} # BASH LINE NOT NEEDED
[778]	938	if [ X${Buffered} = Xtrue ] ; then
	939	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	940	elif [ X${Archived} = Xtrue ] ; then
	941	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	942	elif [ X${Tared} = Xtrue ] ; then
	943	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	944	fi
[821]	945	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	946	done
	947	else
	948	if [ X${Buffered} = Xtrue ] ; then
	949	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
	950	elif [ X${Archived} = Xtrue ] ; then
	951	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
	952	elif [ X${Tared} = Xtrue ] ; then
	953	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	954	fi
	955	fi
	956	(( i=i+3 ))
	957	done
[544]	958	else
[778]	959	if [ X${FileName0} != XNONE ] ; then
	960	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	961	else
	962	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	963	fi
[544]	964	fi
[420]	965	fi
[544]	966	done
[420]	967
[544]	968	NbFiles=$( ls * 2> /dev/null \| wc -l )
	969	if [ ${NbFiles} -gt 0 ] ; then
	970	IGCM_sys_Chmod u+rw *
	971	fi
	972
	973	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
[2]	974	}
	975
	976	#=======================================================================
[1409]	977	function IGCM_comp_GetInputBinaryFiles
	978	{
	979	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
	980
	981	# Debug Print :
	982	echo
	983	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
	984	echo
	985
	986	# Clean up previous pass
	987	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
	988
[1411]	989	typeset comp ExeNameIn ExeNameOut byPass
[1409]	990	typeset compilerNmbr compilerUnit compilerFull
[1411]	991	byPass=false
[1409]	992	for comp in ${config_ListOfComponents[*]} ; do
	993	# Define component
	994
	995	# Copy executable for this component
	996	eval ExeNameIn=\${config_Executable_${comp}[0]}
	997	eval ExeNameOut=\${config_Executable_${comp}[1]}
	998
	999	# If missing executable and DRYRUN is set to 0 or 1 then stop!
	1000	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
	1001	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
	1002	fi
	1003
	1004	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
	1005	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1006	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1007	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1008	fi
	1009	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1010	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1011	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1012	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1013	fi
	1014	fi
	1015
	1016	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1017	# Get the compiler version
	1018	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1019	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1020	# Save it
	1021	echo $compilerFull >> ${RUN_DIR}/compiler.txt
[1411]	1022	[ X${compilerFull} = X ] && byPass=true
[1409]	1023	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
[1413]	1024	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
[1409]	1025	fi
	1026	done
	1027
	1028	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
	1029	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
	1030
[1411]	1031	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
[1409]	1032	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
	1033	fi
	1034
[1417]	1035	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 ] ) ; then
	1036	IGCM_debug_Exit "IPSLCM6.0.13 and IPSLCM6.0.14 must be compiled with intel 2017 compiler"
[1415]	1037	fi
	1038
[1409]	1039	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
	1040	}
	1041
	1042	#=======================================================================
[269]	1043	function IGCM_comp_PeriodStart
	1044	{
[544]	1045	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
[269]	1046
[544]	1047	# Debug Print :
	1048	echo
	1049	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
	1050	echo
[269]	1051
[902]	1052	typeset ExeNameIn ExeNameOut
[544]	1053	typeset comp compname comptagname
	1054	for comp in ${config_ListOfComponents[*]} ; do
[902]	1055	# Define component
[544]	1056	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1057	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[269]	1058
[544]	1059	# Copy executable for this component
	1060	eval ExeNameIn=\${config_Executable_${comp}[0]}
	1061	eval ExeNameOut=\${config_Executable_${comp}[1]}
[269]	1062
[544]	1063	# Debug Print
	1064	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
	1065	# UPDATE component
	1066	${comp}_PeriodStart 2> /dev/null
[269]	1067
[544]	1068	done
[269]	1069
[544]	1070	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
[269]	1071	}
	1072
[1166]	1073
	1074
[269]	1075	#=======================================================================
[1166]	1076	function IGCM_comp_modifyFile
	1077	{
	1078	#
	1079	# syntax: IGCM_comp_modifyFile filein key [value]
	1080	#
	1081	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
	1082	#
	1083	# This function is used to replace a pattern in a file for a specific variable.
	1084	#
	1085	# Arguments:
	1086	# - filein : the file in run directory in which the variable should be set
	1087	# - key : the variable to modify
	1088	# - value : the value to set the key equal to
	1089	#
	1090	IGCM_debug_PushStack "IGCM_comp_modifyFile"
	1091
	1092	typeset filein key value pattern
	1093
	1094	# Set local variables and test the arguments
	1095	if [ $# = 3 ] ; then
	1096	# Normal case with 3 arguments
	1097	filein=$1 ; key=$2 ; value=$3
	1098	else
	1099	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
	1100	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1101	return
	1102	fi
	1103	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
	1104
	1105	# Test if the file exist
	1106	if [ ! -f ${filein} ] ; then
	1107	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
	1108	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1109	return
	1110	fi
	1111
	1112	# Read the line with key in the file without the comments
	1113	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
	1114
	1115	# Verify the existance of the pattern
	1116	if [ X"${pattern}" = X ] ; then
	1117	# Variable key is not set in filein, stop.
	1118	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
	1119	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1120	return
	1121	fi
	1122
	1123	# Now change key in filein
[1176]	1124	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
	1125	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
[1166]	1126	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
	1127	\mv ${filein}.tmp ${filein}
	1128
	1129	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1130	}
	1131
	1132	#=======================================================================
[1069]	1133	function IGCM_comp_modifyDefFile
	1134	{
	1135	#
	1136	# syntax: IGCM_comp_modifyDefFile type filein key [value]
	1137	#
	1138	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
	1139	#
	1140	# This function is used to modify a parameter file for a specific variable.
[1075]	1141	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
	1142	# This function can be used in the comp.driver files for the components.
[1069]	1143	#
[1075]	1144	# Arguments:
[1081]	1145	# - type : first argument must be blocker, nonblocker or force
[1075]	1146	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1069]	1147	# otherwise this function will exit.
[1075]	1148	# For "nonblocker" case, the user can remove or modify the variable. For
	1149	# this case, as long as AUTO is not set, no modification will be done.
[1081]	1150	# For "force" case, the variable will be modified even if it is not set to AUTO
[1069]	1151	# - filein : the file in run directory of .def type in which the variable should be set
	1152	# - key : the variable to modify
[1075]	1153	# - value : the value to set the key equal to, optional. If value is not set or if
[1069]	1154	# value=DEFAULT, then a default value must be given in filein using syntax :
	1155	# key= AUTO : DEFAULT=def_value
	1156	#
[1075]	1157	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
[1069]	1158
[1166]	1159	typeset type filein key value
	1160	typeset filelist nb_occ modify
	1161
[1075]	1162	# Set local variables and test the arguments
	1163	if [ $# = 4 ] ; then
	1164	# Normal case with 4 arguments
	1165	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1166	elif [ $# = 3 ] ; then
	1167	# Normal case with 3 arguments
	1168	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1169	else
	1170	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
[1079]	1171	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1172	return
	1173	fi
[1166]	1174	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
[1069]	1175
[1075]	1176	# Test if first argument is correct
[1166]	1177	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1081]	1178	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
[1079]	1179	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1180	return
	1181	fi
[1069]	1182
[1215]	1183	# Test if the file exist.
	1184	# Exit with error if the file does not exist for the case blocker or force.
	1185	# Only return for the case nonblocker.
[1075]	1186	if [ ! -f ${filein} ] ; then
[1215]	1187	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1188	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
	1189	else
	1190	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
	1191	fi
[1079]	1192	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1193	return
	1194	fi
[1069]	1195
[1102]	1196	# Define list of files to test using all files with suffix .def (except used*.def)
	1197	filelist=$( ls *def \| grep -v used )
[1069]	1198
[1075]	1199	# Count number of occurances for the key in all files
[1166]	1200	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
[1069]	1201
[1075]	1202	# Test if key is set several times
[1166]	1203	if [ ${nb_occ} -gt 1 ] ; then
	1204	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
[1079]	1205	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1206	return
	1207	fi
	1208
	1209	# Treatement according to different cases
[1166]	1210	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
[1075]	1211	# Stop if the key is never set and the function is blocker
[1166]	1212	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
	1213	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
	1214	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
[1075]	1215	# The key is not set but it is a nonblocker call so nothing is done.
[1166]	1216	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1217	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
[1081]	1218	modify=no
[1166]	1219	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
[1075]	1220	# Variable key is not set in filein, stop.
[1166]	1221	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1081]	1222	fi
	1223
	1224	# Check if AUTO is set in the filein on the same line as the key variable
[1166]	1225	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1226	# Modification will be done for all cases
	1227	modify=yes
	1228	else
	1229	# The variable was not set to AUTO
[1166]	1230	if [ ${type} = blocker ] ; then
[1156]	1231	# Exit because this is a blocker call
[1166]	1232	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
[1190]	1233	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1156]	1234	return
[1166]	1235	elif [ ${type} = nonblocker ] ; then
[1156]	1236	# Do nothing. Suppose that the user did set the variable correct
[1166]	1237	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
[1156]	1238	modify=no
[1166]	1239	elif [ ${type} = force ] ; then
[1156]	1240	# Force modification
[1166]	1241	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
[1081]	1242	modify=yes
[1156]	1243	fi
[1081]	1244	fi
[1069]	1245
[1081]	1246	# Do the modifcation now
[1166]	1247	if [ ${modify} = yes ] ; then
[1081]	1248
[1156]	1249	# For option DEFAULT, read default value from file.
[1166]	1250	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1251	# Case to set DEFAULT value
	1252	# Read default value from filein
[1166]	1253	value=$( grep ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
[1069]	1254
[1166]	1255	if [ X"${value}" = X ] ; then
	1256	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
	1257	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
	1258	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1259	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
	1260	return
[1075]	1261	fi
[1156]	1262	fi
[1069]	1263
[1156]	1264	# Now change key in filein
[1166]	1265	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
	1266	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
	1267	\mv ${filein}.tmp ${filein}
[1075]	1268	fi
[1079]	1269	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1069]	1270	}
	1271
	1272	#=======================================================================
[1085]	1273	function IGCM_comp_modifyNamelist
	1274	{
	1275	#
	1276	# syntax: IGCM_comp_modifyNamelist type filein key [value]
	1277	#
	1278	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
	1279	#
	1280	# This function is used to modify a parameter file for a specific variable.
[1155]	1281	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
[1085]	1282	# This function can be used in the comp.driver files for the components.
	1283	#
	1284	# Arguments:
	1285	# - type : first argument must be blocker, nonblocker or force
	1286	# For "blocker" case, the variable must be attributed the keyworld AUTO
	1287	# otherwise this function will exit.
	1288	# For "nonblocker" case, the user can remove or modify the variable. For
	1289	# this case, as long as AUTO is not set, no modification will be done.
	1290	# For "force" case, the variable will be modified even if it is not set to AUTO
	1291	# - filein : the file in run directory of .def type in which the variable should be set
	1292	# - key : the variable to modify
	1293	# - value : the value to set the key equal to, optional. If value is not set or if
	1294	# value=DEFAULT, then a default value must be given in filein using syntax :
	1295	# key= AUTO : DEFAULT=def_value
	1296	#
	1297	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
	1298
[1166]	1299	typeset type filein key value pattern modify
	1300
[1085]	1301	# Set local variables and test the arguments
	1302	if [ $# = 4 ] ; then
	1303	# Normal case with 4 arguments
	1304	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1305	elif [ $# = 3 ] ; then
	1306	# Normal case with 3 arguments
	1307	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1308	else
	1309	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
	1310	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1311	return
	1312	fi
[1166]	1313	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
[1085]	1314
	1315	# Test if first argument is correct
[1166]	1316	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1085]	1317	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
	1318	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1319	return
	1320	fi
	1321
[1215]	1322	# Test if the file exist.
	1323	# Exit with error if the file does not exist for the case blocker or force.
	1324	# Only return for the case nonblocker.
[1085]	1325	if [ ! -f ${filein} ] ; then
[1215]	1326	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1327	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
	1328	else
	1329	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
	1330	fi
[1085]	1331	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1332	return
	1333	fi
	1334
	1335	# Read the line with key in the file without the comments
[1166]	1336	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
[1155]	1337
[1085]	1338	# Verify the existance of the pattern
	1339	if [ X"$pattern" = X ] ; then
[1156]	1340	# Variable key is not set in filein, stop.
[1166]	1341	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1156]	1342	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1343	return
[1085]	1344	fi
[1155]	1345
[1085]	1346	# Check if the variable is set to AUTO in the filein
	1347	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1348	# Modification will be done for all cases
	1349	modify=yes
	1350	else
	1351	# The variable was not set to AUTO
[1166]	1352	if [ ${type} = blocker ] ; then
[1156]	1353	# Exit because this is a blocker call
[1166]	1354	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
[1156]	1355	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1356	return
[1166]	1357	elif [ ${type} = nonblocker ] ; then
[1156]	1358	# Do nothing. Suppose that the user did set the variable correct
[1166]	1359	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
[1156]	1360	modify=no
[1166]	1361	elif [ ${type} = force ] ; then
[1156]	1362	# Force modification
[1166]	1363	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
[1085]	1364	modify=yes
[1156]	1365	fi
[1085]	1366	fi
	1367
	1368	# Do the modifcation now
[1166]	1369	if [ ${modify} = yes ] ; then
[1085]	1370
[1156]	1371	# For option DEFAULT, read default value from file.
[1166]	1372	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1373	# Case to set DEFAULT value
	1374	# Read default value from filein
	1375	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
[1085]	1376
[1166]	1377	if [ X"${value}" = X ] ; then
	1378	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
	1379	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
	1380	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1381	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1382	return
[1085]	1383	fi
[1156]	1384	fi
[1085]	1385
[1156]	1386	# Now change key in filein
[1166]	1387	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
	1388	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
	1389	\mv ${filein}.tmp ${filein}
[1085]	1390	fi
	1391	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1392	}
	1393
	1394	#=======================================================================
[1074]	1395	function IGCM_comp_modifyXmlFile
	1396	{
	1397	#
	1398	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
	1399	#
	1400	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
	1401	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
	1402	#
	1403	# This function is used to modify the value for a specific attribute and variable id.
[1155]	1404	# The file must be a valid xml file.
[1075]	1405	# This function can be used in the comp.driver files for the components.
[1074]	1406	#
[1075]	1407	# Arguments:
	1408	# - type : first argument must be blocker, nonblocker or force.
	1409	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1074]	1410	# otherwise this function will exit.
[1075]	1411	# For "nonblocker" case, the user can remove or modify the variable. For
[1074]	1412	# this case, as long as AUTO is not set, no modification will be done.
[1075]	1413	# For "force" case, the variable will be modified even if it is not set to AUTO
[1074]	1414	# - filein : the file in run directory of .xml type in which the variable should be set
	1415	# - keyid : the variable to modify
	1416	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
	1417	# - value : the value to set in the filein
	1418	#
[1075]	1419	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
[1074]	1420
[1166]	1421	typeset type filein keyid keyattrib value modify
	1422
[1075]	1423	# Set local variables and test the arguments
	1424	if [ $# = 5 ] ; then
	1425	# Normal case with 4 arguments
	1426	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
	1427	else
	1428	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
[1089]	1429	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1430	return
	1431	fi
[1166]	1432	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
[1074]	1433
[1075]	1434	# Test if first argument is correct
[1166]	1435	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1075]	1436	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
[1089]	1437	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1438	return
	1439	fi
[1074]	1440
[1215]	1441	# Test if the file exist.
	1442	# Exit with error if the file does not exist for the case blocker or force.
	1443	# Only return for the case nonblocker.
[1075]	1444	if [ ! -f ${filein} ] ; then
[1215]	1445	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1446	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
	1447	else
	1448	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
	1449	fi
[1089]	1450	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1451	return
	1452	fi
	1453
[1386]	1454	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
[1166]	1455	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
[1386]	1456	if [ ${type} = nonblocker ] ; then
	1457	# This is a nonblocker case, print warning but do nothing else
	1458	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1459	else
	1460	# This is a blocker or force case : stop now
	1461	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
	1462	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
	1463	return
	1464	fi
[1075]	1465	fi
	1466
	1467	# Check if AUTO is set on the same line as keyid and keyattrib
[1166]	1468	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
[1394]	1469	# Modification will be done
[1075]	1470	modify=yes
	1471	else
[1166]	1472	if [ ${type} = blocker ] ; then
[1075]	1473	# Exit, the variable must be set to AUTO
[1166]	1474	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
[1089]	1475	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1476	return
[1166]	1477	elif [ ${type} = nonblocker ] ; then
[1075]	1478	# Nothing will be done
	1479	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
	1480	modify=no
[1166]	1481	elif [ ${type} = force ] ; then
[1075]	1482	# Force modification
[1166]	1483	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
[1075]	1484	modify=yes
[1074]	1485	fi
[1075]	1486	fi
[1074]	1487
[1075]	1488	# Do the modifcation now
[1166]	1489	if [ ${modify} = yes ] ; then
	1490	if [ ${keyattrib} = NONE ] ; then
[1075]	1491	# Case to modify the variable itself
	1492	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
[1166]	1493	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
[1074]	1494	else
[1156]	1495	# Check if keyattrib is set on the same line as keyid
[1166]	1496	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
[1156]	1497	# Case to modify the attribute value
	1498	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
[1166]	1499	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
[1156]	1500	else
	1501	# Case to add the attribute and its value
	1502	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
[1166]	1503	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
[1156]	1504	fi
[1074]	1505	fi
[1166]	1506	\mv ${filein}.tmp ${filein}
[1075]	1507	fi
	1508	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1074]	1509	}
	1510
	1511	#=======================================================================
[2]	1512	function IGCM_comp_Update
	1513	{
[544]	1514	IGCM_debug_PushStack "IGCM_comp_Update"
[2]	1515
[1409]	1516	# Debug Print :
[544]	1517	echo
	1518	IGCM_debug_Print 1 "IGCM_comp_Update"
	1519	echo
[2]	1520
[544]	1521	typeset comp compname comptagname
	1522	for comp in ${config_ListOfComponents[*]} ; do
[902]	1523	# Define component
[544]	1524	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1525	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1526
[544]	1527	# Debug Print
	1528	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
	1529	# UPDATE component
	1530	${comp}_Update
[2]	1531
[1413]	1532	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
	1533	if [ -f timeseries_def_${compname}.xml ]; then
	1534	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
	1535	for line in $( cat ts.temp.${compname}.txt ); do
	1536	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
	1537	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
	1538	case ${output_freq} in
	1539	Y\|y)
	1540	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
	1541	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
	1542	;;
	1543	MO\|mo)
	1544	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
	1545	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
	1546	;;
	1547	D\|d)
	1548	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
	1549	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
	1550	;;
	1551	S\|s)
	1552	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
	1553	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
	1554	;;
	1555	esac
	1556	done
	1557	fi
	1558
	1559	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
	1560	if [ -f dr2xml_${compname}.xml ]; then
	1561	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
	1562	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
	1563
[1420]	1564	# Modify path from dr2xml_{compname}.xml
	1565	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
[1413]	1566
[1420]	1567	# Overwrite the original file
	1568	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
[1422]	1569	fi
[544]	1570	done
[2]	1571
[544]	1572	IGCM_debug_PopStack "IGCM_comp_Update"
[2]	1573	}
	1574
	1575	#=======================================================================
	1576	function IGCM_comp_Finalize
	1577	{
[544]	1578	IGCM_debug_PushStack "IGCM_comp_Finalize"
[2]	1579
[544]	1580	# Debug Print :
	1581	echo
	1582	IGCM_debug_Print 1 "IGCM_comp_Finalize"
	1583	echo
[2]	1584
[544]	1585	typeset ListTextName TextName0
	1586	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
	1587	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
[1165]	1588	typeset -Z4 j4 #BASH declare j4
[544]	1589	typeset list_file nlist_file
	1590	typeset compactoutputs
[429]	1591
[1165]	1592	# Initialize array hosting list of rebuilded files to copy
	1593	unset rebuildedActionsList
	1594
	1595	# Text compacting options
[544]	1596	compactoutputs=false
	1597	if [ X${JobType} != XRUN ] ; then
	1598	compactoutputs=true
	1599	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
	1600	compactoutputs=true
	1601	fi
[433]	1602
[1043]	1603	# Prepare headers for the shell dedicated to offline rebuild
	1604	if [ X${AsynchronousRebuild} = Xtrue ] ; then
	1605	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1606	if [ ${DRYRUN} -le 1 ] ; then
	1607	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1608	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1609	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1610	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1611	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1612	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1613	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1614	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1615	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1616	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1617	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1618	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1619	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1620	fi
	1621	fi
	1622
[544]	1623	for comp in ${config_ListOfComponents[*]} ; do
[902]	1624	# Define component
[544]	1625	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1626	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1627
[544]	1628	# Debug Print
	1629	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
	1630	# FINALIZE component
	1631	${comp}_Finalize
[2]	1632
[778]	1633	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	1634
[804]	1635	# Save Output Text files of models
	1636	#---------------------------------
	1637	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
	1638	IGCM_card_DefineArrayFromOption ${card} OutputText List
	1639	ListTextName=${compname}_OutputText_List
	1640
	1641	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
	1642	if [ X${TextName0} != X${NULL_STR} ] ; then
	1643	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
	1644
	1645	(( i=0 ))
	1646	until [ $i -eq $NbFiles ]; do
	1647	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
	1648	eval file_out=${PREFIX}_${file_in}
	1649
	1650	(( i=i+1 ))
	1651
	1652	unset list_file
	1653	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
	1654	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
	1655	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 )
	1656	nlist_file=${#list_file[@]}
	1657	if [ ${nlist_file} -gt 1 ] ; then
	1658	if ( ${compactoutputs} ) ; then
	1659	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
	1660	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
	1661	echo ${list_file[*]} > ${file_out}
	1662	echo "" >> ${file_out}
	1663
	1664	(( i_ = 0 ))
[1080]	1665	for file in ${list_file[@]} ; do
[804]	1666	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
	1667	echo "\| " ${i_} " " ${file} >> ${file_out}
	1668	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
[999]	1669	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
[804]	1670	echo "" >> ${file_out}
	1671	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1672	(( i_ = i_ + 1 ))
	1673	done
[1080]	1674	if ( ${ExecutionFail} ) ; then
	1675	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
	1676	fi
	1677
[804]	1678	if [ X${Pack} = Xtrue ] ; then
	1679	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
	1680	else
	1681	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
	1682	fi
[1080]	1683
[804]	1684	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
[1080]	1685	else
	1686	for file in ${list_file[@]} ; do
	1687	if ( ${ExecutionFail} ) ; then
	1688	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
	1689	fi
[804]	1690
	1691	if [ X${Pack} = Xtrue ] ; then
	1692	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
	1693	else
	1694	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
	1695	fi
[1080]	1696
[804]	1697	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1698	done
	1699	fi
	1700	else
	1701	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
	1702	eval IGCM_sys_Mv ${file_in}* ${file_in}
	1703	fi
[1080]	1704
	1705	if ( ${ExecutionFail} ) ; then
	1706	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
	1707	fi
	1708
[804]	1709	if [ X${Pack} = Xtrue ] ; then
	1710	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
	1711	else
	1712	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
	1713	fi
	1714	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1715	fi
	1716	done
	1717	fi
	1718
[544]	1719	# Save Restarts files
	1720	#--------------------
	1721	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
	1722	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	1723	ListFilesName=${compname}_RestartFiles_List
	1724	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	1725
[544]	1726	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	1727	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[778]	1728
[544]	1729	(( i=0 ))
	1730	until [ $i -ge $NbFiles ]; do
[778]	1731	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1732	eval file_in=${file_in_}
[2]	1733
[778]	1734	(( i_ = i+1 ))
	1735	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1736	eval file_out=${file_out_}
[151]	1737
[778]	1738	(( i_ = i+2 ))
	1739	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1740	eval file_outin=${file_outin_}
[151]	1741
[778]	1742	generic_restart_file_name_in=$( basename ${file_in} .nc )
	1743	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
	1744	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
[2]	1745
[902]	1746	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
[778]	1747	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	1748	j=0 # BASH LINE NOT NEEDED
	1749	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	1750	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	1751	j4=${j} # BASH LINE NOT NEEDED
[778]	1752	if [ X${Pack} = Xtrue ] ; then
	1753	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1754	else
	1755	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1756	fi
	1757	if [ ! ${file_in} = ${file_outin} ] ; then
	1758	if ( ${ExitFlag} ) ; then
	1759	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
	1760	else
	1761	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
	1762	fi
	1763	fi
[821]	1764	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	1765	done
	1766	else
	1767	if [ X${Pack} = Xtrue ] ; then
	1768	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1769	else
	1770	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1771	fi
	1772	if [ ! ${file_in} = ${file_outin} ] ; then
	1773	if ( ${ExitFlag} ) ; then
	1774	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
	1775	else
	1776	IGCM_sys_Mv ${file_in} ${file_outin}
	1777	fi
	1778	fi
	1779	fi
	1780
	1781	(( i=i+3 ))
[544]	1782	done
	1783	else
	1784	if [ X${FileName0} != XNONE ] ; then
[778]	1785	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
[544]	1786	else
[778]	1787	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
[544]	1788	fi
	1789	fi
[2]	1790
[544]	1791	# Save Output files
	1792	#------------------
	1793	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
	1794	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	1795	ListFilesName=${compname}_OutputFiles_List
	1796	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	1797
[544]	1798	if [ X${FileName0} != X${NULL_STR} ] ; then
	1799	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[149]	1800
[544]	1801	(( i=0 ))
	1802	until [ $i -ge $NbFiles ]; do
[778]	1803	SaveOnArchive=true
	1804	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1805	eval file_in=${file_in_}
	1806	(( i_ = i+1 ))
	1807	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1808	eval file_out=${file_out_}
	1809	#
	1810	# Override file_out path remplacing R_SAVE by R_BUFR
	1811	#
	1812	if [ X${Pack} = Xtrue ] ; then
	1813	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
	1814	fi
	1815	#
	1816	# Not necessarily the best option. /!\ Potential side effects /!\
	1817	#
	1818	(( i_ = i+2 ))
	1819	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1820	#
	1821	generic_file_name=$( basename ${file_in} .nc )
	1822	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
	1823	#
	1824	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
[804]	1825	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
[778]	1826	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
	1827	elif [ ${nb_rebuild_file} -gt 1 ] ; then
[804]	1828	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
[778]	1829	if [ X${AsynchronousRebuild} = Xfalse ] ; then
	1830	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
[1388]	1831	#
	1832	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
	1833	if [ ${file_in} = output.abort.nc ] ; then
	1834	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
	1835	else
	1836	IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc
	1837	fi
[778]	1838	else
	1839	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
[980]	1840	IGCM_sys_Mv ${generic_file_name}_[0-9]*.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
[544]	1841
[778]	1842	# Prepare the shell dedicated to offline rebuild
	1843	if [ $DRYRUN -le 1 ]; then
[694]	1844	if [ ${file_in} = histstn.nc ] ; then
	1845	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1846	else
[980]	1847	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[694]	1848	fi
[1206]	1849	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1850	fi
	1851	#
	1852	# Load Patch we need to apply and apply
	1853	if [ $DRYRUN -le 1 ]; then
	1854	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
[1080]	1855	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1856	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1857	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1858	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1859	done
	1860	fi
	1861	fi
	1862	#
	1863	if [ $DRYRUN -le 1 ]; then
	1864	if [ X${Pack} = Xtrue ] ; then
[1165]	1865	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
[778]	1866	else
[1165]	1867	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
[778]	1868	fi
[1206]	1869	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
[1165]	1870	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
[778]	1871	fi
	1872	SaveOnArchive=false
	1873	fi
	1874	fi
	1875	#
	1876	if [ ${SaveOnArchive} = true ] ; then
	1877	#
	1878	# Rebuild has been done online or it was not needed
	1879	#
	1880	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
	1881	#
	1882	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
[1289]	1883	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
[778]	1884	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1885	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
	1886	#
	1887	if [ $DRYRUN -le 1 ]; then
[1080]	1888	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1889	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1890	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1891	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1892	done
	1893	#
	1894	if [ X${Pack} = Xtrue ] ; then
	1895	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1896	else
	1897	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1898	fi
[1206]	1899	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1900	#
	1901	fi
	1902	else
	1903	#
	1904	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
	1905	#
	1906	if [ X${Pack} = Xtrue ] ; then
	1907	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
	1908	else
	1909	IGCM_sys_Put_Out ${file_in} ${file_out}
	1910	fi
	1911	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1912	if [ ${nb_rebuild_file} -gt 1 ] ; then
	1913	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
	1914	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
	1915	done
	1916	fi
	1917	fi
	1918	fi
	1919	(( i=i+3 ))
[544]	1920	done
	1921	fi
	1922	echo
	1923	done
[1165]	1924	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
	1925	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
[1166]	1926	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1165]	1927	i=0
	1928	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
	1929	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1930	(( i=i+1 ))
	1931	done
	1932	fi
[544]	1933	IGCM_debug_PopStack "IGCM_comp_Finalize"
[2]	1934	}

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