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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1580

Last change on this file since 1580 was 1580, checked in by acosce, 15 months ago
remove test on IPSLCM config for CMIP6 workflow - not useful for redhat8
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
File size: 79.0 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
[544]	650	done
[2]	651
[544]	652	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
[2]	653	}
	654
	655	#=======================================================================
	656	function IGCM_comp_GetInputRestartFiles
	657	{
[544]	658	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
[2]	659
[544]	660	# Debug Print :
	661	echo
	662	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
	663	echo
[2]	664
[590]	665	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
	666	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
[902]	667	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
[544]	668	typeset file_in file_out file_in_ file_out_ file_in_Name
	669	typeset -Z4 j4
[821]	670	#BASH declare j4
[2]	671
[778]	672	IsMatching=""
	673
[544]	674	for comp in ${config_ListOfComponents[*]} ; do
[902]	675	# Define component
[544]	676	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	677	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
	678	#
	679	card=${SUBMIT_DIR}/COMP/${compname}.card
	680	#
	681	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	682	ListFilesName=${compname}_RestartFiles_List
	683	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	684
[544]	685	# Debug Print :
	686	IGCM_debug_Print 3 "restart ${compname}"
[2]	687
[544]	688	if ( ${FirstInitialize} ) ; then
[2]	689
[1401]	690	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[1446]	691	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
[1538]	692	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
[1447]	693	CompOldName=IOS
	694	config_IOS_Restart="n"
	695	do_start="n"
[1449]	696	config_IOS_RestartDate=-1
	697	config_IOS_RestartJobName=${NULL_STR}
	698	config_IOS_RestartPath=${NULL_STR}
[1447]	699	else
[1446]	700	eval config_${comp}_Restart="y"
	701	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
	702	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
	703	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
	704	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
	705	eval CompOldName=${comp}
	706	fi
[544]	707	else
[778]	708	# Read component Restarts parameters
	709	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	710	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
[2]	711
[778]	712	if [ "${do_start}" = "y" ] ; then
	713	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
	714	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
	715	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
	716	else
	717	eval config_${comp}_RestartDate=-1
	718	eval config_${comp}_RestartJobName=${NULL_STR}
	719	eval config_${comp}_RestartPath=${NULL_STR}
	720	fi
[849]	721
[778]	722	eval CompOldName=\${config_${comp}_OldName}
	723	if [ X${CompOldName} = X ] ; then
	724	eval CompOldName=${comp}
	725	fi
	726
	727	# Reinitialize IsMatching to allow searching for a different tar file for each component.
	728	IsMatching=""
	729	TarFileFound=""
[544]	730	fi
[2]	731
[544]	732	if [ "${do_start}" = "y" ] ; then
[2]	733
[672]	734	# Restore Restarts files
	735	#-----------------------
[778]	736	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	737	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	738
[778]	739	(( i=1 ))
	740	until [ $i -gt $NbFiles ]; do
	741	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	742	eval file_in=${file_in_}
	743	(( i_ = i+1 ))
	744	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	745	eval file_out=${file_out_}
	746
	747	eval Date_tmp=\${config_${comp}_RestartDate}
	748	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
[672]	749	# will be re-use
	750	eval RestartPath=\${config_${comp}_RestartPath}
	751	eval RestartJobName=\${config_${comp}_RestartJobName}
	752	#
[778]	753	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
	754	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
[2]	755
[778]	756	extension_in=$( echo ${file_in_Name##*.} )
	757	extension_out=$( echo ${file_out##*.} )
[672]	758
[778]	759	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	760	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
[2]	761
[778]	762	Path_OUT=${Path_r}/${generic_restart_file_name_in}
	763
[672]	764	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	765	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
[778]	766	Buffered=true
	767	Archived=false
	768	Tared=false
	769	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
[672]	770	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	771	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	772	Buffered=false
	773	Archived=true
	774	Tared=false
	775	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
[672]	776	else
[897]	777	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
	778	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
[902]	779	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
[778]	780	Buffered=false
	781	Archived=false
	782	Tared=true
[672]	783	# Look after the tar file we want if we did not found it already
[778]	784	if [ X${IsMatching} = X ] ; then
[947]	785	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
	786	if [ $? ] ; then
[897]	787	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
	788	IsMatching=$( echo ${PotentialTarFile##*/} \| \
	789	sed "s:_restart::" \| \
	790	sed "s:^${RestartJobName}_::" \| \
	791	sed "s:\.tar$::" \| \
	792	gawk -F_ -v restartdate=${Date_r} \
	793	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	794	if [ ! X${IsMatching} = X ] ; then
	795	TarFileFound=${PotentialTarFile}
	796	break
	797	fi
	798	done
[1017]	799	fi
	800	# Stop here if nothing has been found
	801	if [ X${TarFileFound} = X ] ; then
[902]	802	IGCM_debug_Print 3 "Restart files were not found!"
	803	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	804	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
[897]	805	IGCM_debug_Exit "Please double check restart settings in config.card"
	806	IGCM_debug_Verif_Exit
	807	fi
[778]	808	fi
[918]	809	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	810	TarFileLocation=$( basename ${TarFileFound} )
[801]	811	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	812	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	813	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	814	fi
[672]	815
	816	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	817	j=0 # BASH LINE NOT NEEDED
	818	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	819	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	820	j4=${j} # BASH LINE NOT NEEDED
[778]	821	if [ X${Buffered} = Xtrue ] ; then
	822	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	823	elif [ X${Archived} = Xtrue ] ; then
	824	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	825	elif [ X${Tared} = Xtrue ] ; then
	826	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	827	fi
[821]	828	(( j=j+1 )) #BASH LINE NOT NEEDED
[778]	829	done
[740]	830
[1248]	831	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
	832	if [ X${OCE_PROC_MPI} != X ] ; then
	833	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
[1380]	834	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
[740]	835	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
	836	fi
	837	fi
[778]	838	else
	839	if [ X${Buffered} = Xtrue ] ; then
	840	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
	841	elif [ X${Archived} = Xtrue ] ; then
	842	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
	843	elif [ X${Tared} = Xtrue ] ; then
	844	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	845	fi
	846	fi
	847	(( i=i+3 ))
	848	done
	849	else
	850	if [ X${FileName0} != XNONE ] ; then
	851	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	852	else
	853	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	854	fi
	855	fi
[544]	856	fi
[893]	857	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
[544]	858	# if not FirstInitialize and first loop of this job
[2]	859
[544]	860	# Restore Restarts files
	861	#-----------------------
	862	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
[778]	863	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	864
[778]	865	(( i=1 ))
	866	until [ $i -gt $NbFiles ]; do
	867	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	868	eval file_in=${file_in_}
	869	(( i_ = i+1 ))
	870	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	871	eval file_out=${file_out_}
[2]	872
[1028]	873	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
[662]	874
[778]	875	extension_in=$( echo ${file_in_Name##*.} )
	876	extension_out=$( echo ${file_out##*.} )
[67]	877
[778]	878	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	879	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
	880
	881	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
	882	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
	883
[662]	884	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	885	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
[778]	886	Buffered=true
	887	Archived=false
	888	Tared=false
	889	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
[672]	890	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	891	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	892	Buffered=false
	893	Archived=true
	894	Tared=false
	895	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
	896	else
[897]	897	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
[902]	898	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
[778]	899	Buffered=false
	900	Archived=false
	901	Tared=true
	902	# Look after the tar file we want if we did not found it already
	903	if [ X${IsMatching} = X ] ; then
[801]	904	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
[778]	905	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	906	if [ ! X${IsMatching} = X ] ; then
	907	TarFileFound=${PotentialTarFile}
	908	break
	909	fi
	910	done
	911	fi
[1017]	912	# Stop here if nothing has been found
	913	if [ X${TarFileFound} = X ] ; then
	914	IGCM_debug_Print 3 "Restart files were not found!"
	915	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	916	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
	917	IGCM_debug_Exit "Please double check restart settings in config.card"
	918	IGCM_debug_Verif_Exit
	919	fi
[918]	920	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	921	TarFileLocation=$( basename ${TarFileFound} )
[801]	922	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	923	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	924	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	925	fi
[41]	926
[778]	927	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	928	j=0 # BASH LINE NOT NEEDED
	929	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	930	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	931	j4=${j} # BASH LINE NOT NEEDED
[778]	932	if [ X${Buffered} = Xtrue ] ; then
	933	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	934	elif [ X${Archived} = Xtrue ] ; then
	935	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	936	elif [ X${Tared} = Xtrue ] ; then
	937	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	938	fi
[821]	939	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	940	done
	941	else
	942	if [ X${Buffered} = Xtrue ] ; then
	943	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
	944	elif [ X${Archived} = Xtrue ] ; then
	945	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
	946	elif [ X${Tared} = Xtrue ] ; then
	947	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	948	fi
	949	fi
	950	(( i=i+3 ))
	951	done
[544]	952	else
[778]	953	if [ X${FileName0} != XNONE ] ; then
	954	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	955	else
	956	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	957	fi
[544]	958	fi
[420]	959	fi
[544]	960	done
[420]	961
[544]	962	NbFiles=$( ls * 2> /dev/null \| wc -l )
	963	if [ ${NbFiles} -gt 0 ] ; then
	964	IGCM_sys_Chmod u+rw *
	965	fi
	966
	967	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
[2]	968	}
	969
	970	#=======================================================================
[1409]	971	function IGCM_comp_GetInputBinaryFiles
	972	{
	973	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
	974
	975	# Debug Print :
	976	echo
	977	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
	978	echo
	979
	980	# Clean up previous pass
	981	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
	982
[1411]	983	typeset comp ExeNameIn ExeNameOut byPass
[1409]	984	typeset compilerNmbr compilerUnit compilerFull
[1411]	985	byPass=false
[1409]	986	for comp in ${config_ListOfComponents[*]} ; do
	987	# Define component
	988
	989	# Copy executable for this component
	990	eval ExeNameIn=\${config_Executable_${comp}[0]}
	991	eval ExeNameOut=\${config_Executable_${comp}[1]}
[1486]	992	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
	993	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
	994	# The executable is set in config.card and is different from ""
	995	# Use eval to expand ExeNameIn if variables are used in the name
	996	eval ExeNameIn=${ExeNameIn}
	997	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
	998	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
	999	fi
[1409]	1000	fi
	1001
	1002	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
	1003	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1004	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1005	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1006	fi
	1007	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1008	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1009	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1010	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1011	fi
	1012	fi
	1013
	1014	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1015	# Get the compiler version
	1016	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1017	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1018	# Save it
	1019	echo $compilerFull >> ${RUN_DIR}/compiler.txt
[1411]	1020	[ X${compilerFull} = X ] && byPass=true
[1409]	1021	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
[1413]	1022	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
[1409]	1023	fi
	1024	done
	1025
	1026	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
	1027	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
	1028
[1411]	1029	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
[1409]	1030	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
	1031	fi
	1032
[1415]	1033
[1409]	1034	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
	1035	}
	1036
	1037	#=======================================================================
[269]	1038	function IGCM_comp_PeriodStart
	1039	{
[544]	1040	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
[269]	1041
[544]	1042	# Debug Print :
	1043	echo
	1044	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
	1045	echo
[269]	1046
[902]	1047	typeset ExeNameIn ExeNameOut
[544]	1048	typeset comp compname comptagname
	1049	for comp in ${config_ListOfComponents[*]} ; do
[902]	1050	# Define component
[544]	1051	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1052	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[269]	1053
[544]	1054	# Copy executable for this component
	1055	eval ExeNameIn=\${config_Executable_${comp}[0]}
[1486]	1056	eval ExeNameIn=${ExeNameIn}
[544]	1057	eval ExeNameOut=\${config_Executable_${comp}[1]}
[269]	1058
[544]	1059	# Debug Print
	1060	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
	1061	# UPDATE component
	1062	${comp}_PeriodStart 2> /dev/null
[269]	1063
[544]	1064	done
[269]	1065
[544]	1066	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
[269]	1067	}
	1068
[1166]	1069
	1070
[269]	1071	#=======================================================================
[1166]	1072	function IGCM_comp_modifyFile
	1073	{
	1074	#
	1075	# syntax: IGCM_comp_modifyFile filein key [value]
	1076	#
	1077	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
	1078	#
	1079	# This function is used to replace a pattern in a file for a specific variable.
	1080	#
	1081	# Arguments:
	1082	# - filein : the file in run directory in which the variable should be set
	1083	# - key : the variable to modify
	1084	# - value : the value to set the key equal to
	1085	#
	1086	IGCM_debug_PushStack "IGCM_comp_modifyFile"
	1087
	1088	typeset filein key value pattern
	1089
	1090	# Set local variables and test the arguments
	1091	if [ $# = 3 ] ; then
	1092	# Normal case with 3 arguments
	1093	filein=$1 ; key=$2 ; value=$3
	1094	else
	1095	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
	1096	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1097	return
	1098	fi
	1099	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
	1100
	1101	# Test if the file exist
	1102	if [ ! -f ${filein} ] ; then
	1103	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
	1104	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1105	return
	1106	fi
	1107
	1108	# Read the line with key in the file without the comments
	1109	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
	1110
	1111	# Verify the existance of the pattern
	1112	if [ X"${pattern}" = X ] ; then
	1113	# Variable key is not set in filein, stop.
	1114	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
	1115	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1116	return
	1117	fi
	1118
	1119	# Now change key in filein
[1176]	1120	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
	1121	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
[1166]	1122	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
	1123	\mv ${filein}.tmp ${filein}
	1124
	1125	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1126	}
	1127
	1128	#=======================================================================
[1069]	1129	function IGCM_comp_modifyDefFile
	1130	{
	1131	#
	1132	# syntax: IGCM_comp_modifyDefFile type filein key [value]
	1133	#
	1134	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
	1135	#
	1136	# This function is used to modify a parameter file for a specific variable.
[1075]	1137	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
	1138	# This function can be used in the comp.driver files for the components.
[1069]	1139	#
[1075]	1140	# Arguments:
[1081]	1141	# - type : first argument must be blocker, nonblocker or force
[1075]	1142	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1069]	1143	# otherwise this function will exit.
[1075]	1144	# For "nonblocker" case, the user can remove or modify the variable. For
	1145	# this case, as long as AUTO is not set, no modification will be done.
[1081]	1146	# For "force" case, the variable will be modified even if it is not set to AUTO
[1069]	1147	# - filein : the file in run directory of .def type in which the variable should be set
	1148	# - key : the variable to modify
[1075]	1149	# - value : the value to set the key equal to, optional. If value is not set or if
[1069]	1150	# value=DEFAULT, then a default value must be given in filein using syntax :
	1151	# key= AUTO : DEFAULT=def_value
	1152	#
[1075]	1153	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
[1069]	1154
[1166]	1155	typeset type filein key value
	1156	typeset filelist nb_occ modify
	1157
[1075]	1158	# Set local variables and test the arguments
	1159	if [ $# = 4 ] ; then
	1160	# Normal case with 4 arguments
	1161	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1162	elif [ $# = 3 ] ; then
	1163	# Normal case with 3 arguments
	1164	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1165	else
	1166	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
[1079]	1167	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1168	return
	1169	fi
[1166]	1170	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
[1069]	1171
[1075]	1172	# Test if first argument is correct
[1166]	1173	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1081]	1174	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
[1079]	1175	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1176	return
	1177	fi
[1069]	1178
[1215]	1179	# Test if the file exist.
	1180	# Exit with error if the file does not exist for the case blocker or force.
	1181	# Only return for the case nonblocker.
[1075]	1182	if [ ! -f ${filein} ] ; then
[1215]	1183	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1184	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
	1185	else
	1186	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
	1187	fi
[1079]	1188	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1189	return
	1190	fi
[1069]	1191
[1102]	1192	# Define list of files to test using all files with suffix .def (except used*.def)
	1193	filelist=$( ls *def \| grep -v used )
[1069]	1194
[1075]	1195	# Count number of occurances for the key in all files
[1166]	1196	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
[1069]	1197
[1075]	1198	# Test if key is set several times
[1166]	1199	if [ ${nb_occ} -gt 1 ] ; then
	1200	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
[1079]	1201	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1202	return
	1203	fi
	1204
	1205	# Treatement according to different cases
[1166]	1206	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
[1075]	1207	# Stop if the key is never set and the function is blocker
[1166]	1208	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
	1209	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
	1210	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
[1075]	1211	# The key is not set but it is a nonblocker call so nothing is done.
[1166]	1212	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1213	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
[1081]	1214	modify=no
[1166]	1215	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
[1075]	1216	# Variable key is not set in filein, stop.
[1166]	1217	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1081]	1218	fi
	1219
	1220	# Check if AUTO is set in the filein on the same line as the key variable
[1166]	1221	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1222	# Modification will be done for all cases
	1223	modify=yes
	1224	else
	1225	# The variable was not set to AUTO
[1166]	1226	if [ ${type} = blocker ] ; then
[1156]	1227	# Exit because this is a blocker call
[1166]	1228	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
[1190]	1229	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1156]	1230	return
[1166]	1231	elif [ ${type} = nonblocker ] ; then
[1156]	1232	# Do nothing. Suppose that the user did set the variable correct
[1166]	1233	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
[1156]	1234	modify=no
[1166]	1235	elif [ ${type} = force ] ; then
[1156]	1236	# Force modification
[1166]	1237	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
[1081]	1238	modify=yes
[1156]	1239	fi
[1081]	1240	fi
[1069]	1241
[1081]	1242	# Do the modifcation now
[1166]	1243	if [ ${modify} = yes ] ; then
[1081]	1244
[1156]	1245	# For option DEFAULT, read default value from file.
[1166]	1246	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1247	# Case to set DEFAULT value
	1248	# Read default value from filein
[1423]	1249	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
[1069]	1250
[1166]	1251	if [ X"${value}" = X ] ; then
	1252	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
	1253	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
	1254	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1255	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
	1256	return
[1075]	1257	fi
[1156]	1258	fi
[1069]	1259
[1156]	1260	# Now change key in filein
[1166]	1261	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
	1262	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
	1263	\mv ${filein}.tmp ${filein}
[1075]	1264	fi
[1079]	1265	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1069]	1266	}
	1267
	1268	#=======================================================================
[1085]	1269	function IGCM_comp_modifyNamelist
	1270	{
	1271	#
	1272	# syntax: IGCM_comp_modifyNamelist type filein key [value]
	1273	#
	1274	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
	1275	#
	1276	# This function is used to modify a parameter file for a specific variable.
[1155]	1277	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
[1085]	1278	# This function can be used in the comp.driver files for the components.
	1279	#
	1280	# Arguments:
	1281	# - type : first argument must be blocker, nonblocker or force
	1282	# For "blocker" case, the variable must be attributed the keyworld AUTO
	1283	# otherwise this function will exit.
	1284	# For "nonblocker" case, the user can remove or modify the variable. For
	1285	# this case, as long as AUTO is not set, no modification will be done.
	1286	# For "force" case, the variable will be modified even if it is not set to AUTO
	1287	# - filein : the file in run directory of .def type in which the variable should be set
	1288	# - key : the variable to modify
	1289	# - value : the value to set the key equal to, optional. If value is not set or if
	1290	# value=DEFAULT, then a default value must be given in filein using syntax :
	1291	# key= AUTO : DEFAULT=def_value
	1292	#
	1293	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
	1294
[1166]	1295	typeset type filein key value pattern modify
	1296
[1085]	1297	# Set local variables and test the arguments
	1298	if [ $# = 4 ] ; then
	1299	# Normal case with 4 arguments
	1300	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1301	elif [ $# = 3 ] ; then
	1302	# Normal case with 3 arguments
	1303	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1304	else
	1305	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
	1306	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1307	return
	1308	fi
[1166]	1309	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
[1085]	1310
	1311	# Test if first argument is correct
[1166]	1312	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1085]	1313	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
	1314	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1315	return
	1316	fi
	1317
[1215]	1318	# Test if the file exist.
	1319	# Exit with error if the file does not exist for the case blocker or force.
	1320	# Only return for the case nonblocker.
[1085]	1321	if [ ! -f ${filein} ] ; then
[1215]	1322	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1323	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
	1324	else
	1325	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
	1326	fi
[1085]	1327	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1328	return
	1329	fi
	1330
	1331	# Read the line with key in the file without the comments
[1166]	1332	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
[1155]	1333
[1085]	1334	# Verify the existance of the pattern
	1335	if [ X"$pattern" = X ] ; then
[1156]	1336	# Variable key is not set in filein, stop.
[1166]	1337	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1156]	1338	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1339	return
[1085]	1340	fi
[1155]	1341
[1085]	1342	# Check if the variable is set to AUTO in the filein
	1343	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1344	# Modification will be done for all cases
	1345	modify=yes
	1346	else
	1347	# The variable was not set to AUTO
[1166]	1348	if [ ${type} = blocker ] ; then
[1156]	1349	# Exit because this is a blocker call
[1166]	1350	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
[1156]	1351	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1352	return
[1166]	1353	elif [ ${type} = nonblocker ] ; then
[1156]	1354	# Do nothing. Suppose that the user did set the variable correct
[1166]	1355	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
[1156]	1356	modify=no
[1166]	1357	elif [ ${type} = force ] ; then
[1156]	1358	# Force modification
[1166]	1359	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
[1085]	1360	modify=yes
[1156]	1361	fi
[1085]	1362	fi
	1363
	1364	# Do the modifcation now
[1166]	1365	if [ ${modify} = yes ] ; then
[1085]	1366
[1156]	1367	# For option DEFAULT, read default value from file.
[1166]	1368	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1369	# Case to set DEFAULT value
	1370	# Read default value from filein
	1371	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
[1085]	1372
[1166]	1373	if [ X"${value}" = X ] ; then
	1374	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
	1375	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
	1376	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1377	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1378	return
[1085]	1379	fi
[1156]	1380	fi
[1085]	1381
[1156]	1382	# Now change key in filein
[1166]	1383	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
	1384	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
	1385	\mv ${filein}.tmp ${filein}
[1085]	1386	fi
	1387	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1388	}
	1389
	1390	#=======================================================================
[1074]	1391	function IGCM_comp_modifyXmlFile
	1392	{
	1393	#
	1394	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
	1395	#
	1396	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
	1397	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
	1398	#
	1399	# This function is used to modify the value for a specific attribute and variable id.
[1155]	1400	# The file must be a valid xml file.
[1075]	1401	# This function can be used in the comp.driver files for the components.
[1074]	1402	#
[1075]	1403	# Arguments:
	1404	# - type : first argument must be blocker, nonblocker or force.
	1405	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1074]	1406	# otherwise this function will exit.
[1075]	1407	# For "nonblocker" case, the user can remove or modify the variable. For
[1074]	1408	# this case, as long as AUTO is not set, no modification will be done.
[1075]	1409	# For "force" case, the variable will be modified even if it is not set to AUTO
[1074]	1410	# - filein : the file in run directory of .xml type in which the variable should be set
	1411	# - keyid : the variable to modify
	1412	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
	1413	# - value : the value to set in the filein
	1414	#
[1075]	1415	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
[1074]	1416
[1166]	1417	typeset type filein keyid keyattrib value modify
	1418
[1075]	1419	# Set local variables and test the arguments
	1420	if [ $# = 5 ] ; then
	1421	# Normal case with 4 arguments
	1422	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
	1423	else
	1424	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
[1089]	1425	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1426	return
	1427	fi
[1166]	1428	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
[1074]	1429
[1075]	1430	# Test if first argument is correct
[1166]	1431	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1075]	1432	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
[1089]	1433	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1434	return
	1435	fi
[1074]	1436
[1215]	1437	# Test if the file exist.
	1438	# Exit with error if the file does not exist for the case blocker or force.
	1439	# Only return for the case nonblocker.
[1075]	1440	if [ ! -f ${filein} ] ; then
[1215]	1441	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1442	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
	1443	else
	1444	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
	1445	fi
[1089]	1446	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1447	return
	1448	fi
	1449
[1386]	1450	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
[1166]	1451	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
[1386]	1452	if [ ${type} = nonblocker ] ; then
	1453	# This is a nonblocker case, print warning but do nothing else
	1454	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1455	else
	1456	# This is a blocker or force case : stop now
	1457	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
	1458	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
	1459	return
	1460	fi
[1075]	1461	fi
	1462
	1463	# Check if AUTO is set on the same line as keyid and keyattrib
[1166]	1464	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
[1394]	1465	# Modification will be done
[1075]	1466	modify=yes
	1467	else
[1166]	1468	if [ ${type} = blocker ] ; then
[1075]	1469	# Exit, the variable must be set to AUTO
[1166]	1470	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
[1089]	1471	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1472	return
[1166]	1473	elif [ ${type} = nonblocker ] ; then
[1075]	1474	# Nothing will be done
	1475	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
	1476	modify=no
[1166]	1477	elif [ ${type} = force ] ; then
[1075]	1478	# Force modification
[1166]	1479	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
[1075]	1480	modify=yes
[1074]	1481	fi
[1075]	1482	fi
[1074]	1483
[1075]	1484	# Do the modifcation now
[1166]	1485	if [ ${modify} = yes ] ; then
	1486	if [ ${keyattrib} = NONE ] ; then
[1075]	1487	# Case to modify the variable itself
	1488	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
[1166]	1489	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
[1074]	1490	else
[1156]	1491	# Check if keyattrib is set on the same line as keyid
[1166]	1492	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
[1156]	1493	# Case to modify the attribute value
	1494	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
[1166]	1495	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
[1156]	1496	else
	1497	# Case to add the attribute and its value
	1498	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
[1166]	1499	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
[1156]	1500	fi
[1074]	1501	fi
[1166]	1502	\mv ${filein}.tmp ${filein}
[1075]	1503	fi
	1504	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1074]	1505	}
	1506
	1507	#=======================================================================
[2]	1508	function IGCM_comp_Update
	1509	{
[544]	1510	IGCM_debug_PushStack "IGCM_comp_Update"
[2]	1511
[1409]	1512	# Debug Print :
[544]	1513	echo
	1514	IGCM_debug_Print 1 "IGCM_comp_Update"
	1515	echo
[2]	1516
[544]	1517	typeset comp compname comptagname
	1518	for comp in ${config_ListOfComponents[*]} ; do
[902]	1519	# Define component
[544]	1520	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1521	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1522
[544]	1523	# Debug Print
	1524	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
	1525	# UPDATE component
	1526	${comp}_Update
[2]	1527
[1413]	1528	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
	1529	if [ -f timeseries_def_${compname}.xml ]; then
	1530	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
	1531	for line in $( cat ts.temp.${compname}.txt ); do
	1532	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
	1533	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
	1534	case ${output_freq} in
	1535	Y\|y)
	1536	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
	1537	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
	1538	;;
	1539	MO\|mo)
	1540	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
	1541	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
	1542	;;
	1543	D\|d)
	1544	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
	1545	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
	1546	;;
	1547	S\|s)
	1548	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
	1549	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
	1550	;;
	1551	esac
	1552	done
	1553	fi
	1554
	1555	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
	1556	if [ -f dr2xml_${compname}.xml ]; then
[1535]	1557	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
	1558	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
	1559	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
	1560	# Modify path from dr2xml_{compname}.xml
	1561	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
[1552]	1562	${libIGCM}/libIGCM_post/xios_parser.py -v modifydr2xmlIPSL --newPath ${CMIP6_DIR} --splitLastDate ${EndYear_p1} --JobName ${config_UserChoices_JobName} --ModelName ${config_UserChoices_ModelName} --ModelVersion ${config_UserChoices_LongName} --ExperimentName ${config_UserChoices_ExperimentName} --file dr2xml_${compname}.xml
[1535]	1563	else
	1564	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
	1565	fi
	1566	# Overwrite the original file
	1567	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
[1467]	1568	fi
[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
[1429]	1836	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
[1388]	1837	fi
[778]	1838	else
	1839	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
[1429]	1840	IGCM_sys_Mv ${generic_file_name}_????.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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