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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1572

Last change on this file since 1572 was 1552, checked in by aclsce, 2 years ago
Modified to use CMIP6 workflow for non CMIP6 runs.
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: 79.8 KB

Rev	Line
[2]	1	#!/bin/ksh
	2
	3	#**************************************************************
	4	# Author: Sebastien Denvil, Martial Mancip
[373]	5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
	6	# $Revision:: $ Revision of last commit
	7	# $Author:: $ Author of last commit
	8	# $Date:: $ Date of last commit
[2]	9	# IPSL (2006)
	10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
	11	#
	12	#**************************************************************
	13
	14	#========================================================================
	15	function IGCM_comp_Initialize
	16	{
[544]	17	IGCM_debug_PushStack "IGCM_comp_Initialize"
[2]	18
[778]	19	# Debug Print :
[544]	20	echo
	21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
	22	echo
[2]	23
[1244]	24	typeset comp compname comptagname auxprint card_UserChoices first_option option i j
[544]	25	for comp in ${config_ListOfComponents[*]} ; do
[2]	26
[902]	27	# Define component
[544]	28	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
	29	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	30	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[457]	31
[615]	32	# Debug Print
	33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
	34
[1244]	35	# ${compname}.card PATH
[544]	36	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	37
[544]	38	# Manage component executable
	39	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
[2]	40
[849]	41	# Define all options in section [comp]
	42	IGCM_debug_Print 3 " DefineArrayFromSection : ${comp}"
	43	IGCM_card_DefineArrayFromSection ${SUBMIT_DIR}/config.card ${comp}
	44	eval config_comp=\${config_${comp}[*]} > /dev/null 2>&1
	45	for option in ${config_comp[*]} ; do
[902]	46	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
[849]	47	done
	48	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
	49
[544]	50	# Debug Print :
	51	eval auxprint=\${config_${comp}_WriteFrequency}
	52	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
	53	#2> /dev/null
[2]	54
[544]	55	# Debug Print :
	56	IGCM_debug_Print 2 "Initialize following component library"
[522]	57
[544]	58	# Source drivers in directory DRIVER if it exist
	59	# else source them from directory COMP
	60	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
	61	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
	62	# Source component library
	63	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
	64	else
	65	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
	66	# Source component library
	67	. ${SUBMIT_DIR}/COMP/${compname}.driver
	68	fi
	69	IGCM_debug_Print 3 "With tag : ${comptagname}"
[2]	70
[544]	71	# Debug Print
	72	IGCM_debug_Print 3 "Initialize ${comp} output directory."
[2]	73
[544]	74	# Define ARCHIVED Dirs
	75	eval R_OUT_${comp}=${R_SAVE}/${comp}
	76	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
[2]	77
[544]	78	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
	79	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
[2]	80
[1413]	81	eval R_OUT_${comp}_A=\${R_OUT_${comp}}/Analyse
	82	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_A}
	83
[544]	84	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
[804]	85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
[2]	86
[544]	87	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
[804]	88	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
[2]	89
[544]	90	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
	91	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
	92	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
	93	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
	94
[1413]	95	eval R_OUT_${comp}_A_H=\${R_OUT_${comp}_A}/TS_HF
	96	eval R_OUT_${comp}_A_D=\${R_OUT_${comp}_A}/TS_DA
	97	eval R_OUT_${comp}_A_M=\${R_OUT_${comp}_A}/TS_MO
	98	eval R_OUT_${comp}_A_Y=\${R_OUT_${comp}_A}/TS_YE
	99
[544]	100	# Define BUFFERED Dirs
[1022]	101	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
[804]	102	eval R_BUF_${comp}=${R_BUFR}/${comp}
	103	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
[544]	104
[804]	105	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
	106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
[544]	107
[1413]	108	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
	109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
	110
[804]	111	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
	112	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
[544]	113
[804]	114	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
	115	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
[544]	116
[804]	117	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
	118	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
	119	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
	120	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
[1413]	121
	122	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
	123	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
	124	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
	125	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
	126
	127	# Define CMIP6 Dirs
[1431]	128	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
[804]	129	fi
[544]	130
	131	# Read UserChoices section of component card
	132	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
	133	IGCM_card_DefineArrayFromSection ${card} UserChoices
	134	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
[804]	135
[544]	136	# If section is not empty we define corresponding variables
	137	if [ X${first_option} != X"Error:" ] ; then
	138	if [ X${card_UserChoices[0]} != X ] ; then
[778]	139	unset card_UserChoices
[544]	140	fi
[833]	141	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
[544]	142	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
	143	for option in ${card_UserChoices[*]} ; do
[778]	144	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
	145	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
[544]	146	done
	147	fi
	148
	149	# Read and Build Output File stuff
	150	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
	151	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	152	ListFilesName=${compname}_OutputFiles_List
	153	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
	154	#
	155	if [ X${FileName0} != X${NULL_STR} ] ; then
	156	#
	157	#IGCM_debug_Print 1 "Component : ${compname}"
	158	#
	159	# INITIALISATION
	160	#
	161	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
	162	#
	163	i=2
	164	#
	165	until [ $i -ge $NbFiles ]; do
[778]	166	#
	167	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
	168	#
	169	if [ X${flag_post} != XNONE ] ; then
	170	#
[544]	171	# First of all
	172	#
[778]	173	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
[1151]	174	# This section is mandatory
	175	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
	176	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
	177	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
	178	IGCM_debug_Verif_Exit
	179	fi
[778]	180	#
	181	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
	182	#
	183	# variable option allready typeset above
	184	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
	185	if [ ${option} = Seasonal ] ; then
	186	FoundSeasonal=true
	187	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
	188	fi
	189	done
	190	#
	191	if [ ! X${FoundSeasonal} = Xtrue ] ; then
	192	eval ${compname}_${flag_post}_Seasonal=ON
	193	fi
	194	#
	195	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
	196	Seasonal=true
	197	fi
	198
	199	# Dimension = vide si vieille card.
	200	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
	201	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
	202	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
	203	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
	204	ListDimension[0]=2D
	205	ListDimension[1]=3D
	206	TimeSeries=false
	207	iLoop=${#ListDimension[*]}
	208	j=0
	209	until [ $j -ge ${iLoop} ]; do
	210	Dimension=${ListDimension[${j}]}
	211	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
	212	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
[544]	213	#
[778]	214	# Time series WITHOUT chunk
	215	#
	216	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
	217	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
	218	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
	219	eval TimeSeries${Dimension}=true
	220	fi
	221	fi
	222	#
	223	# Time series WITH chunk
	224	#
	225	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
	226	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
	227	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
	228	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
	229	eval TimeSeriesChunck${Dimension}=true
[829]	230	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
	231	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
	232	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
	233	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
[778]	234	fi
	235	fi
	236	(( j=j+1 ))
	237	done
	238	else
	239	ListDimension[0]=""
	240	TimeSeries=true
	241	TimeSeries2D=false
	242	TimeSeries3D=false
	243	TimeSeriesChunck2D=false
	244	TimeSeriesChunck3D=false
	245	fi
	246	fi
	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
[1504]	1033	# Test on compiler version for IPSLCM6* configuration on irene (only for CMIP6 production)
	1034	if [ ${SYSTEM} = irene ]; then
[1520]	1035	if ( [ X"$( 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 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.0.15 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM6.1 )" != "X" ] && [ X${compilerFull} != XV17 ] ) \|\| ( [ X"$( echo ${config_UserChoices_LongName} \| grep IPSLCM5A2.1 )" != "X" ] && [ X${compilerFull} != XV17 ] ) ; then
	1036	IGCM_debug_Exit "IPSLCM6.0.13, IPSLCM6.0.14, IPSLCM6.0.15, IPSLCM6.1 and IPSLCM5A2.1 must be compiled with intel 2017 compiler"
[1504]	1037	fi
[1415]	1038	fi
	1039
[1409]	1040	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
	1041	}
	1042
	1043	#=======================================================================
[269]	1044	function IGCM_comp_PeriodStart
	1045	{
[544]	1046	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
[269]	1047
[544]	1048	# Debug Print :
	1049	echo
	1050	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
	1051	echo
[269]	1052
[902]	1053	typeset ExeNameIn ExeNameOut
[544]	1054	typeset comp compname comptagname
	1055	for comp in ${config_ListOfComponents[*]} ; do
[902]	1056	# Define component
[544]	1057	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1058	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[269]	1059
[544]	1060	# Copy executable for this component
	1061	eval ExeNameIn=\${config_Executable_${comp}[0]}
[1486]	1062	eval ExeNameIn=${ExeNameIn}
[544]	1063	eval ExeNameOut=\${config_Executable_${comp}[1]}
[269]	1064
[544]	1065	# Debug Print
	1066	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
	1067	# UPDATE component
	1068	${comp}_PeriodStart 2> /dev/null
[269]	1069
[544]	1070	done
[269]	1071
[544]	1072	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
[269]	1073	}
	1074
[1166]	1075
	1076
[269]	1077	#=======================================================================
[1166]	1078	function IGCM_comp_modifyFile
	1079	{
	1080	#
	1081	# syntax: IGCM_comp_modifyFile filein key [value]
	1082	#
	1083	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
	1084	#
	1085	# This function is used to replace a pattern in a file for a specific variable.
	1086	#
	1087	# Arguments:
	1088	# - filein : the file in run directory in which the variable should be set
	1089	# - key : the variable to modify
	1090	# - value : the value to set the key equal to
	1091	#
	1092	IGCM_debug_PushStack "IGCM_comp_modifyFile"
	1093
	1094	typeset filein key value pattern
	1095
	1096	# Set local variables and test the arguments
	1097	if [ $# = 3 ] ; then
	1098	# Normal case with 3 arguments
	1099	filein=$1 ; key=$2 ; value=$3
	1100	else
	1101	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
	1102	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1103	return
	1104	fi
	1105	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
	1106
	1107	# Test if the file exist
	1108	if [ ! -f ${filein} ] ; then
	1109	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
	1110	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1111	return
	1112	fi
	1113
	1114	# Read the line with key in the file without the comments
	1115	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
	1116
	1117	# Verify the existance of the pattern
	1118	if [ X"${pattern}" = X ] ; then
	1119	# Variable key is not set in filein, stop.
	1120	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
	1121	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1122	return
	1123	fi
	1124
	1125	# Now change key in filein
[1176]	1126	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
	1127	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
[1166]	1128	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
	1129	\mv ${filein}.tmp ${filein}
	1130
	1131	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1132	}
	1133
	1134	#=======================================================================
[1069]	1135	function IGCM_comp_modifyDefFile
	1136	{
	1137	#
	1138	# syntax: IGCM_comp_modifyDefFile type filein key [value]
	1139	#
	1140	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
	1141	#
	1142	# This function is used to modify a parameter file for a specific variable.
[1075]	1143	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
	1144	# This function can be used in the comp.driver files for the components.
[1069]	1145	#
[1075]	1146	# Arguments:
[1081]	1147	# - type : first argument must be blocker, nonblocker or force
[1075]	1148	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1069]	1149	# otherwise this function will exit.
[1075]	1150	# For "nonblocker" case, the user can remove or modify the variable. For
	1151	# this case, as long as AUTO is not set, no modification will be done.
[1081]	1152	# For "force" case, the variable will be modified even if it is not set to AUTO
[1069]	1153	# - filein : the file in run directory of .def type in which the variable should be set
	1154	# - key : the variable to modify
[1075]	1155	# - value : the value to set the key equal to, optional. If value is not set or if
[1069]	1156	# value=DEFAULT, then a default value must be given in filein using syntax :
	1157	# key= AUTO : DEFAULT=def_value
	1158	#
[1075]	1159	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
[1069]	1160
[1166]	1161	typeset type filein key value
	1162	typeset filelist nb_occ modify
	1163
[1075]	1164	# Set local variables and test the arguments
	1165	if [ $# = 4 ] ; then
	1166	# Normal case with 4 arguments
	1167	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1168	elif [ $# = 3 ] ; then
	1169	# Normal case with 3 arguments
	1170	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1171	else
	1172	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
[1079]	1173	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1174	return
	1175	fi
[1166]	1176	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
[1069]	1177
[1075]	1178	# Test if first argument is correct
[1166]	1179	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1081]	1180	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
[1079]	1181	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1182	return
	1183	fi
[1069]	1184
[1215]	1185	# Test if the file exist.
	1186	# Exit with error if the file does not exist for the case blocker or force.
	1187	# Only return for the case nonblocker.
[1075]	1188	if [ ! -f ${filein} ] ; then
[1215]	1189	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1190	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
	1191	else
	1192	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
	1193	fi
[1079]	1194	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1195	return
	1196	fi
[1069]	1197
[1102]	1198	# Define list of files to test using all files with suffix .def (except used*.def)
	1199	filelist=$( ls *def \| grep -v used )
[1069]	1200
[1075]	1201	# Count number of occurances for the key in all files
[1166]	1202	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
[1069]	1203
[1075]	1204	# Test if key is set several times
[1166]	1205	if [ ${nb_occ} -gt 1 ] ; then
	1206	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
[1079]	1207	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1208	return
	1209	fi
	1210
	1211	# Treatement according to different cases
[1166]	1212	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
[1075]	1213	# Stop if the key is never set and the function is blocker
[1166]	1214	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
	1215	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
	1216	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
[1075]	1217	# The key is not set but it is a nonblocker call so nothing is done.
[1166]	1218	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1219	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
[1081]	1220	modify=no
[1166]	1221	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
[1075]	1222	# Variable key is not set in filein, stop.
[1166]	1223	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1081]	1224	fi
	1225
	1226	# Check if AUTO is set in the filein on the same line as the key variable
[1166]	1227	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1228	# Modification will be done for all cases
	1229	modify=yes
	1230	else
	1231	# The variable was not set to AUTO
[1166]	1232	if [ ${type} = blocker ] ; then
[1156]	1233	# Exit because this is a blocker call
[1166]	1234	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
[1190]	1235	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1156]	1236	return
[1166]	1237	elif [ ${type} = nonblocker ] ; then
[1156]	1238	# Do nothing. Suppose that the user did set the variable correct
[1166]	1239	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
[1156]	1240	modify=no
[1166]	1241	elif [ ${type} = force ] ; then
[1156]	1242	# Force modification
[1166]	1243	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
[1081]	1244	modify=yes
[1156]	1245	fi
[1081]	1246	fi
[1069]	1247
[1081]	1248	# Do the modifcation now
[1166]	1249	if [ ${modify} = yes ] ; then
[1081]	1250
[1156]	1251	# For option DEFAULT, read default value from file.
[1166]	1252	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1253	# Case to set DEFAULT value
	1254	# Read default value from filein
[1423]	1255	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
[1069]	1256
[1166]	1257	if [ X"${value}" = X ] ; then
	1258	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
	1259	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
	1260	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1261	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
	1262	return
[1075]	1263	fi
[1156]	1264	fi
[1069]	1265
[1156]	1266	# Now change key in filein
[1166]	1267	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
	1268	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
	1269	\mv ${filein}.tmp ${filein}
[1075]	1270	fi
[1079]	1271	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1069]	1272	}
	1273
	1274	#=======================================================================
[1085]	1275	function IGCM_comp_modifyNamelist
	1276	{
	1277	#
	1278	# syntax: IGCM_comp_modifyNamelist type filein key [value]
	1279	#
	1280	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
	1281	#
	1282	# This function is used to modify a parameter file for a specific variable.
[1155]	1283	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
[1085]	1284	# This function can be used in the comp.driver files for the components.
	1285	#
	1286	# Arguments:
	1287	# - type : first argument must be blocker, nonblocker or force
	1288	# For "blocker" case, the variable must be attributed the keyworld AUTO
	1289	# otherwise this function will exit.
	1290	# For "nonblocker" case, the user can remove or modify the variable. For
	1291	# this case, as long as AUTO is not set, no modification will be done.
	1292	# For "force" case, the variable will be modified even if it is not set to AUTO
	1293	# - filein : the file in run directory of .def type in which the variable should be set
	1294	# - key : the variable to modify
	1295	# - value : the value to set the key equal to, optional. If value is not set or if
	1296	# value=DEFAULT, then a default value must be given in filein using syntax :
	1297	# key= AUTO : DEFAULT=def_value
	1298	#
	1299	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
	1300
[1166]	1301	typeset type filein key value pattern modify
	1302
[1085]	1303	# Set local variables and test the arguments
	1304	if [ $# = 4 ] ; then
	1305	# Normal case with 4 arguments
	1306	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1307	elif [ $# = 3 ] ; then
	1308	# Normal case with 3 arguments
	1309	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1310	else
	1311	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
	1312	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1313	return
	1314	fi
[1166]	1315	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
[1085]	1316
	1317	# Test if first argument is correct
[1166]	1318	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1085]	1319	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
	1320	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1321	return
	1322	fi
	1323
[1215]	1324	# Test if the file exist.
	1325	# Exit with error if the file does not exist for the case blocker or force.
	1326	# Only return for the case nonblocker.
[1085]	1327	if [ ! -f ${filein} ] ; then
[1215]	1328	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1329	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
	1330	else
	1331	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
	1332	fi
[1085]	1333	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1334	return
	1335	fi
	1336
	1337	# Read the line with key in the file without the comments
[1166]	1338	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
[1155]	1339
[1085]	1340	# Verify the existance of the pattern
	1341	if [ X"$pattern" = X ] ; then
[1156]	1342	# Variable key is not set in filein, stop.
[1166]	1343	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1156]	1344	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1345	return
[1085]	1346	fi
[1155]	1347
[1085]	1348	# Check if the variable is set to AUTO in the filein
	1349	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1350	# Modification will be done for all cases
	1351	modify=yes
	1352	else
	1353	# The variable was not set to AUTO
[1166]	1354	if [ ${type} = blocker ] ; then
[1156]	1355	# Exit because this is a blocker call
[1166]	1356	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
[1156]	1357	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1358	return
[1166]	1359	elif [ ${type} = nonblocker ] ; then
[1156]	1360	# Do nothing. Suppose that the user did set the variable correct
[1166]	1361	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
[1156]	1362	modify=no
[1166]	1363	elif [ ${type} = force ] ; then
[1156]	1364	# Force modification
[1166]	1365	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
[1085]	1366	modify=yes
[1156]	1367	fi
[1085]	1368	fi
	1369
	1370	# Do the modifcation now
[1166]	1371	if [ ${modify} = yes ] ; then
[1085]	1372
[1156]	1373	# For option DEFAULT, read default value from file.
[1166]	1374	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1375	# Case to set DEFAULT value
	1376	# Read default value from filein
	1377	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
[1085]	1378
[1166]	1379	if [ X"${value}" = X ] ; then
	1380	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
	1381	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
	1382	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1383	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1384	return
[1085]	1385	fi
[1156]	1386	fi
[1085]	1387
[1156]	1388	# Now change key in filein
[1166]	1389	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
	1390	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
	1391	\mv ${filein}.tmp ${filein}
[1085]	1392	fi
	1393	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1394	}
	1395
	1396	#=======================================================================
[1074]	1397	function IGCM_comp_modifyXmlFile
	1398	{
	1399	#
	1400	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
	1401	#
	1402	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
	1403	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
	1404	#
	1405	# This function is used to modify the value for a specific attribute and variable id.
[1155]	1406	# The file must be a valid xml file.
[1075]	1407	# This function can be used in the comp.driver files for the components.
[1074]	1408	#
[1075]	1409	# Arguments:
	1410	# - type : first argument must be blocker, nonblocker or force.
	1411	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1074]	1412	# otherwise this function will exit.
[1075]	1413	# For "nonblocker" case, the user can remove or modify the variable. For
[1074]	1414	# this case, as long as AUTO is not set, no modification will be done.
[1075]	1415	# For "force" case, the variable will be modified even if it is not set to AUTO
[1074]	1416	# - filein : the file in run directory of .xml type in which the variable should be set
	1417	# - keyid : the variable to modify
	1418	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
	1419	# - value : the value to set in the filein
	1420	#
[1075]	1421	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
[1074]	1422
[1166]	1423	typeset type filein keyid keyattrib value modify
	1424
[1075]	1425	# Set local variables and test the arguments
	1426	if [ $# = 5 ] ; then
	1427	# Normal case with 4 arguments
	1428	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
	1429	else
	1430	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
[1089]	1431	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1432	return
	1433	fi
[1166]	1434	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
[1074]	1435
[1075]	1436	# Test if first argument is correct
[1166]	1437	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1075]	1438	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
[1089]	1439	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1440	return
	1441	fi
[1074]	1442
[1215]	1443	# Test if the file exist.
	1444	# Exit with error if the file does not exist for the case blocker or force.
	1445	# Only return for the case nonblocker.
[1075]	1446	if [ ! -f ${filein} ] ; then
[1215]	1447	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1448	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
	1449	else
	1450	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
	1451	fi
[1089]	1452	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1453	return
	1454	fi
	1455
[1386]	1456	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
[1166]	1457	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
[1386]	1458	if [ ${type} = nonblocker ] ; then
	1459	# This is a nonblocker case, print warning but do nothing else
	1460	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1461	else
	1462	# This is a blocker or force case : stop now
	1463	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
	1464	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
	1465	return
	1466	fi
[1075]	1467	fi
	1468
	1469	# Check if AUTO is set on the same line as keyid and keyattrib
[1166]	1470	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
[1394]	1471	# Modification will be done
[1075]	1472	modify=yes
	1473	else
[1166]	1474	if [ ${type} = blocker ] ; then
[1075]	1475	# Exit, the variable must be set to AUTO
[1166]	1476	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
[1089]	1477	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1478	return
[1166]	1479	elif [ ${type} = nonblocker ] ; then
[1075]	1480	# Nothing will be done
	1481	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
	1482	modify=no
[1166]	1483	elif [ ${type} = force ] ; then
[1075]	1484	# Force modification
[1166]	1485	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
[1075]	1486	modify=yes
[1074]	1487	fi
[1075]	1488	fi
[1074]	1489
[1075]	1490	# Do the modifcation now
[1166]	1491	if [ ${modify} = yes ] ; then
	1492	if [ ${keyattrib} = NONE ] ; then
[1075]	1493	# Case to modify the variable itself
	1494	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
[1166]	1495	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
[1074]	1496	else
[1156]	1497	# Check if keyattrib is set on the same line as keyid
[1166]	1498	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
[1156]	1499	# Case to modify the attribute value
	1500	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
[1166]	1501	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
[1156]	1502	else
	1503	# Case to add the attribute and its value
	1504	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
[1166]	1505	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
[1156]	1506	fi
[1074]	1507	fi
[1166]	1508	\mv ${filein}.tmp ${filein}
[1075]	1509	fi
	1510	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1074]	1511	}
	1512
	1513	#=======================================================================
[2]	1514	function IGCM_comp_Update
	1515	{
[544]	1516	IGCM_debug_PushStack "IGCM_comp_Update"
[2]	1517
[1409]	1518	# Debug Print :
[544]	1519	echo
	1520	IGCM_debug_Print 1 "IGCM_comp_Update"
	1521	echo
[2]	1522
[544]	1523	typeset comp compname comptagname
	1524	for comp in ${config_ListOfComponents[*]} ; do
[902]	1525	# Define component
[544]	1526	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1527	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1528
[544]	1529	# Debug Print
	1530	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
	1531	# UPDATE component
	1532	${comp}_Update
[2]	1533
[1413]	1534	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
	1535	if [ -f timeseries_def_${compname}.xml ]; then
	1536	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
	1537	for line in $( cat ts.temp.${compname}.txt ); do
	1538	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
	1539	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
	1540	case ${output_freq} in
	1541	Y\|y)
	1542	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
	1543	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
	1544	;;
	1545	MO\|mo)
	1546	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
	1547	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
	1548	;;
	1549	D\|d)
	1550	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
	1551	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
	1552	;;
	1553	S\|s)
	1554	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
	1555	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
	1556	;;
	1557	esac
	1558	done
	1559	fi
	1560
	1561	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
	1562	if [ -f dr2xml_${compname}.xml ]; then
[1535]	1563	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
	1564	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
	1565	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
	1566	# Modify path from dr2xml_{compname}.xml
	1567	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
[1552]	1568	${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]	1569	else
	1570	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
	1571	fi
	1572	# Overwrite the original file
	1573	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
[1467]	1574	fi
[1422]	1575	fi
[544]	1576	done
[2]	1577
[544]	1578	IGCM_debug_PopStack "IGCM_comp_Update"
[2]	1579	}
	1580
	1581	#=======================================================================
	1582	function IGCM_comp_Finalize
	1583	{
[544]	1584	IGCM_debug_PushStack "IGCM_comp_Finalize"
[2]	1585
[544]	1586	# Debug Print :
	1587	echo
	1588	IGCM_debug_Print 1 "IGCM_comp_Finalize"
	1589	echo
[2]	1590
[544]	1591	typeset ListTextName TextName0
	1592	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
	1593	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
[1165]	1594	typeset -Z4 j4 #BASH declare j4
[544]	1595	typeset list_file nlist_file
	1596	typeset compactoutputs
[429]	1597
[1165]	1598	# Initialize array hosting list of rebuilded files to copy
	1599	unset rebuildedActionsList
	1600
	1601	# Text compacting options
[544]	1602	compactoutputs=false
	1603	if [ X${JobType} != XRUN ] ; then
	1604	compactoutputs=true
	1605	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
	1606	compactoutputs=true
	1607	fi
[433]	1608
[1043]	1609	# Prepare headers for the shell dedicated to offline rebuild
	1610	if [ X${AsynchronousRebuild} = Xtrue ] ; then
	1611	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1612	if [ ${DRYRUN} -le 1 ] ; then
	1613	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1614	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1615	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1616	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1617	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1618	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1619	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1620	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1621	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1622	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1623	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1624	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1625	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1626	fi
	1627	fi
	1628
[544]	1629	for comp in ${config_ListOfComponents[*]} ; do
[902]	1630	# Define component
[544]	1631	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1632	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1633
[544]	1634	# Debug Print
	1635	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
	1636	# FINALIZE component
	1637	${comp}_Finalize
[2]	1638
[778]	1639	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	1640
[804]	1641	# Save Output Text files of models
	1642	#---------------------------------
	1643	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
	1644	IGCM_card_DefineArrayFromOption ${card} OutputText List
	1645	ListTextName=${compname}_OutputText_List
	1646
	1647	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
	1648	if [ X${TextName0} != X${NULL_STR} ] ; then
	1649	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
	1650
	1651	(( i=0 ))
	1652	until [ $i -eq $NbFiles ]; do
	1653	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
	1654	eval file_out=${PREFIX}_${file_in}
	1655
	1656	(( i=i+1 ))
	1657
	1658	unset list_file
	1659	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
	1660	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
	1661	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 )
	1662	nlist_file=${#list_file[@]}
	1663	if [ ${nlist_file} -gt 1 ] ; then
	1664	if ( ${compactoutputs} ) ; then
	1665	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
	1666	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
	1667	echo ${list_file[*]} > ${file_out}
	1668	echo "" >> ${file_out}
	1669
	1670	(( i_ = 0 ))
[1080]	1671	for file in ${list_file[@]} ; do
[804]	1672	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
	1673	echo "\| " ${i_} " " ${file} >> ${file_out}
	1674	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
[999]	1675	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
[804]	1676	echo "" >> ${file_out}
	1677	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1678	(( i_ = i_ + 1 ))
	1679	done
[1080]	1680	if ( ${ExecutionFail} ) ; then
	1681	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
	1682	fi
	1683
[804]	1684	if [ X${Pack} = Xtrue ] ; then
	1685	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
	1686	else
	1687	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
	1688	fi
[1080]	1689
[804]	1690	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
[1080]	1691	else
	1692	for file in ${list_file[@]} ; do
	1693	if ( ${ExecutionFail} ) ; then
	1694	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
	1695	fi
[804]	1696
	1697	if [ X${Pack} = Xtrue ] ; then
	1698	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
	1699	else
	1700	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
	1701	fi
[1080]	1702
[804]	1703	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1704	done
	1705	fi
	1706	else
	1707	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
	1708	eval IGCM_sys_Mv ${file_in}* ${file_in}
	1709	fi
[1080]	1710
	1711	if ( ${ExecutionFail} ) ; then
	1712	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
	1713	fi
	1714
[804]	1715	if [ X${Pack} = Xtrue ] ; then
	1716	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
	1717	else
	1718	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
	1719	fi
	1720	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1721	fi
	1722	done
	1723	fi
	1724
[544]	1725	# Save Restarts files
	1726	#--------------------
	1727	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
	1728	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	1729	ListFilesName=${compname}_RestartFiles_List
	1730	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	1731
[544]	1732	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	1733	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[778]	1734
[544]	1735	(( i=0 ))
	1736	until [ $i -ge $NbFiles ]; do
[778]	1737	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1738	eval file_in=${file_in_}
[2]	1739
[778]	1740	(( i_ = i+1 ))
	1741	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1742	eval file_out=${file_out_}
[151]	1743
[778]	1744	(( i_ = i+2 ))
	1745	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1746	eval file_outin=${file_outin_}
[151]	1747
[778]	1748	generic_restart_file_name_in=$( basename ${file_in} .nc )
	1749	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
	1750	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
[2]	1751
[902]	1752	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
[778]	1753	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	1754	j=0 # BASH LINE NOT NEEDED
	1755	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	1756	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	1757	j4=${j} # BASH LINE NOT NEEDED
[778]	1758	if [ X${Pack} = Xtrue ] ; then
	1759	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1760	else
	1761	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1762	fi
	1763	if [ ! ${file_in} = ${file_outin} ] ; then
	1764	if ( ${ExitFlag} ) ; then
	1765	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
	1766	else
	1767	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
	1768	fi
	1769	fi
[821]	1770	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	1771	done
	1772	else
	1773	if [ X${Pack} = Xtrue ] ; then
	1774	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1775	else
	1776	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1777	fi
	1778	if [ ! ${file_in} = ${file_outin} ] ; then
	1779	if ( ${ExitFlag} ) ; then
	1780	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
	1781	else
	1782	IGCM_sys_Mv ${file_in} ${file_outin}
	1783	fi
	1784	fi
	1785	fi
	1786
	1787	(( i=i+3 ))
[544]	1788	done
	1789	else
	1790	if [ X${FileName0} != XNONE ] ; then
[778]	1791	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
[544]	1792	else
[778]	1793	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
[544]	1794	fi
	1795	fi
[2]	1796
[544]	1797	# Save Output files
	1798	#------------------
	1799	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
	1800	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	1801	ListFilesName=${compname}_OutputFiles_List
	1802	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	1803
[544]	1804	if [ X${FileName0} != X${NULL_STR} ] ; then
	1805	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[149]	1806
[544]	1807	(( i=0 ))
	1808	until [ $i -ge $NbFiles ]; do
[778]	1809	SaveOnArchive=true
	1810	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1811	eval file_in=${file_in_}
	1812	(( i_ = i+1 ))
	1813	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1814	eval file_out=${file_out_}
	1815	#
	1816	# Override file_out path remplacing R_SAVE by R_BUFR
	1817	#
	1818	if [ X${Pack} = Xtrue ] ; then
	1819	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
	1820	fi
	1821	#
	1822	# Not necessarily the best option. /!\ Potential side effects /!\
	1823	#
	1824	(( i_ = i+2 ))
	1825	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1826	#
	1827	generic_file_name=$( basename ${file_in} .nc )
	1828	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
	1829	#
	1830	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
[804]	1831	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
[778]	1832	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
	1833	elif [ ${nb_rebuild_file} -gt 1 ] ; then
[804]	1834	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
[778]	1835	if [ X${AsynchronousRebuild} = Xfalse ] ; then
	1836	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
[1388]	1837	#
	1838	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
	1839	if [ ${file_in} = output.abort.nc ] ; then
	1840	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
	1841	else
[1429]	1842	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
[1388]	1843	fi
[778]	1844	else
	1845	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
[1429]	1846	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
[544]	1847
[778]	1848	# Prepare the shell dedicated to offline rebuild
	1849	if [ $DRYRUN -le 1 ]; then
[694]	1850	if [ ${file_in} = histstn.nc ] ; then
	1851	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1852	else
[980]	1853	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[694]	1854	fi
[1206]	1855	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1856	fi
	1857	#
	1858	# Load Patch we need to apply and apply
	1859	if [ $DRYRUN -le 1 ]; then
	1860	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
[1080]	1861	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1862	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1863	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1864	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1865	done
	1866	fi
	1867	fi
	1868	#
	1869	if [ $DRYRUN -le 1 ]; then
	1870	if [ X${Pack} = Xtrue ] ; then
[1165]	1871	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
[778]	1872	else
[1165]	1873	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
[778]	1874	fi
[1206]	1875	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
[1165]	1876	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
[778]	1877	fi
	1878	SaveOnArchive=false
	1879	fi
	1880	fi
	1881	#
	1882	if [ ${SaveOnArchive} = true ] ; then
	1883	#
	1884	# Rebuild has been done online or it was not needed
	1885	#
	1886	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
	1887	#
	1888	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
[1289]	1889	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
[778]	1890	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1891	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
	1892	#
	1893	if [ $DRYRUN -le 1 ]; then
[1080]	1894	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1895	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1896	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1897	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1898	done
	1899	#
	1900	if [ X${Pack} = Xtrue ] ; then
	1901	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1902	else
	1903	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1904	fi
[1206]	1905	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1906	#
	1907	fi
	1908	else
	1909	#
	1910	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
	1911	#
	1912	if [ X${Pack} = Xtrue ] ; then
	1913	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
	1914	else
	1915	IGCM_sys_Put_Out ${file_in} ${file_out}
	1916	fi
	1917	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1918	if [ ${nb_rebuild_file} -gt 1 ] ; then
	1919	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
	1920	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
	1921	done
	1922	fi
	1923	fi
	1924	fi
	1925	(( i=i+3 ))
[544]	1926	done
	1927	fi
	1928	echo
	1929	done
[1165]	1930	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
	1931	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
[1166]	1932	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1165]	1933	i=0
	1934	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
	1935	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1936	(( i=i+1 ))
	1937	done
	1938	fi
[544]	1939	IGCM_debug_PopStack "IGCM_comp_Finalize"
[2]	1940	}

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