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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1448

Last change on this file since 1448 was 1447, checked in by sdipsl, 6 years ago
Fix the Adhoc exception for CMIP6
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: 79.6 KB

Rev	Line
[2]	1	#!/bin/ksh
	2
	3	#**************************************************************
	4	# Author: Sebastien Denvil, Martial Mancip
[373]	5	# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr Martial.Mancip__at__ipsl.jussieu.fr
	6	# $Revision:: $ Revision of last commit
	7	# $Author:: $ Author of last commit
	8	# $Date:: $ Date of last commit
[2]	9	# IPSL (2006)
	10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
	11	#
	12	#**************************************************************
	13
	14	#========================================================================
	15	function IGCM_comp_Initialize
	16	{
[544]	17	IGCM_debug_PushStack "IGCM_comp_Initialize"
[2]	18
[778]	19	# Debug Print :
[544]	20	echo
	21	IGCM_debug_Print 1 "IGCM_comp_Initialize"
	22	echo
[2]	23
[1244]	24	typeset comp compname comptagname auxprint card_UserChoices first_option option i j
[544]	25	for comp in ${config_ListOfComponents[*]} ; do
[2]	26
[902]	27	# Define component
[544]	28	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
	29	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	30	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[457]	31
[615]	32	# Debug Print
	33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
	34
[1244]	35	# ${compname}.card PATH
[544]	36	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	37
[544]	38	# Manage component executable
	39	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
[2]	40
[849]	41	# Define all options in section [comp]
	42	IGCM_debug_Print 3 " DefineArrayFromSection : ${comp}"
	43	IGCM_card_DefineArrayFromSection ${SUBMIT_DIR}/config.card ${comp}
	44	eval config_comp=\${config_${comp}[*]} > /dev/null 2>&1
	45	for option in ${config_comp[*]} ; do
[902]	46	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
[849]	47	done
	48	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
	49
[544]	50	# Debug Print :
	51	eval auxprint=\${config_${comp}_WriteFrequency}
	52	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
	53	#2> /dev/null
[2]	54
[544]	55	# Debug Print :
	56	IGCM_debug_Print 2 "Initialize following component library"
[522]	57
[544]	58	# Source drivers in directory DRIVER if it exist
	59	# else source them from directory COMP
	60	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
	61	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
	62	# Source component library
	63	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
	64	else
	65	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
	66	# Source component library
	67	. ${SUBMIT_DIR}/COMP/${compname}.driver
	68	fi
	69	IGCM_debug_Print 3 "With tag : ${comptagname}"
[2]	70
[544]	71	# Debug Print
	72	IGCM_debug_Print 3 "Initialize ${comp} output directory."
[2]	73
[544]	74	# Define ARCHIVED Dirs
	75	eval R_OUT_${comp}=${R_SAVE}/${comp}
	76	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
[2]	77
[544]	78	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
	79	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
[2]	80
[1413]	81	eval R_OUT_${comp}_A=\${R_OUT_${comp}}/Analyse
	82	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_A}
	83
[544]	84	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
[804]	85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
[2]	86
[544]	87	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
[804]	88	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
[2]	89
[544]	90	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
	91	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
	92	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
	93	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
	94
[1413]	95	eval R_OUT_${comp}_A_H=\${R_OUT_${comp}_A}/TS_HF
	96	eval R_OUT_${comp}_A_D=\${R_OUT_${comp}_A}/TS_DA
	97	eval R_OUT_${comp}_A_M=\${R_OUT_${comp}_A}/TS_MO
	98	eval R_OUT_${comp}_A_Y=\${R_OUT_${comp}_A}/TS_YE
	99
[544]	100	# Define BUFFERED Dirs
[1022]	101	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
[804]	102	eval R_BUF_${comp}=${R_BUFR}/${comp}
	103	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
[544]	104
[804]	105	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
	106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
[544]	107
[1413]	108	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
	109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
	110
[804]	111	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
	112	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
[544]	113
[804]	114	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
	115	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
[544]	116
[804]	117	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
	118	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
	119	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
	120	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
[1413]	121
	122	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
	123	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
	124	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
	125	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
	126
	127	# Define CMIP6 Dirs
[1431]	128	eval CMIP6_BUF_${comp}=${R_CMIP}/CMIP6/${comp}
[804]	129	fi
[544]	130
	131	# Read UserChoices section of component card
	132	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
	133	IGCM_card_DefineArrayFromSection ${card} UserChoices
	134	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
[804]	135
[544]	136	# If section is not empty we define corresponding variables
	137	if [ X${first_option} != X"Error:" ] ; then
	138	if [ X${card_UserChoices[0]} != X ] ; then
[778]	139	unset card_UserChoices
[544]	140	fi
[833]	141	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
[544]	142	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
	143	for option in ${card_UserChoices[*]} ; do
[778]	144	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
	145	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
[544]	146	done
	147	fi
	148
	149	# Read and Build Output File stuff
	150	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
	151	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	152	ListFilesName=${compname}_OutputFiles_List
	153	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
	154	#
	155	if [ X${FileName0} != X${NULL_STR} ] ; then
	156	#
	157	#IGCM_debug_Print 1 "Component : ${compname}"
	158	#
	159	# INITIALISATION
	160	#
	161	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
	162	#
	163	i=2
	164	#
	165	until [ $i -ge $NbFiles ]; do
[778]	166	#
	167	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
	168	#
	169	if [ X${flag_post} != XNONE ] ; then
	170	#
[544]	171	# First of all
	172	#
[778]	173	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
[1151]	174	# This section is mandatory
	175	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
	176	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
	177	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
	178	IGCM_debug_Verif_Exit
	179	fi
[778]	180	#
	181	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
	182	#
	183	# variable option allready typeset above
	184	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
	185	if [ ${option} = Seasonal ] ; then
	186	FoundSeasonal=true
	187	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
	188	fi
	189	done
	190	#
	191	if [ ! X${FoundSeasonal} = Xtrue ] ; then
	192	eval ${compname}_${flag_post}_Seasonal=ON
	193	fi
	194	#
	195	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
	196	Seasonal=true
	197	fi
	198
	199	# Dimension = vide si vieille card.
	200	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
	201	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
	202	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
	203	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
	204	ListDimension[0]=2D
	205	ListDimension[1]=3D
	206	TimeSeries=false
	207	iLoop=${#ListDimension[*]}
	208	j=0
	209	until [ $j -ge ${iLoop} ]; do
	210	Dimension=${ListDimension[${j}]}
	211	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
	212	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
[544]	213	#
[778]	214	# Time series WITHOUT chunk
	215	#
	216	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
	217	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
	218	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
	219	eval TimeSeries${Dimension}=true
	220	fi
	221	fi
	222	#
	223	# Time series WITH chunk
	224	#
	225	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
	226	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
	227	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
	228	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
	229	eval TimeSeriesChunck${Dimension}=true
[829]	230	eval CHUNCK${Dimension}_COMP[\${#CHUNCK${Dimension}_COMP[*]}]=${comp}
	231	eval CHUNCK${Dimension}_FLAG[\${#CHUNCK${Dimension}_FLAG[*]}]=${i}
	232	eval CHUNCK${Dimension}_NAME[\${#CHUNCK${Dimension}_NAME[*]}]=${flag_post}
	233	eval CHUNCK${Dimension}_SIZE[\${#CHUNCK${Dimension}_SIZE[*]}]=${chunck_size}
[778]	234	fi
	235	fi
	236	(( j=j+1 ))
	237	done
	238	else
	239	ListDimension[0]=""
	240	TimeSeries=true
	241	TimeSeries2D=false
	242	TimeSeries3D=false
	243	TimeSeriesChunck2D=false
	244	TimeSeriesChunck3D=false
	245	fi
	246	fi
	247	(( i=i+3 ))
[544]	248	done
	249	fi
	250	# Debug Print
	251	IGCM_debug_Print 3 "Initialize ${compname} with driver."
	252	# INIT component
	253	${comp}_Initialize
	254	echo
	255	done
[2]	256
[544]	257	IGCM_debug_PopStack "IGCM_comp_Initialize"
[2]	258	}
	259
	260	#=======================================================================
	261	function IGCM_comp_PrepareDeletedFiles
	262	{
[544]	263	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
[778]	264
[544]	265	if [ X${2} != X. ] ; then
	266	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
	267	else
	268	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
	269	fi
[2]	270
[544]	271	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
[2]	272	}
	273
	274	#=======================================================================
[1338]	275	function IGCM_comp_PrepareXiosFiles
	276	{
	277	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
	278
	279	typeset file
	280	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
	281
	282	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
	283	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
	284	fi
	285	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
	286	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
	287	fi
[1413]	288	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
	289	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
	290	fi
[1338]	291
	292	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
	293	}
	294
	295	#=======================================================================
[2]	296	function IGCM_comp_GetInputInitialStateFiles
	297	{
[544]	298	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
[2]	299
[544]	300	# Debug Print :
	301	echo
	302	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
	303	echo
[2]	304
[902]	305	# Only the first time step need InitialStateFiles
[544]	306	# otherwise it's BoundaryConditions
	307	if ( ${FirstInitialize} ) ; then
[902]	308	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	309	typeset file_in_ file_in file_out_ file_out do_init
[544]	310	for comp in ${config_ListOfComponents[*]} ; do
	311	# Initialize
	312	do_init="y"
	313	# Do we need to bring initial state file for this component
[1401]	314	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[778]	315	eval do_init="n"
[544]	316	else
[778]	317	# Read component Restarts parameters
	318	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	319	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
	320	if [ "${do_start}" = "y" ] ; then
	321	do_init="n"
	322	else
	323	do_init="y"
	324	fi
[544]	325	fi
[2]	326
[544]	327	if [ "${do_init}" = "y" ] ; then
[902]	328	# Define component
[778]	329	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	330	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	331
[778]	332	# Debug Print :
	333	IGCM_debug_Print 3 "Initialisation files ${compname}"
[2]	334
[778]	335	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	336
[778]	337	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
	338	ListFilesName=${compname}_InitialStateFiles_List
[2]	339
[778]	340	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
	341	if [ X${FileName0} != X${NULL_STR} ] ; then
	342	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
	343	(( i=0 ))
	344	until [ $i -ge $NbFiles ]; do
	345	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	346	eval file_in=${file_in_}
	347	(( i_ = i+1 ))
	348	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	349	eval file_out=${file_out_}
[2]	350
[778]	351	IGCM_sys_IsFileArchived ${file_in}
	352	if [ $? = 0 ] ; then
	353	IGCM_sys_Get ${file_in} ${file_out}
	354	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	355	else
	356	IGCM_sys_Cp ${file_in} ${file_out}
	357	fi
	358	(( i=i+2 ))
	359	done
	360	fi
[544]	361	fi
	362	done
	363	fi
	364	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
[2]	365	}
	366
	367	#=======================================================================
[247]	368	# Definition of Smooth modulo function
[902]	369	# usage :
[247]	370	# IGCM_SmoothModulo StringModulo value
	371	#
	372	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
	373	# [min]:[modulo:][max]
	374	# where :
[902]	375	# [] value are optionnals;
[247]	376	# empty min equal 1
	377	# empty max equal infinity
	378	# modulo not given or empty equal 1
	379	# empty string or just ':' equal always.
	380	#
	381	# value : the value to test with the definition
	382	#
[902]	383	# return : true(1)/false(0)
[247]	384	function IGCM_SmoothModulo
	385	{
[544]	386	IGCM_debug_PushStack "IGCM_SmoothModulo"
	387	typeset defVector ModValue
[247]	388
[544]	389	eval set +A defVector -- $( echo "${1}" \| \
	390	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
[247]	391
[544]	392	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
	393	arr[1]=${defVector[0]}
	394	arr[2]=${defVector[2]}
[412]	395
[902]	396	# Test limits :
	397	# ${defVector[0]} <= ${2} <= ${defVector[2]}
[544]	398	# or ${defVector[2]} == -1
	399	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
	400	# Test modulo
	401	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
	402	if [ ${ModValue} -eq 0 ] ; then
	403	arr[3]=true
	404	echo ${arr[@]}
	405	IGCM_debug_PopStack "IGCM_SmoothModulo"
	406	return 1
[247]	407	else
[544]	408	arr[3]=false
	409	echo ${arr[@]}
	410	IGCM_debug_PopStack "IGCM_SmoothModulo"
	411	return 0
[247]	412	fi
[544]	413	else
	414	arr[3]=false
	415	echo ${arr[@]}
	416	IGCM_debug_PopStack "IGCM_SmoothModulo"
	417	return 0
	418	fi
[247]	419	}
	420
	421	#=======================================================================
	422	function IGCM_comp_GetInputSmoothFiles
	423	{
[544]	424	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
[247]	425
[544]	426	# Debug Print :
	427	echo
	428	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
	429	echo
[247]	430
[544]	431	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
	432	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
[247]	433
[544]	434	for comp in ${config_ListOfComponents[*]} ; do
	435	# Define component
	436	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	437	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[247]	438
[544]	439	# Debug Print :
	440	IGCM_debug_Print 3 "Smooth files ${compname}"
[247]	441
[544]	442	card=${SUBMIT_DIR}/COMP/${compname}.card
[247]	443
[544]	444	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
	445	ListFilesName=${compname}_SmoothFiles_List
	446	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[247]	447
[544]	448	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
	449	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[247]	450
[544]	451	(( i=0 ))
	452	until [ $i -ge $NbFiles ]; do
[778]	453	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	454	eval file_in=${file_in_}
	455	(( i_ = i+1 ))
	456	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	457	eval file_out=${file_out_}
[247]	458
[778]	459	# define CumulPeriod definition for this file
	460	(( i__ = i+2 ))
	461	eval SmoothDef=\${${ListFilesName}[$i__]}
	462	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
	463	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
	464	j=1
	465	for val in ${aux} ; do
	466	[ ${j} -eq 1 ] && SmoothMin=${val}
	467	[ ${j} -eq 2 ] && SmoothMax=${val}
	468	[ ${j} -eq 3 ] && ret=${val}
	469	(( j=j+1 ))
	470	done
	471	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
	472	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
[548]	473
[778]	474	IGCM_sys_IsFileArchived ${file_in}
	475	if [ $? = 0 ] ; then
	476	IGCM_sys_Get ${file_in} ${file_out}
	477	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	478	else
	479	IGCM_sys_Cp ${file_in} ${file_out}
	480	fi
	481	fi
	482	(( i=i+3 ))
[544]	483	done
	484	fi
	485	done
[778]	486
[544]	487	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
[247]	488	}
	489
	490	#=======================================================================
[2]	491	function IGCM_comp_GetInputBoundaryFiles
	492	{
[544]	493	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
[2]	494
[544]	495	# Debug Print :
	496	echo
	497	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
	498	echo
[2]	499
[902]	500	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	501	typeset file_in_ file_in file_out_ file_out
[2]	502
[544]	503	if [ ${Period} = 1 ]; then
	504	ListFixBoundary=" "
	505	fi
[2]	506
[544]	507	for comp in ${config_ListOfComponents[*]} ; do
[2]	508
[544]	509	# Define component
	510	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	511	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	512
[544]	513	# Debug Print :
	514	IGCM_debug_Print 3 "Boundary files ${compname}"
[2]	515
[544]	516	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	517
[544]	518	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
	519	ListFilesName=${compname}_BoundaryFiles_List
	520	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	521
[544]	522	if [ X${FileName0} != X${NULL_STR} ] ; then
	523	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	524
[544]	525	(( i=0 ))
	526	until [ $i -ge $NbFiles ]; do
[778]	527	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	528	eval file_in=${file_in_}
	529	(( i_ = i+1 ))
	530	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	531	eval file_out=${file_out_}
[2]	532
[778]	533	IGCM_sys_IsFileArchived ${file_in}
	534	if [ $? = 0 ] ; then
	535	IGCM_sys_Get ${file_in} ${file_out}
[809]	536	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[778]	537	else
	538	IGCM_sys_Cp ${file_in} ${file_out}
	539	fi
[2]	540
[778]	541	(( i=i+2 ))
[544]	542	done
	543	fi
[2]	544
[544]	545	# Get non deleted files
	546	if [ ${Period} = 1 ]; then
[2]	547
[544]	548	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
	549	ListFilesName=${compname}_BoundaryFiles_ListNonDel
	550	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	551
[544]	552	if [ X${FileName0} != X${NULL_STR} ] ; then
[778]	553	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	554
[778]	555	(( i=0 ))
	556	until [ $i -ge $NbFiles ]; do
	557	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	558	eval file_in=${file_in_}
	559	(( i_ = i+1 ))
	560	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	561	eval file_out=${file_out_}
[2]	562
[778]	563	IGCM_sys_IsFileArchived ${file_in}
	564	if [ $? = 0 ] ; then
	565	IGCM_sys_Get ${file_in} ${file_out}
	566	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	567	else
	568	IGCM_sys_Cp ${file_in} ${file_out}
	569	fi
[2]	570
[778]	571	if [ X${file_out} != X. ] ; then
	572	ListFixBoundary=${ListFixBoundary}" "${file_out}
	573	else
	574	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
	575	fi
	576
	577	(( i=i+2 ))
	578	done
[544]	579	fi
	580	fi
	581	done
[778]	582
[544]	583	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
[2]	584	}
	585
	586	#=======================================================================
	587	function IGCM_comp_DelFixeBoundaryFiles
	588	{
[544]	589	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	590
[544]	591	# Debug Print :
	592	echo
	593	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
	594	echo
[2]	595
[544]	596	ls -l ${ListFixBoundary}
	597	rm -f ${ListFixBoundary}
[2]	598
[544]	599	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	600	}
	601
	602	#=======================================================================
	603	function IGCM_comp_GetInputParametersFiles
	604	{
[544]	605	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
[2]	606
[544]	607	# Debug Print :
	608	echo
	609	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
	610	echo
[2]	611
[544]	612	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
	613	for comp in ${config_ListOfComponents[*]} ; do
[902]	614	# Define component
[544]	615	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	616	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	617
[1338]	618	# Initialize array hosting file_def and field_def files to check and/or modify
	619	unset FieldDef
	620	unset FileDef
	621
[544]	622	# Debug Print :
	623	IGCM_debug_Print 3 "Parameters ${compname}"
[2]	624
[778]	625	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	626
[544]	627	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
	628	ListFilesName=${compname}_ParametersFiles_List
	629	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	630
[544]	631	if [ X${FileName0} != X${NULL_STR} ] ; then
	632	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	633
[544]	634	(( i=0 ))
	635	until [ $i -ge $NbFiles ]; do
[778]	636	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	637	eval file_in=${file_in_}
	638	(( i_ = i+1 ))
	639	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
[902]	640	eval file_out=${file_out_}
[2]	641
[902]	642	IGCM_sys_Cp ${file_in} ${file_out}
[778]	643	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[1338]	644	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
[2]	645
[778]	646	(( i=i+2 ))
[544]	647	done
	648	fi
[1338]	649
	650	if [ ${#FileDef[@]} -ne 0 ] ; then
	651	# Check XMLs coherency now
[1339]	652	IGCM_debug_Print 1 "${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}"
	653	${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}
[1338]	654	if [ $? = 0 ] ; then
[1339]	655	IGCM_debug_Print 1 "${compname} XIOS XMLs are consistent"
[1338]	656	else
[1373]	657	IGCM_debug_Print 1 "${compname} XIOS XMLs ARE NOT consistent"
	658	if [ X${config_Post_ParserXIOS} = XTRUE ] ; then
	659	IGCM_debug_Print 1 "Try to fix it:"
	660	IGCM_debug_Print 3 "${libIGCM}/libIGCM_post/xios_parser.py -v modify --field ${FieldDef[]} --file ${FileDef[]}"
	661	${libIGCM}/libIGCM_post/xios_parser.py -vv modify --field ${FieldDef[]} --file ${FileDef[]}
	662	[ $? != 0 ] && IGCM_debug_Exit "Failed to fix XIOS xml files for ${compname}"
	663	fi
[1338]	664	fi
	665	fi
[544]	666	done
[2]	667
[544]	668	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
[2]	669	}
	670
	671	#=======================================================================
	672	function IGCM_comp_GetInputRestartFiles
	673	{
[544]	674	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
[2]	675
[544]	676	# Debug Print :
	677	echo
	678	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
	679	echo
[2]	680
[590]	681	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
	682	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
[902]	683	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
[544]	684	typeset file_in file_out file_in_ file_out_ file_in_Name
	685	typeset -Z4 j4
[821]	686	#BASH declare j4
[2]	687
[778]	688	IsMatching=""
	689
[544]	690	for comp in ${config_ListOfComponents[*]} ; do
[902]	691	# Define component
[544]	692	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	693	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
	694	#
	695	card=${SUBMIT_DIR}/COMP/${compname}.card
	696	#
	697	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	698	ListFilesName=${compname}_RestartFiles_List
	699	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	700
[544]	701	# Debug Print :
	702	IGCM_debug_Print 3 "restart ${compname}"
[2]	703
[544]	704	if ( ${FirstInitialize} ) ; then
[2]	705
[1401]	706	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[1446]	707	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
[1447]	708	if ( [ X${comp} = XIOS ] && [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] )
	709	CompOldName=IOS
	710	config_IOS_Restart="n"
	711	do_start="n"
	712	config_${comp}_RestartDate=-1
	713	config_${comp}_RestartJobName=${NULL_STR}
	714	config_${comp}_RestartPath=${NULL_STR}
	715	else
[1446]	716	eval config_${comp}_Restart="y"
	717	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
	718	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
	719	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
	720	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
	721	eval CompOldName=${comp}
	722	fi
[544]	723	else
[778]	724	# Read component Restarts parameters
	725	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	726	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
[2]	727
[778]	728	if [ "${do_start}" = "y" ] ; then
	729	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
	730	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
	731	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
	732	else
	733	eval config_${comp}_RestartDate=-1
	734	eval config_${comp}_RestartJobName=${NULL_STR}
	735	eval config_${comp}_RestartPath=${NULL_STR}
	736	fi
[849]	737
[778]	738	eval CompOldName=\${config_${comp}_OldName}
	739	if [ X${CompOldName} = X ] ; then
	740	eval CompOldName=${comp}
	741	fi
	742
	743	# Reinitialize IsMatching to allow searching for a different tar file for each component.
	744	IsMatching=""
	745	TarFileFound=""
[544]	746	fi
[2]	747
[544]	748	if [ "${do_start}" = "y" ] ; then
[2]	749
[672]	750	# Restore Restarts files
	751	#-----------------------
[778]	752	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	753	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	754
[778]	755	(( i=1 ))
	756	until [ $i -gt $NbFiles ]; do
	757	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	758	eval file_in=${file_in_}
	759	(( i_ = i+1 ))
	760	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	761	eval file_out=${file_out_}
	762
	763	eval Date_tmp=\${config_${comp}_RestartDate}
	764	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
[672]	765	# will be re-use
	766	eval RestartPath=\${config_${comp}_RestartPath}
	767	eval RestartJobName=\${config_${comp}_RestartJobName}
	768	#
[778]	769	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
	770	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
[2]	771
[778]	772	extension_in=$( echo ${file_in_Name##*.} )
	773	extension_out=$( echo ${file_out##*.} )
[672]	774
[778]	775	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	776	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
[2]	777
[778]	778	Path_OUT=${Path_r}/${generic_restart_file_name_in}
	779
[672]	780	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	781	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
[778]	782	Buffered=true
	783	Archived=false
	784	Tared=false
	785	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
[672]	786	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	787	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	788	Buffered=false
	789	Archived=true
	790	Tared=false
	791	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
[672]	792	else
[897]	793	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
	794	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
[902]	795	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
[778]	796	Buffered=false
	797	Archived=false
	798	Tared=true
[672]	799	# Look after the tar file we want if we did not found it already
[778]	800	if [ X${IsMatching} = X ] ; then
[947]	801	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
	802	if [ $? ] ; then
[897]	803	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
	804	IsMatching=$( echo ${PotentialTarFile##*/} \| \
	805	sed "s:_restart::" \| \
	806	sed "s:^${RestartJobName}_::" \| \
	807	sed "s:\.tar$::" \| \
	808	gawk -F_ -v restartdate=${Date_r} \
	809	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	810	if [ ! X${IsMatching} = X ] ; then
	811	TarFileFound=${PotentialTarFile}
	812	break
	813	fi
	814	done
[1017]	815	fi
	816	# Stop here if nothing has been found
	817	if [ X${TarFileFound} = X ] ; then
[902]	818	IGCM_debug_Print 3 "Restart files were not found!"
	819	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	820	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
[897]	821	IGCM_debug_Exit "Please double check restart settings in config.card"
	822	IGCM_debug_Verif_Exit
	823	fi
[778]	824	fi
[918]	825	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	826	TarFileLocation=$( basename ${TarFileFound} )
[801]	827	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	828	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	829	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	830	fi
[672]	831
	832	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	833	j=0 # BASH LINE NOT NEEDED
	834	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	835	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	836	j4=${j} # BASH LINE NOT NEEDED
[778]	837	if [ X${Buffered} = Xtrue ] ; then
	838	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	839	elif [ X${Archived} = Xtrue ] ; then
	840	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	841	elif [ X${Tared} = Xtrue ] ; then
	842	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	843	fi
[821]	844	(( j=j+1 )) #BASH LINE NOT NEEDED
[778]	845	done
[740]	846
[1248]	847	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
	848	if [ X${OCE_PROC_MPI} != X ] ; then
	849	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
[1380]	850	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
[740]	851	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
	852	fi
	853	fi
[778]	854	else
	855	if [ X${Buffered} = Xtrue ] ; then
	856	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
	857	elif [ X${Archived} = Xtrue ] ; then
	858	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
	859	elif [ X${Tared} = Xtrue ] ; then
	860	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	861	fi
	862	fi
	863	(( i=i+3 ))
	864	done
	865	else
	866	if [ X${FileName0} != XNONE ] ; then
	867	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	868	else
	869	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	870	fi
	871	fi
[544]	872	fi
[893]	873	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
[544]	874	# if not FirstInitialize and first loop of this job
[2]	875
[544]	876	# Restore Restarts files
	877	#-----------------------
	878	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
[778]	879	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	880
[778]	881	(( i=1 ))
	882	until [ $i -gt $NbFiles ]; do
	883	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	884	eval file_in=${file_in_}
	885	(( i_ = i+1 ))
	886	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	887	eval file_out=${file_out_}
[2]	888
[1028]	889	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
[662]	890
[778]	891	extension_in=$( echo ${file_in_Name##*.} )
	892	extension_out=$( echo ${file_out##*.} )
[67]	893
[778]	894	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	895	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
	896
	897	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
	898	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
	899
[662]	900	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	901	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
[778]	902	Buffered=true
	903	Archived=false
	904	Tared=false
	905	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
[672]	906	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	907	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	908	Buffered=false
	909	Archived=true
	910	Tared=false
	911	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
	912	else
[897]	913	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
[902]	914	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
[778]	915	Buffered=false
	916	Archived=false
	917	Tared=true
	918	# Look after the tar file we want if we did not found it already
	919	if [ X${IsMatching} = X ] ; then
[801]	920	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
[778]	921	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	922	if [ ! X${IsMatching} = X ] ; then
	923	TarFileFound=${PotentialTarFile}
	924	break
	925	fi
	926	done
	927	fi
[1017]	928	# Stop here if nothing has been found
	929	if [ X${TarFileFound} = X ] ; then
	930	IGCM_debug_Print 3 "Restart files were not found!"
	931	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	932	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
	933	IGCM_debug_Exit "Please double check restart settings in config.card"
	934	IGCM_debug_Verif_Exit
	935	fi
[918]	936	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	937	TarFileLocation=$( basename ${TarFileFound} )
[801]	938	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	939	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	940	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	941	fi
[41]	942
[778]	943	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	944	j=0 # BASH LINE NOT NEEDED
	945	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	946	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	947	j4=${j} # BASH LINE NOT NEEDED
[778]	948	if [ X${Buffered} = Xtrue ] ; then
	949	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	950	elif [ X${Archived} = Xtrue ] ; then
	951	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	952	elif [ X${Tared} = Xtrue ] ; then
	953	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	954	fi
[821]	955	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	956	done
	957	else
	958	if [ X${Buffered} = Xtrue ] ; then
	959	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
	960	elif [ X${Archived} = Xtrue ] ; then
	961	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
	962	elif [ X${Tared} = Xtrue ] ; then
	963	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	964	fi
	965	fi
	966	(( i=i+3 ))
	967	done
[544]	968	else
[778]	969	if [ X${FileName0} != XNONE ] ; then
	970	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	971	else
	972	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	973	fi
[544]	974	fi
[420]	975	fi
[544]	976	done
[420]	977
[544]	978	NbFiles=$( ls * 2> /dev/null \| wc -l )
	979	if [ ${NbFiles} -gt 0 ] ; then
	980	IGCM_sys_Chmod u+rw *
	981	fi
	982
	983	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
[2]	984	}
	985
	986	#=======================================================================
[1409]	987	function IGCM_comp_GetInputBinaryFiles
	988	{
	989	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
	990
	991	# Debug Print :
	992	echo
	993	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
	994	echo
	995
	996	# Clean up previous pass
	997	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
	998
[1411]	999	typeset comp ExeNameIn ExeNameOut byPass
[1409]	1000	typeset compilerNmbr compilerUnit compilerFull
[1411]	1001	byPass=false
[1409]	1002	for comp in ${config_ListOfComponents[*]} ; do
	1003	# Define component
	1004
	1005	# Copy executable for this component
	1006	eval ExeNameIn=\${config_Executable_${comp}[0]}
	1007	eval ExeNameOut=\${config_Executable_${comp}[1]}
	1008
	1009	# If missing executable and DRYRUN is set to 0 or 1 then stop!
	1010	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
	1011	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
	1012	fi
	1013
	1014	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
	1015	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1016	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1017	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1018	fi
	1019	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1020	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1021	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1022	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1023	fi
	1024	fi
	1025
	1026	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1027	# Get the compiler version
	1028	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1029	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1030	# Save it
	1031	echo $compilerFull >> ${RUN_DIR}/compiler.txt
[1411]	1032	[ X${compilerFull} = X ] && byPass=true
[1409]	1033	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
[1413]	1034	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
[1409]	1035	fi
	1036	done
	1037
	1038	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
	1039	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
	1040
[1411]	1041	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
[1409]	1042	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
	1043	fi
	1044
[1428]	1045	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 ] ) ; then
	1046	IGCM_debug_Exit "IPSLCM6.0.13, IPSLCM6.0.14, IPSLCM6.0.15 and IPSLCM6.1 must be compiled with intel 2017 compiler"
[1415]	1047	fi
	1048
[1409]	1049	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
	1050	}
	1051
	1052	#=======================================================================
[269]	1053	function IGCM_comp_PeriodStart
	1054	{
[544]	1055	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
[269]	1056
[544]	1057	# Debug Print :
	1058	echo
	1059	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
	1060	echo
[269]	1061
[902]	1062	typeset ExeNameIn ExeNameOut
[544]	1063	typeset comp compname comptagname
	1064	for comp in ${config_ListOfComponents[*]} ; do
[902]	1065	# Define component
[544]	1066	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1067	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[269]	1068
[544]	1069	# Copy executable for this component
	1070	eval ExeNameIn=\${config_Executable_${comp}[0]}
	1071	eval ExeNameOut=\${config_Executable_${comp}[1]}
[269]	1072
[544]	1073	# Debug Print
	1074	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
	1075	# UPDATE component
	1076	${comp}_PeriodStart 2> /dev/null
[269]	1077
[544]	1078	done
[269]	1079
[544]	1080	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
[269]	1081	}
	1082
[1166]	1083
	1084
[269]	1085	#=======================================================================
[1166]	1086	function IGCM_comp_modifyFile
	1087	{
	1088	#
	1089	# syntax: IGCM_comp_modifyFile filein key [value]
	1090	#
	1091	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
	1092	#
	1093	# This function is used to replace a pattern in a file for a specific variable.
	1094	#
	1095	# Arguments:
	1096	# - filein : the file in run directory in which the variable should be set
	1097	# - key : the variable to modify
	1098	# - value : the value to set the key equal to
	1099	#
	1100	IGCM_debug_PushStack "IGCM_comp_modifyFile"
	1101
	1102	typeset filein key value pattern
	1103
	1104	# Set local variables and test the arguments
	1105	if [ $# = 3 ] ; then
	1106	# Normal case with 3 arguments
	1107	filein=$1 ; key=$2 ; value=$3
	1108	else
	1109	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
	1110	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1111	return
	1112	fi
	1113	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
	1114
	1115	# Test if the file exist
	1116	if [ ! -f ${filein} ] ; then
	1117	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
	1118	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1119	return
	1120	fi
	1121
	1122	# Read the line with key in the file without the comments
	1123	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
	1124
	1125	# Verify the existance of the pattern
	1126	if [ X"${pattern}" = X ] ; then
	1127	# Variable key is not set in filein, stop.
	1128	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
	1129	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1130	return
	1131	fi
	1132
	1133	# Now change key in filein
[1176]	1134	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
	1135	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
[1166]	1136	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
	1137	\mv ${filein}.tmp ${filein}
	1138
	1139	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1140	}
	1141
	1142	#=======================================================================
[1069]	1143	function IGCM_comp_modifyDefFile
	1144	{
	1145	#
	1146	# syntax: IGCM_comp_modifyDefFile type filein key [value]
	1147	#
	1148	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
	1149	#
	1150	# This function is used to modify a parameter file for a specific variable.
[1075]	1151	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
	1152	# This function can be used in the comp.driver files for the components.
[1069]	1153	#
[1075]	1154	# Arguments:
[1081]	1155	# - type : first argument must be blocker, nonblocker or force
[1075]	1156	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1069]	1157	# otherwise this function will exit.
[1075]	1158	# For "nonblocker" case, the user can remove or modify the variable. For
	1159	# this case, as long as AUTO is not set, no modification will be done.
[1081]	1160	# For "force" case, the variable will be modified even if it is not set to AUTO
[1069]	1161	# - filein : the file in run directory of .def type in which the variable should be set
	1162	# - key : the variable to modify
[1075]	1163	# - value : the value to set the key equal to, optional. If value is not set or if
[1069]	1164	# value=DEFAULT, then a default value must be given in filein using syntax :
	1165	# key= AUTO : DEFAULT=def_value
	1166	#
[1075]	1167	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
[1069]	1168
[1166]	1169	typeset type filein key value
	1170	typeset filelist nb_occ modify
	1171
[1075]	1172	# Set local variables and test the arguments
	1173	if [ $# = 4 ] ; then
	1174	# Normal case with 4 arguments
	1175	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1176	elif [ $# = 3 ] ; then
	1177	# Normal case with 3 arguments
	1178	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1179	else
	1180	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
[1079]	1181	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1182	return
	1183	fi
[1166]	1184	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
[1069]	1185
[1075]	1186	# Test if first argument is correct
[1166]	1187	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1081]	1188	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
[1079]	1189	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1190	return
	1191	fi
[1069]	1192
[1215]	1193	# Test if the file exist.
	1194	# Exit with error if the file does not exist for the case blocker or force.
	1195	# Only return for the case nonblocker.
[1075]	1196	if [ ! -f ${filein} ] ; then
[1215]	1197	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1198	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
	1199	else
	1200	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
	1201	fi
[1079]	1202	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1203	return
	1204	fi
[1069]	1205
[1102]	1206	# Define list of files to test using all files with suffix .def (except used*.def)
	1207	filelist=$( ls *def \| grep -v used )
[1069]	1208
[1075]	1209	# Count number of occurances for the key in all files
[1166]	1210	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
[1069]	1211
[1075]	1212	# Test if key is set several times
[1166]	1213	if [ ${nb_occ} -gt 1 ] ; then
	1214	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
[1079]	1215	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1216	return
	1217	fi
	1218
	1219	# Treatement according to different cases
[1166]	1220	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
[1075]	1221	# Stop if the key is never set and the function is blocker
[1166]	1222	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
	1223	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
	1224	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
[1075]	1225	# The key is not set but it is a nonblocker call so nothing is done.
[1166]	1226	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1227	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
[1081]	1228	modify=no
[1166]	1229	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
[1075]	1230	# Variable key is not set in filein, stop.
[1166]	1231	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1081]	1232	fi
	1233
	1234	# Check if AUTO is set in the filein on the same line as the key variable
[1166]	1235	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1236	# Modification will be done for all cases
	1237	modify=yes
	1238	else
	1239	# The variable was not set to AUTO
[1166]	1240	if [ ${type} = blocker ] ; then
[1156]	1241	# Exit because this is a blocker call
[1166]	1242	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
[1190]	1243	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1156]	1244	return
[1166]	1245	elif [ ${type} = nonblocker ] ; then
[1156]	1246	# Do nothing. Suppose that the user did set the variable correct
[1166]	1247	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
[1156]	1248	modify=no
[1166]	1249	elif [ ${type} = force ] ; then
[1156]	1250	# Force modification
[1166]	1251	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
[1081]	1252	modify=yes
[1156]	1253	fi
[1081]	1254	fi
[1069]	1255
[1081]	1256	# Do the modifcation now
[1166]	1257	if [ ${modify} = yes ] ; then
[1081]	1258
[1156]	1259	# For option DEFAULT, read default value from file.
[1166]	1260	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1261	# Case to set DEFAULT value
	1262	# Read default value from filein
[1423]	1263	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
[1069]	1264
[1166]	1265	if [ X"${value}" = X ] ; then
	1266	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
	1267	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
	1268	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1269	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
	1270	return
[1075]	1271	fi
[1156]	1272	fi
[1069]	1273
[1156]	1274	# Now change key in filein
[1166]	1275	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
	1276	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
	1277	\mv ${filein}.tmp ${filein}
[1075]	1278	fi
[1079]	1279	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1069]	1280	}
	1281
	1282	#=======================================================================
[1085]	1283	function IGCM_comp_modifyNamelist
	1284	{
	1285	#
	1286	# syntax: IGCM_comp_modifyNamelist type filein key [value]
	1287	#
	1288	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
	1289	#
	1290	# This function is used to modify a parameter file for a specific variable.
[1155]	1291	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
[1085]	1292	# This function can be used in the comp.driver files for the components.
	1293	#
	1294	# Arguments:
	1295	# - type : first argument must be blocker, nonblocker or force
	1296	# For "blocker" case, the variable must be attributed the keyworld AUTO
	1297	# otherwise this function will exit.
	1298	# For "nonblocker" case, the user can remove or modify the variable. For
	1299	# this case, as long as AUTO is not set, no modification will be done.
	1300	# For "force" case, the variable will be modified even if it is not set to AUTO
	1301	# - filein : the file in run directory of .def type in which the variable should be set
	1302	# - key : the variable to modify
	1303	# - value : the value to set the key equal to, optional. If value is not set or if
	1304	# value=DEFAULT, then a default value must be given in filein using syntax :
	1305	# key= AUTO : DEFAULT=def_value
	1306	#
	1307	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
	1308
[1166]	1309	typeset type filein key value pattern modify
	1310
[1085]	1311	# Set local variables and test the arguments
	1312	if [ $# = 4 ] ; then
	1313	# Normal case with 4 arguments
	1314	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1315	elif [ $# = 3 ] ; then
	1316	# Normal case with 3 arguments
	1317	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1318	else
	1319	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
	1320	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1321	return
	1322	fi
[1166]	1323	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
[1085]	1324
	1325	# Test if first argument is correct
[1166]	1326	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1085]	1327	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
	1328	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1329	return
	1330	fi
	1331
[1215]	1332	# Test if the file exist.
	1333	# Exit with error if the file does not exist for the case blocker or force.
	1334	# Only return for the case nonblocker.
[1085]	1335	if [ ! -f ${filein} ] ; then
[1215]	1336	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1337	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
	1338	else
	1339	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
	1340	fi
[1085]	1341	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1342	return
	1343	fi
	1344
	1345	# Read the line with key in the file without the comments
[1166]	1346	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
[1155]	1347
[1085]	1348	# Verify the existance of the pattern
	1349	if [ X"$pattern" = X ] ; then
[1156]	1350	# Variable key is not set in filein, stop.
[1166]	1351	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1156]	1352	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1353	return
[1085]	1354	fi
[1155]	1355
[1085]	1356	# Check if the variable is set to AUTO in the filein
	1357	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1358	# Modification will be done for all cases
	1359	modify=yes
	1360	else
	1361	# The variable was not set to AUTO
[1166]	1362	if [ ${type} = blocker ] ; then
[1156]	1363	# Exit because this is a blocker call
[1166]	1364	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
[1156]	1365	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1366	return
[1166]	1367	elif [ ${type} = nonblocker ] ; then
[1156]	1368	# Do nothing. Suppose that the user did set the variable correct
[1166]	1369	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
[1156]	1370	modify=no
[1166]	1371	elif [ ${type} = force ] ; then
[1156]	1372	# Force modification
[1166]	1373	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
[1085]	1374	modify=yes
[1156]	1375	fi
[1085]	1376	fi
	1377
	1378	# Do the modifcation now
[1166]	1379	if [ ${modify} = yes ] ; then
[1085]	1380
[1156]	1381	# For option DEFAULT, read default value from file.
[1166]	1382	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1383	# Case to set DEFAULT value
	1384	# Read default value from filein
	1385	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
[1085]	1386
[1166]	1387	if [ X"${value}" = X ] ; then
	1388	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
	1389	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
	1390	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1391	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1392	return
[1085]	1393	fi
[1156]	1394	fi
[1085]	1395
[1156]	1396	# Now change key in filein
[1166]	1397	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
	1398	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
	1399	\mv ${filein}.tmp ${filein}
[1085]	1400	fi
	1401	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1402	}
	1403
	1404	#=======================================================================
[1074]	1405	function IGCM_comp_modifyXmlFile
	1406	{
	1407	#
	1408	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
	1409	#
	1410	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
	1411	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
	1412	#
	1413	# This function is used to modify the value for a specific attribute and variable id.
[1155]	1414	# The file must be a valid xml file.
[1075]	1415	# This function can be used in the comp.driver files for the components.
[1074]	1416	#
[1075]	1417	# Arguments:
	1418	# - type : first argument must be blocker, nonblocker or force.
	1419	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1074]	1420	# otherwise this function will exit.
[1075]	1421	# For "nonblocker" case, the user can remove or modify the variable. For
[1074]	1422	# this case, as long as AUTO is not set, no modification will be done.
[1075]	1423	# For "force" case, the variable will be modified even if it is not set to AUTO
[1074]	1424	# - filein : the file in run directory of .xml type in which the variable should be set
	1425	# - keyid : the variable to modify
	1426	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
	1427	# - value : the value to set in the filein
	1428	#
[1075]	1429	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
[1074]	1430
[1166]	1431	typeset type filein keyid keyattrib value modify
	1432
[1075]	1433	# Set local variables and test the arguments
	1434	if [ $# = 5 ] ; then
	1435	# Normal case with 4 arguments
	1436	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
	1437	else
	1438	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
[1089]	1439	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1440	return
	1441	fi
[1166]	1442	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
[1074]	1443
[1075]	1444	# Test if first argument is correct
[1166]	1445	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1075]	1446	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
[1089]	1447	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1448	return
	1449	fi
[1074]	1450
[1215]	1451	# Test if the file exist.
	1452	# Exit with error if the file does not exist for the case blocker or force.
	1453	# Only return for the case nonblocker.
[1075]	1454	if [ ! -f ${filein} ] ; then
[1215]	1455	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1456	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
	1457	else
	1458	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
	1459	fi
[1089]	1460	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1461	return
	1462	fi
	1463
[1386]	1464	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
[1166]	1465	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
[1386]	1466	if [ ${type} = nonblocker ] ; then
	1467	# This is a nonblocker case, print warning but do nothing else
	1468	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1469	else
	1470	# This is a blocker or force case : stop now
	1471	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
	1472	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
	1473	return
	1474	fi
[1075]	1475	fi
	1476
	1477	# Check if AUTO is set on the same line as keyid and keyattrib
[1166]	1478	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
[1394]	1479	# Modification will be done
[1075]	1480	modify=yes
	1481	else
[1166]	1482	if [ ${type} = blocker ] ; then
[1075]	1483	# Exit, the variable must be set to AUTO
[1166]	1484	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
[1089]	1485	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1486	return
[1166]	1487	elif [ ${type} = nonblocker ] ; then
[1075]	1488	# Nothing will be done
	1489	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
	1490	modify=no
[1166]	1491	elif [ ${type} = force ] ; then
[1075]	1492	# Force modification
[1166]	1493	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
[1075]	1494	modify=yes
[1074]	1495	fi
[1075]	1496	fi
[1074]	1497
[1075]	1498	# Do the modifcation now
[1166]	1499	if [ ${modify} = yes ] ; then
	1500	if [ ${keyattrib} = NONE ] ; then
[1075]	1501	# Case to modify the variable itself
	1502	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
[1166]	1503	sed -e "s/\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\)/\1${value}\3/" ${filein} > ${filein}.tmp
[1074]	1504	else
[1156]	1505	# Check if keyattrib is set on the same line as keyid
[1166]	1506	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
[1156]	1507	# Case to modify the attribute value
	1508	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
[1166]	1509	sed -e "/id=\"${keyid}\"/s/\(${keyattrib}=\"\)[^\"]*\(\"\)/\1${value}\2/" ${filein} > ${filein}.tmp
[1156]	1510	else
	1511	# Case to add the attribute and its value
	1512	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
[1166]	1513	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
[1156]	1514	fi
[1074]	1515	fi
[1166]	1516	\mv ${filein}.tmp ${filein}
[1075]	1517	fi
	1518	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1074]	1519	}
	1520
	1521	#=======================================================================
[2]	1522	function IGCM_comp_Update
	1523	{
[544]	1524	IGCM_debug_PushStack "IGCM_comp_Update"
[2]	1525
[1409]	1526	# Debug Print :
[544]	1527	echo
	1528	IGCM_debug_Print 1 "IGCM_comp_Update"
	1529	echo
[2]	1530
[544]	1531	typeset comp compname comptagname
	1532	for comp in ${config_ListOfComponents[*]} ; do
[902]	1533	# Define component
[544]	1534	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1535	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1536
[544]	1537	# Debug Print
	1538	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
	1539	# UPDATE component
	1540	${comp}_Update
[2]	1541
[1413]	1542	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
	1543	if [ -f timeseries_def_${compname}.xml ]; then
	1544	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
	1545	for line in $( cat ts.temp.${compname}.txt ); do
	1546	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
	1547	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
	1548	case ${output_freq} in
	1549	Y\|y)
	1550	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
	1551	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
	1552	;;
	1553	MO\|mo)
	1554	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
	1555	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
	1556	;;
	1557	D\|d)
	1558	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
	1559	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
	1560	;;
	1561	S\|s)
	1562	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
	1563	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
	1564	;;
	1565	esac
	1566	done
	1567	fi
	1568
	1569	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
	1570	if [ -f dr2xml_${compname}.xml ]; then
	1571	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
	1572	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
	1573
[1420]	1574	# Modify path from dr2xml_{compname}.xml
	1575	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
[1413]	1576
[1420]	1577	# Overwrite the original file
	1578	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
[1422]	1579	fi
[544]	1580	done
[2]	1581
[544]	1582	IGCM_debug_PopStack "IGCM_comp_Update"
[2]	1583	}
	1584
	1585	#=======================================================================
	1586	function IGCM_comp_Finalize
	1587	{
[544]	1588	IGCM_debug_PushStack "IGCM_comp_Finalize"
[2]	1589
[544]	1590	# Debug Print :
	1591	echo
	1592	IGCM_debug_Print 1 "IGCM_comp_Finalize"
	1593	echo
[2]	1594
[544]	1595	typeset ListTextName TextName0
	1596	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
	1597	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
[1165]	1598	typeset -Z4 j4 #BASH declare j4
[544]	1599	typeset list_file nlist_file
	1600	typeset compactoutputs
[429]	1601
[1165]	1602	# Initialize array hosting list of rebuilded files to copy
	1603	unset rebuildedActionsList
	1604
	1605	# Text compacting options
[544]	1606	compactoutputs=false
	1607	if [ X${JobType} != XRUN ] ; then
	1608	compactoutputs=true
	1609	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
	1610	compactoutputs=true
	1611	fi
[433]	1612
[1043]	1613	# Prepare headers for the shell dedicated to offline rebuild
	1614	if [ X${AsynchronousRebuild} = Xtrue ] ; then
	1615	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1616	if [ ${DRYRUN} -le 1 ] ; then
	1617	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1618	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1619	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1620	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1621	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1622	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1623	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1624	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1625	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1626	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1627	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1628	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1629	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1630	fi
	1631	fi
	1632
[544]	1633	for comp in ${config_ListOfComponents[*]} ; do
[902]	1634	# Define component
[544]	1635	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1636	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1637
[544]	1638	# Debug Print
	1639	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
	1640	# FINALIZE component
	1641	${comp}_Finalize
[2]	1642
[778]	1643	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	1644
[804]	1645	# Save Output Text files of models
	1646	#---------------------------------
	1647	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
	1648	IGCM_card_DefineArrayFromOption ${card} OutputText List
	1649	ListTextName=${compname}_OutputText_List
	1650
	1651	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
	1652	if [ X${TextName0} != X${NULL_STR} ] ; then
	1653	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
	1654
	1655	(( i=0 ))
	1656	until [ $i -eq $NbFiles ]; do
	1657	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
	1658	eval file_out=${PREFIX}_${file_in}
	1659
	1660	(( i=i+1 ))
	1661
	1662	unset list_file
	1663	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
	1664	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
	1665	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 )
	1666	nlist_file=${#list_file[@]}
	1667	if [ ${nlist_file} -gt 1 ] ; then
	1668	if ( ${compactoutputs} ) ; then
	1669	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
	1670	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
	1671	echo ${list_file[*]} > ${file_out}
	1672	echo "" >> ${file_out}
	1673
	1674	(( i_ = 0 ))
[1080]	1675	for file in ${list_file[@]} ; do
[804]	1676	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
	1677	echo "\| " ${i_} " " ${file} >> ${file_out}
	1678	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
[999]	1679	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
[804]	1680	echo "" >> ${file_out}
	1681	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1682	(( i_ = i_ + 1 ))
	1683	done
[1080]	1684	if ( ${ExecutionFail} ) ; then
	1685	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
	1686	fi
	1687
[804]	1688	if [ X${Pack} = Xtrue ] ; then
	1689	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
	1690	else
	1691	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
	1692	fi
[1080]	1693
[804]	1694	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
[1080]	1695	else
	1696	for file in ${list_file[@]} ; do
	1697	if ( ${ExecutionFail} ) ; then
	1698	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
	1699	fi
[804]	1700
	1701	if [ X${Pack} = Xtrue ] ; then
	1702	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
	1703	else
	1704	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
	1705	fi
[1080]	1706
[804]	1707	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1708	done
	1709	fi
	1710	else
	1711	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
	1712	eval IGCM_sys_Mv ${file_in}* ${file_in}
	1713	fi
[1080]	1714
	1715	if ( ${ExecutionFail} ) ; then
	1716	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
	1717	fi
	1718
[804]	1719	if [ X${Pack} = Xtrue ] ; then
	1720	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
	1721	else
	1722	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
	1723	fi
	1724	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1725	fi
	1726	done
	1727	fi
	1728
[544]	1729	# Save Restarts files
	1730	#--------------------
	1731	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
	1732	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	1733	ListFilesName=${compname}_RestartFiles_List
	1734	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	1735
[544]	1736	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	1737	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[778]	1738
[544]	1739	(( i=0 ))
	1740	until [ $i -ge $NbFiles ]; do
[778]	1741	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1742	eval file_in=${file_in_}
[2]	1743
[778]	1744	(( i_ = i+1 ))
	1745	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1746	eval file_out=${file_out_}
[151]	1747
[778]	1748	(( i_ = i+2 ))
	1749	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1750	eval file_outin=${file_outin_}
[151]	1751
[778]	1752	generic_restart_file_name_in=$( basename ${file_in} .nc )
	1753	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
	1754	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
[2]	1755
[902]	1756	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
[778]	1757	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	1758	j=0 # BASH LINE NOT NEEDED
	1759	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	1760	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	1761	j4=${j} # BASH LINE NOT NEEDED
[778]	1762	if [ X${Pack} = Xtrue ] ; then
	1763	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1764	else
	1765	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1766	fi
	1767	if [ ! ${file_in} = ${file_outin} ] ; then
	1768	if ( ${ExitFlag} ) ; then
	1769	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
	1770	else
	1771	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
	1772	fi
	1773	fi
[821]	1774	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	1775	done
	1776	else
	1777	if [ X${Pack} = Xtrue ] ; then
	1778	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1779	else
	1780	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1781	fi
	1782	if [ ! ${file_in} = ${file_outin} ] ; then
	1783	if ( ${ExitFlag} ) ; then
	1784	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
	1785	else
	1786	IGCM_sys_Mv ${file_in} ${file_outin}
	1787	fi
	1788	fi
	1789	fi
	1790
	1791	(( i=i+3 ))
[544]	1792	done
	1793	else
	1794	if [ X${FileName0} != XNONE ] ; then
[778]	1795	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
[544]	1796	else
[778]	1797	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
[544]	1798	fi
	1799	fi
[2]	1800
[544]	1801	# Save Output files
	1802	#------------------
	1803	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
	1804	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	1805	ListFilesName=${compname}_OutputFiles_List
	1806	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	1807
[544]	1808	if [ X${FileName0} != X${NULL_STR} ] ; then
	1809	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[149]	1810
[544]	1811	(( i=0 ))
	1812	until [ $i -ge $NbFiles ]; do
[778]	1813	SaveOnArchive=true
	1814	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1815	eval file_in=${file_in_}
	1816	(( i_ = i+1 ))
	1817	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1818	eval file_out=${file_out_}
	1819	#
	1820	# Override file_out path remplacing R_SAVE by R_BUFR
	1821	#
	1822	if [ X${Pack} = Xtrue ] ; then
	1823	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
	1824	fi
	1825	#
	1826	# Not necessarily the best option. /!\ Potential side effects /!\
	1827	#
	1828	(( i_ = i+2 ))
	1829	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1830	#
	1831	generic_file_name=$( basename ${file_in} .nc )
	1832	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
	1833	#
	1834	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
[804]	1835	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
[778]	1836	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
	1837	elif [ ${nb_rebuild_file} -gt 1 ] ; then
[804]	1838	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
[778]	1839	if [ X${AsynchronousRebuild} = Xfalse ] ; then
	1840	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
[1388]	1841	#
	1842	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
	1843	if [ ${file_in} = output.abort.nc ] ; then
	1844	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
	1845	else
[1429]	1846	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
[1388]	1847	fi
[778]	1848	else
	1849	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
[1429]	1850	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
[544]	1851
[778]	1852	# Prepare the shell dedicated to offline rebuild
	1853	if [ $DRYRUN -le 1 ]; then
[694]	1854	if [ ${file_in} = histstn.nc ] ; then
	1855	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1856	else
[980]	1857	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[694]	1858	fi
[1206]	1859	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1860	fi
	1861	#
	1862	# Load Patch we need to apply and apply
	1863	if [ $DRYRUN -le 1 ]; then
	1864	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
[1080]	1865	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1866	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1867	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1868	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1869	done
	1870	fi
	1871	fi
	1872	#
	1873	if [ $DRYRUN -le 1 ]; then
	1874	if [ X${Pack} = Xtrue ] ; then
[1165]	1875	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
[778]	1876	else
[1165]	1877	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
[778]	1878	fi
[1206]	1879	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
[1165]	1880	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
[778]	1881	fi
	1882	SaveOnArchive=false
	1883	fi
	1884	fi
	1885	#
	1886	if [ ${SaveOnArchive} = true ] ; then
	1887	#
	1888	# Rebuild has been done online or it was not needed
	1889	#
	1890	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
	1891	#
	1892	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
[1289]	1893	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
[778]	1894	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1895	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
	1896	#
	1897	if [ $DRYRUN -le 1 ]; then
[1080]	1898	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1899	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1900	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1901	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1902	done
	1903	#
	1904	if [ X${Pack} = Xtrue ] ; then
	1905	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1906	else
	1907	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1908	fi
[1206]	1909	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1910	#
	1911	fi
	1912	else
	1913	#
	1914	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
	1915	#
	1916	if [ X${Pack} = Xtrue ] ; then
	1917	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
	1918	else
	1919	IGCM_sys_Put_Out ${file_in} ${file_out}
	1920	fi
	1921	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1922	if [ ${nb_rebuild_file} -gt 1 ] ; then
	1923	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
	1924	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
	1925	done
	1926	fi
	1927	fi
	1928	fi
	1929	(( i=i+3 ))
[544]	1930	done
	1931	fi
	1932	echo
	1933	done
[1165]	1934	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
	1935	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
[1166]	1936	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1165]	1937	i=0
	1938	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
	1939	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1940	(( i=i+1 ))
	1941	done
	1942	fi
[544]	1943	IGCM_debug_PopStack "IGCM_comp_Finalize"
[2]	1944	}

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