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libIGCM_comp.ksh @ 1603

Last change on this file since 1603 was 1603, checked in by aclsce, 8 months ago

Changed libIGCM behaviour in case of pb in pack_output.job : now, we exit from the job if there is any problem, whatever we are in PROD, DEVT, TEST mode.
Specification of pack frequency per file :

In order to reduce the number of inodes, it is possible to specify by file the frequency of packing. The syntax to do that is in the 4th column of OutputFiles? section of the component.card, for example as follows in lmdz.card :
[OutputFiles?]
List= (histmth.nc, ${R_OUT_ATM_O_M}/${PREFIX}_1M_histmth.nc, Post_1M_histmth, 100Y), \

(histday.nc, ${R_OUT_ATM_O_D}/${PREFIX}_1D_histday.nc, Post_1D_histday, 10Y), \

...

In this example, histmth files will be packed every 100 years and histday files will be packed every 10 years.
The pack frequency you defined in config.card is the frequency of pack by default, that means if a specific frequency of pack is specified for a file in a component.card, this file will be packed at the specific frequency whereas all other files will be packed at global pack frequency (specified in config.card) and in this case, the frequency pack (from the config.card) is the frequency the pack_output job will be launched at.
There is a constraint to use this fonctionality : the Packfrequency you defined in config.card must be greater or equal to the pack frequencies you specified for each type of file in component.card, otherwise the computing job will be stopped (with an explicit error message).
Surpack mode :
A surpack mode functionality is available through the use of pack_output.job. To enable this functionality, you have to put "surpack_mode=y" (default value is n). The way to use is similar to restart post-processing pack_output jobs, as indicated here : http://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/CheckDebug#RestartPack_output. You can either use a global pack frequency in config.card or specific pack frequency per file, as explained above.

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: 79.3 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
[1603]	247	((i_ = i +1))
	248	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	249	eval Testvar=${Testvar_}
	250	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
	251	((i = i+4))
	252	else
[778]	253	(( i=i+3 ))
[1603]	254	fi
[544]	255	done
	256	fi
	257	# Debug Print
	258	IGCM_debug_Print 3 "Initialize ${compname} with driver."
	259	# INIT component
	260	${comp}_Initialize
	261	echo
	262	done
[2]	263
[544]	264	IGCM_debug_PopStack "IGCM_comp_Initialize"
[2]	265	}
	266
	267	#=======================================================================
	268	function IGCM_comp_PrepareDeletedFiles
	269	{
[544]	270	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
[778]	271
[544]	272	if [ X${2} != X. ] ; then
	273	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
	274	else
	275	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
	276	fi
[2]	277
[544]	278	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
[2]	279	}
	280
	281	#=======================================================================
[1338]	282	function IGCM_comp_PrepareXiosFiles
	283	{
	284	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
	285
	286	typeset file
	287	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
	288
	289	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
	290	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
	291	fi
	292	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
	293	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
	294	fi
[1413]	295	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
	296	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
	297	fi
[1338]	298
	299	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
	300	}
	301
	302	#=======================================================================
[2]	303	function IGCM_comp_GetInputInitialStateFiles
	304	{
[544]	305	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
[2]	306
[544]	307	# Debug Print :
	308	echo
	309	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
	310	echo
[2]	311
[902]	312	# Only the first time step need InitialStateFiles
[544]	313	# otherwise it's BoundaryConditions
	314	if ( ${FirstInitialize} ) ; then
[902]	315	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	316	typeset file_in_ file_in file_out_ file_out do_init
[544]	317	for comp in ${config_ListOfComponents[*]} ; do
	318	# Initialize
	319	do_init="y"
	320	# Do we need to bring initial state file for this component
[1401]	321	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[778]	322	eval do_init="n"
[544]	323	else
[778]	324	# Read component Restarts parameters
	325	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	326	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
	327	if [ "${do_start}" = "y" ] ; then
	328	do_init="n"
	329	else
	330	do_init="y"
	331	fi
[544]	332	fi
[2]	333
[544]	334	if [ "${do_init}" = "y" ] ; then
[902]	335	# Define component
[778]	336	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	337	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	338
[778]	339	# Debug Print :
	340	IGCM_debug_Print 3 "Initialisation files ${compname}"
[2]	341
[778]	342	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	343
[778]	344	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
	345	ListFilesName=${compname}_InitialStateFiles_List
[2]	346
[778]	347	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
	348	if [ X${FileName0} != X${NULL_STR} ] ; then
	349	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
	350	(( i=0 ))
	351	until [ $i -ge $NbFiles ]; do
	352	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	353	eval file_in=${file_in_}
	354	(( i_ = i+1 ))
	355	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	356	eval file_out=${file_out_}
[2]	357
[778]	358	IGCM_sys_IsFileArchived ${file_in}
	359	if [ $? = 0 ] ; then
	360	IGCM_sys_Get ${file_in} ${file_out}
	361	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	362	else
	363	IGCM_sys_Cp ${file_in} ${file_out}
	364	fi
	365	(( i=i+2 ))
	366	done
	367	fi
[544]	368	fi
	369	done
	370	fi
	371	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
[2]	372	}
	373
	374	#=======================================================================
[247]	375	# Definition of Smooth modulo function
[902]	376	# usage :
[247]	377	# IGCM_SmoothModulo StringModulo value
	378	#
	379	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
	380	# [min]:[modulo:][max]
	381	# where :
[902]	382	# [] value are optionnals;
[247]	383	# empty min equal 1
	384	# empty max equal infinity
	385	# modulo not given or empty equal 1
	386	# empty string or just ':' equal always.
	387	#
	388	# value : the value to test with the definition
	389	#
[902]	390	# return : true(1)/false(0)
[247]	391	function IGCM_SmoothModulo
	392	{
[544]	393	IGCM_debug_PushStack "IGCM_SmoothModulo"
	394	typeset defVector ModValue
[247]	395
[544]	396	eval set +A defVector -- $( echo "${1}" \| \
	397	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
[247]	398
[544]	399	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
	400	arr[1]=${defVector[0]}
	401	arr[2]=${defVector[2]}
[412]	402
[902]	403	# Test limits :
	404	# ${defVector[0]} <= ${2} <= ${defVector[2]}
[544]	405	# or ${defVector[2]} == -1
	406	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
	407	# Test modulo
	408	ModValue=$( expr $ ${2} - ${defVector[0]} $ % ${defVector[1]} )
	409	if [ ${ModValue} -eq 0 ] ; then
	410	arr[3]=true
	411	echo ${arr[@]}
	412	IGCM_debug_PopStack "IGCM_SmoothModulo"
	413	return 1
[247]	414	else
[544]	415	arr[3]=false
	416	echo ${arr[@]}
	417	IGCM_debug_PopStack "IGCM_SmoothModulo"
	418	return 0
[247]	419	fi
[544]	420	else
	421	arr[3]=false
	422	echo ${arr[@]}
	423	IGCM_debug_PopStack "IGCM_SmoothModulo"
	424	return 0
	425	fi
[247]	426	}
	427
	428	#=======================================================================
	429	function IGCM_comp_GetInputSmoothFiles
	430	{
[544]	431	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
[247]	432
[544]	433	# Debug Print :
	434	echo
	435	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
	436	echo
[247]	437
[544]	438	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
	439	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
[247]	440
[544]	441	for comp in ${config_ListOfComponents[*]} ; do
	442	# Define component
	443	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	444	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[247]	445
[544]	446	# Debug Print :
	447	IGCM_debug_Print 3 "Smooth files ${compname}"
[247]	448
[544]	449	card=${SUBMIT_DIR}/COMP/${compname}.card
[247]	450
[544]	451	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
	452	ListFilesName=${compname}_SmoothFiles_List
	453	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[247]	454
[544]	455	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
	456	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[247]	457
[544]	458	(( i=0 ))
	459	until [ $i -ge $NbFiles ]; do
[778]	460	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	461	eval file_in=${file_in_}
	462	(( i_ = i+1 ))
	463	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	464	eval file_out=${file_out_}
[247]	465
[778]	466	# define CumulPeriod definition for this file
	467	(( i__ = i+2 ))
	468	eval SmoothDef=\${${ListFilesName}[$i__]}
	469	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
	470	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
	471	j=1
	472	for val in ${aux} ; do
	473	[ ${j} -eq 1 ] && SmoothMin=${val}
	474	[ ${j} -eq 2 ] && SmoothMax=${val}
	475	[ ${j} -eq 3 ] && ret=${val}
	476	(( j=j+1 ))
	477	done
	478	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
	479	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
[548]	480
[778]	481	IGCM_sys_IsFileArchived ${file_in}
	482	if [ $? = 0 ] ; then
	483	IGCM_sys_Get ${file_in} ${file_out}
	484	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	485	else
	486	IGCM_sys_Cp ${file_in} ${file_out}
	487	fi
	488	fi
	489	(( i=i+3 ))
[544]	490	done
	491	fi
	492	done
[778]	493
[544]	494	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
[247]	495	}
	496
	497	#=======================================================================
[2]	498	function IGCM_comp_GetInputBoundaryFiles
	499	{
[544]	500	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
[2]	501
[544]	502	# Debug Print :
	503	echo
	504	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
	505	echo
[2]	506
[902]	507	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
	508	typeset file_in_ file_in file_out_ file_out
[2]	509
[544]	510	if [ ${Period} = 1 ]; then
	511	ListFixBoundary=" "
	512	fi
[2]	513
[544]	514	for comp in ${config_ListOfComponents[*]} ; do
[2]	515
[544]	516	# Define component
	517	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	518	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	519
[544]	520	# Debug Print :
	521	IGCM_debug_Print 3 "Boundary files ${compname}"
[2]	522
[544]	523	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	524
[544]	525	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
	526	ListFilesName=${compname}_BoundaryFiles_List
	527	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	528
[544]	529	if [ X${FileName0} != X${NULL_STR} ] ; then
	530	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	531
[544]	532	(( i=0 ))
	533	until [ $i -ge $NbFiles ]; do
[778]	534	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	535	eval file_in=${file_in_}
	536	(( i_ = i+1 ))
	537	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	538	eval file_out=${file_out_}
[2]	539
[778]	540	IGCM_sys_IsFileArchived ${file_in}
	541	if [ $? = 0 ] ; then
	542	IGCM_sys_Get ${file_in} ${file_out}
[809]	543	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[778]	544	else
	545	IGCM_sys_Cp ${file_in} ${file_out}
	546	fi
[2]	547
[778]	548	(( i=i+2 ))
[544]	549	done
	550	fi
[2]	551
[544]	552	# Get non deleted files
	553	if [ ${Period} = 1 ]; then
[2]	554
[544]	555	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
	556	ListFilesName=${compname}_BoundaryFiles_ListNonDel
	557	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	558
[544]	559	if [ X${FileName0} != X${NULL_STR} ] ; then
[778]	560	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	561
[778]	562	(( i=0 ))
	563	until [ $i -ge $NbFiles ]; do
	564	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	565	eval file_in=${file_in_}
	566	(( i_ = i+1 ))
	567	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	568	eval file_out=${file_out_}
[2]	569
[778]	570	IGCM_sys_IsFileArchived ${file_in}
	571	if [ $? = 0 ] ; then
	572	IGCM_sys_Get ${file_in} ${file_out}
	573	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
	574	else
	575	IGCM_sys_Cp ${file_in} ${file_out}
	576	fi
[2]	577
[778]	578	if [ X${file_out} != X. ] ; then
	579	ListFixBoundary=${ListFixBoundary}" "${file_out}
	580	else
	581	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
	582	fi
	583
	584	(( i=i+2 ))
	585	done
[544]	586	fi
	587	fi
	588	done
[778]	589
[544]	590	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
[2]	591	}
	592
	593	#=======================================================================
	594	function IGCM_comp_DelFixeBoundaryFiles
	595	{
[544]	596	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	597
[544]	598	# Debug Print :
	599	echo
	600	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
	601	echo
[2]	602
[544]	603	ls -l ${ListFixBoundary}
	604	rm -f ${ListFixBoundary}
[2]	605
[544]	606	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
[2]	607	}
	608
	609	#=======================================================================
	610	function IGCM_comp_GetInputParametersFiles
	611	{
[544]	612	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
[2]	613
[544]	614	# Debug Print :
	615	echo
	616	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
	617	echo
[2]	618
[544]	619	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
	620	for comp in ${config_ListOfComponents[*]} ; do
[902]	621	# Define component
[544]	622	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	623	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	624
[1338]	625	# Initialize array hosting file_def and field_def files to check and/or modify
	626	unset FieldDef
	627	unset FileDef
	628
[544]	629	# Debug Print :
	630	IGCM_debug_Print 3 "Parameters ${compname}"
[2]	631
[778]	632	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	633
[544]	634	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
	635	ListFilesName=${compname}_ParametersFiles_List
	636	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	637
[544]	638	if [ X${FileName0} != X${NULL_STR} ] ; then
	639	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	640
[544]	641	(( i=0 ))
	642	until [ $i -ge $NbFiles ]; do
[778]	643	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	644	eval file_in=${file_in_}
	645	(( i_ = i+1 ))
	646	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
[902]	647	eval file_out=${file_out_}
[2]	648
[902]	649	IGCM_sys_Cp ${file_in} ${file_out}
[778]	650	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
[1338]	651	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
[2]	652
[778]	653	(( i=i+2 ))
[544]	654	done
	655	fi
[1338]	656
[544]	657	done
[2]	658
[544]	659	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
[2]	660	}
	661
	662	#=======================================================================
	663	function IGCM_comp_GetInputRestartFiles
	664	{
[544]	665	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
[2]	666
[544]	667	# Debug Print :
	668	echo
	669	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
	670	echo
[2]	671
[590]	672	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
	673	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
[902]	674	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
[544]	675	typeset file_in file_out file_in_ file_out_ file_in_Name
	676	typeset -Z4 j4
[821]	677	#BASH declare j4
[2]	678
[778]	679	IsMatching=""
	680
[544]	681	for comp in ${config_ListOfComponents[*]} ; do
[902]	682	# Define component
[544]	683	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	684	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
	685	#
	686	card=${SUBMIT_DIR}/COMP/${compname}.card
	687	#
	688	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	689	ListFilesName=${compname}_RestartFiles_List
	690	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	691
[544]	692	# Debug Print :
	693	IGCM_debug_Print 3 "restart ${compname}"
[2]	694
[544]	695	if ( ${FirstInitialize} ) ; then
[2]	696
[1401]	697	if ( [ "${config_Restarts_OverRule}" = "y" ] \|\| [ "${config_Restarts_OverRule}" = "Y" ] ) ; then
[1446]	698	# Adhoc exception for CMIP6 : exclude XIOS from the restart overrule mechanism.
[1538]	699	if ( [ X${comp} = XIOS ] ) && ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
[1447]	700	CompOldName=IOS
	701	config_IOS_Restart="n"
	702	do_start="n"
[1449]	703	config_IOS_RestartDate=-1
	704	config_IOS_RestartJobName=${NULL_STR}
	705	config_IOS_RestartPath=${NULL_STR}
[1447]	706	else
[1446]	707	eval config_${comp}_Restart="y"
	708	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
	709	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
	710	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
	711	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
	712	eval CompOldName=${comp}
	713	fi
[544]	714	else
[778]	715	# Read component Restarts parameters
	716	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
	717	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
[2]	718
[778]	719	if [ "${do_start}" = "y" ] ; then
	720	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
	721	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
	722	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
	723	else
	724	eval config_${comp}_RestartDate=-1
	725	eval config_${comp}_RestartJobName=${NULL_STR}
	726	eval config_${comp}_RestartPath=${NULL_STR}
	727	fi
[849]	728
[778]	729	eval CompOldName=\${config_${comp}_OldName}
	730	if [ X${CompOldName} = X ] ; then
	731	eval CompOldName=${comp}
	732	fi
	733
	734	# Reinitialize IsMatching to allow searching for a different tar file for each component.
	735	IsMatching=""
	736	TarFileFound=""
[544]	737	fi
[2]	738
[544]	739	if [ "${do_start}" = "y" ] ; then
[2]	740
[672]	741	# Restore Restarts files
	742	#-----------------------
[778]	743	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	744	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	745
[778]	746	(( i=1 ))
	747	until [ $i -gt $NbFiles ]; do
	748	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	749	eval file_in=${file_in_}
	750	(( i_ = i+1 ))
	751	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	752	eval file_out=${file_out_}
	753
	754	eval Date_tmp=\${config_${comp}_RestartDate}
	755	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
[672]	756	# will be re-use
	757	eval RestartPath=\${config_${comp}_RestartPath}
	758	eval RestartJobName=\${config_${comp}_RestartJobName}
	759	#
[778]	760	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
	761	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
[2]	762
[778]	763	extension_in=$( echo ${file_in_Name##*.} )
	764	extension_out=$( echo ${file_out##*.} )
[672]	765
[778]	766	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	767	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
[2]	768
[778]	769	Path_OUT=${Path_r}/${generic_restart_file_name_in}
	770
[672]	771	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	772	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
[778]	773	Buffered=true
	774	Archived=false
	775	Tared=false
	776	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
[672]	777	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	778	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	779	Buffered=false
	780	Archived=true
	781	Tared=false
	782	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
[672]	783	else
[897]	784	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
	785	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
[902]	786	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
[778]	787	Buffered=false
	788	Archived=false
	789	Tared=true
[672]	790	# Look after the tar file we want if we did not found it already
[778]	791	if [ X${IsMatching} = X ] ; then
[947]	792	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
	793	if [ $? ] ; then
[897]	794	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
	795	IsMatching=$( echo ${PotentialTarFile##*/} \| \
	796	sed "s:_restart::" \| \
	797	sed "s:^${RestartJobName}_::" \| \
	798	sed "s:\.tar$::" \| \
	799	gawk -F_ -v restartdate=${Date_r} \
	800	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	801	if [ ! X${IsMatching} = X ] ; then
	802	TarFileFound=${PotentialTarFile}
	803	break
	804	fi
	805	done
[1017]	806	fi
	807	# Stop here if nothing has been found
	808	if [ X${TarFileFound} = X ] ; then
[902]	809	IGCM_debug_Print 3 "Restart files were not found!"
	810	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	811	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
[897]	812	IGCM_debug_Exit "Please double check restart settings in config.card"
	813	IGCM_debug_Verif_Exit
	814	fi
[778]	815	fi
[918]	816	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	817	TarFileLocation=$( basename ${TarFileFound} )
[801]	818	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	819	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	820	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	821	fi
[672]	822
	823	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	824	j=0 # BASH LINE NOT NEEDED
	825	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	826	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	827	j4=${j} # BASH LINE NOT NEEDED
[778]	828	if [ X${Buffered} = Xtrue ] ; then
	829	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	830	elif [ X${Archived} = Xtrue ] ; then
	831	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	832	elif [ X${Tared} = Xtrue ] ; then
	833	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	834	fi
[821]	835	(( j=j+1 )) #BASH LINE NOT NEEDED
[778]	836	done
[740]	837
[1248]	838	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
	839	if [ X${OCE_PROC_MPI} != X ] ; then
	840	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
[1380]	841	IGCM_sys_rebuild_nemo ${generic_restart_file_name_out} ${nb_restart_file} ${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
[740]	842	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
	843	fi
	844	fi
[778]	845	else
	846	if [ X${Buffered} = Xtrue ] ; then
	847	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
	848	elif [ X${Archived} = Xtrue ] ; then
	849	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
	850	elif [ X${Tared} = Xtrue ] ; then
	851	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	852	fi
	853	fi
	854	(( i=i+3 ))
	855	done
	856	else
	857	if [ X${FileName0} != XNONE ] ; then
	858	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	859	else
	860	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	861	fi
	862	fi
[544]	863	fi
[893]	864	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
[544]	865	# if not FirstInitialize and first loop of this job
[2]	866
[544]	867	# Restore Restarts files
	868	#-----------------------
	869	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
[778]	870	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[2]	871
[778]	872	(( i=1 ))
	873	until [ $i -gt $NbFiles ]; do
	874	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	875	eval file_in=${file_in_}
	876	(( i_ = i+1 ))
	877	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	878	eval file_out=${file_out_}
[2]	879
[1028]	880	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
[662]	881
[778]	882	extension_in=$( echo ${file_in_Name##*.} )
	883	extension_out=$( echo ${file_out##*.} )
[67]	884
[778]	885	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
	886	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
	887
	888	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
	889	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
	890
[662]	891	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	892	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
[778]	893	Buffered=true
	894	Archived=false
	895	Tared=false
	896	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
[672]	897	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
[897]	898	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
[778]	899	Buffered=false
	900	Archived=true
	901	Tared=false
	902	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
	903	else
[897]	904	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
[902]	905	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
[778]	906	Buffered=false
	907	Archived=false
	908	Tared=true
	909	# Look after the tar file we want if we did not found it already
	910	if [ X${IsMatching} = X ] ; then
[801]	911	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
[778]	912	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
	913	if [ ! X${IsMatching} = X ] ; then
	914	TarFileFound=${PotentialTarFile}
	915	break
	916	fi
	917	done
	918	fi
[1017]	919	# Stop here if nothing has been found
	920	if [ X${TarFileFound} = X ] ; then
	921	IGCM_debug_Print 3 "Restart files were not found!"
	922	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
	923	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
	924	IGCM_debug_Exit "Please double check restart settings in config.card"
	925	IGCM_debug_Verif_Exit
	926	fi
[918]	927	IGCM_sys_PrepareTaredRestart ${TarFileFound}
	928	TarFileLocation=$( basename ${TarFileFound} )
[801]	929	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
	930	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
[778]	931	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
	932	fi
[41]	933
[778]	934	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	935	j=0 # BASH LINE NOT NEEDED
	936	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	937	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	938	j4=${j} # BASH LINE NOT NEEDED
[778]	939	if [ X${Buffered} = Xtrue ] ; then
	940	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	941	elif [ X${Archived} = Xtrue ] ; then
	942	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	943	elif [ X${Tared} = Xtrue ] ; then
	944	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
	945	fi
[821]	946	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	947	done
	948	else
	949	if [ X${Buffered} = Xtrue ] ; then
	950	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
	951	elif [ X${Archived} = Xtrue ] ; then
	952	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
	953	elif [ X${Tared} = Xtrue ] ; then
	954	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
	955	fi
	956	fi
	957	(( i=i+3 ))
	958	done
[544]	959	else
[778]	960	if [ X${FileName0} != XNONE ] ; then
	961	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
	962	else
	963	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
	964	fi
[544]	965	fi
[420]	966	fi
[544]	967	done
[420]	968
[544]	969	NbFiles=$( ls * 2> /dev/null \| wc -l )
	970	if [ ${NbFiles} -gt 0 ] ; then
	971	IGCM_sys_Chmod u+rw *
	972	fi
	973
	974	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
[2]	975	}
	976
	977	#=======================================================================
[1409]	978	function IGCM_comp_GetInputBinaryFiles
	979	{
	980	IGCM_debug_PushStack "IGCM_comp_GetInputBinaryFiles"
	981
	982	# Debug Print :
	983	echo
	984	IGCM_debug_Print 1 "IGCM_comp_GetInputBinaryFiles"
	985	echo
	986
	987	# Clean up previous pass
	988	[ -f ${RUN_DIR}/compiler.txt ] && rm -f ${RUN_DIR}/compiler.txt
	989
[1411]	990	typeset comp ExeNameIn ExeNameOut byPass
[1409]	991	typeset compilerNmbr compilerUnit compilerFull
[1411]	992	byPass=false
[1409]	993	for comp in ${config_ListOfComponents[*]} ; do
	994	# Define component
	995
	996	# Copy executable for this component
	997	eval ExeNameIn=\${config_Executable_${comp}[0]}
	998	eval ExeNameOut=\${config_Executable_${comp}[1]}
[1486]	999	# Test if missing executable and DRYRUN is set to 0 or 1, then stop!
	1000	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] ; then
	1001	# The executable is set in config.card and is different from ""
	1002	# Use eval to expand ExeNameIn if variables are used in the name
	1003	eval ExeNameIn=${ExeNameIn}
	1004	if [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
	1005	IGCM_debug_Exit "IGCM_comp_GetInputBinaryFiles missing executable ${ExeNameIn}"
	1006	fi
[1409]	1007	fi
	1008
	1009	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
	1010	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
	1011	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1012	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
	1013	fi
	1014	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; 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	fi
	1020
	1021	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
	1022	# Get the compiler version
	1023	compilerFull=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1024	compilerVersion=$( strings ${RUN_DIR}/${ExeNameOut} \| grep "RTL Message Catalog" \| gawk '{print $6}' \| gawk -F. '{print $1}' )
	1025	# Save it
	1026	echo $compilerFull >> ${RUN_DIR}/compiler.txt
[1411]	1027	[ X${compilerFull} = X ] && byPass=true
[1409]	1028	IGCM_debug_Print 1 "${RUN_DIR}/${ExeNameOut} has been compiled with ${compilerFull}"
[1413]	1029	IGCM_debug_Print 1 "Compiler is ${compilerVersion}"
[1409]	1030	fi
	1031	done
	1032
	1033	compilerNmbr=$( cat ${RUN_DIR}/compiler.txt \| wc -l )
	1034	compilerUnit=$( cat ${RUN_DIR}/compiler.txt \| sort \| uniq -c )
	1035
[1411]	1036	if ( [ ${compilerNmbr} -ne ${compilerUnit} ] && [ ! X${byPass} = Xtrue ] ); then
[1409]	1037	IGCM_debug_Exit "Binaries has not been compiled with the same compiler version"
	1038	fi
	1039
[1415]	1040
[1409]	1041	IGCM_debug_PopStack "IGCM_comp_GetInputBinaryFiles"
	1042	}
	1043
	1044	#=======================================================================
[269]	1045	function IGCM_comp_PeriodStart
	1046	{
[544]	1047	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
[269]	1048
[544]	1049	# Debug Print :
	1050	echo
	1051	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
	1052	echo
[269]	1053
[902]	1054	typeset ExeNameIn ExeNameOut
[544]	1055	typeset comp compname comptagname
	1056	for comp in ${config_ListOfComponents[*]} ; do
[902]	1057	# Define component
[544]	1058	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1059	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[269]	1060
[544]	1061	# Copy executable for this component
	1062	eval ExeNameIn=\${config_Executable_${comp}[0]}
[1486]	1063	eval ExeNameIn=${ExeNameIn}
[544]	1064	eval ExeNameOut=\${config_Executable_${comp}[1]}
[269]	1065
[544]	1066	# Debug Print
	1067	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
	1068	# UPDATE component
	1069	${comp}_PeriodStart 2> /dev/null
[269]	1070
[544]	1071	done
[269]	1072
[544]	1073	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
[269]	1074	}
	1075
[1166]	1076
	1077
[269]	1078	#=======================================================================
[1166]	1079	function IGCM_comp_modifyFile
	1080	{
	1081	#
	1082	# syntax: IGCM_comp_modifyFile filein key [value]
	1083	#
	1084	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
	1085	#
	1086	# This function is used to replace a pattern in a file for a specific variable.
	1087	#
	1088	# Arguments:
	1089	# - filein : the file in run directory in which the variable should be set
	1090	# - key : the variable to modify
	1091	# - value : the value to set the key equal to
	1092	#
	1093	IGCM_debug_PushStack "IGCM_comp_modifyFile"
	1094
	1095	typeset filein key value pattern
	1096
	1097	# Set local variables and test the arguments
	1098	if [ $# = 3 ] ; then
	1099	# Normal case with 3 arguments
	1100	filein=$1 ; key=$2 ; value=$3
	1101	else
	1102	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
	1103	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1104	return
	1105	fi
	1106	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
	1107
	1108	# Test if the file exist
	1109	if [ ! -f ${filein} ] ; then
	1110	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
	1111	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1112	return
	1113	fi
	1114
	1115	# Read the line with key in the file without the comments
	1116	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
	1117
	1118	# Verify the existance of the pattern
	1119	if [ X"${pattern}" = X ] ; then
	1120	# Variable key is not set in filein, stop.
	1121	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
	1122	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1123	return
	1124	fi
	1125
	1126	# Now change key in filein
[1176]	1127	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
	1128	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
[1166]	1129	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
	1130	\mv ${filein}.tmp ${filein}
	1131
	1132	IGCM_debug_PopStack "IGCM_comp_modifyFile"
	1133	}
	1134
	1135	#=======================================================================
[1069]	1136	function IGCM_comp_modifyDefFile
	1137	{
	1138	#
	1139	# syntax: IGCM_comp_modifyDefFile type filein key [value]
	1140	#
	1141	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
	1142	#
	1143	# This function is used to modify a parameter file for a specific variable.
[1075]	1144	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
	1145	# This function can be used in the comp.driver files for the components.
[1069]	1146	#
[1075]	1147	# Arguments:
[1081]	1148	# - type : first argument must be blocker, nonblocker or force
[1075]	1149	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1069]	1150	# otherwise this function will exit.
[1075]	1151	# For "nonblocker" case, the user can remove or modify the variable. For
	1152	# this case, as long as AUTO is not set, no modification will be done.
[1081]	1153	# For "force" case, the variable will be modified even if it is not set to AUTO
[1069]	1154	# - filein : the file in run directory of .def type in which the variable should be set
	1155	# - key : the variable to modify
[1075]	1156	# - value : the value to set the key equal to, optional. If value is not set or if
[1069]	1157	# value=DEFAULT, then a default value must be given in filein using syntax :
	1158	# key= AUTO : DEFAULT=def_value
	1159	#
[1075]	1160	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
[1069]	1161
[1166]	1162	typeset type filein key value
	1163	typeset filelist nb_occ modify
	1164
[1075]	1165	# Set local variables and test the arguments
	1166	if [ $# = 4 ] ; then
	1167	# Normal case with 4 arguments
	1168	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1169	elif [ $# = 3 ] ; then
	1170	# Normal case with 3 arguments
	1171	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1172	else
	1173	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
[1079]	1174	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1175	return
	1176	fi
[1166]	1177	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
[1069]	1178
[1075]	1179	# Test if first argument is correct
[1166]	1180	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1081]	1181	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
[1079]	1182	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1183	return
	1184	fi
[1069]	1185
[1215]	1186	# Test if the file exist.
	1187	# Exit with error if the file does not exist for the case blocker or force.
	1188	# Only return for the case nonblocker.
[1075]	1189	if [ ! -f ${filein} ] ; then
[1215]	1190	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1191	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
	1192	else
	1193	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
	1194	fi
[1079]	1195	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1196	return
	1197	fi
[1069]	1198
[1102]	1199	# Define list of files to test using all files with suffix .def (except used*.def)
	1200	filelist=$( ls *def \| grep -v used )
[1069]	1201
[1075]	1202	# Count number of occurances for the key in all files
[1166]	1203	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
[1069]	1204
[1075]	1205	# Test if key is set several times
[1166]	1206	if [ ${nb_occ} -gt 1 ] ; then
	1207	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
[1079]	1208	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1075]	1209	return
	1210	fi
	1211
	1212	# Treatement according to different cases
[1166]	1213	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
[1075]	1214	# Stop if the key is never set and the function is blocker
[1166]	1215	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
	1216	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
	1217	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
[1075]	1218	# The key is not set but it is a nonblocker call so nothing is done.
[1166]	1219	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1220	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
[1081]	1221	modify=no
[1166]	1222	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
[1075]	1223	# Variable key is not set in filein, stop.
[1166]	1224	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1081]	1225	fi
	1226
	1227	# Check if AUTO is set in the filein on the same line as the key variable
[1166]	1228	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1229	# Modification will be done for all cases
	1230	modify=yes
	1231	else
	1232	# The variable was not set to AUTO
[1166]	1233	if [ ${type} = blocker ] ; then
[1156]	1234	# Exit because this is a blocker call
[1166]	1235	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
[1190]	1236	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1156]	1237	return
[1166]	1238	elif [ ${type} = nonblocker ] ; then
[1156]	1239	# Do nothing. Suppose that the user did set the variable correct
[1166]	1240	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
[1156]	1241	modify=no
[1166]	1242	elif [ ${type} = force ] ; then
[1156]	1243	# Force modification
[1166]	1244	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
[1081]	1245	modify=yes
[1156]	1246	fi
[1081]	1247	fi
[1069]	1248
[1081]	1249	# Do the modifcation now
[1166]	1250	if [ ${modify} = yes ] ; then
[1081]	1251
[1156]	1252	# For option DEFAULT, read default value from file.
[1166]	1253	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1254	# Case to set DEFAULT value
	1255	# Read default value from filein
[1423]	1256	value=$( grep -w ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
[1069]	1257
[1166]	1258	if [ X"${value}" = X ] ; then
	1259	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
	1260	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
	1261	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1262	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
	1263	return
[1075]	1264	fi
[1156]	1265	fi
[1069]	1266
[1156]	1267	# Now change key in filein
[1166]	1268	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
	1269	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
	1270	\mv ${filein}.tmp ${filein}
[1075]	1271	fi
[1079]	1272	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
[1069]	1273	}
	1274
	1275	#=======================================================================
[1085]	1276	function IGCM_comp_modifyNamelist
	1277	{
	1278	#
	1279	# syntax: IGCM_comp_modifyNamelist type filein key [value]
	1280	#
	1281	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
	1282	#
	1283	# This function is used to modify a parameter file for a specific variable.
[1155]	1284	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
[1085]	1285	# This function can be used in the comp.driver files for the components.
	1286	#
	1287	# Arguments:
	1288	# - type : first argument must be blocker, nonblocker or force
	1289	# For "blocker" case, the variable must be attributed the keyworld AUTO
	1290	# otherwise this function will exit.
	1291	# For "nonblocker" case, the user can remove or modify the variable. For
	1292	# this case, as long as AUTO is not set, no modification will be done.
	1293	# For "force" case, the variable will be modified even if it is not set to AUTO
	1294	# - filein : the file in run directory of .def type in which the variable should be set
	1295	# - key : the variable to modify
	1296	# - value : the value to set the key equal to, optional. If value is not set or if
	1297	# value=DEFAULT, then a default value must be given in filein using syntax :
	1298	# key= AUTO : DEFAULT=def_value
	1299	#
	1300	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
	1301
[1166]	1302	typeset type filein key value pattern modify
	1303
[1085]	1304	# Set local variables and test the arguments
	1305	if [ $# = 4 ] ; then
	1306	# Normal case with 4 arguments
	1307	type=$1 ; filein=$2 ; key=$3 ; value=$4
	1308	elif [ $# = 3 ] ; then
	1309	# Normal case with 3 arguments
	1310	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
	1311	else
	1312	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
	1313	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1314	return
	1315	fi
[1166]	1316	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
[1085]	1317
	1318	# Test if first argument is correct
[1166]	1319	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1085]	1320	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
	1321	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1322	return
	1323	fi
	1324
[1215]	1325	# Test if the file exist.
	1326	# Exit with error if the file does not exist for the case blocker or force.
	1327	# Only return for the case nonblocker.
[1085]	1328	if [ ! -f ${filein} ] ; then
[1215]	1329	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1330	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
	1331	else
	1332	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
	1333	fi
[1085]	1334	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1335	return
	1336	fi
	1337
	1338	# Read the line with key in the file without the comments
[1166]	1339	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
[1155]	1340
[1085]	1341	# Verify the existance of the pattern
	1342	if [ X"$pattern" = X ] ; then
[1156]	1343	# Variable key is not set in filein, stop.
[1166]	1344	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
[1156]	1345	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1346	return
[1085]	1347	fi
[1155]	1348
[1085]	1349	# Check if the variable is set to AUTO in the filein
	1350	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
[1156]	1351	# Modification will be done for all cases
	1352	modify=yes
	1353	else
	1354	# The variable was not set to AUTO
[1166]	1355	if [ ${type} = blocker ] ; then
[1156]	1356	# Exit because this is a blocker call
[1166]	1357	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
[1156]	1358	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1359	return
[1166]	1360	elif [ ${type} = nonblocker ] ; then
[1156]	1361	# Do nothing. Suppose that the user did set the variable correct
[1166]	1362	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
[1156]	1363	modify=no
[1166]	1364	elif [ ${type} = force ] ; then
[1156]	1365	# Force modification
[1166]	1366	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
[1085]	1367	modify=yes
[1156]	1368	fi
[1085]	1369	fi
	1370
	1371	# Do the modifcation now
[1166]	1372	if [ ${modify} = yes ] ; then
[1085]	1373
[1156]	1374	# For option DEFAULT, read default value from file.
[1166]	1375	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
[1156]	1376	# Case to set DEFAULT value
	1377	# Read default value from filein
	1378	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
[1085]	1379
[1166]	1380	if [ X"${value}" = X ] ; then
	1381	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
	1382	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
	1383	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
[1156]	1384	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1385	return
[1085]	1386	fi
[1156]	1387	fi
[1085]	1388
[1156]	1389	# Now change key in filein
[1166]	1390	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
	1391	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
	1392	\mv ${filein}.tmp ${filein}
[1085]	1393	fi
	1394	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
	1395	}
	1396
	1397	#=======================================================================
[1074]	1398	function IGCM_comp_modifyXmlFile
	1399	{
	1400	#
	1401	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
	1402	#
	1403	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
	1404	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
	1405	#
	1406	# This function is used to modify the value for a specific attribute and variable id.
[1155]	1407	# The file must be a valid xml file.
[1075]	1408	# This function can be used in the comp.driver files for the components.
[1074]	1409	#
[1075]	1410	# Arguments:
	1411	# - type : first argument must be blocker, nonblocker or force.
	1412	# For "blocker" case, the variable must be attributed the keyworld AUTO
[1074]	1413	# otherwise this function will exit.
[1075]	1414	# For "nonblocker" case, the user can remove or modify the variable. For
[1074]	1415	# this case, as long as AUTO is not set, no modification will be done.
[1075]	1416	# For "force" case, the variable will be modified even if it is not set to AUTO
[1074]	1417	# - filein : the file in run directory of .xml type in which the variable should be set
	1418	# - keyid : the variable to modify
	1419	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
	1420	# - value : the value to set in the filein
	1421	#
[1075]	1422	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
[1074]	1423
[1166]	1424	typeset type filein keyid keyattrib value modify
	1425
[1075]	1426	# Set local variables and test the arguments
	1427	if [ $# = 5 ] ; then
	1428	# Normal case with 4 arguments
	1429	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
	1430	else
	1431	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
[1089]	1432	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1433	return
	1434	fi
[1166]	1435	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
[1074]	1436
[1075]	1437	# Test if first argument is correct
[1166]	1438	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
[1075]	1439	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
[1089]	1440	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1441	return
	1442	fi
[1074]	1443
[1215]	1444	# Test if the file exist.
	1445	# Exit with error if the file does not exist for the case blocker or force.
	1446	# Only return for the case nonblocker.
[1075]	1447	if [ ! -f ${filein} ] ; then
[1215]	1448	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
	1449	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
	1450	else
	1451	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
	1452	fi
[1089]	1453	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1454	return
	1455	fi
	1456
[1386]	1457	# Test if keyid is set in filein. If not exit for case all cases(blocker, force) except nonblocker.
[1166]	1458	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
[1386]	1459	if [ ${type} = nonblocker ] ; then
	1460	# This is a nonblocker case, print warning but do nothing else
	1461	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${keyid} is not set in ${filein}. This is a nonblocker call so nothing is done."
	1462	else
	1463	# This is a blocker or force case : stop now
	1464	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
	1465	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
	1466	return
	1467	fi
[1075]	1468	fi
	1469
	1470	# Check if AUTO is set on the same line as keyid and keyattrib
[1166]	1471	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
[1394]	1472	# Modification will be done
[1075]	1473	modify=yes
	1474	else
[1166]	1475	if [ ${type} = blocker ] ; then
[1075]	1476	# Exit, the variable must be set to AUTO
[1166]	1477	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
[1089]	1478	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1075]	1479	return
[1166]	1480	elif [ ${type} = nonblocker ] ; then
[1075]	1481	# Nothing will be done
	1482	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
	1483	modify=no
[1166]	1484	elif [ ${type} = force ] ; then
[1075]	1485	# Force modification
[1166]	1486	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
[1075]	1487	modify=yes
[1074]	1488	fi
[1075]	1489	fi
[1074]	1490
[1075]	1491	# Do the modifcation now
[1166]	1492	if [ ${modify} = yes ] ; then
	1493	if [ ${keyattrib} = NONE ] ; then
[1075]	1494	# Case to modify the variable itself
	1495	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
[1166]	1496	sed -e "s/$<[^\"]\"${keyid}\".>$$[^<]$$<[^>]$/\1${value}\3/" ${filein} > ${filein}.tmp
[1074]	1497	else
[1156]	1498	# Check if keyattrib is set on the same line as keyid
[1166]	1499	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
[1156]	1500	# Case to modify the attribute value
	1501	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
[1166]	1502	sed -e "/id=\"${keyid}\"/s/$${keyattrib}=\"$[^\"]*$\"$/\1${value}\2/" ${filein} > ${filein}.tmp
[1156]	1503	else
	1504	# Case to add the attribute and its value
	1505	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
[1166]	1506	sed -e "/id=\"${keyid}\"/s/\/>/ ${keyattrib}=\"${value}\"\/>/" ${filein} > ${filein}.tmp
[1156]	1507	fi
[1074]	1508	fi
[1166]	1509	\mv ${filein}.tmp ${filein}
[1075]	1510	fi
	1511	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
[1074]	1512	}
	1513
	1514	#=======================================================================
[2]	1515	function IGCM_comp_Update
	1516	{
[544]	1517	IGCM_debug_PushStack "IGCM_comp_Update"
[2]	1518
[1409]	1519	# Debug Print :
[544]	1520	echo
	1521	IGCM_debug_Print 1 "IGCM_comp_Update"
	1522	echo
[2]	1523
[544]	1524	typeset comp compname comptagname
	1525	for comp in ${config_ListOfComponents[*]} ; do
[902]	1526	# Define component
[544]	1527	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1528	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1529
[544]	1530	# Debug Print
	1531	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
	1532	# UPDATE component
	1533	${comp}_Update
[2]	1534
[1413]	1535	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
	1536	if [ -f timeseries_def_${compname}.xml ]; then
	1537	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
	1538	for line in $( cat ts.temp.${compname}.txt ); do
	1539	output_freq=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
	1540	id=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
	1541	case ${output_freq} in
	1542	Y\|y)
	1543	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
	1544	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
	1545	;;
	1546	MO\|mo)
	1547	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
	1548	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
	1549	;;
	1550	D\|d)
	1551	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
	1552	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
	1553	;;
	1554	S\|s)
	1555	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
	1556	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
	1557	;;
	1558	esac
	1559	done
	1560	fi
	1561
	1562	# Read TimeSeries information from XML files, prepare CMIP6 TS directories and do modifications in dr2xml_${compname}.xml
	1563	if [ -f dr2xml_${compname}.xml ]; then
[1535]	1564	if ( [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] \|\| [ X${config_Post_dr2xmlIPSL} = XTRUE ] ) ; then
	1565	eval IGCM_sys_Mkdir \${CMIP6_BUF_${comp}}
	1566	eval CMIP6_DIR=\${CMIP6_BUF_${comp}}
	1567	# Modify path from dr2xml_{compname}.xml
	1568	if [ X${config_Post_dr2xmlIPSL} = XTRUE ]; then
[1552]	1569	${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]	1570	else
	1571	${libIGCM}/libIGCM_post/xios_parser.py -v modifyPath --newPath ${CMIP6_DIR} --file dr2xml_${compname}.xml
	1572	fi
	1573	# Overwrite the original file
	1574	IGCM_sys_Mv modified.dr2xml_${compname}.xml dr2xml_${compname}.xml
[1467]	1575	fi
[1422]	1576	fi
[544]	1577	done
[2]	1578
[544]	1579	IGCM_debug_PopStack "IGCM_comp_Update"
[2]	1580	}
	1581
	1582	#=======================================================================
	1583	function IGCM_comp_Finalize
	1584	{
[544]	1585	IGCM_debug_PushStack "IGCM_comp_Finalize"
[2]	1586
[544]	1587	# Debug Print :
	1588	echo
	1589	IGCM_debug_Print 1 "IGCM_comp_Finalize"
	1590	echo
[2]	1591
[544]	1592	typeset ListTextName TextName0
	1593	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
	1594	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
[1165]	1595	typeset -Z4 j4 #BASH declare j4
[544]	1596	typeset list_file nlist_file
	1597	typeset compactoutputs
[429]	1598
[1165]	1599	# Initialize array hosting list of rebuilded files to copy
	1600	unset rebuildedActionsList
	1601
	1602	# Text compacting options
[544]	1603	compactoutputs=false
	1604	if [ X${JobType} != XRUN ] ; then
	1605	compactoutputs=true
	1606	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
	1607	compactoutputs=true
	1608	fi
[433]	1609
[1043]	1610	# Prepare headers for the shell dedicated to offline rebuild
	1611	if [ X${AsynchronousRebuild} = Xtrue ] ; then
	1612	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1613	if [ ${DRYRUN} -le 1 ] ; then
	1614	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1615	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1616	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1617	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1618	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1619	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1620	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1621	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1622	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1623	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1624	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1625	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1626	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1627	fi
	1628	fi
	1629
[544]	1630	for comp in ${config_ListOfComponents[*]} ; do
[902]	1631	# Define component
[544]	1632	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
	1633	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
[2]	1634
[544]	1635	# Debug Print
	1636	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
	1637	# FINALIZE component
	1638	${comp}_Finalize
[2]	1639
[778]	1640	card=${SUBMIT_DIR}/COMP/${compname}.card
[2]	1641
[804]	1642	# Save Output Text files of models
	1643	#---------------------------------
	1644	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
	1645	IGCM_card_DefineArrayFromOption ${card} OutputText List
	1646	ListTextName=${compname}_OutputText_List
	1647
	1648	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
	1649	if [ X${TextName0} != X${NULL_STR} ] ; then
	1650	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
	1651
	1652	(( i=0 ))
	1653	until [ $i -eq $NbFiles ]; do
	1654	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
	1655	eval file_out=${PREFIX}_${file_in}
	1656
	1657	(( i=i+1 ))
	1658
	1659	unset list_file
	1660	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
	1661	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
	1662	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 )
	1663	nlist_file=${#list_file[@]}
	1664	if [ ${nlist_file} -gt 1 ] ; then
	1665	if ( ${compactoutputs} ) ; then
	1666	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
	1667	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
	1668	echo ${list_file[*]} > ${file_out}
	1669	echo "" >> ${file_out}
	1670
	1671	(( i_ = 0 ))
[1080]	1672	for file in ${list_file[@]} ; do
[804]	1673	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
	1674	echo "\| " ${i_} " " ${file} >> ${file_out}
	1675	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
[999]	1676	cat ${file} \| sed "s/$.*$/${i_}\1/" >> ${file_out}
[804]	1677	echo "" >> ${file_out}
	1678	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1679	(( i_ = i_ + 1 ))
	1680	done
[1080]	1681	if ( ${ExecutionFail} ) ; then
	1682	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
	1683	fi
	1684
[804]	1685	if [ X${Pack} = Xtrue ] ; then
	1686	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
	1687	else
	1688	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
	1689	fi
[1080]	1690
[804]	1691	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
[1080]	1692	else
	1693	for file in ${list_file[@]} ; do
	1694	if ( ${ExecutionFail} ) ; then
	1695	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
	1696	fi
[804]	1697
	1698	if [ X${Pack} = Xtrue ] ; then
	1699	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
	1700	else
	1701	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
	1702	fi
[1080]	1703
[804]	1704	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
	1705	done
	1706	fi
	1707	else
	1708	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
	1709	eval IGCM_sys_Mv ${file_in}* ${file_in}
	1710	fi
[1080]	1711
	1712	if ( ${ExecutionFail} ) ; then
	1713	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
	1714	fi
	1715
[804]	1716	if [ X${Pack} = Xtrue ] ; then
	1717	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
	1718	else
	1719	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
	1720	fi
	1721	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1722	fi
	1723	done
	1724	fi
	1725
[544]	1726	# Save Restarts files
	1727	#--------------------
	1728	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
	1729	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
	1730	ListFilesName=${compname}_RestartFiles_List
	1731	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[778]	1732
[544]	1733	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
	1734	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[778]	1735
[544]	1736	(( i=0 ))
	1737	until [ $i -ge $NbFiles ]; do
[778]	1738	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1739	eval file_in=${file_in_}
[2]	1740
[778]	1741	(( i_ = i+1 ))
	1742	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1743	eval file_out=${file_out_}
[151]	1744
[778]	1745	(( i_ = i+2 ))
	1746	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1747	eval file_outin=${file_outin_}
[151]	1748
[778]	1749	generic_restart_file_name_in=$( basename ${file_in} .nc )
	1750	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
	1751	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
[2]	1752
[902]	1753	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
[778]	1754	if [ ${nb_restart_file} -gt 1 ] ; then
[821]	1755	j=0 # BASH LINE NOT NEEDED
	1756	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
	1757	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
	1758	j4=${j} # BASH LINE NOT NEEDED
[778]	1759	if [ X${Pack} = Xtrue ] ; then
	1760	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1761	else
	1762	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
	1763	fi
	1764	if [ ! ${file_in} = ${file_outin} ] ; then
	1765	if ( ${ExitFlag} ) ; then
	1766	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
	1767	else
	1768	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
	1769	fi
	1770	fi
[821]	1771	(( j=j+1 )) # BASH LINE NOT NEEDED
[778]	1772	done
	1773	else
	1774	if [ X${Pack} = Xtrue ] ; then
	1775	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1776	else
	1777	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
	1778	fi
	1779	if [ ! ${file_in} = ${file_outin} ] ; then
	1780	if ( ${ExitFlag} ) ; then
	1781	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
	1782	else
	1783	IGCM_sys_Mv ${file_in} ${file_outin}
	1784	fi
	1785	fi
	1786	fi
	1787
	1788	(( i=i+3 ))
[544]	1789	done
	1790	else
	1791	if [ X${FileName0} != XNONE ] ; then
[778]	1792	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
[544]	1793	else
[778]	1794	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
[544]	1795	fi
	1796	fi
[2]	1797
[544]	1798	# Save Output files
	1799	#------------------
	1800	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
	1801	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
	1802	ListFilesName=${compname}_OutputFiles_List
	1803	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
[2]	1804
[544]	1805	if [ X${FileName0} != X${NULL_STR} ] ; then
	1806	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
[149]	1807
[544]	1808	(( i=0 ))
	1809	until [ $i -ge $NbFiles ]; do
[778]	1810	SaveOnArchive=true
	1811	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
	1812	eval file_in=${file_in_}
	1813	(( i_ = i+1 ))
	1814	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1815	eval file_out=${file_out_}
	1816	#
	1817	# Override file_out path remplacing R_SAVE by R_BUFR
	1818	#
	1819	if [ X${Pack} = Xtrue ] ; then
	1820	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
	1821	fi
	1822	#
	1823	# Not necessarily the best option. /!\ Potential side effects /!\
	1824	#
	1825	(( i_ = i+2 ))
	1826	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1827	#
	1828	generic_file_name=$( basename ${file_in} .nc )
	1829	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
	1830	#
	1831	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
[804]	1832	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
[778]	1833	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
	1834	elif [ ${nb_rebuild_file} -gt 1 ] ; then
[804]	1835	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
[778]	1836	if [ X${AsynchronousRebuild} = Xfalse ] ; then
	1837	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
[1388]	1838	#
	1839	# for output.abort file, let use rebuild_NEMO : 13s instead of 20 mn.
	1840	if [ ${file_in} = output.abort.nc ] ; then
	1841	IGCM_sys_rebuild_nemo ${generic_file_name} ${nb_rebuild_file} "nc" ${generic_file_name}_[0-9]*.nc
	1842	else
[1429]	1843	IGCM_sys_rebuild ${file_in} ${generic_file_name}_????.nc
[1388]	1844	fi
[778]	1845	else
	1846	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
[1429]	1847	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
[544]	1848
[778]	1849	# Prepare the shell dedicated to offline rebuild
	1850	if [ $DRYRUN -le 1 ]; then
[694]	1851	if [ ${file_in} = histstn.nc ] ; then
	1852	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1853	else
[980]	1854	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[694]	1855	fi
[1206]	1856	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1857	fi
	1858	#
	1859	# Load Patch we need to apply and apply
	1860	if [ $DRYRUN -le 1 ]; then
	1861	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
[1080]	1862	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1863	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1864	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1865	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1866	done
	1867	fi
	1868	fi
	1869	#
	1870	if [ $DRYRUN -le 1 ]; then
	1871	if [ X${Pack} = Xtrue ] ; then
[1165]	1872	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
[778]	1873	else
[1165]	1874	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
[778]	1875	fi
[1206]	1876	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
[1165]	1877	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
[778]	1878	fi
	1879	SaveOnArchive=false
	1880	fi
	1881	fi
	1882	#
	1883	if [ ${SaveOnArchive} = true ] ; then
	1884	#
	1885	# Rebuild has been done online or it was not needed
	1886	#
	1887	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
	1888	#
	1889	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
[1289]	1890	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
[778]	1891	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
	1892	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
	1893	#
	1894	if [ $DRYRUN -le 1 ]; then
[1080]	1895	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
[778]	1896	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1897	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1206]	1898	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1899	done
	1900	#
	1901	if [ X${Pack} = Xtrue ] ; then
	1902	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1903	else
	1904	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1905	fi
[1206]	1906	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[778]	1907	#
	1908	fi
	1909	else
	1910	#
	1911	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
	1912	#
	1913	if [ X${Pack} = Xtrue ] ; then
	1914	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
	1915	else
	1916	IGCM_sys_Put_Out ${file_in} ${file_out}
	1917	fi
	1918	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
	1919	if [ ${nb_rebuild_file} -gt 1 ] ; then
	1920	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
	1921	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
	1922	done
	1923	fi
	1924	fi
	1925	fi
[1603]	1926	((i_ = i_ +1))
	1927	eval Testvar_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
	1928	eval Testvar=${Testvar_}
	1929	if [[ ${Testvar} =~ [0-9][DMY]$ ]] ; then
	1930	((i = i+4))
	1931	else
[778]	1932	(( i=i+3 ))
[1603]	1933	fi
[544]	1934	done
	1935	fi
	1936	echo
	1937	done
[1165]	1938	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
	1939	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
[1166]	1940	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
[1165]	1941	i=0
	1942	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
	1943	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
	1944	(( i=i+1 ))
	1945	done
	1946	fi
[544]	1947	IGCM_debug_PopStack "IGCM_comp_Finalize"
[2]	1948	}

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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1603

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