Context Navigation

source: tags/libIGCM_v2.5/libIGCM_comp/libIGCM_comp.ksh @ 1456

Last change on this file since 1456 was 1166, checked in by sdipsl, 9 years ago
the metrics template need more information create IGCM_comp_modifyFile function to simply replace pattern in files code cleanup
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: 71.4 KB

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

Note: See TracBrowser for help on using the repository browser.

Download in other formats: