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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 1388

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

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