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source: trunk/libIGCM/libIGCM_comp/libIGCM_comp.ksh @ 159

Last change on this file since 159 was 159, checked in by sdipsl, 15 years ago
Bugfix with test regarding Patch files and empty option Bugfix with rebuildFromWorkdir Job
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 `Date Author Revision`
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1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
5	# Contact: Sebastien.Denvil@ipsl.jussieu.fr Martial.Mancip@ipsl.jussieu.fr
6	# $Date$
7	# $Author$
8	# $Revision$
9	# IPSL (2006)
10	# This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11	# History:
12	# Modification:
13	#
14	#**************************************************************
15
16	#========================================================================
17	function IGCM_comp_Initialize
18	{
19	IGCM_debug_PushStack "IGCM_comp_Initialize"
20
21	# Debug Print :
22	echo
23	IGCM_debug_Print 1 "IGCM_comp_Initialize :"
24	echo
25
26	typeset comp compname comptagname CompatibilityTag auxprint card_UserChoices first_option i j
27	for comp in ${config_ListOfComponents[*]} ; do
28	# Debug Print
29	IGCM_debug_Print 1 ${comp}
30	# Define component
31	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
32	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
33	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
34
35	# Read libIGCM compatibility version in ${compname}.card
36	card=${SUBMIT_DIR}/COMP/${compname}.card
37	IGCM_card_DefineVariableFromOption ${card} Compatibility libIGCM
38	eval CompatibilityTag=\${${compname}_Compatibility_libIGCM} > /dev/null 2>&1
39
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	# Read component Write Frequency in config.card
48	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} WriteFrequency
49	# Debug Print :
50	eval auxprint=\${config_${comp}_WriteFrequency}
51	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
52	#2> /dev/null
53
54	# Debug Print :
55	IGCM_debug_Print 1 "Initialize following component library :"
56	IGCM_debug_Print 1 ${SUBMIT_DIR}/COMP/${compname}.driver
57	IGCM_debug_Print 3 "With tag : ${comptagname}"
58	# Source component library
59	. ${SUBMIT_DIR}/COMP/${compname}.driver
60
61	# Debug Print
62	IGCM_debug_Print 3 "Initialize ${comp} output directory."
63	# Define Dirs
64	eval R_OUT_${comp}=${R_SAVE}/${comp}
65	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
66
67	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
68	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
69
70	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
71	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
72
73	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
74	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
75
76	eval R_OUT_${comp}_O_I=\${R_OUT_${comp}_O}/INS
77	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
78	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
79	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
80	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
81
82	# Read UserChoices section of component card
83	IGCM_debug_Print 1 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
84	IGCM_card_DefineArrayFromSection ${card} UserChoices
85	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
86	if [ X${first_option} != X"Error:" ] ; then
87	eval IGCM_debug_Print 2 "${compname}_UserChoices_Options:" \${${compname}_UserChoices[*]}
88	if [ X${card_UserChoices[0]} != X ] ; then
89	unset card_UserChoices
90	fi
91	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
92	typeset option
93	for option in ${card_UserChoices[*]} ; do
94	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
95	eval IGCM_debug_Print 3 "${compname}_UserChoices_values: ${option} \${card_UserChoices_${option}}"
96	done
97	fi
98
99	# Read and Build Output File stuff
100	IGCM_debug_Print 1 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
101	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
102	ListFilesName=${compname}_OutputFiles_List
103	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
104	#
105	if [ X${FileName0} != X${NULL_STR} ] ; then
106	#
107	#IGCM_debug_Print 1 "Component : ${compname}"
108	#
109	# INITIALISATION
110	#
111	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
112	i=2
113	#
114	until [ $i -ge $NbFiles ]; do
115	#
116	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
117	#
118	if [ X${flag_post} != XNONE ] ; then
119	# A mettre demain (11/08/2009) : dÃ©pendance Dimension 2D:3D
120	# Dimension = vide si vieille card.
121	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
122	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
123	if [ "$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = "Option not found ${flag_post}" ] ; then
124	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
125	ListDimension[0]=2D
126	ListDimension[1]=3D
127	TimeSeries=false
128	iLoop=${#ListDimension[*]}
129	j=0
130	until [ $j -ge ${iLoop} ]; do
131	Dimension=${ListDimension[${j}]}
132	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
133	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
134	#
135	# Time series WITHOUT chunk
136	#
137	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
138	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
139	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post} according to ${card}"
140	eval TimeSeries${Dimension}=true
141	fi
142	fi
143	#
144	# Time series WITH chunk
145	#
146	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
147	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
148	if [ ! ${chunck_size} = NONE ] ; then
149	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post} according to ${card}"
150	eval TimeSeriesChunck${Dimension}=true
151	eval set +A CHUNCK${Dimension}_COMP \${CHUNCK${Dimension}_COMP[*]} ${comp}
152	eval set +A CHUNCK${Dimension}_FLAG \${CHUNCK${Dimension}_FLAG[*]} ${i}
153	eval set +A CHUNCK${Dimension}_SIZE \${CHUNCK${Dimension}_SIZE[*]} ${chunck_size}
154	fi
155	fi
156	(( j=j+1 ))
157	done
158	else
159	ListDimension[0]=""
160	TimeSeries=true
161	TimeSeries2D=false
162	TimeSeries3D=false
163	TimeSeriesChunck2D=false
164	TimeSeriesChunck3D=false
165	fi
166	fi
167	(( i=i+3 ))
168	done
169	fi
170	# Debug Print
171	IGCM_debug_Print 3 "Initialize ${compname} with driver."
172	# INIT component
173	${comp}_Initialize
174	echo
175	done
176	echo "-----"
177	echo
178	IGCM_debug_Print 1 "DefineArrayFromOption : ListOfComponents"
179	IGCM_debug_PrintVariables 3 config_ListOfComponents
180
181	IGCM_debug_PopStack "IGCM_comp_Initialize"
182	}
183
184	#=======================================================================
185	function IGCM_comp_PrepareDeletedFiles
186	{
187	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
188
189	if [ X${2} != X. ] ; then
190	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
191	else
192	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
193	fi
194
195	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
196	}
197
198	#=======================================================================
199	function IGCM_comp_GetInputInitialStateFiles
200	{
201	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
202
203	# Debug Print :
204	echo
205	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles :"
206	echo
207
208	# Only the first time step need InitialStateFiles
209	# otherwise it's BoundaryConditions
210	if ( ${FirstInitialize} ) ; then
211	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
212	typeset file_in_ file_in file_out_ file_out do_init
213	for comp in ${config_ListOfComponents[*]} ; do
214	# Initialize
215	do_init="y"
216	# Do we need to bring initial state file for this component
217	if [ "${config_Restarts_OverRule}" = "y" ] ; then
218	eval do_init="n"
219	else
220	# Read component Restarts parameters
221	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
222	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
223	if [ "${do_start}" = "y" ] ; then
224	do_init="n"
225	else
226	do_init="y"
227	fi
228	fi
229
230	if [ "${do_init}" = "y" ] ; then
231	# Define component
232	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
233	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
234
235	# Debug Print :
236	IGCM_debug_Print 3 "Initialisation files ${compname}"
237
238	card=${SUBMIT_DIR}/COMP/${compname}.card
239
240	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
241	ListFilesName=${compname}_InitialStateFiles_List
242
243	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
244	if [ X${FileName0} != X${NULL_STR} ] ; then
245	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
246
247	(( i=0 ))
248	until [ $i -ge $NbFiles ]; do
249	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
250	eval file_in=${file_in_}
251	(( i_ = i+1 ))
252	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
253	eval file_out=${file_out_}
254
255	IGCM_sys_Get ${file_in} ${file_out}
256	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
257
258	(( i=i+2 ))
259	done
260	fi
261	fi
262	done
263	fi
264	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
265	}
266
267	#=======================================================================
268	function IGCM_comp_GetInputBoundaryFiles
269	{
270	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
271
272	# Debug Print :
273	echo
274	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles :"
275	echo
276
277	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
278	typeset file_in_ file_in file_out_ file_out
279
280	if [ ${Period} = 1 ]; then
281	ListFixBoundary=" "
282	fi
283
284	for comp in ${config_ListOfComponents[*]} ; do
285
286	echo "-----"
287	# Define component
288	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
289	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
290
291	# Debug Print :
292	IGCM_debug_Print 3 "Boundary files ${compname}"
293
294	card=${SUBMIT_DIR}/COMP/${compname}.card
295
296	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
297	ListFilesName=${compname}_BoundaryFiles_List
298	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
299
300	if [ X${FileName0} != X${NULL_STR} ] ; then
301	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
302
303	(( i=0 ))
304	until [ $i -ge $NbFiles ]; do
305	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
306	eval file_in=${file_in_}
307	(( i_ = i+1 ))
308	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
309	eval file_out=${file_out_}
310
311	IGCM_sys_Get ${file_in} ${file_out}
312	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
313
314	(( i=i+2 ))
315	done
316	fi
317
318	# Get non deleted files
319	if [ ${Period} = 1 ]; then
320
321	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
322	ListFilesName=${compname}_BoundaryFiles_ListNonDel
323	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
324
325	if [ X${FileName0} != X${NULL_STR} ] ; then
326	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
327
328	(( i=0 ))
329	until [ $i -ge $NbFiles ]; do
330	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
331	eval file_in=${file_in_}
332	(( i_ = i+1 ))
333	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
334	eval file_out=${file_out_}
335
336	IGCM_sys_Get ${file_in} ${file_out}
337
338	if [ X${file_out} != X. ] ; then
339	ListFixBoundary=${ListFixBoundary}" "${file_out}
340	else
341	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
342	fi
343
344	(( i=i+2 ))
345	done
346	fi
347	fi
348	done
349
350	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
351	}
352
353	#=======================================================================
354	function IGCM_comp_DelFixeBoundaryFiles
355	{
356	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
357
358	# Debug Print :
359	echo
360	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles :"
361	echo
362
363	ls -l ${ListFixBoundary}
364	rm -f ${ListFixBoundary}
365
366	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
367	}
368
369	#=======================================================================
370	function IGCM_comp_GetInputParametersFiles
371	{
372	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
373
374	# Debug Print :
375	echo
376	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles :"
377	echo
378
379	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
380	for comp in ${config_ListOfComponents[*]} ; do
381	# Define component
382	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
383	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
384
385	# Debug Print :
386	IGCM_debug_Print 3 "Parameters ${compname}"
387
388	card=${SUBMIT_DIR}/COMP/${compname}.card
389
390	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
391	ListFilesName=${compname}_ParametersFiles_List
392	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
393
394	if [ X${FileName0} != X${NULL_STR} ] ; then
395	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
396
397	(( i=0 ))
398	until [ $i -ge $NbFiles ]; do
399	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
400	eval file_in=${file_in_}
401	(( i_ = i+1 ))
402	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
403	eval file_out=${file_out_}
404
405	IGCM_sys_Cp ${file_in} ${file_out}
406	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
407
408	(( i=i+2 ))
409	done
410	fi
411	done
412
413	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
414	}
415
416	#=======================================================================
417	function IGCM_comp_GetInputRestartFiles
418	{
419	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
420
421	# Debug Print :
422	echo
423	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles :"
424	echo
425
426	typeset Date_tmp Date_r Path_r do_start CompOldName Path_temp
427	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
428	typeset file_in file_out file_in_ file_out_ file_in_Name
429	typeset -Z4 j4
430
431	for comp in ${config_ListOfComponents[*]} ; do
432	# Define component
433	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
434	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
435	#
436	card=${SUBMIT_DIR}/COMP/${compname}.card
437	#
438	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
439	ListFilesName=${compname}_RestartFiles_List
440	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
441
442	# Debug Print :
443	IGCM_debug_Print 3 "restart ${compname}"
444
445	if ( ${FirstInitialize} ) ; then
446
447	if [ "${config_Restarts_OverRule}" = "y" ] ; then
448	eval config_${comp}_Restart="y"
449	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
450	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
451	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
452	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
453	eval CompOldName=${comp}
454	else
455	# Read component Restarts parameters
456	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
457	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
458
459	if [ "${do_start}" = "y" ] ; then
460	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
461	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
462	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
463	else
464	eval config_${comp}_RestartDate=-1
465	eval config_${comp}_RestartJobName=${NULL_STR}
466	eval config_${comp}_RestartPath=${NULL_STR}
467	fi
468	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} OldName
469	eval CompOldName=\${config_${comp}_OldName}
470	if [ X${CompOldName} = X ] ; then
471	eval CompOldName=${comp}
472	fi
473	fi
474
475	if [ "${do_start}" = "y" ] ; then
476
477	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
478	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
479
480	(( i=1 ))
481	until [ $i -gt $NbFiles ]; do
482	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
483	eval file_in=${file_in_}
484
485	(( i_ = i+1 ))
486	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
487	eval file_out=${file_out_}
488
489	eval Date_tmp=\${config_${comp}_RestartDate}
490	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
491	eval Path_r=\${config_${comp}_RestartPath}/\${config_${comp}_RestartJobName}/${CompOldName}/Restart
492	eval file_in_Name=\${config_${comp}_RestartJobName}_${Date_r}_${file_in}
493
494	generic_restart_file_name_in=$( basename ${file_in_Name} .nc )
495	generic_restart_file_name_out=$( basename ${file_out} .nc )
496
497	eval Path_temp=\${Path_r}/${generic_restart_file_name_in}
498	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_temp}_????.nc)
499
500	if [ ${nb_restart_file} -gt 1 ] ; then
501	j=0
502	until [ $j -ge $nb_restart_file ]; do
503	j4=${j}
504	eval IGCM_sys_Get ${Path_r}/${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
505	#IGCM_comp_PrepareDeletedFiles ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
506	#eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${generic_restart_file_name_out}_${j4}.nc" > /dev/null 2>&1
507	(( j=j+1 ))
508	done
509	else
510	eval IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
511	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
512	fi
513
514	(( i=i+3 ))
515	done
516	else
517	if [ X${FileName0} != XNONE ] ; then
518	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
519	else
520	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
521	fi
522	fi
523	fi
524	elif [ ${Period} -eq 1 ] ; then
525	# if not FirstInitialize and first loop of this job
526
527	# Restore Restarts files
528	#-----------------------
529	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
530	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
531
532	(( i=1 ))
533	until [ $i -gt $NbFiles ]; do
534	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
535	eval file_in=${file_in_}
536	(( i_ = i+1 ))
537	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
538	eval file_out=${file_out_}
539
540	file_in_Name=${run_Configuration_OldPrefix}_${file_in}
541
542	generic_restart_file_name_in=$( basename ${file_in_Name} .nc )
543	generic_restart_file_name_out=$( basename ${file_out} .nc )
544
545	eval Path_temp=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
546	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_temp}_????.nc)
547
548	if [ ${nb_restart_file} -gt 1 ] ; then
549	j=0
550	until [ $j -ge $nb_restart_file ]; do
551	j4=${j}
552	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
553	#IGCM_comp_PrepareDeletedFiles ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
554	#eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${generic_restart_file_name_out}_${j4}.nc" > /dev/null 2>&1
555
556	(( j=j+1 ))
557	done
558	else
559	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
560	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
561	fi
562
563	(( i=i+3 ))
564	done
565	else
566	if [ X${FileName0} != XNONE ] ; then
567	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
568	else
569	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
570	fi
571	fi
572	fi
573	done
574	IGCM_sys_Chmod u+rw *
575
576	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
577	}
578
579	#=======================================================================
580	function IGCM_comp_Update
581	{
582	IGCM_debug_PushStack "IGCM_comp_Update"
583
584	# Debug Print :
585	echo
586	IGCM_debug_Print 1 "IGCM_comp_Update :"
587	echo
588
589	typeset ExeNameIn ExeNameOut
590	typeset comp compname comptagname
591	for comp in ${config_ListOfComponents[*]} ; do
592	# Define component
593	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
594	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
595
596	# Copy executable for this component
597	eval ExeNameIn=\${config_Executable_${comp}[0]}
598	eval ExeNameOut=\${config_Executable_${comp}[1]}
599
600	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
601	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
602	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
603	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
604	fi
605	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
606	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
607	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
608	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
609	fi
610	fi
611
612	# Debug Print
613	IGCM_debug_Print 3 "Update ${compname} Parameter Files."
614	# UPDATE component
615	${comp}_Update
616
617	done
618
619	IGCM_debug_PopStack "IGCM_comp_Update"
620	}
621
622	#=======================================================================
623	function IGCM_comp_Finalize
624	{
625	IGCM_debug_PushStack "IGCM_comp_Finalize"
626
627	# Debug Print :
628	echo
629	IGCM_debug_Print 1 "IGCM_comp_Finalize :"
630	echo
631
632	typeset ListTextName TextName0
633	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
634	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
635	typeset -Z4 j4
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	# Debug Print
642	IGCM_debug_Print 1 "Finalize ${compname} component."
643	# FINALIZE component
644	${comp}_Finalize
645
646	card=${SUBMIT_DIR}/COMP/${compname}.card
647
648	# Save Restarts files
649	#--------------------
650	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
651	ListFilesName=${compname}_RestartFiles_List
652	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
653
654	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
655	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
656
657	(( i=0 ))
658	until [ $i -ge $NbFiles ]; do
659	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
660	eval file_in=${file_in_}
661
662	(( i_ = i+1 ))
663	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
664	eval file_out=${file_out_}
665
666	(( i_ = i+2 ))
667	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
668	eval file_outin=${file_outin_}
669
670	generic_restart_file_name_in=$( basename ${file_in} .nc )
671	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
672	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
673
674	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
675	if [ ${nb_restart_file} -gt 1 ] ; then
676	j=0
677	until [ $j -ge $nb_restart_file ]; do
678	j4=${j}
679	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
680	[ ! ${file_in} = ${file_outin} ] && IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
681	#eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${generic_restart_file_name_in}_${j4}.nc" > /dev/null 2>&1
682	(( j=j+1 ))
683	done
684	else
685	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
686	[ ! ${file_in} = ${file_outin} ] && IGCM_sys_Mv ${file_in} ${file_outin}
687	#eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
688	fi
689
690	(( i=i+3 ))
691	done
692	else
693	if [ X${FileName0} != XNONE ] ; then
694	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
695	else
696	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
697	fi
698	fi
699
700	# Save Output files
701	#------------------
702	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
703	ListFilesName=${compname}_OutputFiles_List
704	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
705
706	if [ X${FileName0} != X${NULL_STR} ] ; then
707	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
708
709	(( i=0 ))
710	until [ $i -ge $NbFiles ]; do
711	SaveOnArchive=true
712	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
713	eval file_in=${file_in_}
714	(( i_ = i+1 ))
715	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
716	eval file_out=${file_out_}
717	(( i_ = i+2 ))
718	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
719	#
720	generic_file_name=$( basename ${file_in} .nc )
721	nb_rebuild_file=$( ls \| grep "^${generic_file_name}[_0-9]*.nc" \| wc -l )
722	#
723	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
724	IGCM_debug_Print 2 "Parallelism with 1 process. Rebuilding ${file_in} not needed"
725	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
726	elif [ ${nb_rebuild_file} -gt 1 ] ; then
727	IGCM_debug_Print 2 "Parallelism detected rebuilding ${file_in} is needed"
728	if ( [ X${config_Post_RebuildFrequency} = X${NULL_STR} ] \|\| [ X${config_Post_RebuildFrequency} = XNONE ] ) ; then
729	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
730	IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc
731	else
732	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
733	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
734	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
735
736	# Prepare headers for the shell dedicated to offline rebuild
737	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
738	echo \#!/bin/ksh > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
739	echo function IGCM_FlushRebuild >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
740	echo { >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
741	echo IGCM_debug_PushStack "IGCM_FlushRebuild" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
742	echo echo >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
743	echo IGCM_debug_Print 1 "IGCM_FlushRebuild" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
744	echo echo >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
745	fi
746	# Prepare the shell dedicated to offline rebuild
747	echo IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
748	echo IGCM_debug_Verif_Exit >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
749	#
750	# Load Patch we need to apply and apply
751	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
752	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
753	echo . ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
754	echo IGCM_${Patch} ${file_in} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
755	done
756	fi
757	#
758	echo IGCM_sys_Put_Out ${file_in} ${file_out} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
759	echo IGCM_debug_Verif_Exit >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
760	echo IGCM_sys_Rm ${generic_file_name}_*.nc >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
761	SaveOnArchive=false
762	fi
763	fi
764	#
765	if [ ${SaveOnArchive} = true ] ; then
766	#
767	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
768	#
769	if ( [ ! X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) = X${NULL_STR} ] && [ ! X${config_Post_RebuildFrequency} = X ] && [ ! X${config_Post_RebuildFrequency} = XNONE ] ) ; then
770	if [ -f ${file_in} ] ; then
771	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
772	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
773	#
774	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
775	echo . ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
776	echo IGCM_${Patch} ${file_in} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
777	done
778	#
779	echo IGCM_sys_Put_Out ${file_in} ${file_out} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
780	echo IGCM_debug_Verif_Exit >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
781	#
782	fi
783	else
784	IGCM_sys_Put_Out ${file_in} ${file_out}
785	[ $? -eq 0 ] && eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
786	if [ ${nb_rebuild_file} -gt 1 ] ; then
787	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
788	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
789	done
790	fi
791	fi
792	fi
793	(( i=i+3 ))
794	done
795	fi
796
797	# Save Output Text files of models
798	#---------------------------------
799
800	IGCM_card_DefineArrayFromOption ${card} OutputText List
801	ListTextName=${compname}_OutputText_List
802
803	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
804	if [ X${TextName0} != X${NULL_STR} ] ; then
805	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
806
807	(( i=0 ))
808	until [ $i -eq $NbFiles ]; do
809	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
810	(( i=i+1 ))
811
812	nb_text_file=$( ls ${file_in}* 2>/dev/null \| wc -l )
813	if [ ${nb_text_file} -gt 1 ] ; then
814	list_file=$( ls ${file_in}* )
815	for file in ${list_file}
816	do
817	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
818	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
819	done
820	else
821	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
822	eval IGCM_sys_Mv ${file_in}* ${file_in}
823	fi
824	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${PREFIX}_${file_in}
825	[ $? -eq 0 ] && eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
826	fi
827	done
828	fi
829	done
830
831	IGCM_debug_PopStack "IGCM_comp_Finalize"
832	}

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