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source: tags/libIGCM_v1_4/libIGCM_comp/libIGCM_comp.ksh

Last change on this file was 168, checked in by sdipsl, 15 years ago
Bugfix with monitoring submission OM : bugfix with StandAlone? mode
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	# Dimension = vide si vieille card.
120	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
121	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
122	if [ "$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = "Option not found ${flag_post}" ] ; then
123	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
124	ListDimension[0]=2D
125	ListDimension[1]=3D
126	TimeSeries=false
127	iLoop=${#ListDimension[*]}
128	j=0
129	until [ $j -ge ${iLoop} ]; do
130	Dimension=${ListDimension[${j}]}
131	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
132	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
133	#
134	# Time series WITHOUT chunk
135	#
136	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
137	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
138	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post} according to ${card}"
139	eval TimeSeries${Dimension}=true
140	fi
141	fi
142	#
143	# Time series WITH chunk
144	#
145	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
146	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
147	if [ ! ${chunck_size} = NONE ] ; then
148	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post} according to ${card}"
149	eval TimeSeriesChunck${Dimension}=true
150	eval set +A CHUNCK${Dimension}_COMP \${CHUNCK${Dimension}_COMP[*]} ${comp}
151	eval set +A CHUNCK${Dimension}_FLAG \${CHUNCK${Dimension}_FLAG[*]} ${i}
152	eval set +A CHUNCK${Dimension}_SIZE \${CHUNCK${Dimension}_SIZE[*]} ${chunck_size}
153	fi
154	fi
155	(( j=j+1 ))
156	done
157	else
158	ListDimension[0]=""
159	TimeSeries=true
160	TimeSeries2D=false
161	TimeSeries3D=false
162	TimeSeriesChunck2D=false
163	TimeSeriesChunck3D=false
164	fi
165	fi
166	(( i=i+3 ))
167	done
168	fi
169	# Debug Print
170	IGCM_debug_Print 3 "Initialize ${compname} with driver."
171	# INIT component
172	${comp}_Initialize
173	echo
174	done
175	echo "-----"
176	echo
177	IGCM_debug_Print 1 "DefineArrayFromOption : ListOfComponents"
178	IGCM_debug_PrintVariables 3 config_ListOfComponents
179
180	IGCM_debug_PopStack "IGCM_comp_Initialize"
181	}
182
183	#=======================================================================
184	function IGCM_comp_PrepareDeletedFiles
185	{
186	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
187
188	if [ X${2} != X. ] ; then
189	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
190	else
191	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
192	fi
193
194	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
195	}
196
197	#=======================================================================
198	function IGCM_comp_GetInputInitialStateFiles
199	{
200	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
201
202	# Debug Print :
203	echo
204	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles :"
205	echo
206
207	# Only the first time step need InitialStateFiles
208	# otherwise it's BoundaryConditions
209	if ( ${FirstInitialize} ) ; then
210	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
211	typeset file_in_ file_in file_out_ file_out do_init
212	for comp in ${config_ListOfComponents[*]} ; do
213	# Initialize
214	do_init="y"
215	# Do we need to bring initial state file for this component
216	if [ "${config_Restarts_OverRule}" = "y" ] ; then
217	eval do_init="n"
218	else
219	# Read component Restarts parameters
220	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
221	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
222	if [ "${do_start}" = "y" ] ; then
223	do_init="n"
224	else
225	do_init="y"
226	fi
227	fi
228
229	if [ "${do_init}" = "y" ] ; then
230	# Define component
231	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
232	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
233
234	# Debug Print :
235	IGCM_debug_Print 3 "Initialisation files ${compname}"
236
237	card=${SUBMIT_DIR}/COMP/${compname}.card
238
239	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
240	ListFilesName=${compname}_InitialStateFiles_List
241
242	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
243	if [ X${FileName0} != X${NULL_STR} ] ; then
244	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
245
246	(( i=0 ))
247	until [ $i -ge $NbFiles ]; do
248	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
249	eval file_in=${file_in_}
250	(( i_ = i+1 ))
251	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
252	eval file_out=${file_out_}
253
254	IGCM_sys_Get ${file_in} ${file_out}
255	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
256
257	(( i=i+2 ))
258	done
259	fi
260	fi
261	done
262	fi
263	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
264	}
265
266	#=======================================================================
267	function IGCM_comp_GetInputBoundaryFiles
268	{
269	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
270
271	# Debug Print :
272	echo
273	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles :"
274	echo
275
276	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
277	typeset file_in_ file_in file_out_ file_out
278
279	if [ ${Period} = 1 ]; then
280	ListFixBoundary=" "
281	fi
282
283	for comp in ${config_ListOfComponents[*]} ; do
284
285	echo "-----"
286	# Define component
287	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
288	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
289
290	# Debug Print :
291	IGCM_debug_Print 3 "Boundary files ${compname}"
292
293	card=${SUBMIT_DIR}/COMP/${compname}.card
294
295	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
296	ListFilesName=${compname}_BoundaryFiles_List
297	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
298
299	if [ X${FileName0} != X${NULL_STR} ] ; then
300	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
301
302	(( i=0 ))
303	until [ $i -ge $NbFiles ]; do
304	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
305	eval file_in=${file_in_}
306	(( i_ = i+1 ))
307	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
308	eval file_out=${file_out_}
309
310	IGCM_sys_Get ${file_in} ${file_out}
311	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
312
313	(( i=i+2 ))
314	done
315	fi
316
317	# Get non deleted files
318	if [ ${Period} = 1 ]; then
319
320	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
321	ListFilesName=${compname}_BoundaryFiles_ListNonDel
322	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
323
324	if [ X${FileName0} != X${NULL_STR} ] ; then
325	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
326
327	(( i=0 ))
328	until [ $i -ge $NbFiles ]; do
329	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
330	eval file_in=${file_in_}
331	(( i_ = i+1 ))
332	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
333	eval file_out=${file_out_}
334
335	IGCM_sys_Get ${file_in} ${file_out}
336
337	if [ X${file_out} != X. ] ; then
338	ListFixBoundary=${ListFixBoundary}" "${file_out}
339	else
340	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
341	fi
342
343	(( i=i+2 ))
344	done
345	fi
346	fi
347	done
348
349	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
350	}
351
352	#=======================================================================
353	function IGCM_comp_DelFixeBoundaryFiles
354	{
355	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
356
357	# Debug Print :
358	echo
359	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles :"
360	echo
361
362	ls -l ${ListFixBoundary}
363	rm -f ${ListFixBoundary}
364
365	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
366	}
367
368	#=======================================================================
369	function IGCM_comp_GetInputParametersFiles
370	{
371	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
372
373	# Debug Print :
374	echo
375	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles :"
376	echo
377
378	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
379	for comp in ${config_ListOfComponents[*]} ; do
380	# Define component
381	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
382	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
383
384	# Debug Print :
385	IGCM_debug_Print 3 "Parameters ${compname}"
386
387	card=${SUBMIT_DIR}/COMP/${compname}.card
388
389	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
390	ListFilesName=${compname}_ParametersFiles_List
391	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
392
393	if [ X${FileName0} != X${NULL_STR} ] ; then
394	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
395
396	(( i=0 ))
397	until [ $i -ge $NbFiles ]; do
398	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
399	eval file_in=${file_in_}
400	(( i_ = i+1 ))
401	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
402	eval file_out=${file_out_}
403
404	IGCM_sys_Cp ${file_in} ${file_out}
405	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
406
407	(( i=i+2 ))
408	done
409	fi
410	done
411
412	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
413	}
414
415	#=======================================================================
416	function IGCM_comp_GetInputRestartFiles
417	{
418	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
419
420	# Debug Print :
421	echo
422	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles :"
423	echo
424
425	typeset Date_tmp Date_r Path_r do_start CompOldName Path_temp
426	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
427	typeset file_in file_out file_in_ file_out_ file_in_Name
428	typeset -Z4 j4
429
430	for comp in ${config_ListOfComponents[*]} ; do
431	# Define component
432	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
433	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
434	#
435	card=${SUBMIT_DIR}/COMP/${compname}.card
436	#
437	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
438	ListFilesName=${compname}_RestartFiles_List
439	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
440
441	# Debug Print :
442	IGCM_debug_Print 3 "restart ${compname}"
443
444	if ( ${FirstInitialize} ) ; then
445
446	if [ "${config_Restarts_OverRule}" = "y" ] ; then
447	eval config_${comp}_Restart="y"
448	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
449	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
450	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
451	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
452	eval CompOldName=${comp}
453	else
454	# Read component Restarts parameters
455	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
456	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
457
458	if [ "${do_start}" = "y" ] ; then
459	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
460	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
461	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
462	else
463	eval config_${comp}_RestartDate=-1
464	eval config_${comp}_RestartJobName=${NULL_STR}
465	eval config_${comp}_RestartPath=${NULL_STR}
466	fi
467	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} OldName
468	eval CompOldName=\${config_${comp}_OldName}
469	if [ X${CompOldName} = X ] ; then
470	eval CompOldName=${comp}
471	fi
472	fi
473
474	if [ "${do_start}" = "y" ] ; then
475
476	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
477	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
478
479	(( i=1 ))
480	until [ $i -gt $NbFiles ]; do
481	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
482	eval file_in=${file_in_}
483
484	(( i_ = i+1 ))
485	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
486	eval file_out=${file_out_}
487
488	eval Date_tmp=\${config_${comp}_RestartDate}
489	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
490	eval Path_r=\${config_${comp}_RestartPath}/\${config_${comp}_RestartJobName}/${CompOldName}/Restart
491	eval file_in_Name=\${config_${comp}_RestartJobName}_${Date_r}_${file_in}
492
493	generic_restart_file_name_in=$( basename ${file_in_Name} .nc )
494	generic_restart_file_name_out=$( basename ${file_out} .nc )
495
496	eval Path_temp=\${Path_r}/${generic_restart_file_name_in}
497	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_temp}_????.nc)
498
499	if [ ${nb_restart_file} -gt 1 ] ; then
500	j=0
501	until [ $j -ge $nb_restart_file ]; do
502	j4=${j}
503	eval IGCM_sys_Get ${Path_r}/${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
504	#IGCM_comp_PrepareDeletedFiles ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
505	#eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${generic_restart_file_name_out}_${j4}.nc" > /dev/null 2>&1
506	(( j=j+1 ))
507	done
508	else
509	eval IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
510	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
511	fi
512
513	(( i=i+3 ))
514	done
515	else
516	if [ X${FileName0} != XNONE ] ; then
517	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
518	else
519	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
520	fi
521	fi
522	fi
523	elif [ ${Period} -eq 1 ] ; then
524	# if not FirstInitialize and first loop of this job
525
526	# Restore Restarts files
527	#-----------------------
528	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
529	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
530
531	(( i=1 ))
532	until [ $i -gt $NbFiles ]; do
533	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
534	eval file_in=${file_in_}
535	(( i_ = i+1 ))
536	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
537	eval file_out=${file_out_}
538
539	file_in_Name=${run_Configuration_OldPrefix}_${file_in}
540
541	generic_restart_file_name_in=$( basename ${file_in_Name} .nc )
542	generic_restart_file_name_out=$( basename ${file_out} .nc )
543
544	eval Path_temp=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
545	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_temp}_????.nc)
546
547	if [ ${nb_restart_file} -gt 1 ] ; then
548	j=0
549	until [ $j -ge $nb_restart_file ]; do
550	j4=${j}
551	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
552	#IGCM_comp_PrepareDeletedFiles ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
553	#eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${generic_restart_file_name_out}_${j4}.nc" > /dev/null 2>&1
554
555	(( j=j+1 ))
556	done
557	else
558	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
559	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
560	fi
561
562	(( i=i+3 ))
563	done
564	else
565	if [ X${FileName0} != XNONE ] ; then
566	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
567	else
568	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
569	fi
570	fi
571	fi
572	done
573	IGCM_sys_Chmod u+rw *
574
575	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
576	}
577
578	#=======================================================================
579	function IGCM_comp_Update
580	{
581	IGCM_debug_PushStack "IGCM_comp_Update"
582
583	# Debug Print :
584	echo
585	IGCM_debug_Print 1 "IGCM_comp_Update :"
586	echo
587
588	typeset ExeNameIn ExeNameOut
589	typeset comp compname comptagname
590	for comp in ${config_ListOfComponents[*]} ; do
591	# Define component
592	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
593	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
594
595	# Copy executable for this component
596	eval ExeNameIn=\${config_Executable_${comp}[0]}
597	eval ExeNameOut=\${config_Executable_${comp}[1]}
598
599	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
600	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
601	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
602	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
603	fi
604	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
605	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
606	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
607	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
608	fi
609	fi
610
611	# Debug Print
612	IGCM_debug_Print 3 "Update ${compname} Parameter Files."
613	# UPDATE component
614	${comp}_Update
615
616	done
617
618	IGCM_debug_PopStack "IGCM_comp_Update"
619	}
620
621	#=======================================================================
622	function IGCM_comp_Finalize
623	{
624	IGCM_debug_PushStack "IGCM_comp_Finalize"
625
626	# Debug Print :
627	echo
628	IGCM_debug_Print 1 "IGCM_comp_Finalize :"
629	echo
630
631	typeset ListTextName TextName0
632	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
633	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
634	typeset -Z4 j4
635	for comp in ${config_ListOfComponents[*]} ; do
636	# Define component
637	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
638	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
639
640	# Debug Print
641	IGCM_debug_Print 1 "Finalize ${compname} component."
642	# FINALIZE component
643	${comp}_Finalize
644
645	card=${SUBMIT_DIR}/COMP/${compname}.card
646
647	# Save Restarts files
648	#--------------------
649	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
650	ListFilesName=${compname}_RestartFiles_List
651	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
652
653	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
654	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
655
656	(( i=0 ))
657	until [ $i -ge $NbFiles ]; do
658	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
659	eval file_in=${file_in_}
660
661	(( i_ = i+1 ))
662	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
663	eval file_out=${file_out_}
664
665	(( i_ = i+2 ))
666	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
667	eval file_outin=${file_outin_}
668
669	generic_restart_file_name_in=$( basename ${file_in} .nc )
670	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
671	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
672
673	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
674	if [ ${nb_restart_file} -gt 1 ] ; then
675	j=0
676	until [ $j -ge $nb_restart_file ]; do
677	j4=${j}
678	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
679	[ ! ${file_in} = ${file_outin} ] && IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
680	#eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${generic_restart_file_name_in}_${j4}.nc" > /dev/null 2>&1
681	(( j=j+1 ))
682	done
683	else
684	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
685	[ ! ${file_in} = ${file_outin} ] && IGCM_sys_Mv ${file_in} ${file_outin}
686	#eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
687	fi
688
689	(( i=i+3 ))
690	done
691	else
692	if [ X${FileName0} != XNONE ] ; then
693	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
694	else
695	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
696	fi
697	fi
698
699	# Save Output files
700	#------------------
701	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
702	ListFilesName=${compname}_OutputFiles_List
703	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
704
705	if [ X${FileName0} != X${NULL_STR} ] ; then
706	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
707
708	(( i=0 ))
709	until [ $i -ge $NbFiles ]; do
710	SaveOnArchive=true
711	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
712	eval file_in=${file_in_}
713	(( i_ = i+1 ))
714	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
715	eval file_out=${file_out_}
716	(( i_ = i+2 ))
717	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
718	#
719	generic_file_name=$( basename ${file_in} .nc )
720	nb_rebuild_file=$( ls \| grep "^${generic_file_name}[_0-9]*.nc" \| wc -l )
721	#
722	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
723	IGCM_debug_Print 2 "Parallelism with 1 process. Rebuilding ${file_in} not needed"
724	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
725	elif [ ${nb_rebuild_file} -gt 1 ] ; then
726	IGCM_debug_Print 2 "Parallelism detected rebuilding ${file_in} is needed"
727	if ( [ X${config_Post_RebuildFrequency} = X${NULL_STR} ] \|\| [ X${config_Post_RebuildFrequency} = XNONE ] ) ; then
728	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
729	IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc
730	else
731	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
732	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
733	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
734
735	# Prepare headers for the shell dedicated to offline rebuild
736	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
737	echo \#!/bin/ksh > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
738	echo function IGCM_FlushRebuild >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
739	echo { >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
740	echo IGCM_debug_PushStack "IGCM_FlushRebuild" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
741	echo echo >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
742	echo IGCM_debug_Print 1 "IGCM_FlushRebuild" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
743	echo echo >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
744	fi
745	# Prepare the shell dedicated to offline rebuild
746	echo IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
747	echo IGCM_debug_Verif_Exit >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
748	#
749	# Load Patch we need to apply and apply
750	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
751	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
752	echo . ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
753	echo IGCM_${Patch} ${file_in} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
754	done
755	fi
756	#
757	echo IGCM_sys_Put_Out ${file_in} ${file_out} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
758	echo IGCM_debug_Verif_Exit >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
759	echo IGCM_sys_Rm ${generic_file_name}_*.nc >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
760	SaveOnArchive=false
761	fi
762	fi
763	#
764	if [ ${SaveOnArchive} = true ] ; then
765	#
766	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
767	#
768	if ( [ ! X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) = X${NULL_STR} ] && [ ! X${config_Post_RebuildFrequency} = X ] && [ ! X${config_Post_RebuildFrequency} = XNONE ] ) ; then
769	if [ -f ${file_in} ] ; then
770	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
771	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
772	#
773	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
774	echo . ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
775	echo IGCM_${Patch} ${file_in} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
776	done
777	#
778	echo IGCM_sys_Put_Out ${file_in} ${file_out} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
779	echo IGCM_debug_Verif_Exit >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
780	#
781	fi
782	else
783	IGCM_sys_Put_Out ${file_in} ${file_out}
784	[ $? -eq 0 ] && eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
785	if [ ${nb_rebuild_file} -gt 1 ] ; then
786	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
787	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
788	done
789	fi
790	fi
791	fi
792	(( i=i+3 ))
793	done
794	fi
795
796	# Save Output Text files of models
797	#---------------------------------
798
799	IGCM_card_DefineArrayFromOption ${card} OutputText List
800	ListTextName=${compname}_OutputText_List
801
802	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
803	if [ X${TextName0} != X${NULL_STR} ] ; then
804	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
805
806	(( i=0 ))
807	until [ $i -eq $NbFiles ]; do
808	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
809	(( i=i+1 ))
810
811	nb_text_file=$( ls ${file_in}* 2>/dev/null \| wc -l )
812	if [ ${nb_text_file} -gt 1 ] ; then
813	list_file=$( ls ${file_in}* )
814	for file in ${list_file}
815	do
816	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
817	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
818	done
819	else
820	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
821	eval IGCM_sys_Mv ${file_in}* ${file_in}
822	fi
823	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${PREFIX}_${file_in}
824	[ $? -eq 0 ] && eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
825	fi
826	done
827	fi
828	done
829
830	IGCM_debug_PopStack "IGCM_comp_Finalize"
831	}

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