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libIGCM_comp.ksh @ 603

Last change on this file since 603 was 603, checked in by mafoipsl, 12 years ago
Take into account [599] change from trunk.
Property licence set to The following licence information concerns ONLY the libIGCM tools ================================================================== Copyright © Centre National de la Recherche Scientifique CNRS Commissariat à l'Énergie Atomique CEA libIGCM : Library for Portable Models Computation of IGCM Group. IGCM Group is the french IPSL Global Climate Model Group. This library is a set of shell scripts and functions whose purpose is the management of the initialization, the launch, the transfer of output files, the post-processing and the monitoring of datas produce by any numerical program on any plateforme. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. Property svn:keywords set to `Revision Author Date`
File size: 43.8 KB

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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 CompatibilityTag auxprint card_UserChoices first_option option i j
25	for comp in ${config_ListOfComponents[*]} ; do
26	# Debug Print
27	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
28
29	# Define component
30	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
31	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
32	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
33
34	# Read libIGCM compatibility version in ${compname}.card
35	card=${SUBMIT_DIR}/COMP/${compname}.card
36	IGCM_card_DefineVariableFromOption ${card} Compatibility libIGCM
37
38	eval CompatibilityTag=\${${compname}_Compatibility_libIGCM} > /dev/null 2>&1
39	if [ ! "${CompatibilityTag}" = "${libIGCM_CurrentTag}" ] ; then
40	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 ."
41	fi
42
43	# Manage component executable
44	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
45
46	# Read component Write Frequency in config.card
47	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} WriteFrequency
48	# Debug Print :
49	eval auxprint=\${config_${comp}_WriteFrequency}
50	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
51	#2> /dev/null
52
53	# Debug Print :
54	IGCM_debug_Print 2 "Initialize following component library"
55
56	# Source drivers in directory DRIVER if it exist
57	# else source them from directory COMP
58	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
59	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
60	# Source component library
61	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
62	else
63	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
64	# Source component library
65	. ${SUBMIT_DIR}/COMP/${compname}.driver
66	fi
67	IGCM_debug_Print 3 "With tag : ${comptagname}"
68
69	# Debug Print
70	IGCM_debug_Print 3 "Initialize ${comp} output directory."
71
72	# Define ARCHIVED Dirs
73	eval R_OUT_${comp}=${R_SAVE}/${comp}
74	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
75
76	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
77	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
78
79	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
80	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
81
82	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
83	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
84
85	eval R_OUT_${comp}_O_I=\${R_OUT_${comp}_O}/INS
86	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
87	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
88	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
89	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
90
91	# Define BUFFERED Dirs
92	eval R_BUF_${comp}=${R_BUFR}/${comp}
93	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
94
95	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
96	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
97
98	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
99	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
100
101	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
102	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
103
104	eval R_BUF_${comp}_O_I=\${R_BUF_${comp}_O}/INS
105	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
106	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
107	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
108	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
109
110	# Read UserChoices section of component card
111	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
112	IGCM_card_DefineArrayFromSection ${card} UserChoices
113	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
114	# If section is not empty we define corresponding variables
115	if [ X${first_option} != X"Error:" ] ; then
116	if [ X${card_UserChoices[0]} != X ] ; then
117	unset card_UserChoices
118	fi
119	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
120	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
121	for option in ${card_UserChoices[*]} ; do
122	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
123	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
124	done
125	fi
126
127	# Read and Build Output File stuff
128	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
129	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
130	ListFilesName=${compname}_OutputFiles_List
131	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
132	#
133	if [ X${FileName0} != X${NULL_STR} ] ; then
134	#
135	#IGCM_debug_Print 1 "Component : ${compname}"
136	#
137	# INITIALISATION
138	#
139	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
140	#
141	i=2
142	#
143	until [ $i -ge $NbFiles ]; do
144	#
145	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
146	#
147	if [ X${flag_post} != XNONE ] ; then
148	#
149	# First of all
150	#
151	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
152	#
153	# Seasonal case : If option Seasonal is not found (old cards) put SEASONAL ON by default
154	#
155	# variable option allready typeset above
156	for option in $( eval echo \${${compname}_${flag_post}[*]} ) ; do
157	if [ ${option} = Seasonal ] ; then
158	FoundSeasonal=true
159	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
160	fi
161	done
162	#
163	if [ ! X${FoundSeasonal} = Xtrue ] ; then
164	eval ${compname}_${flag_post}_Seasonal=ON
165	fi
166	#
167	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
168	Seasonal=true
169	fi
170
171	# Dimension = vide si vieille card.
172	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars
173	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
174	if [ X"$( eval echo \${${compname}_${flag_post}_TimeSeriesVars[*]} )" = X"Option not" ] ; then
175	# New TimeSeriesVar description, with 2D, 3D and associate ChunckJob.
176	ListDimension[0]=2D
177	ListDimension[1]=3D
178	TimeSeries=false
179	iLoop=${#ListDimension[*]}
180	j=0
181	until [ $j -ge ${iLoop} ]; do
182	Dimension=${ListDimension[${j}]}
183	IGCM_card_DefineArrayFromOption ${card} ${flag_post} TimeSeriesVars${Dimension}
184	IGCM_card_DefineVariableFromOption ${card} ${flag_post} ChunckJob${Dimension}
185	#
186	# Time series WITHOUT chunk
187	#
188	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
189	if [ $( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} ) = NONE ] ; then
190	IGCM_debug_Print 3 "${Dimension} time series activated for ${flag_post}"
191	eval TimeSeries${Dimension}=true
192	fi
193	fi
194	#
195	# Time series WITH chunk
196	#
197	if [ ! $( eval echo \${${compname}_${flag_post}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
198	chunck_size=$( eval echo \${${compname}_${flag_post}_ChunckJob${Dimension}} )
199	if [ ! ${chunck_size} = NONE ] && [ ! ${chunck_size} = OFF ] ; then
200	IGCM_debug_Print 3 "${Dimension} time series activated with chunck for ${flag_post}"
201	eval TimeSeriesChunck${Dimension}=true
202	eval set +A CHUNCK${Dimension}_COMP \${CHUNCK${Dimension}_COMP[*]} ${comp}
203	eval set +A CHUNCK${Dimension}_FLAG \${CHUNCK${Dimension}_FLAG[*]} ${i}
204	eval set +A CHUNCK${Dimension}_NAME \${CHUNCK${Dimension}_NAME[*]} ${flag_post}
205	eval set +A CHUNCK${Dimension}_SIZE \${CHUNCK${Dimension}_SIZE[*]} ${chunck_size}
206	fi
207	fi
208	(( j=j+1 ))
209	done
210	else
211	ListDimension[0]=""
212	TimeSeries=true
213	TimeSeries2D=false
214	TimeSeries3D=false
215	TimeSeriesChunck2D=false
216	TimeSeriesChunck3D=false
217	fi
218	fi
219	(( i=i+3 ))
220	done
221	fi
222	# Debug Print
223	IGCM_debug_Print 3 "Initialize ${compname} with driver."
224	# INIT component
225	${comp}_Initialize
226	echo
227	done
228
229	IGCM_debug_PopStack "IGCM_comp_Initialize"
230	}
231
232	#=======================================================================
233	function IGCM_comp_PrepareDeletedFiles
234	{
235	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
236
237	if [ X${2} != X. ] ; then
238	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
239	else
240	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
241	fi
242
243	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
244	}
245
246	#=======================================================================
247	function IGCM_comp_GetInputInitialStateFiles
248	{
249	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
250
251	# Debug Print :
252	echo
253	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
254	echo
255
256	# Only the first time step need InitialStateFiles
257	# otherwise it's BoundaryConditions
258	if ( ${FirstInitialize} ) ; then
259	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
260	typeset file_in_ file_in file_out_ file_out do_init
261	for comp in ${config_ListOfComponents[*]} ; do
262	# Initialize
263	do_init="y"
264	# Do we need to bring initial state file for this component
265	if [ "${config_Restarts_OverRule}" = "y" ] ; then
266	eval do_init="n"
267	else
268	# Read component Restarts parameters
269	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
270	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
271	if [ "${do_start}" = "y" ] ; then
272	do_init="n"
273	else
274	do_init="y"
275	fi
276	fi
277
278	if [ "${do_init}" = "y" ] ; then
279	# Define component
280	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
281	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
282
283	# Debug Print :
284	IGCM_debug_Print 3 "Initialisation files ${compname}"
285
286	card=${SUBMIT_DIR}/COMP/${compname}.card
287
288	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
289	ListFilesName=${compname}_InitialStateFiles_List
290
291	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
292	if [ X${FileName0} != X${NULL_STR} ] ; then
293	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
294	(( i=0 ))
295	until [ $i -ge $NbFiles ]; do
296	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
297	eval file_in=${file_in_}
298	(( i_ = i+1 ))
299	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
300	eval file_out=${file_out_}
301
302	IGCM_sys_IsFileArchived ${file_in}
303	if [ $? = 0 ] ; then
304	IGCM_sys_Get ${file_in} ${file_out}
305	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
306	else
307	IGCM_sys_Cp ${file_in} ${file_out}
308	fi
309	(( i=i+2 ))
310	done
311	fi
312	fi
313	done
314	fi
315	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
316	}
317
318	#=======================================================================
319	# Definition of Smooth modulo function
320	# usage :
321	# IGCM_SmoothModulo StringModulo value
322	#
323	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
324	# [min]:[modulo:][max]
325	# where :
326	# [] value are optionnals;
327	# empty min equal 1
328	# empty max equal infinity
329	# modulo not given or empty equal 1
330	# empty string or just ':' equal always.
331	#
332	# value : the value to test with the definition
333	#
334	# return : true(1)/false(0)
335	function IGCM_SmoothModulo
336	{
337	IGCM_debug_PushStack "IGCM_SmoothModulo"
338	typeset defVector ModValue
339
340	eval set +A defVector -- $( echo "${1}" \| \
341	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
342
343	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
344	arr[1]=${defVector[0]}
345	arr[2]=${defVector[2]}
346
347	# Test limits :
348	# ${defVector[0]} <= ${2} <= ${defVector[2]}
349	# or ${defVector[2]} == -1
350	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
351	# Test modulo
352	ModValue=$( expr $ ${2} - ${defVector[0]} $ % ${defVector[1]} )
353	if [ ${ModValue} -eq 0 ] ; then
354	arr[3]=true
355	echo ${arr[@]}
356	IGCM_debug_PopStack "IGCM_SmoothModulo"
357	return 1
358	else
359	arr[3]=false
360	echo ${arr[@]}
361	IGCM_debug_PopStack "IGCM_SmoothModulo"
362	return 0
363	fi
364	else
365	arr[3]=false
366	echo ${arr[@]}
367	IGCM_debug_PopStack "IGCM_SmoothModulo"
368	return 0
369	fi
370	}
371
372	#=======================================================================
373	function IGCM_comp_GetInputSmoothFiles
374	{
375	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
376
377	# Debug Print :
378	echo
379	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
380	echo
381
382	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
383	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
384
385	for comp in ${config_ListOfComponents[*]} ; do
386	# Define component
387	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
388	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
389
390	# Debug Print :
391	IGCM_debug_Print 3 "Smooth files ${compname}"
392
393	card=${SUBMIT_DIR}/COMP/${compname}.card
394
395	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
396	ListFilesName=${compname}_SmoothFiles_List
397	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
398
399	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
400	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
401
402	(( i=0 ))
403	until [ $i -ge $NbFiles ]; do
404	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
405	eval file_in=${file_in_}
406	(( i_ = i+1 ))
407	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
408	eval file_out=${file_out_}
409
410	# define CumulPeriod definition for this file
411	(( i__ = i+2 ))
412	eval SmoothDef=\${${ListFilesName}[$i__]}
413	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
414	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
415	j=1
416	for val in ${aux} ; do
417	[ ${j} -eq 1 ] && SmoothMin=${val}
418	[ ${j} -eq 2 ] && SmoothMax=${val}
419	[ ${j} -eq 3 ] && ret=${val}
420	(( j=j+1 ))
421	done
422	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
423	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
424
425	IGCM_sys_IsFileArchived ${file_in}
426	if [ $? = 0 ] ; then
427	IGCM_sys_Get ${file_in} ${file_out}
428	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
429	else
430	IGCM_sys_Cp ${file_in} ${file_out}
431	fi
432	fi
433	(( i=i+3 ))
434	done
435	fi
436	done
437
438	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
439	}
440
441	#=======================================================================
442	function IGCM_comp_GetInputBoundaryFiles
443	{
444	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
445
446	# Debug Print :
447	echo
448	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
449	echo
450
451	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
452	typeset file_in_ file_in file_out_ file_out
453
454	if [ ${Period} = 1 ]; then
455	ListFixBoundary=" "
456	fi
457
458	for comp in ${config_ListOfComponents[*]} ; do
459
460	# Define component
461	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
462	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
463
464	# Debug Print :
465	IGCM_debug_Print 3 "Boundary files ${compname}"
466
467	card=${SUBMIT_DIR}/COMP/${compname}.card
468
469	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
470	ListFilesName=${compname}_BoundaryFiles_List
471	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
472
473	if [ X${FileName0} != X${NULL_STR} ] ; then
474	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
475
476	(( i=0 ))
477	until [ $i -ge $NbFiles ]; do
478	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
479	eval file_in=${file_in_}
480	(( i_ = i+1 ))
481	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
482	eval file_out=${file_out_}
483
484	IGCM_sys_IsFileArchived ${file_in}
485	if [ $? = 0 ] ; then
486	IGCM_sys_Get ${file_in} ${file_out}
487	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
488	else
489	IGCM_sys_Cp ${file_in} ${file_out}
490	fi
491
492	(( i=i+2 ))
493	done
494	fi
495
496	# Get non deleted files
497	if [ ${Period} = 1 ]; then
498
499	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
500	ListFilesName=${compname}_BoundaryFiles_ListNonDel
501	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
502
503	if [ X${FileName0} != X${NULL_STR} ] ; then
504	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
505
506	(( i=0 ))
507	until [ $i -ge $NbFiles ]; do
508	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
509	eval file_in=${file_in_}
510	(( i_ = i+1 ))
511	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
512	eval file_out=${file_out_}
513
514	IGCM_sys_IsFileArchived ${file_in}
515	if [ $? = 0 ] ; then
516	IGCM_sys_Get ${file_in} ${file_out}
517	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
518	else
519	IGCM_sys_Cp ${file_in} ${file_out}
520	fi
521
522	if [ X${file_out} != X. ] ; then
523	ListFixBoundary=${ListFixBoundary}" "${file_out}
524	else
525	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
526	fi
527
528	(( i=i+2 ))
529	done
530	fi
531	fi
532	done
533
534	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
535	}
536
537	#=======================================================================
538	function IGCM_comp_DelFixeBoundaryFiles
539	{
540	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
541
542	# Debug Print :
543	echo
544	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
545	echo
546
547	ls -l ${ListFixBoundary}
548	rm -f ${ListFixBoundary}
549
550	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
551	}
552
553	#=======================================================================
554	function IGCM_comp_GetInputParametersFiles
555	{
556	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
557
558	# Debug Print :
559	echo
560	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
561	echo
562
563	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
564	for comp in ${config_ListOfComponents[*]} ; do
565	# Define component
566	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
567	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
568
569	# Debug Print :
570	IGCM_debug_Print 3 "Parameters ${compname}"
571
572	card=${SUBMIT_DIR}/COMP/${compname}.card
573
574	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
575	ListFilesName=${compname}_ParametersFiles_List
576	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
577
578	if [ X${FileName0} != X${NULL_STR} ] ; then
579	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
580
581	(( i=0 ))
582	until [ $i -ge $NbFiles ]; do
583	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
584	eval file_in=${file_in_}
585	(( i_ = i+1 ))
586	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
587	eval file_out=${file_out_}
588
589	IGCM_sys_Cp ${file_in} ${file_out}
590	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
591
592	(( i=i+2 ))
593	done
594	fi
595	done
596
597	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
598	}
599
600	#=======================================================================
601	function IGCM_comp_GetInputRestartFiles
602	{
603	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
604
605	# Debug Print :
606	echo
607	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
608	echo
609
610	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
611	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
612	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
613	typeset file_in file_out file_in_ file_out_ file_in_Name
614	typeset -Z4 j4
615
616	for comp in ${config_ListOfComponents[*]} ; do
617	# Define component
618	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
619	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
620	#
621	card=${SUBMIT_DIR}/COMP/${compname}.card
622	#
623	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
624	ListFilesName=${compname}_RestartFiles_List
625	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
626
627	# Debug Print :
628	IGCM_debug_Print 3 "restart ${compname}"
629
630	if ( ${FirstInitialize} ) ; then
631
632	if [ "${config_Restarts_OverRule}" = "y" ] ; then
633	eval config_${comp}_Restart="y"
634	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
635	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
636	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
637	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
638	eval CompOldName=${comp}
639	else
640	# Read component Restarts parameters
641	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
642	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
643
644	if [ "${do_start}" = "y" ] ; then
645	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
646	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
647	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
648	else
649	eval config_${comp}_RestartDate=-1
650	eval config_${comp}_RestartJobName=${NULL_STR}
651	eval config_${comp}_RestartPath=${NULL_STR}
652	fi
653	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} OldName
654	eval CompOldName=\${config_${comp}_OldName}
655	if [ X${CompOldName} = X ] ; then
656	eval CompOldName=${comp}
657	fi
658	fi
659
660	if [ "${do_start}" = "y" ] ; then
661
662	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
663	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
664
665	(( i=1 ))
666	until [ $i -gt $NbFiles ]; do
667	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
668	eval file_in=${file_in_}
669
670	(( i_ = i+1 ))
671	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
672	eval file_out=${file_out_}
673
674	eval Date_tmp=\${config_${comp}_RestartDate}
675	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
676	eval Path_r=\${config_${comp}_RestartPath}/\${config_${comp}_RestartJobName}/${CompOldName}/Restart
677	eval file_in_Name=\${config_${comp}_RestartJobName}_${Date_r}_${file_in}
678
679	generic_restart_file_name_in=$( basename ${file_in_Name} .nc )
680	generic_restart_file_name_out=$( basename ${file_out} .nc )
681
682	eval Path_OUT=\${Path_r}/${generic_restart_file_name_in}
683	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.nc)
684
685	if [ ${nb_restart_file} -gt 1 ] ; then
686	j=0
687	until [ $j -ge $nb_restart_file ]; do
688	j4=${j}
689	eval IGCM_sys_Get ${Path_r}/${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
690	#IGCM_comp_PrepareDeletedFiles ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
691	#eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${generic_restart_file_name_out}_${j4}.nc" > /dev/null 2>&1
692	(( j=j+1 ))
693	done
694	else
695	eval IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
696	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
697	fi
698
699	(( i=i+3 ))
700	done
701	else
702	if [ X${FileName0} != XNONE ] ; then
703	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
704	else
705	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
706	fi
707	fi
708	fi
709	elif [ ${Period} -eq 1 ] ; then
710	# if not FirstInitialize and first loop of this job
711
712	# Restore Restarts files
713	#-----------------------
714	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
715	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
716
717	(( i=1 ))
718	until [ $i -gt $NbFiles ]; do
719	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
720	eval file_in=${file_in_}
721	(( i_ = i+1 ))
722	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
723	eval file_out=${file_out_}
724
725	file_in_Name=${run_Configuration_OldPrefix}_${file_in}
726
727	generic_restart_file_name_in=$( basename ${file_in_Name} .nc )
728	generic_restart_file_name_out=$( basename ${file_out} .nc )
729
730	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
731	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
732
733	if [ -f ${Path_BUF}*.nc ] ; then
734	IGCM_debug_Print 3 "Buffered restart"
735	Buffered=true
736	Archived=false
737	Tared=false
738	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.nc)
739	elif [ -f ${Path_OUT}*.nc ] ; then
740	IGCM_debug_Print 3 "Archived restart"
741	Buffered=false
742	Archived=true
743	Tared=false
744	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.nc)
745	else
746	IGCM_debug_Print 3 "Tared restart"
747	Buffered=false
748	Archived=false
749	Tared=true
750	# Look after the tar file we want if we did not found it already
751	if [ X${IsMatching} = X ] ; then
752	for PotentialTarFile in $( find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" ) ; do
753	IsMatching=$( echo $( basename ${PotentialTarFile} ) \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
754	if [ ! X${IsMatching} = X ] ; then
755	TarFileFound=${PotentialTarFile}
756	break
757	fi
758	done
759	fi
760	tar xvf ${TarFileFound} ${comp}_${generic_restart_file_name_in}*.nc
761	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.nc )
762	fi
763
764	if [ ${nb_restart_file} -gt 1 ] ; then
765	j=0
766	until [ $j -ge $nb_restart_file ]; do
767	j4=${j}
768	if [ X${Buffered} = Xtrue ] ; then
769	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
770	elif [ X${Archived} = Xtrue ] ; then
771	IGCM_sys_Get ${Path_OUT}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
772	elif [ X${Tared} = Xtrue ] ; then
773	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_out}_${j4}.nc
774	fi
775	(( j=j+1 ))
776	done
777	else
778	if [ X${Buffered} = Xtrue ] ; then
779	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
780	elif [ X${Archived} = Xtrue ] ; then
781	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
782	elif [ X${Tared} = Xtrue ] ; then
783	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
784	fi
785	fi
786	(( i=i+3 ))
787	done
788	else
789	if [ X${FileName0} != XNONE ] ; then
790	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
791	else
792	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
793	fi
794	fi
795	fi
796	done
797
798	NbFiles=$( ls * 2> /dev/null \| wc -l )
799	if [ ${NbFiles} -gt 0 ] ; then
800	IGCM_sys_Chmod u+rw *
801	fi
802
803	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
804	}
805
806	#=======================================================================
807	function IGCM_comp_PeriodStart
808	{
809	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
810
811	# Debug Print :
812	echo
813	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
814	echo
815
816	typeset ExeNameIn ExeNameOut
817	typeset comp compname comptagname
818	for comp in ${config_ListOfComponents[*]} ; do
819	# Define component
820	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
821	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
822
823	# Copy executable for this component
824	eval ExeNameIn=\${config_Executable_${comp}[0]}
825	eval ExeNameOut=\${config_Executable_${comp}[1]}
826
827	# Debug Print
828	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
829	# UPDATE component
830	${comp}_PeriodStart 2> /dev/null
831
832	done
833
834	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
835	}
836
837	#=======================================================================
838	function IGCM_comp_Update
839	{
840	IGCM_debug_PushStack "IGCM_comp_Update"
841
842	# Debug Print :
843	echo
844	IGCM_debug_Print 1 "IGCM_comp_Update"
845	echo
846
847	typeset ExeNameIn ExeNameOut
848	typeset comp compname comptagname
849	for comp in ${config_ListOfComponents[*]} ; do
850	# Define component
851	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
852	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
853
854	# Copy executable for this component
855	eval ExeNameIn=\${config_Executable_${comp}[0]}
856	eval ExeNameOut=\${config_Executable_${comp}[1]}
857
858	# If missing executable and DRYRUN is set to 0 or 1 then stop!
859	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
860	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
861	fi
862
863	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
864	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
865	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
866	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
867	fi
868	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
869	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
870	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
871	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
872	fi
873	fi
874
875	# Debug Print
876	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
877	# UPDATE component
878	${comp}_Update
879
880	done
881
882	IGCM_debug_PopStack "IGCM_comp_Update"
883	}
884
885	#=======================================================================
886	function IGCM_comp_Finalize
887	{
888	IGCM_debug_PushStack "IGCM_comp_Finalize"
889
890	# Debug Print :
891	echo
892	IGCM_debug_Print 1 "IGCM_comp_Finalize"
893	echo
894
895	typeset ListTextName TextName0
896	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
897	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
898	typeset -Z4 j4
899	typeset list_file nlist_file
900	typeset compactoutputs
901
902	compactoutputs=false
903	if [ X${JobType} != XRUN ] ; then
904	compactoutputs=true
905	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
906	compactoutputs=true
907	fi
908
909	for comp in ${config_ListOfComponents[*]} ; do
910	# Define component
911	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
912	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
913
914	# Debug Print
915	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
916	# FINALIZE component
917	${comp}_Finalize
918
919	card=${SUBMIT_DIR}/COMP/${compname}.card
920
921	# Save Restarts files
922	#--------------------
923	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
924	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
925	ListFilesName=${compname}_RestartFiles_List
926	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
927
928	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
929	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
930
931	(( i=0 ))
932	until [ $i -ge $NbFiles ]; do
933	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
934	eval file_in=${file_in_}
935
936	(( i_ = i+1 ))
937	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
938	eval file_out=${file_out_}
939
940	(( i_ = i+2 ))
941	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
942	eval file_outin=${file_outin_}
943
944	generic_restart_file_name_in=$( basename ${file_in} .nc )
945	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
946	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
947
948	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
949	if [ ${nb_restart_file} -gt 1 ] ; then
950	j=0
951	until [ $j -ge $nb_restart_file ]; do
952	j4=${j}
953	if [ X${Pack} = Xtrue ] ; then
954	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
955	else
956	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
957	fi
958	if [ ! ${file_in} = ${file_outin} ] ; then
959	if ( ${ExitFlag} ) ; then
960	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
961	else
962	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
963	fi
964	fi
965	(( j=j+1 ))
966	done
967	else
968	if [ X${Pack} = Xtrue ] ; then
969	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
970	else
971	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
972	fi
973	if [ ! ${file_in} = ${file_outin} ] ; then
974	if ( ${ExitFlag} ) ; then
975	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
976	else
977	IGCM_sys_Mv ${file_in} ${file_outin}
978	fi
979	fi
980	fi
981
982	(( i=i+3 ))
983	done
984	else
985	if [ X${FileName0} != XNONE ] ; then
986	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
987	else
988	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
989	fi
990	fi
991
992	# Save Output files
993	#------------------
994	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
995	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
996	ListFilesName=${compname}_OutputFiles_List
997	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
998
999	if [ X${FileName0} != X${NULL_STR} ] ; then
1000	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1001
1002	(( i=0 ))
1003	until [ $i -ge $NbFiles ]; do
1004	SaveOnArchive=true
1005	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1006	eval file_in=${file_in_}
1007	(( i_ = i+1 ))
1008	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1009	eval file_out=${file_out_}
1010	#
1011	# Override file_out path remplacing R_SAVE by R_BUFR
1012	#
1013	if [ X${Pack} = Xtrue ] ; then
1014	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1015	fi
1016	#
1017	# Not necessarily the best option. /!\ Potential side effects /!\
1018	#
1019	(( i_ = i+2 ))
1020	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1021	#
1022	generic_file_name=$( basename ${file_in} .nc )
1023	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1024	#
1025	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1026	IGCM_debug_Print 2 "Parallelism with 1 process. Rebuilding ${file_in} not needed"
1027	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1028	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1029	IGCM_debug_Print 2 "Parallelism detected rebuilding ${file_in} is needed"
1030	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1031	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1032	IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc
1033	else
1034	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1035	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1036	IGCM_sys_Mv ${generic_file_name}_????.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1037
1038	# Prepare headers for the shell dedicated to offline rebuild
1039	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1040	if [ $DRYRUN -le 1 ]; then
1041	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1042	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1043	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1044	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1045	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1046	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1047	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1048	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1049	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1050	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1051	fi
1052	fi
1053	# Prepare the shell dedicated to offline rebuild
1054	if [ $DRYRUN -le 1 ]; then
1055	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1056	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1057	fi
1058	#
1059	# Load Patch we need to apply and apply
1060	if [ $DRYRUN -le 1 ]; then
1061	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1062	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1063	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1064	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1065	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1066	done
1067	fi
1068	fi
1069	#
1070	if [ $DRYRUN -le 1 ]; then
1071	if [ X${Pack} = Xtrue ] ; then
1072	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1073	else
1074	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1075	fi
1076	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1077	echo "IGCM_sys_Rm ${generic_file_name}_*.nc " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1078	fi
1079	SaveOnArchive=false
1080	fi
1081	fi
1082	#
1083	if [ ${SaveOnArchive} = true ] ; then
1084	#
1085	# Rebuild has been done online or it was not needed
1086	#
1087	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1088	#
1089	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1090	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1091	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1092	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1093	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1094	#
1095	if [ $DRYRUN -le 1 ]; then
1096	if [ ! -f ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh ] ; then
1097	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1098	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1099	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1100	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1101	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1102	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1103	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1104	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1105	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1106	fi
1107	#
1108	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ); do
1109	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1110	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1111	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1112	done
1113	#
1114	if [ X${Pack} = Xtrue ] ; then
1115	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1116	else
1117	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1118	fi
1119	echo "IGCM_debug_Verif_Exit_Post " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1120	#
1121	fi
1122	else
1123	#
1124	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1125	#
1126	if [ X${Pack} = Xtrue ] ; then
1127	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1128	else
1129	IGCM_sys_Put_Out ${file_in} ${file_out}
1130	fi
1131	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1132	if [ ${nb_rebuild_file} -gt 1 ] ; then
1133	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1134	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1135	done
1136	fi
1137	fi
1138	fi
1139	(( i=i+3 ))
1140	done
1141	fi
1142
1143	# Save Output Text files of models
1144	#---------------------------------
1145	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1146	IGCM_card_DefineArrayFromOption ${card} OutputText List
1147	ListTextName=${compname}_OutputText_List
1148
1149	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1150	if [ X${TextName0} != X${NULL_STR} ] ; then
1151	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1152
1153	(( i=0 ))
1154	until [ $i -eq $NbFiles ]; do
1155	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1156	eval file_out=${PREFIX}_${file_in}
1157
1158	(( i=i+1 ))
1159
1160	unset list_file
1161	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1162	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1163	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 )
1164	nlist_file=${#list_file[@]}
1165	if [ ${nlist_file} -gt 1 ] ; then
1166	if ( ${compactoutputs} ) ; then
1167	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1168	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1169	echo ${list_file[*]} > ${file_out}
1170	echo "" >> ${file_out}
1171
1172	(( i_ = 0 ))
1173	for file in ${list_file[@]}
1174	do
1175	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1176	echo "\| " ${i_} " " ${file} >> ${file_out}
1177	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1178	cat ${file} \| sed "s/$.*$/${i_}\1/" ${file} >> ${file_out}
1179	echo "" >> ${file_out}
1180	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1181	(( i_ = i_ + 1 ))
1182	done
1183	if [ X${Pack} = Xtrue ] ; then
1184	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1185	else
1186	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1187	fi
1188	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1189
1190	if ( ${ExecutionFail} ) ; then
1191	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1192	fi
1193	else
1194	for file in ${list_file[@]}
1195	do
1196	if [ X${Pack} = Xtrue ] ; then
1197	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1198	else
1199	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1200	fi
1201	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1202
1203	if ( ${ExecutionFail} ) ; then
1204	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1205	fi
1206	done
1207	fi
1208	else
1209	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1210	eval IGCM_sys_Mv ${file_in}* ${file_in}
1211	fi
1212	if [ X${Pack} = Xtrue ] ; then
1213	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1214	else
1215	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1216	fi
1217	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1218
1219	if ( ${ExecutionFail} ) ; then
1220	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1221	fi
1222	fi
1223	done
1224	fi
1225	echo
1226	done
1227	IGCM_debug_PopStack "IGCM_comp_Finalize"
1228	}

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source: branches/libIGCM_MPI_OpenMP/libIGCM_comp/libIGCM_comp.ksh @ 603

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