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source: tags/libIGCM_v3.0_beta1/libIGCM_comp/libIGCM_comp.ksh @ 1375

Last change on this file since 1375 was 1375, checked in by sdipsl, 7 years ago
Populate the first bunch of modifications in libIGCM_v3.0_beta1 repo
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: 73.1 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 auxprint card_UserChoices first_option option i j
25	for comp in ${config_ListOfComponents[*]} ; do
26
27	# Define component
28	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card ListOfComponents ${comp}
29	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
30	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
31
32	# Debug Print
33	IGCM_debug_Print 1 "Initialize ${comp} : ${compname} component."
34
35	# ${compname}.card PATH
36	card=${SUBMIT_DIR}/COMP/${compname}.card
37
38	# Manage component executable
39	IGCM_card_DefineArrayFromOption ${SUBMIT_DIR}/config.card Executable ${comp}
40
41	# Define all options in section [comp]
42	IGCM_debug_Print 3 " DefineArrayFromSection : ${comp}"
43	IGCM_card_DefineArrayFromSection ${SUBMIT_DIR}/config.card ${comp}
44	eval config_comp=\${config_${comp}[*]} > /dev/null 2>&1
45	for option in ${config_comp[*]} ; do
46	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} ${option}
47	done
48	IGCM_debug_Print 3 " Found in section config_${comp} : ${config_comp[*]} "
49
50	# Debug Print :
51	eval auxprint=\${config_${comp}_WriteFrequency}
52	IGCM_debug_Print 1 "Write frequency for ${compname} : ${auxprint} "
53	#2> /dev/null
54
55	# Debug Print :
56	IGCM_debug_Print 2 "Initialize following component library"
57
58	# Source drivers in directory DRIVER if it exist
59	# else source them from directory COMP
60	if [ -d ${SUBMIT_DIR}/DRIVER ] ; then
61	IGCM_debug_Print 2 ${SUBMIT_DIR}/DRIVER/${compname}.driver
62	# Source component library
63	. ${SUBMIT_DIR}/DRIVER/${compname}.driver
64	else
65	IGCM_debug_Print 2 ${SUBMIT_DIR}/COMP/${compname}.driver
66	# Source component library
67	. ${SUBMIT_DIR}/COMP/${compname}.driver
68	fi
69	IGCM_debug_Print 3 "With tag : ${comptagname}"
70
71	# Debug Print
72	IGCM_debug_Print 3 "Initialize ${comp} output directory."
73
74	# Define ARCHIVED Dirs
75	eval R_OUT_${comp}=${R_SAVE}/${comp}
76	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}}
77
78	eval R_OUT_${comp}_O=\${R_OUT_${comp}}/Output
79	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_O}
80
81	eval R_OUT_${comp}_A=\${R_OUT_${comp}}/Analyse
82	eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_A}
83
84	eval R_OUT_${comp}_R=\${R_OUT_${comp}}/Restart
85	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_R}
86
87	eval R_OUT_${comp}_D=\${R_OUT_${comp}}/Debug
88	[ ${config_Post_PackFrequency} = NONE ] && eval IGCM_sys_MkdirArchive \${R_OUT_${comp}_D}
89
90	eval R_OUT_${comp}_O_H=\${R_OUT_${comp}_O}/HF
91	eval R_OUT_${comp}_O_D=\${R_OUT_${comp}_O}/DA
92	eval R_OUT_${comp}_O_M=\${R_OUT_${comp}_O}/MO
93	eval R_OUT_${comp}_O_Y=\${R_OUT_${comp}_O}/YE
94
95	eval R_OUT_${comp}_A_H=\${R_OUT_${comp}_A}/TS_HF
96	eval R_OUT_${comp}_A_D=\${R_OUT_${comp}_A}/TS_DA
97	eval R_OUT_${comp}_A_M=\${R_OUT_${comp}_A}/TS_MO
98	eval R_OUT_${comp}_A_Y=\${R_OUT_${comp}_A}/TS_YE
99
100	# Define BUFFERED Dirs
101	if ( [ ! ${config_Post_PackFrequency} = NONE ] \|\| [ X${config_UserChoices_SpaceName} = XTEST ] ) ; then
102	eval R_BUF_${comp}=${R_BUFR}/${comp}
103	eval IGCM_sys_Mkdir \${R_BUF_${comp}}
104
105	eval R_BUF_${comp}_O=\${R_BUF_${comp}}/Output
106	eval IGCM_sys_Mkdir \${R_BUF_${comp}_O}
107
108	eval R_BUF_${comp}_A=\${R_BUF_${comp}}/Analyse
109	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A}
110
111	eval R_BUF_${comp}_R=\${R_BUF_${comp}}/Restart
112	eval IGCM_sys_Mkdir \${R_BUF_${comp}_R}
113
114	eval R_BUF_${comp}_D=\${R_BUF_${comp}}/Debug
115	eval IGCM_sys_Mkdir \${R_BUF_${comp}_D}
116
117	eval R_BUF_${comp}_O_H=\${R_BUF_${comp}_O}/HF
118	eval R_BUF_${comp}_O_D=\${R_BUF_${comp}_O}/DA
119	eval R_BUF_${comp}_O_M=\${R_BUF_${comp}_O}/MO
120	eval R_BUF_${comp}_O_Y=\${R_BUF_${comp}_O}/YE
121
122	eval R_BUF_${comp}_A_H=\${R_BUF_${comp}_A}/TS_HF
123	eval R_BUF_${comp}_A_D=\${R_BUF_${comp}_A}/TS_DA
124	eval R_BUF_${comp}_A_M=\${R_BUF_${comp}_A}/TS_MO
125	eval R_BUF_${comp}_A_Y=\${R_BUF_${comp}_A}/TS_YE
126	fi
127
128	# Read UserChoices section of component card
129	IGCM_debug_Print 2 "DefineArrayFromSection : ${compname}_UserChoices ${card}"
130	IGCM_card_DefineArrayFromSection ${card} UserChoices
131	eval first_option=\${${compname}_UserChoices[0]} > /dev/null 2>&1
132
133	# If section is not empty we define corresponding variables
134	if [ X${first_option} != X"Error:" ] ; then
135	if [ X${card_UserChoices[0]} != X ] ; then
136	unset card_UserChoices
137	fi
138	eval set +A card_UserChoices -- \${${compname}_UserChoices[*]} > /dev/null 2>&1
139	IGCM_debug_Print 3 "${compname}_UserChoices_values:"
140	for option in ${card_UserChoices[*]} ; do
141	IGCM_card_DefineVariableFromOption ${card} UserChoices ${option}
142	eval IGCM_debug_Print 3 "${option}=\${${compname}_UserChoices_${option}}"
143	done
144	fi
145
146	# Read and Build Output File stuff
147	IGCM_debug_Print 2 "DefineArrayFromOption : ${compname}_OutputFiles ${card}"
148	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
149	ListFilesName=${compname}_OutputFiles_List
150	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
151	#
152	if [ X${FileName0} != X${NULL_STR} ] ; then
153	#
154	#IGCM_debug_Print 1 "Component : ${compname}"
155	#
156	# INITIALISATION
157	#
158	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
159	#
160	i=2
161	#
162	until [ $i -ge $NbFiles ]; do
163	#
164	eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
165	#
166	if [ X${flag_post} != XNONE ] ; then
167	#
168	# First of all
169	#
170	IGCM_card_DefineArrayFromSection ${card} ${flag_post}
171	# This section is mandatory
172	if [ "X$( eval echo \${${compname}_${flag_post}[@]} )" = "X" ] ; then
173	IGCM_debug_Print 1 "IGCM_card_DefineArrayFromSection ${card} ${flag_post}"
174	IGCM_debug_Exit "${flag_post} section do not exist in ${card}. Please check your card."
175	IGCM_debug_Verif_Exit
176	fi
177
178	# Do have seasonal average enabled
179	IGCM_card_DefineVariableFromOption ${card} ${flag_post} Seasonal
180	if [ $( eval echo \${${compname}_${flag_post}_Seasonal} ) = ON ] ; then
181	Seasonal=true
182	fi
183
184	# Read the Patches Option
185	IGCM_card_DefineArrayFromOption ${card} ${flag_post} Patches
186	fi
187	(( i=i+3 ))
188	done
189	fi
190	# Debug Print
191	IGCM_debug_Print 3 "Initialize ${compname} with driver."
192	# INIT component
193	${comp}_Initialize
194	echo
195	done
196
197	IGCM_debug_PopStack "IGCM_comp_Initialize"
198	}
199
200	#=======================================================================
201	function IGCM_comp_PrepareDeletedFiles
202	{
203	IGCM_debug_PushStack "IGCM_comp_PrepareDeletedFiles" $@
204
205	if [ X${2} != X. ] ; then
206	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${2} ) > /dev/null 2>&1
207	else
208	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=$( basename ${1} ) > /dev/null 2>&1
209	fi
210
211	IGCM_debug_PopStack "IGCM_comp_PrepareDeletedFiles"
212	}
213
214	#=======================================================================
215	function IGCM_comp_PrepareXiosFiles
216	{
217	IGCM_debug_PushStack "IGCM_comp_PrepareXiosFiles" $@
218
219	typeset file
220	[ X${2} != X. ] && file=$( basename ${2} ) \|\| file=$( basename ${1} )
221
222	if [ $( echo ${file} \| grep "^field_def_" \| wc -l ) = 1 ] ; then
223	eval FieldDef[${#FieldDef[@]}]=${file} > /dev/null 2>&1
224	fi
225	if [ $( echo ${file} \| grep "^file_def_" \| wc -l ) = 1 ] ; then
226	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
227	fi
228	if [ $( echo ${file} \| grep "^timeseries_def_" \| wc -l ) = 1 ] ; then
229	eval FileDef[${#FileDef[@]}]=${file} > /dev/null 2>&1
230	fi
231
232	IGCM_debug_PopStack "IGCM_comp_PrepareXiosFiles"
233	}
234
235	#=======================================================================
236	function IGCM_comp_GetInputInitialStateFiles
237	{
238	IGCM_debug_PushStack "IGCM_comp_GetInputInitialStateFiles"
239
240	# Debug Print :
241	echo
242	IGCM_debug_Print 1 "IGCM_comp_GetInputInitialStateFiles"
243	echo
244
245	# Only the first time step need InitialStateFiles
246	# otherwise it's BoundaryConditions
247	if ( ${FirstInitialize} ) ; then
248	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
249	typeset file_in_ file_in file_out_ file_out do_init
250	for comp in ${config_ListOfComponents[*]} ; do
251	# Initialize
252	do_init="y"
253	# Do we need to bring initial state file for this component
254	if [ "${config_Restarts_OverRule}" = "y" ] ; then
255	eval do_init="n"
256	else
257	# Read component Restarts parameters
258	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
259	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
260	if [ "${do_start}" = "y" ] ; then
261	do_init="n"
262	else
263	do_init="y"
264	fi
265	fi
266
267	if [ "${do_init}" = "y" ] ; then
268	# Define component
269	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
270	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
271
272	# Debug Print :
273	IGCM_debug_Print 3 "Initialisation files ${compname}"
274
275	card=${SUBMIT_DIR}/COMP/${compname}.card
276
277	IGCM_card_DefineArrayFromOption ${card} InitialStateFiles List
278	ListFilesName=${compname}_InitialStateFiles_List
279
280	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
281	if [ X${FileName0} != X${NULL_STR} ] ; then
282	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
283	(( i=0 ))
284	until [ $i -ge $NbFiles ]; do
285	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
286	eval file_in=${file_in_}
287	(( i_ = i+1 ))
288	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
289	eval file_out=${file_out_}
290
291	IGCM_sys_IsFileArchived ${file_in}
292	if [ $? = 0 ] ; then
293	IGCM_sys_Get ${file_in} ${file_out}
294	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
295	else
296	IGCM_sys_Cp ${file_in} ${file_out}
297	fi
298	(( i=i+2 ))
299	done
300	fi
301	fi
302	done
303	fi
304	IGCM_debug_PopStack "IGCM_comp_GetInputInitialStateFiles"
305	}
306
307	#=======================================================================
308	# Definition of Smooth modulo function
309	# usage :
310	# IGCM_SmoothModulo StringModulo value
311	#
312	# StringModulo : A string of min max and modulo like definition of Scilab vectors.
313	# [min]:[modulo:][max]
314	# where :
315	# [] value are optionnals;
316	# empty min equal 1
317	# empty max equal infinity
318	# modulo not given or empty equal 1
319	# empty string or just ':' equal always.
320	#
321	# value : the value to test with the definition
322	#
323	# return : true(1)/false(0)
324	function IGCM_SmoothModulo
325	{
326	IGCM_debug_PushStack "IGCM_SmoothModulo"
327	typeset defVector ModValue
328
329	eval set +A defVector -- $( echo "${1}" \| \
330	gawk -F ':' '{print ($1 == "" ? 1 : $1) " " (NF==3 ? ($2 == "" ? 1 : $2) : 1) " " (NF==3 ? ($3 == "" ? -1 : $3) : ($2 == "" ? -1 : $2))}' )
331
332	# Save Smooth Min and Max. Needed to call IGCM_sys_Get when appropriate
333	arr[1]=${defVector[0]}
334	arr[2]=${defVector[2]}
335
336	# Test limits :
337	# ${defVector[0]} <= ${2} <= ${defVector[2]}
338	# or ${defVector[2]} == -1
339	if ( [ ${2} -ge ${defVector[0]} ] && ( [ ${2} -le ${defVector[2]} ] \|\| [ ${defVector[2]} -lt 0 ] ) ) ; then
340	# Test modulo
341	ModValue=$( expr \( ${2} - ${defVector[0]} \) % ${defVector[1]} )
342	if [ ${ModValue} -eq 0 ] ; then
343	arr[3]=true
344	echo ${arr[@]}
345	IGCM_debug_PopStack "IGCM_SmoothModulo"
346	return 1
347	else
348	arr[3]=false
349	echo ${arr[@]}
350	IGCM_debug_PopStack "IGCM_SmoothModulo"
351	return 0
352	fi
353	else
354	arr[3]=false
355	echo ${arr[@]}
356	IGCM_debug_PopStack "IGCM_SmoothModulo"
357	return 0
358	fi
359	}
360
361	#=======================================================================
362	function IGCM_comp_GetInputSmoothFiles
363	{
364	IGCM_debug_PushStack "IGCM_comp_GetInputSmoothFiles"
365
366	# Debug Print :
367	echo
368	IGCM_debug_Print 1 "IGCM_comp_GetInputSmoothFiles"
369	echo
370
371	typeset comp compname comptagname card ListFilesName FileName0 NbFiles j i i_ i__
372	typeset file_in_ file_in file_out_ file_out ret SmoothDef aux val
373
374	for comp in ${config_ListOfComponents[*]} ; do
375	# Define component
376	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
377	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
378
379	# Debug Print :
380	IGCM_debug_Print 3 "Smooth files ${compname}"
381
382	card=${SUBMIT_DIR}/COMP/${compname}.card
383
384	IGCM_card_DefineArrayFromOption ${card} SmoothFiles List
385	ListFilesName=${compname}_SmoothFiles_List
386	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
387
388	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != X"Section" ] ) ; then
389	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
390
391	(( i=0 ))
392	until [ $i -ge $NbFiles ]; do
393	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
394	eval file_in=${file_in_}
395	(( i_ = i+1 ))
396	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
397	eval file_out=${file_out_}
398
399	# define CumulPeriod definition for this file
400	(( i__ = i+2 ))
401	eval SmoothDef=\${${ListFilesName}[$i__]}
402	IGCM_debug_Print 3 " ${file_in} ${SmoothDef}"
403	aux=$( IGCM_SmoothModulo ${SmoothDef} ${CumulPeriod} )
404	j=1
405	for val in ${aux} ; do
406	[ ${j} -eq 1 ] && SmoothMin=${val}
407	[ ${j} -eq 2 ] && SmoothMax=${val}
408	[ ${j} -eq 3 ] && ret=${val}
409	(( j=j+1 ))
410	done
411	[ ${SmoothMax} -eq -1 ] && SmoothMax=${CumulPeriod}
412	if ( [ X${ret} = Xtrue ] \|\| ( [ ${Period} -eq 1 ] && [ ${CumulPeriod} -ge ${SmoothMin} ] && [ ${CumulPeriod} -le ${SmoothMax} ] ) ) ; then
413
414	IGCM_sys_IsFileArchived ${file_in}
415	if [ $? = 0 ] ; then
416	IGCM_sys_Get ${file_in} ${file_out}
417	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
418	else
419	IGCM_sys_Cp ${file_in} ${file_out}
420	fi
421	fi
422	(( i=i+3 ))
423	done
424	fi
425	done
426
427	IGCM_debug_PopStack "IGCM_comp_GetInputSmoothFiles"
428	}
429
430	#=======================================================================
431	function IGCM_comp_GetInputBoundaryFiles
432	{
433	IGCM_debug_PushStack "IGCM_comp_GetInputBoundaryFiles"
434
435	# Debug Print :
436	echo
437	IGCM_debug_Print 1 "IGCM_comp_GetInputBoundaryFiles"
438	echo
439
440	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
441	typeset file_in_ file_in file_out_ file_out
442
443	if [ ${Period} = 1 ]; then
444	ListFixBoundary=" "
445	fi
446
447	for comp in ${config_ListOfComponents[*]} ; do
448
449	# Define component
450	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
451	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
452
453	# Debug Print :
454	IGCM_debug_Print 3 "Boundary files ${compname}"
455
456	card=${SUBMIT_DIR}/COMP/${compname}.card
457
458	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles List
459	ListFilesName=${compname}_BoundaryFiles_List
460	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
461
462	if [ X${FileName0} != X${NULL_STR} ] ; then
463	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
464
465	(( i=0 ))
466	until [ $i -ge $NbFiles ]; do
467	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
468	eval file_in=${file_in_}
469	(( i_ = i+1 ))
470	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
471	eval file_out=${file_out_}
472
473	IGCM_sys_IsFileArchived ${file_in}
474	if [ $? = 0 ] ; then
475	IGCM_sys_Get ${file_in} ${file_out}
476	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
477	else
478	IGCM_sys_Cp ${file_in} ${file_out}
479	fi
480
481	(( i=i+2 ))
482	done
483	fi
484
485	# Get non deleted files
486	if [ ${Period} = 1 ]; then
487
488	IGCM_card_DefineArrayFromOption ${card} BoundaryFiles ListNonDel
489	ListFilesName=${compname}_BoundaryFiles_ListNonDel
490	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
491
492	if [ X${FileName0} != X${NULL_STR} ] ; then
493	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
494
495	(( i=0 ))
496	until [ $i -ge $NbFiles ]; do
497	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
498	eval file_in=${file_in_}
499	(( i_ = i+1 ))
500	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
501	eval file_out=${file_out_}
502
503	IGCM_sys_IsFileArchived ${file_in}
504	if [ $? = 0 ] ; then
505	IGCM_sys_Get ${file_in} ${file_out}
506	#IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
507	else
508	IGCM_sys_Cp ${file_in} ${file_out}
509	fi
510
511	if [ X${file_out} != X. ] ; then
512	ListFixBoundary=${ListFixBoundary}" "${file_out}
513	else
514	ListFixBoundary=${ListFixBoundary}" "$( basename ${file_in} )
515	fi
516
517	(( i=i+2 ))
518	done
519	fi
520	fi
521	done
522
523	IGCM_debug_PopStack "IGCM_comp_GetInputBoundaryFiles"
524	}
525
526	#=======================================================================
527	function IGCM_comp_DelFixeBoundaryFiles
528	{
529	IGCM_debug_PushStack "IGCM_comp_DelFixeBoundaryFiles"
530
531	# Debug Print :
532	echo
533	IGCM_debug_Print 1 "IGCM_comp_DelFixeBoundaryFiles"
534	echo
535
536	ls -l ${ListFixBoundary}
537	rm -f ${ListFixBoundary}
538
539	IGCM_debug_PopStack "IGCM_comp_DelFixeBoundaryFiles"
540	}
541
542	#=======================================================================
543	function IGCM_comp_GetInputParametersFiles
544	{
545	IGCM_debug_PushStack "IGCM_comp_GetInputParametersFiles"
546
547	# Debug Print :
548	echo
549	IGCM_debug_Print 1 "IGCM_comp_GetInputParametersFiles"
550	echo
551
552	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_ file_in file_out
553	for comp in ${config_ListOfComponents[*]} ; do
554	# Define component
555	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
556	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
557
558	# Initialize array hosting file_def and field_def files to check and/or modify
559	unset FieldDef
560	unset FileDef
561
562	# Debug Print :
563	IGCM_debug_Print 3 "Parameters ${compname}"
564
565	card=${SUBMIT_DIR}/COMP/${compname}.card
566
567	IGCM_card_DefineArrayFromOption ${card} ParametersFiles List
568	ListFilesName=${compname}_ParametersFiles_List
569	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
570
571	if [ X${FileName0} != X${NULL_STR} ] ; then
572	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
573
574	(( i=0 ))
575	until [ $i -ge $NbFiles ]; do
576	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
577	eval file_in=${file_in_}
578	(( i_ = i+1 ))
579	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
580	eval file_out=${file_out_}
581
582	IGCM_sys_Cp ${file_in} ${file_out}
583	IGCM_comp_PrepareDeletedFiles ${file_in} ${file_out}
584	IGCM_comp_PrepareXiosFiles ${file_in} ${file_out}
585
586	(( i=i+2 ))
587	done
588	fi
589
590	if [ ${#FileDef[@]} -ne 0 ] ; then
591	# Check XMLs coherency now
592	IGCM_debug_Print 1 "${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}"
593	${libIGCM}/libIGCM_post/xios_parser.py check --field ${FieldDef[]} --file ${FileDef[]}
594	if [ $? = 0 ] ; then
595	IGCM_debug_Print 1 "${compname} XIOS XMLs are consistent"
596	else
597	IGCM_debug_Print 1 "${compname} XIOS XMLs ARE NOT consistent"
598	if [ X${config_Post_ParserXIOS} = XTRUE ] ; then
599	IGCM_debug_Print 1 "Try to fix it:"
600	IGCM_debug_Print 3 "${libIGCM}/libIGCM_post/xios_parser.py -v modify --field ${FieldDef[]} --file ${FileDef[]}"
601	${libIGCM}/libIGCM_post/xios_parser.py -vv modify --field ${FieldDef[]} --file ${FileDef[]}
602	[ $? != 0 ] && IGCM_debug_Exit "Failed to fix XIOS xml files for ${compname}"
603	fi
604	fi
605	fi
606	done
607
608	IGCM_debug_PopStack "IGCM_comp_GetInputParametersFiles"
609	}
610
611	#=======================================================================
612	function IGCM_comp_GetInputRestartFiles
613	{
614	IGCM_debug_PushStack "IGCM_comp_GetInputRestartFiles"
615
616	# Debug Print :
617	echo
618	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles"
619	echo
620
621	typeset Date_tmp Date_r Path_r do_start CompOldName Path_OUT Path_BUF
622	typeset Buffered Archived Tared PotentialTarFile IsMatching TarFileFound
623	typeset comp compname comptagname card ListFilesName FileName0 NbFiles i i_
624	typeset file_in file_out file_in_ file_out_ file_in_Name
625	typeset -Z4 j4
626	#BASH declare j4
627
628	IsMatching=""
629
630	for comp in ${config_ListOfComponents[*]} ; do
631	# Define component
632	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
633	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
634	#
635	card=${SUBMIT_DIR}/COMP/${compname}.card
636	#
637	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
638	ListFilesName=${compname}_RestartFiles_List
639	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
640
641	# Debug Print :
642	IGCM_debug_Print 3 "restart ${compname}"
643
644	if ( ${FirstInitialize} ) ; then
645
646	if [ "${config_Restarts_OverRule}" = "y" ] ; then
647	eval config_${comp}_Restart="y"
648	eval config_${comp}_RestartDate=${config_Restarts_RestartDate}
649	eval config_${comp}_RestartJobName=${config_Restarts_RestartJobName}
650	eval config_${comp}_RestartPath=${config_Restarts_RestartPath}
651	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
652	eval CompOldName=${comp}
653	else
654	# Read component Restarts parameters
655	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} Restart
656	eval do_start=\${config_${comp}_Restart} > /dev/null 2>&1
657
658	if [ "${do_start}" = "y" ] ; then
659	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartDate
660	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartJobName
661	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ${comp} RestartPath
662	else
663	eval config_${comp}_RestartDate=-1
664	eval config_${comp}_RestartJobName=${NULL_STR}
665	eval config_${comp}_RestartPath=${NULL_STR}
666	fi
667
668	eval CompOldName=\${config_${comp}_OldName}
669	if [ X${CompOldName} = X ] ; then
670	eval CompOldName=${comp}
671	fi
672
673	# Reinitialize IsMatching to allow searching for a different tar file for each component.
674	IsMatching=""
675	TarFileFound=""
676	fi
677
678	if [ "${do_start}" = "y" ] ; then
679
680	# Restore Restarts files
681	#-----------------------
682	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
683	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
684
685	(( i=1 ))
686	until [ $i -gt $NbFiles ]; do
687	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
688	eval file_in=${file_in_}
689	(( i_ = i+1 ))
690	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
691	eval file_out=${file_out_}
692
693	eval Date_tmp=\${config_${comp}_RestartDate}
694	Date_r=$( IGCM_date_ConvertFormatToGregorian ${Date_tmp} )
695	# will be re-use
696	eval RestartPath=\${config_${comp}_RestartPath}
697	eval RestartJobName=\${config_${comp}_RestartJobName}
698	#
699	Path_r=${RestartPath}/${RestartJobName}/${CompOldName}/Restart
700	file_in_Name=${RestartJobName}_${Date_r}_${file_in}
701
702	extension_in=$( echo ${file_in_Name##*.} )
703	extension_out=$( echo ${file_out##*.} )
704
705	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
706	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
707
708	Path_OUT=${Path_r}/${generic_restart_file_name_in}
709
710	if [ $( IGCM_sys_TestFileBuffer ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
711	IGCM_debug_Print 3 "Buffered restart ${Path_OUT}*.${extension_in} "
712	Buffered=true
713	Archived=false
714	Tared=false
715	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_OUT}_????.${extension_in})
716	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
717	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
718	Buffered=false
719	Archived=true
720	Tared=false
721	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
722	else
723	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
724	IGCM_debug_Print 3 "${Path_OUT}*.${extension_in} do not exist"
725	IGCM_debug_Print 3 "Restart files will now be searched for in : ${RestartPath}/${RestartJobName}/RESTART"
726	Buffered=false
727	Archived=false
728	Tared=true
729	# Look after the tar file we want if we did not found it already
730	if [ X${IsMatching} = X ] ; then
731	IGCM_sys_TestDirArchive ${RestartPath}/${RestartJobName}/RESTART
732	if [ $? ] ; then
733	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${RestartPath}/${RestartJobName}/RESTART -name "${RestartJobName}_restart.tar" -print" ) ; do
734	IsMatching=$( echo ${PotentialTarFile##*/} \| \
735	sed "s:_restart::" \| \
736	sed "s:^${RestartJobName}_::" \| \
737	sed "s:\.tar$::" \| \
738	gawk -F_ -v restartdate=${Date_r} \
739	'{if (($1 <= restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
740	if [ ! X${IsMatching} = X ] ; then
741	TarFileFound=${PotentialTarFile}
742	break
743	fi
744	done
745	fi
746	# Stop here if nothing has been found
747	if [ X${TarFileFound} = X ] ; then
748	IGCM_debug_Print 3 "Restart files were not found!"
749	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
750	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
751	IGCM_debug_Exit "Please double check restart settings in config.card"
752	IGCM_debug_Verif_Exit
753	fi
754	fi
755	IGCM_sys_PrepareTaredRestart ${TarFileFound}
756	TarFileLocation=$( basename ${TarFileFound} )
757	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
758	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
759	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
760	fi
761
762	if [ ${nb_restart_file} -gt 1 ] ; then
763	j=0 # BASH LINE NOT NEEDED
764	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
765	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
766	j4=${j} # BASH LINE NOT NEEDED
767	if [ X${Buffered} = Xtrue ] ; then
768	IGCM_sys_GetBuffer ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
769	elif [ X${Archived} = Xtrue ] ; then
770	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
771	elif [ X${Tared} = Xtrue ] ; then
772	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
773	fi
774	(( j=j+1 )) #BASH LINE NOT NEEDED
775	done
776
777	# OCE SPECIFIC TO REBUILD RESTART WHEN NUMBER OF RESTART FILES DONT MATCH MPI PROCESS
778	if [ X${OCE_PROC_MPI} != X ] ; then
779	if [ ${OCE_PROC_MPI} -ne ${nb_restart_file} ] ; then
780	IGCM_sys_rebuild ${generic_restart_file_name_out}.${extension_out} ${generic_restart_file_name_out}_????.${extension_out}
781	IGCM_sys_Rm ${generic_restart_file_name_out}_????.${extension_out}
782	fi
783	fi
784	else
785	if [ X${Buffered} = Xtrue ] ; then
786	IGCM_sys_GetBuffer ${Path_r}/${file_in_Name} ${file_out}
787	elif [ X${Archived} = Xtrue ] ; then
788	IGCM_sys_Get ${Path_r}/${file_in_Name} ${file_out}
789	elif [ X${Tared} = Xtrue ] ; then
790	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
791	fi
792	fi
793	(( i=i+3 ))
794	done
795	else
796	if [ X${FileName0} != XNONE ] ; then
797	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
798	else
799	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
800	fi
801	fi
802	fi
803	elif ( [ ${Period} -eq 1 ] && [ ${DRYRUN} -eq 0 ] ) ; then
804	# if not FirstInitialize and first loop of this job
805
806	# Restore Restarts files
807	#-----------------------
808	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
809	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
810
811	(( i=1 ))
812	until [ $i -gt $NbFiles ]; do
813	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
814	eval file_in=${file_in_}
815	(( i_ = i+1 ))
816	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
817	eval file_out=${file_out_}
818
819	file_in_Name=${config_UserChoices_JobName}_${LastPeriodDateEnd}_${file_in}
820
821	extension_in=$( echo ${file_in_Name##*.} )
822	extension_out=$( echo ${file_out##*.} )
823
824	generic_restart_file_name_in=$( basename ${file_in_Name} .${extension_in} )
825	generic_restart_file_name_out=$( basename ${file_out} .${extension_out} )
826
827	eval Path_BUF=\${R_BUF_${comp}_R}/${generic_restart_file_name_in}
828	eval Path_OUT=\${R_OUT_${comp}_R}/${generic_restart_file_name_in}
829
830	if [ $( IGCM_sys_TestFileBuffer ${Path_BUF}*.${extension_in} ; echo $? ) = 0 ] ; then
831	IGCM_debug_Print 3 "Buffered restart ${Path_BUF}*.${extension_in}"
832	Buffered=true
833	Archived=false
834	Tared=false
835	nb_restart_file=$(IGCM_sys_CountFileBuffer ${Path_BUF}_????.${extension_in})
836	elif [ $( IGCM_sys_TestFileArchive ${Path_OUT}*.${extension_in} ; echo $? ) = 0 ] ; then
837	IGCM_debug_Print 3 "Archived restart ${Path_OUT}*.${extension_in}"
838	Buffered=false
839	Archived=true
840	Tared=false
841	nb_restart_file=$(IGCM_sys_CountFileArchive ${Path_OUT}_????.${extension_in})
842	else
843	IGCM_debug_Print 3 "No restart file in the buffer nor in the archive directory"
844	IGCM_debug_Print 3 "Restart files will now be searched for in : ${R_SAVE}/RESTART"
845	Buffered=false
846	Archived=false
847	Tared=true
848	# Look after the tar file we want if we did not found it already
849	if [ X${IsMatching} = X ] ; then
850	for PotentialTarFile in $( IGCM_sys_RshArchive "find ${R_SAVE}/RESTART -name "${config_UserChoices_JobName}_*_restart.tar" -print" ) ; do
851	IsMatching=$( echo ${PotentialTarFile##*/} \| sed "s:^${config_UserChoices_JobName}_::" \| sed "s:\.restart\.tar$::" \| gawk -F_ -v restartdate=${LastPeriodDateEnd} '{if (($1 < restartdate) && ($2 >= restartdate)) {print $1"_"$2}}' )
852	if [ ! X${IsMatching} = X ] ; then
853	TarFileFound=${PotentialTarFile}
854	break
855	fi
856	done
857	fi
858	# Stop here if nothing has been found
859	if [ X${TarFileFound} = X ] ; then
860	IGCM_debug_Print 3 "Restart files were not found!"
861	IGCM_debug_Print 3 "Restart files have been searched for in buffer and archive directory."
862	IGCM_debug_Print 3 "They have been searched for in packed and unpacked format."
863	IGCM_debug_Exit "Please double check restart settings in config.card"
864	IGCM_debug_Verif_Exit
865	fi
866	IGCM_sys_PrepareTaredRestart ${TarFileFound}
867	TarFileLocation=$( basename ${TarFileFound} )
868	IGCM_debug_Print 1 "tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}"
869	tar xvf ${TarFileLocation} ${comp}_${generic_restart_file_name_in}*.${extension_in}
870	nb_restart_file=$( IGCM_sys_CountFileBuffer ${comp}_${generic_restart_file_name_in}_????.${extension_in} )
871	fi
872
873	if [ ${nb_restart_file} -gt 1 ] ; then
874	j=0 # BASH LINE NOT NEEDED
875	#BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
876	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
877	j4=${j} # BASH LINE NOT NEEDED
878	if [ X${Buffered} = Xtrue ] ; then
879	IGCM_sys_GetBuffer ${Path_BUF}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
880	elif [ X${Archived} = Xtrue ] ; then
881	IGCM_sys_Get ${Path_OUT}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
882	elif [ X${Tared} = Xtrue ] ; then
883	IGCM_sys_Mv ${comp}_${generic_restart_file_name_in}_${j4}.${extension_in} ${generic_restart_file_name_out}_${j4}.${extension_out}
884	fi
885	(( j=j+1 )) # BASH LINE NOT NEEDED
886	done
887	else
888	if [ X${Buffered} = Xtrue ] ; then
889	eval IGCM_sys_GetBuffer \${R_BUF_${comp}_R}/${file_in_Name} ${file_out}
890	elif [ X${Archived} = Xtrue ] ; then
891	eval IGCM_sys_Get \${R_OUT_${comp}_R}/${file_in_Name} ${file_out}
892	elif [ X${Tared} = Xtrue ] ; then
893	IGCM_sys_Mv ${comp}_${file_in_Name} ${file_out}
894	fi
895	fi
896	(( i=i+3 ))
897	done
898	else
899	if [ X${FileName0} != XNONE ] ; then
900	IGCM_debug_Exit "IGCM_comp_GetInputRestartFiles : No file in list for ${compname}."
901	else
902	IGCM_debug_Print 1 "IGCM_comp_GetInputRestartFiles : NONE specified in Restart List ${compname}."
903	fi
904	fi
905	fi
906	done
907
908	NbFiles=$( ls * 2> /dev/null \| wc -l )
909	if [ ${NbFiles} -gt 0 ] ; then
910	IGCM_sys_Chmod u+rw *
911	fi
912
913	IGCM_debug_PopStack "IGCM_comp_GetInputRestartFiles"
914	}
915
916	#=======================================================================
917	function IGCM_comp_PeriodStart
918	{
919	IGCM_debug_PushStack "IGCM_comp_PeriodStart"
920
921	# Debug Print :
922	echo
923	IGCM_debug_Print 1 "IGCM_comp_PeriodStart"
924	echo
925
926	typeset ExeNameIn ExeNameOut
927	typeset comp compname comptagname
928	for comp in ${config_ListOfComponents[*]} ; do
929	# Define component
930	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
931	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
932
933	# Copy executable for this component
934	eval ExeNameIn=\${config_Executable_${comp}[0]}
935	eval ExeNameOut=\${config_Executable_${comp}[1]}
936
937	# Debug Print
938	IGCM_debug_Print 3 "PeriodStart ${compname} Driver Function (if any)."
939	# UPDATE component
940	${comp}_PeriodStart 2> /dev/null
941
942	done
943
944	IGCM_debug_PopStack "IGCM_comp_PeriodStart"
945	}
946
947
948
949	#=======================================================================
950	function IGCM_comp_modifyFile
951	{
952	#
953	# syntax: IGCM_comp_modifyFile filein key [value]
954	#
955	# For example : IGCM_comp_modifyFile metrics_template.py case_id \'SE_${YEARS}\'
956	#
957	# This function is used to replace a pattern in a file for a specific variable.
958	#
959	# Arguments:
960	# - filein : the file in run directory in which the variable should be set
961	# - key : the variable to modify
962	# - value : the value to set the key equal to
963	#
964	IGCM_debug_PushStack "IGCM_comp_modifyFile"
965
966	typeset filein key value pattern
967
968	# Set local variables and test the arguments
969	if [ $# = 3 ] ; then
970	# Normal case with 3 arguments
971	filein=$1 ; key=$2 ; value=$3
972	else
973	IGCM_debug_Exit "IGCM_comp_modifyFile: Bad number of arguments."
974	IGCM_debug_PopStack "IGCM_comp_modifyFile"
975	return
976	fi
977	IGCM_debug_Print 1 "Entering IGCM_comp_modifyFile with arguments: ${filein} ${key} ${value}"
978
979	# Test if the file exist
980	if [ ! -f ${filein} ] ; then
981	IGCM_debug_Exit "IGCM_comp_modifyFile: ${filein} does not exist."
982	IGCM_debug_PopStack "IGCM_comp_modifyFile"
983	return
984	fi
985
986	# Read the line with key in the file without the comments
987	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
988
989	# Verify the existance of the pattern
990	if [ X"${pattern}" = X ] ; then
991	# Variable key is not set in filein, stop.
992	IGCM_debug_Exit "IGCM_comp_modifyFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
993	IGCM_debug_PopStack "IGCM_comp_modifyFile"
994	return
995	fi
996
997	# Now change key in filein
998	#sed -e "s:${pattern}:${key}=${value}:" ${filein} > ${filein}.tmp
999	sed -e "s:^ ${key} =.*:${key}=${value}:" ${filein} > ${filein}.tmp
1000	IGCM_debug_Print 1 "IGCM_comp_modifyFile: In ${filein} set ${key}=${value}"
1001	\mv ${filein}.tmp ${filein}
1002
1003	IGCM_debug_PopStack "IGCM_comp_modifyFile"
1004	}
1005
1006	#=======================================================================
1007	function IGCM_comp_modifyDefFile
1008	{
1009	#
1010	# syntax: IGCM_comp_modifyDefFile type filein key [value]
1011	#
1012	# For example : IGCM_comp_modifyDefFile blocker run.def day_step 1200
1013	#
1014	# This function is used to modify a parameter file for a specific variable.
1015	# The file must be a ".def" file, i.e. with IOIPSL parameter file syntax.
1016	# This function can be used in the comp.driver files for the components.
1017	#
1018	# Arguments:
1019	# - type : first argument must be blocker, nonblocker or force
1020	# For "blocker" case, the variable must be attributed the keyworld AUTO
1021	# otherwise this function will exit.
1022	# For "nonblocker" case, the user can remove or modify the variable. For
1023	# this case, as long as AUTO is not set, no modification will be done.
1024	# For "force" case, the variable will be modified even if it is not set to AUTO
1025	# - filein : the file in run directory of .def type in which the variable should be set
1026	# - key : the variable to modify
1027	# - value : the value to set the key equal to, optional. If value is not set or if
1028	# value=DEFAULT, then a default value must be given in filein using syntax :
1029	# key= AUTO : DEFAULT=def_value
1030	#
1031	IGCM_debug_PushStack "IGCM_comp_modifyDefFile"
1032
1033	typeset type filein key value
1034	typeset filelist nb_occ modify
1035
1036	# Set local variables and test the arguments
1037	if [ $# = 4 ] ; then
1038	# Normal case with 4 arguments
1039	type=$1 ; filein=$2 ; key=$3 ; value=$4
1040	elif [ $# = 3 ] ; then
1041	# Normal case with 3 arguments
1042	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1043	else
1044	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Bad number of arguments."
1045	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1046	return
1047	fi
1048	IGCM_debug_Print 1 "Entering IGCM_comp_modifyDefFile with arguments: ${type} ${filein} ${key} ${value}"
1049
1050	# Test if first argument is correct
1051	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1052	IGCM_debug_Exit "IGCM_comp_modifyDefFile: Error in first argument must be blocker, nonblocker or force"
1053	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1054	return
1055	fi
1056
1057	# Test if the file exist.
1058	# Exit with error if the file does not exist for the case blocker or force.
1059	# Only return for the case nonblocker.
1060	if [ ! -f ${filein} ] ; then
1061	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1062	IGCM_debug_Exit "IGCM_comp_modifyDefFile: ${filein} does not exist."
1063	else
1064	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${filein} does not exist. Nothing will be done for this file."
1065	fi
1066	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1067	return
1068	fi
1069
1070	# Define list of files to test using all files with suffix .def (except used*.def)
1071	filelist=$( ls *def \| grep -v used )
1072
1073	# Count number of occurances for the key in all files
1074	nb_occ=$( grep -w ${key} ${filelist} \| grep -v "#" \| wc -l )
1075
1076	# Test if key is set several times
1077	if [ ${nb_occ} -gt 1 ] ; then
1078	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} is set ${nb_occ} times"
1079	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1080	return
1081	fi
1082
1083	# Treatement according to different cases
1084	if [ ${nb_occ} -eq 0 ] && [ ${type} = blocker ] ; then
1085	# Stop if the key is never set and the function is blocker
1086	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Error in ${filein}: Variable=${key} has been removed but this function is blocker. "
1087	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: restore ${filein} for variable ${key}."
1088	elif [ ${nb_occ} -eq 0 ] && [ ${type} = nonblocker ] ; then
1089	# The key is not set but it is a nonblocker call so nothing is done.
1090	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is not set in ${filein}. This is a nonblocker call so nothing is done."
1091	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: Default value for ${key} from the model will be used."
1092	modify=no
1093	elif [ $( grep ${key} ${filein} \| grep -v "\#" \|wc -l ) = 0 ] ; then
1094	# Variable key is not set in filein, stop.
1095	IGCM_debug_Exit "IGCM_comp_modifyDefFile : Variable ${key} is not set in correct file. It should be set in ${filein}."
1096	fi
1097
1098	# Check if AUTO is set in the filein on the same line as the key variable
1099	if [ $( grep -w ${key} ${filein} \| grep -v "\#" \| grep AUTO \| wc -l ) = 1 ] ; then
1100	# Modification will be done for all cases
1101	modify=yes
1102	else
1103	# The variable was not set to AUTO
1104	if [ ${type} = blocker ] ; then
1105	# Exit because this is a blocker call
1106	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} cannot be modified. It should be set to AUTO."
1107	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1108	return
1109	elif [ ${type} = nonblocker ] ; then
1110	# Do nothing. Suppose that the user did set the variable correct
1111	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key} is set by the user. Nothing done."
1112	modify=no
1113	elif [ ${type} = force ] ; then
1114	# Force modification
1115	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile : Variabl=${key} was not set to AUTO. Modification will be forced."
1116	modify=yes
1117	fi
1118	fi
1119
1120	# Do the modifcation now
1121	if [ ${modify} = yes ] ; then
1122
1123	# For option DEFAULT, read default value from file.
1124	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1125	# Case to set DEFAULT value
1126	# Read default value from filein
1127	value=$( grep ${key} ${filein} \| grep -v "\#" \| awk -F"DEFAULT *=" '{print $2}')
1128
1129	if [ X"${value}" = X ] ; then
1130	IGCM_debug_Exit "IGCM_comp_modifyDefFile : The variable ${key} needs a DEFAULT value in ${filein}."
1131	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: The syntax in ${filein} should be:"
1132	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: ${key}=_AUTO_:DEFAULT=def_value"
1133	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1134	return
1135	fi
1136	fi
1137
1138	# Now change key in filein
1139	sed -e "s/^${key}\ =./${key}= ${value}/" ${filein} > ${filein}.tmp
1140	IGCM_debug_Print 1 "IGCM_comp_modifyDefFile: In ${filein} set ${key}=${value}"
1141	\mv ${filein}.tmp ${filein}
1142	fi
1143	IGCM_debug_PopStack "IGCM_comp_modifyDefFile"
1144	}
1145
1146	#=======================================================================
1147	function IGCM_comp_modifyNamelist
1148	{
1149	#
1150	# syntax: IGCM_comp_modifyNamelist type filein key [value]
1151	#
1152	# For example : IGCM_comp_modifyNamelist blocker run.def day_step 1200
1153	#
1154	# This function is used to modify a parameter file for a specific variable.
1155	# The file must be a "namelist" file, i.e. with fortran namelist syntax.
1156	# This function can be used in the comp.driver files for the components.
1157	#
1158	# Arguments:
1159	# - type : first argument must be blocker, nonblocker or force
1160	# For "blocker" case, the variable must be attributed the keyworld AUTO
1161	# otherwise this function will exit.
1162	# For "nonblocker" case, the user can remove or modify the variable. For
1163	# this case, as long as AUTO is not set, no modification will be done.
1164	# For "force" case, the variable will be modified even if it is not set to AUTO
1165	# - filein : the file in run directory of .def type in which the variable should be set
1166	# - key : the variable to modify
1167	# - value : the value to set the key equal to, optional. If value is not set or if
1168	# value=DEFAULT, then a default value must be given in filein using syntax :
1169	# key= AUTO : DEFAULT=def_value
1170	#
1171	IGCM_debug_PushStack "IGCM_comp_modifyNamelist"
1172
1173	typeset type filein key value pattern modify
1174
1175	# Set local variables and test the arguments
1176	if [ $# = 4 ] ; then
1177	# Normal case with 4 arguments
1178	type=$1 ; filein=$2 ; key=$3 ; value=$4
1179	elif [ $# = 3 ] ; then
1180	# Normal case with 3 arguments
1181	type=$1 ; filein=$2 ; key=$3; value="DEFAULT"
1182	else
1183	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Bad number of arguments."
1184	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1185	return
1186	fi
1187	IGCM_debug_Print 1 "Entering IGCM_comp_modifyNamelist with arguments: ${type} ${filein} ${key} ${value}"
1188
1189	# Test if first argument is correct
1190	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1191	IGCM_debug_Exit "IGCM_comp_modifyNamelist: Error in first argument must be blocker, nonblocker or force"
1192	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1193	return
1194	fi
1195
1196	# Test if the file exist.
1197	# Exit with error if the file does not exist for the case blocker or force.
1198	# Only return for the case nonblocker.
1199	if [ ! -f ${filein} ] ; then
1200	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1201	IGCM_debug_Exit "IGCM_comp_modifyNamelist: ${filein} does not exist."
1202	else
1203	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${filein} does not exist. Nothing will be done for this file."
1204	fi
1205	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1206	return
1207	fi
1208
1209	# Read the line with key in the file without the comments
1210	pattern=$( grep "^ ${key} =" ${filein} \| sed -e "s% \!.%%" )
1211
1212	# Verify the existance of the pattern
1213	if [ X"$pattern" = X ] ; then
1214	# Variable key is not set in filein, stop.
1215	IGCM_debug_Exit "IGCM_comp_modifyNamelist : Variable ${key} is not set in correct file. It should be set in ${filein}."
1216	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1217	return
1218	fi
1219
1220	# Check if the variable is set to AUTO in the filein
1221	if [ $( echo $pattern \| grep AUTO \| wc -l ) = 1 ] ; then
1222	# Modification will be done for all cases
1223	modify=yes
1224	else
1225	# The variable was not set to AUTO
1226	if [ ${type} = blocker ] ; then
1227	# Exit because this is a blocker call
1228	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} cannot be modified. It should be set to AUTO."
1229	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1230	return
1231	elif [ ${type} = nonblocker ] ; then
1232	# Do nothing. Suppose that the user did set the variable correct
1233	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key} is set by the user. Nothing done."
1234	modify=no
1235	elif [ ${type} = force ] ; then
1236	# Force modification
1237	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist : Variabl=${key} was not set to AUTO. Modification will be forced."
1238	modify=yes
1239	fi
1240	fi
1241
1242	# Do the modifcation now
1243	if [ ${modify} = yes ] ; then
1244
1245	# For option DEFAULT, read default value from file.
1246	if [ X"${value}" = XDEFAULT ] \|\| [ X"${value}" = X ] ; then
1247	# Case to set DEFAULT value
1248	# Read default value from filein
1249	value=$( echo $pattern \| awk -F"DEFAULT *=" '{print $2}')
1250
1251	if [ X"${value}" = X ] ; then
1252	IGCM_debug_Exit "IGCM_comp_modifyNamelist : The variable ${key} needs a DEFAULT value in ${filein}."
1253	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: The syntax in ${filein} should be:"
1254	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: ${key}=_AUTO_:DEFAULT=def_value"
1255	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1256	return
1257	fi
1258	fi
1259
1260	# Now change key in filein
1261	sed -e "s/${pattern}/ ${key}=${value}/" ${filein} > ${filein}.tmp
1262	IGCM_debug_Print 1 "IGCM_comp_modifyNamelist: In ${filein} set ${key}=${value}"
1263	\mv ${filein}.tmp ${filein}
1264	fi
1265	IGCM_debug_PopStack "IGCM_comp_modifyNamelist"
1266	}
1267
1268	#=======================================================================
1269	function IGCM_comp_modifyXmlFile
1270	{
1271	#
1272	# syntax: IGCM_comp_modifyXmlFile type filein keyid keyattrib value
1273	#
1274	# For example : IGCM_comp_modifyXmlFile force file_def_orchidee.xml sechiba2 enabled .TRUE.
1275	# or IGCM_comp_modifyXmlFile blocker iodef.xml using_server NONE false
1276	#
1277	# This function is used to modify the value for a specific attribute and variable id.
1278	# The file must be a valid xml file.
1279	# This function can be used in the comp.driver files for the components.
1280	#
1281	# Arguments:
1282	# - type : first argument must be blocker, nonblocker or force.
1283	# For "blocker" case, the variable must be attributed the keyworld AUTO
1284	# otherwise this function will exit.
1285	# For "nonblocker" case, the user can remove or modify the variable. For
1286	# this case, as long as AUTO is not set, no modification will be done.
1287	# For "force" case, the variable will be modified even if it is not set to AUTO
1288	# - filein : the file in run directory of .xml type in which the variable should be set
1289	# - keyid : the variable to modify
1290	# - keyattrib : the attribute name to modify. If NONE, then the variable itself will be modified
1291	# - value : the value to set in the filein
1292	#
1293	IGCM_debug_PushStack "IGCM_comp_modifyXmlFile"
1294
1295	typeset type filein keyid keyattrib value modify
1296
1297	# Set local variables and test the arguments
1298	if [ $# = 5 ] ; then
1299	# Normal case with 4 arguments
1300	type=$1 ; filein=$2 ; keyid=$3 ; keyattrib=$4 ; value=$5
1301	else
1302	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Bad number of arguments."
1303	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1304	return
1305	fi
1306	IGCM_debug_Print 1 "Entering IGCM_comp_modifyXmlFile with arguments: type=${type} file=${filein}, id=${keyid} attribute=${keyattrib}, value=${value}"
1307
1308	# Test if first argument is correct
1309	if [ ${type} != blocker ] && [ ${type} != nonblocker ] && [ ${type} != force ] ; then
1310	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: Error in first argument must be blocker, nonblocker or force"
1311	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1312	return
1313	fi
1314
1315	# Test if the file exist.
1316	# Exit with error if the file does not exist for the case blocker or force.
1317	# Only return for the case nonblocker.
1318	if [ ! -f ${filein} ] ; then
1319	if [ ${type} = blocker ] \|\| [ ${type} = force ] ; then
1320	IGCM_debug_Exit "IGCM_comp_modifyXmlFile: ${filein} does not exist."
1321	else
1322	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile: ${filein} does not exist. Nothing will be done for this file."
1323	fi
1324	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1325	return
1326	fi
1327
1328	# Test if keyid is set in filein, otherwise exit
1329	if [ $( grep -w ${keyid} ${filein} \| wc -l ) = 0 ] ; then
1330	# Variable key is not set in filein, stop.
1331	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : ${keyid} is not set in the file. Bad syntax of ${filein} file."
1332	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1333	return
1334	fi
1335
1336	# Check if AUTO is set on the same line as keyid and keyattrib
1337	if [ $( grep -w ${keyid} ${filein} \| grep AUTO \| wc -l ) = 1 ] ; then
1338	# Modifification will be done
1339	modify=yes
1340	else
1341	if [ ${type} = blocker ] ; then
1342	# Exit, the variable must be set to AUTO
1343	IGCM_debug_Exit "IGCM_comp_modifyXmlFile : blocker function. The ${keyattrib} for ${keyid} must be set to AUTO in ${filein}."
1344	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1345	return
1346	elif [ ${type} = nonblocker ] ; then
1347	# Nothing will be done
1348	IGCM_debug_Print 1 "Nonblocker nothing is done for ${filein}, id=${keyid} and attribute ${keyattrib}"
1349	modify=no
1350	elif [ ${type} = force ] ; then
1351	# Force modification
1352	IGCM_debug_Print 1 "IGCM_comp_modifyXmlFile : Attribute=${keyattrib} for id=${keyid} was not set to AUTO. Modification will be forced."
1353	modify=yes
1354	fi
1355	fi
1356
1357	# Do the modifcation now
1358	if [ ${modify} = yes ] ; then
1359	if [ ${keyattrib} = NONE ] ; then
1360	# Case to modify the variable itself
1361	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting the variable=${value}"
1362	sed -e "s:\(<[^\"]\"${keyid}\".>\)\([^<]\)\(<[^>]\):\1${value}\3:" ${filein} > ${filein}.tmp
1363	else
1364	# Check if keyattrib is set on the same line as keyid
1365	if [ $( grep -w ${keyid} ${filein} \| grep ${keyattrib} \| wc -l ) = 1 ] ; then
1366	# Case to modify the attribute value
1367	IGCM_debug_Print 1 "Now modify ${filein} for id=${keyid} by setting attribute to ${keyattrib}=${value}"
1368	sed -e "/id=\"${keyid}\"/s:\(${keyattrib}=\"\)[^\"]*\(\"\):\1${value}\2:" ${filein} > ${filein}.tmp
1369	else
1370	# Case to add the attribute and its value
1371	IGCM_debug_Print 1 "Now add in ${filein} for id=${keyid} the attribute ${keyattrib} to the value ${value}"
1372	sed -e "/id=\"${keyid}\"/s:\/>: ${keyattrib}=\"${value}\"\/>:" ${filein} > ${filein}.tmp
1373	fi
1374	fi
1375	\mv ${filein}.tmp ${filein}
1376	fi
1377	IGCM_debug_PopStack "IGCM_comp_modifyXmlFile"
1378	}
1379
1380	#=======================================================================
1381	function IGCM_comp_Update
1382	{
1383	IGCM_debug_PushStack "IGCM_comp_Update"
1384
1385	# Debug Print :
1386	echo
1387	IGCM_debug_Print 1 "IGCM_comp_Update"
1388	echo
1389
1390	typeset ExeNameIn ExeNameOut
1391	typeset comp compname comptagname
1392	for comp in ${config_ListOfComponents[*]} ; do
1393	# Define component
1394	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1395	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1396
1397	# Copy executable for this component
1398	eval ExeNameIn=\${config_Executable_${comp}[0]}
1399	eval ExeNameOut=\${config_Executable_${comp}[1]}
1400
1401	# If missing executable and DRYRUN is set to 0 or 1 then stop!
1402	if [ ${DRYRUN} -le 1 ] && [ X${ExeNameIn} != X\"\" ] && [ ! -f ${R_EXE}/${ExeNameIn} ] ; then
1403	IGCM_debug_Exit "IGCM_comp_Update missing executable ${ExeNameIn}"
1404	fi
1405
1406	if [ ${Period} -eq 1 ] && [ -f ${R_EXE}/${ExeNameIn} ] ; then
1407	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1408	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1409	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1410	fi
1411	elif [ -f ${R_EXE}/${ExeNameIn} ] && [ ! -f ${RUN_DIR}/${ExeNameOut} ] ; then
1412	eval IGCM_sys_Cp ${R_EXE}/${ExeNameIn} ${ExeNameOut}
1413	if [ -f ${RUN_DIR}/${ExeNameOut} ] ; then
1414	eval IGCM_sys_Chmod +rx ${RUN_DIR}/${ExeNameOut}
1415	fi
1416	fi
1417
1418	# Debug Print
1419	IGCM_debug_Print 1 "Update ${compname} Parameter Files."
1420	# UPDATE component
1421	${comp}_Update
1422
1423	set -vx
1424
1425	# Read TimeSeries information from XML files, prepare TS directories and do modifications in timeseries_def_${compname}.xml
1426	if [ -f timeseries_def_${compname}.xml ]; then
1427	${libIGCM}/libIGCM_post/xios_parser.py tsquery --file timeseries_def_${compname}.xml > ts.temp.${compname}.txt
1428	for line in $( cat ts.temp.${compname}.txt ); do
1429	id=$( echo ${line} \| awk -F "," '{print $1}' \| awk -F "=" '{print $2}' )
1430	output_freq=$( echo ${line} \| awk -F "," '{print $2}' \| awk -F "=" '{print $2}' )
1431	case ${output_freq} in
1432	Y\|y)
1433	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_Y}
1434	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_Y}/${config_UserChoices_JobName}
1435	;;
1436	MO\|mo)
1437	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_M}
1438	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_M}/${config_UserChoices_JobName}
1439	;;
1440	D\|d)
1441	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_D}
1442	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_D}/${config_UserChoices_JobName}
1443	;;
1444	S\|s)
1445	eval IGCM_sys_Mkdir \${R_BUF_${comp}_A_H}
1446	eval IGCM_comp_modifyXmlFile nonblocker timeseries_def_${compname}.xml ${id} ts_prefix \${R_BUF_${comp}_A_H}/${config_UserChoices_JobName}
1447	;;
1448	esac
1449	done
1450	fi
1451
1452	set +vx
1453
1454	done
1455
1456	IGCM_debug_PopStack "IGCM_comp_Update"
1457	}
1458
1459	#=======================================================================
1460	function IGCM_comp_Finalize
1461	{
1462	IGCM_debug_PushStack "IGCM_comp_Finalize"
1463
1464	# Debug Print :
1465	echo
1466	IGCM_debug_Print 1 "IGCM_comp_Finalize"
1467	echo
1468
1469	typeset ListTextName TextName0
1470	typeset comp compname comptagname card ListFilesName FileName0 NbFiles SaveOnArchive
1471	typeset i i_ file_in file_in_ file_out file_out_ file_outin file_outin_ generic_file_name nb_rebuild_file
1472	typeset -Z4 j4 #BASH declare j4
1473	typeset list_file nlist_file
1474	typeset compactoutputs
1475
1476	# Initialize array hosting list of rebuilded files to copy
1477	unset rebuildedActionsList
1478
1479	# Text compacting options
1480	compactoutputs=false
1481	if [ X${JobType} != XRUN ] ; then
1482	compactoutputs=true
1483	elif [ X${config_UserChoices_CompactText} != Xn ] ; then
1484	compactoutputs=true
1485	fi
1486
1487	# Prepare headers for the shell dedicated to offline rebuild
1488	if [ X${AsynchronousRebuild} = Xtrue ] ; then
1489	[ ! -d ${RUN_DIR}/REBUILD_${PeriodDateBegin} ] && IGCM_sys_Mkdir ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1490	if [ ${DRYRUN} -le 1 ] ; then
1491	echo "#!/bin/ksh " > ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1492	echo "function IGCM_FlushRebuild " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1493	echo "{ " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1494	echo "IGCM_debug_PushStack \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1495	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1496	echo "IGCM_debug_Print 1 \"IGCM_FlushRebuild\" " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1497	echo "echo " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1498	echo "export R_SAVE=${R_SAVE} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1499	echo "export R_BUFR=${R_BUFR} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1500	echo "export R_OUT_KSH=${R_OUT_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1501	echo "export R_BUF_KSH=${R_BUF_KSH} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1502	echo "export config_UserChoices_JobName=${config_UserChoices_JobName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1503	echo "export config_UserChoices_SpaceName=${config_UserChoices_SpaceName} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1504	fi
1505	fi
1506
1507	for comp in ${config_ListOfComponents[*]} ; do
1508	# Define component
1509	eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
1510	eval comptagname=\${config_ListOfComponents_${comp}[1]} > /dev/null 2>&1
1511
1512	# Debug Print
1513	IGCM_debug_Print 1 "Finalize ${comp} : ${compname} component."
1514	# FINALIZE component
1515	${comp}_Finalize
1516
1517	card=${SUBMIT_DIR}/COMP/${compname}.card
1518
1519	# Save Output Text files of models
1520	#---------------------------------
1521	IGCM_debug_Print 2 "Save Output Text files for ${comp} : ${compname} component."
1522	IGCM_card_DefineArrayFromOption ${card} OutputText List
1523	ListTextName=${compname}_OutputText_List
1524
1525	eval TextName0=\${${ListTextName}[0]} > /dev/null 2>&1
1526	if [ X${TextName0} != X${NULL_STR} ] ; then
1527	eval NbFiles=\${#${ListTextName}[@]} > /dev/null 2>&1
1528
1529	(( i=0 ))
1530	until [ $i -eq $NbFiles ]; do
1531	eval file_in=\${${ListTextName}[$i]} > /dev/null 2>&1
1532	eval file_out=${PREFIX}_${file_in}
1533
1534	(( i=i+1 ))
1535
1536	unset list_file
1537	#set +A list_file -- $( ls ${file_in}* \| sort 2>/dev/null )
1538	# result for a a1 a10 a2 with file_in=a a a1 a2 a10
1539	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 )
1540	nlist_file=${#list_file[@]}
1541	if [ ${nlist_file} -gt 1 ] ; then
1542	if ( ${compactoutputs} ) ; then
1543	IGCM_debug_Print 2 "Parallelism of Text Output with ${nlist_file} files."
1544	IGCM_debug_Print 2 "Compact files in ${file_out} : " ${list_file[*]}
1545	echo ${list_file[*]} > ${file_out}
1546	echo "" >> ${file_out}
1547
1548	(( i_ = 0 ))
1549	for file in ${list_file[@]} ; do
1550	echo "_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ " >> ${file_out}
1551	echo "\| " ${i_} " " ${file} >> ${file_out}
1552	echo "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - " >> ${file_out}
1553	cat ${file} \| sed "s/\(.*\)/${i_}\1/" >> ${file_out}
1554	echo "" >> ${file_out}
1555	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1556	(( i_ = i_ + 1 ))
1557	done
1558	if ( ${ExecutionFail} ) ; then
1559	IGCM_sys_Cp ${file_out} ${SUBMIT_DIR}/Debug
1560	fi
1561
1562	if [ X${Pack} = Xtrue ] ; then
1563	eval IGCM_sys_PutBuffer_Out ${file_out} \${R_BUF_${comp}_D}/${file_out}
1564	else
1565	eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}_D}/${file_out}
1566	fi
1567
1568	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_out}" > /dev/null 2>&1
1569	else
1570	for file in ${list_file[@]} ; do
1571	if ( ${ExecutionFail} ) ; then
1572	IGCM_sys_Cp ${file} ${SUBMIT_DIR}/Debug/${PREFIX}_${file}
1573	fi
1574
1575	if [ X${Pack} = Xtrue ] ; then
1576	eval IGCM_sys_PutBuffer_Out ${file} \${R_BUF_${comp}_D}/${PREFIX}_${file}
1577	else
1578	eval IGCM_sys_Put_Out ${file} \${R_OUT_${comp}_D}/${PREFIX}_${file}
1579	fi
1580
1581	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file}" > /dev/null 2>&1
1582	done
1583	fi
1584	else
1585	if ( [ -f ${file_in}_0000 ] \|\| [ -f ${file_in}0 ] ) ; then
1586	eval IGCM_sys_Mv ${file_in}* ${file_in}
1587	fi
1588
1589	if ( ${ExecutionFail} ) ; then
1590	IGCM_sys_Cp ${file_in} ${SUBMIT_DIR}/Debug/${file_out}
1591	fi
1592
1593	if [ X${Pack} = Xtrue ] ; then
1594	eval IGCM_sys_PutBuffer_Out ${file_in} \${R_BUF_${comp}_D}/${file_out}
1595	else
1596	eval IGCM_sys_Put_Out ${file_in} \${R_OUT_${comp}_D}/${file_out}
1597	fi
1598	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1599	fi
1600	done
1601	fi
1602
1603	# Save Restarts files
1604	#--------------------
1605	IGCM_debug_Print 2 "Save Restart files for ${comp} : ${compname} component."
1606	IGCM_card_DefineArrayFromOption ${card} RestartFiles List
1607	ListFilesName=${compname}_RestartFiles_List
1608	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1609
1610	if ( [ X${FileName0} != X${NULL_STR} ] && [ X${FileName0} != XNONE ] ) ; then
1611	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1612
1613	(( i=0 ))
1614	until [ $i -ge $NbFiles ]; do
1615	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1616	eval file_in=${file_in_}
1617
1618	(( i_ = i+1 ))
1619	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1620	eval file_out=${file_out_}
1621
1622	(( i_ = i+2 ))
1623	eval file_outin_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1624	eval file_outin=${file_outin_}
1625
1626	generic_restart_file_name_in=$( basename ${file_in} .nc )
1627	generic_restart_file_name_out=$( basename ${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out} .nc )
1628	generic_restart_file_name_outin=$( basename ${file_outin} .nc )
1629
1630	nb_restart_file=$( ls ${generic_restart_file_name_in}_????.nc 2>/dev/null \| wc -l )
1631	if [ ${nb_restart_file} -gt 1 ] ; then
1632	j=0 # BASH LINE NOT NEEDED
1633	# BASH for j4 in in $( eval echo {0000..$(( nb_restart_file - 1 ))} ) ; do
1634	until [ $j -ge ${nb_restart_file} ]; do # BASH LINE NOT NEEDED
1635	j4=${j} # BASH LINE NOT NEEDED
1636	if [ X${Pack} = Xtrue ] ; then
1637	eval IGCM_sys_PutBuffer_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_BUF_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1638	else
1639	eval IGCM_sys_Put_Rest ${generic_restart_file_name_in}_${j4}.nc \${R_OUT_${comp}_R}/${generic_restart_file_name_out}_${j4}.nc
1640	fi
1641	if [ ! ${file_in} = ${file_outin} ] ; then
1642	if ( ${ExitFlag} ) ; then
1643	echo "IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc not executed."
1644	else
1645	IGCM_sys_Mv ${generic_restart_file_name_in}_${j4}.nc ${generic_restart_file_name_outin}_${j4}.nc
1646	fi
1647	fi
1648	(( j=j+1 )) # BASH LINE NOT NEEDED
1649	done
1650	else
1651	if [ X${Pack} = Xtrue ] ; then
1652	eval IGCM_sys_PutBuffer_Rest ${file_in} \${R_BUF_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1653	else
1654	eval IGCM_sys_Put_Rest ${file_in} \${R_OUT_${comp}_R}/${config_UserChoices_JobName}_${PeriodDateEnd}_${file_out}
1655	fi
1656	if [ ! ${file_in} = ${file_outin} ] ; then
1657	if ( ${ExitFlag} ) ; then
1658	echo "IGCM_sys_Mv ${file_in} ${file_outin} not executed."
1659	else
1660	IGCM_sys_Mv ${file_in} ${file_outin}
1661	fi
1662	fi
1663	fi
1664
1665	(( i=i+3 ))
1666	done
1667	else
1668	if [ X${FileName0} != XNONE ] ; then
1669	IGCM_debug_Exit "IGCM_comp_Finalize : No file in restart list for ${compname}."
1670	else
1671	IGCM_debug_Print 1 "IGCM_comp_Finalize : NONE specified in Restart List ${compname}."
1672	fi
1673	fi
1674
1675	# Save Output files
1676	#------------------
1677	IGCM_debug_Print 2 "Save Output files for ${comp} : ${compname} component."
1678	IGCM_card_DefineArrayFromOption ${card} OutputFiles List
1679	ListFilesName=${compname}_OutputFiles_List
1680	eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
1681
1682	if [ X${FileName0} != X${NULL_STR} ] ; then
1683	eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
1684
1685	(( i=0 ))
1686	until [ $i -ge $NbFiles ]; do
1687	SaveOnArchive=true
1688	eval file_in_=\${${ListFilesName}[$i]} > /dev/null 2>&1
1689	eval file_in=${file_in_}
1690	(( i_ = i+1 ))
1691	eval file_out_=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1692	eval file_out=${file_out_}
1693	#
1694	# Override file_out path remplacing R_SAVE by R_BUFR
1695	#
1696	if [ X${Pack} = Xtrue ] ; then
1697	file_out=$( echo $file_out \| sed "s:^$R_SAVE:$R_BUFR:" )
1698	fi
1699	#
1700	# Not necessarily the best option. /!\ Potential side effects /!\
1701	#
1702	(( i_ = i+2 ))
1703	eval flag_post=\${${ListFilesName}[$i_]} > /dev/null 2>&1
1704	#
1705	generic_file_name=$( basename ${file_in} .nc )
1706	nb_rebuild_file=$( ls \| grep "^${generic_file_name}_[0-9]*.nc" \| wc -l )
1707	#
1708	if ( [ ${nb_rebuild_file} -eq 1 ] && [ -f ${generic_file_name}_0000.nc ] ) ; then
1709	IGCM_debug_Print 2 "Parallelism with 1 file. Rebuilding ${file_in} not needed"
1710	IGCM_sys_Mv ${generic_file_name}_0000.nc ${file_in}
1711	elif [ ${nb_rebuild_file} -gt 1 ] ; then
1712	IGCM_debug_Print 2 "Parallelism detected and rebuilding ${file_in} is needed"
1713	if [ X${AsynchronousRebuild} = Xfalse ] ; then
1714	IGCM_debug_Print 2 "Rebuilding ${file_in} online"
1715	IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc
1716	else
1717	IGCM_debug_Print 2 "Preparing offline rebuild for ${file_in}"
1718	IGCM_sys_Mv ${generic_file_name}_[0-9]*.nc ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1719
1720	# Prepare the shell dedicated to offline rebuild
1721	if [ $DRYRUN -le 1 ]; then
1722	if [ ${file_in} = histstn.nc ] ; then
1723	echo "IGCM_sys_rebuild_station ${file_in} ${generic_file_name}_*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1724	else
1725	echo "IGCM_sys_rebuild ${file_in} ${generic_file_name}_[0-9]*.nc" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1726	fi
1727	echo "IGCM_debug_Verif_Exit" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1728	fi
1729	#
1730	# Load Patch we need to apply and apply
1731	if [ $DRYRUN -le 1 ]; then
1732	if [ X$( eval echo \${${compname}_${flag_post}_Patches[0]} ) != X${NULL_STR} ]; then
1733	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1734	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1735	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1736	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1737	done
1738	fi
1739	fi
1740	#
1741	if [ $DRYRUN -le 1 ]; then
1742	if [ X${Pack} = Xtrue ] ; then
1743	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_PutBuffer_Out ${file_in} ${file_out}"
1744	else
1745	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_sys_Put_Out ${file_in} ${file_out}"
1746	fi
1747	rebuildedActionsList[${#rebuildedActionsList[*]}]="IGCM_debug_Verif_Exit"
1748	rebuildedActionsList[${#rebuildedActionsList[]}]="IGCM_sys_Rm ${generic_file_name}_[0-9].nc"
1749	fi
1750	SaveOnArchive=false
1751	fi
1752	fi
1753	#
1754	if [ ${SaveOnArchive} = true ] ; then
1755	#
1756	# Rebuild has been done online or it was not needed
1757	#
1758	# If we need to apply a patch we use TMP DIRECTORY before ARCHIVING if asynchronous rebuild is on
1759	#
1760	thereisapatch=$( eval echo \${${compname}_${flag_post}_Patches[0]} )
1761	if ( [ ! X${thereisapatch} = X${NULL_STR} ] && [ ! X${thereisapatch} = X ] && [ X${AsynchronousRebuild} = Xtrue ] && [ -f ${file_in} ] ) ; then
1762	IGCM_sys_Mv ${file_in} ${RUN_DIR}/REBUILD_${PeriodDateBegin}
1763	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=REBUILD_${PeriodDateBegin}/${file_in} > /dev/null 2>&1
1764	#
1765	if [ $DRYRUN -le 1 ]; then
1766	for Patch in $( eval echo \${${compname}_${flag_post}_Patches[*]} ) ; do
1767	echo ". ${libIGCM_POST}/libIGCM_post/IGCM_${Patch}.ksh" >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1768	echo "IGCM_${Patch} ${file_in} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1769	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1770	done
1771	#
1772	if [ X${Pack} = Xtrue ] ; then
1773	echo "IGCM_sys_PutBuffer_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1774	else
1775	echo "IGCM_sys_Put_Out ${file_in} ${file_out} " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1776	fi
1777	echo "IGCM_debug_Verif_Exit " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1778	#
1779	fi
1780	else
1781	#
1782	# No Patch, No Asynchronous rebuild, online rebuild has been done or was not needed
1783	#
1784	if [ X${Pack} = Xtrue ] ; then
1785	IGCM_sys_PutBuffer_Out ${file_in} ${file_out}
1786	else
1787	IGCM_sys_Put_Out ${file_in} ${file_out}
1788	fi
1789	eval FileToBeDeleted[${#FileToBeDeleted[@]}]="${file_in}" > /dev/null 2>&1
1790	if [ ${nb_rebuild_file} -gt 1 ] ; then
1791	for DelFile in $( ls \| grep "${generic_file_name}[_0-9]*.nc" ) ; do
1792	eval FileToBeDeleted[${#FileToBeDeleted[@]}]=${DelFile} > /dev/null 2>&1
1793	done
1794	fi
1795	fi
1796	fi
1797	(( i=i+3 ))
1798	done
1799	fi
1800	echo
1801	done
1802	# Append the sync call and the copy sequence to the IGCM_FlushRebuild function if needed
1803	if [ ${#rebuildedActionsList[*]} -ne 0 ] ; then
1804	echo "IGCM_sys_sync " >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1805	i=0
1806	until [ ${i} -ge ${#rebuildedActionsList[*]} ]; do
1807	echo ${rebuildedActionsList[$i]} >> ${RUN_DIR}/REBUILD_${PeriodDateBegin}/rebuild.ksh
1808	(( i=i+1 ))
1809	done
1810	fi
1811	IGCM_debug_PopStack "IGCM_comp_Finalize"
1812	}

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