source: branches/libIGCM_MPI_OpenMP/AA_pack_restart

Last change on this file was 612, checked in by mafoipsl, 12 years ago

Pack_restart : keep last restart of pack (This will reduce the need of packed restart and tar) and add delete of the last restart of the previous pack.
  • Property svn:keywords set to Revision Author Date
File size: 14.2 KB
Line 
1#-Q- cesium #!/bin/ksh
2#-Q- cesium ######################
3#-Q- cesium ## CESIUM   CEA ##
4#-Q- cesium ######################
5#-Q- cesium #MSUB -r PACKRESTART    # Nom du job
6#-Q- cesium #MSUB -N 1              # Reservation du noeud
7#-Q- cesium #MSUB -n 1              # Reservation du processus
8#-Q- cesium #MSUB -T 86400          # Limite de temps elapsed du job
9#-Q- cesium #MSUB -E "-j o"
10#-Q- cesium #MSUB -E "-S /bin/ksh"
11#-Q- platine #!/usr/bin/ksh
12#-Q- platine ###################
13#-Q- platine ## PLATINE   CEA ##
14#-Q- platine ###################
15#-Q- platine #BSUB -J PACKRESTART            # Nom du job
16#-Q- platine #BSUB -N                        # message a la fin du job
17#-Q- platine #BSUB -n 1                      # reservation des processeurs pour le job
18#-Q- platine #BSUB -W 4:00                   # Limite temps
19#-Q- platine #BSUB -q post                   # Passage en queue post
20#-Q- platine #BSUB -L /bin/ksh
21#-Q- sx8brodie #!/bin/ksh
22#-Q- sx8brodie #######################
23#-Q- sx8brodie ## SX8BRODIE   IDRIS ##
24#-Q- sx8brodie #######################
25#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
26#-Q- sx8brodie # @ wall_clock_limit = 10:00:00
27#-Q- sx8brodie # Nom du travail LoadLeveler
28#-Q- sx8brodie # @ job_name   = PACKRESTART
29#-Q- sx8brodie # Fichier de sortie standard du travail
30#-Q- sx8brodie # @ output     = $(job_name).$(jobid)
31#-Q- sx8brodie # Fichier de sortie d'erreur du travail
32#-Q- sx8brodie # @ error      =  $(job_name).$(jobid)
33#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
34#-Q- sx8brodie # @ notification = error
35#-Q- sx8brodie # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
36#-Q- sx8brodie # @ queue
37#-Q- aix6 #!/bin/ksh
38#-Q- aix6 #######################
39#-Q- aix6 ##   VARGAS   IDRIS  ##
40#-Q- aix6 #######################
41#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
42#-Q- aix6 # @ wall_clock_limit = 10:00:00
43#-Q- aix6 # Nom du travail LoadLeveler
44#-Q- aix6 # @ job_name   = PACKRESTART
45#-Q- aix6 # Fichier de sortie standard du travail
46#-Q- aix6 # @ output     = $(job_name).$(jobid)
47#-Q- aix6 # Fichier de sortie d'erreur du travail
48#-Q- aix6 # @ error      =  $(job_name).$(jobid)
49#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
50#-Q- aix6 # @ notification = error
51#-Q- aix6 # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
52#-Q- aix6 # @ queue
53#-Q- ulam #!/bin/ksh
54#-Q- ulam #######################
55#-Q- ulam ##   VARGAS   IDRIS  ##
56#-Q- ulam #######################
57#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
58#-Q- ulam # @ wall_clock_limit = 10:00:00
59#-Q- ulam # Nom du travail LoadLeveler
60#-Q- ulam # @ job_name   = PACKRESTART
61#-Q- ulam # Fichier de sortie standard du travail
62#-Q- ulam # @ output     = $(job_name).$(jobid)
63#-Q- ulam # Fichier de sortie d'erreur du travail
64#-Q- ulam # @ error      =  $(job_name).$(jobid)
65#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
66#-Q- ulam # @ notification = error
67#-Q- ulam # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
68#-Q- ulam # @ queue
69#-Q- sx8mercure #!/bin/ksh
70#-Q- sx8mercure ######################
71#-Q- sx8mercure ## SX8MERCURE   CEA ##
72#-Q- sx8mercure ######################
73#-Q- sx8mercure #PBS -N PACKRESTART          # Nom du job
74#-Q- sx8mercure #PBS -j o                    # regroupement des stdout et stderr
75#-Q- sx8mercure #PBS -S /usr/bin/ksh         # shell de soumission
76#-Q- sx8mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
77#-Q- sx8mercure #PBS -l cputim_job=24:00:00  # Limite temps a 1 heures
78#-Q- sx8mercure #PBS -q scalaire
79#-Q- sx9mercure #!/bin/ksh
80#-Q- sx9mercure ######################
81#-Q- sx9mercure ## SX9MERCURE  CCRT ##
82#-Q- sx9mercure ######################
83#-Q- sx9mercure #PBS -N PACKRESTART          # Nom du job
84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr
85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission
86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
87#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures
88#-Q- sx9mercure #PBS -q scalaire
89#-Q- titane #!/bin/ksh
90#-Q- titane ######################
91#-Q- titane ## TITANE   CEA     ##
92#-Q- titane ######################
93#-Q- titane #MSUB -r PACKRESTART    # Nom du job
94#-Q- titane #MSUB -eo
95#-Q- titane #MSUB -n 1              # Reservation du processus
96#-Q- titane #MSUB -T 86400          # Limite de temps elapsed du job
97#-Q- titane #MSUB -q mono
98#-Q- lxiv8 ######################
99#-Q- lxiv8 ## OBELIX      LSCE ##
100#-Q- lxiv8 ######################
101#-Q- lxiv8 #PBS -N PACKRESTART
102#-Q- lxiv8 #PBS -m a
103#-Q- lxiv8 #PBS -j oe
104#-Q- lxiv8 #PBS -q medium
105#-Q- lxiv8 #PBS -o PACKRESTART.$$
106#-Q- lxiv8 #PBS -S /bin/ksh
107#-Q- default #!/bin/ksh
108#-Q- default ##################
109#-Q- default ## DEFAULT HOST ##
110#-Q- default ##################
111
112#**************************************************************
113# Author: Sebastien Denvil
114# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
115# $Revision::                                          $ Revision of last commit
116# $Author::                                            $ Author of last commit
117# $Date::                                              $ Date of last commit
118# IPSL (2006)
119#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
120#
121#**************************************************************
122
123#set -eu
124#set -vx
125
126date
127
128########################################################################
129
130#D- Flag to determine if this job in a standalone mode
131#D- Default : value from AA_job if any
132StandAlone=${StandAlone:=true}
133
134#D- Path to libIGCM
135#D- Default : value from AA_job if any
136# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
137# WARNING you must check MirrorlibIGCM variable in sys library.
138# WARNING If this variable is true, you must use libIGCM_POST path instead
139# WARNING of your running libIGCM directory.
140libIGCM=${libIGCM:=::modipsl::/libIGCM}
141
142#-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer.
143MASTER=${MASTER:=mercure|titane|brodie|vargas}
144
145#D- Flag to determine begin date for restart pack
146#D- Default : value from AA_job if any
147DateBegin=${DateBegin:=20000101}
148
149#D- Flag to determine end date for restart pack
150#D- Default : value from AA_job if any
151DateEnd=${DateEnd:=20691231}
152
153#D- Flag to determine pack period
154#D- Default : value from AA_job if any
155PeriodPack=${PeriodPack:=10Y}
156
157#D- Uncomment to run interactively
158#D- For testing purpose, will be remove
159#SUBMIT_DIR=${PWD}
160#RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test
161
162#D- Increased verbosity (1, 2, 3)
163#D- Default : value from AA_job if any
164Verbosity=${Verbosity:=3}
165
166#D- Low level debug : to bypass lib test checks and stack construction
167#D- Default : value from AA_job if any
168DEBUG_debug=${DEBUG_debug:=false}
169
170#D- Keep following comments for now. Will be remove.
171
172#on veut archiver les fichiers restart
173#Dans le cadre du demenagement ils seront renommes
174#ATM/Restart/****.nc
175#OCE/Restart/****.nc
176#...
177#sous la forme
178#RESTART/ATM_****.nc
179#RESTART/OCE_****.nc
180#Attention de bien conserver les dates d'origines
181#
182#Dans le cadre de la production nouvelle chaine
183#ils auront directement le bon nom
184#
185#On veut egalement que l'archive soit par periode de temps
186# cette periode est definie par la taille du pack donc connue
187# en entree du script (1M, 1Y, 5Y, 10Y etc...)
188#
189# $1= PATH/config_card d'une simulation avec
190# TagName/JobName/ExperimentName/SpaceName/DateBegin/DateEnd
191# $2=PeriodPack en M/m ou Y/y
192
193########################################################################
194
195. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
196( ${DEBUG_debug} ) && IGCM_debug_Check
197. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
198( ${DEBUG_debug} ) && IGCM_card_Check
199. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
200( ${DEBUG_debug} ) && IGCM_date_Check
201#-------
202. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
203. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
204
205########################################################################
206
207#set -vx
208
209RUN_DIR=${RUN_DIR_PATH}
210IGCM_sys_MkdirWork ${RUN_DIR}
211IGCM_sys_Cd ${RUN_DIR}
212
213# ------------------------------------------------------------------
214# Test if all was right before proceeding further
215# ------------------------------------------------------------------
216IGCM_debug_Verif_Exit_Post
217
218if [ ${StandAlone} = true ] ; then
219    CARD_DIR=${SUBMIT_DIR}
220else
221    CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
222    IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH}
223fi
224
225#====================================================
226# First of all
227#
228# Read config.card
229
230IGCM_card_DefineArrayFromSection     ${CARD_DIR}/config.card UserChoices
231typeset option
232for option in ${config_UserChoices[*]} ; do
233  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
234done
235#
236echo
237IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices"
238IGCM_debug_PrintVariables 3 config_UserChoices_JobName
239IGCM_debug_PrintVariables 3 config_UserChoices_LongName
240IGCM_debug_PrintVariables 3 config_UserChoices_TagName
241IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
242IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
243IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
244IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
245IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
246IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
247echo
248
249#====================================================
250# Prepare environment
251#R_SAVE        : Job output storage directory
252#R_BUFR        : Job output buffered directory
253#STORE_RESTART : Where we store tar files
254
255if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
256  FreeName=$( echo ${config_UserChoices_JobName} | sed 's/.*_//' )
257  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
258  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
259else
260  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
261  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
262fi
263IGCM_sys_TestDirArchive ${R_SAVE}
264[ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive"
265
266#STORE_RESTART=/ccc/store/cont003/dsm/p86denv/.../RESTART
267STORE_RESTART=${R_SAVE}/RESTART
268IGCM_sys_MkdirArchive ${STORE_RESTART}
269
270#cd ${STORE_RESTART}
271#rm -f *
272
273# Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure)
274JobName=${config_UserChoices_JobName}
275echo $JobName $R_BUFR $DateBegin $DateEnd
276
277# Clear txt file lists
278rm -f ${RUN_DIR}/liste_restart_files.txt
279rm -f ${RUN_DIR}/new_liste_restart_files.txt
280rm -f ${RUN_DIR}/liste_pack_*.txt
281
282# Create sorted restart list to work with
283find ${R_BUFR}/*/Restart -name "*nc" | sort >> ${RUN_DIR}/liste_restart_files.txt
284
285# Rename restart files we will work with using symlinks
286#gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("cp --preserve " $0 " "dest_name)}' ${RUN_DIR}/liste_restart_files.txt
287gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("ln -s " $0 " "dest_name)}' ${RUN_DIR}/liste_restart_files.txt
288
289# List renamed restart files
290find ${RUN_DIR} -name "*.nc" -ls | sort -k 11 > ${RUN_DIR}/new_liste_restart_files.txt
291
292# ------------------------------------------------------------------
293# Test if all was right before proceeding further
294# ------------------------------------------------------------------
295IGCM_debug_Verif_Exit_Post
296
297# Init loop
298date_begin_pack=${DateBegin}
299date_end_simulation=${DateEnd}
300number_pack=1
301
302IGCM_debug_PrintVariables 3 date_begin_pack
303IGCM_debug_PrintVariables 3 date_end_simulation
304
305# last restart of the previous period : to be deleted
306typeset date_end_previous
307date_end_previous=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} -1 )
308
309while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do
310
311  IGCM_debug_PrintVariables 3 number_pack
312
313  DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} )
314  date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) )
315
316  for file in $( gawk '{print $11}' ${RUN_DIR}/new_liste_restart_files.txt ); do
317    extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_//" )
318    date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' )
319#   warning demenagement. delete last restart of the previous pack
320    [  ${date_file} -eq ${date_end_previous} ] && echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${number_pack}.txt
321#   echo pack number ${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack}
322    if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then
323      echo $( basename ${file} ) >> ${RUN_DIR}/liste_pack_${number_pack}.txt
324#   warning demenagement. do not delete last restart of this pack
325      [ ${date_file} -eq ${date_end_pack} ] || echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${number_pack}.txt
326#   Will not work. Need to find a better ordering.
327#   elif [ ${date_file} -ge ${date_end_pack} ] ; then
328#     break
329    fi
330  done
331
332  # Create tar files
333  IGCM_debug_Print 1 "Tar ongoing"
334  tar -cvf ${JobName}_${date_begin_pack}_${date_end_pack}_restart.tar --dereference --files-from ${RUN_DIR}/liste_pack_${number_pack}.txt
335  # Save it
336  IGCM_sys_Put_Out ${JobName}_${date_begin_pack}_${date_end_pack}_restart.tar ${STORE_RESTART}
337  # Clean it
338  IGCM_sys_Rm ${JobName}_${date_begin_pack}_${date_end_pack}_restart.tar
339  # Clean links
340  cat ${RUN_DIR}/liste_pack_${number_pack}.txt | xargs rm
341  # Clean files links pointed to
342  cat ${RUN_DIR}/liste_remove_pack_${number_pack}.txt | xargs rm
343  # Save the list of files that has been pack (tar)
344  mv ${RUN_DIR}/liste_pack_${number_pack}.txt ${STORE_RESTART}
345  IGCM_debug_Print 1 "Tar and cleaning done"
346
347  (( number_pack = number_pack + 1 ))
348
349  # Add 1 day to date_end_pack to have the new date_begin_pack
350  date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 )
351
352done
353
354# Clean RUN_DIR_PATH (necessary for cesium and titane only)
355IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
356
357date
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