source: trunk/libIGCM/AA_pack_restart @ 1464

Last change on this file since 1464 was 1460, checked in by jgipsl, 6 years ago

Change in headers at irene : removed temporary settings -E '--licenses=fs_unshare,fs_work,fs_store,fs_scratch' and now use option -m store,work,scratch. The temporary settings were needed because a bug with resubmitting jobs at workdir/irene. This has been fixed by TGCC.

  • 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: 11.9 KB
Line 
1#-Q- curie ######################
2#-Q- curie ## CURIE   TGCC/CEA ##
3#-Q- curie ######################
4#-Q- curie #MSUB -r PACKRESTART    # Nom du job
5#-Q- curie #MSUB -eo
6#-Q- curie #MSUB -n 1              # Reservation du processus
7#-Q- curie #MSUB -T 7200          # Limite de temps elapsed du job
8#-Q- curie #MSUB -q ::default_node::
9#-Q- curie #MSUB -c ::default_core::
10#-Q- curie #MSUB -Q normal
11#-Q- curie #MSUB -A ::default_project::
12#-Q- curie set +x
13#-Q- irene ######################
14#-Q- irene ## IRENE   TGCC/CEA ##
15#-Q- irene ######################
16#-Q- irene #MSUB -r PACKRESTART    # Job name
17#-Q- irene #MSUB -eo
18#-Q- irene #MSUB -n 1              # Number of cores
19#-Q- irene #MSUB -T 7200           # Maximum elapsed time
20#-Q- irene #MSUB -q skylake
21#-Q- irene #MSUB -c 4
22#-Q- irene #MSUB -Q normal
23#-Q- irene #MSUB -A ::default_project::
24#-Q- irene #MSUB -m store,work,scratch
25#-Q- irene set +x
26#-Q- ada #!/bin/ksh
27#-Q- ada #######################
28#-Q- ada ## ADA         IDRIS ##
29#-Q- ada #######################
30#-Q- ada # @ job_type = mpich
31#-Q- ada # @ requirements = (Feature == "prepost")
32#-Q- ada # Temps Elapsed max. d'une requete hh:mm:ss
33#-Q- ada # @ wall_clock_limit = 10:00:00
34#-Q- ada # Nom du travail LoadLeveler
35#-Q- ada # @ job_name   = PACKRESTART
36#-Q- ada # Fichier de sortie standard du travail
37#-Q- ada # @ output     = $(job_name).$(jobid)
38#-Q- ada # Fichier de sortie d'erreur du travail
39#-Q- ada # @ error      =  $(job_name).$(jobid)
40#-Q- ada # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
41#-Q- ada # @ notification = error
42#-Q- ada # @ environment  = $DEBUG_debug ; $BigBrother ; $postProcessingStopLevel ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $POST_DIR ; $Script_Post_Output ; $SUBMIT_DIR ; $PeriodDateBegin ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER ; wall_clock_limit=$(wall_clock_limit)
43#-Q- ada # @ queue
44#-Q- lxiv8 ######################
45#-Q- lxiv8 ## OBELIX      LSCE ##
46#-Q- lxiv8 ######################
47#-Q- lxiv8 #PBS -N PACKRESTART
48#-Q- lxiv8 #PBS -m a
49#-Q- lxiv8 #PBS -j oe
50#-Q- lxiv8 #PBS -q medium
51#-Q- lxiv8 #PBS -o PACKRESTART.$$
52#-Q- lxiv8 #PBS -S /bin/ksh
53#-Q- ifort_CICLAD ######################
54#-Q- ifort_CICLAD ##   CICLAD    IPSL ##
55#-Q- ifort_CICLAD ######################
56#-Q- ifort_CICLAD #PBS -N PACKRESTART
57#-Q- ifort_CICLAD #PBS -m a
58#-Q- ifort_CICLAD #PBS -j oe
59#-Q- ifort_CICLAD #PBS -q std
60#-Q- ifort_CICLAD #PBS -S /bin/ksh
61#-Q- default #!/bin/ksh
62#-Q- default ##################
63#-Q- default ## DEFAULT HOST ##
64#-Q- default ##################
65
66#**************************************************************
67# Author: Sebastien Denvil
68# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
69# $Revision::                                          $ Revision of last commit
70# $Author::                                            $ Author of last commit
71# $Date::                                              $ Date of last commit
72# IPSL (2006)
73#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
74#
75#**************************************************************
76
77#set -eu
78#set -vx
79
80date
81
82#D- Task type DO NOT CHANGE (computing, post-processing or checking)
83TaskType=post-processing
84
85########################################################################
86
87#D- Flag to determine if this job in a standalone mode
88#D- Default : value from AA_job if any
89StandAlone=${StandAlone:=true}
90
91#D- Path to libIGCM
92#D- Default : value from AA_job if any
93# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
94# WARNING you must check MirrorlibIGCM variable in sys library.
95# WARNING If this variable is true, you must use libIGCM_POST path instead
96# WARNING of your running libIGCM directory.
97libIGCM=${libIGCM:=::modipsl::/libIGCM}
98
99#-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer.
100MASTER=${MASTER:=ada|curie}
101
102#D- Flag to determine begin date for restart pack
103#D- Default : value from AA_job if any
104DateBegin=${DateBegin:=20000101}
105
106#D- Flag to determine end date for restart pack
107#D- Default : value from AA_job if any
108DateEnd=${DateEnd:=20691231}
109
110#D- Flag to determine pack period
111#D- Default : value from AA_job if any
112PeriodPack=${PeriodPack:=10Y}
113
114#D- Uncomment to run interactively
115#D- For testing purpose, will be remove
116#SUBMIT_DIR=${PWD}
117#RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test
118
119#D- Increased verbosity (1, 2, 3)
120#D- Default : value from AA_job if any
121Verbosity=${Verbosity:=3}
122
123#D- Low level debug : to bypass lib test checks and stack construction
124#D- Default : value from AA_job if any
125DEBUG_debug=${DEBUG_debug:=false}
126
127#D- Keep following comments for now. Will be remove.
128
129#on veut archiver les fichiers restart
130#Dans le cadre du demenagement ils seront renommes
131#ATM/Restart/****.nc
132#OCE/Restart/****.nc
133#...
134#sous la forme
135#RESTART/ATM_****.nc
136#RESTART/OCE_****.nc
137#Attention de bien conserver les dates d'origines
138#
139#Dans le cadre de la production nouvelle chaine
140#ils auront directement le bon nom
141#
142#On veut egalement que l'archive soit par periode de temps
143# cette periode est definie par la taille du pack donc connue
144# en entree du script (1M, 1Y, 5Y, 10Y etc...)
145#
146# $1= PATH/config_card d'une simulation avec
147# TagName/JobName/ExperimentName/SpaceName/DateBegin/DateEnd
148# $2=PeriodPack en M/m ou Y/y
149
150########################################################################
151
152. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
153. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
154. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
155#-------
156. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
157. ${libIGCM}/libIGCM_config/libIGCM_config.ksh
158. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
159#-------
160RUN_DIR=${RUN_DIR_PATH}
161IGCM_sys_MkdirWork ${RUN_DIR}
162IGCM_sys_Cd ${RUN_DIR}
163#-------
164( ${DEBUG_debug} ) && IGCM_debug_Check
165( ${DEBUG_debug} ) && IGCM_card_Check
166( ${DEBUG_debug} ) && IGCM_date_Check
167
168########################################################################
169
170#set -vx
171
172# ------------------------------------------------------------------
173# Test if all was right before proceeding further
174# ------------------------------------------------------------------
175IGCM_debug_Verif_Exit
176
177if [ ${StandAlone} = true ] ; then
178    CARD_DIR=${SUBMIT_DIR}
179else
180    CARD_DIR=${RUN_DIR_PATH}
181    IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
182    IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card    ${RUN_DIR_PATH}
183    IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP        ${RUN_DIR_PATH}
184    IGCM_sys_Get_Master ${SUBMIT_DIR}/POST        ${RUN_DIR_PATH}
185fi
186
187#==================================
188# First of all
189#
190# Read libIGCM compatibility version in config.card
191# Read UserChoices section
192# Read Ensemble section
193# Read Post section
194# Define all netcdf output directories
195#==================================
196IGCM_config_CommonConfiguration ${CARD_DIR}/config.card
197
198# ------------------------------------------------------------------
199# Activate BigBrother so as to supervise this job
200# ------------------------------------------------------------------
201IGCM_debug_BigBro_Initialize
202
203#==================================
204# Test and set up directories
205#==================================
206IGCM_sys_TestDirArchive ${R_SAVE}
207[ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive"
208
209STORE_RESTART=${R_SAVE}/RESTART
210IGCM_sys_MkdirArchive ${STORE_RESTART}
211
212# Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure)
213JobName=${config_UserChoices_JobName}
214echo $JobName $R_BUFR $DateBegin $DateEnd
215
216# Clear txt file lists
217rm -f ${RUN_DIR}/liste_restart_files.txt
218rm -f ${RUN_DIR}/new_liste_restart_files.txt
219rm -f ${RUN_DIR}/liste_pack_*.txt
220rm -f ${RUN_DIR}/liste_pack_light_*.txt
221
222# Create sorted restart list to work with
223find ${R_BUFR}/*/Restart -name "*.*" | sort >> ${RUN_DIR}/liste_restart_files.txt
224
225# Rename restart files we will work with using symlinks
226#gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("cp --preserve " $0 " "dest_name)}' ${RUN_DIR}/liste_restart_files.txt
227gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("ln -s " $0 " "dest_name)}' ${RUN_DIR}/liste_restart_files.txt
228
229# List renamed restart files
230find ${RUN_DIR} -maxdepth 1 -mindepth 1 -name "???_*${JobName}*" -ls | sort -k 11 > ${RUN_DIR}/new_liste_restart_files.txt
231
232# ------------------------------------------------------------------
233# Test if all was right before proceeding further
234# ------------------------------------------------------------------
235IGCM_debug_Verif_Exit
236
237# Init loop
238date_begin_pack=${DateBegin}
239date_end_simulation=${DateEnd}
240number_pack=1
241
242IGCM_debug_PrintVariables 3 date_begin_pack
243IGCM_debug_PrintVariables 3 date_end_simulation
244
245# last restart of the previous period : to be deleted
246typeset date_end_previous
247date_end_previous=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} -1 )
248
249while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do
250
251  IGCM_debug_PrintVariables 3 number_pack
252
253  DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} )
254  date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) )
255
256  for file in $( gawk '{print $11}' ${RUN_DIR}/new_liste_restart_files.txt ); do
257    extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_//" )
258    date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' )
259    # warning demenagement. delete last restart of the previous pack
260    [  ${date_file} -eq ${date_end_previous} ] && echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${date_begin_pack}_${date_end_pack}.txt
261    # echo pack number ${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack}
262    if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then
263      echo $( basename ${file} ) >> ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt
264      # warning demenagement. do not delete last restart of this pack
265      [ ${date_file} -eq ${date_end_pack} ] || echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${date_begin_pack}_${date_end_pack}.txt
266    fi
267    # light pack list of restarts files that will be used
268    if [ X${config_Post_LightRestartPack} = XTRUE ] ; then
269      if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${PeriodDateBegin} ] ; then
270        echo $( basename ${file} ) >> ${RUN_DIR}/liste_pack_light_${date_begin_pack}_${date_end_pack}.txt
271      fi
272    fi
273  done
274
275  # Create tar files
276  IGCM_debug_Print 1 "Tar ongoing"
277  if [ X${config_Post_LightRestartPack} = XTRUE ] ; then
278    tar -cvf ${JobName}_${date_begin_pack}_${date_end_pack}_restart.tar --dereference --files-from ${RUN_DIR}/liste_pack_light_${date_begin_pack}_${date_end_pack}.txt
279  else
280    tar -cvf ${JobName}_${date_begin_pack}_${date_end_pack}_restart.tar --dereference --files-from ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt
281  fi
282  # Save it
283  IGCM_sys_Put_Out ${JobName}_${date_begin_pack}_${date_end_pack}_restart.tar ${STORE_RESTART}
284  # Clean it
285  IGCM_sys_Rm ${JobName}_${date_begin_pack}_${date_end_pack}_restart.tar
286  # ------------------------------------------------------------------
287  # Test if all was right before proceeding cleaning
288  # ------------------------------------------------------------------
289  IGCM_debug_Verif_Exit
290  # Clean links
291  cat ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt | xargs rm
292  # Clean files links pointed to
293  cat ${RUN_DIR}/liste_remove_pack_${date_begin_pack}_${date_end_pack}.txt | xargs rm
294  # Save the list of files that has been pack (tar)
295  #mv ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt ${STORE_RESTART}
296  IGCM_debug_Print 1 "Tar and cleaning done"
297
298  (( number_pack = number_pack + 1 ))
299
300  # Add 1 day to date_end_pack to have the new date_begin_pack
301  date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 )
302
303done
304
305# Clean RUN_DIR_PATH (necessary for cesium and titane only)
306IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
307
308# ------------------------------------------------------------------
309# Finalize BigBrother to inform that the jobs end
310# ------------------------------------------------------------------
311IGCM_debug_BigBro_Finalize
312
313date
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