source: trunk/libIGCM/AA_pack_restart

Last change on this file was 1612, checked in by aclsce, 4 months ago

Needed to define Script_Post_Output variable in stand alone mode in order to handle exit in case of error
  • 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: 13.5 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 -o PACKRESTART.out_%I
6#-Q- curie #MSUB -e PACKRESTART.out_%I
7#-Q- curie #MSUB -n 1              # Reservation du processus
8#-Q- curie #MSUB -T 7200          # Limite de temps elapsed du job
9#-Q- curie #MSUB -q ::default_node::
10#-Q- curie #MSUB -c ::default_core::
11#-Q- curie #MSUB -Q normal
12#-Q- curie #MSUB -A ::default_project::
13#-Q- curie set +x
14#-Q- irene ######################
15#-Q- irene ## IRENE   TGCC/CEA ##
16#-Q- irene ######################
17#-Q- irene #MSUB -r PACKRESTART    # Job name
18#-Q- irene #MSUB -o PACKRESTART.out_%I
19#-Q- irene #MSUB -e PACKRESTART.out_%I
20#-Q- irene #MSUB -n 1              # Number of cores
21#-Q- irene #MSUB -T 7200           # Maximum elapsed time
22#-Q- irene #MSUB -q ::default_node::
23#-Q- irene #MSUB -c ::default_core::
24#-Q- irene #MSUB -Q normal
25#-Q- irene #MSUB -A ::default_post_project::
26#-Q- irene #MSUB -m store,work,scratch
27#-Q- irene set +x
28#-Q- irene-amd ##########################
29#-Q- irene-amd ## IRENE-ROME  TGCC/CEA ##
30#-Q- irene-amd ##########################
31#-Q- irene-amd #MSUB -r PACKRESTART     # Job name
32#-Q- irene-amd #MSUB -o PACKRESTART.out_%I
33#-Q- irene-amd #MSUB -e PACKRESTART.out_%I
34#-Q- irene-amd #MSUB -n 1              # Number of cores
35#-Q- irene-amd #MSUB -T 7200          # Maximum elapsed time
36#-Q- irene-amd #MSUB -q ::default_node::
37#-Q- irene-amd #MSUB -c ::default_core::
38#-Q- irene-amd #MSUB -Q normal
39#-Q- irene-amd #MSUB -A ::default_post_project::
40#-Q- irene-amd #MSUB -m store,work,scratch
41#-Q- irene-amd set +x
42#-Q- jeanzay #!/bin/ksh
43#-Q- jeanzay ######################
44#-Q- jeanzay ## JEANZAY    IDRIS ##
45#-Q- jeanzay ######################
46#-Q- jeanzay #SBATCH --job-name=PACKRESTART         # Job Name
47#-Q- jeanzay #SBATCH --output=PACKRESTART.out_%J    # standard output
48#-Q- jeanzay #SBATCH --error=PACKRESTART.out_%J     # error output
49#-Q- jeanzay #SBATCH -N  1                        # Number of core
50#-Q- jeanzay #SBATCH --partition=prepost          # Post-processing partition
51#-Q- jeanzay #SBATCH --time=10:00:00                # Wall clock limit (seconds)
52#-Q- jeanzay #SBATCH --account ::default_project::@cpu
53#-Q- jeanzay set +x
54#-Q- ada #!/bin/ksh
55#-Q- ada #######################
56#-Q- ada ## ADA         IDRIS ##
57#-Q- ada #######################
58#-Q- ada # @ job_type = mpich
59#-Q- ada # @ requirements = (Feature == "prepost")
60#-Q- ada # Temps Elapsed max. d'une requete hh:mm:ss
61#-Q- ada # @ wall_clock_limit = 10:00:00
62#-Q- ada # Nom du travail LoadLeveler
63#-Q- ada # @ job_name   = PACKRESTART
64#-Q- ada # Fichier de sortie standard du travail
65#-Q- ada # @ output     = $(job_name).$(jobid)
66#-Q- ada # Fichier de sortie d'erreur du travail
67#-Q- ada # @ error      =  $(job_name).$(jobid)
68#-Q- ada # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
69#-Q- ada # @ notification = error
70#-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)
71#-Q- ada # @ queue
72#-Q- obelix ######################
73#-Q- obelix ## OBELIX      LSCE ##
74#-Q- obelix ######################
75#-Q- obelix #PBS -N PACKRESTART
76#-Q- obelix #PBS -m a
77#-Q- obelix #PBS -j oe
78#-Q- obelix #PBS -q medium
79#-Q- obelix #PBS -o PACKRESTART.$$
80#-Q- obelix #PBS -S /bin/ksh
81#-Q- ifort_CICLAD ######################
82#-Q- ifort_CICLAD ##   CICLAD    IPSL ##
83#-Q- ifort_CICLAD ######################
84#-Q- ifort_CICLAD #PBS -N PACKRESTART
85#-Q- ifort_CICLAD #PBS -m a
86#-Q- ifort_CICLAD #PBS -j oe
87#-Q- ifort_CICLAD #PBS -q std
88#-Q- ifort_CICLAD #PBS -S /bin/ksh
89#-Q- default #!/bin/ksh
90#-Q- default ##################
91#-Q- default ## DEFAULT HOST ##
92#-Q- default ##################
93
94#**************************************************************
95# Author: Sebastien Denvil
96# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
97# $Revision::                                          $ Revision of last commit
98# $Author::                                            $ Author of last commit
99# $Date::                                              $ Date of last commit
100# IPSL (2006)
101#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
102#
103#**************************************************************
104
105#set -eu
106#set -vx
107
108date
109
110#D- Task type DO NOT CHANGE (computing, post-processing or checking)
111TaskType=post-processing
112
113########################################################################
114
115#D- Flag to determine if this job in a standalone mode
116#D- Default : value from AA_job if any
117StandAlone=${StandAlone:=true}
118
119#D- Path to libIGCM
120#D- Default : value from AA_job if any
121# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
122# WARNING you must check MirrorlibIGCM variable in sys library.
123# WARNING If this variable is true, you must use libIGCM_POST path instead
124# WARNING of your running libIGCM directory.
125libIGCM=${libIGCM:=::modipsl::/libIGCM}
126
127#-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer.
128MASTER=${MASTER:=ada|curie}
129
130#D- Flag to determine begin date for restart pack
131#D- Default : value from AA_job if any
132DateBegin=${DateBegin:=20000101}
133
134#D- Flag to determine end date for restart pack
135#D- Default : value from AA_job if any
136DateEnd=${DateEnd:=20691231}
137
138#D- Flag to determine pack period
139#D- Default : value from AA_job if any
140PeriodPack=${PeriodPack:=10Y}
141
142#D- Uncomment to run interactively
143#D- For testing purpose, will be remove
144#SUBMIT_DIR=${PWD}
145#RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test
146
147#D- Increased verbosity (1, 2, 3)
148#D- Default : value from AA_job if any
149Verbosity=${Verbosity:=3}
150
151#D- Low level debug : to bypass lib test checks and stack construction
152#D- Default : value from AA_job if any
153DEBUG_debug=${DEBUG_debug:=false}
154
155#D- Needed to define this variable in order to handle exit in case of error
156Script_Post_Output=${Script_Post_Output:=pack_restart}
157
158
159#D- Keep following comments for now. Will be remove.
160
161#on veut archiver les fichiers restart
162#Dans le cadre du demenagement ils seront renommes
163#ATM/Restart/****.nc
164#OCE/Restart/****.nc
165#...
166#sous la forme
167#RESTART/ATM_****.nc
168#RESTART/OCE_****.nc
169#Attention de bien conserver les dates d'origines
170#
171#Dans le cadre de la production nouvelle chaine
172#ils auront directement le bon nom
173#
174#On veut egalement que l'archive soit par periode de temps
175# cette periode est definie par la taille du pack donc connue
176# en entree du script (1M, 1Y, 5Y, 10Y etc...)
177#
178# $1= PATH/config_card d'une simulation avec
179# TagName/JobName/ExperimentName/SpaceName/DateBegin/DateEnd
180# $2=PeriodPack en M/m ou Y/y
181
182########################################################################
183
184. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
185. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
186. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
187#-------
188. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
189. ${libIGCM}/libIGCM_config/libIGCM_config.ksh
190. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
191#-------
192RUN_DIR=${RUN_DIR_PATH}
193IGCM_sys_MkdirWork ${RUN_DIR}
194IGCM_sys_Cd ${RUN_DIR}
195#-------
196( ${DEBUG_debug} ) && IGCM_debug_Check
197( ${DEBUG_debug} ) && IGCM_card_Check
198( ${DEBUG_debug} ) && IGCM_date_Check
199
200########################################################################
201
202#set -vx
203
204# ------------------------------------------------------------------
205# Test if all was right before proceeding further
206# ------------------------------------------------------------------
207IGCM_debug_Verif_Exit
208
209if [ ${StandAlone} = true ] ; then
210    CARD_DIR=${SUBMIT_DIR}
211else
212    CARD_DIR=${RUN_DIR_PATH}
213    IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
214    IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card    ${RUN_DIR_PATH}
215    IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP        ${RUN_DIR_PATH}
216    IGCM_sys_Get_Master ${SUBMIT_DIR}/POST        ${RUN_DIR_PATH}
217fi
218
219#==================================
220# First of all
221#
222# Read libIGCM compatibility version in config.card
223# Read UserChoices section
224# Read Ensemble section
225# Read Post section
226# Define all netcdf output directories
227#==================================
228IGCM_config_CommonConfiguration ${CARD_DIR}/config.card
229
230# ------------------------------------------------------------------
231# Activate BigBrother so as to supervise this job
232# ------------------------------------------------------------------
233IGCM_debug_BigBro_Initialize
234
235#==================================
236# Test and set up directories
237#==================================
238IGCM_sys_TestDirArchive ${R_SAVE}
239[ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive"
240
241STORE_RESTART=${R_SAVE}/RESTART
242IGCM_sys_MkdirArchive ${STORE_RESTART}
243
244# Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure)
245JobName=${config_UserChoices_JobName}
246echo $JobName $R_BUFR $DateBegin $DateEnd
247
248# Clear txt file lists
249rm -f ${RUN_DIR}/liste_restart_files.txt
250rm -f ${RUN_DIR}/new_liste_restart_files.txt
251rm -f ${RUN_DIR}/liste_pack_*.txt
252rm -f ${RUN_DIR}/liste_pack_light_*.txt
253
254# Create sorted restart list to work with
255find ${R_BUFR}/*/Restart -name "*.*" | sort >> ${RUN_DIR}/liste_restart_files.txt
256
257# Rename restart files we will work with using symlinks
258#gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("cp --preserve " $0 " "dest_name)}' ${RUN_DIR}/liste_restart_files.txt
259gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("ln -s " $0 " "dest_name)}' ${RUN_DIR}/liste_restart_files.txt
260
261# List renamed restart files
262find ${RUN_DIR} -maxdepth 1 -mindepth 1 -name "???_*${JobName}*" -ls | sort -k 11 > ${RUN_DIR}/new_liste_restart_files.txt
263
264# ------------------------------------------------------------------
265# Test if all was right before proceeding further
266# ------------------------------------------------------------------
267IGCM_debug_Verif_Exit
268
269# Init loop
270date_begin_pack=${DateBegin}
271date_end_simulation=${DateEnd}
272number_pack=1
273
274IGCM_debug_PrintVariables 3 date_begin_pack
275IGCM_debug_PrintVariables 3 date_end_simulation
276
277# last restart of the previous period : to be deleted
278typeset date_end_previous
279date_end_previous=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} -1 )
280
281while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do
282
283  IGCM_debug_PrintVariables 3 number_pack
284
285  DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} )
286  date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) )
287
288  for file in $( gawk '{print $11}' ${RUN_DIR}/new_liste_restart_files.txt ); do
289    extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_//" )
290    date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' )
291    # warning demenagement. delete last restart of the previous pack
292    [  ${date_file} -eq ${date_end_previous} ] && echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${date_begin_pack}_${date_end_pack}.txt
293    # echo pack number ${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack}
294    if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then
295      echo $( basename ${file} ) >> ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt
296      # warning demenagement. do not delete last restart of this pack
297      [ ${date_file} -eq ${date_end_pack} ] || echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${date_begin_pack}_${date_end_pack}.txt
298    fi
299    # light pack list of restarts files that will be used
300    if [ X${config_Post_LightRestartPack} = XTRUE ] ; then
301      if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${PeriodDateBegin} ] ; then
302        echo $( basename ${file} ) >> ${RUN_DIR}/liste_pack_light_${date_begin_pack}_${date_end_pack}.txt
303      fi
304    fi
305  done
306
307  # Create tar files
308  IGCM_debug_Print 1 "Tar ongoing"
309  if [ X${config_Post_LightRestartPack} = XTRUE ] ; then
310    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
311  else
312    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
313  fi
314  # Test return code of tar
315  [ $? != 0 ] && IGCM_debug_Exit "tar failed in pack_restart job"
316  # Save it
317  IGCM_sys_Put_Out ${JobName}_${date_begin_pack}_${date_end_pack}_restart.tar ${STORE_RESTART}
318  # Clean it
319  IGCM_sys_Rm ${JobName}_${date_begin_pack}_${date_end_pack}_restart.tar
320  # ------------------------------------------------------------------
321  # Test if all was right before proceeding cleaning
322  # ------------------------------------------------------------------
323  IGCM_debug_Verif_Exit
324  # Clean links
325  cat ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt | xargs rm
326  # Clean files links pointed to
327  cat ${RUN_DIR}/liste_remove_pack_${date_begin_pack}_${date_end_pack}.txt | xargs rm
328  # Save the list of files that has been pack (tar)
329  #mv ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt ${STORE_RESTART}
330  IGCM_debug_Print 1 "Tar and cleaning done"
331
332  (( number_pack = number_pack + 1 ))
333
334  # Add 1 day to date_end_pack to have the new date_begin_pack
335  date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 )
336
337done
338
339# Clean RUN_DIR_PATH (necessary for cesium and titane only)
340IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
341
342# ------------------------------------------------------------------
343# Finalize BigBrother to inform that the jobs end
344# ------------------------------------------------------------------
345IGCM_debug_BigBro_Finalize
346
347date
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