source: trunk/libIGCM/AA_pack_debug @ 640

Last change on this file since 640 was 640, checked in by mafoipsl, 12 years ago

Add norerun option on SX front-end. Transfer specific files ie config.card COMP ... with IGCM_sys_Get_Master and modify IGCM_sys_Get_Master to allow file transfer. tested on ulam and SX front-end.
  • Property svn:keywords set to Revision Author Date
File size: 14.8 KB
Line 
1#-Q- cesium #!/bin/ksh
2#-Q- cesium ######################
3#-Q- cesium ## CESIUM   CEA ##
4#-Q- cesium ######################
5#-Q- cesium #MSUB -r PACKDEBUG    # 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- curie ######################
12#-Q- curie ## CURIE   TGCC/CEA ##
13#-Q- curie ######################
14#-Q- curie #MSUB -r PACKDEBUG      # Nom du job               
15#-Q- curie #MSUB -eo
16#-Q- curie #MSUB -n 1              # Reservation du processus
17#-Q- curie #MSUB -T 86400          # Limite de temps elapsed du job
18#-Q- platine #!/usr/bin/ksh
19#-Q- platine ###################
20#-Q- platine ## PLATINE   CEA ##
21#-Q- platine ###################
22#-Q- platine #BSUB -J PACKDEBUG            # Nom du job
23#-Q- platine #BSUB -N                        # message a la fin du job
24#-Q- platine #BSUB -n 1                      # reservation des processeurs pour le job
25#-Q- platine #BSUB -W 4:00                   # Limite temps
26#-Q- platine #BSUB -q post                   # Passage en queue post
27#-Q- platine #BSUB -L /bin/ksh
28#-Q- sx8brodie #!/bin/ksh
29#-Q- sx8brodie #######################
30#-Q- sx8brodie ## SX8BRODIE   IDRIS ##
31#-Q- sx8brodie #######################
32#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
33#-Q- sx8brodie # @ wall_clock_limit = 10:00:00
34#-Q- sx8brodie # Nom du travail LoadLeveler
35#-Q- sx8brodie # @ job_name   = PACKDEBUG
36#-Q- sx8brodie # Fichier de sortie standard du travail
37#-Q- sx8brodie # @ output     = $(job_name).$(jobid)
38#-Q- sx8brodie # Fichier de sortie d'erreur du travail
39#-Q- sx8brodie # @ error      =  $(job_name).$(jobid)
40#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
41#-Q- sx8brodie # @ notification = error
42#-Q- sx8brodie # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
43#-Q- sx8brodie # @ queue
44#-Q- aix6 #!/bin/ksh
45#-Q- aix6 #######################
46#-Q- aix6 ##   VARGAS   IDRIS  ##
47#-Q- aix6 #######################
48#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
49#-Q- aix6 # @ wall_clock_limit = 10:00:00
50#-Q- aix6 # Nom du travail LoadLeveler
51#-Q- aix6 # @ job_name   = PACKDEBUG
52#-Q- aix6 # Fichier de sortie standard du travail
53#-Q- aix6 # @ output     = $(job_name).$(jobid)
54#-Q- aix6 # Fichier de sortie d'erreur du travail
55#-Q- aix6 # @ error      =  $(job_name).$(jobid)
56#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
57#-Q- aix6 # @ notification = error
58#-Q- aix6 # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
59#-Q- aix6 # @ queue
60#-Q- ulam #!/bin/ksh
61#-Q- ulam #######################
62#-Q- ulam ##   VARGAS   IDRIS  ##
63#-Q- ulam #######################
64#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
65#-Q- ulam # @ wall_clock_limit = 10:00:00
66#-Q- ulam # Nom du travail LoadLeveler
67#-Q- ulam # @ job_name   = PACKDEBUG
68#-Q- ulam # Fichier de sortie standard du travail
69#-Q- ulam # @ output     = $(job_name).$(jobid)
70#-Q- ulam # Fichier de sortie d'erreur du travail
71#-Q- ulam # @ error      =  $(job_name).$(jobid)
72#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
73#-Q- ulam # @ notification = error
74#-Q- ulam # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
75#-Q- ulam # @ queue
76#-Q- sx8mercure #!/bin/ksh
77#-Q- sx8mercure ######################
78#-Q- sx8mercure ## SX8MERCURE   CEA ##
79#-Q- sx8mercure ######################
80#-Q- sx8mercure #PBS -N PACKDEBUG          # Nom du job
81#-Q- sx8mercure #PBS -j o                    # regroupement des stdout et stderr
82#-Q- sx8mercure #PBS -S /usr/bin/ksh         # shell de soumission
83#-Q- sx8mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
84#-Q- sx8mercure #PBS -l cputim_job=24:00:00  # Limite temps a 1 heures
85#-Q- sx8mercure #PBS -q scalaire
86#-Q- sx8mercure #PBS -r n
87#-Q- sx9mercure #!/bin/ksh
88#-Q- sx9mercure ######################
89#-Q- sx9mercure ## SX9MERCURE  CCRT ##
90#-Q- sx9mercure ######################
91#-Q- sx9mercure #PBS -N PACKDEBUG          # Nom du job
92#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr
93#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission
94#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
95#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures
96#-Q- sx9mercure #PBS -q scalaire
97#-Q- sx9mercure #PBS -r n
98#-Q- titane #!/bin/ksh
99#-Q- titane ######################
100#-Q- titane ## TITANE   CEA     ##
101#-Q- titane ######################
102#-Q- titane #MSUB -r PACKDEBUG    # Nom du job
103#-Q- titane #MSUB -eo
104#-Q- titane #MSUB -n 1              # Reservation du processus
105#-Q- titane #MSUB -T 86400          # Limite de temps elapsed du job
106#-Q- titane #MSUB -q mono
107#-Q- lxiv8 ######################
108#-Q- lxiv8 ## OBELIX      LSCE ##
109#-Q- lxiv8 ######################
110#-Q- lxiv8 #PBS -N PACKDEBUG
111#-Q- lxiv8 #PBS -m a
112#-Q- lxiv8 #PBS -j oe
113#-Q- lxiv8 #PBS -q medium
114#-Q- lxiv8 #PBS -o PACKDEBUG.$$
115#-Q- lxiv8 #PBS -S /bin/ksh
116#-Q- default #!/bin/ksh
117#-Q- default ##################
118#-Q- default ## DEFAULT HOST ##
119#-Q- default ##################
120
121#**************************************************************
122# Author: Sebastien Denvil
123# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
124# $Revision::                                          $ Revision of last commit
125# $Author::                                            $ Author of last commit
126# $Date::                                              $ Date of last commit
127# IPSL (2006)
128#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
129#
130#**************************************************************
131
132#set -eu
133#set -vx
134
135date
136
137########################################################################
138
139#D- Flag to determine if this job in a standalone mode
140#D- Default : value from AA_job if any
141StandAlone=${StandAlone:=true}
142
143#D- Path to libIGCM
144#D- Default : value from AA_job if any
145# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
146# WARNING you must check MirrorlibIGCM variable in sys library.
147# WARNING If this variable is true, you must use libIGCM_POST path instead
148# WARNING of your running libIGCM directory.
149libIGCM=${libIGCM:=::modipsl::/libIGCM}
150
151#-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer.
152MASTER=${MASTER:=mercure|titane|brodie|vargas}
153
154#D- Flag to determine begin date for restart pack
155#D- Default : value from AA_job if any
156DateBegin=${DateBegin:=20000101}
157
158#D- Flag to determine end date for restart pack
159#D- Default : value from AA_job if any
160DateEnd=${DateEnd:=20691231}
161
162#D- Flag to determine pack period
163#D- Default : value from AA_job if any
164PeriodPack=${PeriodPack:=10Y}
165
166#D- Uncomment to run interactively
167#D- For testing purpose, will be remove
168#SUBMIT_DIR=${PWD}
169#RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test
170
171#D- Increased verbosity (1, 2, 3)
172#D- Default : value from AA_job if any
173Verbosity=${Verbosity:=3}
174
175#D- Low level debug : to bypass lib test checks and stack construction
176#D- Default : value from AA_job if any
177DEBUG_debug=${DEBUG_debug:=false}
178
179#D- Keep following comments for now. Will be remove.
180
181#on veut archiver les fichiers restart
182#Dans le cadre du demenagement ils seront renommes
183#ATM/Restart/****.nc
184#OCE/Restart/****.nc
185#...
186#sous la forme
187#RESTART/ATM_****.nc
188#RESTART/OCE_****.nc
189#Attention de bien conserver les dates d'origines
190#
191#Dans le cadre de la production nouvelle chaine
192#ils auront directement le bon nom
193#
194#On veut egalement que l'archive soit par periode de temps
195# cette periode est definie par la taille du pack donc connue
196# en entree du script (1M, 1Y, 5Y, 10Y etc...)
197#
198# $1= PATH/config_card d'une simulation avec
199# TagName/JobName/ExperimentName/SpaceName/DateBegin/DateEnd
200# $2=PeriodPack en M/m ou Y/y
201
202########################################################################
203
204. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
205( ${DEBUG_debug} ) && IGCM_debug_Check
206. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
207( ${DEBUG_debug} ) && IGCM_card_Check
208. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
209( ${DEBUG_debug} ) && IGCM_date_Check
210#-------
211. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
212. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
213
214########################################################################
215
216#set -vx
217
218RUN_DIR=${RUN_DIR_PATH}
219IGCM_sys_MkdirWork ${RUN_DIR}
220IGCM_sys_Cd ${RUN_DIR}
221
222# ------------------------------------------------------------------
223# Test if all was right before proceeding further
224# ------------------------------------------------------------------
225IGCM_debug_Verif_Exit_Post
226
227if [ ${StandAlone} = true ] ; then
228    CARD_DIR=${SUBMIT_DIR}
229else
230    CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
231    IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
232    IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card    ${RUN_DIR_PATH}
233    IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP        ${RUN_DIR_PATH}
234    IGCM_sys_Get_Master ${SUBMIT_DIR}/POST        ${RUN_DIR_PATH}
235fi
236
237#====================================================
238# First of all
239#
240# Read config.card
241IGCM_card_DefineArrayFromSection     ${CARD_DIR}/config.card UserChoices
242typeset option
243for option in ${config_UserChoices[*]} ; do
244  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
245done
246#
247echo
248IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices"
249IGCM_debug_PrintVariables 3 config_UserChoices_JobName
250IGCM_debug_PrintVariables 3 config_UserChoices_LongName
251IGCM_debug_PrintVariables 3 config_UserChoices_TagName
252IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
253IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
254IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
255IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
256IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
257IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
258echo
259
260#====================================================
261# Prepare environment
262#R_SAVE      : Job output storage directory
263#R_BUFR      : Job output buffered directory
264#STORE_DEBUG : Where we store tar files
265
266if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
267  FreeName=$( echo ${config_UserChoices_JobName} | sed 's/.*_//' )
268  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
269  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
270else
271  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
272  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
273fi
274IGCM_sys_TestDirArchive ${R_SAVE}
275[ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive"
276
277#STORE_DEBUG=/ccc/store/cont003/dsm/p86denv/.../DEBUG
278STORE_DEBUG=${R_SAVE}/DEBUG
279IGCM_sys_MkdirArchive ${STORE_DEBUG}
280
281#cd ${STORE_DEBUG}
282#rm -f *
283
284# Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure)
285JobName=${config_UserChoices_JobName}
286echo $JobName $DateBegin $DateEnd
287
288# Clear txt file lists
289rm -f ${RUN_DIR}/liste_debug_files.txt
290rm -f ${RUN_DIR}/liste_out_files.txt
291rm -f ${RUN_DIR}/new_liste_debug_files.txt
292rm -f ${RUN_DIR}/liste_pack_*.txt
293
294# Create sorted debug list to work with
295find ${R_BUFR}/*/Debug -type f | sort >> ${RUN_DIR}/liste_debug_files.txt
296
297# Rename debug files we will work with using symlinks. use ???_ prefix ie NF-2
298#gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("cp --preserve " $0 " "dest_name)}' ${RUN_DIR}/liste_debug_files.txt
299gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("ln -s " $0 " "dest_name)}' ${RUN_DIR}/liste_debug_files.txt
300
301# Add out_ : output of execution files
302find ${R_BUFR}/Out -type f -name '*out_*' | sort >> ${RUN_DIR}/liste_out_files.txt
303
304# Rename out files we will work with using symlinks. use Out_ prefix ie NF-1
305gawk -F/ '{dest_name=$(NF-1)("_") $(NF); system("ln -s " $0 " "dest_name)}' ${RUN_DIR}/liste_out_files.txt
306
307# List renamed debug files. Exclude Job_xxx files.
308find ${RUN_DIR} -maxdepth 1 -mindepth 1 -name "???_*${JobName}*" -ls | sort -k 11 > ${RUN_DIR}/new_liste_debug_files.txt
309
310# ------------------------------------------------------------------
311# Test if all was right before proceeding further
312# ------------------------------------------------------------------
313IGCM_debug_Verif_Exit_Post
314
315# Init loop
316date_begin_pack=${DateBegin}
317date_end_simulation=${DateEnd}
318number_pack=1
319
320IGCM_debug_PrintVariables 3 date_begin_pack
321IGCM_debug_PrintVariables 3 date_end_simulation
322
323while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do
324
325  IGCM_debug_PrintVariables 3 number_pack
326
327  DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} )
328  date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) )
329
330  for file in $( gawk '{print $11}' ${RUN_DIR}/new_liste_debug_files.txt ); do
331    extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_[0-9]*_//" )
332    date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' )
333#   echo pack n°${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack}
334    if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then
335        echo $( basename ${file} ) >> ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt
336        echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${date_begin_pack}_${date_end_pack}.txt
337#    Will not work. Need to find a better ordering.
338#    elif [ ${date_file} -ge ${date_end_pack} ] ; then
339#      break
340    fi
341  done
342
343  # Create tar files
344  IGCM_debug_Print 1 "Tar ongoing"
345  tar -cvf ${JobName}_${date_begin_pack}_${date_end_pack}_debug.tar --dereference --files-from ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt
346  # Save it
347  IGCM_sys_Put_Out ${JobName}_${date_begin_pack}_${date_end_pack}_debug.tar ${STORE_DEBUG}
348  # Clean it
349  IGCM_sys_Rm ${JobName}_${date_begin_pack}_${date_end_pack}_debug.tar
350  # Clean links
351  cat ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt | xargs rm
352  # Clean files links pointed to
353  cat ${RUN_DIR}/liste_remove_pack_${date_begin_pack}_${date_end_pack}.txt | xargs rm
354  # Save the list of files that has been pack (tar)
355  #mv ${RUN_DIR}/liste_pack_${date_begin_pack}_${date_end_pack}.txt ${STORE_DEBUG}
356  IGCM_debug_Print 1 "Tar and cleaning done"
357
358  (( number_pack = number_pack + 1 ))
359
360  # Add 1 day to date_end_pack to have the new date_begin_pack
361  date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 )
362
363done
364
365# Clean RUN_DIR_PATH (necessary for cesium and titane only)
366IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
367
368date
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