source: tags/libIGCM_v2.0_beta1/AA_pack_output @ 1170

Last change on this file since 1170 was 653, checked in by sdipsl, 12 years ago
  • Bugfix : when asking only for chunked time series job was not submitted
  • Bugfix : when in pack case seasonal job was not submitted if no time series were active
  • Cosmetics
  • Property svn:keywords set to Revision Author Date
File size: 16.1 KB
Line 
1#-Q- cesium #!/bin/ksh
2#-Q- cesium ######################
3#-Q- cesium ## CESIUM   CEA ##
4#-Q- cesium ######################
5#-Q- cesium #MSUB -r PACKOUTPUT    # 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 PACKOUTPUT     # 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- curie #MSUB -E '--no-requeue'
19#-Q- platine #!/usr/bin/ksh
20#-Q- platine ###################
21#-Q- platine ## PLATINE   CEA ##
22#-Q- platine ###################
23#-Q- platine #BSUB -J PACKOUTPUT            # Nom du job
24#-Q- platine #BSUB -N                        # message a la fin du job
25#-Q- platine #BSUB -n 1                      # reservation des processeurs pour le job
26#-Q- platine #BSUB -W 4:00                   # Limite temps
27#-Q- platine #BSUB -q post                   # Passage en queue post
28#-Q- platine #BSUB -L /bin/ksh
29#-Q- sx8brodie #!/bin/ksh
30#-Q- sx8brodie #######################
31#-Q- sx8brodie ## SX8BRODIE   IDRIS ##
32#-Q- sx8brodie #######################
33#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
34#-Q- sx8brodie # @ wall_clock_limit = 10:00:00
35#-Q- sx8brodie # Nom du travail LoadLeveler
36#-Q- sx8brodie # @ job_name   = PACKOUTPUT
37#-Q- sx8brodie # Fichier de sortie standard du travail
38#-Q- sx8brodie # @ output     = $(job_name).$(jobid)
39#-Q- sx8brodie # Fichier de sortie d'erreur du travail
40#-Q- sx8brodie # @ error      =  $(job_name).$(jobid)
41#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
42#-Q- sx8brodie # @ notification = error
43#-Q- sx8brodie # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
44#-Q- sx8brodie # @ queue
45#-Q- aix6 #!/bin/ksh
46#-Q- aix6 #######################
47#-Q- aix6 ##   VARGAS   IDRIS  ##
48#-Q- aix6 #######################
49#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
50#-Q- aix6 # @ wall_clock_limit = 10:00:00
51#-Q- aix6 # Nom du travail LoadLeveler
52#-Q- aix6 # @ job_name   = PACKOUTPUT
53#-Q- aix6 # Fichier de sortie standard du travail
54#-Q- aix6 # @ output     = $(job_name).$(jobid)
55#-Q- aix6 # Fichier de sortie d'erreur du travail
56#-Q- aix6 # @ error      =  $(job_name).$(jobid)
57#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
58#-Q- aix6 # @ notification = error
59#-Q- aix6 # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
60#-Q- aix6 # @ queue
61#-Q- ulam #!/bin/ksh
62#-Q- ulam #######################
63#-Q- ulam ##   VARGAS   IDRIS  ##
64#-Q- ulam #######################
65#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
66#-Q- ulam # @ wall_clock_limit = 10:00:00
67#-Q- ulam # Nom du travail LoadLeveler
68#-Q- ulam # @ job_name   = PACKOUTPUT
69#-Q- ulam # Fichier de sortie standard du travail
70#-Q- ulam # @ output     = $(job_name).$(jobid)
71#-Q- ulam # Fichier de sortie d'erreur du travail
72#-Q- ulam # @ error      =  $(job_name).$(jobid)
73#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
74#-Q- ulam # @ notification = error
75#-Q- ulam # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
76#-Q- ulam # @ queue
77#-Q- sx8mercure #!/bin/ksh
78#-Q- sx8mercure ######################
79#-Q- sx8mercure ## SX8MERCURE   CEA ##
80#-Q- sx8mercure ######################
81#-Q- sx8mercure #PBS -N PACKOUTPUT          # Nom du job
82#-Q- sx8mercure #PBS -j o                    # regroupement des stdout et stderr
83#-Q- sx8mercure #PBS -S /usr/bin/ksh         # shell de soumission
84#-Q- sx8mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
85#-Q- sx8mercure #PBS -l cputim_job=24:00:00  # Limite temps a 1 heures
86#-Q- sx8mercure #PBS -q scalaire
87#-Q- sx8mercure #PBS -r n
88#-Q- sx9mercure #!/bin/ksh
89#-Q- sx9mercure ######################
90#-Q- sx9mercure ## SX9MERCURE  CCRT ##
91#-Q- sx9mercure ######################
92#-Q- sx9mercure #PBS -N PACKOUTPUT          # Nom du job
93#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr
94#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission
95#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
96#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures
97#-Q- sx9mercure #PBS -q scalaire
98#-Q- sx9mercure #PBS -r n
99#-Q- titane #!/bin/ksh
100#-Q- titane ######################
101#-Q- titane ## TITANE   CEA     ##
102#-Q- titane ######################
103#-Q- titane #MSUB -r PACKOUTPUT    # Nom du job
104#-Q- titane #MSUB -eo
105#-Q- titane #MSUB -n 1              # Reservation du processus
106#-Q- titane #MSUB -T 86400          # Limite de temps elapsed du job
107#-Q- titane #MSUB -q mono
108#-Q- titane #MSUB -E '-rn'
109#-Q- lxiv8 ######################
110#-Q- lxiv8 ## OBELIX      LSCE ##
111#-Q- lxiv8 ######################
112#-Q- lxiv8 #PBS -N PACKOUTPUT
113#-Q- lxiv8 #PBS -m a
114#-Q- lxiv8 #PBS -j oe
115#-Q- lxiv8 #PBS -q medium
116#-Q- lxiv8 #PBS -o PACKOUTPUT.$$
117#-Q- lxiv8 #PBS -S /bin/ksh
118#-Q- default #!/bin/ksh
119#-Q- default ##################
120#-Q- default ## DEFAULT HOST ##
121#-Q- default ##################
122
123#**************************************************************
124# Author: Sebastien Denvil
125# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
126# $Revision::                                          $ Revision of last commit
127# $Author::                                            $ Author of last commit
128# $Date::                                              $ Date of last commit
129# IPSL (2006)
130#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
131#
132#**************************************************************
133
134#set -eu
135#set -vx
136
137date
138
139########################################################################
140
141#D- Flag to determine if this job in a standalone mode
142#D- Default : value from AA_job if any
143StandAlone=${StandAlone:=true}
144
145#D- Path to libIGCM
146#D- Default : value from AA_job if any
147# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
148# WARNING you must check MirrorlibIGCM variable in sys library.
149# WARNING If this variable is true, you must use libIGCM_POST path instead
150# WARNING of your running libIGCM directory.
151libIGCM=${libIGCM:=::modipsl::/libIGCM}
152
153#-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer.
154MASTER=${MASTER:=mercure|titane|brodie|vargas}
155
156#D- Flag to determine begin date for restart pack
157#D- Default : value from AA_job if any
158DateBegin=${DateBegin:=20000101}
159
160#D- Flag to determine end date for restart pack
161#D- Default : value from AA_job if any
162DateEnd=${DateEnd:=20691231}
163
164#D- Flag to determine pack period
165#D- Default : value from AA_job if any
166PeriodPack=${PeriodPack:=10Y}
167
168#D- Uncomment to run interactively
169#D- For testing purpose, will be remove
170#SUBMIT_DIR=${PWD}
171#RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test
172
173#D- Increased verbosity (1, 2, 3)
174#D- Default : value from AA_job if any
175Verbosity=${Verbosity:=3}
176
177#D- Low level debug : to bypass lib test checks and stack construction
178#D- Default : value from AA_job if any
179DEBUG_debug=${DEBUG_debug:=false}
180
181########################################################################
182
183. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
184( ${DEBUG_debug} ) && IGCM_debug_Check
185. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
186( ${DEBUG_debug} ) && IGCM_card_Check
187. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
188( ${DEBUG_debug} ) && IGCM_date_Check
189#-------
190. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
191. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
192
193########################################################################
194
195#set -vx
196
197RUN_DIR=${RUN_DIR_PATH}
198IGCM_sys_MkdirWork ${RUN_DIR}
199IGCM_sys_Cd ${RUN_DIR}
200
201# ------------------------------------------------------------------
202# Test if all was right before proceeding further
203# ------------------------------------------------------------------
204IGCM_debug_Verif_Exit_Post
205
206if [ ${StandAlone} = true ] ; then
207    CARD_DIR=${SUBMIT_DIR}
208else
209    CARD_DIR=${RUN_DIR_PATH}
210    IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
211    IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card    ${RUN_DIR_PATH}
212    IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP        ${RUN_DIR_PATH}
213    IGCM_sys_Get_Master ${SUBMIT_DIR}/POST        ${RUN_DIR_PATH}
214fi
215
216#====================================================
217# First of all
218#
219# Read config.card
220
221IGCM_card_DefineArrayFromSection     ${CARD_DIR}/config.card UserChoices
222typeset option
223for option in ${config_UserChoices[*]} ; do
224  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
225done
226#
227echo
228IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices"
229IGCM_debug_PrintVariables 3 config_UserChoices_JobName
230IGCM_debug_PrintVariables 3 config_UserChoices_LongName
231IGCM_debug_PrintVariables 3 config_UserChoices_TagName
232IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
233IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
234IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
235IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
236IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
237IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
238echo
239
240# Get ListOfComponents to drive the loop over find
241IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
242
243#====================================================
244#R_SAVE : Job output storage directory
245#R_BUFR : Job output buffered directory
246
247if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
248  FreeName=$( echo ${config_UserChoices_JobName} | sed 's/.*_//' )
249  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
250  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
251else
252  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
253  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
254fi
255IGCM_sys_TestDirArchive ${R_SAVE}
256[ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive"
257
258# Where to store used file list /!\ TEMPORARY /!\
259STORE_DEBUG=${R_SAVE}/DEBUG
260
261# Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure)
262JobName=${config_UserChoices_JobName}
263echo $JobName $DateBegin $DateEnd
264
265# ------------------------------------------------------------------
266# Test if all was right before proceeding further
267# ------------------------------------------------------------------
268IGCM_debug_Verif_Exit_Post
269
270IGCM_debug_Print 1 "Check coherence between PackFrequency and PeriodLength"
271IGCM_post_CheckModuloFrequency PeriodPack config_UserChoices_PeriodLength NbPeriodPerFrequency
272# ------------------------------------------------------------------
273# Test if all was right before proceeding further
274# ------------------------------------------------------------------
275IGCM_debug_Verif_Exit_Post
276
277IGCM_debug_Print 1 "We must process ${NbPeriodPerFrequency} files for each pack"
278
279# Init loop
280date_begin_pack=${DateBegin}
281date_end_simulation=${DateEnd}
282number_pack=1
283
284IGCM_debug_PrintVariables 3 date_begin_pack
285IGCM_debug_PrintVariables 3 date_end_simulation
286
287while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do
288
289  IGCM_debug_PrintVariables 3 number_pack
290  DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} )
291  date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) )
292
293  for comp in ${config_ListOfComponents[*]} ; do
294    dirList=$( find ${R_BUFR}/${comp}/Output -maxdepth 1 -mindepth 1 -type d )
295    for dir in ${dirList} ; do
296      # dirID is like ATM.Output.MO
297      dirID=$( echo $dir | sed "s:${R_BUFR}/::" | sed "s:/:.:g" )
298      # Sort what's in the directory
299      find ${dir} -type f -name "${JobName}*.nc" -ls | sort -k 11 > liste_files.${dirID}.txt
300      # How much file type. Example : 1M_histmthCOSP.nc, 1M_histmth.nc, 1M_histmthNMC.nc, 1M_paramLMDZ_phy.nc
301      # /!\ fileType include the .nc extension /!\
302      fileType=$( gawk '{print $11}' liste_files.${dirID}.txt | gawk -F$dir/ '{print $2}' | sed "s:${JobName}_[0-9]\{8,9\}_[0-9]\{8,9\}_::g" | sort | uniq )
303      # Loop over the file type and pack them when in between date_begin_pack and date_end_pack
304      for myType in ${fileType} ; do
305        grep ${myType} liste_files.${dirID}.txt > liste_files.${dirID}.${myType}.txt
306        nbfile=0
307        for file in $( gawk '{print $11}' liste_files.${dirID}.${myType}.txt ); do
308          extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_[0-9]*_//" )
309          date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' )
310          # echo pack n°${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack}
311          if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then
312            echo ${file} >> liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt
313            ncdump -h ${file} | grep -E 'float|double' | cut -f 1 -d '(' | cut -f 2 -d ' ' >> liste_variables_${myType}_${date_begin_pack}_${date_end_pack}.txt
314            (( nbfile = nbfile + 1 ))
315          fi
316        done
317        # Select list of variables to work with
318        list_var=$( cat liste_variables_${myType}_${date_begin_pack}_${date_end_pack}.txt | sort | uniq -c | awk -v nbfile=$nbfile '{if ($1 != nbfile) {print $2}}' | paste -s -d ',' )
319        liste_file_tmp=$( for i in $( cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ) ; do basename $i ; done )
320        # Create packed files
321        IGCM_debug_Print 1 "Ncrcat ongoing for ${dir} and ${myType}"
322        if [ ! ${nbfile} = ${NbPeriodPerFrequency} ] ; then
323          IGCM_debug_Print 1 "Number of files to process is not equal to what it should be"
324          IGCM_debug_Print 1 "We found ${nbfile} files and it should have been ${NbPeriodPerFrequency} files"
325          IGCM_debug_Exit "ERROR in number of files to process. STOP HERE INCLUDING THE COMPUTING JOB"
326          IGCM_debug_Verif_Exit
327        fi
328        output=${JobName}_${date_begin_pack}_${date_end_pack}_${myType}
329        #cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs ncrcat -v ${list_var} -o ${output}
330        if [ X${list_var} = X ] ; then
331          IGCM_sys_ncrcat -p ${dir} ${liste_file_tmp} --output ${output}
332        else
333          IGCM_sys_ncrcat -x -v ${list_var} -p ${dir} ${liste_file_tmp} --output ${output}
334        fi
335        # ------------------------------------------------------------------
336        # Test if all was right before proceeding further
337        # ------------------------------------------------------------------
338        IGCM_debug_Verif_Exit_Post
339        # Save it
340        IGCM_sys_Put_Out ${output} ${R_SAVE}/$( echo $dir | sed "s:${R_BUFR}/::" )/${output}
341        # ------------------------------------------------------------------
342        # Test if all was right before proceeding further
343        # ------------------------------------------------------------------
344        IGCM_debug_Verif_Exit_Post
345        # Clean file produced by ncrcat
346        IGCM_sys_Rm ${output}
347        # Clean files used by ncrcat
348        cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs rm
349        # Save the list of files that has been pack (ncrcat)
350        #mv liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ${STORE_DEBUG}
351        IGCM_debug_Print 1 "Ncrcat and cleaning done for ${dir} and ${myType}"
352        echo
353      done
354    done
355  done
356  (( number_pack = number_pack + 1 ))
357  # Add 1 day to date_end_pack to have the new date_begin_pack
358  date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 )
359done
360
361# Flush post-processing submission
362if [ -f ${R_BUFR}/FlushPost_${DateEnd}.ksh ] ; then
363  . ${R_BUFR}/FlushPost_${DateEnd}.ksh
364  IGCM_FlushPost
365  #IGCM_sys_Rm -f ${R_BUFR}/FlushPost_${DateEnd}.ksh
366fi
367
368# Clean RUN_DIR_PATH (necessary for cesium and titane only)
369IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
370
371date
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