source: tags/libIGCM_v2.0_beta4/AA_pack_output @ 1170

Last change on this file since 1170 was 681, checked in by mafoipsl, 12 years ago

On curie : Computing job on -q standard ie thin nodes, post-processing jobs on -q large ie large nodes. Stop default echo of commands.
  • Property svn:keywords set to Revision Author Date
File size: 17.8 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- curie #MSUB -q large
20#-Q- curie set +x
21#-Q- platine #!/usr/bin/ksh
22#-Q- platine ###################
23#-Q- platine ## PLATINE   CEA ##
24#-Q- platine ###################
25#-Q- platine #BSUB -J PACKOUTPUT            # Nom du job
26#-Q- platine #BSUB -N                        # message a la fin du job
27#-Q- platine #BSUB -n 1                      # reservation des processeurs pour le job
28#-Q- platine #BSUB -W 4:00                   # Limite temps
29#-Q- platine #BSUB -q post                   # Passage en queue post
30#-Q- platine #BSUB -L /bin/ksh
31#-Q- sx8brodie #!/bin/ksh
32#-Q- sx8brodie #######################
33#-Q- sx8brodie ## SX8BRODIE   IDRIS ##
34#-Q- sx8brodie #######################
35#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
36#-Q- sx8brodie # @ wall_clock_limit = 10:00:00
37#-Q- sx8brodie # Nom du travail LoadLeveler
38#-Q- sx8brodie # @ job_name   = PACKOUTPUT
39#-Q- sx8brodie # Fichier de sortie standard du travail
40#-Q- sx8brodie # @ output     = $(job_name).$(jobid)
41#-Q- sx8brodie # Fichier de sortie d'erreur du travail
42#-Q- sx8brodie # @ error      =  $(job_name).$(jobid)
43#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
44#-Q- sx8brodie # @ notification = error
45#-Q- sx8brodie # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
46#-Q- sx8brodie # @ queue
47#-Q- aix6 #!/bin/ksh
48#-Q- aix6 #######################
49#-Q- aix6 ##   VARGAS   IDRIS  ##
50#-Q- aix6 #######################
51#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
52#-Q- aix6 # @ wall_clock_limit = 10:00:00
53#-Q- aix6 # Nom du travail LoadLeveler
54#-Q- aix6 # @ job_name   = PACKOUTPUT
55#-Q- aix6 # Fichier de sortie standard du travail
56#-Q- aix6 # @ output     = $(job_name).$(jobid)
57#-Q- aix6 # Fichier de sortie d'erreur du travail
58#-Q- aix6 # @ error      =  $(job_name).$(jobid)
59#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
60#-Q- aix6 # @ notification = error
61#-Q- aix6 # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
62#-Q- aix6 # @ queue
63#-Q- ulam #!/bin/ksh
64#-Q- ulam #######################
65#-Q- ulam ##   VARGAS   IDRIS  ##
66#-Q- ulam #######################
67#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
68#-Q- ulam # @ wall_clock_limit = 10:00:00
69#-Q- ulam # Nom du travail LoadLeveler
70#-Q- ulam # @ job_name   = PACKOUTPUT
71#-Q- ulam # Fichier de sortie standard du travail
72#-Q- ulam # @ output     = $(job_name).$(jobid)
73#-Q- ulam # Fichier de sortie d'erreur du travail
74#-Q- ulam # @ error      =  $(job_name).$(jobid)
75#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
76#-Q- ulam # @ notification = error
77#-Q- ulam # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
78#-Q- ulam # @ queue
79#-Q- sx8mercure #!/bin/ksh
80#-Q- sx8mercure ######################
81#-Q- sx8mercure ## SX8MERCURE   CEA ##
82#-Q- sx8mercure ######################
83#-Q- sx8mercure #PBS -N PACKOUTPUT          # Nom du job
84#-Q- sx8mercure #PBS -j o                    # regroupement des stdout et stderr
85#-Q- sx8mercure #PBS -S /usr/bin/ksh         # shell de soumission
86#-Q- sx8mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
87#-Q- sx8mercure #PBS -l cputim_job=24:00:00  # Limite temps a 1 heures
88#-Q- sx8mercure #PBS -q scalaire
89#-Q- sx8mercure #PBS -r n
90#-Q- sx9mercure #!/bin/ksh
91#-Q- sx9mercure ######################
92#-Q- sx9mercure ## SX9MERCURE  CCRT ##
93#-Q- sx9mercure ######################
94#-Q- sx9mercure #PBS -N PACKOUTPUT          # Nom du job
95#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr
96#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission
97#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
98#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures
99#-Q- sx9mercure #PBS -q scalaire
100#-Q- sx9mercure #PBS -r n
101#-Q- titane #!/bin/ksh
102#-Q- titane ######################
103#-Q- titane ## TITANE   CEA     ##
104#-Q- titane ######################
105#-Q- titane #MSUB -r PACKOUTPUT    # Nom du job
106#-Q- titane #MSUB -eo
107#-Q- titane #MSUB -n 1              # Reservation du processus
108#-Q- titane #MSUB -T 86400          # Limite de temps elapsed du job
109#-Q- titane #MSUB -q mono
110#-Q- titane #MSUB -E '-rn'
111#-Q- lxiv8 ######################
112#-Q- lxiv8 ## OBELIX      LSCE ##
113#-Q- lxiv8 ######################
114#-Q- lxiv8 #PBS -N PACKOUTPUT
115#-Q- lxiv8 #PBS -m a
116#-Q- lxiv8 #PBS -j oe
117#-Q- lxiv8 #PBS -q medium
118#-Q- lxiv8 #PBS -o PACKOUTPUT.$$
119#-Q- lxiv8 #PBS -S /bin/ksh
120#-Q- default #!/bin/ksh
121#-Q- default ##################
122#-Q- default ## DEFAULT HOST ##
123#-Q- default ##################
124
125#**************************************************************
126# Author: Sebastien Denvil
127# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
128# $Revision::                                          $ Revision of last commit
129# $Author::                                            $ Author of last commit
130# $Date::                                              $ Date of last commit
131# IPSL (2006)
132#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
133#
134#**************************************************************
135
136#set -eu
137#set -vx
138
139date
140
141########################################################################
142
143#D- Flag to determine if this job in a standalone mode
144#D- Default : value from AA_job if any
145StandAlone=${StandAlone:=true}
146
147#D- Path to libIGCM
148#D- Default : value from AA_job if any
149# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
150# WARNING you must check MirrorlibIGCM variable in sys library.
151# WARNING If this variable is true, you must use libIGCM_POST path instead
152# WARNING of your running libIGCM directory.
153libIGCM=${libIGCM:=::modipsl::/libIGCM}
154
155#-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer.
156MASTER=${MASTER:=mercure|titane|brodie|vargas}
157
158#D- Flag to determine begin date for restart pack
159#D- Default : value from AA_job if any
160DateBegin=${DateBegin:=20000101}
161
162#D- Flag to determine end date for restart pack
163#D- Default : value from AA_job if any
164DateEnd=${DateEnd:=20691231}
165
166#D- Flag to determine pack period
167#D- Default : value from AA_job if any
168PeriodPack=${PeriodPack:=10Y}
169
170#D- Uncomment to run interactively
171#D- For testing purpose, will be remove
172#SUBMIT_DIR=${PWD}
173#RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test
174
175#D- Increased verbosity (1, 2, 3)
176#D- Default : value from AA_job if any
177Verbosity=${Verbosity:=3}
178
179#D- Low level debug : to bypass lib test checks and stack construction
180#D- Default : value from AA_job if any
181DEBUG_debug=${DEBUG_debug:=false}
182
183########################################################################
184
185. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
186( ${DEBUG_debug} ) && IGCM_debug_Check
187. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
188( ${DEBUG_debug} ) && IGCM_card_Check
189. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
190( ${DEBUG_debug} ) && IGCM_date_Check
191#-------
192. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
193. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
194
195########################################################################
196
197#set -vx
198
199RUN_DIR=${RUN_DIR_PATH}
200IGCM_sys_MkdirWork ${RUN_DIR}
201IGCM_sys_Cd ${RUN_DIR}
202
203# ------------------------------------------------------------------
204# Test if all was right before proceeding further
205# ------------------------------------------------------------------
206IGCM_debug_Verif_Exit_Post
207
208if [ ${StandAlone} = true ] ; then
209    CARD_DIR=${SUBMIT_DIR}
210else
211    CARD_DIR=${RUN_DIR_PATH}
212    IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
213    IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card    ${RUN_DIR_PATH}
214    IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP        ${RUN_DIR_PATH}
215    IGCM_sys_Get_Master ${SUBMIT_DIR}/POST        ${RUN_DIR_PATH}
216fi
217
218#====================================================
219# First of all
220#
221# Read config.card
222
223IGCM_card_DefineArrayFromSection     ${CARD_DIR}/config.card UserChoices
224typeset option
225for option in ${config_UserChoices[*]} ; do
226  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
227done
228#
229IGCM_card_DefineArrayFromSection     ${CARD_DIR}/config.card Ensemble
230typeset option
231for option in ${config_Ensemble[*]} ; do
232  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Ensemble ${option}
233done
234#
235echo
236IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices"
237IGCM_debug_PrintVariables 3 config_UserChoices_JobName
238IGCM_debug_PrintVariables 3 config_UserChoices_LongName
239IGCM_debug_PrintVariables 3 config_UserChoices_TagName
240IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
241IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
242IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
243IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
244IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
245IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
246IGCM_debug_PrintVariables 3 config_Ensemble_EnsembleName
247IGCM_debug_PrintVariables 3 config_Ensemble_EnsembleDate
248echo
249
250# Get ListOfComponents to drive the loop over find
251IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
252
253#====================================================
254#R_SAVE : Job output storage directory
255#R_BUFR : Job output buffered directory
256
257if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
258  FreeName=$( echo ${config_UserChoices_JobName} | sed 's/.*_//' )
259  if ( [ ! X${config_Ensemble_EnsembleName} = X ] && [ ! X${config_Ensemble_EnsembleDate} = X ] ) ; then
260    R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${config_Ensemble_EnsembleName}/${config_Ensemble_EnsembleDate}/${FreeName}
261    R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${config_Ensemble_EnsembleName}/${config_Ensemble_EnsembleDate}/${FreeName}
262  else
263    R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
264    R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
265  fi
266else
267  if ( [ ! X${config_Ensemble_EnsembleName} = X ] && [ ! X${config_Ensemble_EnsembleDate} = X ] ) ; then
268    R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_Ensemble_EnsembleName}/${config_Ensemble_EnsembleDate}/${config_UserChoices_JobName}
269    R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_Ensemble_EnsembleName}/${config_Ensemble_EnsembleDate}/${config_UserChoices_JobName}
270  else
271    R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
272    R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
273  fi
274fi
275IGCM_sys_TestDirArchive ${R_SAVE}
276[ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive"
277
278# Where to store used file list /!\ TEMPORARY /!\
279STORE_DEBUG=${R_SAVE}/DEBUG
280
281# Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure)
282JobName=${config_UserChoices_JobName}
283echo $JobName $DateBegin $DateEnd
284
285# ------------------------------------------------------------------
286# Test if all was right before proceeding further
287# ------------------------------------------------------------------
288IGCM_debug_Verif_Exit_Post
289
290IGCM_debug_Print 1 "Check coherence between PackFrequency and PeriodLength"
291IGCM_post_CheckModuloFrequency PeriodPack config_UserChoices_PeriodLength NbPeriodPerFrequency
292# ------------------------------------------------------------------
293# Test if all was right before proceeding further
294# ------------------------------------------------------------------
295IGCM_debug_Verif_Exit_Post
296
297IGCM_debug_Print 1 "We must process ${NbPeriodPerFrequency} files for each pack"
298
299# Init loop
300date_begin_pack=${DateBegin}
301date_end_simulation=${DateEnd}
302number_pack=1
303
304IGCM_debug_PrintVariables 3 date_begin_pack
305IGCM_debug_PrintVariables 3 date_end_simulation
306
307while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do
308
309  IGCM_debug_PrintVariables 3 number_pack
310  DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} )
311  date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) )
312
313  for comp in ${config_ListOfComponents[*]} ; do
314    dirList=$( find ${R_BUFR}/${comp}/Output -maxdepth 1 -mindepth 1 -type d )
315    for dir in ${dirList} ; do
316      # dirID is like ATM.Output.MO
317      dirID=$( echo $dir | sed "s:${R_BUFR}/::" | sed "s:/:.:g" )
318      # Sort what's in the directory
319      find ${dir} -type f -name "${JobName}*.nc" -ls | sort -k 11 > liste_files.${dirID}.txt
320      # How much file type. Example : 1M_histmthCOSP.nc, 1M_histmth.nc, 1M_histmthNMC.nc, 1M_paramLMDZ_phy.nc
321      # /!\ fileType include the .nc extension /!\
322      fileType=$( 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 )
323      # Loop over the file type and pack them when in between date_begin_pack and date_end_pack
324      for myType in ${fileType} ; do
325        grep ${myType} liste_files.${dirID}.txt > liste_files.${dirID}.${myType}.txt
326        nbfile=0
327        for file in $( gawk '{print $11}' liste_files.${dirID}.${myType}.txt ); do
328          extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_[0-9]*_//" )
329          date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' )
330          # echo pack n°${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack}
331          if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then
332            echo ${file} >> liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt
333            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
334            (( nbfile = nbfile + 1 ))
335          fi
336        done
337
338        if ( [ X${StandAlone} = Xtrue ] && [ ${nbfile} = 0 ] ) ; then
339          IGCM_debug_Print 1 "We found ${nbfile} files to process"
340          IGCM_debug_Print 1 "We should have found ${NbPeriodPerFrequency} files"
341          IGCM_debug_Print 1 "As we are in StandAlone mode we consider the job has been done and move to the next file type"
342          continue
343        fi
344
345        # Select list of variables to work with
346        list_var=$( cat liste_variables_${myType}_${date_begin_pack}_${date_end_pack}.txt | sort | uniq -c | awk -v nbfile=$nbfile '{if ($1 != nbfile) {print $2}}' | paste -s -d ',' )
347        liste_file_tmp=$( for i in $( cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ) ; do basename $i ; done )
348        # Create packed files
349        IGCM_debug_Print 1 "Ncrcat ongoing for ${dir} and ${myType}"
350        if [ ! ${nbfile} = ${NbPeriodPerFrequency} ] ; then
351          IGCM_debug_Print 1 "Number of files to process is not equal to what it should be"
352          IGCM_debug_Print 1 "We found ${nbfile} files and it should have been ${NbPeriodPerFrequency} files"
353          IGCM_debug_Exit "ERROR in number of files to process. STOP HERE INCLUDING THE COMPUTING JOB"
354          IGCM_debug_Verif_Exit
355        fi
356        output=${JobName}_${date_begin_pack}_${date_end_pack}_${myType}
357        #cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs ncrcat -v ${list_var} -o ${output}
358        if [ X${list_var} = X ] ; then
359          IGCM_sys_ncrcat -p ${dir} ${liste_file_tmp} --output ${output}
360        else
361          IGCM_sys_ncrcat -x -v ${list_var} -p ${dir} ${liste_file_tmp} --output ${output}
362        fi
363        # ------------------------------------------------------------------
364        # Test if all was right before proceeding further
365        # ------------------------------------------------------------------
366        IGCM_debug_Verif_Exit_Post
367        # Save it
368        IGCM_sys_Put_Out ${output} ${R_SAVE}/$( echo $dir | sed "s:${R_BUFR}/::" )/${output}
369        # ------------------------------------------------------------------
370        # Test if all was right before proceeding further
371        # ------------------------------------------------------------------
372        IGCM_debug_Verif_Exit_Post
373        # Clean file produced by ncrcat
374        IGCM_sys_Rm ${output}
375        # Clean files used by ncrcat
376        cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs rm
377        # Save the list of files that has been pack (ncrcat)
378        #mv liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ${STORE_DEBUG}
379        IGCM_debug_Print 1 "Ncrcat and cleaning done for ${dir} and ${myType}"
380        echo
381      done
382    done
383  done
384  (( number_pack = number_pack + 1 ))
385  # Add 1 day to date_end_pack to have the new date_begin_pack
386  date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 )
387done
388
389# Flush post-processing submission
390if [ -f ${R_BUFR}/FlushPost_${DateEnd}.ksh ] ; then
391  . ${R_BUFR}/FlushPost_${DateEnd}.ksh
392  IGCM_FlushPost
393  #IGCM_sys_Rm -f ${R_BUFR}/FlushPost_${DateEnd}.ksh
394fi
395
396# Clean RUN_DIR_PATH (necessary for cesium and titane only)
397IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
398
399date
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