source: trunk/libIGCM/AA_pack_output @ 704

Last change on this file since 704 was 704, checked in by jgipsl, 12 years ago

=> Added "#MSUB -Q normal" in headings for jobs at curie : When submitting a job in test queue (#MSUB -Q test) all sub jobs will also be subbmitted in test queue if nothingelse is specified.

=> Changed in AA_job : use /bin/ksh at curie due to specific usage in SPINUP configuration.

=> Correct directory in libIGCM_sys_obelix.
  • 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 #MSUB -Q normal
21#-Q- curie set +x
22#-Q- platine #!/usr/bin/ksh
23#-Q- platine ###################
24#-Q- platine ## PLATINE   CEA ##
25#-Q- platine ###################
26#-Q- platine #BSUB -J PACKOUTPUT            # Nom du job
27#-Q- platine #BSUB -N                        # message a la fin du job
28#-Q- platine #BSUB -n 1                      # reservation des processeurs pour le job
29#-Q- platine #BSUB -W 4:00                   # Limite temps
30#-Q- platine #BSUB -q post                   # Passage en queue post
31#-Q- platine #BSUB -L /bin/ksh
32#-Q- sx8brodie #!/bin/ksh
33#-Q- sx8brodie #######################
34#-Q- sx8brodie ## SX8BRODIE   IDRIS ##
35#-Q- sx8brodie #######################
36#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
37#-Q- sx8brodie # @ wall_clock_limit = 10:00:00
38#-Q- sx8brodie # Nom du travail LoadLeveler
39#-Q- sx8brodie # @ job_name   = PACKOUTPUT
40#-Q- sx8brodie # Fichier de sortie standard du travail
41#-Q- sx8brodie # @ output     = $(job_name).$(jobid)
42#-Q- sx8brodie # Fichier de sortie d'erreur du travail
43#-Q- sx8brodie # @ error      =  $(job_name).$(jobid)
44#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
45#-Q- sx8brodie # @ notification = error
46#-Q- sx8brodie # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
47#-Q- sx8brodie # @ queue
48#-Q- aix6 #!/bin/ksh
49#-Q- aix6 #######################
50#-Q- aix6 ##   VARGAS   IDRIS  ##
51#-Q- aix6 #######################
52#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
53#-Q- aix6 # @ wall_clock_limit = 10:00:00
54#-Q- aix6 # Nom du travail LoadLeveler
55#-Q- aix6 # @ job_name   = PACKOUTPUT
56#-Q- aix6 # Fichier de sortie standard du travail
57#-Q- aix6 # @ output     = $(job_name).$(jobid)
58#-Q- aix6 # Fichier de sortie d'erreur du travail
59#-Q- aix6 # @ error      =  $(job_name).$(jobid)
60#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
61#-Q- aix6 # @ notification = error
62#-Q- aix6 # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
63#-Q- aix6 # @ queue
64#-Q- ulam #!/bin/ksh
65#-Q- ulam #######################
66#-Q- ulam ##   VARGAS   IDRIS  ##
67#-Q- ulam #######################
68#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
69#-Q- ulam # @ wall_clock_limit = 10:00:00
70#-Q- ulam # Nom du travail LoadLeveler
71#-Q- ulam # @ job_name   = PACKOUTPUT
72#-Q- ulam # Fichier de sortie standard du travail
73#-Q- ulam # @ output     = $(job_name).$(jobid)
74#-Q- ulam # Fichier de sortie d'erreur du travail
75#-Q- ulam # @ error      =  $(job_name).$(jobid)
76#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
77#-Q- ulam # @ notification = error
78#-Q- ulam # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
79#-Q- ulam # @ queue
80#-Q- sx8mercure #!/bin/ksh
81#-Q- sx8mercure ######################
82#-Q- sx8mercure ## SX8MERCURE   CEA ##
83#-Q- sx8mercure ######################
84#-Q- sx8mercure #PBS -N PACKOUTPUT          # Nom du job
85#-Q- sx8mercure #PBS -j o                    # regroupement des stdout et stderr
86#-Q- sx8mercure #PBS -S /usr/bin/ksh         # shell de soumission
87#-Q- sx8mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
88#-Q- sx8mercure #PBS -l cputim_job=48:00:00  # Limite temps a 1 heures
89#-Q- sx8mercure #PBS -q scalaire
90#-Q- sx8mercure #PBS -r n
91#-Q- sx9mercure #!/bin/ksh
92#-Q- sx9mercure ######################
93#-Q- sx9mercure ## SX9MERCURE  CCRT ##
94#-Q- sx9mercure ######################
95#-Q- sx9mercure #PBS -N PACKOUTPUT          # Nom du job
96#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr
97#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission
98#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
99#-Q- sx9mercure #PBS -l elapstim_req=48:00:00  # Limite temps a 1 heures
100#-Q- sx9mercure #PBS -q scalaire
101#-Q- sx9mercure #PBS -r n
102#-Q- titane #!/bin/ksh
103#-Q- titane ######################
104#-Q- titane ## TITANE   CEA     ##
105#-Q- titane ######################
106#-Q- titane #MSUB -r PACKOUTPUT    # Nom du job
107#-Q- titane #MSUB -eo
108#-Q- titane #MSUB -n 1              # Reservation du processus
109#-Q- titane #MSUB -T 86400          # Limite de temps elapsed du job
110#-Q- titane #MSUB -q mono
111#-Q- titane #MSUB -E '-rn'
112#-Q- lxiv8 ######################
113#-Q- lxiv8 ## OBELIX      LSCE ##
114#-Q- lxiv8 ######################
115#-Q- lxiv8 #PBS -N PACKOUTPUT
116#-Q- lxiv8 #PBS -m a
117#-Q- lxiv8 #PBS -j oe
118#-Q- lxiv8 #PBS -q medium
119#-Q- lxiv8 #PBS -o PACKOUTPUT.$$
120#-Q- lxiv8 #PBS -S /bin/ksh
121#-Q- default #!/bin/ksh
122#-Q- default ##################
123#-Q- default ## DEFAULT HOST ##
124#-Q- default ##################
125
126#**************************************************************
127# Author: Sebastien Denvil
128# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
129# $Revision::                                          $ Revision of last commit
130# $Author::                                            $ Author of last commit
131# $Date::                                              $ Date of last commit
132# IPSL (2006)
133#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
134#
135#**************************************************************
136
137#set -eu
138#set -vx
139
140date
141
142########################################################################
143
144#D- Flag to determine if this job in a standalone mode
145#D- Default : value from AA_job if any
146StandAlone=${StandAlone:=true}
147
148#D- Path to libIGCM
149#D- Default : value from AA_job if any
150# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
151# WARNING you must check MirrorlibIGCM variable in sys library.
152# WARNING If this variable is true, you must use libIGCM_POST path instead
153# WARNING of your running libIGCM directory.
154libIGCM=${libIGCM:=::modipsl::/libIGCM}
155
156#-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer.
157MASTER=${MASTER:=mercure|titane|brodie|vargas}
158
159#D- Flag to determine begin date for restart pack
160#D- Default : value from AA_job if any
161DateBegin=${DateBegin:=20000101}
162
163#D- Flag to determine end date for restart pack
164#D- Default : value from AA_job if any
165DateEnd=${DateEnd:=20691231}
166
167#D- Flag to determine pack period
168#D- Default : value from AA_job if any
169PeriodPack=${PeriodPack:=10Y}
170
171#D- Uncomment to run interactively
172#D- For testing purpose, will be remove
173#SUBMIT_DIR=${PWD}
174#RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test
175
176#D- Increased verbosity (1, 2, 3)
177#D- Default : value from AA_job if any
178Verbosity=${Verbosity:=3}
179
180#D- Low level debug : to bypass lib test checks and stack construction
181#D- Default : value from AA_job if any
182DEBUG_debug=${DEBUG_debug:=false}
183
184########################################################################
185
186. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
187( ${DEBUG_debug} ) && IGCM_debug_Check
188. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
189( ${DEBUG_debug} ) && IGCM_card_Check
190. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
191( ${DEBUG_debug} ) && IGCM_date_Check
192#-------
193. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
194. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
195
196########################################################################
197
198#set -vx
199
200RUN_DIR=${RUN_DIR_PATH}
201IGCM_sys_MkdirWork ${RUN_DIR}
202IGCM_sys_Cd ${RUN_DIR}
203
204# ------------------------------------------------------------------
205# Test if all was right before proceeding further
206# ------------------------------------------------------------------
207IGCM_debug_Verif_Exit_Post
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 config.card
223
224IGCM_card_DefineArrayFromSection     ${CARD_DIR}/config.card UserChoices
225typeset option
226for option in ${config_UserChoices[*]} ; do
227  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
228done
229#
230IGCM_card_DefineArrayFromSection     ${CARD_DIR}/config.card Ensemble
231typeset option
232for option in ${config_Ensemble[*]} ; do
233  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Ensemble ${option}
234done
235#
236echo
237IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices"
238IGCM_debug_PrintVariables 3 config_UserChoices_JobName
239IGCM_debug_PrintVariables 3 config_UserChoices_LongName
240IGCM_debug_PrintVariables 3 config_UserChoices_TagName
241IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
242IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
243IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
244IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
245IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
246IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
247IGCM_debug_PrintVariables 3 config_Ensemble_EnsembleName
248IGCM_debug_PrintVariables 3 config_Ensemble_EnsembleDate
249echo
250
251# Get ListOfComponents to drive the loop over find
252IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
253
254#====================================================
255#R_SAVE : Job output storage directory
256#R_BUFR : Job output buffered directory
257
258if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
259  FreeName=$( echo ${config_UserChoices_JobName} | sed 's/.*_//' )
260  if ( [ ! X${config_Ensemble_EnsembleName} = X ] && [ ! X${config_Ensemble_EnsembleDate} = X ] ) ; then
261    R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${config_Ensemble_EnsembleName}/${config_Ensemble_EnsembleDate}/${FreeName}
262    R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${config_Ensemble_EnsembleName}/${config_Ensemble_EnsembleDate}/${FreeName}
263  else
264    R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
265    R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
266  fi
267else
268  if ( [ ! X${config_Ensemble_EnsembleName} = X ] && [ ! X${config_Ensemble_EnsembleDate} = X ] ) ; then
269    R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_Ensemble_EnsembleName}/${config_Ensemble_EnsembleDate}/${config_UserChoices_JobName}
270    R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_Ensemble_EnsembleName}/${config_Ensemble_EnsembleDate}/${config_UserChoices_JobName}
271  else
272    R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
273    R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
274  fi
275fi
276IGCM_sys_TestDirArchive ${R_SAVE}
277[ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive"
278
279# Where to store used file list /!\ TEMPORARY /!\
280STORE_DEBUG=${R_SAVE}/DEBUG
281
282# Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure)
283JobName=${config_UserChoices_JobName}
284echo $JobName $DateBegin $DateEnd
285
286# ------------------------------------------------------------------
287# Test if all was right before proceeding further
288# ------------------------------------------------------------------
289IGCM_debug_Verif_Exit_Post
290
291IGCM_debug_Print 1 "Check coherence between PackFrequency and PeriodLength"
292IGCM_post_CheckModuloFrequency PeriodPack config_UserChoices_PeriodLength NbPeriodPerFrequency
293# ------------------------------------------------------------------
294# Test if all was right before proceeding further
295# ------------------------------------------------------------------
296IGCM_debug_Verif_Exit_Post
297
298IGCM_debug_Print 1 "We must process ${NbPeriodPerFrequency} files for each pack"
299
300# Init loop
301date_begin_pack=${DateBegin}
302date_end_simulation=${DateEnd}
303number_pack=1
304
305IGCM_debug_PrintVariables 3 date_begin_pack
306IGCM_debug_PrintVariables 3 date_end_simulation
307
308while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do
309
310  IGCM_debug_PrintVariables 3 number_pack
311  DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} )
312  date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) )
313
314  for comp in ${config_ListOfComponents[*]} ; do
315    dirList=$( find ${R_BUFR}/${comp}/Output -maxdepth 1 -mindepth 1 -type d )
316    for dir in ${dirList} ; do
317      # dirID is like ATM.Output.MO
318      dirID=$( echo $dir | sed "s:${R_BUFR}/::" | sed "s:/:.:g" )
319      # Sort what's in the directory
320      find ${dir} -type f -name "${JobName}*.nc" -ls | sort -k 11 > liste_files.${dirID}.txt
321      # How much file type. Example : 1M_histmthCOSP.nc, 1M_histmth.nc, 1M_histmthNMC.nc, 1M_paramLMDZ_phy.nc
322      # /!\ fileType include the .nc extension /!\
323      fileType=$( 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 )
324      # Loop over the file type and pack them when in between date_begin_pack and date_end_pack
325      for myType in ${fileType} ; do
326        grep ${myType} liste_files.${dirID}.txt > liste_files.${dirID}.${myType}.txt
327        nbfile=0
328        for file in $( gawk '{print $11}' liste_files.${dirID}.${myType}.txt ); do
329          extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_[0-9]*_//" )
330          date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' )
331          # echo pack n°${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack}
332          if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then
333            echo ${file} >> liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt
334            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
335            (( nbfile = nbfile + 1 ))
336          fi
337        done
338
339        if ( [ X${StandAlone} = Xtrue ] && [ ${nbfile} = 0 ] ) ; then
340          IGCM_debug_Print 1 "We found ${nbfile} files to process"
341          IGCM_debug_Print 1 "We should have found ${NbPeriodPerFrequency} files"
342          IGCM_debug_Print 1 "As we are in StandAlone mode we consider the job has been done and move to the next file type"
343          continue
344        fi
345
346        # Select list of variables to work with
347        list_var=$( cat liste_variables_${myType}_${date_begin_pack}_${date_end_pack}.txt | sort | uniq -c | awk -v nbfile=$nbfile '{if ($1 != nbfile) {print $2}}' | paste -s -d ',' )
348        liste_file_tmp=$( for i in $( cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ) ; do basename $i ; done )
349        # Create packed files
350        IGCM_debug_Print 1 "Ncrcat ongoing for ${dir} and ${myType}"
351        if [ ! ${nbfile} = ${NbPeriodPerFrequency} ] ; then
352          IGCM_debug_Print 1 "Number of files to process is not equal to what it should be"
353          IGCM_debug_Print 1 "We found ${nbfile} files and it should have been ${NbPeriodPerFrequency} files"
354          IGCM_debug_Exit "ERROR in number of files to process. STOP HERE INCLUDING THE COMPUTING JOB"
355          IGCM_debug_Verif_Exit
356        fi
357        output=${JobName}_${date_begin_pack}_${date_end_pack}_${myType}
358        #cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs ncrcat -v ${list_var} -o ${output}
359        if [ X${list_var} = X ] ; then
360          IGCM_sys_ncrcat -p ${dir} ${liste_file_tmp} --output ${output}
361        else
362          IGCM_sys_ncrcat -x -v ${list_var} -p ${dir} ${liste_file_tmp} --output ${output}
363        fi
364        # ------------------------------------------------------------------
365        # Test if all was right before proceeding further
366        # ------------------------------------------------------------------
367        IGCM_debug_Verif_Exit_Post
368        # Save it
369        IGCM_sys_Put_Out ${output} ${R_SAVE}/$( echo $dir | sed "s:${R_BUFR}/::" )/${output}
370        # Clean file produced by ncrcat
371        IGCM_sys_Rm ${output}
372        # ------------------------------------------------------------------
373        # Test if all was right before proceeding further
374        # ------------------------------------------------------------------
375        IGCM_debug_Verif_Exit_Post
376        # Clean files used by ncrcat
377        cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs rm
378        # Save the list of files that has been pack (ncrcat)
379        #mv liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ${STORE_DEBUG}
380        IGCM_debug_Print 1 "Ncrcat and cleaning done for ${dir} and ${myType}"
381        echo
382      done
383    done
384  done
385  (( number_pack = number_pack + 1 ))
386  # Add 1 day to date_end_pack to have the new date_begin_pack
387  date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 )
388done
389
390# Flush post-processing submission
391if [ -f ${R_BUFR}/FlushPost_${DateEnd}.ksh ] ; then
392  . ${R_BUFR}/FlushPost_${DateEnd}.ksh
393  IGCM_FlushPost
394  #IGCM_sys_Rm -f ${R_BUFR}/FlushPost_${DateEnd}.ksh
395fi
396
397# Clean RUN_DIR_PATH (necessary for cesium and titane only)
398IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
399
400date
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