source: trunk/libIGCM/AA_create_ts @ 1274

Last change on this file since 1274 was 1274, checked in by mafoipsl, 9 years ago

For curie :

  • Add a new option in AA_post_jobs header on curie : "-c ::default_core::" with the number of core reserved.
  • Add 3 options to ins_job :
    • -p projet
    • -q standard/xlarge : with xlarge as default value. except for gencmip6 project
    • -c number of cores (default value is : 4 on standard node or 8 on xlarge node)
  • For batch usage, it's possible to set these options on ins_job command line. See Usage.
  • By default, 3 questions are asked interactively to the user.

With 4 or 8 cores per job we want to limit the number of simultaneous running jobs on one node
and eventually limit SCRATCH congestion.
  • 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: 31.2 KB
Line 
1#-Q- curie ######################
2#-Q- curie ## CURIE   TGCC/CEA ##
3#-Q- curie ######################
4#-Q- curie #MSUB -r TS             # Nom du job
5#-Q- curie #MSUB -eo
6#-Q- curie #MSUB -n 1              # Reservation du processus
7#-Q- curie #MSUB -T 80000          # Limite de temps elapsed du job
8#-Q- curie #MSUB -q ::default_node::
9#-Q- curie #MSUB -c ::default_core::
10#-Q- curie #MSUB -Q normal
11#-Q- curie #MSUB -A ::default_project::
12#-Q- curie set +x
13#-Q- ada #!/bin/ksh
14#-Q- ada #######################
15#-Q- ada ## ADA         IDRIS ##
16#-Q- ada #######################
17#-Q- ada # @ job_type = serial
18#-Q- ada # @ requirements = (Feature == "prepost")
19#-Q- ada # Temps Elapsed max. d'une requete hh:mm:ss
20#-Q- ada # @ wall_clock_limit = 20:00:00
21#-Q- ada # Nom du travail LoadLeveler
22#-Q- ada # @ job_name   = TS
23#-Q- ada # Fichier de sortie standard du travail
24#-Q- ada # @ output     = $(job_name).$(jobid)
25#-Q- ada # Fichier de sortie d'erreur du travail
26#-Q- ada # @ error      =  $(job_name).$(jobid)
27#-Q- ada # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
28#-Q- ada # @ notification = error
29#-Q- ada # @ environment  = $DEBUG_debug ; $BigBrother ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $POST_DIR ; $Script_Post_Output ; $MASTER ; $RebuildFrequency ; $DateBegin ; $PeriodDateEnd ; $StandAlone ; $CompletedFlag ; $TsTask ; $CompToRead ; $FlagToRead ; $RESOL_ATM ; $RESOL_OCE ; $RESOL_ICE ; $RESOL_MBG ; $RESOL_SRF ; $RESOL_SBG ; wall_clock_limit=$(wall_clock_limit)
30#-Q- ada # @ queue
31#-Q- lxiv8 ######################
32#-Q- lxiv8 ## OBELIX      LSCE ##
33#-Q- lxiv8 ######################
34#-Q- lxiv8 #PBS -N TS
35#-Q- lxiv8 #PBS -m a
36#-Q- lxiv8 #PBS -j oe
37#-Q- lxiv8 #PBS -q medium
38#-Q- lxiv8 #PBS -o TS.$$
39#-Q- lxiv8 #PBS -S /bin/ksh
40#-Q- ifort_CICLAD ######################
41#-Q- ifort_CICLAD ##   CICLAD    IPSL ##
42#-Q- ifort_CICLAD ######################
43#-Q- ifort_CICLAD #PBS -N TS
44#-Q- ifort_CICLAD #PBS -m a
45#-Q- ifort_CICLAD #PBS -j oe
46#-Q- ifort_CICLAD #PBS -q h12
47#-Q- ifort_CICLAD #PBS -S /bin/ksh
48#-Q- default #!/bin/ksh
49#-Q- default ##################
50#-Q- default ## DEFAULT HOST ##
51#-Q- default ##################
52
53#**************************************************************
54# Author: Sebastien Denvil
55# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
56# $Revision::                                          $ Revision of last commit
57# $Author::                                            $ Author of last commit
58# $Date::                                              $ Date of last commit
59# IPSL (2006)
60#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
61#
62#**************************************************************
63
64#set -eu
65#set -vx
66
67date
68
69#-Q- ada export OMP_NUM_THREADS=1
70
71#D- Task type (computing or post-processing)
72TaskType=post-processing
73
74########################################################################
75
76#D- Flag to determine if this job in a standalone mode
77#D- Default : value from AA_job if any
78StandAlone=${StandAlone:=true}
79
80#D- Path to libIGCM
81#D- Default : value from AA_job if any
82libIGCM=${libIGCM:=::modipsl::/libIGCM}
83
84#D- Flag to determine allready produced time series. Empty if you start from the beginning
85#D- Default : Value from AA_job if any. Usefull in StandAlone case if you want to continue a time series
86CompletedFlag=${CompletedFlag:=}
87
88#D- Flag to determine task type this script will perform.
89#D- Possible Value : 2D, 3D, Chunck2D, Chunck3D
90#D- Default : Value from AA_job if any. Usefull in StandAlone case.
91TsTask=${TsTask:=2D}
92if [ X${TsTask} = Xempty ] ; then
93  TsTask=""
94fi
95
96#D- Flag to determine if rebuild process has been performed asynchronously
97#D- Possible value true or false.
98#D- If true raw files has allready been patched by rebuild job
99#D- If false create_ts will patch the raw files
100#D- Default : Value from AA_job if any. Usefull in StandAlone case.
101RebuildFrequency=${RebuildFrequency:=true}
102
103#D- Flag to determine job's output directory
104#D- Default : value from libIGCM_post.ksh if any
105POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
106
107#D- Increased verbosity (1, 2, 3)
108#D- Default : value from AA_job if any
109Verbosity=${Verbosity:=3}
110
111#D- Low level debug : to bypass lib test checks and stack construction
112#D- Default : value from AA_job if any
113DEBUG_debug=${DEBUG_debug:=false}
114
115#D- TEMPORARY Flag to determine atmospheric resolution
116#D- Default : value from atmospheric driver if any
117RESOL_ATM=ALL
118
119#D- Flag to determine surface resolution
120#D- Default : value from surface driver if any
121RESOL_SRF=ALL
122
123#D- Flag to determine surface resolution
124#D- Default : value from surface driver if any
125RESOL_SBG=ALL
126
127#D- TEMPORARY Flag to determine ocean resolution
128#D- Default : value from ocean driver if any
129RESOL_OCE=${RESOL_OCE:=ORCA2}
130
131#D- TEMPORARY Flag to determine ice resolution
132#D- Default : value from ice driver if any
133RESOL_ICE=${RESOL_ICE:=ORCA2}
134
135#D- TEMPORARY Flag to determine marine biogeochemistry resolution
136#D- Default : value from ice driver if any
137RESOL_MBG=${RESOL_MBG:=ORCA2}
138
139########################################################################
140
141. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
142. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
143. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
144#-------
145. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
146. ${libIGCM}/libIGCM_config/libIGCM_config.ksh
147#-------
148IGCM_sys_MkdirWork ${RUN_DIR_PATH}
149IGCM_sys_Cd ${RUN_DIR_PATH}
150#-------
151( ${DEBUG_debug} ) && IGCM_debug_Check
152( ${DEBUG_debug} ) && IGCM_card_Check
153( ${DEBUG_debug} ) && IGCM_date_Check
154
155########################################################################
156
157#set -vx
158
159# Useful cleaning function
160MENAGE ()
161{
162  [ -f $3 ] && ( IGCM_sys_RshArchive rm -f $1/$2 ;)
163}
164
165########################################################################
166
167# ------------------------------------------------------------------
168# Test if all was right before proceeding further
169# ------------------------------------------------------------------
170IGCM_debug_Verif_Exit
171
172if [ ${StandAlone} = true ] ; then
173  CARD_DIR=${SUBMIT_DIR}
174else
175  CARD_DIR=${RUN_DIR_PATH}
176
177  IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
178
179  IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card    ${RUN_DIR_PATH}
180
181  IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP        ${RUN_DIR_PATH}
182
183  IGCM_sys_Get_Master ${SUBMIT_DIR}/POST        ${RUN_DIR_PATH}
184fi
185
186#==================================
187# First of all
188#
189# Read libIGCM compatibility version in config.card
190# Read UserChoices section
191# Read Ensemble section
192# Read Post section
193# Define all netcdf output directories
194#==================================
195IGCM_config_CommonConfiguration ${CARD_DIR}/config.card
196
197# ------------------------------------------------------------------
198# Activate BigBrother so as to supervise this job
199# ------------------------------------------------------------------
200IGCM_debug_BigBro_Initialize
201
202#==================================
203# Define default value to keep compatibility with previous card: means before changes due to TGCC
204if [ X${PackDefault} = Xtrue ] ; then
205  [ X${config_Post_PackFrequency} = X ] && config_Post_PackFrequency=${config_Post_RebuildFrequency}
206else
207  config_Post_PackFrequency=NONE
208fi
209
210#==================================
211# If pack is active then PackFrequency overule the config_UserChoices_PeriodLength
212if ( [ ! X${config_Post_PackFrequency} = X${NULL_STR} ] && [ ! X${config_Post_PackFrequency} = XNONE ] ) ; then
213  config_UserChoices_PeriodLength=${config_Post_PackFrequency}
214fi
215
216#
217# Determine component to take care of depending on kind of task create_ts will perform
218#
219[ ${CompToRead} ] && set -A config_ListOfComponents ${CompToRead} || IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
220#
221# Determine period for time series. Default : value from AA_job or from launch_TS if any
222#
223[ X${CompletedFlag} = X ] || CompletedFlag=$( IGCM_date_ConvertFormatToGregorian ${CompletedFlag} )
224
225DateBegin=${DateBegin:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateBegin} )}
226#
227PeriodDateEnd=${PeriodDateEnd:=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} )}
228#
229# Determine Dimension of the produced time series : 2D or 3D
230if (   [ X${TsTask} = XChunck2D ] || [ X${TsTask} = X2D ] ) ; then
231  Dimension=2D
232elif ( [ X${TsTask} = XChunck3D ] || [ X${TsTask} = X3D ] ) ; then
233  Dimension=3D
234else
235  Dimension=""
236fi
237
238# ------------------------------------------------------------------
239#D- Test if all was right before entering the loop
240# ------------------------------------------------------------------
241IGCM_debug_Verif_Exit
242
243########################################################################
244#      Depending on requested time series fill following variables :
245#
246#                           - LISTE_FILE_${comp}[*]
247#                           - LISTE_VARS_${file}[*]
248#                           - LISTE_AXIS_${file}[*]
249#                           - LISTE_PATCH_${file}[*]
250########################################################################
251
252#
253# For each selected component determine which files need post-processing
254#
255DoJob=false
256for comp in ${config_ListOfComponents[*]} ; do
257  #
258  ActiveComp=false
259  #
260  IGCM_card_DefineArrayFromOption ${CARD_DIR}/config.card ListOfComponents ${comp}
261  eval compname=\${config_ListOfComponents_${comp}[0]} > /dev/null 2>&1
262  #
263  card=${CARD_DIR}/COMP/${compname}.card
264
265  IGCM_card_DefineArrayFromOption ${card} OutputFiles List
266  #
267  ListFilesName=${compname}_OutputFiles_List
268  eval FileName0=\${${ListFilesName}[0]} > /dev/null 2>&1
269  #
270  if [ X${FileName0} != X${NULL_STR} ] ; then
271    #
272    #IGCM_debug_Print 1 "Component      : ${compname}"
273    #
274    # INITIALISATION
275    #
276    typeset i
277    if [ ${FlagToRead} ] ; then
278      ((NbFiles=${FlagToRead}))
279      ((i=${NbFiles}))
280    else
281      eval NbFiles=\${#${ListFilesName}[@]} > /dev/null 2>&1
282      i=2
283    fi
284    #
285    until [ $i -gt $NbFiles ]; do
286      #
287      eval flag_post=\${${ListFilesName}[$i]} > /dev/null 2>&1
288      #
289      if [ X${flag_post} != XNONE ] ; then
290        #
291        # For each comp and each file who needs post-processing
292        # determine which variables need time series.
293        #
294        FILE=$( echo ${flag_post} | awk "-FPost_" '{print $2}' )
295        IGCM_card_DefineArrayFromOption ${card}    Post_${FILE} TimeSeriesVars${Dimension}
296        IGCM_card_DefineVariableFromOption ${card} Post_${FILE} ChunckJob${Dimension}
297        #
298        # If TimeSeriesVars list is empty we skip
299        #
300        if [ $( eval echo \${${compname}_Post_${FILE}_TimeSeriesVars${Dimension}} ) = ${NULL_STR} ] ; then
301          #
302          IGCM_debug_Print 3 "Nothing to do for ${FILE} according to ${card}"
303          IGCM_debug_Print 3 "TimeSeriesVars${Dimension} for ${FILE} is empty"
304          (( i=i+3 ))
305          continue
306          #
307        fi
308        #
309        # If files/variables has been switch off by ChunckJob${Dimension}=0 we skip
310        #
311        if [ X$( eval echo \${${compname}_Post_${FILE}_ChunckJob${Dimension}} ) = XOFF ] ; then
312          IGCM_debug_Print 3 "Nothing to do for ${FILE} according to ${card}"
313          IGCM_debug_Print 3 "ChunckJob${Dimension}=OFF for ${FILE} so it has been switched off"
314          (( i=i+3 ))
315          continue
316        fi
317        #
318          # If we are not a Chunck type task, we skip files/variables handled by chunck task
319          #
320        if ( [ ! X${TsTask} = XChunck${Dimension} ] && [ ! X${TsTask} = X ] && [ ! XChunck${Dimension} = XChunck ] ) ; then
321          if [ ! $( eval echo \${${compname}_Post_${FILE}_ChunckJob${Dimension}} ) = NONE ] ; then
322            IGCM_debug_Print 3 "Nothing to do for ${FILE} TimeSeriesVars${Dimension} according to ${card}"
323            IGCM_debug_Print 3 "Let another chunck task do the job $( eval echo \${${compname}_Post_${FILE}_ChunckJob${Dimension}} )"
324            (( i=i+3 ))
325            continue
326          fi
327        fi
328        #
329        # Now on we know we have things to do
330        #
331
332        #
333        #  We need coordinates axis to properly fill produced time series
334        #
335        IGCM_card_DefineArrayFromOption ${card} Post_${FILE} GatherWithInternal
336        #
337        if [ $( eval echo \${${compname}_Post_${FILE}_GatherWithInternal} ) = ${NULL_STR} ] ; then
338          #
339          IGCM_debug_Print 1 "ERROR !! We miss coordinate axis for ${FILE} according to ${card}"
340          IGCM_debug_Print 1 "So no time series will be produced for ${FILE} !!"
341          (( i=i+3 ))
342          continue
343          #
344        fi
345        #
346        # We need LIST of variables not allready produced (useful for standalone mode)
347        #
348        FlagDir=$( echo ${FILE} | awk -F "_" '{print $1}' )
349        case ${FlagDir} in
350          *Y)  TS_Dir=TS_YE  ;;
351          *M)  TS_Dir=TS_MO  ;;
352          *D)  TS_Dir=TS_DA  ;;
353          HF)  TS_Dir=TS_HF  ;;
354          3H)  TS_Dir=TS_HF  ;;
355          INS) TS_Dir=TS_INS ;;
356        esac
357        #
358        count=0
359        for var in $( eval echo \${${compname}_Post_${FILE}_TimeSeriesVars${Dimension}[*]} ) ; do
360          #
361          DIRECTORY=${R_SAVE}/${comp}/Analyse/${TS_Dir}
362          TestedFile=${config_UserChoices_JobName}_${DateBegin}_${PeriodDateEnd}_${FlagDir}_${var}.nc
363          #
364          IGCM_sys_TestFileArchive ${DIRECTORY}/${TestedFile}
365          if [ ! $? = 0 ] ; then
366            eval set +A LISTE_VARS_${FILE} \${LISTE_VARS_${FILE}[*]} ${var}
367            ActiveComp=true
368            (( count = count + 1 ))
369          fi
370        done
371        #
372        if [ ${count} -gt 0 ] ; then
373          #
374          eval set +A LISTE_FILE_${comp} \${LISTE_FILE_${comp}[*]} ${FILE}
375          eval set +A LISTE_AXIS_${FILE} \${${compname}_Post_${FILE}_GatherWithInternal[*]}
376          #
377          if [ ! X${RebuildFrequency} = Xtrue ] ; then
378            IGCM_card_DefineArrayFromOption ${card} Post_${FILE} Patches
379            eval set +A LISTE_PATCHES_${FILE} \${${compname}_Post_${FILE}_Patches[*]}
380            if [ X$( eval echo \${LISTE_PATCHES_${FILE}[0]} ) !=  X${NULL_STR} ]; then
381              for Patch in $( eval echo \${LISTE_PATCHES_${FILE}[*]} ); do
382                if [ Xload${Patch} != X ] ; then
383                  . ${libIGCM}/libIGCM_post/IGCM_${Patch}.ksh
384                  eval load${Patch}=loaded
385                fi
386              done
387            fi
388          fi
389        fi
390      fi
391      (( i=i+3 ))
392    done
393  fi
394  #
395  if [ ${ActiveComp} = true ] ; then
396    set +A ActiveListOfComponents ${ActiveListOfComponents[*]} ${comp}
397  fi
398done
399
400set -A config_ListOfComponents ${ActiveListOfComponents[*]}
401[ ! -z "${ActiveListOfComponents}" ] && DoJob=true
402
403########################################################################
404#
405#               IS THERE SOME ALLREADY PRODUCED TIME SERIES ?
406#                 IF SO BRING THEM IN THE WORKING DIRECTORY
407#
408# PS : Keep in mind that IGCM_sys_Get here is a weak link :
409#      - especially for IDRiS
410#      - no special protection against "command too long" !
411#      - libIGCM_sys should handle that or modify following code part
412#
413########################################################################
414
415if [ ${StandAlone} != true ] ; then
416  Running_Flag=$( IGCM_sys_RshMaster "IGCM_card_DefineVariableFromOption \
417  ${SUBMIT_DIR}/run.card PostProcessing TimeSeriesRunning ; \
418  echo \${run_PostProcessing_TimeSeriesRunning}" )
419
420  #if [ X${Running_Flag} = Xy ] ; then
421  #  # Time Series Job allready running
422  #  IGCM_debug_Print 1 "Time Series Job allready running exit"
423  #  exit
424  #fi
425  # Now run.card know we are running
426
427
428
429
430  IGCM_sys_RshMaster IGCM_card_WriteOption ${SUBMIT_DIR}/run.card PostProcessing TimeSeriesRunning "y"
431
432
433
434
435
436  # Get information from last execution
437  #CompletedFlag=$( IGCM_sys_RshMaster \
438  # "IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/run.card PostProcessing TimeSeriesCompleted ;\
439  #        echo \${run_PostProcessing_TimeSeriesCompleted}" )
440fi
441
442# Is it the first submission or not ?
443
444if ( [ X${CompletedFlag} = X ] || [ X${CompletedFlag} = X$( IGCM_date_AddDaysToGregorianDate ${DateBegin} -1 ) ] ) ; then
445  # First Time Series Submission
446  FIRST_PASS=TRUE
447  Length=$( IGCM_date_DaysInPreviousPeriod ${DateBegin} ${config_UserChoices_PeriodLength} begin)
448  DATE_FIN_JOB_B=$( IGCM_date_AddDaysToGregorianDate ${DateBegin} $(( Length - 1 )) )
449else
450  # Last Completed Time Series
451  FIRST_PASS=FALSE
452  DATE_FIN_JOB_B=${CompletedFlag}
453  date=${DateBegin}_${DATE_FIN_JOB_B}
454  #
455  for comp in ${config_ListOfComponents[*]} ; do
456    #
457    IGCM_sys_Mkdir ${RUN_DIR_PATH}/${comp}
458    #
459    IGCM_sys_Cd ${RUN_DIR_PATH}/${comp}
460    #
461    unset liste_file
462    #
463    file_path=${R_SAVE}/${comp}/Analyse
464    #
465    i=0
466    file=${NULL_STR}
467    #
468    for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
469      #
470      # Determine in which output can we find file
471      # IE : Analyse/TS or Analyse/DA2TS or ...
472      #
473      FlagDir=$( echo ${file} | awk -F "_" '{print $1}' )
474      case ${FlagDir} in
475        *Y)  TS_Dir=TS_YE  ;;
476        *M)  TS_Dir=TS_MO  ;;
477        *D)  TS_Dir=TS_DA  ;;
478        HF)  TS_Dir=TS_HF  ;;
479        3H)  TS_Dir=TS_HF  ;;
480        INS) TS_Dir=TS_INS ;;
481      esac
482      for var in $( eval echo \${LISTE_VARS_${file}[*]} ) ; do
483        #
484        IGCM_sys_TestFileArchive ${file_path}/${TS_Dir}/${config_UserChoices_JobName}_${date}_${FlagDir}_${var}.nc
485        if [ $? = 0 ] ; then
486          liste_file[${#liste_file[*]}]=${file_path}/${TS_Dir}/${config_UserChoices_JobName}_${date}_${FlagDir}_${var}.nc
487        else
488          IGCM_debug_Print 1 "WARNING ${file_path}/${TS_Dir}/${config_UserChoices_JobName}_${date}_${FlagDir}_${var}.nc dont exist"
489        fi
490        #
491      done
492    done
493    if [ X${file} != X${NULL_STR} ] ; then
494      IGCM_sys_Get /l liste_file[*] ${RUN_DIR_PATH}/${comp}
495      IGCM_debug_Verif_Exit
496    fi
497  done
498  #
499  LEVEL=0
500  #
501fi
502
503########################################################################
504#
505#                          DEFINE LOOP PARAMETERS
506#
507########################################################################
508
509DATE_COUNT=${DATE_FIN_JOB_B}
510DATE_FIN_JOB_B_LOOP=${DATE_FIN_JOB_B}
511
512( [ -n "${LEVEL}" ] && [ ${LEVEL} -eq 0 ] ) && NBRE_FILE_TOT=0 || NBRE_FILE_TOT=1
513
514if [ ${DoJob} = true ] ; then
515  while [ ${DATE_COUNT} -lt ${PeriodDateEnd} ] ; do
516    (( NBRE_FILE_TOT = NBRE_FILE_TOT + 1 ))
517    Length=$( IGCM_date_DaysInNextPeriod ${DATE_COUNT} ${config_UserChoices_PeriodLength} )
518    DATE_COUNT=$( IGCM_date_AddDaysToGregorianDate ${DATE_COUNT} ${Length} )
519  done
520else
521  NBRE_FILE_TOT=0
522fi
523
524if [ ${NBRE_FILE_TOT} -le ${UNIX_MAX_LIMIT} ] ; then
525  NBRE_TOUR=1
526elif [ ${NBRE_FILE_TOT}%${UNIX_MAX_LIMIT} -eq 0 ] ; then
527  let NBRE_TOUR=${NBRE_FILE_TOT}/${UNIX_MAX_LIMIT}
528else
529  let NBRE_TOUR=${NBRE_FILE_TOT}/${UNIX_MAX_LIMIT}+1
530fi
531
532CURRENT_LOOP=1
533# THIS LOOP GIVES PARAMETERS FOR THE DATE'S LOOP ie : DATE_COURANTE, DATE_FIN.
534# WE HAVE 3 LEVELS
535#    - LEVEL 1 : JUST ONE LOOP TO COMPLETE
536#    - LEVEL 2 : WE ARE IN THE "DEEP" LOOP
537#    - LEVEL 3 : WE ARE IN THE LAST LOOP
538
539while [ ${CURRENT_LOOP} -le  ${NBRE_TOUR} ] ; do
540
541  if [ ${NBRE_FILE_TOT} -le ${UNIX_MAX_LIMIT} ] ; then
542    # - LEVEL 1 : JUST ONE LOOP TO COMPLETE
543    NBRE_FILE_LOOP=${NBRE_FILE_TOT}
544
545    if [ ${FIRST_PASS} = TRUE ] ; then
546      DATE_COURANTE=${DATE_FIN_JOB_B_LOOP}
547    else
548      Length=$( IGCM_date_DaysInNextPeriod ${DATE_FIN_JOB_B_LOOP} ${config_UserChoices_PeriodLength} )
549      DATE_COURANTE=$( IGCM_date_AddDaysToGregorianDate ${DATE_FIN_JOB_B_LOOP} ${Length} )
550    fi
551
552    DATE_FIN=${PeriodDateEnd}
553    DATE_FIN_JOB_B_LOOP_PREC=${DATE_FIN_JOB_B_LOOP}
554
555    [ -n "${DATE_LOOP}" ] && DATE_FIN_JOB_B_LOOP=${DATE_LOOP}
556    [ -n "${LEVEL}" ] && FLAG_B="TRUE" || FLAG_B="FALSE"
557
558    LEVEL=1
559    DEPOT="TRUE"
560  elif [ ${CURRENT_LOOP} -ne  ${NBRE_TOUR} ] ; then
561    # - LEVEL 2 : WE ARE IN THE "DEEP" LOOP
562    NBRE_FILE_LOOP=${UNIX_MAX_LIMIT}
563
564    if [ ! ${FIRST_PASS} = TRUE ] && [ ${CURRENT_LOOP} -eq 1 ] ; then
565      Length=$( IGCM_date_DaysInNextPeriod ${DATE_FIN_JOB_B_LOOP} ${config_UserChoices_PeriodLength} )
566      DATE_COURANTE=$( IGCM_date_AddDaysToGregorianDate ${DATE_FIN_JOB_B_LOOP} ${Length} )
567    elif [ -z "${DATE_COURANTE}" ] ; then
568      DATE_COURANTE=${DATE_FIN_JOB_B}
569    else
570      Length=$( IGCM_date_DaysInNextPeriod ${DATE_FIN} ${config_UserChoices_PeriodLength} )
571      DATE_COURANTE=$( IGCM_date_AddDaysToGregorianDate ${DATE_FIN} ${Length} )
572    fi
573
574    (( TotLength = 0 ))
575    COMPTEUR=1
576    DATE_LOOP=${DATE_COURANTE}
577
578    while [ ${COMPTEUR} -lt ${NBRE_FILE_LOOP} ] ; do
579      #
580      Length=$( IGCM_date_DaysInNextPeriod ${DATE_LOOP} ${config_UserChoices_PeriodLength} )
581      DATE_LOOP=$( IGCM_date_AddDaysToGregorianDate ${DATE_LOOP} ${Length} )
582      (( TotLength = TotLength + Length ))
583      (( COMPTEUR = COMPTEUR + 1 ))
584      #
585    done # while [ ${COMPTEUR} -le ${NBRE_FILE_LOOP} ] done
586    DATE_FIN=$( IGCM_date_AddDaysToGregorianDate ${DATE_COURANTE} ${TotLength} )
587
588    [ -n "${DATE_LOOP}" ] && DATE_FIN_JOB_B_LOOP_PREC=${DATE_FIN_JOB_B_LOOP} ; DATE_FIN_JOB_B_LOOP=${DATE_LOOP}
589    [ -n "${LEVEL}" ] && [ ${LEVEL} -eq 0 ] && FLAG_B="TRUE" || [ ${CURRENT_LOOP} -gt 1 ] && FLAG_B="TRUE" || FLAG_B="FALSE"
590    DEPOT="FALSE"
591    LEVEL=2
592  else
593    # - LEVEL 3 : WE ARE IN THE LAST LOOP
594    NBRE_FILE_LOOP=$(( ${NBRE_FILE_TOT} % ( ${UNIX_MAX_LIMIT} * ( ${CURRENT_LOOP} - 1 ) ) ))
595    [ ${NBRE_FILE_LOOP} -eq 0 ] && NBRE_FILE_LOOP=${UNIX_MAX_LIMIT}
596
597    Length=$( IGCM_date_DaysInNextPeriod ${DATE_FIN} ${config_UserChoices_PeriodLength} )
598    DATE_COURANTE=$(IGCM_date_AddDaysToGregorianDate ${DATE_FIN} ${Length} )
599    DATE_FIN=${PeriodDateEnd}
600    [ -n "${DATE_LOOP}" ] && DATE_FIN_JOB_B_LOOP_PREC=${DATE_FIN_JOB_B_LOOP} ; DATE_FIN_JOB_B_LOOP=${DATE_LOOP}
601
602    LEVEL=3
603    DEPOT="TRUE"
604    FLAG_B="TRUE"
605  fi
606
607  # THEN FOR EACH FILE TYPE WE LOOP BETWEEN DATE_COURANTE AND DATE_FIN.
608  for comp in ${config_ListOfComponents[*]} ; do
609    #
610    IGCM_sys_Mkdir ${RUN_DIR_PATH}/${comp}
611      #
612    IGCM_sys_Cd ${RUN_DIR_PATH}/${comp}
613    #
614    eval R_OUT_${comp}=${R_SAVE}/${comp}
615    #
616    i=0
617    #
618    for file in $( eval echo \${LISTE_FILE_${comp}[*]} ); do
619      #
620      # Determine in which output we can find file
621      # IE : Output/MO or Output/DA or ...
622      #
623      FlagDir=$( echo ${file} | awk -F "_" '{print $1}' )
624      case ${FlagDir} in
625        *Y)    TS_Dir=TS_YE  ; FreqDir=YE  ;;
626        *M)    TS_Dir=TS_MO  ; FreqDir=MO  ;;
627        *D)    TS_Dir=TS_DA  ; FreqDir=DA  ;;
628        HF)    TS_Dir=TS_HF  ; FreqDir=HF  ;;
629        3H)    TS_Dir=TS_HF  ; FreqDir=HF  ;;
630        INS)   TS_Dir=TS_INS ; FreqDir=INS ;;
631        *)     IGCM_debug_Print 1 "Error in FlagDir=${FlagDir} for file ${file}."
632               IGCM_debug_Exit "Job create_ts" ;;
633      esac
634
635      # Initialize array
636      unset liste_file
637      unset liste_file_tmp
638      eval file_path=\${R_OUT_${comp}}/Output/${FreqDir}/
639
640      COMPTEUR=1
641      MissingFile=FALSE
642      DATE_LOOP=${DATE_COURANTE}
643
644      while [ ${COMPTEUR} -le ${NBRE_FILE_LOOP} ] ; do
645        #
646        Length1=$( IGCM_date_DaysInPreviousPeriod ${DATE_LOOP} ${config_UserChoices_PeriodLength} end)
647        DATE_TAB=$(  IGCM_date_AddDaysToGregorianDate ${DATE_LOOP} $(( 1 - Length1 )) )_${DATE_LOOP}
648
649        Length2=$( IGCM_date_DaysInNextPeriod ${DATE_LOOP} ${config_UserChoices_PeriodLength} )
650        DATE_LOOP=$( IGCM_date_AddDaysToGregorianDate ${DATE_LOOP} ${Length2} )
651
652        IGCM_sys_TestFileArchive ${file_path}${config_UserChoices_JobName}_${DATE_TAB}_${file}.nc
653        if [ $? = 0 ] ; then
654          liste_file[${#liste_file[*]}]=${file_path}${config_UserChoices_JobName}_${DATE_TAB}_${file}.nc
655          liste_file_tmp[${#liste_file_tmp[*]}]=${config_UserChoices_JobName}_${DATE_TAB}_${file}.nc
656        else
657          IGCM_debug_Print 1 "WARNING ${file_path}${config_UserChoices_JobName}_${DATE_TAB}_${file}.nc dont exist"
658          MissingFile=TRUE
659        fi
660        (( COMPTEUR = COMPTEUR + 1 ))
661        #
662      done # while [ ${COMPTEUR} -le ${NBRE_FILE_LOOP} ] done
663
664      # We skip this file type if one of them is missing.
665      if [ "${MissingFile}" = "TRUE" ] ; then
666        IGCM_debug_Print 1 "WARNING We skip ${file} type processing"
667        continue
668      fi
669
670      DATE_LOOP=$( IGCM_date_AddDaysToGregorianDate ${DATE_LOOP} -${Length2} )
671
672      # Get selected files
673      IGCM_sys_Get /l liste_file[*] ${RUN_DIR_PATH}/${comp}
674      IGCM_debug_Verif_Exit
675
676      # Apply IGCM_Patch if needed
677      if [ ! X${RebuildFrequency} = Xtrue ] ; then
678        if [ X$( eval echo \${LISTE_PATCHES_${file}[0]} ) !=  X${NULL_STR} ]; then
679          for file_t in $( eval echo ${liste_file_tmp[*]} ); do
680            for Patch in $( eval echo \${LISTE_PATCHES_${file}[*]} ); do
681              IGCM_${Patch} ${file_t}
682              IGCM_debug_Verif_Exit
683            done
684          done
685        fi
686      fi
687
688      # WE CAN CONCATENATE FILES AT THIS POINT
689      [ "${FLAG_B}" = "TRUE" ] && DATE_BUILD_B=${DateBegin}_${DATE_FIN_JOB_B_LOOP_PREC}
690      Length=$( IGCM_date_DaysInPreviousPeriod ${DATE_COURANTE} ${config_UserChoices_PeriodLength} end)
691      DATE_BUILD1=$( IGCM_date_AddDaysToGregorianDate ${DATE_COURANTE} -$(( Length - 1 )) )
692      DATE_BUILD=${DATE_BUILD1}_${DATE_FIN}
693      DATE_BUILD_END=${DateBegin}_${DATE_FIN}
694
695      liste_coord=" "
696      for axis in $( eval echo \${LISTE_AXIS_${file}[*]} ); do
697        liste_coord=${liste_coord}${axis}","
698      done
699
700      # Time axis must be the last dimension
701      time_axis=${axis}
702
703      # SWITCH BETWEEN MODEL TO FIT PARTICULAR CASE
704      for var in $( eval echo \${LISTE_VARS_${file}[*]} ) ; do
705        #
706        # We skip variables not in the first file of the list.
707        # Seems overkill to test thel all... but will do if needed
708        ncdump -hv ${var} ${liste_file_tmp[0]} > /dev/null 2>&1
709        if [ ! $? = 0 ] ; then
710          IGCM_debug_Print 1 "WARNING We skip ${var}, not present within ${liste_file_tmp[0]}"
711          continue
712        fi
713        #
714        if [ "${FLAG_B}" = "TRUE" ] ; then
715          # WE CONCATENATE WITH EXISTING FILES
716          file1=${config_UserChoices_JobName}_${DATE_BUILD_B}_${FlagDir}_${var}.nc
717          file_out=${config_UserChoices_JobName}_${DATE_BUILD_END}_${FlagDir}_${var}.nc
718          IGCM_sys_ncrcat --hst -v ${liste_coord}${var} ${file1} ${liste_file_tmp[*]} ${file_out}
719          IGCM_debug_Verif_Exit
720          #
721          IGCM_sys_Rm ${file1}
722          if [ ! "${DEPOT}" = "TRUE" ] ; then
723            eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}}/Analyse/${TS_Dir}/${file_out}
724            # "${file1} = file_before ?
725            [ ! "${file1}" = "${config_UserChoices_JobName}_${DateBegin}_${DATE_FIN_JOB_B}_${FlagDir}_${var}.nc" ] && eval MENAGE \${R_OUT_${comp}}/Analyse/${TS_Dir} ${file1} ${file_out}
726          fi
727        else
728          # OR NOT
729          file_out=${config_UserChoices_JobName}_${DATE_BUILD}_${FlagDir}_${var}.nc
730          IGCM_sys_ncrcat --hst -v ${liste_coord}${var} ${liste_file_tmp[*]} ${file_out}
731          IGCM_debug_Verif_Exit
732        fi
733
734        #
735        if [ "${DEPOT}" = "TRUE" ] ; then
736          # YEARLY AVERAGE DERIVED FROM MONTHLY MEAN
737          if ( [ ${FlagDir} = "1M" ] && [ -f ${file_out} ] ) ; then
738            file_before_YE=${config_UserChoices_JobName}_${DateBegin}_${DATE_FIN_JOB_B}_1Y_${var}.nc
739            file_out_YE=${config_UserChoices_JobName}_${DATE_BUILD_END}_1Y_${var}.nc
740            #
741            # Compute yearly average considering calendar
742            IGCM_sys_cdo yearmonmean -selvar,${var} ${file_out} ${file_out_YE}
743            # Extract all ancillary variables except $var, they will be appended after the cdo command
744            # Needed because cdo applies calculs on all variables
745            IGCM_sys_ncks -Oh -x -v ${var} ${file_out} ${file_out_YE%%.nc}_tmp1.nc
746            # This will remove the time axis because cdo rewrites severely with only considered useful variables
747            IGCM_sys_cdo -mulc,1 ${file_out_YE%%.nc}_tmp1.nc ${file_out_YE%%.nc}_tmp2.nc 2>/dev/null
748            if [ $? -eq 0 ] ; then
749              # Now append all ancillary variables if previous cdo operator ok
750              IGCM_sys_ncks -h -A ${file_out_YE%%.nc}_tmp2.nc ${file_out_YE}
751            fi
752
753            # Put global history attribut
754            IGCM_sys_ncatted -Oh -a history,global,o,c,"build by libIGCM/create_ts" ${file_out_YE}
755            IGCM_debug_Verif_Exit
756            #
757            eval IGCM_sys_Put_Out ${file_out_YE} \${R_OUT_${comp}}/Analyse/TS_MO_YE/${file_out_YE}
758            [ "${FLAG_B}" = "TRUE" ] && eval MENAGE \${R_OUT_${comp}}/Analyse/TS_MO_YE/ ${file_before_YE} ${file_out_YE}
759            IGCM_sys_Rm ${file_out_YE%%.nc}_tmp*.nc
760          fi
761          # WE PUT FINAL FILE ON FILE SYSTEM
762          [ "${FLAG_B}" = "FALSE" ] && file_out=${config_UserChoices_JobName}_${DATE_BUILD}_${FlagDir}_${var}.nc
763          file_before=${config_UserChoices_JobName}_${DateBegin}_${DATE_FIN_JOB_B}_${FlagDir}_${var}.nc
764          #
765          eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}}/Analyse/${TS_Dir}/${file_out}
766          [ "${FLAG_B}" = "TRUE" ] && eval MENAGE \${R_OUT_${comp}}/Analyse/${TS_Dir} ${file_before} ${file_out}
767          if [ ! "X${file1}" = "X" ] ; then
768            [ ! "${file1}" = "${config_UserChoices_JobName}_${DateBegin}_${DATE_FIN_JOB_B}_${FlagDir}_${var}.nc" ] && eval MENAGE \${R_OUT_${comp}}/Analyse/${TS_Dir} ${file1} ${file_out}
769          fi
770          #
771          [ -f ${file_out} ] && IGCM_sys_Rm ${file_out}
772          #
773        fi
774        #
775      done                              # for var in ${liste_var} ; do
776      IGCM_sys_Rm ${liste_file_tmp[*]}
777    done                                # for file in ${liste_file_brut} do
778  done                                  # for comp in ${config_ListOfComponents[*]} ; do
779  # GO AHEAD IN DEEPEST LOOP
780  (( CURRENT_LOOP = CURRENT_LOOP + 1 ))
781done                                    # while [ ${CURRENT_LOOP} -le  ${NBRE_TOUR} ] do
782# FINISH
783
784# DODS copy
785for comp in ${config_ListOfComponents[*]} ; do
786  for TS_Dir in TS_YE TS_MO TS_MO_YE TS_DA TS_HF TS_INS ; do
787    IGCM_sys_TestDirArchive ${R_SAVE}/${comp}/Analyse/${TS_Dir}
788    [ $? = 0 ] && IGCM_sys_Put_Dods ${comp}/Analyse/${TS_Dir}
789  done
790done
791
792export DEBUG_debug; export BigBrother ; export libIGCM; export SUBMIT_DIR; export POST_DIR; export Script_Output ;
793export StandAlone ; export RESOL_ATM; export RESOL_OCE ; export RESOL_ICE ; export RESOL_MBG ; export RESOL_SRF ;
794export RESOL_SBG
795listVarEnv="DEBUG_debug,BigBrother,libIGCM,SUBMIT_DIR,POST_DIR,Script_Post_Output,StandAlone,RESOL_ATM,RESOL_OCE,RESOL_ICE,RESOL_MBG,RESOL_SRF,RESOL_SBG"
796export listVarEnv
797
798#D-
799# --------------------------------------------------------------------
800#D- Test if all was right
801# --------------------------------------------------------------------
802IGCM_debug_Verif_Exit
803# --------------------------------------------------------------------
804#D- Submit MONITORING
805# --------------------------------------------------------------------
806if ( [ X${TsTask} = X2D ] || [ X${TsTask} = X3D ] || [ X${TsTask} = X ] ) ; then
807  Script_Post_Output=monitoring.${PeriodDateEnd}
808  IGCM_sys_QsubPost monitoring
809fi
810
811#D-
812# --------------------------------------------------------------------
813#D- Update the run.card
814# --------------------------------------------------------------------
815if [ ${StandAlone} != true ] ; then
816  # Put in run.card end period of time series
817  [ X"${DATE_FIN}" = X ] || IGCM_sys_RshMaster IGCM_card_WriteOption ${SUBMIT_DIR}/run.card PostProcessing TimeSeriesCompleted "${DATE_FIN}"
818  # We have finish the job !
819  IGCM_sys_RshMaster IGCM_card_WriteOption ${SUBMIT_DIR}/run.card PostProcessing TimeSeriesRunning "n"
820fi
821
822# Clean RUN_DIR_PATH (necessary for cesium and titane only)
823IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
824
825# ------------------------------------------------------------------
826# Finalize BigBrother to inform that the jobs end
827# ------------------------------------------------------------------
828IGCM_debug_BigBro_Finalize
829
830date
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