source: trunk/libIGCM/AA_pack_output @ 628

Last change on this file since 628 was 628, checked in by sdipsl, 12 years ago
  • Depending on the user selected workflow, compute job or rebuild job or pack_output job will submit the post-processing.
  • Tests are ongoing (SX9 + Titane)
  • Property svn:keywords set to Revision Author Date
File size: 15.0 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- platine #!/usr/bin/ksh
19#-Q- platine ###################
20#-Q- platine ## PLATINE   CEA ##
21#-Q- platine ###################
22#-Q- platine #BSUB -J PACKOUTPUT            # Nom du job
23#-Q- platine #BSUB -N                        # message a la fin du job
24#-Q- platine #BSUB -n 1                      # reservation des processeurs pour le job
25#-Q- platine #BSUB -W 4:00                   # Limite temps
26#-Q- platine #BSUB -q post                   # Passage en queue post
27#-Q- platine #BSUB -L /bin/ksh
28#-Q- sx8brodie #!/bin/ksh
29#-Q- sx8brodie #######################
30#-Q- sx8brodie ## SX8BRODIE   IDRIS ##
31#-Q- sx8brodie #######################
32#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
33#-Q- sx8brodie # @ wall_clock_limit = 10:00:00
34#-Q- sx8brodie # Nom du travail LoadLeveler
35#-Q- sx8brodie # @ job_name   = PACKOUTPUT
36#-Q- sx8brodie # Fichier de sortie standard du travail
37#-Q- sx8brodie # @ output     = $(job_name).$(jobid)
38#-Q- sx8brodie # Fichier de sortie d'erreur du travail
39#-Q- sx8brodie # @ error      =  $(job_name).$(jobid)
40#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
41#-Q- sx8brodie # @ notification = error
42#-Q- sx8brodie # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
43#-Q- sx8brodie # @ queue
44#-Q- aix6 #!/bin/ksh
45#-Q- aix6 #######################
46#-Q- aix6 ##   VARGAS   IDRIS  ##
47#-Q- aix6 #######################
48#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
49#-Q- aix6 # @ wall_clock_limit = 10:00:00
50#-Q- aix6 # Nom du travail LoadLeveler
51#-Q- aix6 # @ job_name   = PACKOUTPUT
52#-Q- aix6 # Fichier de sortie standard du travail
53#-Q- aix6 # @ output     = $(job_name).$(jobid)
54#-Q- aix6 # Fichier de sortie d'erreur du travail
55#-Q- aix6 # @ error      =  $(job_name).$(jobid)
56#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
57#-Q- aix6 # @ notification = error
58#-Q- aix6 # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
59#-Q- aix6 # @ queue
60#-Q- ulam #!/bin/ksh
61#-Q- ulam #######################
62#-Q- ulam ##   VARGAS   IDRIS  ##
63#-Q- ulam #######################
64#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
65#-Q- ulam # @ wall_clock_limit = 10:00:00
66#-Q- ulam # Nom du travail LoadLeveler
67#-Q- ulam # @ job_name   = PACKOUTPUT
68#-Q- ulam # Fichier de sortie standard du travail
69#-Q- ulam # @ output     = $(job_name).$(jobid)
70#-Q- ulam # Fichier de sortie d'erreur du travail
71#-Q- ulam # @ error      =  $(job_name).$(jobid)
72#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
73#-Q- ulam # @ notification = error
74#-Q- ulam # @ environment  = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER
75#-Q- ulam # @ queue
76#-Q- sx8mercure #!/bin/ksh
77#-Q- sx8mercure ######################
78#-Q- sx8mercure ## SX8MERCURE   CEA ##
79#-Q- sx8mercure ######################
80#-Q- sx8mercure #PBS -N PACKOUTPUT          # Nom du job
81#-Q- sx8mercure #PBS -j o                    # regroupement des stdout et stderr
82#-Q- sx8mercure #PBS -S /usr/bin/ksh         # shell de soumission
83#-Q- sx8mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
84#-Q- sx8mercure #PBS -l cputim_job=24:00:00  # Limite temps a 1 heures
85#-Q- sx8mercure #PBS -q scalaire
86#-Q- sx9mercure #!/bin/ksh
87#-Q- sx9mercure ######################
88#-Q- sx9mercure ## SX9MERCURE  CCRT ##
89#-Q- sx9mercure ######################
90#-Q- sx9mercure #PBS -N PACKOUTPUT          # Nom du job
91#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr
92#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission
93#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
94#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures
95#-Q- sx9mercure #PBS -q scalaire
96#-Q- titane #!/bin/ksh
97#-Q- titane ######################
98#-Q- titane ## TITANE   CEA     ##
99#-Q- titane ######################
100#-Q- titane #MSUB -r PACKOUTPUT    # Nom du job
101#-Q- titane #MSUB -eo
102#-Q- titane #MSUB -n 1              # Reservation du processus
103#-Q- titane #MSUB -T 86400          # Limite de temps elapsed du job
104#-Q- titane #MSUB -q mono
105#-Q- lxiv8 ######################
106#-Q- lxiv8 ## OBELIX      LSCE ##
107#-Q- lxiv8 ######################
108#-Q- lxiv8 #PBS -N PACKOUTPUT
109#-Q- lxiv8 #PBS -m a
110#-Q- lxiv8 #PBS -j oe
111#-Q- lxiv8 #PBS -q medium
112#-Q- lxiv8 #PBS -o PACKOUTPUT.$$
113#-Q- lxiv8 #PBS -S /bin/ksh
114#-Q- default #!/bin/ksh
115#-Q- default ##################
116#-Q- default ## DEFAULT HOST ##
117#-Q- default ##################
118
119#**************************************************************
120# Author: Sebastien Denvil
121# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
122# $Revision::                                          $ Revision of last commit
123# $Author::                                            $ Author of last commit
124# $Date::                                              $ Date of last commit
125# IPSL (2006)
126#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
127#
128#**************************************************************
129
130#set -eu
131#set -vx
132
133date
134
135########################################################################
136
137#D- Flag to determine if this job in a standalone mode
138#D- Default : value from AA_job if any
139StandAlone=${StandAlone:=true}
140
141#D- Path to libIGCM
142#D- Default : value from AA_job if any
143# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
144# WARNING you must check MirrorlibIGCM variable in sys library.
145# WARNING If this variable is true, you must use libIGCM_POST path instead
146# WARNING of your running libIGCM directory.
147libIGCM=${libIGCM:=::modipsl::/libIGCM}
148
149#-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer.
150MASTER=${MASTER:=mercure|titane|brodie|vargas}
151
152#D- Flag to determine begin date for restart pack
153#D- Default : value from AA_job if any
154DateBegin=${DateBegin:=20000101}
155
156#D- Flag to determine end date for restart pack
157#D- Default : value from AA_job if any
158DateEnd=${DateEnd:=20691231}
159
160#D- Flag to determine pack period
161#D- Default : value from AA_job if any
162PeriodPack=${PeriodPack:=10Y}
163
164#D- Uncomment to run interactively
165#D- For testing purpose, will be remove
166#SUBMIT_DIR=${PWD}
167#RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test
168
169#D- Increased verbosity (1, 2, 3)
170#D- Default : value from AA_job if any
171Verbosity=${Verbosity:=3}
172
173#D- Low level debug : to bypass lib test checks and stack construction
174#D- Default : value from AA_job if any
175DEBUG_debug=${DEBUG_debug:=false}
176
177########################################################################
178
179. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
180( ${DEBUG_debug} ) && IGCM_debug_Check
181. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
182( ${DEBUG_debug} ) && IGCM_card_Check
183. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
184( ${DEBUG_debug} ) && IGCM_date_Check
185#-------
186. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
187. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
188
189########################################################################
190
191#set -vx
192
193RUN_DIR=${RUN_DIR_PATH}
194IGCM_sys_MkdirWork ${RUN_DIR}
195IGCM_sys_Cd ${RUN_DIR}
196
197# ------------------------------------------------------------------
198# Test if all was right before proceeding further
199# ------------------------------------------------------------------
200IGCM_debug_Verif_Exit_Post
201
202if [ ${StandAlone} = true ] ; then
203    CARD_DIR=${SUBMIT_DIR}
204else
205    CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
206    IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH}
207fi
208
209#====================================================
210# First of all
211#
212# Read config.card
213
214IGCM_card_DefineArrayFromSection     ${CARD_DIR}/config.card UserChoices
215typeset option
216for option in ${config_UserChoices[*]} ; do
217  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
218done
219#
220echo
221IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices"
222IGCM_debug_PrintVariables 3 config_UserChoices_JobName
223IGCM_debug_PrintVariables 3 config_UserChoices_LongName
224IGCM_debug_PrintVariables 3 config_UserChoices_TagName
225IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
226IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
227IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
228IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
229IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
230IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
231echo
232
233# Get ListOfComponents to drive the loop over find
234IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
235
236#====================================================
237#R_SAVE : Job output storage directory
238#R_BUFR : Job output buffered directory
239
240if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
241  FreeName=$( echo ${config_UserChoices_JobName} | sed 's/.*_//' )
242  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
243  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
244else
245  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
246  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
247fi
248IGCM_sys_TestDirArchive ${R_SAVE}
249[ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive"
250
251# Where to store used file list /!\ TEMPORARY /!\
252STORE_DEBUG=${R_SAVE}/DEBUG
253
254# Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure)
255JobName=${config_UserChoices_JobName}
256echo $JobName $DateBegin $DateEnd
257
258# ------------------------------------------------------------------
259# Test if all was right before proceeding further
260# ------------------------------------------------------------------
261IGCM_debug_Verif_Exit_Post
262
263# Init loop
264date_begin_pack=${DateBegin}
265date_end_simulation=${DateEnd}
266number_pack=1
267
268IGCM_debug_PrintVariables 3 date_begin_pack
269IGCM_debug_PrintVariables 3 date_end_simulation
270
271while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do
272
273  IGCM_debug_PrintVariables 3 number_pack
274  DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} )
275  date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) )
276
277  for comp in ${config_ListOfComponents[*]} ; do
278    dirList=$( find ${R_BUFR}/${comp}/Output -maxdepth 1 -mindepth 1 -type d )
279    for dir in ${dirList} ; do
280      # dirID is like ATM.Output.MO
281      dirID=$( echo $dir | sed "s:${R_BUFR}/::" | sed "s:/:.:g" )
282      # Sort what's in the directory
283      find ${dir} -type f -name "${JobName}*.nc" -ls | sort -k 11 > liste_files.${dirID}.txt
284      # How much file type. Example : 1M_histmthCOSP.nc, 1M_histmth.nc, 1M_histmthNMC.nc, 1M_paramLMDZ_phy.nc
285      # /!\ fileType include the .nc extension /!\
286      fileType=$( 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 )
287      # Loop over the file type and pack them when in between date_begin_pack and date_end_pack
288      for myType in ${fileType} ; do
289        grep ${myType} liste_files.${dirID}.txt > liste_files.${dirID}.${myType}.txt
290        nbfile=0
291        for file in $( gawk '{print $11}' liste_files.${dirID}.${myType}.txt ); do
292          extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_[0-9]*_//" )
293          date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' )
294          # echo pack n°${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack}
295          if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then
296            echo ${file} >> liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt
297            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
298            (( nbfile = nbfile + 1 ))
299          fi
300        done
301        # Select list of variables to work with
302        list_var=$( cat liste_variables_${myType}_${date_begin_pack}_${date_end_pack}.txt | sort | uniq -c | awk -v nbfile=$nbfile '{if ($1 != nbfile) {print $2}}' | paste -s -d ',' )
303        liste_file_tmp=$( for i in $( cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ) ; do basename $i ; done )
304        # Create packed files
305        IGCM_debug_Print 1 "Ncrcat ongoing for ${dir} and ${myType}"
306        output=${JobName}_${date_begin_pack}_${date_end_pack}_${myType}
307        #cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs ncrcat -v ${list_var} -o ${output}
308        if [ X${list_var} = X ] ; then
309          IGCM_sys_ncrcat -p ${dir} ${liste_file_tmp} --output ${output}
310        else
311          IGCM_sys_ncrcat -x -v ${list_var} -p ${dir} ${liste_file_tmp} --output ${output}
312        fi
313        # ------------------------------------------------------------------
314        # Test if all was right before proceeding further
315        # ------------------------------------------------------------------
316        IGCM_debug_Verif_Exit_Post
317        # Save it
318        IGCM_sys_Put_Out ${output} ${R_SAVE}/$( echo $dir | sed "s:${R_BUFR}/::" )/${output}
319        # ------------------------------------------------------------------
320        # Test if all was right before proceeding further
321        # ------------------------------------------------------------------
322        IGCM_debug_Verif_Exit_Post
323        # Clean file produced by ncrcat
324        IGCM_sys_Rm ${output}
325        # Clean files used by ncrcat
326        cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs rm
327        # Save the list of files that has been pack (ncrcat)
328        mv liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ${STORE_DEBUG}
329        IGCM_debug_Print 1 "Ncrcat and cleaning done for ${dir} and ${myType}"
330      done
331    done
332  done
333  (( number_pack = number_pack + 1 ))
334  # Add 1 day to date_end_pack to have the new date_begin_pack
335  date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 )
336done
337
338# Flush post-processing submission
339if [ -f ${R_BUFR}/FlushPost_${DateEnd}.ksh ] ; then
340  . ${R_BUFR}/FlushPost_${DateEnd}.ksh
341  IGCM_FlushPost
342  #IGCM_sys_Rm -f ${R_BUFR}/FlushPost_${DateEnd}.ksh
343fi
344
345# Clean RUN_DIR_PATH (necessary for cesium and titane only)
346IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
347
348date
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