source: trunk/libIGCM/AA_pack_output @ 640

Last change on this file since 640 was 640, checked in by mafoipsl, 12 years ago

Add norerun option on SX front-end. Transfer specific files ie config.card COMP ... with IGCM_sys_Get_Master and modify IGCM_sys_Get_Master to allow file transfer. tested on ulam and SX front-end.
  • Property svn:keywords set to Revision Author Date
File size: 15.2 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- sx8mercure #PBS -r n
87#-Q- sx9mercure #!/bin/ksh
88#-Q- sx9mercure ######################
89#-Q- sx9mercure ## SX9MERCURE  CCRT ##
90#-Q- sx9mercure ######################
91#-Q- sx9mercure #PBS -N PACKOUTPUT          # Nom du job
92#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr
93#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission
94#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
95#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures
96#-Q- sx9mercure #PBS -q scalaire
97#-Q- sx9mercure #PBS -r n
98#-Q- titane #!/bin/ksh
99#-Q- titane ######################
100#-Q- titane ## TITANE   CEA     ##
101#-Q- titane ######################
102#-Q- titane #MSUB -r PACKOUTPUT    # Nom du job
103#-Q- titane #MSUB -eo
104#-Q- titane #MSUB -n 1              # Reservation du processus
105#-Q- titane #MSUB -T 86400          # Limite de temps elapsed du job
106#-Q- titane #MSUB -q mono
107#-Q- lxiv8 ######################
108#-Q- lxiv8 ## OBELIX      LSCE ##
109#-Q- lxiv8 ######################
110#-Q- lxiv8 #PBS -N PACKOUTPUT
111#-Q- lxiv8 #PBS -m a
112#-Q- lxiv8 #PBS -j oe
113#-Q- lxiv8 #PBS -q medium
114#-Q- lxiv8 #PBS -o PACKOUTPUT.$$
115#-Q- lxiv8 #PBS -S /bin/ksh
116#-Q- default #!/bin/ksh
117#-Q- default ##################
118#-Q- default ## DEFAULT HOST ##
119#-Q- default ##################
120
121#**************************************************************
122# Author: Sebastien Denvil
123# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
124# $Revision::                                          $ Revision of last commit
125# $Author::                                            $ Author of last commit
126# $Date::                                              $ Date of last commit
127# IPSL (2006)
128#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
129#
130#**************************************************************
131
132#set -eu
133#set -vx
134
135date
136
137########################################################################
138
139#D- Flag to determine if this job in a standalone mode
140#D- Default : value from AA_job if any
141StandAlone=${StandAlone:=true}
142
143#D- Path to libIGCM
144#D- Default : value from AA_job if any
145# WARNING For StandAlone use : To run this script on some machine (ulam and cesium)
146# WARNING you must check MirrorlibIGCM variable in sys library.
147# WARNING If this variable is true, you must use libIGCM_POST path instead
148# WARNING of your running libIGCM directory.
149libIGCM=${libIGCM:=::modipsl::/libIGCM}
150
151#-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer.
152MASTER=${MASTER:=mercure|titane|brodie|vargas}
153
154#D- Flag to determine begin date for restart pack
155#D- Default : value from AA_job if any
156DateBegin=${DateBegin:=20000101}
157
158#D- Flag to determine end date for restart pack
159#D- Default : value from AA_job if any
160DateEnd=${DateEnd:=20691231}
161
162#D- Flag to determine pack period
163#D- Default : value from AA_job if any
164PeriodPack=${PeriodPack:=10Y}
165
166#D- Uncomment to run interactively
167#D- For testing purpose, will be remove
168#SUBMIT_DIR=${PWD}
169#RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test
170
171#D- Increased verbosity (1, 2, 3)
172#D- Default : value from AA_job if any
173Verbosity=${Verbosity:=3}
174
175#D- Low level debug : to bypass lib test checks and stack construction
176#D- Default : value from AA_job if any
177DEBUG_debug=${DEBUG_debug:=false}
178
179########################################################################
180
181. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
182( ${DEBUG_debug} ) && IGCM_debug_Check
183. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
184( ${DEBUG_debug} ) && IGCM_card_Check
185. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
186( ${DEBUG_debug} ) && IGCM_date_Check
187#-------
188. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
189. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
190
191########################################################################
192
193#set -vx
194
195RUN_DIR=${RUN_DIR_PATH}
196IGCM_sys_MkdirWork ${RUN_DIR}
197IGCM_sys_Cd ${RUN_DIR}
198
199# ------------------------------------------------------------------
200# Test if all was right before proceeding further
201# ------------------------------------------------------------------
202IGCM_debug_Verif_Exit_Post
203
204if [ ${StandAlone} = true ] ; then
205    CARD_DIR=${SUBMIT_DIR}
206else
207    CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
208    IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH}
209    IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card    ${RUN_DIR_PATH}
210    IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP        ${RUN_DIR_PATH}
211    IGCM_sys_Get_Master ${SUBMIT_DIR}/POST        ${RUN_DIR_PATH}
212fi
213
214#====================================================
215# First of all
216#
217# Read config.card
218
219IGCM_card_DefineArrayFromSection     ${CARD_DIR}/config.card UserChoices
220typeset option
221for option in ${config_UserChoices[*]} ; do
222  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
223done
224#
225echo
226IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices"
227IGCM_debug_PrintVariables 3 config_UserChoices_JobName
228IGCM_debug_PrintVariables 3 config_UserChoices_LongName
229IGCM_debug_PrintVariables 3 config_UserChoices_TagName
230IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
231IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
232IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
233IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
234IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
235IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
236echo
237
238# Get ListOfComponents to drive the loop over find
239IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents
240
241#====================================================
242#R_SAVE : Job output storage directory
243#R_BUFR : Job output buffered directory
244
245if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then
246  FreeName=$( echo ${config_UserChoices_JobName} | sed 's/.*_//' )
247  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
248  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
249else
250  R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
251  R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
252fi
253IGCM_sys_TestDirArchive ${R_SAVE}
254[ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive"
255
256# Where to store used file list /!\ TEMPORARY /!\
257STORE_DEBUG=${R_SAVE}/DEBUG
258
259# Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure)
260JobName=${config_UserChoices_JobName}
261echo $JobName $DateBegin $DateEnd
262
263# ------------------------------------------------------------------
264# Test if all was right before proceeding further
265# ------------------------------------------------------------------
266IGCM_debug_Verif_Exit_Post
267
268# Init loop
269date_begin_pack=${DateBegin}
270date_end_simulation=${DateEnd}
271number_pack=1
272
273IGCM_debug_PrintVariables 3 date_begin_pack
274IGCM_debug_PrintVariables 3 date_end_simulation
275
276while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do
277
278  IGCM_debug_PrintVariables 3 number_pack
279  DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} )
280  date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) )
281
282  for comp in ${config_ListOfComponents[*]} ; do
283    dirList=$( find ${R_BUFR}/${comp}/Output -maxdepth 1 -mindepth 1 -type d )
284    for dir in ${dirList} ; do
285      # dirID is like ATM.Output.MO
286      dirID=$( echo $dir | sed "s:${R_BUFR}/::" | sed "s:/:.:g" )
287      # Sort what's in the directory
288      find ${dir} -type f -name "${JobName}*.nc" -ls | sort -k 11 > liste_files.${dirID}.txt
289      # How much file type. Example : 1M_histmthCOSP.nc, 1M_histmth.nc, 1M_histmthNMC.nc, 1M_paramLMDZ_phy.nc
290      # /!\ fileType include the .nc extension /!\
291      fileType=$( 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 )
292      # Loop over the file type and pack them when in between date_begin_pack and date_end_pack
293      for myType in ${fileType} ; do
294        grep ${myType} liste_files.${dirID}.txt > liste_files.${dirID}.${myType}.txt
295        nbfile=0
296        for file in $( gawk '{print $11}' liste_files.${dirID}.${myType}.txt ); do
297          extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_[0-9]*_//" )
298          date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' )
299          # echo pack n°${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack}
300          if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then
301            echo ${file} >> liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt
302            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
303            (( nbfile = nbfile + 1 ))
304          fi
305        done
306        # Select list of variables to work with
307        list_var=$( cat liste_variables_${myType}_${date_begin_pack}_${date_end_pack}.txt | sort | uniq -c | awk -v nbfile=$nbfile '{if ($1 != nbfile) {print $2}}' | paste -s -d ',' )
308        liste_file_tmp=$( for i in $( cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ) ; do basename $i ; done )
309        # Create packed files
310        IGCM_debug_Print 1 "Ncrcat ongoing for ${dir} and ${myType}"
311        output=${JobName}_${date_begin_pack}_${date_end_pack}_${myType}
312        #cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs ncrcat -v ${list_var} -o ${output}
313        if [ X${list_var} = X ] ; then
314          IGCM_sys_ncrcat -p ${dir} ${liste_file_tmp} --output ${output}
315        else
316          IGCM_sys_ncrcat -x -v ${list_var} -p ${dir} ${liste_file_tmp} --output ${output}
317        fi
318        # ------------------------------------------------------------------
319        # Test if all was right before proceeding further
320        # ------------------------------------------------------------------
321        IGCM_debug_Verif_Exit_Post
322        # Save it
323        IGCM_sys_Put_Out ${output} ${R_SAVE}/$( echo $dir | sed "s:${R_BUFR}/::" )/${output}
324        # ------------------------------------------------------------------
325        # Test if all was right before proceeding further
326        # ------------------------------------------------------------------
327        IGCM_debug_Verif_Exit_Post
328        # Clean file produced by ncrcat
329        IGCM_sys_Rm ${output}
330        # Clean files used by ncrcat
331        cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs rm
332        # Save the list of files that has been pack (ncrcat)
333        #mv liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ${STORE_DEBUG}
334        IGCM_debug_Print 1 "Ncrcat and cleaning done for ${dir} and ${myType}"
335      done
336    done
337  done
338  (( number_pack = number_pack + 1 ))
339  # Add 1 day to date_end_pack to have the new date_begin_pack
340  date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 )
341done
342
343# Flush post-processing submission
344if [ -f ${R_BUFR}/FlushPost_${DateEnd}.ksh ] ; then
345  . ${R_BUFR}/FlushPost_${DateEnd}.ksh
346  IGCM_FlushPost
347  #IGCM_sys_Rm -f ${R_BUFR}/FlushPost_${DateEnd}.ksh
348fi
349
350# Clean RUN_DIR_PATH (necessary for cesium and titane only)
351IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
352
353date
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