source: TOOLS/EXTRAlibIGCM/AA_stomate_flux_correction @ 1836

Last change on this file since 1836 was 1500, checked in by mafoipsl, 13 years ago

Move AA_stomate_flux_correction into EXTRAlibIGCM directory.
  • Property svn:keywords set to Date Author Revision
File size: 16.3 KB
Line 
1#-Q- cesium #!/bin/ksh
2#-Q- cesium ######################
3#-Q- cesium ## CESIUM   CEA ##
4#-Q- cesium ######################
5#-Q- cesium #MSUB -r SBGcorr             # 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- platine #!/usr/bin/ksh
12#-Q- platine ###################
13#-Q- platine ## PLATINE   CEA ##
14#-Q- platine ###################
15#-Q- platine #BSUB -J SBGcorr                     # Nom du job
16#-Q- platine #BSUB -N                        # message a la fin du job
17#-Q- platine #BSUB -n 1                      # reservation des processeurs pour le job
18#-Q- platine #BSUB -W 1:00                   # Limite temps
19#-Q- platine #BSUB -q post                   # Passage en queue post
20#-Q- sx8brodie #!/bin/ksh
21#-Q- sx8brodie #######################
22#-Q- sx8brodie ## SX8BRODIE   IDRIS ##
23#-Q- sx8brodie #######################
24#-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss
25#-Q- sx8brodie # @ wall_clock_limit = 20:00:00
26#-Q- sx8brodie # Nom du travail LoadLeveler
27#-Q- sx8brodie # @ job_name   = SBGcorr
28#-Q- sx8brodie # Fichier de sortie standard du travail       
29#-Q- sx8brodie # @ output     = $(job_name).$(jobid)
30#-Q- sx8brodie # Fichier de sortie d'erreur du travail
31#-Q- sx8brodie # @ error      =  $(job_name).$(jobid)
32#-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
33#-Q- sx8brodie # @ notification = error
34#-Q- sx8brodie # @ environment  = $CURRENT_LOOP ; $imin ; $imax
35#-Q- sx8brodie # @ queue
36#-Q- aix6 #!/bin/ksh
37#-Q- aix6 #######################
38#-Q- aix6 ##   VARGAS   IDRIS  ##
39#-Q- aix6 #######################
40#-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss
41#-Q- aix6 # @ wall_clock_limit = 20:00:00
42#-Q- aix6 # Nom du travail LoadLeveler
43#-Q- aix6 # @ job_name   = SBGcorr
44#-Q- aix6 # Fichier de sortie standard du travail
45#-Q- aix6 # @ output     = $(job_name).$(jobid)
46#-Q- aix6 # Fichier de sortie d'erreur du travail
47#-Q- aix6 # @ error      =  $(job_name).$(jobid)
48#-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
49#-Q- aix6 # @ notification = error
50#-Q- aix6 # @ environment  = $CURRENT_LOOP ; $imin ; $imax
51#-Q- aix6 # @ queue
52#-Q- ulam #!/bin/ksh
53#-Q- ulam #######################
54#-Q- ulam ##   ULAM   IDRIS  ##
55#-Q- ulam #######################
56#-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss
57#-Q- ulam # @ wall_clock_limit = 20:00:00
58#-Q- ulam # Nom du travail LoadLeveler
59#-Q- ulam # @ job_name   = SBGcorr
60#-Q- ulam # Fichier de sortie standard du travail
61#-Q- ulam # @ output     = $(job_name).$(jobid)
62#-Q- ulam # Fichier de sortie d'erreur du travail
63#-Q- ulam # @ error      =  $(job_name).$(jobid)
64#-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.)
65#-Q- ulam # @ notification = error
66#-Q- ulam # @ environment  = $CURRENT_LOOP ; $imin ; $imax
67#-Q- ulam # @ queue
68#-Q- sx8mercure ######################
69#-Q- sx8mercure ## SX8MERCURE   CEA ##
70#-Q- sx8mercure ######################
71#-Q- sx8mercure #PBS -N SBGcorr                   # Nom du job
72#-Q- sx8mercure #PBS -j o                    # regroupement des stdout et stderr
73#-Q- sx8mercure #PBS -S /usr/bin/ksh         # shell de soumission
74#-Q- sx8mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go
75#-Q- sx8mercure #PBS -l cputim_job=24:00:00   # Limite temps a 2 heures
76#-Q- sx8mercure #PBS -q scalaire
77#-Q- sx9mercure #!/bin/ksh
78#-Q- sx9mercure #########################
79#-Q- sx9mercure ## CESIUM FOR SX9  CEA ##
80#-Q- sx9mercure #########################
81#-Q- sx9mercure #MSUB -r SBGcorr             # Nom du job               
82#-Q- sx9mercure #MSUB -N 1              # Reservation du noeud
83#-Q- sx9mercure #MSUB -n 1              # Reservation du processus
84#-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job
85#-Q- sx9mercure #MSUB -E "-j o"
86#-Q- sx9mercure #MSUB -E "-S /bin/ksh"
87#-Q- titane #!/bin/ksh
88#-Q- titane ######################
89#-Q- titane ## TITANE   CEA ##
90#-Q- titane ######################
91#-Q- titane #MSUB -r SBGcorr             # Nom du job               
92#-Q- titane #MSUB -N 1              # Reservation du noeud
93#-Q- titane #MSUB -n 1              # Reservation du processus
94#-Q- titane #MSUB -T 86400          # Limite de temps elapsed du job
95#-Q- titane #MSUB -E "-j o"
96#-Q- titane #MSUB -E "-S /bin/ksh"
97#-Q- lxiv8 ######################
98#-Q- lxiv8 ## OBELIX      LSCE ##
99#-Q- lxiv8 ######################
100#-Q- lxiv8 #PBS -N SBGcorr
101#-Q- lxiv8 #PBS -m a
102#-Q- lxiv8 #PBS -j oe
103#-Q- lxiv8 #PBS -q medium
104#-Q- lxiv8 #PBS -o SBGcorr.$$
105#-Q- lxiv8 #PBS -S /bin/ksh
106#-Q- default #!/bin/ksh
107#-Q- default ##################
108#-Q- default ## DEFAULT HOST ##
109#-Q- default ##################
110
111#**************************************************************
112# Author: Martial Mancip
113# Contact: Martial.Mancip__at__ipsl.jussieu.fr
114# $Revision::                                          $ Revision of last commit
115# $Author::                                            $ Author of last commit
116# $Date::                                              $ Date of last commit
117# IPSL (2006)
118#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
119#
120#**************************************************************
121
122
123#**************************************************************
124# usage :
125#
126#  This script is only used for correction of stomate_ipcc_history files created
127# with orchidee_1_9_5 version of ORCHIDEE model checkouted before 05/08/10 :   
128# Version of ORCHIDEE/src_stomate/stomate_lpj.f90 before CVS 1.26 had a bug
129# that give a wrong Land Cover Change (fLuc) variable and a wrong nbp balance variable.
130# This file will correct all those IPCC CMIP5 history files in a simulation.
131# You must read 'Documentation' paragraph below to parameter the chain of jobs for
132# specific schedulers.
133#
134# To protect IPCC history files if this script crash, we first move original files
135# in SAVE_${loopmmin} directories.
136# YOU have to destroy them by hand after corrected all your run.
137#
138# This script must only be used in a libIGCM directory
139#     (but submit from a CONFIG directory).
140#
141# Default parameters in this job are given for mercure CCRT X64 frontend. 
142#
143#**************************************************************
144
145
146
147
148date
149
150#-Q- sx8brodie export OMP_NUM_THREADS=1
151#-Q- aix6 export OMP_NUM_THREADS=1
152#-Q- ulam export OMP_NUM_THREADS=1
153
154########################################################################
155
156#D- Low level debug : to bypass lib test checks and stack construction
157#D- Default : value from AA_job if any
158libIGCM=${libIGCM:=::modipsl::/libIGCM}
159# WARNING for StandAlone used : To run this script on some machine,
160# you must check MirrorlibIGCM variable in sys library.
161# If this variable is true, you must use libIGCM_POST path instead
162# of your running libIGCM directory.
163
164
165#D- Flag to determine job's output directory
166#D- Default : value from libIGCM_post.ksh if any
167POST_DIR=${POST_DIR:=${PBS_O_WORKDIR:=$(pwd)}}
168
169#D- Increased verbosity (1, 2, 3)
170#D- Default : value from AA_job if any
171Verbosity=${Verbosity:=3}
172
173#D- Experience type : DEB(ug), DEV(elopment), RUN (default)
174JobType=RUN
175
176
177### Documentation :
178##      1) To start again this script in StandAlone mode
179##         (because it fails with a problem with the system or a timeout, for example),
180##         you must check the initialisation of three variables after the "Start loop" line :
181##    CURRENT_LOOP=${CURRENT_LOOP:=1} give the iteration to begin the main loop
182##    imin=${imin:=0}                 give the corresponding min index in the list of stomate_history files
183##    imax=${imax:=${NbFilesLOOP}}    give the corresponding max index in the list of stomate_history files
184##         nb: the main loop is parametered by UNIX_MAX_LIMIT (in system library) value.
185##    imax is a factor of NbFilesLOOP = UNIX_MAX_LIMIT / 2 value
186##    imin is the previous imax (see previous output of the script if exist)
187##      2) This script will re-submit itself automaticly after calculate the next values of those three variables.
188
189##   To prevent timeout because of a large number of files (long simulation) and maximum elapse time
190## in the PBS queue, you must give the correct value of next line LOOP_MAX variable.
191## It gives the maximum of iterations of the MAIN LOOP during the elapse time required in the PBS.
192LOOP_MAX=15
193#
194## For example: if UNIX_MAX_LIMIT=360 and the number of stomate_history for a run if 3800,
195##              the number of files that has to be demigrated if 7600 (stomate_history + stomate_ipcc_history).
196##              The NBRE_TOUR (see previous output) calculate is 22.
197##              If the elasped time required is 24H (86400s) and each 10 years (120x2 = 240 files) take one hour,
198##              you must give LOOP_MAX= 240 * 24 / 360 = 16 max.
199##              To prevent system slow, the default value is 15.
200
201
202########################################################################
203
204. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
205      ( ${DEBUG_debug} ) && IGCM_debug_Check
206. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
207     ( ${DEBUG_debug} ) && IGCM_card_Check
208. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
209     ( ${DEBUG_debug} ) && IGCM_date_Check
210#-------
211. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
212
213########################################################################
214
215#set -vx
216
217IGCM_sys_MkdirWork ${RUN_DIR_PATH}
218IGCM_sys_Cd ${RUN_DIR_PATH}
219
220
221#
222# First of all
223#
224IGCM_card_DefineArrayFromSection       ${SUBMIT_DIR}/config.card UserChoices
225typeset option
226for option in ${config_UserChoices[*]} ; do
227    IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card UserChoices ${option}
228done
229#
230echo
231IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices"
232IGCM_debug_PrintVariables 3 config_UserChoices_JobName
233IGCM_debug_PrintVariables 3 config_UserChoices_LongName
234IGCM_debug_PrintVariables 3 config_UserChoices_TagName
235IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName
236IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName
237IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
238IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
239IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
240IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
241echo
242
243#==================================
244#R_SAVE : Job output directory
245if ( [ ! X${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_DODS=${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}
249else
250    R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName}
251    R_DODS=${config_UserChoices_TagName}/${config_UserChoices_JobName}
252fi
253
254
255########################################################################
256#
257#                          DEFINE LOOP PARAMETERS
258#
259########################################################################
260
261R_OUT_SBG=${R_SAVE}/SBG
262file_path=${R_OUT_SBG}/Output/MO
263
264set +A LISTE_FILE_SBG -- $( IGCM_sys_RshArchive "find ${file_path} -name \"*stomate_history.nc\" " )
265CountLISTE_FILE_SBG=${#LISTE_FILE_SBG[@]}
266echo "Nombre de stomate_history : " ${CountLISTE_FILE_SBG}
267
268NBRE_FILE_TOT=$(( 2 * CountLISTE_FILE_SBG ))
269echo "Nombre de fichiers à démigrer : " ${NBRE_FILE_TOT}
270
271if [ ${NBRE_FILE_TOT} -le ${UNIX_MAX_LIMIT} ] ; then
272    NBRE_TOUR=1
273    NbFilesLOOP=${CountLISTE_FILE_SBG}
274elif [ ${NBRE_FILE_TOT}%${UNIX_MAX_LIMIT} -eq 0 ] ; then
275    (( NBRE_TOUR = NBRE_FILE_TOT / UNIX_MAX_LIMIT ))
276    (( NbFilesLOOP = UNIX_MAX_LIMIT / 2 ))
277else
278    (( NBRE_TOUR = NBRE_FILE_TOT / UNIX_MAX_LIMIT + 1 ))
279    (( NbFilesLOOP = UNIX_MAX_LIMIT / 2 ))
280fi
281echo "NBRE_TOUR = ${NBRE_TOUR} "
282echo "NbFilesLOOP = ${NbFilesLOOP} "
283
284########################################################################
285#
286#                          START THE MAIN LOOP
287#
288########################################################################
289
290# PARAMETERS OF THE LOOP :
291# Cumultate CURRENT LOOP number over submitions
292CURRENT_LOOP=${CURRENT_LOOP:=1}
293# min index for list of local files
294imin=${imin:=0}
295# max index for list of local files
296imax=${imax:=${NbFilesLOOP}}
297
298# DEPEND OF THE ELAPSED TIME RESERVED FOR LOOP_MAX ITERATIONS
299LOOP_MAX=${LOOP_MAX:=NBRE_TOUR}
300
301IGCM_debug_Verif_Exit_Post
302
303# MAIN LOOP
304# LOCAL CURRENT LOOP number less than LOOP_MAX
305CURRENT_LOOP0=1
306while [ ${CURRENT_LOOP} -le ${NBRE_TOUR} ] ; do
307
308    echo "###############################################################"
309    echo "CURRENT_LOOP : " ${CURRENT_LOOP}
310    echo "imin/imax : " $imin " / " $imax
311   
312    unset liste_file
313    unset liste_file_local
314    unset liste_file_ipcc
315    unset liste_file_ipcc_local
316   
317    (( i = imin ))
318    while [ ${i} -lt ${imax} ] ; do
319        file=${LISTE_FILE_SBG[${i}]}
320        file_ipcc=$( echo ${file} | sed -e "s/stomate_history/stomate_ipcc_history/" )
321
322        liste_file[${#liste_file[*]}]=${file}
323        liste_file_local[${#liste_file_local[*]}]=$( basename ${file} )
324        RET=$?
325        if [ ${RET} -gt 0 ] ; then
326            echo "erreur basename liste_file_local " ${file}
327            echo "file = " ${file}
328            exit 1
329        fi
330        liste_file[${#liste_file[*]}]=${file_ipcc}
331
332        liste_file_ipcc[${#liste_file_ipcc[*]}]=${file_ipcc}
333        liste_file_ipcc_local[${#liste_file_ipcc_local[*]}]=$( basename ${file_ipcc} )
334        RET=$?
335        if [ ${RET} -gt 0 ] ; then
336            echo "erreur basename liste_file_ipcc_local " ${file_ipcc}
337            echo "file = " ${file_ipcc}
338            exit 3
339        fi
340
341        (( i = i + 1 ))
342    done
343    #echo ${liste_file_local[@]}
344    #echo ${liste_file[@]}
345
346    # Get selected files
347    IGCM_sys_Get /l liste_file[*] ${RUN_DIR_PATH}
348    IGCM_debug_Verif_Exit_Post
349
350    # chmod sur dépÃŽt
351    IGCM_sys_RshArchive "mkdir ${file_path}/SAVE_${imin}"
352    IGCM_sys_RshArchive "mv ${liste_file_ipcc[@]} ${file_path}/SAVE_${imin}"
353
354    # Faire le nco/ncap2
355    (( i = imin ))
356    while [ ${i} -lt ${imax} ] ; do
357        file=$( basename ${LISTE_FILE_SBG[${i}]} )
358        RET=$?
359        if [ ${RET} -gt 0 ] ; then
360            echo "erreur basename"
361            echo "i, imin, imax = " i imin imax
362            echo "file = " ${file}
363            exit 4
364        fi
365        file_ipcc=$( echo ${file} | sed -e "s/stomate_history/stomate_ipcc_history/" )
366        ls -la ${file_ipcc}
367
368        IGCM_sys_ncks -a -A -x -v GPP ${file} stomate.nc
369        IGCM_sys_ncks -a -A ${file_ipcc} stomate.nc
370
371        IGCM_sys_Cp ${file_ipcc} _${file_ipcc}
372        IGCM_sys_Chmod u+w _${file_ipcc}
373
374        IGCM_sys_ncap2 -s 'fLuc=float(fLuc*0.+(CONVFLUX+CFLUX_PROD10+CFLUX_PROD100)/1e3/86400*CONTFRAC)' \
375                       -s 'nbp=float(nbp*0.f+(gpp-ra-rh-fFire-fLuc-fHarvest))' -v stomate.nc stomate1.nc
376        IGCM_debug_Verif_Exit_Post
377
378        IGCM_sys_ncks -a -A stomate1.nc _${file_ipcc}
379        IGCM_sys_Mv -f _${file_ipcc} ${file_ipcc}
380        IGCM_sys_Chmod u-w ${file_ipcc}
381
382        ls -la ${file_ipcc}
383        IGCM_sys_Rm stomate.nc stomate1.nc
384        IGCM_debug_Verif_Exit_Post
385
386        # Put_Out des fichiers ipcc corrigés
387        IGCM_sys_Put_Out ${file_ipcc} ${file_path}/${file_ipcc}
388
389        (( i = i + 1 ))
390    done
391
392    # Nettoyage
393    IGCM_sys_Rm ${liste_file_local[*]}
394
395
396    # GO AHEAD IN DEEPEST LOOP
397    (( imin = imax ))
398    (( CURRENT_LOOP = CURRENT_LOOP + 1 ))
399    (( CURRENT_LOOP0 = CURRENT_LOOP0 + 1 ))
400    if [ ${CURRENT_LOOP} -lt ${NBRE_TOUR} ] ; then
401        (( imax = imax + ${NbFilesLOOP} ))
402    else
403        if [ ${CURRENT_LOOP} -eq ${NBRE_TOUR} ] ; then
404            echo "Last loop : "
405            if [ ${NBRE_FILE_TOT}%${UNIX_MAX_LIMIT} -eq 0 ] ; then
406                (( imax = imax + ${NbFilesLOOP} ))
407            else
408                (( imax = imax + ( NBRE_FILE_TOT % UNIX_MAX_LIMIT ) / 2 ))
409            fi
410        fi
411    fi
412    echo "imin NEW = " ${imin}
413    echo "imax NEW = " ${imax}
414    echo "CURRENT_LOOP = " ${CURRENT_LOOP}
415
416    if ( [ ${CURRENT_LOOP} -le ${NBRE_TOUR} ] && \
417         [ ${CURRENT_LOOP0} -gt ${LOOP_MAX} ] ) ; then
418        export CURRENT_LOOP
419        export imin
420        export imax
421        IGCM_sys_Cd ${SUBMIT_DIR}
422        Script_Post_Output=SBGcorr.${imin}.${imax}
423        listVarEnv="CURRENT_LOOP,imin,imax"
424        echo "Submit next job."
425        IGCM_sys_QsubPost stomate_flux_correction
426        break ;
427    fi
428done                 # while [ ${CURRENT_LOOP} -le  ${LOOP_MAX} ] do
429# FINISH
430
431
432#D-
433# --------------------------------------------------------------------
434#D- Test if all was right
435# --------------------------------------------------------------------
436IGCM_debug_Verif_Exit_Post
437
438# Clean RUN_DIR_PATH (necessary for cesium)
439IGCM_sys_Cd ${SUBMIT_DIR}
440IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}
441
442date
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