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lance_batch.ksh in tags/nemo_v3_2/nemo_v3_2/NVTK/INSTALL/JOBS – NEMO

source: tags/nemo_v3_2/nemo_v3_2/NVTK/INSTALL/JOBS/lance_batch.ksh @ 1878

Last change on this file since 1878 was 1878, checked in by flavoni, 14 years ago

initial test for nemogcm
File size: 11.6 KB
Line 
1#!/bin/ksh
2# $Id: lance_batch.ksh 1576 2009-08-04 13:56:13Z ctlod $
3######################################################
4# Original : C. Talandier for NEMO team
5# Contact  : nemo_st@locean-ipsl.upmc.fr
6#
7# INPUT ARGS: 9
8#     - CONF  : configuration name (ORCA2_LIM, GYRE ..)
9#     - MTIME : timing/no timing (timing or notiming)
10#     - JOBTOL: jobs to launch: all, long, 1_short or gtime
11#     - OWNEXP: name of the experience performed
12#     - PRC   : total number of processors
13#     - REFTAG: reference tag name to be compare to
14#     - USE_IOMPUT: true of false (default false)
15#     - USE_IOSERVER: true of false (default false)
16#     - NB_PROCS_IOSERVER: (default 0)
17#
18# WORK: This script aims to (for each standard configuration) :
19#
20#    I.   Take into account target's specificities
21#         Variables below must be filled for a new target
22#         - W_XX   = name of target
23#         - LAUN   = name of jobs launcher command
24#         - LLJOBS = name of jobs listing command
25#         - LSUB   = name of running command
26#         - LPERF  = name of timing command for the whole run
27#         - LJTIM  = required time for a one year run (/proc)
28#         - LJTIMJ = required time for a one year run (job)
29#         - CMDGET = name of specific command to retrieve files
30#         - SYMBOL = identifier associated to a platform which
31#                    is used to name all outputs files
32#                    Ex: For Brodie, this symbol could be "B_" so
33#                    file names looks like B_solver.stat ...
34#
35#    II.  Build jobs
36#         - based on specific header depending on target, it must
37#           be provided for a new target following samples
38#           jhd_[target_name]_mon for mono-processors runs
39#           jhd_[target_name]_mpi for multi-processors MPI runs
40#           jhd_[target_name]_omp for multi-processors OPen-MP runs
41#
42#    III. Launch jobs
43#         to test both reproductibility and restartability
44#         for each configuration NAME_CONF
45#         & for each run type [mon, mpi, omp]
46#         3 runs will be launched:
47#              - LONG
48#              - 1_SHORT
49#              - 2_SHORT
50#
51#    IV. Launch cron job
52#         Since no jobs (for a given configuration) are in
53#         the batch queue, this cron will launch the assessment.ksh
54#         script
55#
56##########################################################
57#set -xv
58##########################################################
59##### Begin Users modifications
60##########################################################
61# IODIR     : directory where to get ORCA2_LIM_nemo_v3.1.tar
62##########################################################
63IODIR=/u/rech/eee/reee512/NEMO/
64TARGET=sx8brodie
65##########################################################
66##### End   Users modifications
67##########################################################
68
69CONF=$1
70MTIME=$2
71JOBTOL=$3
72OWNEXP=$4
73PRC=$5
74REFTAG=$6
75USE_IOMPUT=${7:-false}
76USE_IOSERVER=${8:-false}
77NB_PROCS_IOSERVER=${9:-0}
78[ "${USE_IOMPUT}" = "false" ] && USE_IOSERVER=false
79[ "${USE_IOSERVER}" = "false" ] && NB_PROCS_IOSERVER=0
80RUN=$(basename `pwd`)
81[ "${RUN}" = "mon" ] && PRC=1
82if [[ ( "${TARGET}" = "sx8brodie" ) || ( "${TARGET}" = "sx8mercure" ) ]]
83then
84    if [ $(( ${PRC} + ${NB_PROCS_IOSERVER} )) -gt 8 ]
85    then
86   echo NVTK is not made to use more than 1 node on SX8 machines...
87   echo please, reduce the number of cpu used by NEMO or/and the ioserver
88   exit 1
89    fi
90fi
91# ---------------------------------------------------------------
92#  I. Take into account target's specificities
93#     Select appropriate target lines in Job_${CONF}.ksh
94# ---------------------------------------------------------------
95if   [ ${TARGET} = 'sx8brodie' ]; then
96    W_XX='#-T- sx8brodie'
97    LAUN='qsub '
98    LLJOBS=qstat
99    LSUB="mpirun -np ${PRC}"
100    LPERF=
101    LJTIM='01:20:00'
102    LJTIMJ='01:40:00'
103    CMDGET=mfget
104    SYMBOL=B_
105elif [ ${TARGET} = 'sx8mercure' ]; then
106    W_XX='#-T- sx8mercure'
107    LAUN='qsub '
108    LLJOBS=qstat
109    LSUB="mpirun -np ${PRC}"
110    LPERF=
111    LJTIM='01:20:00'
112    LJTIMJ='01:40:00'
113    CMDGET=cp
114    SYMBOL=M_
115elif [ ${TARGET} = 'aix6' ]; then
116    W_XX='#-T- aix6'
117    LAUN='llsubmit '
118    LLJOBS=Qstat
119    LSUB=
120    LPERF="poe hpmcount -o perfs_mpi.txt" 
121    LJTIM='01:10:00'
122    LJTIMJ=
123    CMDGET=mfget
124    SYMBOL=V_
125elif [ ${TARGET} = 'osxxlf' ]; then
126    W_XX='#-T- osxxlf'
127    LAUN='./'
128    LLJOBS=
129    LSUB="mpirun -np ${PRC}"
130    LPERF=
131    LJTIM=
132    LJTIMJ=
133    CMDGET=cp
134    SYMBOL=D_
135else
136    echo '  #######################################'
137    echo '  You must give a target name :'
138    echo '  sx8brodie, aix6 or add one'
139    echo '  Have a look in lance_batch.ksh script'
140    echo '  #######################################'
141    stop
142fi
143
144sed -e "s%^$W_XX *%%" job_${CONF}.ksh | grep -v '^#-T- ' > job_${CONF}.$$
145
146# --------------------------------------------------------------
147# II. Build jobs
148#     Adapt header (batch jobs) and concatanate it with core job
149# --------------------------------------------------------------
150if [ ${CONF} == 'ORCA2_LIM' ] ; then
151    CONFS=ORCA2
152elif [ ${CONF} == 'ORCA2_LIM3' ] ; then
153    CONFS=OR2L3
154elif [ ${CONF} == 'GYRE' ] ; then
155    CONFS=GYREO
156elif [ ${CONF} == 'GYRE_LOBSTER' ] ; then
157    CONFS=GYREL
158elif [ ${CONF} == 'ORCA2_LIM_PISCES' ] ; then
159    CONFS=OR2LP
160elif [ ${CONF} == 'ORCA2_OFF_PISCES' ] ; then
161    CONFS=OR2OP
162elif [ ${CONF} == 'ZAGRIF' ] ; then
163    CONFS=ZAGRI
164else
165    CONFS=${CONF}
166fi
167
168case ${TARGET} in
169    'osxxlf' )
170   cp jhd_${TARGET}_${RUN} jhd_${TARGET}_${RUN}_tmp  ;;
171    'aix6' )
172   CAR_JNAM=$( grep '\# @ job_name' jhd_${TARGET}_${RUN} )
173   CAR_JMPI=$( grep '\# @ total_tasks' jhd_${TARGET}_${RUN} )
174   sed -e "s%$CAR_JNAM%\# @ job_name = ${RUN}${CONFS}%" \
175       -e "s%$CAR_JMPI%\# @ total_tasks = $(( ${PRC} + ${NB_PROCS_IOSERVER} ))%" \
176       jhd_${TARGET}_${RUN} > jhd_${TARGET}_${RUN}_tmp  ;;
177    'sx8brodie' )
178   CAR_JNAM=$( grep '\#PBS -N ' jhd_${TARGET}_${RUN} )
179   CAR_JNAMO=$( grep '\#PBS -o ' jhd_${TARGET}_${RUN} )
180   CAR_JNAME=$( grep '\#PBS -e ' jhd_${TARGET}_${RUN} )
181   if [ ${RUN} = 'mpi' -o ${RUN} = 'omp' ] ; then
182       CAR_JMPI=$( grep '\#PBS -l cpunum_job' jhd_${TARGET}_${RUN} )
183       sed -e "s%$CAR_JNAM%\#PBS -N  ${RUN}${CONFS}%" \
184      -e "s%$CAR_JNAMO%\#PBS -o  ${RUN}${CONFS}_std%" \
185      -e "s%$CAR_JNAME%\#PBS -e  ${RUN}${CONFS}_err%" \
186      -e "s%$CAR_JMPI%\#PBS -l cpunum_job=$(( ${PRC} + ${NB_PROCS_IOSERVER} ))%" \
187      jhd_${TARGET}_${RUN} > jhd_${TARGET}_${RUN}_tmp
188   else
189       sed -e "s%$CAR_JNAM%\#PBS -N  ${RUN}${CONFS}%" \
190      -e "s%$CAR_JNAMO%\#PBS -o  ${RUN}${CONFS}_std%" \
191      -e "s%$CAR_JNAME%\#PBS -e  ${RUN}${CONFS}_err%" \
192      jhd_${TARGET}_${RUN} > jhd_${TARGET}_${RUN}_tmp
193   fi ;;
194    'sx8mercure' )
195   CAR_JNAM=$( grep '\#PBS -N ' jhd_${TARGET}_${RUN} )
196   CAR_JNAMO=$( grep '\#PBS -o ' jhd_${TARGET}_${RUN} )
197   CAR_JNAME=$( grep '\#PBS -e ' jhd_${TARGET}_${RUN} )
198   if [ ${RUN} = 'mpi' -o ${RUN} = 'omp' ] ; then
199       CAR_JMPI=$( grep '\#PBS -l cpunum_job' jhd_${TARGET}_${RUN} )
200       sed -e "s%$CAR_JNAM%\#PBS -N  ${RUN}${CONFS}%" \
201      -e "s%$CAR_JNAMO%\#PBS -o  ${RUN}${CONFS}_std%" \
202      -e "s%$CAR_JNAME%\#PBS -e  ${RUN}${CONFS}_err%" \
203      -e "s%$CAR_JMPI%\#PBS -l cpunum_job=$(( ${PRC} + ${NB_PROCS_IOSERVER} ))%" \
204      jhd_${TARGET}_${RUN} > jhd_${TARGET}_${RUN}_tmp
205   else
206       sed -e "s%$CAR_JNAM%\#PBS -N  ${RUN}${CONFS}%" \
207      -e "s%$CAR_JNAMO%\#PBS -o  ${RUN}${CONFS}_std%" \
208      -e "s%$CAR_JNAME%\#PBS -e  ${RUN}${CONFS}_err%" \
209      jhd_${TARGET}_${RUN} > jhd_${TARGET}_${RUN}_tmp
210   fi ;;
211esac
212
213cat jhd_${TARGET}_${RUN}_tmp job_${CONF}.$$ > job_tmp_${RUN}.ksh
214rm -f job_${CONF}.$$ jhd_${TARGET}_${RUN}_tmp
215
216# -----------------------------------------------------------------------------
217# III. Launch jobs
218#      The 3 following jobs are created for the run [type]=mon,mpi,omp :
219#      - "job_[type]_long.ksh"      ---> long run
220#      - "job_[type]_1_short.ksh"   ---> stream 1 run
221#      - "job_[type]_2_short.ksh"   ---> stream 2 run
222#      - "job_[type]_gtime.ksh"     ---> one year run
223#      The first 2 as the last one are immediatly launched whereas "job_[type]_2_short.ksh"
224#      is launched only when the "job_[type]_1_short.ksh" short run is finished
225# -----------------------------------------------------------------------------
226jobnam[0]=long ; jobnam[1]=1_short ; jobnam[2]=2_short ; jobnam[3]=gtime
227dirjob[0]=LONG ; dirjob[1]=1_SHORT ; dirjob[2]=2_SHORT ; dirjob[3]=GTIME
228
229case ${JOBTOL} in
230    'all' )
231   if [ ${MTIME} = 'timing' ] ; then
232       ind=0
233       iloop=4
234   else
235       ind=0
236       iloop=3
237   fi 
238   ;;
239    'long' )
240   ind=0
241   iloop=1 ;;
242    'short' )
243   ind=1
244   iloop=3 ;;
245    'gtime' )
246   ind=3
247   iloop=4 ;;
248esac
249
250chwd () { 
251    word=$( grep "^ *${1}" job_tmp_${RUN}.ksh | cut -f 1 -d " " )
252    if [ "${word}" != "" ] 
253   then
254   sed -e "s@${word}@${1%=*}=\"${2}\"@" job_tmp_${RUN}.ksh > tmp$$
255   mv tmp$$ job_tmp_${RUN}.ksh
256    fi
257}
258
259chwd "RUN=xxx"              "${RUN}"
260chwd "NB_PROCS=xxx"          ${PRC}
261chwd "LAUNCH=xxx"           "${LAUN}"
262chwd "LEXE=xxx"             "${LSUB}"
263chwd "CPERF=xxx"            "${LPERF}"
264chwd "D_INPUT=xxx"          "${IODIR}"
265chwd "D_GET=xxx"            "${CMDGET}"
266chwd "REF_TAG=xxx"          "${REFTAG}" 
267chwd "MYO_EXP=xxx"          "${OWNEXP}"
268chwd "TSYMB=xxx"            "${SYMBOL}"
269chwd "USE_IOMPUT=xxx"        ${USE_IOMPUT}
270chwd "USE_IOSERVER=xxx"      ${USE_IOSERVER}
271chwd "NB_PROCS_IOSERVER=xxx" ${NB_PROCS_IOSERVER}
272
273while [ $ind -lt ${iloop} ]
274  do
275 
276  chwd "type=" "${jobnam[$ind]}" 
277  cp job_tmp_${RUN}.ksh job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh
278 
279  if [ ${jobnam[$ind]} = 'gtime' ] ; then
280     
281      case ${TARGET} in
282     'aix6' )
283         CAR_JTIM=$( grep '\# @ wall_clock_limit' job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh )
284         sed -e "s%$CAR_JTIM%\# @ wall_clock_limit = ${LJTIM}%" \
285        job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh > job_${RUN}_${jobnam[$ind]}.ksh_tmp  ;;
286     'sx8brodie' )
287         CAR_JTIMP=$( grep '\#PBS -l cputim_prc' job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh )
288         CAR_JTIMJ=$( grep '\#PBS -l cputim_job' job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh )
289         sed -e "s%$CAR_JTIMP%\#PBS -l cputim_prc=${LJTIM}%" \
290        -e "s%$CAR_JTIMJ%\#PBS -l cputim_job=${LJTIMJ}%" \
291        job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh > job_${RUN}_${jobnam[$ind]}.ksh_tmp  ;;
292     'sx8mercure' )
293         CAR_JTIMP=$( grep '\#PBS -l cputim_prc' job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh )
294         CAR_JTIMJ=$( grep '\#PBS -l cputim_job' job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh )
295         sed -e "s%$CAR_JTIMP%\#PBS -l cputim_prc=${LJTIM}%" \
296        -e "s%$CAR_JTIMJ%\#PBS -l cputim_job=${LJTIMJ}%" \
297        job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh > job_${RUN}_${jobnam[$ind]}.ksh_tmp  ;;
298      esac
299      mv job_${RUN}_${jobnam[$ind]}.ksh_tmp job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh
300     
301  fi
302 
303  chmod 750 job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh
304 
305  if [ ! -d ${dirjob[$ind]}/$OWNEXP ] ;  then
306      mkdir ${dirjob[$ind]}/$OWNEXP
307  fi
308  mv job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh ${dirjob[$ind]}/${OWNEXP}/.
309 
310  if [ ${jobnam[$ind]} != '2_short' ] ; then
311      cd ${dirjob[$ind]}/${OWNEXP}
312      ${LAUN}job_${RUN}_${jobnam[$ind]}_${OWNEXP}.ksh &
313      cd ../..
314  fi
315 
316  let ind=$ind+1
317done
318rm -f job_tmp_${RUN}.ksh
319
320# List all jobs submitted
321${LLJOBS}
322
323# -----------------------------------------------------------------------------
324# IV. Launch cron to be able to launch the assessment step
325# -----------------------------------------------------------------------------
326if [ ${RUN} == 'mon' ] ; then
327    cd ..
328   
329    CAR_LJOB_tmp=$( grep 'LJOBS=' cron_jobs.ksh )
330    CAR_LJOB=`echo $CAR_LJOB_tmp | cut -f 1 -d " " `
331   
332    sed    -e "s%$CAR_LJOB%LJOBS=${LLJOBS}%" cron_jobs.ksh > cron_jobs.$$
333    mv cron_jobs.$$ cron_jobs.ksh &&  rm -rf cron_jobs.$$
334    chmod 744 cron_jobs.ksh
335   
336    if [ ${TARGET} != 'osxxlf' ]; then
337        ./cron_jobs.ksh ${OWNEXP} ${CONFS} &
338    fi
339fi
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