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all_functions.sh in utils/CI/sette_ticket2304 – NEMO

source: utils/CI/sette_ticket2304/all_functions.sh @ 12238

Last change on this file since 12238 was 12238, checked in by mathiot, 4 years ago

stop sette execution if one of the namelist variable cannot be updated in namelist cfg because of missing namelist group #2304
  • Property svn:executable set to *
  • Property svn:keywords set to Id
File size: 17.8 KB
Line 
1######################################################
2# Author : Simona Flavoni for NEMO
3# Contact : sflod@locean-ipsl.upmc.fr
4#
5# ----------------------------------------------------------------------
6# NEMO/SETTE , NEMO Consortium (2010)
7# Software governed by the CeCILL licence     (NEMOGCM/NEMO_CeCILL.txt)
8# ----------------------------------------------------------------------
9#
10# Some scripts called by sette.sh
11# all_functions.sh   : all functions used by sette.sh 
12######################################################
13#set -x
14#set -o posix
15#set -u
16#set -e
17#+
18#
19# ================
20# all_functions.sh
21# ================
22#
23# ----------------------------------------------
24# Set of functions used by sette.sh (NEMO tests)
25# ----------------------------------------------
26#
27# SYNOPSIS
28# ========
29#
30# ::
31#
32#  $ ./set_namelist INPUT_NAMELIST VARIABLE VALUE
33#  $ post_test_tidyup
34#
35#
36# DESCRIPTION
37# ===========
38#
39# function superegrep
40#   input variable value
41#
42# function set_namelist
43#   input namelist_name variable value
44#   output namelist
45#
46# function post_test_tidyup
47#   creates nemo_validation tree, and save output & debug files
48#   this function creates tree of validation in NEMO_VALIDATION_DIR as follows :
49#
50# NEMO_VALIDATION_DIR/WCONFIG_NAME/WCOMPILER_NAME/REVISION_NUMBER(or DATE)/TEST_NAME
51#
52# NEMO_VALIDATION_DIR           : is choosen in param.cfg
53#
54# WCONFIG_NAME                  : set by makenemo at the moment of compilation
55#
56# WCOMPILER_NAME                : set by makenemo at the moment of compilation
57#
58# REVISION_NUMBER(or DATE)      : revision number by svn info, if problems with svn date is taken
59#
60# TEST_NAME                     : set in sette.sh for each configuration to be tested (directory TEST_NAME is created under ${NEW_CONF} directory )
61#
62# EXAMPLES
63# ========
64#
65# ::
66#
67#  $ ./set_namelist namelist          nn_itend        75
68#  $ ./set_namelist namelist_ice      cn_icerst_in  \"00101231_restart_ice\"
69#  $ post_test_tidyup
70#
71#
72# TODO
73# ====
74#
75# option debug
76#
77#
78# EVOLUTIONS
79# ==========
80#
81# $Id$
82#
83#   * creation
84#-
85# function to find namelists parameters
86supergrep () {
87            grep "^ *$1 *=" $2 | sed -e "s% *\!.*%%"
88    }
89
90usage=" Usage : set_namelist input_namelist variable_name value"
91usage=" if value is a string ths is neede syntax : ./set_namelist namelist_name var_name \"new_value\" "
92
93# define validation dir
94set_valid_dir () {
95    LANG=en_US
96    REVISION_NB=`LC_MESSAGES=${LANG} ${SVN_CMD} info ${SETTE_DIR}/.. | grep "Last Changed Rev" | awk '{print $NF}'`
97    if [ ${#REVISION_NB} -eq 0 ]
98    then
99        echo "some problems with ${SVN_CMD} info command"
100        echo "some problems with ${SVN_CMD} info command" >> ${SETTE_DIR}/output.sette
101        REVISION_NB=`date +%Y%m%d`
102        echo "put in ${REVISION_NB} date"
103        echo "put in ${REVISION_NB} date" >> ${SETTE_DIR}/output.sette
104    else
105    echo "value of revision number of NEMOGCM: ${REVISION_NB}"
106    fi
107    [ `${SVN_CMD} status -q ${SETTE_DIR}/../{cfg,tests,src} | wc -l` -ge 1 ] && REVISION_NB=${REVISION_NB}+
108    NEMO_VALID=${NEMO_VALIDATION_DIR}/W${NEW_CONF}/${CMP_NAM}/${REVISION_NB}/${TEST_NAME}
109}
110
111# clean valid dir (move old ocean_output/run.stat and tracer to avoid checking them in case something wrong happen.
112clean_valid_dir () {
113#   set_valid_dir # already done in sette_ref/sette_test
114   echo "validation directory is : $NEMO_VALID"
115   if [ -d $NEMO_VALID ] ; then
116      [ -f ${NEMO_VALID}/ocean.output ] && mv ${NEMO_VALID}/ocean.output ${NEMO_VALID}/ocean.output_old
117      [ -f ${NEMO_VALID}/run.stat ]     && mv ${NEMO_VALID}/run.stat     ${NEMO_VALID}/run.stat_old
118      [ -f ${NEMO_VALID}/tracer.stat ]  && mv ${NEMO_VALID}/tracer.stat  ${NEMO_VALID}/tracer.stat_old
119   fi
120}
121
122# function to set namelists parameters
123set_namelist () {
124   minargcount=3
125   if [ ${#} -lt ${minargcount} ]
126   then
127      echo "not enough arguments for set_namelist"
128      echo "${usage}"
129      exit 1
130   fi
131   unset minargcount
132   if [  ! -f ${SETTE_DIR}/output.sette ] ; then
133                touch ${SETTE_DIR}/output.sette
134        fi
135
136        echo "executing script : set_namelist $@" >> ${SETTE_DIR}/output.sette
137        echo "################" >> ${SETTE_DIR}/output.sette
138     
139   VAR_NAME=$( supergrep $2 ${EXE_DIR}/$1 )
140   if [ ${#VAR_NAME} -eq 0 ] 
141   then
142      echo "doing \"set_namelist $@\". "  >> ${SETTE_DIR}/output.sette
143      echo "variable: \"$2\" not found in \"${EXE_DIR}/$1\" "  >> ${SETTE_DIR}/output.sette
144                NAMREF=$( basename $1 _cfg )_ref
145      echo "doing more : search in ${EXE_DIR}/$NAMREF " >> ${SETTE_DIR}/output.sette
146                VAR_NAME=$( supergrep $2 ${EXE_DIR}/$NAMREF )
147           if [ ${#VAR_NAME} -eq 0 ] 
148           then
149                    echo " variable $VAR_NAME not found in ${EXE_DIR}/$1 nor in ${EXE_DIR}/$NAMREF "
150                    echo " check your variable name "
151            echo "exit"
152            echo "error in executing script : set_namelist $@" >> ${SETTE_DIR}/output.sette
153            echo "....." >> ${SETTE_DIR}/output.sette
154            exit 1
155                fi
156                LINEVAR=$( grep -s -n "$VAR_NAME" ${EXE_DIR}/$NAMREF | awk -F: '{ { print $1} }' )
157                echo " $VAR_NAME found in ${EXE_DIR}/$NAMREF at line $LINEVAR " >> ${SETTE_DIR}/output.sette
158#   search for namelist group name
159                NAMGRP=$( head -n$LINEVAR ${EXE_DIR}/$NAMREF | grep --line-buffered "^&nam" | tail -1 | awk -F" " '{ { print $1} }' ) 
160                echo " variable $VAR_NAME will be added in $NAMGRP namelist-group of namelist file ${EXE_DIR}/$1 " >> ${SETTE_DIR}/output.sette
161# Add $VARNAME in namelist file ${EXE_DIR}/$1 in namelist group $NAMGRP
162# on mac osx, replace sed --posix by gsed (available with mac port)
163                sed --posix "/${NAMGRP} /a\ ${VAR_NAME} " ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp || gsed --posix "/${NAMGRP} /a\ ${VAR_NAME} " ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
164# if file not empty replace ${EXE_DIR}/$1
165                # check if namelist group present in namelist_cfg
166                NGRP=$(grep ${NAMGRP} ${EXE_DIR}/$1 | wc -l )
167                if [ ${NGRP} -eq 0 ]; then
168                   echo ''
169                   echo "+++++ Cannot update ${2} because group ${NAMGRP} is missing in ${EXE_DIR}/$1  +++++ "     
170                   echo ''
171                   exit 42
172                fi
173                if [ -s ${EXE_DIR}/$1.tmp ] ; then
174                   mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1 
175                else
176                echo "file ${EXE_DIR}/$1.tmp is empty. sed command went wrong "; exit 200
177                fi
178   fi
179
180        ARGS_LST="${@:3}"
181        sed -e "s;${VAR_NAME}.*;${VAR_NAME};" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
182        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
183        sed -e "s;${VAR_NAME};$2=${ARGS_LST};"  ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
184        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
185
186        echo "finished script : set_namelist $@" >> ${SETTE_DIR}/output.sette
187        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
188        echo "                " >> ${SETTE_DIR}/output.sette
189}
190
191
192# function to tidy up after each test and populate the NEMO_VALIDATION store
193post_test_tidyup () {
194# Save current exit status of caller script
195    RUN_STATUS=$? 
196    echo "Exit status: ${RUN_STATUS}" 
197#
198# requires the following variables defined and exported from the calling script:
199#  SETTE_DIR
200#  INPUT_DIR
201#  EXE_DIR
202#  CONFIG_DIR
203#  NEMO_VALIDATION_DIR
204#  NEW_CONF
205#  CMP_NAM
206#  TEST_NAME
207echo "SETTE directory is : ${SETTE_DIR}"
208echo "INPUT directory is : ${INPUT_DIR}"
209echo "EXECUTION directory is : ${EXE_DIR}"
210echo "CONFIG directory is : ${CONFIG_DIR}"
211echo "VALIDATION directory is : ${NEMO_VALID}"
212echo "NEW CONFIGURATION is : ${NEW_CONF}"
213echo "COMPILER is : ${CMP_NAM}"
214echo "TEST is : ${TEST_NAME}"
215echo "TOOLS directory is : ${TOOLS_DIR}"
216################################################################
217# SMALL DEBUG
218    EXIT_STATUS=${RUN_STATUS}
219    if [ ! -r ${EXE_DIR}/ocean.output ]
220        then
221        grep "E R R O R" ${EXE_DIR}/ocean.output && echo "Some ERRORS at execution time, see ${EXE_DIR}/ocean.output"
222        EXIT_STATUS=2
223        # exit 2 Error now catch in the report
224    fi
225
226    if [ ! -r ${EXE_DIR}/time.step ]
227        then
228        echo "file time.step does not exist"   >> ${SETTE_DIR}/output.sette
229        echo "some problems during execution of model"  >> ${SETTE_DIR}/output.sette
230        EXIT_STATUS=1
231        # exit 1 Error now catch in the report
232    else
233        echo "file time.step exists"  >> ${SETTE_DIR}/output.sette
234        echo "execution of model time step loop started"   >> ${SETTE_DIR}/output.sette
235    fi
236
237################################################################
238
239################################################################
240#
241# Creation of NEMO_VALIDATION tree
242#    set_valid_dir already done in sette_reference_config
243    mkdir -p ${NEMO_VALIDATION_DIR}
244    if [ -d ${NEMO_VALIDATION_DIR} ] ; then
245   echo "created ${NEMO_VALIDATION_DIR} directory"   >> ${SETTE_DIR}/output.sette
246    else
247   echo "problems in creating ${NEMO_VALIDATION_DIR} directory"   >> ${SETTE_DIR}/output.sette
248   echo "EXIT,"
249   exit 1
250    fi
251#
252# Exit before populating validation directory if the model run has
253# returned a non-zero exit status
254# On CRAY NEMO exit is not the expected 999 or 123456 (let this bloc in case useful later on).
255#    case ${EXIT_STATUS} in
256#        0|123456|999) echo " NEMO finished with exit code $EXIT_STATUS " ; post_test_tidyup ;;
257#        *) echo " NEMO abort on an unexpected error (segmentation fault or whatever) $EXIT_STATUS "
258#    esac
259
260    [ ${EXIT_STATUS} -ne 0 ] && exit ${EXIT_STATUS} 
261#
262# Save output & debug files in NEMO_VALIDATION tree
263    echo "saving ocean & ice output, run.stat, tracer.stat files ...." >> ${SETTE_DIR}/output.sette
264    echo "            " >> ${SETTE_DIR}/output.sette
265    [ -f ${EXE_DIR}/ocean.output ] && cp ${EXE_DIR}/*ocean.output ${NEMO_VALIDATION_DIR}/.
266    [ -f ${EXE_DIR}/run.stat ] && cp ${EXE_DIR}/*run.stat ${NEMO_VALIDATION_DIR}/.
267    [ -f ${EXE_DIR}/output.namelist.dyn ] && cp ${EXE_DIR}/*output.nam* ${NEMO_VALIDATION_DIR}/.
268    [ -f ${EXE_DIR}/tracer.stat ] && cp ${EXE_DIR}/*tracer.stat ${NEMO_VALIDATION_DIR}/.
269
270    if [ -n "$(ls ${NEMO_VALIDATION_DIR}/*run*)" ] ; then
271   echo "moved run.stat in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
272   echo "moved run.stat in ${NEMO_VALIDATION_DIR} directory" 
273    else
274   echo "problem in looking for run.stat file in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
275   echo "run.stat IS NOT in ${NEMO_VALIDATION_DIR} directory" 
276    fi
277    if [ -n "$(ls ${NEMO_VALIDATION_DIR}/*ocean.output*)" ] ; then
278   echo "moved ocean.output in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
279   echo "moved ocean.output in ${NEMO_VALIDATION_DIR} directory" 
280    else
281   echo "problem in looking for ocean.output file in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
282   echo "ocean.output IS NOT in ${NEMO_VALIDATION_DIR} directory" 
283    fi
284    if [ -n "$(ls ${NEMO_VALIDATION_DIR}/*tracer.stat*)" ] ; then
285        echo "moved tracer.stat in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
286        echo "moved tracer.stat in ${NEMO_VALIDATION_DIR} directory"
287    else
288        echo "problem in looking for tracer.stat file in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
289        echo "tracer.stat IS NOT in ${NEMO_VALIDATION_DIR} directory"
290    fi
291}
292
293#############################################################
294# extra functions to manipulate settings in the iodef.xml file
295#
296# Examples:
297#   set_xio_file_type    iodef.xml one_file
298#   set_xio_using_server iodef.xml true
299#   set_xio_buffer_size  iodef.xml 50000000
300#   set_xio_field_defs   iodef.xml
301#
302#############################################################
303
304usage2=" Usage : set_xio_file_type input_iodef.xml one_file||multiple_file"
305usage3=" Usage : set_xio_using_server input_iodef.xml true||false"
306usage4=" Usage : set_xio_buffer_size input_iodef.xml int_buffer_size"
307usage5=" Usage : set_xio_field_defs input_iodef.xml"
308
309set_xio_file_type () {
310        minargcount=2
311        if [ ${#} -lt ${minargcount} ]
312        then
313                echo "not enough arguments for set_xio_file_type"
314                echo "${usage2}"
315                exit 1
316        fi
317        if [ $2 != "one_file" ] && [ $2 != "multiple_file" ]
318        then
319                echo "unrecognised argument for set_xio_file_type"
320                echo "${usage2}"
321                echo $2
322                exit 1
323        fi
324        unset minargcount
325        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
326                touch ${SETTE_DIR}/output.sette
327        fi
328
329        echo "executing script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
330        echo "################" >> ${SETTE_DIR}/output.sette
331
332        VAR_NAME=$( grep "^.*<.*file_definition.*type.*=" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
333        if [ ${#VAR_NAME} -eq 0 ]
334        then
335                echo "doing \"set_xio_file_type $@\". "
336                echo "xml_tag: file_definition with variable: type is empty"
337                echo "confirm that an appropriate file_definition is in \"${EXE_DIR}/$1\" "
338                echo "exit"
339                echo "error in executing script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
340                echo "....." >> ${SETTE_DIR}/output.sette
341                exit 1
342        fi
343        if [ $2 == "one_file" ] 
344        then
345           sed -e "s:multiple_file:one_file:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
346        else
347           sed -e "s:one_file:multiple_file:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
348        fi
349        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
350
351        echo "finished script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
352        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
353        echo "                " >> ${SETTE_DIR}/output.sette
354}
355
356set_xio_using_server () {
357        minargcount=2
358        if [ ${#} -lt ${minargcount} ]
359        then
360                echo "not enough arguments for set_xio_using_server"
361                echo "${usage2}"
362                exit 1
363        fi
364        if [ $2 != "true" ] && [ $2 != "false" ]
365        then
366                echo "unrecognised argument for set_xio_using_server"
367                echo "${usage2}"
368                echo $2
369                exit 1
370        fi
371        unset minargcount
372        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
373                touch ${SETTE_DIR}/output.sette
374        fi
375
376        echo "executing script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
377        echo "################" >> ${SETTE_DIR}/output.sette
378
379        VAR_NAME=$( grep "^.*<.*variable id.*=.*using_server.*=.*bool" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
380        if [ ${#VAR_NAME} -eq 0 ]
381        then
382                echo "doing \"set_xio_using_server $@\". "
383                echo "xml_tag: "variable id=using_server" with variable: bool is empty"
384                echo "confirm that an appropriate variable id is in \"${EXE_DIR}/$1\" "
385                echo "exit"
386                echo "error in executing script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
387                echo "....." >> ${SETTE_DIR}/output.sette
388                exit 1
389        fi
390        if [ $2 == "false" ]
391        then
392           sed -e "/using_server/s:true:false:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
393           export USING_MPMD=no
394        else
395           sed -e "/using_server/s:false:true:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
396           export USING_MPMD=yes
397        fi
398        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
399
400        echo "finished script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
401        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
402        echo "                " >> ${SETTE_DIR}/output.sette
403}
404
405set_xio_buffer_size () {
406        minargcount=2
407        if [ ${#} -lt ${minargcount} ]
408        then
409                echo "not enough arguments for set_xio_buffer_size"
410                echo "${usage4}"
411                exit 1
412        fi
413        unset minargcount
414        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
415                touch ${SETTE_DIR}/output.sette
416        fi
417
418        echo "executing script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
419        echo "################" >> ${SETTE_DIR}/output.sette
420
421        VAR_NAME=$( grep "^.*<.*variable id.*=.*buffer_size.*=.*integer" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
422        if [ ${#VAR_NAME} -eq 0 ]
423        then
424                echo "doing \"set_xio_buffer_size $@\". "
425                echo "xml_tag: "variable id=buffer_size" with variable: integer is empty"
426                echo "confirm that an appropriate variable id is in \"${EXE_DIR}/$1\" "
427                echo "exit"
428                echo "error in executing script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
429                echo "....." >> ${SETTE_DIR}/output.sette
430                exit 1
431        fi
432        sed -e "/buffer_size/s:>.*<:>$2<:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
433        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
434
435        echo "finished script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
436        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
437        echo "                " >> ${SETTE_DIR}/output.sette
438}
439
440set_xio_field_defs () {
441        minargcount=1
442        if [ ${#} -lt ${minargcount} ]
443        then
444                echo "not enough arguments for set_xio_field_defs"
445                echo "${usage5}"
446                exit 1
447        fi
448        unset minargcount
449        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
450                touch ${SETTE_DIR}/output.sette
451        fi
452
453        echo "executing script : set_xio_field_defs $@" >> ${SETTE_DIR}/output.sette
454        echo "################" >> ${SETTE_DIR}/output.sette
455
456
457        [ -f ${EXE_DIR}/field_def_nemo-oce.xml ] || sed -i '/field_def_nemo-oce/d' $1
458        [ -f ${EXE_DIR}/field_def_nemo-ice.xml ] || sed -i '/field_def_nemo-ice/d' $1
459        [ -f ${EXE_DIR}/field_def_nemo-pisces.xml ] || sed -i '/field_def_nemo-pisces/d' $1
460
461        echo "finished script : set_xio_field_defs $@" >> ${SETTE_DIR}/output.sette
462        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
463        echo "                " >> ${SETTE_DIR}/output.sette
464}
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