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all_functions.sh in utils/CI/sette – NEMO

source: utils/CI/sette/all_functions.sh @ 12474

Last change on this file since 12474 was 11161, checked in by mathiot, 5 years ago

merge fix_sette_ticket2239 : major simplification/improvement of SETTE (see README.rst for all the details), tested with the latest version of the trunk (r11160) (ticket #2239)

  • Property svn:executable set to *
  • Property svn:keywords set to Id
File size: 17.4 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                if [ -s ${EXE_DIR}/$1.tmp ] ; then
166                   mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1 
167                else
168                echo "file ${EXE_DIR}/$1.tmp is empty. sed command went wrong "; exit 200
169                fi
170   fi
171
172        ARGS_LST="${@:3}"
173        sed -e "s;${VAR_NAME}.*;${VAR_NAME};" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
174        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
175        sed -e "s;${VAR_NAME};$2=${ARGS_LST};"  ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
176        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
177
178        echo "finished script : set_namelist $@" >> ${SETTE_DIR}/output.sette
179        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
180        echo "                " >> ${SETTE_DIR}/output.sette
181}
182
183
184# function to tidy up after each test and populate the NEMO_VALIDATION store
185post_test_tidyup () {
186# Save current exit status of caller script
187    RUN_STATUS=$? 
188    echo "Exit status: ${RUN_STATUS}" 
189#
190# requires the following variables defined and exported from the calling script:
191#  SETTE_DIR
192#  INPUT_DIR
193#  EXE_DIR
194#  CONFIG_DIR
195#  NEMO_VALIDATION_DIR
196#  NEW_CONF
197#  CMP_NAM
198#  TEST_NAME
199echo "SETTE directory is : ${SETTE_DIR}"
200echo "INPUT directory is : ${INPUT_DIR}"
201echo "EXECUTION directory is : ${EXE_DIR}"
202echo "CONFIG directory is : ${CONFIG_DIR}"
203echo "VALIDATION directory is : ${NEMO_VALID}"
204echo "NEW CONFIGURATION is : ${NEW_CONF}"
205echo "COMPILER is : ${CMP_NAM}"
206echo "TEST is : ${TEST_NAME}"
207echo "TOOLS directory is : ${TOOLS_DIR}"
208################################################################
209# SMALL DEBUG
210    EXIT_STATUS=${RUN_STATUS}
211    if [ ! -r ${EXE_DIR}/ocean.output ]
212        then
213        grep "E R R O R" ${EXE_DIR}/ocean.output && echo "Some ERRORS at execution time, see ${EXE_DIR}/ocean.output"
214        EXIT_STATUS=2
215        # exit 2 Error now catch in the report
216    fi
217
218    if [ ! -r ${EXE_DIR}/time.step ]
219        then
220        echo "file time.step does not exist"   >> ${SETTE_DIR}/output.sette
221        echo "some problems during execution of model"  >> ${SETTE_DIR}/output.sette
222        EXIT_STATUS=1
223        # exit 1 Error now catch in the report
224    else
225        echo "file time.step exists"  >> ${SETTE_DIR}/output.sette
226        echo "execution of model time step loop started"   >> ${SETTE_DIR}/output.sette
227    fi
228
229################################################################
230
231################################################################
232#
233# Creation of NEMO_VALIDATION tree
234#    set_valid_dir already done in sette_reference_config
235    mkdir -p ${NEMO_VALIDATION_DIR}
236    if [ -d ${NEMO_VALIDATION_DIR} ] ; then
237   echo "created ${NEMO_VALIDATION_DIR} directory"   >> ${SETTE_DIR}/output.sette
238    else
239   echo "problems in creating ${NEMO_VALIDATION_DIR} directory"   >> ${SETTE_DIR}/output.sette
240   echo "EXIT,"
241   exit 1
242    fi
243#
244# Exit before populating validation directory if the model run has
245# returned a non-zero exit status
246# On CRAY NEMO exit is not the expected 999 or 123456 (let this bloc in case useful later on).
247#    case ${EXIT_STATUS} in
248#        0|123456|999) echo " NEMO finished with exit code $EXIT_STATUS " ; post_test_tidyup ;;
249#        *) echo " NEMO abort on an unexpected error (segmentation fault or whatever) $EXIT_STATUS "
250#    esac
251
252    [ ${EXIT_STATUS} -ne 0 ] && exit ${EXIT_STATUS} 
253#
254# Save output & debug files in NEMO_VALIDATION tree
255    echo "saving ocean & ice output, run.stat, tracer.stat files ...." >> ${SETTE_DIR}/output.sette
256    echo "            " >> ${SETTE_DIR}/output.sette
257    [ -f ${EXE_DIR}/ocean.output ] && cp ${EXE_DIR}/*ocean.output ${NEMO_VALIDATION_DIR}/.
258    [ -f ${EXE_DIR}/run.stat ] && cp ${EXE_DIR}/*run.stat ${NEMO_VALIDATION_DIR}/.
259    [ -f ${EXE_DIR}/output.namelist.dyn ] && cp ${EXE_DIR}/*output.nam* ${NEMO_VALIDATION_DIR}/.
260    [ -f ${EXE_DIR}/tracer.stat ] && cp ${EXE_DIR}/*tracer.stat ${NEMO_VALIDATION_DIR}/.
261
262    if [ -n "$(ls ${NEMO_VALIDATION_DIR}/*run*)" ] ; then
263   echo "moved run.stat in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
264   echo "moved run.stat in ${NEMO_VALIDATION_DIR} directory" 
265    else
266   echo "problem in looking for run.stat file in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
267   echo "run.stat IS NOT in ${NEMO_VALIDATION_DIR} directory" 
268    fi
269    if [ -n "$(ls ${NEMO_VALIDATION_DIR}/*ocean.output*)" ] ; then
270   echo "moved ocean.output in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
271   echo "moved ocean.output in ${NEMO_VALIDATION_DIR} directory" 
272    else
273   echo "problem in looking for ocean.output file in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
274   echo "ocean.output IS NOT in ${NEMO_VALIDATION_DIR} directory" 
275    fi
276    if [ -n "$(ls ${NEMO_VALIDATION_DIR}/*tracer.stat*)" ] ; then
277        echo "moved tracer.stat in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
278        echo "moved tracer.stat in ${NEMO_VALIDATION_DIR} directory"
279    else
280        echo "problem in looking for tracer.stat file in ${NEMO_VALIDATION_DIR} directory"  >> ${SETTE_DIR}/output.sette
281        echo "tracer.stat IS NOT in ${NEMO_VALIDATION_DIR} directory"
282    fi
283}
284
285#############################################################
286# extra functions to manipulate settings in the iodef.xml file
287#
288# Examples:
289#   set_xio_file_type    iodef.xml one_file
290#   set_xio_using_server iodef.xml true
291#   set_xio_buffer_size  iodef.xml 50000000
292#   set_xio_field_defs   iodef.xml
293#
294#############################################################
295
296usage2=" Usage : set_xio_file_type input_iodef.xml one_file||multiple_file"
297usage3=" Usage : set_xio_using_server input_iodef.xml true||false"
298usage4=" Usage : set_xio_buffer_size input_iodef.xml int_buffer_size"
299usage5=" Usage : set_xio_field_defs input_iodef.xml"
300
301set_xio_file_type () {
302        minargcount=2
303        if [ ${#} -lt ${minargcount} ]
304        then
305                echo "not enough arguments for set_xio_file_type"
306                echo "${usage2}"
307                exit 1
308        fi
309        if [ $2 != "one_file" ] && [ $2 != "multiple_file" ]
310        then
311                echo "unrecognised argument for set_xio_file_type"
312                echo "${usage2}"
313                echo $2
314                exit 1
315        fi
316        unset minargcount
317        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
318                touch ${SETTE_DIR}/output.sette
319        fi
320
321        echo "executing script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
322        echo "################" >> ${SETTE_DIR}/output.sette
323
324        VAR_NAME=$( grep "^.*<.*file_definition.*type.*=" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
325        if [ ${#VAR_NAME} -eq 0 ]
326        then
327                echo "doing \"set_xio_file_type $@\". "
328                echo "xml_tag: file_definition with variable: type is empty"
329                echo "confirm that an appropriate file_definition is in \"${EXE_DIR}/$1\" "
330                echo "exit"
331                echo "error in executing script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
332                echo "....." >> ${SETTE_DIR}/output.sette
333                exit 1
334        fi
335        if [ $2 == "one_file" ] 
336        then
337           sed -e "s:multiple_file:one_file:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
338        else
339           sed -e "s:one_file:multiple_file:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
340        fi
341        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
342
343        echo "finished script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
344        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
345        echo "                " >> ${SETTE_DIR}/output.sette
346}
347
348set_xio_using_server () {
349        minargcount=2
350        if [ ${#} -lt ${minargcount} ]
351        then
352                echo "not enough arguments for set_xio_using_server"
353                echo "${usage2}"
354                exit 1
355        fi
356        if [ $2 != "true" ] && [ $2 != "false" ]
357        then
358                echo "unrecognised argument for set_xio_using_server"
359                echo "${usage2}"
360                echo $2
361                exit 1
362        fi
363        unset minargcount
364        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
365                touch ${SETTE_DIR}/output.sette
366        fi
367
368        echo "executing script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
369        echo "################" >> ${SETTE_DIR}/output.sette
370
371        VAR_NAME=$( grep "^.*<.*variable id.*=.*using_server.*=.*bool" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
372        if [ ${#VAR_NAME} -eq 0 ]
373        then
374                echo "doing \"set_xio_using_server $@\". "
375                echo "xml_tag: "variable id=using_server" with variable: bool is empty"
376                echo "confirm that an appropriate variable id is in \"${EXE_DIR}/$1\" "
377                echo "exit"
378                echo "error in executing script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
379                echo "....." >> ${SETTE_DIR}/output.sette
380                exit 1
381        fi
382        if [ $2 == "false" ]
383        then
384           sed -e "/using_server/s:true:false:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
385           export USING_MPMD=no
386        else
387           sed -e "/using_server/s:false:true:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
388           export USING_MPMD=yes
389        fi
390        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
391
392        echo "finished script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
393        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
394        echo "                " >> ${SETTE_DIR}/output.sette
395}
396
397set_xio_buffer_size () {
398        minargcount=2
399        if [ ${#} -lt ${minargcount} ]
400        then
401                echo "not enough arguments for set_xio_buffer_size"
402                echo "${usage4}"
403                exit 1
404        fi
405        unset minargcount
406        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
407                touch ${SETTE_DIR}/output.sette
408        fi
409
410        echo "executing script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
411        echo "################" >> ${SETTE_DIR}/output.sette
412
413        VAR_NAME=$( grep "^.*<.*variable id.*=.*buffer_size.*=.*integer" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
414        if [ ${#VAR_NAME} -eq 0 ]
415        then
416                echo "doing \"set_xio_buffer_size $@\". "
417                echo "xml_tag: "variable id=buffer_size" with variable: integer is empty"
418                echo "confirm that an appropriate variable id is in \"${EXE_DIR}/$1\" "
419                echo "exit"
420                echo "error in executing script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
421                echo "....." >> ${SETTE_DIR}/output.sette
422                exit 1
423        fi
424        sed -e "/buffer_size/s:>.*<:>$2<:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
425        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
426
427        echo "finished script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
428        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
429        echo "                " >> ${SETTE_DIR}/output.sette
430}
431
432set_xio_field_defs () {
433        minargcount=1
434        if [ ${#} -lt ${minargcount} ]
435        then
436                echo "not enough arguments for set_xio_field_defs"
437                echo "${usage5}"
438                exit 1
439        fi
440        unset minargcount
441        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
442                touch ${SETTE_DIR}/output.sette
443        fi
444
445        echo "executing script : set_xio_field_defs $@" >> ${SETTE_DIR}/output.sette
446        echo "################" >> ${SETTE_DIR}/output.sette
447
448
449        [ -f ${EXE_DIR}/field_def_nemo-oce.xml ] || sed -i '/field_def_nemo-oce/d' $1
450        [ -f ${EXE_DIR}/field_def_nemo-ice.xml ] || sed -i '/field_def_nemo-ice/d' $1
451        [ -f ${EXE_DIR}/field_def_nemo-pisces.xml ] || sed -i '/field_def_nemo-pisces/d' $1
452
453        echo "finished script : set_xio_field_defs $@" >> ${SETTE_DIR}/output.sette
454        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
455        echo "                " >> ${SETTE_DIR}/output.sette
456}
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