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all_functions.sh in utils/CI/sette – NEMO

source: utils/CI/sette/all_functions.sh @ 10631

Last change on this file since 10631 was 10631, checked in by smueller, 6 years ago

Slight SETTE enhancement to improve the reliability of restartability and reproducibility tests; see ticket #2226
  • Property svn:executable set to *
  • Property svn:keywords set to Id
File size: 15.8 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# function to set namelists parameters
94set_namelist () {
95   minargcount=3
96   if [ ${#} -lt ${minargcount} ]
97   then
98      echo "not enough arguments for set_namelist"
99      echo "${usage}"
100      exit 1
101   fi
102   unset minargcount
103   if [  ! -f ${SETTE_DIR}/output.sette ] ; then
104                touch ${SETTE_DIR}/output.sette
105        fi
106
107        echo "executing script : set_namelist $@" >> ${SETTE_DIR}/output.sette
108        echo "################" >> ${SETTE_DIR}/output.sette
109     
110   VAR_NAME=$( supergrep $2 ${EXE_DIR}/$1 )
111   if [ ${#VAR_NAME} -eq 0 ] 
112   then
113      echo "doing \"set_namelist $@\". "  >> ${SETTE_DIR}/output.sette
114      echo "variable: \"$2\" not found in \"${EXE_DIR}/$1\" "  >> ${SETTE_DIR}/output.sette
115                NAMREF=$( basename $1 _cfg )_ref
116      echo "doing more : search in ${EXE_DIR}/$NAMREF " >> ${SETTE_DIR}/output.sette
117                VAR_NAME=$( supergrep $2 ${EXE_DIR}/$NAMREF )
118           if [ ${#VAR_NAME} -eq 0 ] 
119           then
120                    echo " variable $VAR_NAME not found in ${EXE_DIR}/$1 nor in ${EXE_DIR}/$NAMREF "
121                    echo " check your variable name "
122            echo "exit"
123            echo "error in executing script : set_namelist $@" >> ${SETTE_DIR}/output.sette
124            echo "....." >> ${SETTE_DIR}/output.sette
125            exit 1
126                fi
127                LINEVAR=$( grep -s -n "$VAR_NAME" ${EXE_DIR}/$NAMREF | awk -F: '{ { print $1} }' )
128                echo " $VAR_NAME found in ${EXE_DIR}/$NAMREF at line $LINEVAR " >> ${SETTE_DIR}/output.sette
129#   search for namelist group name
130                NAMGRP=$( head -n$LINEVAR ${EXE_DIR}/$NAMREF | grep --line-buffered "^&nam" | tail -1 | awk -F" " '{ { print $1} }' ) 
131                echo " variable $VAR_NAME will be added in $NAMGRP namelist-group of namelist file ${EXE_DIR}/$1 " >> ${SETTE_DIR}/output.sette
132# Add $VARNAME in namelist file ${EXE_DIR}/$1 in namelist group $NAMGRP
133# on mac osx, replace sed --posix by gsed (available with mac port)
134                sed --posix "/${NAMGRP} /a\ ${VAR_NAME} " ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp || gsed --posix "/${NAMGRP} /a\ ${VAR_NAME} " ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
135# if file not empty replace ${EXE_DIR}/$1
136                if [ -s ${EXE_DIR}/$1.tmp ] ; then
137                   mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1 
138                else
139                echo "file ${EXE_DIR}/$1.tmp is empty. sed command went wrong "; exit 200
140                fi
141   fi
142
143        sed -e "s:${VAR_NAME}.*:${VAR_NAME}:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
144        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
145        sed -e "s:${VAR_NAME}:$2=$3:"  ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
146        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
147
148        echo "finished script : set_namelist $@" >> ${SETTE_DIR}/output.sette
149        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
150        echo "                " >> ${SETTE_DIR}/output.sette
151}
152
153
154# function to tidy up after each test and populate the NEMO_VALIDATION store
155post_test_tidyup () {
156#
157# requires the following variables defined and exported from the calling script:
158#  SETTE_DIR
159#  INPUT_DIR
160#  EXE_DIR
161#  CONFIG_DIR
162#  NEMO_VALIDATION_DIR
163#  NEW_CONF
164#  CMP_NAM
165#  TEST_NAME
166echo "SETTE directory is : ${SETTE_DIR}"
167echo "INPUT directory is : ${INPUT_DIR}"
168echo "EXECUTION directory is : ${EXE_DIR}"
169echo "CONFIG directory is : ${CONFIG_DIR}"
170echo "VALIDATION directory is : ${NEMO_VALIDATION_DIR}"
171echo "NEW CONFIGURATION is : ${NEW_CONF}"
172echo "COMPILER is : ${CMP_NAM}"
173echo "TEST is : ${TEST_NAME}"
174echo "TOOLS directory is : ${TOOLS_DIR}"
175################################################################
176# SMALL DEBUG
177    if [ ! -r ${EXE_DIR}/ocean.output ]
178        then
179        grep "E R R O R" ${EXE_DIR}/ocean.output && echo "Some ERRORS at execution time, see ${EXE_DIR}/ocean.output"
180        exit 2
181    fi
182
183    if [ ! -r ${EXE_DIR}/time.step ]
184        then
185        echo "file time.step does not exist"   >> ${SETTE_DIR}/output.sette
186        echo "some problems during execution of model"  >> ${SETTE_DIR}/output.sette
187        exit 1
188    else
189        echo "file time.step exists"  >> ${SETTE_DIR}/output.sette
190        echo "execution of model time step loop started"   >> ${SETTE_DIR}/output.sette
191    fi
192
193################################################################
194
195################################################################
196# Creation of NEMO_VALIDATION tree
197    export LANG=en_US
198    REVISION_NB=`svn info ${SETTE_DIR}/.. | grep -i "Last Changed Rev:" | sed -e "s/ //g" | cut -d ":" -f 2`
199    if [ ${#REVISION_NB} -eq 0 ]
200    then
201      echo "some problems with svn info command"
202      echo "some problems with svn info command" >> ${SETTE_DIR}/output.sette
203      REVISION_NB=`date +%Y%m%d`
204      echo "put in ${REVISION_NB} date"
205      echo "put in ${REVISION_NB} date" >> ${SETTE_DIR}/output.sette
206    else
207    echo "value of revision number of NEMOGCM: ${REVISION_NB}"
208    fi
209    cd ${NEMO_VALIDATION_DIR}
210    `mkdir -p ${NEMO_VALIDATION_DIR}/W${NEW_CONF}/${CMP_NAM}/${REVISION_NB}/${TEST_NAME}`
211    NEMO_VALID=${NEMO_VALIDATION_DIR}/W${NEW_CONF}/${CMP_NAM}/${REVISION_NB}/${TEST_NAME}
212    if [ -d ${NEMO_VALID} ] ; then
213   echo "created ${NEMO_VALID} directory"   >> ${SETTE_DIR}/output.sette
214    else
215   echo "problems in creating ${NEMO_VALID} directory"   >> ${SETTE_DIR}/output.sette
216   echo "EXIT,"
217   exit 1
218    fi
219    # Save output & debug files in NEMO_VALIDATION tree
220    echo "saving ocean & ice output, run.stat, tracer.stat files ...." >> ${SETTE_DIR}/output.sette
221    echo "            " >> ${SETTE_DIR}/output.sette
222    [ -f ${EXE_DIR}/ocean.output ] && cp ${EXE_DIR}/*ocean.output ${NEMO_VALID}/.
223    [ -f ${EXE_DIR}/run.stat ] && cp ${EXE_DIR}/*run.stat ${NEMO_VALID}/.
224    [ -f ${EXE_DIR}/output.namelist.dyn ] && cp ${EXE_DIR}/*output.nam* ${NEMO_VALID}/.
225    [ -f ${EXE_DIR}/tracer.stat ] && cp ${EXE_DIR}/*tracer.stat ${NEMO_VALID}/.
226
227    if [ -n "$(ls ${NEMO_VALID}/*run*)" ] ; then
228   echo "moved run.stat in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
229   echo "moved run.stat in ${NEMO_VALID} directory" 
230    else
231   echo "problem in looking for run.stat file in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
232   echo "run.stat IS NOT in ${NEMO_VALID} directory" 
233    fi
234    if [ -n "$(ls ${NEMO_VALID}/*ocean.output*)" ] ; then
235   echo "moved ocean.output in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
236   echo "moved ocean.output in ${NEMO_VALID} directory" 
237    else
238   echo "problem in looking for ocean.output file in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
239   echo "ocean.output IS NOT in ${NEMO_VALID} directory" 
240    fi
241    if [ -n "$(ls ${NEMO_VALID}/*tracer.stat*)" ] ; then
242        echo "moved tracer.stat in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
243        echo "moved tracer.stat in ${NEMO_VALID} directory"
244    else
245        echo "problem in looking for tracer.stat file in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
246        echo "tracer.stat IS NOT in ${NEMO_VALID} directory"
247    fi
248}
249
250#############################################################
251# extra functions to manipulate settings in the iodef.xml file
252#
253# Examples:
254#   set_xio_file_type    iodef.xml one_file
255#   set_xio_using_server iodef.xml true
256#   set_xio_buffer_size  iodef.xml 50000000
257#   set_xio_field_defs   iodef.xml
258#
259#############################################################
260
261usage2=" Usage : set_xio_file_type input_iodef.xml one_file||multiple_file"
262usage3=" Usage : set_xio_using_server input_iodef.xml true||false"
263usage4=" Usage : set_xio_buffer_size input_iodef.xml int_buffer_size"
264usage5=" Usage : set_xio_field_defs input_iodef.xml"
265
266set_xio_file_type () {
267        minargcount=2
268        if [ ${#} -lt ${minargcount} ]
269        then
270                echo "not enough arguments for set_xio_file_type"
271                echo "${usage2}"
272                exit 1
273        fi
274        if [ $2 != "one_file" ] && [ $2 != "multiple_file" ]
275        then
276                echo "unrecognised argument for set_xio_file_type"
277                echo "${usage2}"
278                echo $2
279                exit 1
280        fi
281        unset minargcount
282        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
283                touch ${SETTE_DIR}/output.sette
284        fi
285
286        echo "executing script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
287        echo "################" >> ${SETTE_DIR}/output.sette
288
289        VAR_NAME=$( grep "^.*<.*file_definition.*type.*=" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
290        if [ ${#VAR_NAME} -eq 0 ]
291        then
292                echo "doing \"set_xio_file_type $@\". "
293                echo "xml_tag: file_definition with variable: type is empty"
294                echo "confirm that an appropriate file_definition is in \"${EXE_DIR}/$1\" "
295                echo "exit"
296                echo "error in executing script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
297                echo "....." >> ${SETTE_DIR}/output.sette
298                exit 1
299        fi
300        if [ $2 == "one_file" ] 
301        then
302           sed -e "s:multiple_file:one_file:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
303        else
304           sed -e "s:one_file:multiple_file:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
305        fi
306        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
307
308        echo "finished script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
309        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
310        echo "                " >> ${SETTE_DIR}/output.sette
311}
312
313set_xio_using_server () {
314        minargcount=2
315        if [ ${#} -lt ${minargcount} ]
316        then
317                echo "not enough arguments for set_xio_using_server"
318                echo "${usage2}"
319                exit 1
320        fi
321        if [ $2 != "true" ] && [ $2 != "false" ]
322        then
323                echo "unrecognised argument for set_xio_using_server"
324                echo "${usage2}"
325                echo $2
326                exit 1
327        fi
328        unset minargcount
329        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
330                touch ${SETTE_DIR}/output.sette
331        fi
332
333        echo "executing script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
334        echo "################" >> ${SETTE_DIR}/output.sette
335
336        VAR_NAME=$( grep "^.*<.*variable id.*=.*using_server.*=.*bool" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
337        if [ ${#VAR_NAME} -eq 0 ]
338        then
339                echo "doing \"set_xio_using_server $@\". "
340                echo "xml_tag: "variable id=using_server" with variable: bool is empty"
341                echo "confirm that an appropriate variable id is in \"${EXE_DIR}/$1\" "
342                echo "exit"
343                echo "error in executing script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
344                echo "....." >> ${SETTE_DIR}/output.sette
345                exit 1
346        fi
347        if [ $2 == "false" ]
348        then
349           sed -e "/using_server/s:true:false:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
350           export USING_MPMD=no
351        else
352           sed -e "/using_server/s:false:true:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
353           export USING_MPMD=yes
354        fi
355        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
356
357        echo "finished script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
358        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
359        echo "                " >> ${SETTE_DIR}/output.sette
360}
361
362set_xio_buffer_size () {
363        minargcount=2
364        if [ ${#} -lt ${minargcount} ]
365        then
366                echo "not enough arguments for set_xio_buffer_size"
367                echo "${usage4}"
368                exit 1
369        fi
370        unset minargcount
371        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
372                touch ${SETTE_DIR}/output.sette
373        fi
374
375        echo "executing script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
376        echo "################" >> ${SETTE_DIR}/output.sette
377
378        VAR_NAME=$( grep "^.*<.*variable id.*=.*buffer_size.*=.*integer" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
379        if [ ${#VAR_NAME} -eq 0 ]
380        then
381                echo "doing \"set_xio_buffer_size $@\". "
382                echo "xml_tag: "variable id=buffer_size" with variable: integer is empty"
383                echo "confirm that an appropriate variable id is in \"${EXE_DIR}/$1\" "
384                echo "exit"
385                echo "error in executing script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
386                echo "....." >> ${SETTE_DIR}/output.sette
387                exit 1
388        fi
389        sed -e "/buffer_size/s:>.*<:>$2<:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
390        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
391
392        echo "finished script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
393        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
394        echo "                " >> ${SETTE_DIR}/output.sette
395}
396
397set_xio_field_defs () {
398        minargcount=1
399        if [ ${#} -lt ${minargcount} ]
400        then
401                echo "not enough arguments for set_xio_field_defs"
402                echo "${usage5}"
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_field_defs $@" >> ${SETTE_DIR}/output.sette
411        echo "################" >> ${SETTE_DIR}/output.sette
412
413
414        [ -f ${EXE_DIR}/field_def_nemo-oce.xml ] || sed -i '/field_def_nemo-oce/d' $1
415        [ -f ${EXE_DIR}/field_def_nemo-ice.xml ] || sed -i '/field_def_nemo-ice/d' $1
416        [ -f ${EXE_DIR}/field_def_nemo-pisces.xml ] || sed -i '/field_def_nemo-pisces/d' $1
417
418        echo "finished script : set_xio_field_defs $@" >> ${SETTE_DIR}/output.sette
419        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
420        echo "                " >> ${SETTE_DIR}/output.sette
421}
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