source: branches/2017/dev_merge_2017/NEMOGCM/SETTE/all_functions.sh @ 9019

Last change on this file since 9019 was 9019, checked in by timgraham, 4 years ago

Merge of dev_CNRS_2017 into branch

  • Property svn:executable set to *
  • Property svn:keywords set to Id
File size: 15.8 KB
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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    cd ${CONFIG_DIR}
199    cd ../
200    REVISION_NB=`svn info | grep -i "Last Changed Rev:" | sed -e "s/ //g" | cut -d ":" -f 2`
201    if [ ${#REVISION_NB} -eq 0 ]
202    then
203      echo "some problems with svn info command"
204      echo "some problems with svn info command" >> ${SETTE_DIR}/output.sette
205      REVISION_NB=`date +%Y%m%d`
206      echo "put in ${REVISION_NB} date"
207      echo "put in ${REVISION_NB} date" >> ${SETTE_DIR}/output.sette
208    else
209    echo "value of revision number of NEMOGCM: ${REVISION_NB}"
210    fi
211    cd ${NEMO_VALIDATION_DIR}
212    `mkdir -p ${NEMO_VALIDATION_DIR}/W${NEW_CONF}/${CMP_NAM}/${REVISION_NB}/${TEST_NAME}`
213    NEMO_VALID=${NEMO_VALIDATION_DIR}/W${NEW_CONF}/${CMP_NAM}/${REVISION_NB}/${TEST_NAME}
214    if [ -d ${NEMO_VALID} ] ; then
215   echo "created ${NEMO_VALID} directory"   >> ${SETTE_DIR}/output.sette
216    else
217   echo "problems in creating ${NEMO_VALID} directory"   >> ${SETTE_DIR}/output.sette
218   echo "EXIT,"
219   exit 1
220    fi
221    # Save output & debug files in NEMO_VALIDATION tree
222    echo "saving ocean & ice output, run.stat, tracer.stat files ...." >> ${SETTE_DIR}/output.sette
223    echo "            " >> ${SETTE_DIR}/output.sette
224    [ -f ${EXE_DIR}/ocean.output ] && cp ${EXE_DIR}/*ocean.output ${NEMO_VALID}/.
225    [ -f ${EXE_DIR}/run.stat ] && cp ${EXE_DIR}/*run.stat ${NEMO_VALID}/.
226    [ -f ${EXE_DIR}/output.namelist.dyn ] && cp ${EXE_DIR}/*output.nam* ${NEMO_VALID}/.
227    [ -f ${EXE_DIR}/tracer.stat ] && cp ${EXE_DIR}/*tracer.stat ${NEMO_VALID}/.
228
229    if [ -n "$(ls ${NEMO_VALID}/*run*)" ] ; then
230   echo "moved run.stat in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
231   echo "moved run.stat in ${NEMO_VALID} directory" 
232    else
233   echo "problem in looking for run.stat file in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
234   echo "run.stat IS NOT in ${NEMO_VALID} directory" 
235    fi
236    if [ -n "$(ls ${NEMO_VALID}/*ocean.output*)" ] ; then
237   echo "moved ocean.output in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
238   echo "moved ocean.output in ${NEMO_VALID} directory" 
239    else
240   echo "problem in looking for ocean.output file in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
241   echo "ocean.output IS NOT in ${NEMO_VALID} directory" 
242    fi
243    if [ -n "$(ls ${NEMO_VALID}/*tracer.stat*)" ] ; then
244        echo "moved tracer.stat in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
245        echo "moved tracer.stat in ${NEMO_VALID} directory"
246    else
247        echo "problem in looking for tracer.stat file in ${NEMO_VALID} directory"  >> ${SETTE_DIR}/output.sette
248        echo "tracer.stat IS NOT in ${NEMO_VALID} directory"
249    fi
250}
251
252#############################################################
253# extra functions to manipulate settings in the iodef.xml file
254#
255# Examples:
256#   set_xio_file_type    iodef.xml one_file
257#   set_xio_using_server iodef.xml true
258#   set_xio_buffer_size  iodef.xml 50000000
259#   set_xio_field_defs   iodef.xml
260#
261#############################################################
262
263usage2=" Usage : set_xio_file_type input_iodef.xml one_file||multiple_file"
264usage3=" Usage : set_xio_using_server input_iodef.xml true||false"
265usage4=" Usage : set_xio_buffer_size input_iodef.xml int_buffer_size"
266usage5=" Usage : set_xio_field_defs input_iodef.xml"
267
268set_xio_file_type () {
269        minargcount=2
270        if [ ${#} -lt ${minargcount} ]
271        then
272                echo "not enough arguments for set_xio_file_type"
273                echo "${usage2}"
274                exit 1
275        fi
276        if [ $2 != "one_file" ] && [ $2 != "multiple_file" ]
277        then
278                echo "unrecognised argument for set_xio_file_type"
279                echo "${usage2}"
280                echo $2
281                exit 1
282        fi
283        unset minargcount
284        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
285                touch ${SETTE_DIR}/output.sette
286        fi
287
288        echo "executing script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
289        echo "################" >> ${SETTE_DIR}/output.sette
290
291        VAR_NAME=$( grep "^.*<.*file_definition.*type.*=" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
292        if [ ${#VAR_NAME} -eq 0 ]
293        then
294                echo "doing \"set_xio_file_type $@\". "
295                echo "xml_tag: file_definition with variable: type is empty"
296                echo "confirm that an appropriate file_definition is in \"${EXE_DIR}/$1\" "
297                echo "exit"
298                echo "error in executing script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
299                echo "....." >> ${SETTE_DIR}/output.sette
300                exit 1
301        fi
302        if [ $2 == "one_file" ] 
303        then
304           sed -e "s:multiple_file:one_file:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
305        else
306           sed -e "s:one_file:multiple_file:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
307        fi
308        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
309
310        echo "finished script : set_xio_file_type $@" >> ${SETTE_DIR}/output.sette
311        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
312        echo "                " >> ${SETTE_DIR}/output.sette
313}
314
315set_xio_using_server () {
316        minargcount=2
317        if [ ${#} -lt ${minargcount} ]
318        then
319                echo "not enough arguments for set_xio_using_server"
320                echo "${usage2}"
321                exit 1
322        fi
323        if [ $2 != "true" ] && [ $2 != "false" ]
324        then
325                echo "unrecognised argument for set_xio_using_server"
326                echo "${usage2}"
327                echo $2
328                exit 1
329        fi
330        unset minargcount
331        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
332                touch ${SETTE_DIR}/output.sette
333        fi
334
335        echo "executing script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
336        echo "################" >> ${SETTE_DIR}/output.sette
337
338        VAR_NAME=$( grep "^.*<.*variable id.*=.*using_server.*=.*bool" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
339        if [ ${#VAR_NAME} -eq 0 ]
340        then
341                echo "doing \"set_xio_using_server $@\". "
342                echo "xml_tag: "variable id=using_server" with variable: bool is empty"
343                echo "confirm that an appropriate variable id is in \"${EXE_DIR}/$1\" "
344                echo "exit"
345                echo "error in executing script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
346                echo "....." >> ${SETTE_DIR}/output.sette
347                exit 1
348        fi
349        if [ $2 == "false" ]
350        then
351           sed -e "/using_server/s:true:false:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
352           export USING_MPMD=no
353        else
354           sed -e "/using_server/s:false:true:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
355           export USING_MPMD=yes
356        fi
357        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
358
359        echo "finished script : set_xio_using_server $@" >> ${SETTE_DIR}/output.sette
360        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
361        echo "                " >> ${SETTE_DIR}/output.sette
362}
363
364set_xio_buffer_size () {
365        minargcount=2
366        if [ ${#} -lt ${minargcount} ]
367        then
368                echo "not enough arguments for set_xio_buffer_size"
369                echo "${usage4}"
370                exit 1
371        fi
372        unset minargcount
373        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
374                touch ${SETTE_DIR}/output.sette
375        fi
376
377        echo "executing script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
378        echo "################" >> ${SETTE_DIR}/output.sette
379
380        VAR_NAME=$( grep "^.*<.*variable id.*=.*buffer_size.*=.*integer" ${EXE_DIR}/$1 | sed -e "s% *\!.*%%" )
381        if [ ${#VAR_NAME} -eq 0 ]
382        then
383                echo "doing \"set_xio_buffer_size $@\". "
384                echo "xml_tag: "variable id=buffer_size" with variable: integer is empty"
385                echo "confirm that an appropriate variable id is in \"${EXE_DIR}/$1\" "
386                echo "exit"
387                echo "error in executing script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
388                echo "....." >> ${SETTE_DIR}/output.sette
389                exit 1
390        fi
391        sed -e "/buffer_size/s:>.*<:>$2<:" ${EXE_DIR}/$1 > ${EXE_DIR}/$1.tmp
392        mv ${EXE_DIR}/$1.tmp ${EXE_DIR}/$1
393
394        echo "finished script : set_xio_buffer_size $@" >> ${SETTE_DIR}/output.sette
395        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
396        echo "                " >> ${SETTE_DIR}/output.sette
397}
398
399set_xio_field_defs () {
400        minargcount=1
401        if [ ${#} -lt ${minargcount} ]
402        then
403                echo "not enough arguments for set_xio_field_defs"
404                echo "${usage5}"
405                exit 1
406        fi
407        unset minargcount
408        if [  ! -f ${SETTE_DIR}/output.sette ] ; then
409                touch ${SETTE_DIR}/output.sette
410        fi
411
412        echo "executing script : set_xio_field_defs $@" >> ${SETTE_DIR}/output.sette
413        echo "################" >> ${SETTE_DIR}/output.sette
414
415
416        [ -f ${EXE_DIR}/field_def_nemo-opa.xml ] || sed -i '/field_def_nemo-opa/d' $1
417        [ -f ${EXE_DIR}/field_def_nemo-lim.xml ] || sed -i '/field_def_nemo-lim/d' $1
418        [ -f ${EXE_DIR}/field_def_nemo-pisces.xml ] || sed -i '/field_def_nemo-pisces/d' $1
419
420        echo "finished script : set_xio_field_defs $@" >> ${SETTE_DIR}/output.sette
421        echo "++++++++++++++++" >> ${SETTE_DIR}/output.sette
422        echo "                " >> ${SETTE_DIR}/output.sette
423}
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