| 1 | #!/bin/bash |
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| 2 | |
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| 3 | |
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| 4 | ## Messenger filenames |
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| 5 | file_date=mesg_01_date.txt ; file_rslt=mesg_02_result.txt |
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| 6 | file_stat=mesg_03_status.txt; file_nemo=mesg_04_nemo.txt |
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| 7 | file_xios=mesg_05_xios.txt ; file_cmpf=mesg_06_compiler.txt |
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| 8 | file_lmpi=mesg_07_mpi.txt ; file_ncdf=mesg_08_netcdf.txt |
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| 9 | file_inpt=mesg_09_inputs.txt; file_time=mesg_10_time.txt |
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| 10 | file_memy=mesg_11_memory.txt; file_note=mesg_12_comments.txt |
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| 11 | |
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| 12 | |
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| 13 | ## Functions in order of use |
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| 14 | print_step() { |
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| 15 | local char_nb=$( echo "$1" | wc -c ) |
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| 16 | local outline=$( printf "%${char_nb}s" ) |
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| 17 | |
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| 18 | printf "\nStep.....\n%s\n%s\n" "$1" ${outline// /-} |
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| 19 | } |
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| 20 | |
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| 21 | init_files() { |
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| 22 | echo 'Date' > ${file_date}; echo 'Result' > ${file_rslt} |
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| 23 | echo 'Status' > ${file_stat}; echo 'NEMOGCM rev.' > ${file_nemo} |
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| 24 | echo 'XIOS rev.' > ${file_xios}; echo 'Fortran compiler' > ${file_cmpf} |
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| 25 | echo 'MPI libs' > ${file_lmpi}; echo 'NetCDF libs' > ${file_ncdf} |
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| 26 | echo 'Input files' > ${file_inpt}; echo 'Elapsed time' > ${file_time} |
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| 27 | echo 'Memory usage (P/V)' > ${file_memy}; echo 'Comments' > ${file_note} |
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| 28 | |
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| 29 | ## 'Failed' status with 'Unknown error' by default |
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| 30 | echo ${TRUS_RSLT} \ |
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| 31 | >> ${file_rslt} |
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| 32 | echo 'Unknown error' \ |
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| 33 | >> ${file_stat} |
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| 34 | } |
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| 35 | |
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| 36 | get_date() { |
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| 37 | ## UTC time zone for timestamping |
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| 38 | local dat=$( date -ud "${TRUS_DATE}" +"%F %R %Z" ) |
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| 39 | |
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| 40 | echo $dat \ |
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| 41 | >> ${file_date} |
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| 42 | } |
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| 43 | |
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| 44 | get_nemo_rev() { |
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| 45 | local dir rev_loc |
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| 46 | local rev=0 |
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| 47 | |
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| 48 | ## Loop on essential NEMO directories |
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| 49 | for dir in ${TRUS_CKOT} ${TRUS_XIOS}; do |
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| 50 | |
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| 51 | ## For time being, just get revision from XIOS with no action on directory |
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| 52 | if [ $dir == ${TRUS_XIOS} ]; then |
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| 53 | rev_loc=$( svn info $dir | awk '/Last Changed Rev/ {print $NF}' ) |
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| 54 | echo 'XIOS '${rev_loc} \ |
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| 55 | >> model.log |
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| 56 | echo "<a href=\"https://forge.ipsl.jussieu.fr/ioserver/changeset/${rev_loc}\" target=\"_blank\">${rev_loc}</a>" \ |
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| 57 | >> ${file_xios} |
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| 58 | continue |
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| 59 | fi |
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| 60 | |
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| 61 | echo $dir && ${TRUS_SVNA} ${TRUS_NGCM}/$dir |
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| 62 | rev_loc=$( svn info ${TRUS_NGCM}/$dir | awk '/Last Changed Rev/ {print $NF}' ) |
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| 63 | |
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| 64 | ## Keep last rev. nb |
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| 65 | [ ${rev_loc} -gt $rev ] && rev=${rev_loc} |
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| 66 | done |
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| 67 | |
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| 68 | echo 'NEMOGCM '$rev \ |
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| 69 | >> model.log |
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| 70 | echo "<a href=\"https://forge.ipsl.jussieu.fr/nemo/changeset/$rev\" target=\"_blank\">$rev</a>" \ |
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| 71 | >> ${file_nemo} |
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| 72 | } |
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| 73 | |
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| 74 | get_soft_rel() { |
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| 75 | local soft_rel str |
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| 76 | |
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| 77 | ## Sourcing environment |
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| 78 | if [ -n "${TRUS_ENVI}" ]; then |
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| 79 | if [[ -e ${TRUS_ENVI}.env && $( declare -F | grep ' module' ) ]]; then |
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| 80 | ## .env file if module function is available |
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| 81 | . ${TRUS_ENVI}.env |
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| 82 | else |
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| 83 | ## .path file if existing, if not the given file |
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| 84 | [ -e ${TRUS_ENVI}.path ] && . ${TRUS_ENVI}.path || . ${TRUS_ENVI} |
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| 85 | fi |
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| 86 | fi |
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| 87 | |
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| 88 | ## Problem with `prepend-path` of modulefile that use ':' instead of ' ' as delimiter |
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| 89 | [ $TRUS_HPCC == 'X64_ADA' ] && WRAPPER_LDFLAGS='-L/smplocal/pub/IdrMemMPI/1.4/lib -lidrmem '${WRAPPER_LDFLAGS} |
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| 90 | |
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| 91 | for str in ${TRUS_CMPV} ${TRUS_MPIR} ${TRUS_CDFR} ${TRUS_CDOR}; do |
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| 92 | [ -z "$str" ] && continue |
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| 93 | soft_rel='' |
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| 94 | |
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| 95 | ## Software release: next word after "$soft" in $PATH (case-insensitive) |
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| 96 | soft_rel=$( echo $PATH | sed "s#.*$str\([0-9.a-z_]*\).*#\1#i" ) |
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| 97 | |
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| 98 | ## option --version would work for main compilers (gfortran, intel, pgfortran, ...) |
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| 99 | [ $str == ${TRUS_CMPV} ] && soft_rel=$( $str --version | grep -m1 -oe '\<[0-9. ]*\>' ) |
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| 100 | |
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| 101 | ## Cleaning characters string to display proper soft name |
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| 102 | str=$( echo $str | sed 's#\\##g; s#[/-]$##' ) |
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| 103 | |
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| 104 | echo $str ${soft_rel} \ |
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| 105 | >> model.log |
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| 106 | done |
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| 107 | |
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| 108 | sed -n 3p model.log \ |
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| 109 | >> ${file_cmpf} |
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| 110 | sed -n 4p model.log \ |
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| 111 | >> ${file_lmpi} |
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| 112 | sed -n 5p model.log \ |
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| 113 | >> ${file_ncdf} |
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| 114 | } |
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| 115 | |
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| 116 | get_inputs() { |
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| 117 | # List archive content & extract it by default |
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| 118 | local get_iol=$( eval " |
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| 119 | for archive in ${TRUS_TARF}; do |
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| 120 | tar -tvf ${TRUS_FORC}/\$archive >> inputs_list.txt; |
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| 121 | done |
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| 122 | " ) |
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| 123 | local get_iof=$( eval " |
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| 124 | for archive in ${TRUS_TARF}; do |
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| 125 | tar -vxf ${TRUS_FORC}/\$archive > /dev/null; |
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| 126 | done |
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| 127 | " ) |
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| 128 | |
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| 129 | ## List & copy files in case of personal inputs |
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| 130 | if [ -z "${TRUS_TARF}" ]; then |
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| 131 | get_iol="ls ${TRUS_FORC}/*" |
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| 132 | get_iof="\cp ${TRUS_FORC}/* ." |
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| 133 | fi |
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| 134 | |
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| 135 | ${get_iol}; ${get_iof} |
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| 136 | |
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| 137 | if [ `find -name '*.gz' -print -quit` ]; then |
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| 138 | find . -name '*.gz' -exec gzip -d {} \; |
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| 139 | fi |
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| 140 | } |
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| 141 | |
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| 142 | diff_inputs() { |
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| 143 | local dif file |
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| 144 | local files_list='' mesg='Same' |
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| 145 | |
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| 146 | ## Simple diff |
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| 147 | for file in 'inputs_list.txt' *namelist_* *.xml cpp_*; do |
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| 148 | dif='' |
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| 149 | |
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| 150 | ## Continue even if input file is not in here (see after) |
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| 151 | if [ -e ${TRUS_STOR}/$file ]; then dif=$( diff -q $file ${TRUS_STOR}/$file ); else dif=0; fi |
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| 152 | |
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| 153 | ## Pass over useless file omission in benckmark directory |
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| 154 | [[ -n "$dif" && "$dif" != '0' ]] && { mesg='Different'; echo $dif; files_list+=$file' '; } |
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| 155 | done |
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| 156 | |
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| 157 | [ $mesg == 'Same' ] && echo $mesg |
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| 158 | echo $mesg \ |
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| 159 | >> ${file_inpt} |
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| 160 | |
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| 161 | ## List different files for web comment |
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| 162 | [ -n "${files_list}" ] && echo 'Inputs : '${files_list}'differ<br>' \ |
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| 163 | >> temp_${file_note} |
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| 164 | } |
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| 165 | |
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| 166 | job_pending() { |
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| 167 | local outline=$( printf "%100s" ) time_elapsed=0 time_increment=30 |
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| 168 | |
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| 169 | sleep ${time_increment} |
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| 170 | |
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| 171 | ## Append a log file while pending |
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| 172 | while [[ $( eval ${TRUS_JSTA} ) && ${time_elapsed} -lt ${TRUS_TOUT} ]]; do |
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| 173 | printf "\n%s\n" ${outline// /#} \ |
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| 174 | >> computation.log |
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| 175 | [ -n "${TRUS_JINF}" ] && eval ${TRUS_JINF} \ |
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| 176 | >> computation.log |
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| 177 | sleep ${time_increment} |
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| 178 | time_elapsed=$(( ${time_elapsed} + ${time_increment} )) |
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| 179 | done |
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| 180 | |
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| 181 | sleep ${time_increment} |
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| 182 | |
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| 183 | ## Kill remaining job & stop the test if it's too long |
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| 184 | [ ${time_elapsed} -eq ${TRUS_TOUT} ] && { eval ${TRUS_JKIL} &> /dev/null; get_out 6; } |
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| 185 | } |
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| 186 | |
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| 187 | diff_results() { |
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| 188 | local file |
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| 189 | local files_list='' mesg='Same' |
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| 190 | |
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| 191 | ## Simple diff |
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| 192 | for file in 'ocean.output' *.stat; do |
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| 193 | ## Stop if no benchmark files (ocean.output, eventual stat files) |
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| 194 | [ ! -e ${TRUS_STOR}/$file ] && { TRUS_RSLT='FAILED'; get_out 7; } |
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| 195 | |
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| 196 | diff -q $file ${TRUS_STOR}/$file |
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| 197 | |
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| 198 | ## Continue even if it differs |
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| 199 | [ $? -ne 0 ] && { TRUS_RSLT='FAILED'; mesg='Different'; files_list+=$file' '; } |
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| 200 | done |
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| 201 | |
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| 202 | [ $mesg == 'Same' ] && echo $mesg |
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| 203 | |
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| 204 | ## List different files for web comment |
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| 205 | [ -n "${files_list}" ] && echo 'Results : '${files_list}'differ<br>' \ |
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| 206 | >> temp_${file_note} |
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| 207 | } |
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| 208 | |
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| 209 | diff_restart() { |
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| 210 | local dif filebase filebases ndomain out |
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| 211 | local files_list='' dif_sum='undef' |
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| 212 | |
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| 213 | ## Find all restart files to rebuild |
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| 214 | if [ $( find -regex ".*_restart.*[0-9]\.nc" -print -quit ) ]; then |
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| 215 | filebases=$( find -regextype sed -regex ".*_[0-9]\{4\}\.nc" \ |
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| 216 | | sed 's/\(.*\)_.*/\1/' | sort -u ) |
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| 217 | |
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| 218 | for filebase in ${filebases}; do |
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| 219 | |
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| 220 | ndomain=$( find -regex ".*${name}_[0-9]*.nc" | wc -l | awk '{print $1}' ) |
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| 221 | |
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| 222 | [ ${ndomain} -eq 0 ] && TRUS_RSLT='FAILED' && get_out 8 |
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| 223 | |
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| 224 | ${TRUS_NGCM}/TOOLS/REBUILD_NEMO/rebuild_nemo \ |
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| 225 | -t ${TRUS_NPRO} $filebase ${ndomain} \ |
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| 226 | > /dev/null |
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| 227 | |
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| 228 | ## Possibility of remaining decomposed restarts (even after rebuild) |
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| 229 | [ $? -eq 0 ] && rm -f ${file}_[0-9]*.nc \ |
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| 230 | > /dev/null |
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| 231 | |
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| 232 | dif='' |
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| 233 | |
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| 234 | ## Stop if no benchmark files (restart file) |
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| 235 | if [ -e ${TRUS_STOR}/$file.nc ]; then |
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| 236 | |
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| 237 | out=$( $TRUS_CDOD $name.nc ${TRUS_STOR}/$name.nc 2>&1 ) |
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| 238 | dif=$( echo $out | grep -o "[0-9]* of [0-9]* records" ) |
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| 239 | |
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| 240 | ## Fix for cdo aborting on restarts with different inputs |
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| 241 | if [[ $out =~ 'Abort' ]]; then |
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| 242 | dif=$( echo $out | awk -F: '{print $NF}' ) |
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| 243 | fi |
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| 244 | |
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| 245 | if [ -n "$dif" ]; then |
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| 246 | export TRUS_RSLT='FAILED' |
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| 247 | files_list+=$name' ' && echo $name'.nc: '$dif |
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| 248 | let dif_sum+=$( echo $dif | awk '{print $1}' ) |
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| 249 | fi |
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| 250 | |
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| 251 | done |
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| 252 | |
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| 253 | ## Stop if no benchmark files (ie time.step) |
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| 254 | if [ ${dif_sum} == 'undef' ]; then |
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| 255 | TRUS_RSLT='FAILED' |
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| 256 | get_out 7 |
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| 257 | ## List different files for web comment with sum of different records |
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| 258 | elif [ ${dif_sum} -ne 0 ]; then |
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| 259 | echo 'Restarts: '${files_list}${dif_sum}' record(s) differ<br>' \ |
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| 260 | >> temp_${file_note} |
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| 261 | else |
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| 262 | echo 'Same' |
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| 263 | fi |
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| 264 | |
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| 265 | else |
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| 266 | TRUS_RSLT='FAILED' |
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| 267 | fi |
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| 268 | |
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| 269 | } |
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| 270 | |
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| 271 | get_time() { |
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| 272 | [ -z "${TRUS_JTIM}" ] && return |
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| 273 | |
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| 274 | ## Interest for checking unusual time computation |
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| 275 | local time_cpu=$( eval ${TRUS_JTIM} ) |
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| 276 | |
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| 277 | printf "Elapsed time: " |
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| 278 | echo ${time_cpu} | tee -a ${file_time} |
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| 279 | } |
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| 280 | |
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| 281 | get_memy() { |
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| 282 | [[ -z "${TRUS_JPME}" && -z "${TRUS_JVME}" ]] && return |
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| 283 | |
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| 284 | ## Interest for checking unusual memory usage |
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| 285 | local memory_pmax=$( eval ${TRUS_JPME} ) memory_vmax=$( eval ${TRUS_JVME} ) |
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| 286 | |
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| 287 | printf "Memory max usage (physical/virtual): " |
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| 288 | echo ${memory_pmax}' / '${memory_vmax} | tee -a ${file_memy} |
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| 289 | } |
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| 290 | |
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| 291 | comments() { |
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| 292 | local opat |
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| 293 | local line='' state=$1 |
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| 294 | |
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| 295 | if [ -e ocean.output ]; then |
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| 296 | ## 'W A R N I N G' pattern by default |
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| 297 | opat="-A2 \"^ $state\"" |
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| 298 | [ "$state" == 'E R R O R' ] && opat="-A4 \"$state\"" |
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| 299 | |
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| 300 | ## Select first occurence for web comment |
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| 301 | line=$( eval grep -m1 $opat ocean.output | tr -d '\n' ) |
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| 302 | fi |
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| 303 | |
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| 304 | [ -n "$line" ] && ( echo $line; printf "$line<br>" \ |
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| 305 | >> temp_${file_note} ) |
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| 306 | } |
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| 307 | |
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| 308 | log_make() { |
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| 309 | ## Format comments for web |
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| 310 | [ -e temp_${file_note} ] && cat temp_${file_note} | tr -d '\n' | sed 's/<br>$//' \ |
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| 311 | >> ${file_note} |
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| 312 | |
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| 313 | ## Construct txt file with all messenger files |
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| 314 | paste -d ';' mesg_*.txt | tee ${TRUS_FILE} |
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| 315 | } |
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| 316 | |
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| 317 | prod_publish() { |
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| 318 | local cmd |
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| 319 | local rev=$( awk '/NEMOGCM/ {print $NF}' model.log ) |
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| 320 | |
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| 321 | ## Production mode (-p|--prod) |
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| 322 | if [ ${TRUS_PROD} -eq 1 ]; then |
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| 323 | |
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| 324 | ## Create or append trusting logfile |
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| 325 | if [ -f ${TRUS_HIST} ]; then cmd='tail -1'; else cmd='cat'; fi |
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| 326 | |
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| 327 | $cmd ${TRUS_FILE} \ |
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| 328 | >> ${TRUS_HIST} |
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| 329 | |
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| 330 | ## Send mail only when FAILED |
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| 331 | if [[ ! -z "${TRUS_MAIL}" && ${TRUS_RSLT} == 'FAILED' ]]; then |
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| 332 | |
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| 333 | ## Content |
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| 334 | cat <<END_MAIL \ |
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| 335 | > trusting.mail |
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| 336 | Dear all, |
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| 337 | |
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| 338 | |
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| 339 | The trusting sequence has not completed successfully on new configuration ${TRUS_CONF} based on ${TRUS_REFE}. |
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| 340 | |
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| 341 | Here is the model summary: |
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| 342 | `cat model.log` |
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| 343 | |
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| 344 | First checking would be on the trusting environment files: |
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| 345 | ${TRUS_USER}.cfg & ${TRUS_HPCC}.cfg |
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| 346 | |
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| 347 | For more details, look into the testing folder at: |
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| 348 | ${TRUS_SCRA} |
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| 349 | |
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| 350 | An archive has been created to share the questionable configuration for further studies: |
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| 351 | ${TRUS_STOR}/${TRUS_ARCH} |
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| 352 | |
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| 353 | END_MAIL |
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| 354 | |
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| 355 | ## Send with detailed subject |
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| 356 | mail -s "[NEMO Trusting][$rev][${TRUS_BRAN}][${TRUS_REFE}] ${TRUS_RSLT} ${TRUS_RORR}" ${TRUS_MAIL} \ |
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| 357 | < trusting.mail |
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| 358 | fi |
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| 359 | |
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| 360 | fi |
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| 361 | } |
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| 362 | |
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| 363 | get_out() { |
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| 364 | local time_step=0 |
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| 365 | |
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| 366 | TRUS_RORR=$1 |
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| 367 | |
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| 368 | printf "\n\nEnd of test\n" |
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| 369 | |
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| 370 | ## In case of compilation error |
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| 371 | cd ${TRUS_SCRA} |
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| 372 | |
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| 373 | if [ ${TRUS_RSLT} == 'FAILED' ]; then |
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| 374 | echo 'Failure' |
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| 375 | |
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| 376 | ## Error identification |
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| 377 | case ${TRUS_RORR} in |
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| 378 | ## Compilation |
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| 379 | '1') TRUS_RORR='XIOS compilation failed' ;; '2') TRUS_RORR='NEMO compilation failed';; |
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| 380 | ## Submission |
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| 381 | '3') TRUS_RORR='Missing input files' ;; '4') TRUS_RORR='Job submission error' ;; |
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| 382 | ## Computation |
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| 383 | '5') TRUS_RORR='Crashed at time step' ;; '6') TRUS_RORR='Exceeded time limit' ;; |
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| 384 | ## Results |
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| 385 | '7') TRUS_RORR='Missing previous outputs';; '8') TRUS_RORR='New outputs differ' ;; |
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| 386 | ## Other |
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| 387 | '*') TRUS_RORR='Unknown error' ;; |
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| 388 | esac |
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| 389 | |
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| 390 | else |
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| 391 | echo 'Success' && TRUS_RORR='Code is reliable' |
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| 392 | fi |
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| 393 | |
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| 394 | ## Eventual comments from ocean.output |
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| 395 | if [ "${TRUS_RORR}" == 'Crashed at time step' ]; then |
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| 396 | comments 'E R R O R' |
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| 397 | [ -e time.step ] && time_step=$( grep -o [0-9]* time.step ) |
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| 398 | TRUS_RORR+=' '$time_step |
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| 399 | else |
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| 400 | comments 'W A R N I N G' |
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| 401 | [ "${TRUS_RORR}" == 'Exceeded time limit' ] && TRUS_RORR+=' '$(( ${TRUS_TOUT}/3600 ))'h' |
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| 402 | fi |
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| 403 | |
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| 404 | ## Last messenger files |
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| 405 | #export TRUS_RORR |
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| 406 | sed -i "2 s/.*/$TRUS_RSLT/" ${file_rslt}; sed -i "2 s/.*/$TRUS_RORR/" ${file_stat} |
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| 407 | |
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| 408 | ## Save tested configuration if trusting failed in production mode (-p|--prod) |
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| 409 | if [[ ${TRUS_RSLT} == 'FAILED' && ${TRUS_PROD} -eq 1 ]]; then |
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| 410 | echo 'Creating archive '${TRUS_ARCH}' under '${TRUS_STOR} |
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| 411 | tar -czf ${TRUS_STOR}/${TRUS_ARCH} * \ |
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| 412 | -C ${TRUS_NGCM}/CONFIG/${TRUS_CONF}/MY_SRC . \ |
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| 413 | -C ${TRUS_NGCM}/CONFIG/${TRUS_CONF} cpp_${TRUS_CONF}.fcm |
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| 414 | fi |
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| 415 | |
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| 416 | ## Logfile construct & eventual sending of notification email |
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| 417 | printf "\nTrusting digest:\n----------------\n" |
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| 418 | log_make |
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| 419 | prod_publish |
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| 420 | |
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| 421 | exit 0 |
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| 422 | } |
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