1 | #!/bin/bash |
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2 | # This script sets up and launches a (series of) simulation(s). |
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3 | # RECOMMENDATION: use main.sh to drive it (do not run it directly) |
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4 | |
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5 | set -eu |
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6 | |
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7 | # EXPERT-LEVEL CHOICES, only available in setup.sh, not in main.sh : |
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8 | #################################################################### |
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9 | function define_expert_options { |
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10 | #NOTE : $optim is part of $LMDZname (see definition of LMDZname below), |
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11 | # so that running with "-debug" needs to (re)install the model (install=-install in main.sh) |
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12 | # If you have already installed the model, and only want to recompile the gcm in debug mode, |
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13 | # add "-debug" to the compilation options in the compile.sh script created in the present folder, and run it (./compile.sh gcm) |
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14 | # ALTERNATIVELY : you can remove $optim in the definition of "LMDZname" below |
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15 | optim="" |
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16 | #optim="-debug" |
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17 | |
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18 | #NOTE : "testmode=y" is for running in test mode : |
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19 | # the simulation job "tmp_$SIM" (created on $SCRATCHDIR) is automatically changed for a short run, |
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20 | # and submitted to the Jean-Zay "test" queue : |
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21 | # a/ time=00:10:00 (run time limit = 10 min; for test queue, it must be 30 min maximum) |
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22 | # b/ nday=1 (this line, forcing nday to 1 day, is "hidden" in script_SIMU, by default it is commented out) |
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23 | # c/ #SBATCH --qos=qos_cpu-dev (this line is in script_SIMU, by default it is commented out) |
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24 | #If you want to change "time", or "nday", but still run in "test" mode, modify the "if [ $debug = 1 ]...; fi" further below. |
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25 | testmode=n |
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26 | |
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27 | # Radiative code : "oldrad" or "rrtm" or "ecrad" |
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28 | rad="rrtm" |
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29 | |
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30 | # AEROSOLS : n (=no) / clim (=average 1995-2014) / spla (interactive dust and sea salt) |
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31 | # (WARNING : if you first run the scripts with aerosols=n, then you want to change to =clim , |
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32 | # you'll need to remove the INIT and LIMIT folders that have been created, then run main.sh with init=1 |
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33 | # in order to re-run the initialisation job, which downloads the aerosol files and interpolates them) |
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34 | aerosols="clim" |
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35 | |
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36 | # SURFACE/VEGETATION SCHEME |
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37 | # It is controlled by the single variable "veget" which can have the following values |
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38 | # - "none": bucket scheme |
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39 | # - "CMIP6" or "orch2.0": orchidee version used in CMIP exercise, rev 5661 |
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40 | # - "orch2.2": orchidee version used in IPSLCM7 configuration |
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41 | # - number: orchidee version number : only rev 7983 on branch _2_2, and 7994 on trunk, are available |
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42 | veget="CMIP6" |
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43 | #AS : If you have installed the model with a given "veget" option, and you want to change it : |
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44 | # --> RECOMMENDED : re-install the model from scratch in a new TEST_PROD folder |
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45 | # TODO Amaury: check w/ Adriana what the use case is for lmdz_setup here |
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46 | # --> EXPERT : If you want to keep your previous installation, and not go through the install_lmdz.sh routine, |
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47 | # you will need to (a) install the proper version of ORCHIDEE in the modipsl/modeles directory, and |
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48 | # (b) set the "veget" options (opt_veget, orchidee_rev, suforch) to their proper values |
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49 | # in the file $LMDZD/modipsl/modeles/surface_env |
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50 | # (NB : no need to initialise these vars here: |
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51 | # surface_env is either (re)created when (re)installing the model (run with install=-install), |
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52 | # or it already exists (install=""). |
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53 | |
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54 | # New snow scheme INLANDSIS (y/n) |
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55 | # (this flag activates INLANDSIS compilation; |
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56 | # not yet done : treatment of specific restart and def file) |
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57 | inlandsis="n" |
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58 | |
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59 | # --->>> ALSO PAY ATTENTION TO OUTPUT files, frequency, level ------------- |
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60 | # With IOIPSL : Choose your config.def among the versions available in DEF, |
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61 | # copy it as config.def (the copy is done automatically for "iso"), |
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62 | # edit it and set up output files, frequencies and levels. |
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63 | # NB : For aerosols=spla, output level minimum 4 is required to output the specific variables. |
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64 | # For aerosols=n, the corresponding flags will automatically be set to "n". |
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65 | # With XIOS : adjust DEF/XMLfiles*/file*xml |
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66 | } |
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67 | |
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68 | # /!\ DO NOT EDIT BELOW UNLESS YOU KNOW WHAT YOU ARE DOING /!\ |
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69 | |
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70 | function enable_groupe { # In job scripts, sed platform-specific headers |
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71 | local file="$1" |
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72 | local platform |
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73 | |
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74 | case ${hostname:0:5} in |
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75 | jean-) platform="JZ";; |
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76 | *) echo "Warning: $hostname is not a known job platform (ignore if running locally)"; return 0;; |
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77 | esac |
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78 | |
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79 | sed -i'' -e "s/^#@$platform//" "$file" |
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80 | } |
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81 | |
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82 | function load_install_lib { |
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83 | # Fetch and source install_lmdz.sh to get `myget` |
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84 | if [[ ! -f "install_lmdz.sh" ]]; then |
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85 | wget "http://svn.lmd.jussieu.fr/LMDZ/BOL/script_install_amaury/install_lmdz.sh" # TODO change to normal branch once ready |
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86 | fi |
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87 | # shellcheck disable=SC1090 |
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88 | source <(sed 's/function \(.*\) {/function installlmdz_\1 {/g' install_lmdz.sh) # source with a namespace for functions |
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89 | function myget { installlmdz_myget "$@"; } |
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90 | } |
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91 | |
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92 | function set_default_params { |
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93 | # Default value of script parameters |
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94 | SIM=$(basename "$local")CTL # name |
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95 | phylmd="lmd" #option -p $phylmd for makelmdz |
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96 | |
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97 | cosp="n" # COSP |
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98 | xios="n" #XIOS |
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99 | |
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100 | # Nudging : |
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101 | ok_guide="n" |
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102 | # With nudging, use real calendar (climato=0) and monthly integrations |
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103 | climato=1 |
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104 | freq="mo" # frequence mensuelle mo ou annuelle yr |
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105 | |
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106 | # NB : the run stops in the BEGINNING of mthend (test "next=stopsim") |
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107 | mthini=200001 |
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108 | mthend=200501 |
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109 | resol="144x142x79" |
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110 | |
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111 | version="20230412.trunk" |
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112 | svn="" |
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113 | |
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114 | init=1 |
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115 | |
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116 | LIMIT="LIMIT" |
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117 | |
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118 | ###################################################################### |
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119 | # Choix du nombre de processeurs |
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120 | # NOTES : |
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121 | # omp=8 by default (for Jean-Zay must be a divisor of 40 procs/node), but we need |
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122 | # omp=1 for SPLA (only MPI parallelisation) |
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123 | # omp=2 for veget=CMIP6 beacause of a bug in ORCHIDEE/src_xml/xios_orchidee.f90 |
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124 | ###################################################################### |
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125 | jm=$(echo "$resol" | cut -dx -f2) |
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126 | (( mpi = ( jm + 1 ) / 2 )) |
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127 | omp=8 |
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128 | if [[ $aerosols = "spla" ]]; then omp=1; fi |
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129 | if [[ $veget = "CMIP6" && $xios = "y" ]]; then omp=2; fi |
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130 | if [[ $mpi -gt $NB_MPI_MAX ]]; then mpi=$NB_MPI_MAX; fi |
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131 | if [[ $omp -gt $NB_OMP_MAX ]]; then omp=$NB_OMP_MAX; fi |
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132 | |
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133 | case $rad in |
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134 | oldrad) iflag_rrtm=0; NSW=2;; |
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135 | rrtm) iflag_rrtm=1; NSW=6;; |
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136 | ecrad) iflag_rrtm=2; NSW=6;; |
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137 | esac |
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138 | } |
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139 | |
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140 | function read_cmdline_args { |
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141 | while (($# > 0)); do |
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142 | case $1 in |
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143 | "-h") cat <<........fin |
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144 | setup.sh can be launched/driven by main.sh; some options can only be specified in setup.sh (ex: veget, aerosols). |
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145 | setup.sh [-v version] [-r svn_release] [-init INIT] [-d 96x95x79] [-f mo] [-nudging] |
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146 | -v "version" like 20150828.trunk; see https://lmdz.lmd.jussieu.fr/Distrib/LISMOI.trunk (default <$version>) |
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147 | -r "svn_release" either the svn release number or "last" (default <$svn>) |
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148 | -d IMxJMxLM to run in resolution IM x JM x LM (default <$resol>) |
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149 | -install pour installer et compiler le modele |
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150 | -f mo/yr pour tourner en mensuel ou annuel (default <$freq>) |
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151 | "INIT" 1: creates INIT and LIMIT |
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152 | 0: reads from INIT and LIMIT |
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153 | SIMU: reads from preexisting simulation SIMU and LIMIT (default <$init>) |
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154 | -nudging to run with nudging. Nudging files must be created independently |
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155 | -p the physics to use (default <$phylmd>) |
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156 | -name install folder name (default <$SIM>) |
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157 | Other options available (see "options" section in the script) |
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158 | ........fin |
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159 | exit;; |
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160 | "-v") version="$2"; shift; shift;; |
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161 | "-r") svn=$2; shift; shift;; |
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162 | "-d") resol=$2; shift; shift;; |
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163 | "-f") freq=$2; shift; shift;; |
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164 | "-p") phylmd=$2; shift; shift;; |
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165 | "-name") SIM=$2; shift; shift;; |
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166 | "-cosp") cosp=y; shift;; |
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167 | "-xios") xios=y; shift;; |
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168 | "-init") init=$2; shift; shift;; |
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169 | "-nudging") ok_guide=y; shift;; |
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170 | "-climato") climato=$2; shift; shift;; |
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171 | "-mthini") mthini=$2; shift; shift;; |
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172 | "-mthend") mthend=$2; shift; shift;; |
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173 | *) echo "unexpected $1"; $0 -h; exit |
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174 | esac |
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175 | done |
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176 | |
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177 | # Initialisation |
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178 | if [[ $init = 1 || $init = 0 ]]; then |
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179 | INIT="INIT" |
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180 | else |
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181 | INIT=$init |
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182 | fi |
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183 | |
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184 | yearini=$(echo "$mthini" | cut -c-4) |
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185 | if [[ $freq = yr ]]; then stopsim=$(echo "$mthend" | cut -c-4); else stopsim=$mthend; fi |
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186 | |
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187 | if [[ -d $SIM ]]; then |
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188 | echo "La simulation $SIM existe deja. Il est conseillé d'arrêter et de vérifier." |
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189 | echo "Si vous êtes sûr de vous, vous pouvez la prolonger. Voulez vous la prolonger ? (y/n)" |
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190 | read -r ans |
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191 | if [[ $ans != y ]]; then exit 1; fi |
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192 | fi |
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193 | } |
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194 | |
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195 | function ensure_correct_option_combinations { |
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196 | # AVOID COMBINATIONS OF OPTIONS THAT DON'T WORK in user choices |
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197 | if [[ $ok_guide = y && $climato = 1 ]]; then |
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198 | echo "STOP: Running nudged simulations with climatological SSTs is not planned. Change <climato> to <0> or modify the setup (experts)"; exit 1 |
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199 | fi |
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200 | |
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201 | if [[ $climato = 0 && $freq = yr ]]; then |
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202 | echo "STOP: Running simulations with interannual SSTs is possible only month by month and a true calendar." |
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203 | echo "Change <climato> to <1> or <freq> to <mo> or modify setup.sh (experts)"; exit 1 |
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204 | fi |
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205 | |
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206 | |
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207 | # (Temporary) Constraints for aerosols=spla : |
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208 | # --> resolution 128x88x79 and rad=rrtm |
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209 | if [[ $aerosols = 1 && $resol != "128x88x79" ]]; then |
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210 | echo 'STOP: For now, <aerosols=spla> requires <resol=128x88x79>, and uses the zoomed grid from gcm.def_zNAfrica_BiJe, for which forcing & initial files are available' |
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211 | echo "Right now resol=<$resol>" |
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212 | exit 1 |
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213 | fi |
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214 | } |
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215 | |
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216 | function install_model { |
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217 | mkdir -p "$LMDZD" |
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218 | |
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219 | local ins_xios ins_cosp ins_aero ins_inlandsis |
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220 | if [[ $xios = "y" ]]; then ins_xios="-xios"; else ins_xios=""; fi |
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221 | if [[ $cosp = "y" ]]; then ins_cosp="-cosp v1"; else ins_cosp=""; fi |
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222 | if [[ $aerosols = "spla" ]]; then ins_aero="-spla"; else ins_aero=""; fi |
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223 | if [[ $inlandsis = "y" ]]; then ins_inlandsis="-inlandsis"; else ins_inlandsis=""; fi |
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224 | if [[ -n $svn ]]; then svnopt="-r $svn"; else svnopt=""; fi |
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225 | |
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226 | version_name=LMDZ$(echo "$version" | sed -e 's/-v//g' -e 's/-unstable//' -e 's/-r/r/' -e 's/ //g') |
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227 | LMDZname="${version_name}${svn}OR$veget${ins_xios}" |
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228 | MODEL="$LMDZD/$LMDZname/modipsl/modeles/LMDZ" |
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229 | |
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230 | if [[ -d $MODEL ]]; then echo "Found existing install at MODEL=$MODEL"; fi |
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231 | echo "Installing model" |
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232 | cd "$LMDZD" |
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233 | cp "$local/install_lmdz.sh" . |
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234 | chmod +x install_lmdz.sh |
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235 | # TODO handle arch/env here (used to be -env-file) |
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236 | echo "./install_lmdz.sh -noclean $optim -v $version $svnopt -d $resol -rad $rad -bench 0 -parallel mpi_omp $ins_cosp $ins_xios $ins_aero $ins_inlandsis -name $LMDZname -veget $veget -netcdf 0 -arch $ARCH" >> install_lmdz_options.$$.sh |
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237 | chmod +x install_lmdz_options.$$.sh |
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238 | echo "Running install_lmdz_options.$$.sh" |
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239 | gcm=$MODEL/$(./install_lmdz_options.$$.sh | tee /dev/tty | tail -n 1 | sed -n "s:.* executable is \(.*\.e\).*:\1:p") |
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240 | mv install_lmdz.sh install_lmdz.$$.sh |
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241 | cd "$local" |
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242 | } |
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243 | |
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244 | function setup_def { # modify various .def in ./DEF (+ xios xml as needed) |
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245 | cd "$local" |
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246 | |
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247 | # Utilisation des .def_iso pour LMDZ-ISOtopes |
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248 | if [[ $phylmd = "lmdiso" ]]; then |
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249 | for file_iso in $(ls DEF | grep _iso); do |
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250 | cp DEF/"$file_iso" DEF/"${file_iso%%_iso}" |
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251 | done |
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252 | fi |
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253 | |
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254 | ###################################################################### |
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255 | # Choix de la grille verticale |
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256 | ###################################################################### |
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257 | lm=$(echo "$resol" | cut -dx -f3) |
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258 | if [ ! -f "DEF/L$lm.def" ]; then |
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259 | echo "STOP: Résolution verticale non prévue - créer un fichier DEF/L$lm.def"; exit 1 |
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260 | else |
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261 | sed -i'' -e "s/INCLUDEDEF=L.*.def/INCLUDEDEF=L$lm.def/" DEF/run.def |
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262 | fi |
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263 | |
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264 | ###################################################################### |
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265 | # Changements dans les fichiers DEF/*def |
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266 | # (ils vont se repercuter dans les repertoires de simulation $local/$SIM et de run $SIMRUNDIR) |
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267 | ###################################################################### |
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268 | |
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269 | # Choix du fichier traceur.def coherent avec l'option "aerosols" |
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270 | # NOTE : Le nouveau tracer.def_nospla par defaut n'inclut pas Rn-Pb; |
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271 | # si on les veut, il faut utiliser ci-dessous; a la place, tracer_RN_PB.def |
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272 | #--------------------------------------------------------------------- |
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273 | # NB: Si on change de traceur.def (entre spla et nospla), il faut refaire l'etape "initialisation" (ce0l)? |
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274 | # Normalement les traceurs absents de start* files sont initialises=0 dans le code; verifier pour spla ! |
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275 | if [[ $aerosols = "spla" ]]; then |
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276 | # ancien traceur pour l instant |
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277 | cp DEF/traceur.def_spla DEF/traceur.def |
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278 | elif [[ $phylmd = "lmdiso" ]]; then |
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279 | # nouveau traceur , déjà copié si 'y' |
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280 | cp DEF/tracer.def_nospla DEF/tracer.def |
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281 | fi |
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282 | |
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283 | # TEMPORAIREMENT pour spla on force l'utilisation de gcm.def_zNAfrica_BiJe (avec resolution 128x88x79) |
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284 | #---------------------------------------------------------------------- |
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285 | if [[ $aerosols = spla ]]; then cp DEF/gcm.def_zNAfrica_BiJe DEF/gcm.def; fi |
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286 | |
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287 | # Inscription du choix ok_guide dans DEF/guide.def |
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288 | #--------------------------------------------------------------------- |
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289 | sed -i'' -e 's/ok_guide=.*.$/ok_guide='$ok_guide'/' DEF/guide.def |
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290 | |
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291 | # Inscription du type de calendrier (qui est fonction de $climato) dans DEF/run.def |
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292 | #--------------------------------------------------------------------- |
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293 | # NB Contrairement a ce qui est ecrit dans les fichiers run.def standard, |
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294 | # dans ce tutorial le choix earth_365d n'est pas disponible, et earth_366d s'appelle gregorian |
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295 | if [[ $climato = 0 ]]; then calend="gregorian"; else calend="earth_360d"; fi |
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296 | sed -i'' -e 's/calend=.*.$/calend='$calend'/' DEF/run.def |
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297 | |
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298 | # Changements dans config.def (pre-choisi, et regle pour output si utilisation avec IOIPSL) |
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299 | # cf options veget, aerosols, cosp, xios |
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300 | #--------------------------------------------------------------------- |
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301 | if [[ $veget = none ]]; then VEGET="n"; else VEGET="y"; fi |
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302 | sed -i'' -e 's/VEGET=.*.$/VEGET='$VEGET'/' DEF/config.def |
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303 | |
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304 | if [[ $aerosols = "n" ]]; then |
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305 | # set flag_aerosols=0 and flags ok_ade&co=n |
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306 | sed -i'' -e 's/^ok_cdnc=.*.$/ok_cdnc=n/' -e 's/^ok_ade=.*.$/ok_ade=n/' -e 's/^ok_aie=.*.$/ok_aie=n/' -e 's/^ok_alw=.*.$/ok_alw=n/' -e 's/^flag_aerosol=.*.$/flag_aerosol=0/' DEF/config.def |
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307 | fi |
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308 | |
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309 | # COSP : ok_cosp desactive COSP si on a compile avec; il ne l'active pas si on a compile sans |
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310 | sed -i'' -e 's/ok_cosp.*.$/ok_cosp='$cosp'/' DEF/config.def |
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311 | if [[ $cosp = "y" ]]; then \cp -f "$MODEL"/DefLists/cosp*.txt "$local"/DEF/; fi |
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312 | |
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313 | # Sorties LMDZ en fonction de l'option "xios" |
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314 | sed -i'' -e 's/ok_all_xml=.*.$/ok_all_xml='$xios'/' DEF/config.def |
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315 | |
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316 | # Ajuster physiq.def en fonction de radiative code (default: values for rad=rrtm) |
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317 | # Pour isotopes=y , mettre iflag_ice_thermo=0 au lieu de 1 |
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318 | #--------------------------------------------------------------------- |
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319 | sed -i'' -e 's/iflag_rrtm=.*.$/iflag_rrtm='"$iflag_rrtm"'/' -e 's/NSW=.*.$/NSW='"$NSW"'/' DEF/physiq.def |
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320 | sed -i'' -e 's:directory_name.*$:directory_name="'"$local"'/ecrad_data",:' DEF/namelist_ecrad |
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321 | |
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322 | if [[ $phylmd = "lmdiso" ]]; then iflag_ice_thermo=0; else iflag_ice_thermo=1; fi |
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323 | sed -i -e 's/iflag_ice_thermo=.*.$/iflag_ice_thermo='$iflag_ice_thermo'/' DEF/physiq.def |
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324 | |
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325 | # Choix de orchidee.def en fonction de orchidee_rev; modification pour xios |
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326 | # NOTE separate orchidee_pft.def file for ORCHIDEE trunk post-CMIP6 |
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327 | #--------------------------------------------------------------------- |
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328 | orchidee_def=orchidee.def_6.1 |
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329 | orchidee_pft_def="" |
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330 | if [[ $veget = "7983" ]]; then |
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331 | orchidee_def=orchidee.def_6.2work |
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332 | elif [[ $veget = "7994" ]]; then |
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333 | orchidee_def=orchidee.def_6.4work |
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334 | orchidee_pft_def=orchidee_pft.def_6.4work |
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335 | if ! grep "INCLUDEDEF=orchidee_pft.def" DEF/run.def; then |
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336 | sed -i'' -e 's/INCLUDEDEF=orchidee.def/INCLUDEDEF=orchidee.def\nINCLUDEDEF=orchidee_pft.def/' DEF/run.def; fi |
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337 | fi |
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338 | cp -f DEF/$orchidee_def DEF/orchidee.def |
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339 | if [[ $orchidee_pft_def != "" ]]; then cp -f DEF/$orchidee_pft_def DEF/orchidee_pft.def; fi |
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340 | |
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341 | # Only for veget=CMIP6 it is still possible to use IOIPSL; newer versions of orchidee.def have XIOS_ORCHIDEE_OK = y |
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342 | sed -i'' -e 's/XIOS_ORCHIDEE_OK =.*.$/XIOS_ORCHIDEE_OK = '$xios'/' DEF/orchidee.def |
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343 | |
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344 | ###################################################################### |
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345 | # Si on tourne avec XIOS, mise a jour des fichiers context et field* dans XMLfilesLMDZ |
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346 | # (ils vont se repercuter dans les repertoires de simulation $local/$SIM et de run $SIMRUNDIR) |
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347 | ###################################################################### |
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348 | if [[ $xios = y ]]; then |
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349 | cp -f "$MODEL"/DefLists/context_lmdz.xml "$local"/DEF/XMLfilesLMDZ/. |
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350 | cp -f "$MODEL"/DefLists/field_def_lmdz.xml "$local"/DEF/XMLfilesLMDZ/. |
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351 | if [[ $cosp = y ]]; then cp -f "$MODEL"/DefLists/field_def_cosp1.xml "$local"/DEF/XMLfilesLMDZ/.; fi |
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352 | fi |
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353 | } |
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354 | |
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355 | function setup_ce0l { # Verification de l'existance de l'état initial, compilation eventuelle pour sa creation |
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356 | if [[ ! -d $INIT ]]; then |
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357 | if [[ $init = 0 ]]; then |
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358 | echo "STOP: Récuperer les repertoires $INIT ou lancer avec option -init"; exit 1 |
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359 | else |
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360 | # Compile ce0l |
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361 | cd "$MODEL" |
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362 | sed -e 's/gcm$/ce0l/' compile.sh > compile_ce0l.sh; chmod +x compile_ce0l.sh |
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363 | echo "Compiling ce0l" |
---|
364 | if ! ./compile_ce0l.sh &> ce0l.log; then echo "STOP: ce0l compilation failed, see $MODEL/ce0l.log"; exit 1; fi |
---|
365 | echo "Compiled ce0l" |
---|
366 | ce0l=${gcm/gcm/ce0l} |
---|
367 | |
---|
368 | cd "$local" |
---|
369 | fi |
---|
370 | elif [[ $init = 1 ]]; then |
---|
371 | echo "STOP: Vous essayez d initialiser le modele mais $INIT existe deja"; exit 1 |
---|
372 | fi |
---|
373 | } |
---|
374 | |
---|
375 | function setup_simu { |
---|
376 | SIMRUNTOPDIR="$SIMRUNBASEDIR/$(basename "$local")" |
---|
377 | SIMRUNDIR=$SIMRUNTOPDIR |
---|
378 | mkdir -p "$SIMRUNDIR" |
---|
379 | cd "$SIMRUNDIR" |
---|
380 | echo "La simulation s'exécutera sur $SIMRUNDIR" |
---|
381 | |
---|
382 | ##################################################################### |
---|
383 | # Creation du repertoire $SIM s'il n'existe pas deja |
---|
384 | ##################################################################### |
---|
385 | if [[ ! -d $local/$SIM ]]; then |
---|
386 | mkdir "$local/$SIM" |
---|
387 | cd "$local" |
---|
388 | |
---|
389 | # Edit reb.sh |
---|
390 | cp reb.sh "$local/$SIM/reb.sh"; chmod +x "$local/$SIM/reb.sh" |
---|
391 | sed -i'' -e "s:^rebuild=.*.$:rebuild=$LMDZD/$LMDZname/modipsl/bin/rebuild:" \ |
---|
392 | -e "s/@@groupe/$GROUPE/" "$local/$SIM/reb.sh" |
---|
393 | enable_groupe "$local/$SIM/reb.sh" |
---|
394 | |
---|
395 | # Copy .def |
---|
396 | cp lmdz_env.sh "$local/$SIM/" |
---|
397 | mkdir "$local/$SIM/DEF"; cp DEF/*def DEF/namelis* "$local/$SIM/DEF/" |
---|
398 | #Pour XIOS, respectivement COSP, copier aussi les fichiers *xml / *txt |
---|
399 | if [[ $cosp = "y" ]]; then cp DEF/cosp*txt "$local/$SIM/DEF/"; fi |
---|
400 | if [[ $xios = "y" ]]; then |
---|
401 | cp DEF/XMLfilesLMDZ/*xml "$local/$SIM/DEF/" |
---|
402 | if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml "$local/$SIM/DEF/"; fi |
---|
403 | fi |
---|
404 | chmod u+w "$local/$SIM"/DEF/* |
---|
405 | |
---|
406 | # Gestion du calendrier |
---|
407 | ####################### |
---|
408 | cd "$SIM" |
---|
409 | sed -i'' -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def |
---|
410 | if [[ $freq = "yr" ]]; then date=$yearini; else date=$mthini; fi |
---|
411 | echo "$date a faire" >| etat |
---|
412 | |
---|
413 | # Recuperation des fichiers : executable initiaux et forcages |
---|
414 | ############################################################# |
---|
415 | echo "date: $date" |
---|
416 | for f in start startphy; do |
---|
417 | inf=../$INIT/$f.$date.nc |
---|
418 | if [[ -f $inf || $init = 1 ]]; then ln -s "$inf" ./; else echo "STOP: $inf missing"; exit ; fi; |
---|
419 | done |
---|
420 | for f in sechiba stomate; do |
---|
421 | if [[ -f ../$INIT/start_$f.$date.nc ]]; then ln -sf "../$INIT/start_$f.$date.nc" .; fi |
---|
422 | done |
---|
423 | cp "$gcm" gcm.e |
---|
424 | fi |
---|
425 | cd "$local"/.. |
---|
426 | |
---|
427 | ##################################################################### |
---|
428 | echo "Modification du script de lancement" |
---|
429 | ##################################################################### |
---|
430 | local cput |
---|
431 | if [[ $freq = "yr" ]]; then cput="04:00:00"; else cput="01:00:00"; fi |
---|
432 | local isotopes="n" |
---|
433 | if [[ $phylmd = "lmdiso" ]]; then isotopes="y"; fi |
---|
434 | sed -e "s/@@groupe/$GROUPE/" \ |
---|
435 | -e "s/NOM_SIMU/$SIM/" \ |
---|
436 | -e "s/time=.*.$/time=$cput/" \ |
---|
437 | -e "s/ntasks=.*.$/ntasks=$mpi/" \ |
---|
438 | -e "s/cpus-per-task=.*.$/cpus-per-task=$omp/" \ |
---|
439 | -e "s/nthreads=.*./nthreads=$omp/" \ |
---|
440 | -e "s/MAINDIR=.*.$/MAINDIR=$(basename "$local")/" \ |
---|
441 | -e "s:STORED=.*.*:STORED=$(dirname $local):" \ |
---|
442 | -e "s:SCRATCHD=.*.*:SCRATCHD=$SIMRUNBASEDIR:" \ |
---|
443 | -e "s/stopsim=.*.$/stopsim=$stopsim/" \ |
---|
444 | -e "s/^veget=.*.$/veget=$veget/" \ |
---|
445 | -e "s/^aerosols=.*.$/aerosols=$aerosols/" \ |
---|
446 | -e "s/^isotopes=.*.$/isotopes=$isotopes/" \ |
---|
447 | -e "s/^climato=.*.$/climato=$climato/" \ |
---|
448 | -e "s/^ok_guide=.*.$/ok_guide=$ok_guide/" \ |
---|
449 | "$local/script_SIMU" >| "$SIMRUNDIR/tmp_$SIM" |
---|
450 | |
---|
451 | enable_groupe "$SIMRUNDIR/tmp_$SIM" |
---|
452 | |
---|
453 | if [[ $testmode = "y" ]]; then |
---|
454 | sed -i'' -e "s/time=.*.$/time=00:30:00/" -e "s/#nday=1/nday=1/" -e "s/#@TESTQ//" "$SIMRUNTOPDIR/tmp_$SIM" |
---|
455 | fi |
---|
456 | } |
---|
457 | |
---|
458 | function fetch_simu_init_files { |
---|
459 | ##################################################################### |
---|
460 | echo "Recuperation eventuelle de certains fichiers sur $LMDZ_INIT" |
---|
461 | ##################################################################### |
---|
462 | mkdir -p "$LMDZ_INIT" |
---|
463 | |
---|
464 | #------------------------------------------------------------------- |
---|
465 | # Fichiers ORCHIDEE |
---|
466 | #------------------------------------------------------------------- |
---|
467 | get="myget 3DInputData/Orchidee/" |
---|
468 | cd "$LMDZ_INIT"; |
---|
469 | for file in "PFTmap_IPCC_2000.nc" "cartepente2d_15min.nc" "routing.nc" "routing_simple.nc" "lai2D.nc" "soils_param.nc" "woodharvest_2000.nc" "PFTmap_15PFT.v1_2000.nc"; do |
---|
470 | if [[ ! -f $file ]]; then ${get}$file; fi |
---|
471 | done |
---|
472 | cd - > /dev/null |
---|
473 | # Additionnal files needed for ORCHIDEE trunk post-CMIP6 |
---|
474 | if [[ $veget = 7994 && ! -f $LMDZ_INIT/soil_bulk_and_ph.nc ]]; then |
---|
475 | cd "$LMDZ_INIT" |
---|
476 | ${get}soil_bulk_and_ph.nc; ${get}NITROGEN_for_ORtrunk.tar |
---|
477 | tar -xvf NITROGEN_for_ORtrunk.tar; cd - > /dev/null |
---|
478 | fi |
---|
479 | #------------------------------------------------------------------- |
---|
480 | # Fichiers aerosols/chimie |
---|
481 | #------------------------------------------------------------------- |
---|
482 | if [[ $aerosols = "clim" ]]; then |
---|
483 | get="myget 3DInputData/AerChem/" |
---|
484 | #liste_get="aerosols1850_from_inca.nc aerosols2000_from_inca.nc" |
---|
485 | #aerosols9999_from_inca.nc est un lien vers aerosols1995_2014_ensavg_from_inca.nc |
---|
486 | cd "$LMDZ_INIT" |
---|
487 | for file in "aerosols1850_from_inca.nc" "aerosols9999_from_inca.nc"; do |
---|
488 | if [[ ! -f $file ]]; then ${get}$file; fi |
---|
489 | done |
---|
490 | cd - > /dev/null |
---|
491 | fi |
---|
492 | # For SPLA |
---|
493 | #------------------- |
---|
494 | # Dans ${LMDZ_INIT} on cree folder SPLA_Init et dedans le INITIAL |
---|
495 | # Pour l'instant on copie là-dedans de chez Binta les fichiers a la res zoomNaf; |
---|
496 | # plus tard on y recupererea des fichiers a haute resolution reguliere depuis http:/LMDZ, |
---|
497 | # a regrider ensuite par un script interp_fichiers_spla.sh (comme pour aerosols="clim") |
---|
498 | # Les fichiers (regrides, sauf SOILSPEC.data utilise tel quel) seront mis dans $MAINDIR/INPUT_SPLA (equivalent de INPUT_DUST) |
---|
499 | if [[ $aerosols = "spla" ]]; then |
---|
500 | mkdir -p "${LMDZ_INIT}/SPLA_Init"; mkdir -p "$LMDZ_INIT/SPLA_Init/INITIAL" |
---|
501 | get="cp -p /gpfsstore/rech/gzi/rgzi027/ergon/BIBIAERO/INPUTS_DUST/INITIAL/" |
---|
502 | liste_get="wth.dat cly.dat donnees_lisa.nc SOILSPEC.data \ |
---|
503 | carbon_emissions.nc sulphur_emissions_antro.nc \ |
---|
504 | sulphur_emissions_nat.nc sulphur_emissions_volc.nc" |
---|
505 | |
---|
506 | cd "$LMDZ_INIT/SPLA_Init/INITIAL" |
---|
507 | for file in $liste_get; do |
---|
508 | if [[ ! -f $file ]]; then ${get}$file .; fi |
---|
509 | done |
---|
510 | cd - > /dev/null |
---|
511 | ### |
---|
512 | #Cas particulier des fichiers mensuels dust.nc :A DECIDER : |
---|
513 | #C'est entre le cas des aerosols.clim= 1 seul fichier, annuel, |
---|
514 | # et le cas des vents guidage, pré-interpolés avec era2gcm pour toute la periode, dans MAINDIR/GUIDE. |
---|
515 | # On pourrait (a)demander de precalculer dust.nc aussi, dans MAINDIR/INPUT_SPLA - avec un script à adapter de Jeronimo. Rien a mettre dans SPLA_Init alors. |
---|
516 | # Ou (b) fournir dans SPLA_Init les 12 mois d'un dust.nc climato (an 2006 pour nous ici) à la res EC, et faire juste le regrid vers MAINDIR/INPUT_SPLA |
---|
517 | #ICI pour l'instant je copie les fichiers de chez Binta (repositoire==http...) dans LMDZ_INIT/SPLA_Init, avec test sur mois 01 |
---|
518 | |
---|
519 | if [[ ! -d ${LMDZ_INIT}/SPLA_Init/PERIOD0001 ]]; then |
---|
520 | if [[ ${hostname:0:5} != "jean-" ]]; then echo "PERIOD001 (aerosols=spla) IS ONLY AVAILABLE ON JEANZAY FOR NOW, CONTACT SUPPORT"; exit 1; fi |
---|
521 | cp -pr /gpfsstore/rech/gzi/rgzi027/ergon/BIBIAERO/INPUTS_DUST/PERIOD* "$LMDZ_INIT/SPLA_Init/."; |
---|
522 | fi |
---|
523 | #A la fin on doit avoir dans SPLA_Init les fichiers initiaux dans INITIAL plus les repertoires PERIOD00MM contenant dust.nc |
---|
524 | #Cela doit se retrouver dans script_SIMU qui les copie dans le repertoire de run sur $SCRATCH |
---|
525 | fi |
---|
526 | #------------------------------------------------------------------- |
---|
527 | # Fichiers Init |
---|
528 | #------------------------------------------------------------------- |
---|
529 | get="myget 3DInputData/Init/" |
---|
530 | liste_get="alb_bg_modisopt_2D_ESA_v2.nc reftemp.nc" |
---|
531 | cd "$LMDZ_INIT" |
---|
532 | for file in $liste_get; do |
---|
533 | if [[ ! -f $LMDZ_INIT/$file ]]; then ${get}$file; fi |
---|
534 | done |
---|
535 | cd - > /dev/null |
---|
536 | } |
---|
537 | |
---|
538 | function run_sim_or_init { |
---|
539 | cd "$local" |
---|
540 | |
---|
541 | if [[ $init = 1 ]]; then |
---|
542 | ##################################################################### |
---|
543 | echo "Creation de l etat initial" |
---|
544 | ##################################################################### |
---|
545 | |
---|
546 | # Creation du repertoire INIT et mise en place de liens logiques vers les starts |
---|
547 | # en anticipation de leur création : |
---|
548 | mkdir "$local/$INIT"; cd "$local/$INIT" |
---|
549 | for an in $mthini $yearini; do for f in start startphy; do ln -s "$f.nc" "$f.$an.nc"; done; done |
---|
550 | |
---|
551 | # Creation du repertoire INIT temporaire et rapatriement des fichiers necessaires |
---|
552 | if [[ -d $SIMRUNDIR/$INIT ]]; then mv "$SIMRUNDIR/$INIT" "$SIMRUNDIR/$INIT$$"; fi |
---|
553 | mkdir "$SIMRUNDIR/$INIT"; cp -r "$local/DEF" "$SIMRUNDIR/$INIT/" |
---|
554 | cd "$SIMRUNDIR/$INIT"; cp DEF/*.def .; cp "$local/lmdz_env.sh" . |
---|
555 | if [[ $xios = "y" ]]; then |
---|
556 | cp DEF/XMLfilesLMDZ/*xml . |
---|
557 | if [[ $veget != 'none' ]]; then cp DEF/XMLfilesOR$veget/*xml .; fi |
---|
558 | fi |
---|
559 | sed -e "s/anneeref=.*.$/anneeref=$yearini/" DEF/run.def >| run.def |
---|
560 | |
---|
561 | #------------------------------------------------------------------- |
---|
562 | # Fichiers Limit |
---|
563 | #------------------------------------------------------------------- |
---|
564 | local yrs suf |
---|
565 | if [[ $climato = 0 ]]; then |
---|
566 | # calend est choisi plus haut dans "Changements dans les fichiers DEF/*def" et ecrit dans $MAINDIR/DEF/run.def |
---|
567 | yrini=$(echo "$mthini" | cut -c-4) |
---|
568 | yrend=$(echo "$mthend" | cut -c-4) |
---|
569 | yrs=""; yr=$yrini |
---|
570 | while [[ $yr -le $yrend ]]; do yrs="$yrs $yr"; (( yr = yr + 1 )); done |
---|
571 | suf="360x180_" |
---|
572 | else |
---|
573 | yrs=2000 |
---|
574 | suf="1x1_clim" |
---|
575 | fi |
---|
576 | |
---|
577 | get="myget 3DInputData/Limit/" |
---|
578 | liste_get="Albedo.nc Relief.nc Rugos.nc landiceref.nc" |
---|
579 | for yr in $yrs; do |
---|
580 | if [[ $climato = 0 ]]; then sufyr=$suf$yr; else sufyr=$suf; fi |
---|
581 | liste_get="$liste_get amipbc_sic_$sufyr.nc amipbc_sst_$sufyr.nc" |
---|
582 | done |
---|
583 | echo LISTEGET "$liste_get" |
---|
584 | for file in $liste_get; do |
---|
585 | cd "$LMDZ_INIT" |
---|
586 | if [[ ! -f $LMDZ_INIT/$file ]]; then ${get}$file; fi |
---|
587 | cd - > /dev/null |
---|
588 | ln -s "$LMDZ_INIT/$file" . |
---|
589 | done |
---|
590 | #------------------------------------------------------------------- |
---|
591 | # ECDYN |
---|
592 | #------------------------------------------------------------------- |
---|
593 | get="myget 3DInputData/Init/" |
---|
594 | if [[ ! -f $LMDZ_INIT/ECDYN.nc ]]; then cd "$LMDZ_INIT"; ${get}ECDYN.nc; cd - > /dev/null; fi |
---|
595 | ln -s "$LMDZ_INIT"/ECDYN.nc . |
---|
596 | ln -sf ECDYN.nc ECPHY.nc |
---|
597 | |
---|
598 | # Creation du script d'initialisation |
---|
599 | cat << ...eod >| tmp |
---|
600 | #!/bin/bash |
---|
601 | #@JZ#JeanZay |
---|
602 | #@JZ#SBATCH --job-name=Init # nom du job |
---|
603 | #@JZ#SBATCH -A "$GROUPE"@cpu |
---|
604 | #@JZ#SBATCH --ntasks=1 # Nombre de processus MPI |
---|
605 | #@JZ#SBATCH --cpus-per-task=16 # nombre de threads OpenMP |
---|
606 | #@JZ# /!\ Attention, la ligne suivante est trompeuse mais dans le vocabulaire |
---|
607 | #@JZ# de Slurm "multithread" fait bien référence à l'hyperthreading. |
---|
608 | #@JZ#SBATCH --hint=nomultithread # 1 thread par coeur physique (pas d'hyperthreading) |
---|
609 | #@JZ#SBATCH --time=00:10:00 # Temps d’exécution maximum demandé (HH:MM:SS) |
---|
610 | #@JZ#SBATCH --output=Init%j.out # Nom du fichier de sortie |
---|
611 | #@JZ#SBATCH --error=Init%j.out # Nom du fichier d'erreur (ici commun avec la sortie) |
---|
612 | #@JZ# To submit to dev queue; "time" (above) must be max 2h |
---|
613 | #@JZ# #SBATCH --qos=qos_cpu-dev |
---|
614 | |
---|
615 | # ANCIEN MULTI STEP case \${LOADL_STEP_NAME} in |
---|
616 | |
---|
617 | # ANCIEN MULTI STEP init ) |
---|
618 | |
---|
619 | if [ ! -f lmdz_env.sh ]; then echo "manque fichier lmdz_env.sh"; ls; exit 1; fi |
---|
620 | . lmdz_env.sh |
---|
621 | ulimit -s unlimited |
---|
622 | export OMP_STACKSIZE=800M |
---|
623 | export OMP_NUM_THREADS=1 |
---|
624 | cd $SIMRUNDIR/$INIT |
---|
625 | echo "Executable : $ce0l" |
---|
626 | for yr in $yrs; do |
---|
627 | if [ $climato = 0 ]; then sufyr=$suf\$yr; else sufyr=$suf; fi |
---|
628 | ln -sf amipbc_sic_\$sufyr.nc amipbc_sic_1x1.nc |
---|
629 | ln -sf amipbc_sst_\$sufyr.nc amipbc_sst_1x1.nc |
---|
630 | sed -e 's/anneeref=.*.$/anneeref='\$yr'/' DEF/run.def >| run.def |
---|
631 | echo Starting initialisation |
---|
632 | $RUNCMD 1 $ce0l |
---|
633 | if [ $climato = 0 ]; then mv limit.nc limit.\$yr.nc; fi |
---|
634 | done |
---|
635 | # ANCIEN MULTI STEP ;; |
---|
636 | |
---|
637 | # ANCIEN MULTI STEP interp ) |
---|
638 | if [[ $aerosols = clim ]]; then |
---|
639 | cp $local/interp_aerosols.sh .; chmod +x interp_aerosols.sh |
---|
640 | # Les aerosols de l'annee 2000 ont été remplacés par "9999" qui pointe vers un fichier moyen sur 1995-2014 |
---|
641 | #for year in 2000 1850; do ./interp_aerosols.sh \$year; done |
---|
642 | #mv aerosols.2000.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc |
---|
643 | for year in 9999 1850; do ./interp_aerosols.sh \$year; done |
---|
644 | mv aerosols.9999.nc aerosols.clim.nc; mv aerosols.1850.nc aerosols.nat.nc |
---|
645 | fi |
---|
646 | |
---|
647 | # AS : S'il etait possible d'automatiser l'interpolation de l'input SPLA, ce serait a lancer ici |
---|
648 | #en attendant, on passe au paragraphe suivant où on copie les fichiers à la res ZoomNaf depuis $LMDZ_INIT/SPLA_Init |
---|
649 | #if [ $aerosols = spla ]; then |
---|
650 | #cp $local/futur script interp_aerosols_SPLA.sh .; chmod +x interp_aerosols_SPLA.sh |
---|
651 | #for file in...; do ./interp_aerosols_SPLA.sh \$year; done |
---|
652 | #etc etc etc ... |
---|
653 | #fi |
---|
654 | |
---|
655 | # Copy initial and forcing files in $local/$INIT and $local/$LIMIT; also in $local/INPUT_SPLA if $aerosols=spla |
---|
656 | for f in sta* limit.nc gri*nc; do cp \$f $local/$INIT/\$f; done |
---|
657 | mkdir -p $local/$LIMIT |
---|
658 | for f in limit*.nc ; do cp \$f $local/$LIMIT/\$f; done |
---|
659 | if [ $aerosols = clim ]; then for f in aerosols[.0-9]*nc; do cp \$f $local/$LIMIT/\$f; done; fi |
---|
660 | # |
---|
661 | if [ $aerosols = spla ]; then |
---|
662 | #mkdir -p $local/INPUT_SPLA; pour l'instant on copie $LMDZ_INIT/SPLA_Init en block |
---|
663 | if [ ! -d $local/INPUT_SPLA ]; then cp -pr $LMDZ_INIT/SPLA_Init $local/INPUT_SPLA; fi |
---|
664 | fi |
---|
665 | cd $SIMRUNDIR |
---|
666 | ...eod |
---|
667 | if [[ $ok_guide != "y" ]]; then # Running first simulation automatically except for nudging |
---|
668 | cat << ...eod >> tmp |
---|
669 | $SUBMITCMD tmp_$SIM |
---|
670 | ...eod |
---|
671 | fi |
---|
672 | cat << ...eod >> tmp |
---|
673 | # ANCIEN MULTI STEP esac |
---|
674 | ...eod |
---|
675 | enable_groupe tmp |
---|
676 | echo "###############################################################################" |
---|
677 | echo "Submitting initialisation job <$SUBMITCMD tmp> from $(pwd)" |
---|
678 | chmod +x tmp |
---|
679 | $SUBMITCMD tmp |
---|
680 | echo "###############################################################################" |
---|
681 | |
---|
682 | else #case [ $init != 1 ] |
---|
683 | cd "$SIMRUNDIR" |
---|
684 | echo "###############################################################################" |
---|
685 | echo "Submitting job tmp_$SIM" |
---|
686 | echo "$SUBMITCMD tmp_$SIM" |
---|
687 | $SUBMITCMD "tmp_$SIM" |
---|
688 | echo '###############################################################################' |
---|
689 | fi |
---|
690 | } |
---|
691 | |
---|
692 | # Set up the appropriate environment |
---|
693 | source lmdz_env.sh |
---|
694 | |
---|
695 | # TODO Amaury: commented-out for now // /!\ check w/ Adriana: "groupe@cpu" never appears in seasonal.sh... |
---|
696 | ## Pour les post-traitements |
---|
697 | #sed -i'' -e "s/groupe@cpu/$groupe@cpu/" seasonal.sh |
---|
698 | local=$(pwd) |
---|
699 | |
---|
700 | load_install_lib |
---|
701 | define_expert_options |
---|
702 | set_default_params |
---|
703 | read_cmdline_args "$@" |
---|
704 | ensure_correct_option_combinations |
---|
705 | install_model |
---|
706 | setup_def |
---|
707 | setup_ce0l |
---|
708 | setup_simu |
---|
709 | fetch_simu_init_files |
---|
710 | run_sim_or_init |
---|
711 | |
---|
712 | exit 1 |
---|
713 | |
---|
714 | |
---|
715 | # COMPILATION OPTIONS depending on the user choices and LMDZ revision number $mysvn |
---|
716 | #------------------------------------------------------- |
---|
717 | if [[ $rad = "ecrad" && ! -d ecrad_data ]]; then |
---|
718 | cd "$local"; wget https://lmdz.lmd.jussieu.fr/pub/3DInputData/ecrad/ecrad_data.tar; tar xvf ecrad_data.tar; cd - > /dev/null |
---|
719 | fi |
---|
720 | |
---|
721 | if [[ $rad = "ecrad" && $aerosols != "n" && $mysvn -lt 4489 ]] ; then echo "Les aerosols tropospheriques ne sont pas pris en charge par ecrad avant LMDZ rev 4489, ici rev est $mysvn"; exit 1; fi |
---|
722 | |
---|
723 | # EXIT after (install and) compilation if we are on jean-zay-pp instead of jean-zay ! |
---|
724 | hostname=`hostname` |
---|
725 | if [ ${hostname:0:11} = "jean-zay-pp" ]; then |
---|
726 | echo "You are on jean-zay-pp, here you only can install and compile the model, not run it" |
---|
727 | echo "If you want to run a simulation, log in to jean-zay and launch main.sh again, without install" |
---|
728 | echo `date` |
---|
729 | exit |
---|
730 | fi |
---|
731 | |
---|
732 | |
---|
733 | |
---|
734 | |
---|
735 | |
---|
736 | |
---|
737 | |
---|
738 | |
---|
739 | |
---|
740 | |
---|
741 | |
---|
742 | |
---|
743 | |
---|
744 | |
---|
745 | |
---|
746 | |
---|
747 | if [ $ok_guide = y -a $init = 1 ]; then |
---|
748 | echo Once initialisation is finished, you have to create nudging files |
---|
749 | echo Edit era2gcm.sh and set the desired parameters in section "User choices" |
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750 | echo Make sure you have acces to the chosen ERA files, and the required modules are load |
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751 | echo Then run : ./era2gcm.sh |
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752 | if [ "$aerosols" = "spla" ]; then |
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753 | echo Your aerosol choice is "spla", so you need ERA 10m-winds interpolated on LMDZ grid |
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754 | echo Use script era2gcm_uv10m.sh |
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755 | fi |
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756 | else |
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757 | echo Si tout se passe bien, vous avez initialise et lance automatiquement |
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758 | echo la simulation. |
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759 | echo Si vous voulez modifier les caracteristiques du job, comme le temps |
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760 | echo max ou le nombre de proc, il se trouve sur |
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761 | echo $SIMRUNTOPDIR/$MAINDIR/tmp_$SIM |
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762 | fi |
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763 | |
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764 | ############################################################################### |
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765 | # At the end, print on screen the compilation command, and also in a "compile.sh" script |
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766 | |
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767 | echo "To recompile the model :" |
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768 | echo "run the compile${sufiso}.sh script created in the present folder: ./compile${sufiso}.sh gcm " |
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