| 1 | #!/bin/bash |
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| 2 | ######################################################################## |
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| 3 | ######## Library of bash functions for the PEM launching script ######## |
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| 4 | ######################################################################## |
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| 5 | |
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| 6 | # To end the launching script |
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| 7 | endlaunch() { |
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| 8 | # Restore the previous value of LC_NUMERIC |
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| 9 | LC_NUMERIC=$OLD_LC_NUMERIC |
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| 10 | |
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| 11 | date |
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| 12 | echo "Success: the launching script for the PEM simulation completed normally!" |
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| 13 | exit 0 |
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| 14 | } |
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| 15 | |
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| 16 | # To end the launching script with error |
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| 17 | errlaunch() { |
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| 18 | # Restore the previous value of LC_NUMERIC |
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| 19 | LC_NUMERIC=$OLD_LC_NUMERIC |
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| 20 | |
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| 21 | date |
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| 22 | echo "Error: an issue occured in the launching script for the PEM simulation!" |
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| 23 | exit 1 |
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| 24 | } |
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| 25 | |
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| 26 | # To check what is the job scheduler |
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| 27 | function job_scheduler() { |
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| 28 | if command -v squeue &> /dev/null; then |
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| 29 | echo "SLURM is installed on $machine." |
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| 30 | scheduler="SLURM" |
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| 31 | name_job="#SBATCH --job-name=" |
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| 32 | kill_job="scancel" |
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| 33 | elif command -v qstat &> /dev/null; then |
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| 34 | echo "PBS/TORQUE is installed on $machine." |
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| 35 | scheduler="PBS" |
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| 36 | name_job="#PBS -N " |
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| 37 | kill_job="qdel" |
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| 38 | else |
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| 39 | echo "Error: neither SLURM nor TORQUE/PBS is installed on $machine!" |
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| 40 | echo "You need to adapt the script to your job scheduler or set 'mode' to 0." |
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| 41 | errlaunch |
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| 42 | fi |
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| 43 | } |
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| 44 | |
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| 45 | # To get the number of slopes for the simulation |
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| 46 | get_nslope() { |
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| 47 | ns=1 |
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| 48 | if [ -f "startfi.nc" ]; then |
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| 49 | ns=$(ncdump -h startfi.nc | sed -n 's/.*nslope = \([0-9]*\) ;.*/\1/p') |
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| 50 | else |
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| 51 | for f in run_PCM.def callphys.def; do |
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| 52 | if [[ -f "$f" ]]; then |
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| 53 | while IFS= read -r line; do |
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| 54 | # Remove leading whitespace |
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| 55 | trimmed=$(echo "$line" | sed 's/^[[:space:]]*//') |
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| 56 | # Skip lines that are commented out |
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| 57 | if [[ "$trimmed" == \#* ]]; then |
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| 58 | continue |
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| 59 | fi |
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| 60 | # Check if line contains 'nslope = N' |
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| 61 | if [[ "$trimmed" =~ ^nslope[[:space:]]*=[[:space:]]*([0-9]+) ]]; then |
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| 62 | ns="${BASH_REMATCH[1]}" |
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| 63 | break |
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| 64 | fi |
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| 65 | done < "$f" |
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| 66 | [[ -n "$ns" ]] && break |
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| 67 | fi |
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| 68 | done |
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| 69 | fi |
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| 70 | } |
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| 71 | |
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| 72 | # To modify the xml file according nslope |
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| 73 | modify_xml() { |
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| 74 | tmp="tmp_file_def.xml" |
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| 75 | in_outdaily4pem=false |
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| 76 | in_outyearly4pem=false |
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| 77 | in_outdaily4pem_s=false |
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| 78 | in_outyearly4pem_s=false |
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| 79 | |
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| 80 | sed -i 's/enabled="\.true\.\">/enabled=".false.">/g' file_def_physics_mars.xml |
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| 81 | |
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| 82 | while IFS= read -r line; do |
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| 83 | # Detect file blocks |
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| 84 | case "$line" in |
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| 85 | *'<file id="outdaily4pem"'*) |
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| 86 | in_outdaily4pem=true |
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| 87 | ;; |
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| 88 | *'<file id="outyearly4pem"'*) |
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| 89 | in_outyearly4pem=true |
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| 90 | ;; |
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| 91 | *'<file id="outdaily4pem_s"'*) |
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| 92 | in_outdaily4pem_s=true |
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| 93 | ;; |
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| 94 | *'<file id="outyearly4pem_s"'*) |
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| 95 | in_outyearly4pem_s=true |
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| 96 | ;; |
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| 97 | esac |
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| 98 | |
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| 99 | # Handle enabled attribute |
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| 100 | if [[ $line == *'enabled="'* ]]; then |
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| 101 | if $in_outdaily4pem || $in_outyearly4pem; then |
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| 102 | if [[ $ns -eq 1 ]]; then |
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| 103 | line=' enabled=".true.">' |
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| 104 | else |
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| 105 | line=' enabled=".false.">' |
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| 106 | fi |
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| 107 | elif $in_outdaily4pem_s || $in_outyearly4pem_s; then |
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| 108 | if [[ $ns -eq 1 ]]; then |
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| 109 | line=' enabled=".false.">' |
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| 110 | else |
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| 111 | line=' enabled=".true.">' |
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| 112 | fi |
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| 113 | fi |
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| 114 | fi |
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| 115 | |
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| 116 | # Handle slope variables |
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| 117 | if ( $in_outdaily4pem_s || $in_outyearly4pem_s ) && [[ $line =~ slope([0-9]+) ]]; then |
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| 118 | slope_id="${BASH_REMATCH[1]}" |
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| 119 | if (( 10#$slope_id > ns )); then |
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| 120 | # Ensure the line is commented |
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| 121 | if [[ $line != "<!--"* ]]; then |
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| 122 | line="<!-- $line -->" |
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| 123 | fi |
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| 124 | else |
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| 125 | # Ensure the line is uncommented |
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| 126 | if [[ $line == "<!--"* ]]; then |
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| 127 | line="${line#<!-- }" # remove leading <!-- |
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| 128 | line="${line% -->}" # remove trailing --> |
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| 129 | fi |
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| 130 | fi |
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| 131 | fi |
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| 132 | |
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| 133 | |
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| 134 | # Leaving the file block |
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| 135 | case "$line" in |
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| 136 | *'</file>'*) |
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| 137 | in_outdaily4pem=false |
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| 138 | in_outyearly4pem=false |
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| 139 | in_outdaily4pem_s=false |
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| 140 | in_outyearly4pem_s=false |
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| 141 | ;; |
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| 142 | esac |
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| 143 | |
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| 144 | echo "$line" >> "$tmp" |
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| 145 | done < file_def_physics_mars.xml |
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| 146 | |
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| 147 | mv "$tmp" file_def_physics_mars.xml |
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| 148 | } |
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| 149 | |
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| 150 | # To check if a PCM run is one year |
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| 151 | check_runyear() { |
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| 152 | if [ -f "run_PCM.def" ]; then |
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| 153 | year_sol=$(ncdump -v controle startfi.nc 2>/dev/null | \ |
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| 154 | sed -n '/controle =/,/;/p' | tr -d '[:space:]' | \ |
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| 155 | sed 's/.*=//; s/;//' | tr ',' '\n' | sed -n '14p') |
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| 156 | else |
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| 157 | year_sol=669 # Length of Martian year (sols) |
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| 158 | fi |
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| 159 | sol_in_file=$(awk -F'=' '/^[[:space:]]*(nday|ndt)[[:space:]]*=/ { |
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| 160 | val=$2 |
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| 161 | gsub(/^[[:space:]]+|[[:space:]]+$/,"",val) |
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| 162 | print val |
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| 163 | exit |
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| 164 | }' run_PCM.def) |
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| 165 | |
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| 166 | if [ -z "$sol_in_file" ]; then |
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| 167 | echo "Error: no length of year found in \"run_PCM.def\"!" |
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| 168 | errlaunch |
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| 169 | elif [ "$sol_in_file" -eq "$year_sol" ]; then |
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| 170 | # Good: we do nothing |
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| 171 | : |
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| 172 | else |
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| 173 | echo "Error: length of year mismatch between \"run_PCM.def\" ($sol_in_file) and \"startfi.nc\" ($year_sol)!" |
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| 174 | errlaunch |
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| 175 | fi |
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| 176 | } |
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| 177 | |
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| 178 | # To check if everything necessary for the launching script is ok |
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| 179 | checklaunch() { |
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| 180 | # Save the current value of LC_NUMERIC and set it to a locale that uses a dot as the decimal separator |
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| 181 | OLD_LC_NUMERIC=$LC_NUMERIC |
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| 182 | LC_NUMERIC=en_US.UTF-8 |
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| 183 | |
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| 184 | if [ -v n_mars_years ] && [ ! -z "$n_mars_years" ]; then |
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| 185 | if [ $(echo "$n_mars_years <= 0." | bc -l) -eq 1 ]; then |
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| 186 | echo "Error: 'n_mars_years' must be > 0!" |
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| 187 | errlaunch |
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| 188 | fi |
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| 189 | elif [ -v n_earth_years ] && [ ! -z "$n_earth_years" ]; then |
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| 190 | if [ $(echo "$n_earth_years <= 0." | bc -l) -eq 1 ]; then |
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| 191 | echo "Error: 'n_earth_years' must be > 0!" |
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| 192 | errlaunch |
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| 193 | fi |
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| 194 | else |
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| 195 | echo "Error: the number of years to be simulated is not set!" |
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| 196 | errlaunch |
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| 197 | fi |
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| 198 | if [ $nPCM_ini -lt 2 ] || [ -z "$nPCM_ini" ]; then |
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| 199 | echo "Error: 'nPCM_ini' must be >= 2!" |
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| 200 | errlaunch |
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| 201 | fi |
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| 202 | if [ $nPCM -lt 2 ] || [ -z "$nPCM" ]; then |
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| 203 | echo "Error: 'nPCM' must be >= 2!" |
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| 204 | errlaunch |
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| 205 | fi |
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| 206 | if [ ! -f "PCMrun.job" ]; then |
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| 207 | echo "Error: file \"PCMrun.job\" does not exist in $dir!" |
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| 208 | errlaunch |
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| 209 | fi |
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| 210 | if [ ! -f "PEMrun.job" ]; then |
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| 211 | echo "Error: file \"PEMrun.job\" does not exist in $dir!" |
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| 212 | errlaunch |
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| 213 | fi |
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| 214 | if [ ! -f "run_PCM.def" ]; then |
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| 215 | echo "Error: file \"run_PCM.def\" does not exist in $dir!" |
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| 216 | errlaunch |
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| 217 | fi |
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| 218 | if [ ! -f "run_PEM.def" ]; then |
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| 219 | echo "Error: file \"run_PEM.def\" does not exist in $dir!" |
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| 220 | errlaunch |
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| 221 | fi |
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| 222 | if [ ! -f "context_lmdz_physics.xml" ]; then |
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| 223 | echo "Error: file \"context_lmdz_physics.xml\" does not exist in $dir!" |
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| 224 | errlaunch |
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| 225 | fi |
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| 226 | if [ ! -f "field_def_physics_mars.xml" ]; then |
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| 227 | echo "Error: file \"field_def_physics_mars.xml\" does not exist in $dir!" |
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| 228 | errlaunch |
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| 229 | fi |
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| 230 | if [ ! -f "file_def_physics_mars.xml" ]; then |
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| 231 | echo "Error: file \"file_def_physics_mars.xml\" does not exist in $dir!" |
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| 232 | errlaunch |
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| 233 | fi |
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| 234 | if [ ! -f "iodef.xml" ]; then |
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| 235 | echo "Error: file \"iodef.xml\" does not exist in $dir!" |
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| 236 | errlaunch |
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| 237 | fi |
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| 238 | if [ ! -d "logs" ]; then |
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| 239 | mkdir logs |
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| 240 | fi |
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| 241 | if [ ! -d "starts" ]; then |
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| 242 | mkdir starts |
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| 243 | fi |
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| 244 | if [ ! -d "diags" ]; then |
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| 245 | mkdir diags |
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| 246 | fi |
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| 247 | if [ $mode -ne 0 ]; then |
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| 248 | job_scheduler |
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| 249 | fi |
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| 250 | # Set automatically the XIOS output file for the PEM according to the number of slopes |
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| 251 | get_nslope |
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| 252 | modify_xml |
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| 253 | # Check if a PCM run is one year |
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| 254 | check_runyear |
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| 255 | } |
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| 256 | |
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| 257 | # To convert Earth years into Mars years |
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| 258 | convertyears() { |
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| 259 | myear=686.9725 # Number of Earth days in Martian year |
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| 260 | eyear=365.256363004 # Number of days in Earth year |
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| 261 | convert_years=$(echo "$myear/$eyear" | bc -l) |
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| 262 | convert_years=$(printf "%.4f" $convert_years) # Rounding to the 4th decimal to respect the precision of Martian year |
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| 263 | if [ -v n_mars_years ]; then |
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| 264 | n_myear=$n_mars_years |
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| 265 | echo "Number of years to be simulated: $n_myear Martian years." |
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| 266 | elif [ -v n_earth_years ]; then |
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| 267 | n_myear=$(echo "$n_earth_years/$convert_years" | bc -l) |
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| 268 | echo "Number of years to be simulated: $n_earth_years Earth years = $n_myear Martian years." |
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| 269 | fi |
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| 270 | } |
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| 271 | |
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| 272 | # To initialize the launching script |
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| 273 | initlaunch() { |
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| 274 | echo "This is a chained simulation for PEM and PCM runs in $dir on $machine by $user." |
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| 275 | convertyears |
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| 276 | i_myear=0. |
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| 277 | iPEM=1 |
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| 278 | iPCM=1 |
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| 279 | if [ -f "startfi.nc" ]; then |
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| 280 | cp startfi.nc starts/ |
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| 281 | fi |
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| 282 | if [ -f "start.nc" ]; then |
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| 283 | cp start.nc starts/ |
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| 284 | elif [ -f "start1D.txt" ]; then |
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| 285 | cp start1D.txt starts/ |
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| 286 | fi |
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| 287 | if [ -f "startpem.nc" ]; then |
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| 288 | cp startpem.nc starts/ |
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| 289 | fi |
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| 290 | |
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| 291 | # Create a file to manage years of the chained simulation and store some info from the PEM runs |
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| 292 | echo $i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini > launchPEM.info |
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| 293 | } |
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| 294 | |
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| 295 | # To submit the PCM runs |
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| 296 | # arg1: launching mode |
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| 297 | # arg2: counting method |
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| 298 | # arg3: number of PCM runs to launch |
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| 299 | # arg4: local number of the PCM run from which to start (optional) |
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| 300 | submitPCM() { |
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| 301 | find . -type f -name "PCMrun*.job" ! -name "PCMrun.job" -delete |
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| 302 | ii=1 |
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| 303 | if [ ! -z $4 ]; then |
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| 304 | ii=$4 |
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| 305 | fi |
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| 306 | if [ $(echo "$i_myear < $n_myear" | bc -l) -eq 1 ]; then |
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| 307 | echo "Run \"PCM $iPCM\" ($ii/$3)" |
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| 308 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 309 | sed -i "s/^k=-\?[0-9]\+$/k=$(echo "$ii - $3 + 2" | bc)/" PCMrun.job |
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| 310 | ./PCMrun.job |
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| 311 | if [ $? -ne 0 ]; then |
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| 312 | errlaunch |
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| 313 | fi |
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| 314 | else # Mode: submitting jobs |
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| 315 | cp PCMrun.job PCMrun${iPCM}.job |
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| 316 | sed -i -E "/^$name_job/s/(.*[^0-9])([0-9]+)(_[^0-9]*)?$/\1${iPCM}\3/" PCMrun${iPCM}.job |
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| 317 | sed -i "s/^k=-\?[0-9]\+$/k=$(echo "$ii - $3 + 2" | bc)/" PCMrun${iPCM}.job |
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| 318 | if [[ "$scheduler" == "SLURM" ]]; then |
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| 319 | jobID=$(sbatch --parsable PCMrun${iPCM}.job) |
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| 320 | elif [[ "$scheduler" == "PBS" ]]; then |
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| 321 | jobID=$(qsub PCMrun${iPCM}.job | cut -d. -f1) |
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| 322 | fi |
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| 323 | # Create a file to cancel the dependent jobs of the cycle |
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| 324 | echo "#!/bin/bash" > kill_launchPEM.sh |
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| 325 | chmod +x kill_launchPEM.sh |
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| 326 | echo $kill_job $jobID >> kill_launchPEM.sh |
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| 327 | fi |
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| 328 | ((iPCM++)) |
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| 329 | if [ $2 -ne 0 ]; then # Counting: PCM years taken into account |
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| 330 | i_myear=$(echo "$i_myear + 1." | bc -l) |
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| 331 | fi |
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| 332 | ((ii++)) |
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| 333 | else |
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| 334 | endlaunch |
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| 335 | fi |
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| 336 | for ((i = $ii; i <= $3; i++)); do |
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| 337 | if [ $(echo "$i_myear < $n_myear" | bc -l) -eq 1 ]; then |
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| 338 | echo "Run \"PCM $iPCM\" ($i/$3)" |
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| 339 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 340 | sed -i "s/^k=-\?[0-9]\+$/k=$(echo "$i - $3 + 2" | bc)/" PCMrun.job |
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| 341 | ./PCMrun.job |
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| 342 | if [ $? -ne 0 ]; then |
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| 343 | errlaunch |
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| 344 | fi |
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| 345 | else # Mode: submitting jobs |
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| 346 | cp PCMrun.job PCMrun${iPCM}.job |
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| 347 | sed -i -E "/^$name_job/s/(.*[^0-9])([0-9]+)(_[^0-9]*)?$/\1${iPCM}\3/" PCMrun${iPCM}.job |
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| 348 | sed -i "s/^k=-\?[0-9]\+$/k=$(echo "$i - $3 + 2" | bc)/" PCMrun${iPCM}.job |
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| 349 | if [[ "$scheduler" == "SLURM" ]]; then |
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| 350 | jobID=$(sbatch --parsable --dependency=afterok:${jobID} PCMrun${iPCM}.job) |
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| 351 | elif [[ "$scheduler" == "PBS" ]]; then |
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| 352 | jobID=$(qsub -W depend=afterok:${jobID} PCMrun${iPCM}.job | cut -d. -f1) |
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| 353 | fi |
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| 354 | echo $kill_job $jobID >> kill_launchPEM.sh |
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| 355 | fi |
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| 356 | ((iPCM++)) |
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| 357 | if [ $2 -ne 0 ]; then # Counting: PCM years taken into account |
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| 358 | i_myear=$(echo "$i_myear + 1." | bc -l) |
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| 359 | fi |
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| 360 | else |
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| 361 | endlaunch |
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| 362 | fi |
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| 363 | done |
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| 364 | } |
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| 365 | |
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| 366 | # To submit the PEM run |
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| 367 | # arg1: launching mode |
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| 368 | submitPEM() { |
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| 369 | if [ $(echo "$i_myear < $n_myear" | bc -l) -eq 1 ]; then |
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| 370 | echo "Run \"PEM $iPEM\"" |
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| 371 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 372 | ./PEMrun.job |
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| 373 | if [ $? -ne 0 ]; then |
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| 374 | errlaunch |
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| 375 | fi |
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| 376 | else # Mode: submitting jobs |
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| 377 | sed -i -E "/^$name_job/s/(.*[^0-9])([0-9]+)(_[^0-9]*)?$/\1${iPEM}\3/" PEMrun.job |
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| 378 | if [[ "$scheduler" == "SLURM" ]]; then |
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| 379 | jobID=$(sbatch --parsable PEMrun.job) |
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| 380 | elif [[ "$scheduler" == "PBS" ]]; then |
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| 381 | jobID=$(qsub PEMrun.job | cut -d. -f1) |
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| 382 | fi |
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| 383 | # Create a file to cancel the dependent jobs of the cycle |
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| 384 | echo "#!/bin/bash" > kill_launchPEM.sh |
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| 385 | chmod +x kill_launchPEM.sh |
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| 386 | echo $kill_job $jobID >> kill_launchPEM.sh |
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| 387 | fi |
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| 388 | else |
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| 389 | endlaunch |
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| 390 | fi |
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| 391 | } |
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| 392 | |
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| 393 | # To make one cycle of PCM and PEM runs |
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| 394 | # arg1: launching mode |
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| 395 | # arg2: counting method |
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| 396 | # arg3: number of PCM runs to launch |
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| 397 | # arg4: local number of the PCM run from which to start (optional) |
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| 398 | cyclelaunch() { |
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| 399 | # PCM runs |
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| 400 | submitPCM $1 $2 $3 $4 |
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| 401 | |
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| 402 | # PEM run |
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| 403 | if [ $(echo "$i_myear < $n_myear" | bc -l) -eq 1 ]; then |
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| 404 | echo "Run \"PEM $iPEM\"" |
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| 405 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 406 | ./PEMrun.job |
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| 407 | if [ $? -ne 0 ]; then |
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| 408 | errlaunch |
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| 409 | fi |
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| 410 | else # Mode: submitting jobs |
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| 411 | sed -i -E "/^$name_job/s/(.*[^0-9])([0-9]+)(_[^0-9]*)?$/\1${iPEM}\3/" PEMrun.job |
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| 412 | if [[ "$scheduler" == "SLURM" ]]; then |
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| 413 | jobID=$(sbatch --parsable --dependency=afterok:${jobID} PEMrun.job) |
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| 414 | elif [[ "$scheduler" == "PBS" ]]; then |
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| 415 | jobID=$(qsub -W depend=afterok:${jobID} PEMrun.job | cut -d. -f1) |
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| 416 | fi |
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| 417 | echo $kill_job $jobID >> kill_launchPEM.sh |
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| 418 | fi |
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| 419 | else |
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| 420 | endlaunch |
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| 421 | fi |
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| 422 | } |
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| 423 | |
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| 424 | # To clean files after the starting run of the relaunch |
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| 425 | # arg1: file name prefix to clean |
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| 426 | # arg2: file name extension to clean |
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| 427 | # arg3: file number from which to clean |
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| 428 | cleanfiles() { |
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| 429 | prefix=$1 |
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| 430 | extension=$2 |
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| 431 | if [ -z "$extension" ]; then |
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| 432 | for file in ${prefix}*; do |
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| 433 | num=${file#$prefix} |
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| 434 | if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then |
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| 435 | rm $file |
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| 436 | fi |
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| 437 | done |
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| 438 | else |
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| 439 | for file in ${prefix}*${extension}; do |
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| 440 | num=${file#$prefix} |
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| 441 | num=${num%$extension} |
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| 442 | if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then |
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| 443 | rm $file |
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| 444 | fi |
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| 445 | done |
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| 446 | fi |
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| 447 | } |
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| 448 | |
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| 449 | # To relaunch from PCM run |
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| 450 | # arg1: launching mode |
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| 451 | # arg2: counting method |
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| 452 | relaunchPCM() { |
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| 453 | iPCM=$(($irelaunch + 1)) |
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| 454 | cleanfiles diags/diagfi .nc $irelaunch |
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| 455 | cleanfiles diags/diagsoil .nc $irelaunch |
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| 456 | cleanfiles diags/Xoutdaily4pem .nc $irelaunch |
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| 457 | cleanfiles diags/Xoutyearly4pem .nc $irelaunch |
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| 458 | cleanfiles logs/runPCM .log $irelaunch |
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| 459 | cleanfiles starts/restart1D .txt $irelaunch |
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| 460 | cleanfiles starts/restart .nc $irelaunch |
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| 461 | cleanfiles starts/restartfi .nc $irelaunch |
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| 462 | cp starts/restartfi${irelaunch}.nc startfi.nc |
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| 463 | if [ -f "starts/restart${irelaunch}.nc" ]; then |
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| 464 | cp starts/restart${irelaunch}.nc start.nc |
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| 465 | elif [ -f "starts/restart1D${irelaunch}.txt" ]; then |
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| 466 | cp starts/restart1D${irelaunch}.txt start1D.txt |
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| 467 | fi |
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| 468 | if [ $irelaunch -le $nPCM_ini ]; then |
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| 469 | # PCM relaunch during the initialization cycle |
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| 470 | iPEM=1 |
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| 471 | if [ $2 -ne 0 ]; then # Counting: PCM years taken into account |
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| 472 | i_myear=$irelaunch |
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| 473 | else # Counting: only PEM years count |
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| 474 | i_myear=0 |
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| 475 | fi |
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| 476 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" launchPEM.info |
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| 477 | cleanfiles diags/diagpem .nc $(($iPEM - 1)) |
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| 478 | cleanfiles diags/diagsoilpem .nc $(($iPEM - 1)) |
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| 479 | cleanfiles logs/runPEM .log $(($iPEM - 1)) |
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| 480 | cleanfiles starts/restart1D_postPEM .txt $(($iPEM - 1)) |
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| 481 | cleanfiles starts/restart_postPEM .nc $(($iPEM - 1)) |
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| 482 | cleanfiles starts/restartfi_postPEM .nc $(($iPEM - 1)) |
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| 483 | cleanfiles starts/restartpem .nc $(($iPEM - 1)) |
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| 484 | rm -f startpem.nc |
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| 485 | if [ -f "starts/startpem.nc" ]; then |
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| 486 | cp starts/startpem.nc . |
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| 487 | fi |
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| 488 | if [ $irelaunch -eq $(($nPCM_ini - 1)) ]; then |
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| 489 | cp diags/Xoutdaily4pem${irelaunch}.nc Xoutdaily4pem_Y1.nc |
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| 490 | cp diags/Xoutyearly4pem${irelaunch}.nc Xoutyearly4pem_Y1.nc |
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| 491 | cyclelaunch $1 $2 $nPCM_ini $iPCM |
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| 492 | elif [ $irelaunch -eq $nPCM_ini ]; then |
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| 493 | cp diags/Xoutdaily4pem$(($irelaunch - 1)).nc Xoutdaily4pem_Y1.nc |
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| 494 | cp diags/Xoutyearly4pem$(($irelaunch - 1)).nc Xoutyearly4pem_Y1.nc |
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| 495 | cp diags/Xoutdaily4pem${irelaunch}.nc Xoutdaily4pem_Y2.nc |
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| 496 | cp diags/Xoutyearly4pem${irelaunch}.nc Xoutyearly4pem_Y2.nc |
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| 497 | submitPEM $1 # The next job is a PEM run |
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| 498 | else |
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| 499 | cyclelaunch $1 $2 $nPCM_ini $iPCM |
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| 500 | fi |
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| 501 | else |
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| 502 | # PCM relaunch during a cycle |
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| 503 | iPEM=$(echo "($iPCM - $nPCM_ini)/$nPCM + 1" | bc) |
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| 504 | il=$(echo "($irelaunch - $nPCM_ini + 1)%$nPCM + 1" | bc) |
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| 505 | if [ $2 -ne 0 ]; then # Counting: PCM years taken into account |
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| 506 | i_myear=$(echo "$(awk "NR==$iPEM {printf \"%s\n\", \$3}" "launchPEM.info") + $il" | bc -l) |
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| 507 | else # Counting: only PEM years count |
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| 508 | i_myear=$(awk "NR==$iPEM {printf \"%s\n\", \$3}" "launchPEM.info") |
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| 509 | fi |
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| 510 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" launchPEM.info |
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| 511 | cleanfiles diags/diagpem .nc $(($iPEM - 1)) |
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| 512 | cleanfiles diags/diagsoilpem .nc $(($iPEM - 1)) |
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| 513 | cleanfiles logs/runPEM .log $(($iPEM - 1)) |
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| 514 | cleanfiles starts/restart1D_postPEM .txt $(($iPEM - 1)) |
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| 515 | cleanfiles starts/restart_postPEM .nc $(($iPEM - 1)) |
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| 516 | cleanfiles starts/restartfi_postPEM .nc $(($iPEM - 1)) |
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| 517 | cleanfiles starts/restartpem .nc $(($iPEM - 1)) |
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| 518 | cp starts/restartpem$(($iPEM - 1)).nc startpem.nc |
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| 519 | if [ $il -eq $(($nPCM - 1)) ]; then # Second to last PCM run |
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| 520 | cp diags/Xoutdaily4pem${irelaunch}.nc Xoutdaily4pem_Y1.nc |
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| 521 | cp diags/Xoutyearly4pem${irelaunch}.nc Xoutyearly4pem_Y1.nc |
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| 522 | cyclelaunch $1 $2 $nPCM $(($il + 1)) |
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| 523 | elif [ $il -eq $nPCM ]; then # Last PCM run so the next job is a PEM run |
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| 524 | cp diags/Xoutdaily4pem$(($irelaunch - 1)).nc Xoutdaily4pem_Y1.nc |
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| 525 | cp diags/Xoutyearly4pem$(($irelaunch - 1)).nc Xoutyearly4pem_Y1.nc |
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| 526 | cp diags/Xoutdaily4pem${irelaunch}.nc Xoutdaily4pem_Y2.nc |
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| 527 | cp diags/Xoutyearly4pem${irelaunch}.nc Xoutyearly4pem_Y2.nc |
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| 528 | submitPEM $1 |
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| 529 | else |
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| 530 | cyclelaunch $1 $2 $nPCM $(($il + 1)) |
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| 531 | fi |
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| 532 | fi |
|---|
| 533 | } |
|---|
| 534 | |
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| 535 | # To relaunch from PEM run |
|---|
| 536 | # arg1: launching mode |
|---|
| 537 | # arg2: counting method |
|---|
| 538 | relaunchPEM() { |
|---|
| 539 | iPEM=$(echo "$irelaunch + 1" | bc) |
|---|
| 540 | iPCM=$(echo "$nPCM_ini + $nPCM*($irelaunch - 1) + 1" | bc) |
|---|
| 541 | i_myear=$(awk "NR==$iPEM {printf \"%s\n\", \$3}" "launchPEM.info") |
|---|
| 542 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" launchPEM.info |
|---|
| 543 | cleanfiles diags/diagfi .nc $(($iPCM - 1)) |
|---|
| 544 | cleanfiles diags/diagsoil .nc $(($iPCM - 1)) |
|---|
| 545 | cleanfiles logs/runPCM .log $(($iPCM - 1)) |
|---|
| 546 | cleanfiles starts/restart1D .txt $(($iPCM - 1)) |
|---|
| 547 | cleanfiles starts/restart .nc $(($iPCM - 1)) |
|---|
| 548 | cleanfiles starts/restartfi .nc $(($iPCM - 1)) |
|---|
| 549 | cleanfiles diags/Xoutdaily4pem .nc $(($iPCM - 1)) |
|---|
| 550 | cleanfiles diags/Xoutyearly4pem .nc $(($iPCM - 1)) |
|---|
| 551 | cleanfiles diags/diagpem .nc $irelaunch |
|---|
| 552 | cleanfiles diags/diagsoilpem .nc $irelaunch |
|---|
| 553 | cleanfiles logs/runPEM .log $irelaunch |
|---|
| 554 | cleanfiles starts/restart1D_postPEM .txt $irelaunch |
|---|
| 555 | cleanfiles starts/restart_postPEM .nc $irelaunch |
|---|
| 556 | cleanfiles starts/restartfi_postPEM .nc $irelaunch |
|---|
| 557 | cleanfiles starts/restartpem .nc $irelaunch |
|---|
| 558 | cp starts/restartpem${irelaunch}.nc startpem.nc |
|---|
| 559 | cp starts/restartfi_postPEM${irelaunch}.nc startfi.nc |
|---|
| 560 | if [ -f "starts/restart_postPEM${irelaunch}.nc" ]; then |
|---|
| 561 | cp starts/restart_postPEM${irelaunch}.nc start.nc |
|---|
| 562 | elif [ -f "starts/restart1D_postPEM${irelaunch}.txt" ]; then |
|---|
| 563 | cp starts/restart1D_postPEM${irelaunch}.txt start1D.txt |
|---|
| 564 | fi |
|---|
| 565 | cyclelaunch $1 $2 $nPCM |
|---|
| 566 | } |
|---|
