| 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=$OLD_LC_NUMERIC |
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| 10 | |
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| 11 | date |
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| 12 | echo "Successful end of the launching script for the PEM simulation." |
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| 13 | exit 0 |
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| 14 | } |
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| 15 | |
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| 16 | # To end the launching script with error |
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| 17 | errlaunch() { |
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| 18 | # Restore the previous value of LC_NUMERIC |
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| 19 | LC_NUMERIC=$OLD_LC_NUMERIC |
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| 20 | |
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| 21 | date |
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| 22 | echo "End with error of the launching script for the PEM." |
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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 | name_job="#SBATCH --job-name=" |
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| 31 | kill_job="scancel" |
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| 32 | submit_job="sbatch --parsable" |
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| 33 | submit_dependjob="sbatch --parsable --dependency" |
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| 34 | elif command -v qstat &> /dev/null; then |
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| 35 | echo "PBS/TORQUE is installed on $machine." |
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| 36 | name_job="#PBS -N " |
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| 37 | kill_job="qdel" |
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| 38 | submit_job="qsub" |
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| 39 | submit_dependjob="qsub -W depend" |
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| 40 | else |
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| 41 | echo "Error: neither SLURM nor TORQUE/PBS is installed on $machine!" |
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| 42 | echo "You need to adapt the script to your job scheduler." |
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| 43 | errlaunch |
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| 44 | fi |
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| 45 | } |
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| 46 | |
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| 47 | # To check if everything necessary for the launching script is ok |
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| 48 | checklaunch() { |
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| 49 | # Save the current value of LC_NUMERIC and set it to a locale that uses a dot as the decimal separator |
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| 50 | OLD_LC_NUMERIC=$LC_NUMERIC |
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| 51 | LC_NUMERIC=en_US.UTF-8 |
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| 52 | |
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| 53 | if [ -v n_mars_years ] && [ ! -z "$n_mars_years" ]; then |
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| 54 | if [ $n_mars_years -lt 0. ]; then |
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| 55 | echo "Error: the value of 'n_mars_years' must be >0!" |
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| 56 | errlaunch |
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| 57 | fi |
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| 58 | elif [ -v n_earth_years ] && [ ! -z "$n_earth_years" ]; then |
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| 59 | if [ $n_earth_years -lt 0. ]; then |
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| 60 | echo "Error: the value of 'n_earth_years' must be >0!" |
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| 61 | errlaunch |
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| 62 | fi |
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| 63 | else |
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| 64 | echo "Error: no number of years to be simulated has been set!" |
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| 65 | errlaunch |
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| 66 | fi |
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| 67 | if [ $nPCM_ini -lt 2 ] || [ -z "$nPCM_ini" ]; then |
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| 68 | echo "Error: the value of 'nPCM_ini' must be >1!" |
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| 69 | errlaunch |
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| 70 | fi |
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| 71 | if [ $nPCM -lt 2 ] || [ -z "$nPCM" ]; then |
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| 72 | echo "Error: the value of 'nPCM' must be >1!" |
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| 73 | errlaunch |
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| 74 | fi |
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| 75 | if [ ! -f "PCMrun.job" ]; then |
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| 76 | echo "Error: file \"PCMrun.job\" does not exist in $dir!" |
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| 77 | errlaunch |
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| 78 | fi |
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| 79 | if [ ! -f "PEMrun.job" ]; then |
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| 80 | echo "Error: file \"PEMrun.job\" does not exist in $dir!" |
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| 81 | errlaunch |
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| 82 | fi |
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| 83 | if [ ! -f "run_PCM.def" ]; then |
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| 84 | echo "Error: file \"run_PCM.def\" does not exist in $dir!" |
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| 85 | errlaunch |
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| 86 | fi |
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| 87 | if [ ! -f "run_PEM.def" ]; then |
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| 88 | echo "Error: file \"run_PEM.def\" does not exist in $dir!" |
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| 89 | errlaunch |
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| 90 | fi |
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| 91 | if [ ! -f "context_lmdz_physics.xml" ]; then |
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| 92 | echo "Error: file \"context_lmdz_physics.xml\" does not exist in $dir!" |
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| 93 | errlaunch |
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| 94 | fi |
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| 95 | if [ ! -f "field_def_physics_mars.xml" ]; then |
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| 96 | echo "Error: file \"field_def_physics_mars.xml\" does not exist in $dir!" |
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| 97 | errlaunch |
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| 98 | fi |
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| 99 | if [ ! -f "file_def_physics_mars.xml" ]; then |
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| 100 | echo "Error: file \"file_def_physics_mars.xml\" does not exist in $dir!" |
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| 101 | errlaunch |
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| 102 | fi |
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| 103 | if [ ! -f "iodef.xml" ]; then |
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| 104 | echo "Error: file \"iodef.xml\" does not exist in $dir!" |
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| 105 | errlaunch |
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| 106 | fi |
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| 107 | if [ ! -d "out_PCM" ]; then |
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| 108 | mkdir out_PCM |
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| 109 | fi |
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| 110 | if [ ! -d "out_PEM" ]; then |
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| 111 | mkdir out_PEM |
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| 112 | fi |
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| 113 | if [ ! -d "starts" ]; then |
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| 114 | mkdir starts |
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| 115 | fi |
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| 116 | if [ ! -d "diags" ]; then |
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| 117 | mkdir diags |
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| 118 | fi |
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| 119 | if [ $mode -ne 0 ]; then |
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| 120 | job_scheduler |
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| 121 | fi |
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| 122 | } |
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| 123 | |
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| 124 | # To convert Earth years into Mars years |
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| 125 | convertyears() { |
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| 126 | myear=686.9725 # Number of Earth days in Martian year |
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| 127 | eyear=365.256363004 # Number of days in Earth year |
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| 128 | convert_years=$(echo "$myear/$eyear" | bc -l) |
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| 129 | convert_years=$(printf "%.4f" $convert_years) # Rounding to the 4th decimal to respect the precision of Martian year |
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| 130 | if [ -v n_mars_years ]; then |
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| 131 | n_myear=$n_mars_years |
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| 132 | echo "Number of years to be simulated: $n_myear Martian years." |
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| 133 | elif [ -v n_earth_years ]; then |
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| 134 | n_myear=$(echo "$n_earth_years/$convert_years" | bc -l) |
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| 135 | echo "Number of years to be simulated: $n_earth_years Earth years = $n_myear Martian years." |
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| 136 | fi |
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| 137 | } |
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| 138 | |
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| 139 | # To initialize the launching script |
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| 140 | initlaunch() { |
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| 141 | echo "This is a chained simulation for PEM and PCM runs in $dir on $machine by $user." |
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| 142 | convertyears |
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| 143 | i_myear=0. |
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| 144 | iPEM=1 |
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| 145 | iPCM=1 |
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| 146 | cp startfi.nc starts/ |
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| 147 | if [ -f "start.nc" ]; then |
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| 148 | cp start.nc starts/ |
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| 149 | elif [ -f "star1D.nc" ]; then |
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| 150 | cp star1D.txt starts/ |
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| 151 | fi |
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| 152 | if [ -f "startpem.nc" ]; then |
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| 153 | cp startpem.nc starts/ |
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| 154 | fi |
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| 155 | |
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| 156 | # Create a file to manage years of the chained simulation and store some info from the PEM runs |
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| 157 | echo $i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini > info_PEM.txt |
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| 158 | } |
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| 159 | |
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| 160 | # To submit the PCM runs |
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| 161 | # arg1: launching mode |
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| 162 | # arg2: number of PCM runs to launch |
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| 163 | # arg3: local number of the PCM run from which to start (optional) |
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| 164 | submitPCM() { |
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| 165 | find . -type f -name "PCMrun*.job" ! -name "PCMrun.job" -delete |
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| 166 | ii=1 |
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| 167 | if [ ! -z $3 ]; then |
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| 168 | ii=$3 |
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| 169 | fi |
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| 170 | if [ $(echo "$i_myear < $n_myear" | bc -l) ]; then |
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| 171 | echo "Run PCM $iPCM: call $ii/$2..." |
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| 172 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 173 | sed -i "s/^k=[0-9]\+$/k=$(echo "3 - $nPCM_ini" | bc)/" PCMrun.job |
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| 174 | ./PCMrun.job |
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| 175 | if [ $? -ne 0 ]; then |
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| 176 | errlaunch |
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| 177 | fi |
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| 178 | else # Mode: submitting jobs |
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| 179 | cp PCMrun.job PCMrun${iPCM}.job |
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| 180 | sed -i -E "s/($name_job[^0-9]*[0-9]*[^0-9]*)[0-9]+$/\1${iPCM}/" PCMrun${iPCM}.job |
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| 181 | sed -i "s/^k=[0-9]\+$/k=$(echo "3 - $nPCM_ini" | bc)/" PCMrun${iPCM}.job |
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| 182 | jobID=$(eval "$submit_job PCMrun${iPCM}.job") |
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| 183 | # Create a file to cancel the dependent jobs of the cycle |
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| 184 | echo "#!/bin/bash" > kill_launchPEM.sh |
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| 185 | chmod +x kill_launchPEM.sh |
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| 186 | echo $kill_job $jobID >> kill_launchPEM.sh |
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| 187 | fi |
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| 188 | ((iPCM++)) |
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| 189 | i_myear = $(echo "$i_myear + 1." | bc - l) |
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| 190 | ((ii++)) |
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| 191 | else |
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| 192 | endlaunch |
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| 193 | fi |
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| 194 | for ((i = $ii; i <= $2; i++)); do |
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| 195 | if [ $(echo "$i_myear < $n_myear" | bc -l) ]; then |
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| 196 | echo "Run PCM $iPCM: call $i/$2..." |
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| 197 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 198 | sed -i "s/^k=[0-9]\+$/k=$(echo "$i + 2 - $nPCM_ini" | bc)/" PCMrun.job |
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| 199 | ./PCMrun.job |
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| 200 | if [ $? -ne 0 ]; then |
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| 201 | errlaunch |
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| 202 | fi |
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| 203 | else # Mode: submitting jobs |
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| 204 | cp PCMrun.job PCMrun${iPCM}.job |
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| 205 | sed -i -E "s/($name_job[^0-9]*[0-9]*[^0-9]*)[0-9]+$/\1${iPCM}/" PCMrun${iPCM}.job |
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| 206 | sed -i "s/^k=[0-9]\+$/k=$(echo "$i + 2 - $nPCM_ini" | bc)/" PCMrun${iPCM}.job |
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| 207 | jobID=$(eval "$submit_dependjob=afterok:${jobID} PCMrun${iPCM}.job") |
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| 208 | echo $kill_job $jobID >> kill_launchPEM.sh |
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| 209 | fi |
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| 210 | ((iPCM++)) |
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| 211 | i_myear = $(echo "$i_myear + 1." | bc - l) |
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| 212 | else |
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| 213 | endlaunch |
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| 214 | fi |
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| 215 | done |
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| 216 | } |
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| 217 | |
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| 218 | # To submit the PEM run |
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| 219 | # arg1: launching mode |
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| 220 | submitPEM() { |
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| 221 | if [ $(echo "$i_myear < $n_myear" | bc -l) ]; then |
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| 222 | echo "Run PEM $iPEM" |
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| 223 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 224 | ./PEMrun.job |
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| 225 | if [ $? -ne 0 ]; then |
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| 226 | errlaunch |
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| 227 | fi |
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| 228 | else # Mode: submitting jobs |
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| 229 | sed -i -E "s/($name_job[^0-9]*[0-9]*[^0-9]*)[0-9]+$/\1${iPEM}/" PEMrun.job |
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| 230 | jobID=$(eval "$submit_job PEMrun.job") |
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| 231 | # Create a file to cancel the dependent jobs of the cycle |
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| 232 | echo "#!/bin/bash" > kill_launchPEM.sh |
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| 233 | chmod +x kill_launchPEM.sh |
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| 234 | echo $kill_job $jobID >> kill_launchPEM.sh |
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| 235 | fi |
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| 236 | else |
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| 237 | endlaunch |
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| 238 | fi |
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| 239 | } |
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| 240 | |
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| 241 | # To make one cycle of PCM and PEM runs |
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| 242 | # arg1: launching mode |
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| 243 | # arg2: number of PCM runs to launch |
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| 244 | # arg3: local number of the PCM run from which to start (optional) |
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| 245 | cyclelaunch() { |
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| 246 | # PCM runs |
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| 247 | submitPCM $1 $2 $3 |
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| 248 | |
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| 249 | # PEM run |
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| 250 | if [ $(echo "$i_myear < $n_myear" | bc -l) ]; then |
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| 251 | echo "Run PEM $iPEM" |
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| 252 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 253 | ./PEMrun.job |
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| 254 | if [ $? -ne 0 ]; then |
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| 255 | errlaunch |
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| 256 | fi |
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| 257 | else # Mode: submitting jobs |
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| 258 | sed -i -E "s/($name_job[^0-9]*[0-9]*[^0-9]*)[0-9]+$/\1${iPEM}/" PEMrun.job |
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| 259 | jobID=$(eval "$submit_dependjob=afterok:${jobID} PEMrun.job") |
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| 260 | echo $kill_job $jobID >> kill_launchPEM.sh |
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| 261 | fi |
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| 262 | else |
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| 263 | endlaunch |
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| 264 | fi |
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| 265 | } |
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| 266 | |
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| 267 | # To clean files after the starting run of the relaunch |
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| 268 | # arg1: file name prefix to clean |
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| 269 | # arg2: file name extension to clean |
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| 270 | # arg3: file number from which to clean |
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| 271 | cleanfiles() { |
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| 272 | prefix=$1 |
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| 273 | extension=$2 |
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| 274 | if [ -z "$extension" ]; then |
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| 275 | for file in ${prefix}*; do |
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| 276 | num=${file#$prefix} |
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| 277 | if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then |
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| 278 | rm $file |
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| 279 | fi |
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| 280 | done |
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| 281 | else |
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| 282 | for file in ${prefix}*${extension}; do |
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| 283 | num=${file#$prefix} |
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| 284 | num=${num%$extension} |
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| 285 | if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then |
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| 286 | rm $file |
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| 287 | fi |
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| 288 | done |
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| 289 | fi |
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| 290 | } |
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| 291 | |
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| 292 | # To relaunch from PCM run |
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| 293 | # arg1: launching mode |
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| 294 | relaunchPCM() { |
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| 295 | iPCM=$(($irelaunch + 1)) |
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| 296 | cleanfiles diags/diagfi .nc $irelaunch |
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| 297 | cleanfiles diags/data2reshape .nc $irelaunch |
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| 298 | cleanfiles "out_PCM/run" "" $irelaunch |
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| 299 | cleanfiles starts/restart1D .txt $irelaunch |
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| 300 | cleanfiles starts/restart .nc $irelaunch |
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| 301 | cleanfiles starts/restartfi .nc $irelaunch |
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| 302 | cp starts/restartfi${irelaunch}.nc startfi.nc |
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| 303 | if [ -f "starts/restart${irelaunch}.nc" ]; then |
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| 304 | cp starts/restart${irelaunch}.nc start.nc |
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| 305 | elif [ -f "starts/restart1D${irelaunch}.txt" ]; then |
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| 306 | cp starts/restart1D${irelaunch}.txt start1D.txt |
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| 307 | fi |
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| 308 | if [ $irelaunch -le $nPCM_ini ]; then |
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| 309 | # PCM relaunch during the initialization cycle |
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| 310 | iPEM=1 |
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| 311 | cleanfiles diags/diagpem .nc $iPEM |
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| 312 | cleanfiles "out_PEM/run" "" $iPEM |
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| 313 | cleanfiles starts/restart1D_postPEM .txt $iPEM |
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| 314 | cleanfiles starts/restart_postPEM .nc $iPEM |
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| 315 | cleanfiles starts/restartfi_postPEM .nc $iPEM |
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| 316 | cleanfiles starts/restartpem .nc $iPEM |
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| 317 | i_myear=$irelaunch |
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| 318 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 319 | rm -f startpem.nc |
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| 320 | if [ $irelaunch -eq $(($nPCM_ini - 1)) ]; then |
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| 321 | cp diags/data2reshape${irelaunch}.nc data2reshape_Y1.nc |
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| 322 | cyclelaunch $1 $nPCM_ini $iPCM |
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| 323 | elif [ $irelaunch -eq $nPCM_ini ]; then |
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| 324 | cp diags/data2reshape$(($irelaunch - 1)).nc data2reshape_Y1.nc |
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| 325 | cp diags/data2reshape${irelaunch}.nc data2reshape_Y2.nc |
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| 326 | submitPEM $1 # The next job is a PEM run |
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| 327 | else |
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| 328 | cyclelaunch $1 $nPCM_ini $iPCM |
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| 329 | fi |
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| 330 | else |
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| 331 | # PCM relaunch during a cycle |
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| 332 | iPEM=$(echo "($iPCM - $nPCM_ini)/$nPCM + 1" | bc) |
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| 333 | il=$(echo "($irelaunch - $nPCM_ini + 1)%$nPCM + 1" | bc) |
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| 334 | cleanfiles diags/diagpem .nc $iPEM |
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| 335 | cleanfiles "out_PEM/run" "" $iPEM |
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| 336 | cleanfiles starts/restart1D_postPEM .txt $iPEM |
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| 337 | cleanfiles starts/restart_postPEM .nc $iPEM |
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| 338 | cleanfiles starts/restartfi_postPEM .nc $iPEM |
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| 339 | cleanfiles starts/restartpem .nc $iPEM |
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| 340 | cp starts/restartpem${iPEM}.nc startpem.nc |
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| 341 | if [ $il -eq $(($nPCM - 1)) ]; then # Second to last PCM run |
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| 342 | i_myear=$(($(awk "NR==$iPEM {print \$1}" "info_PEM.txt") + $il)) |
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| 343 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 344 | cp diags/data2reshape${irelaunch}.nc data2reshape_Y1.nc |
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| 345 | cyclelaunch $1 $nPCM $il |
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| 346 | elif [ $il -eq $nPCM ]; then # Last PCM run so the next job is a PEM run |
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| 347 | i_myear=$(($(awk "NR==$iPEM {print \$1}" "info_PEM.txt") + $nPCM)) |
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| 348 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 349 | cp diags/data2reshape$(($irelaunch - 1)).nc data2reshape_Y1.nc |
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| 350 | cp diags/data2reshape${irelaunch}.nc data2reshape_Y2.nc |
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| 351 | submitPEM $1 |
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| 352 | else |
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| 353 | i_myear=$(($(awk "NR==$iPEM {print \$1}" "info_PEM.txt") + $il)) |
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| 354 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 355 | cyclelaunch $1 $nPCM $il |
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| 356 | fi |
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| 357 | fi |
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| 358 | } |
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| 359 | |
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| 360 | # To relaunch from PEM run |
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| 361 | # arg1: launching mode |
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| 362 | relaunchPEM() { |
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| 363 | iPEM=$(echo "$irelaunch + 1" | bc) |
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| 364 | iPCM=$(echo "$nPCM_ini + $nPCM*($irelaunch - 1) + 1" | bc) |
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| 365 | i_myear=$(awk "NR==$(($iPEM + 1)) {print \$1}" "info_PEM.txt") |
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| 366 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 367 | cleanfiles diags/diagfi .nc $(($iPCM - 1)) |
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| 368 | cleanfiles "out_PCM/run" "" $(($iPCM - 1)) |
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| 369 | cleanfiles starts/restart1D .txt $(($iPCM - 1)) |
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| 370 | cleanfiles starts/restart .nc $(($iPCM - 1)) |
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| 371 | cleanfiles starts/restartfi .nc $(($iPCM - 1)) |
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| 372 | cleanfiles diags/data2reshape .nc $(($iPCM - 1)) |
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| 373 | cleanfiles diags/diagpem .nc $irelaunch |
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| 374 | cleanfiles "out_PEM/run" "" $irelaunch |
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| 375 | cleanfiles starts/restart1D_postPEM .txt $irelaunch |
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| 376 | cleanfiles starts/restart_postPEM .nc $irelaunch |
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| 377 | cleanfiles starts/restartfi_postPEM .nc $irelaunch |
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| 378 | cleanfiles starts/restartpem .nc $irelaunch |
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| 379 | cp starts/restartpem${irelaunch}.nc startpem.nc |
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| 380 | cp starts/restartfi_postPEM${irelaunch}.nc startfi.nc |
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| 381 | if [ -f "starts/restart_postPEM${irelaunch}.nc" ]; then |
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| 382 | cp starts/restart_postPEM${irelaunch}.nc start.nc |
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| 383 | elif [ -f "starts/restart1D_postPEM${irelaunch}.txt" ]; then |
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| 384 | cp starts/restart1D_postPEM${irelaunch}.txt start1D.txt |
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| 385 | fi |
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| 386 | cyclelaunch $1 $nPCM |
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| 387 | } |
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