| 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 if SLURM is the job scheduler |
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| 27 | function is_slurm() { |
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| 28 | if [ ! -x $(command -v squeue) ]; then |
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| 29 | echo "Error: the job scheduler is not SLURM on $machine!" |
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| 30 | echo "You need to adapt the script to your case." |
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| 31 | errlaunch |
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| 32 | fi |
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| 33 | } |
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| 34 | |
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| 35 | # To check if everything necessary for the launching script is ok |
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| 36 | checklaunch() { |
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| 37 | # Save the current value of LC_NUMERIC and set it to a locale that uses a dot as the decimal separator |
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| 38 | OLD_LC_NUMERIC=$LC_NUMERIC |
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| 39 | LC_NUMERIC=en_US.UTF-8 |
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| 40 | |
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| 41 | is_slurm |
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| 42 | if [ -v n_mars_years ] && [ ! -z "$n_mars_years" ]; then |
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| 43 | if [ $n_mars_years -lt 1 ]; then |
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| 44 | echo "Error: the value of 'n_mars_years' must be >0!" |
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| 45 | errlaunch |
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| 46 | fi |
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| 47 | elif [ -v n_earth_years ] && [ ! -z "$n_earth_years" ]; then |
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| 48 | if [ $n_earth_years -lt 1 ]; then |
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| 49 | echo "Error: the value of 'n_earth_years' must be >0!" |
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| 50 | errlaunch |
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| 51 | fi |
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| 52 | else |
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| 53 | echo "Error: no number of years to be simulated has been set!" |
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| 54 | errlaunch |
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| 55 | fi |
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| 56 | if [ $nPCM_ini -lt 2 ] || [ -z "$nPCM_ini" ]; then |
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| 57 | echo "Error: the value of 'nPCM_ini' must be >1!" |
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| 58 | errlaunch |
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| 59 | fi |
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| 60 | if [ $nPCM -lt 2 ] || [ -z "$nPCM" ]; then |
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| 61 | echo "Error: the value of 'nPCM' must be >1!" |
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| 62 | errlaunch |
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| 63 | fi |
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| 64 | if [ ! -f "jobPCM.slurm" ]; then |
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| 65 | echo "Error: file \"jobPCM.slurm\" does not exist in $dir!" |
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| 66 | errlaunch |
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| 67 | fi |
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| 68 | if [ ! -f "jobPEM.slurm" ]; then |
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| 69 | echo "Error: file \"$jobPEM.slurm\" does not exist in $dir!" |
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| 70 | errlaunch |
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| 71 | fi |
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| 72 | if [ ! -f "run_PCM.def" ]; then |
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| 73 | echo "Error: file \"run_PCM.def\" does not exist in $dir!" |
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| 74 | errlaunch |
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| 75 | fi |
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| 76 | if [ ! -f "run_PEM.def" ]; then |
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| 77 | echo "Error: file \"run_PEM.def\" does not exist in $dir!" |
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| 78 | errlaunch |
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| 79 | fi |
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| 80 | if [ ! -f "context_lmdz_physics.xml" ]; then |
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| 81 | echo "Error: file \"context_lmdz_physics.xml\" does not exist in $dir!" |
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| 82 | errlaunch |
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| 83 | fi |
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| 84 | if [ ! -f "field_def_physics_mars.xml" ]; then |
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| 85 | echo "Error: file \"field_def_physics_mars.xml\" does not exist in $dir!" |
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| 86 | errlaunch |
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| 87 | fi |
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| 88 | if [ ! -f "file_def_physics_mars.xml" ]; then |
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| 89 | echo "Error: file \"file_def_physics_mars.xml\" does not exist in $dir!" |
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| 90 | errlaunch |
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| 91 | fi |
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| 92 | if [ ! -f "iodef.xml" ]; then |
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| 93 | echo "Error: file \"iodef.xml\" does not exist in $dir!" |
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| 94 | errlaunch |
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| 95 | fi |
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| 96 | if [ ! -d "out_PCM" ]; then |
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| 97 | mkdir out_PCM |
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| 98 | fi |
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| 99 | if [ ! -d "out_PEM" ]; then |
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| 100 | mkdir out_PEM |
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| 101 | fi |
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| 102 | if [ ! -d "starts" ]; then |
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| 103 | mkdir starts |
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| 104 | fi |
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| 105 | if [ ! -d "diags" ]; then |
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| 106 | mkdir diags |
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| 107 | fi |
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| 108 | } |
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| 109 | |
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| 110 | # To initialize the launching script |
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| 111 | initlaunch() { |
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| 112 | echo "This is a chained simulation for PEM and PCM runs in $dir on $machine by $user." |
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| 113 | myear=686.9725 # Number of Earth days in Martian year |
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| 114 | eyear=365.256363004 # Number of days in Earth year |
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| 115 | convert_years=$(echo "$myear/$eyear" | bc -l) |
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| 116 | convert_years=$(printf "%.4f" $convert_years) # Rounding to the 4th decimal to respect the precision of Martian year |
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| 117 | if [ -v n_mars_years ]; then |
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| 118 | n_myear=$n_mars_years |
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| 119 | echo "Number of years to be simulated: $n_myear Martian years." |
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| 120 | elif [ -v n_earth_years ]; then |
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| 121 | n_myear=$(echo "($n_earth_years/$convert_years + 0.999999)/1" | bc) # Ceiling of n_earth_years/convert_years |
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| 122 | echo "Number of years to be simulated: $n_earth_years Earth years = $n_myear Martian years." |
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| 123 | fi |
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| 124 | i_myear=0 |
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| 125 | iPEM=1 |
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| 126 | iPCM=1 |
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| 127 | cp startfi.nc starts/ |
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| 128 | if [ -f "start.nc" ]; then |
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| 129 | cp start.nc starts/ |
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| 130 | elif [ -f "star1D.nc" ]; then |
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| 131 | cp star1D.txt starts/ |
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| 132 | fi |
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| 133 | |
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| 134 | # Create a file to manage years of the chained simulation and store some info from the PEM runs |
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| 135 | echo $i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini > info_PEM.txt |
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| 136 | } |
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| 137 | |
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| 138 | # To submit the PCM runs |
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| 139 | submitPCM() { |
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| 140 | find . -type f -name "jobPCM*.slurm" ! -name "jobPCM.slurm" -delete |
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| 141 | ii=1 |
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| 142 | if [ ! -z $2 ]; then |
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| 143 | ii=$2 |
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| 144 | fi |
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| 145 | if [ $i_myear -lt $n_myear ]; then |
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| 146 | echo "Run PCM $iPCM: call $ii/$1..." |
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| 147 | cp jobPCM.slurm jobPCM${iPCM}.slurm |
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| 148 | sed -i "s/#SBATCH --job-name=jobPCM.*/#SBATCH --job-name=jobPCM${iPCM}/" jobPCM${iPCM}.slurm |
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| 149 | sed -i "s/^k=[0-9]\+$/k=$(echo "3 - $nPCM_ini" | bc -l)/" jobPCM${iPCM}.slurm |
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| 150 | jobID=$(sbatch --parsable jobPCM${iPCM}.slurm) |
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| 151 | # Create a file to cancel the dependent jobs of the cycle |
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| 152 | echo "#!/bin/bash" > kill_launchPEM.sh |
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| 153 | chmod +x kill_launchPEM.sh |
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| 154 | echo "scancel" $jobID >> kill_launchPEM.sh |
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| 155 | ((iPCM++)) |
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| 156 | ((i_myear++)) |
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| 157 | ((ii++)) |
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| 158 | else |
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| 159 | endlaunch |
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| 160 | fi |
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| 161 | for ((i = $ii; i <= $1; i++)); do |
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| 162 | if [ $i_myear -lt $n_myear ]; then |
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| 163 | echo "Run PCM $iPCM: call $i/$1..." |
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| 164 | cp jobPCM.slurm jobPCM${iPCM}.slurm |
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| 165 | sed -i "s/#SBATCH --job-name=jobPCM.*/#SBATCH --job-name=jobPCM${iPCM}/" jobPCM${iPCM}.slurm |
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| 166 | sed -i "s/^k=[0-9]\+$/k=$(echo "$i + 2 - $nPCM_ini" | bc -l)/" jobPCM${iPCM}.slurm |
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| 167 | jobID=$(sbatch --parsable --dependency=afterok:${jobID} jobPCM${iPCM}.slurm) |
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| 168 | echo "scancel" $jobID >> kill_launchPEM.sh |
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| 169 | ((iPCM++)) |
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| 170 | ((i_myear++)) |
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| 171 | else |
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| 172 | endlaunch |
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| 173 | fi |
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| 174 | done |
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| 175 | } |
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| 176 | |
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| 177 | # To submit the PEM run |
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| 178 | submitPEM() { |
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| 179 | if [ $i_myear -lt $n_myear ]; then |
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| 180 | echo "Run PEM $iPEM" |
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| 181 | sed -i "s/#SBATCH --job-name=jobPEM.*/#SBATCH --job-name=jobPEM${iPEM}/" jobPEM.slurm |
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| 182 | jobID=$(sbatch --parsable jobPEM.slurm) |
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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 "scancel" $jobID >> kill_launchPEM.sh |
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| 187 | else |
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| 188 | endlaunch |
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| 189 | fi |
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| 190 | } |
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| 191 | |
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| 192 | # To make one cycle of PCM and PEM runs |
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| 193 | cyclelaunch() { |
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| 194 | # PCM runs |
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| 195 | submitPCM $1 $2 |
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| 196 | |
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| 197 | # PEM run |
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| 198 | if [ $i_myear -lt $n_myear ]; then |
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| 199 | echo "Run PEM $iPEM" |
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| 200 | sed -i "s/#SBATCH --job-name=jobPEM.*/#SBATCH --job-name=jobPEM${iPEM}/" jobPEM.slurm |
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| 201 | jobID=$(sbatch --parsable --dependency=afterok:${jobID} jobPEM.slurm) |
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| 202 | echo "scancel" $jobID >> kill_launchPEM.sh |
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| 203 | else |
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| 204 | endlaunch |
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| 205 | fi |
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| 206 | } |
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| 207 | |
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| 208 | # To clean files after the starting run of the relaunch |
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| 209 | cleanfiles() { |
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| 210 | prefix=$1 |
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| 211 | extension=$2 |
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| 212 | if [ -z "$extension" ]; then |
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| 213 | for file in ${prefix}*; do |
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| 214 | num=${file#$prefix} |
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| 215 | if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then |
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| 216 | rm $file |
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| 217 | fi |
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| 218 | done |
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| 219 | else |
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| 220 | for file in ${prefix}*${extension}; do |
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| 221 | num=${file#$prefix} |
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| 222 | num=${num%$extension} |
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| 223 | if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then |
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| 224 | rm $file |
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| 225 | fi |
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| 226 | done |
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| 227 | fi |
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| 228 | } |
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| 229 | |
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| 230 | # To relaunch from PCM run |
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| 231 | relaunchPCM() { |
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| 232 | iPCM=$(($irelaunch + 1)) |
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| 233 | cleanfiles diags/diagfi .nc $irelaunch |
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| 234 | cleanfiles "out_PCM/run" "" $irelaunch |
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| 235 | cleanfiles starts/restart1D .txt $irelaunch |
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| 236 | cleanfiles starts/restart .nc $irelaunch |
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| 237 | cleanfiles starts/restartfi .nc $irelaunch |
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| 238 | cp starts/restartfi${irelaunch}.nc startfi.nc |
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| 239 | if [ -f "starts/restart${irelaunch}.nc" ]; then |
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| 240 | cp starts/restart${irelaunch}.nc start.nc |
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| 241 | elif [ -f "starts/restart1D${irelaunch}.txt" ]; then |
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| 242 | cp starts/restart1D${irelaunch}.txt start1D.txt |
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| 243 | fi |
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| 244 | if [ $irelaunch -le $nPCM_ini ]; then |
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| 245 | # PCM relaunch during the initialization cycle |
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| 246 | iPEM=1 |
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| 247 | cleanfiles diags/diagpem .nc $iPEM |
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| 248 | cleanfiles "out_PEM/run" "" $iPEM |
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| 249 | cleanfiles starts/restart1D_postPEM .txt $iPEM |
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| 250 | cleanfiles starts/restart_postPEM .nc $iPEM |
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| 251 | cleanfiles starts/restartfi_postPEM .nc $iPEM |
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| 252 | cleanfiles starts/restartpem .nc $iPEM |
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| 253 | i_myear=$irelaunch |
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| 254 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 255 | if [ $irelaunch -eq $(($nPCM_ini - 1)) ]; then |
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| 256 | cp diags/data2reshape${irelaunch}.nc data2reshape_Y1.nc |
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| 257 | cleanfiles diags/data2reshape .nc $irelaunch |
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| 258 | cyclelaunch $nPCM_ini $irelaunch |
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| 259 | elif [ $irelaunch -eq 0 ]; then |
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| 260 | cp diags/data2reshape$(($irelaunch - 1)).nc data2reshape_Y1.nc |
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| 261 | cp diags/data2reshape${irelaunch}.nc data2reshape_Y2.nc |
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| 262 | cleanfiles diags/data2reshape .nc $(($irelaunch - 1)) |
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| 263 | submitPEM # The next job is a PEM run |
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| 264 | else |
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| 265 | cleanfiles diags/data2reshape .nc 0 |
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| 266 | cyclelaunch $nPCM_ini $iPCM |
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| 267 | fi |
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| 268 | else |
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| 269 | # PCM relaunch during a cycle |
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| 270 | iPEM=$((($irelaunch - $nPCM_ini)/$nPCM + 1)) |
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| 271 | il=$(echo "($irelaunch - $nPCM_ini)%$nPCM" | bc -l) |
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| 272 | cleanfiles diags/diagpem .nc $iPEM |
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| 273 | cleanfiles "out_PEM/run" "" $iPEM |
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| 274 | cleanfiles starts/restart1D_postPEM .txt $iPEM |
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| 275 | cleanfiles starts/restart_postPEM .nc $iPEM |
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| 276 | cleanfiles starts/restartfi_postPEM .nc $iPEM |
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| 277 | cleanfiles starts/restartpem .nc $iPEM |
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| 278 | cp starts/restartpem${iPEM}.nc startpem.nc |
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| 279 | if [ $il -eq $(($nPCM - 1)) ]; then |
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| 280 | i_myear=$(($(awk "NR==$iPEM {print \$1}" "info_PEM.txt") + $il)) |
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| 281 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 282 | cp diags/data2reshape${irelaunch}.nc data2reshape_Y1.nc |
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| 283 | cleanfiles diags/data2reshape .nc $irelaunch |
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| 284 | cyclelaunch $nPCM $il |
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| 285 | elif [ $il -eq 0 ]; then |
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| 286 | i_myear=$(($(awk "NR==$iPEM {print \$1}" "info_PEM.txt") + $nPCM)) |
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| 287 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 288 | cp diags/data2reshape$(($irelaunch - 1)).nc data2reshape_Y1.nc |
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| 289 | cp diags/data2reshape${irelaunch}.nc data2reshape_Y2.nc |
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| 290 | cleanfiles diags/data2reshape .nc $(($irelaunch - 1)) |
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| 291 | submitPEM # The next job is a PEM run |
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| 292 | else |
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| 293 | i_myear=$(($(awk "NR==$iPEM {print \$1}" "info_PEM.txt") + $il)) |
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| 294 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 295 | cleanfiles diags/data2reshape .nc $irelaunch |
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| 296 | cyclelaunch $nPCM $il |
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| 297 | fi |
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| 298 | fi |
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| 299 | } |
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| 300 | |
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| 301 | # To relaunch from PEM run |
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| 302 | relaunchPEM() { |
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| 303 | iPEM=$irelaunch |
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| 304 | iPCM=$(($nPCM_ini + ($nPCM - 1)*$irelaunch + 1)) |
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| 305 | i_myear=$(awk "NR==$(($iPEM + 1)) {print \$1}" "info_PEM.txt") |
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| 306 | sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt |
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| 307 | cleanfiles diags/diagfi .nc $(($iPCM - 1)) |
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| 308 | cleanfiles "out_PCM/run" "" $(($iPCM - 1)) |
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| 309 | cleanfiles starts/restart1D .txt $(($iPCM - 1)) |
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| 310 | cleanfiles starts/restart .nc $(($iPCM - 1)) |
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| 311 | cleanfiles starts/restartfi .nc $(($iPCM - 1)) |
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| 312 | cleanfiles diags/data2reshape .nc $(($iPCM - 1)) |
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| 313 | cleanfiles diags/diagpem .nc $irelaunch |
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| 314 | cleanfiles "out_PEM/run" "" $irelaunch |
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| 315 | cleanfiles starts/restart1D_postPEM .txt $irelaunch |
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| 316 | cleanfiles starts/restart_postPEM .nc $irelaunch |
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| 317 | cleanfiles starts/restartfi_postPEM .nc $irelaunch |
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| 318 | cleanfiles starts/restartpem .nc $irelaunch |
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| 319 | cp starts/restartpem${irelaunch}.nc startpem.nc |
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| 320 | cp starts/restartfi_postPEM${irelaunch}.nc startfi.nc |
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| 321 | if [ -f "starts/restart_postPEM${irelaunch}.nc" ]; then |
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| 322 | cp starts/restart_postPEM${irelaunch}.nc start.nc |
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| 323 | elif [ -f "starts/restart1D_postPEM${irelaunch}.txt" ]; then |
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| 324 | cp starts/restart1D_postPEM${irelaunch}.txt start1D.txt |
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| 325 | fi |
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| 326 | cyclelaunch $nPCM |
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| 327 | } |
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