| 1 | #!/bin/bash |
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| 2 | ######################################################################## |
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| 3 | ######## Library of bash functions for the PEM workflow script ######### |
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| 4 | ######################################################################## |
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| 5 | |
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| 6 | # To end the workflow script |
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| 7 | end_workflow() { |
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| 8 | # Restore the previous value of LC_NUMERIC |
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| 9 | LC_NUMERIC=$OLD_LC_NUMERIC |
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| 10 | date |
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| 11 | echo "Success: the PEM workflow script completed normally!" |
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| 12 | exit 0 |
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| 13 | } |
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| 14 | |
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| 15 | # To abort the workflow script with error |
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| 16 | abort_workflow() { |
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| 17 | # Restore the previous value of LC_NUMERIC |
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| 18 | LC_NUMERIC=$OLD_LC_NUMERIC |
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| 19 | |
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| 20 | date |
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| 21 | echo "Error: an issue occured in the PEM workflow script!" |
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| 22 | exit 1 |
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| 23 | } |
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| 24 | |
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| 25 | # To check what is the job scheduler |
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| 26 | function detect_scheduler() { |
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| 27 | if command -v squeue &> /dev/null; then |
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| 28 | echo "SLURM is installed on $machine." |
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| 29 | job_scheduler="SLURM" |
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| 30 | job_name="#SBATCH --job-name=" |
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| 31 | kill_job="scancel" |
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| 32 | elif command -v qstat &> /dev/null; then |
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| 33 | echo "PBS/TORQUE is installed on $machine." |
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| 34 | job_scheduler="PBS" |
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| 35 | job_name="#PBS -N " |
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| 36 | kill_job="qdel" |
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| 37 | else |
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| 38 | echo "Error: neither SLURM nor TORQUE/PBS is installed on $machine!" |
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| 39 | echo "You need to adapt the script to your job job_scheduler or set 'mode' to 0." |
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| 40 | abort_workflow |
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| 41 | fi |
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| 42 | } |
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| 43 | |
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| 44 | # To get the number of slopes for the simulation |
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| 45 | get_nslope() { |
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| 46 | ns=1 |
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| 47 | if [ -f "startfi.nc" ]; then |
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| 48 | ns=$(ncdump -h startfi.nc | sed -n 's/.*nslope = \([0-9]*\) ;.*/\1/p') |
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| 49 | else |
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| 50 | for f in run_pcm.def callphys.def; do |
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| 51 | if [[ -f "$f" ]]; then |
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| 52 | while IFS= read -r line; do |
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| 53 | # Remove leading whitespace |
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| 54 | trimmed=$(echo "$line" | sed 's/^[[:space:]]*//') |
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| 55 | # Skip lines that are commented out |
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| 56 | if [[ "$trimmed" == \#* ]]; then |
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| 57 | continue |
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| 58 | fi |
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| 59 | # Check if line contains 'nslope = N' |
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| 60 | if [[ "$trimmed" =~ ^nslope[[:space:]]*=[[:space:]]*([0-9]+) ]]; then |
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| 61 | ns="${BASH_REMATCH[1]}" |
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| 62 | break |
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| 63 | fi |
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| 64 | done < "$f" |
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| 65 | [[ -n "$ns" ]] && break |
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| 66 | fi |
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| 67 | done |
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| 68 | fi |
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| 69 | } |
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| 70 | |
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| 71 | # To modify the xml file according nslope |
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| 72 | config_xios_outputs() { |
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| 73 | tmp="tmp_file_def.xml" |
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| 74 | in_outdaily4pem=false |
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| 75 | in_outyearly4pem=false |
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| 76 | in_outdaily4pem_s=false |
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| 77 | in_outyearly4pem_s=false |
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| 78 | |
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| 79 | sed -i 's/enabled="\.true\.\">/enabled=".false.">/g' file_def_physics_mars.xml |
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| 80 | |
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| 81 | while IFS= read -r line; do |
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| 82 | # Detect file blocks |
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| 83 | case "$line" in |
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| 84 | *'<file id="outdaily4pem"'*) |
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| 85 | in_outdaily4pem=true |
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| 86 | ;; |
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| 87 | *'<file id="outyearly4pem"'*) |
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| 88 | in_outyearly4pem=true |
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| 89 | ;; |
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| 90 | *'<file id="outdaily4pem_s"'*) |
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| 91 | in_outdaily4pem_s=true |
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| 92 | ;; |
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| 93 | *'<file id="outyearly4pem_s"'*) |
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| 94 | in_outyearly4pem_s=true |
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| 95 | ;; |
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| 96 | esac |
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| 97 | |
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| 98 | # Handle enabled attribute |
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| 99 | if [[ $line == *'enabled="'* ]]; then |
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| 100 | if $in_outdaily4pem || $in_outyearly4pem; then |
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| 101 | if [[ $ns -eq 1 ]]; then |
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| 102 | line=' enabled=".true.">' |
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| 103 | else |
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| 104 | line=' enabled=".false.">' |
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| 105 | fi |
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| 106 | elif $in_outdaily4pem_s || $in_outyearly4pem_s; then |
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| 107 | if [[ $ns -eq 1 ]]; then |
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| 108 | line=' enabled=".false.">' |
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| 109 | else |
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| 110 | line=' enabled=".true.">' |
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| 111 | fi |
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| 112 | fi |
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| 113 | fi |
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| 114 | |
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| 115 | # Handle slope variables |
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| 116 | if ( $in_outdaily4pem_s || $in_outyearly4pem_s ) && [[ $line =~ slope([0-9]+) ]]; then |
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| 117 | slope_id="${BASH_REMATCH[1]}" |
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| 118 | if (( 10#$slope_id > ns )); then |
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| 119 | # Ensure the line is commented |
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| 120 | if [[ $line != "<!--"* ]]; then |
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| 121 | line="<!-- $line -->" |
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| 122 | fi |
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| 123 | else |
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| 124 | # Ensure the line is uncommented |
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| 125 | if [[ $line == "<!--"* ]]; then |
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| 126 | line="${line#<!-- }" # remove leading <!-- |
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| 127 | line="${line% -->}" # remove trailing --> |
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| 128 | fi |
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| 129 | fi |
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| 130 | fi |
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| 131 | |
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| 132 | |
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| 133 | # Leaving the file block |
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| 134 | case "$line" in |
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| 135 | *'</file>'*) |
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| 136 | in_outdaily4pem=false |
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| 137 | in_outyearly4pem=false |
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| 138 | in_outdaily4pem_s=false |
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| 139 | in_outyearly4pem_s=false |
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| 140 | ;; |
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| 141 | esac |
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| 142 | |
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| 143 | echo "$line" >> "$tmp" |
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| 144 | done < file_def_physics_mars.xml |
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| 145 | |
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| 146 | mv "$tmp" file_def_physics_mars.xml |
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| 147 | } |
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| 148 | |
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| 149 | # To check if a PCM run is one year |
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| 150 | check_run_yearly() { |
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| 151 | if [ -f "startfi.nc" ]; then |
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| 152 | year_sol=$(ncdump -v controle startfi.nc 2>/dev/null | \ |
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| 153 | sed -n '/controle =/,/;/p' | tr -d '[:space:]' | \ |
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| 154 | sed 's/.*=//; s/;//' | tr ',' '\n' | sed -n '14p') |
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| 155 | else |
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| 156 | echo "Warning: no \"startfi.nc\" found! So default year_sol=669 (Mars year) is taken..." |
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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 "$sol_in_file" ]; then |
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| 167 | echo "Error: no length of year found in \"run_pcm.def\"!" |
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| 168 | abort_workflow |
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| 169 | elif [ "$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\" ($year_sol)!" |
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| 174 | abort_workflow |
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| 175 | fi |
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| 176 | } |
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| 177 | |
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| 178 | # To check if everything necessary for the workflow script is ok |
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| 179 | check_workflow() { |
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| 180 | # Save the current value of LC_NUMERIC and set it to a locale that uses a dot as the decimal separator |
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| 181 | OLD_LC_NUMERIC=$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_planetary_years ] && [ ! -z "$n_planetary_years" ]; then |
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| 185 | if [ $(echo "$n_planetary_years <= 0." | bc -l) -eq 1 ]; then |
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| 186 | echo "Error: 'n_planetary_years' must be > 0!" |
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| 187 | abort_workflow |
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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 | abort_workflow |
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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 | abort_workflow |
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| 197 | fi |
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| 198 | if [ $n_pcm_runs_ini -lt 2 ] || [ -z "$n_pcm_runs_ini" ]; then |
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| 199 | echo "Error: 'n_pcm_runs_ini' must be >= 2!" |
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| 200 | abort_workflow |
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| 201 | fi |
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| 202 | if [ $n_pcm_runs -lt 2 ] || [ -z "$n_pcm_runs" ]; then |
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| 203 | echo "Error: 'n_pcm_runs' must be >= 2!" |
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| 204 | abort_workflow |
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| 205 | fi |
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| 206 | if [ ! -f "pcm_run.job" ]; then |
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| 207 | echo "Error: file \"pcm_run.job\" does not exist in $dir!" |
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| 208 | abort_workflow |
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| 209 | fi |
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| 210 | if [ ! -f "pem_run.job" ]; then |
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| 211 | echo "Error: file \"pem_run.job\" does not exist in $dir!" |
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| 212 | abort_workflow |
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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 | abort_workflow |
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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 | abort_workflow |
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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 | abort_workflow |
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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 | abort_workflow |
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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 | abort_workflow |
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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 | abort_workflow |
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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 [ $exec_mode -ne 0 ]; then |
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| 248 | detect_scheduler |
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| 249 | fi |
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| 250 | # Set automatically the XIOS output file for the PEM according to the number of slopes |
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| 251 | get_nslope |
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| 252 | config_xios_outputs |
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| 253 | # Check if a PCM run is one year |
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| 254 | check_run_yearly |
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| 255 | } |
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| 256 | |
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| 257 | # To convert Earth years into Mars years |
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| 258 | convert_earth2plnt_years() { |
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| 259 | myear=686.9725 # Number of Earth days in Martian year |
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| 260 | eyear=365.256363004 # Number of days in Earth year |
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| 261 | r_plnt2earth_yr=$(echo "$myear/$eyear" | bc -l) |
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| 262 | r_plnt2earth_yr=$(printf "%.4f" $r_plnt2earth_yr) # Rounding to the 4th decimal to respect the precision of Martian year |
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| 263 | if [ -v n_planetary_years ]; then |
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| 264 | ntot_yr_sim=$n_planetary_years |
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| 265 | echo "Number of years to be simulated: $ntot_yr_sim Martian years." |
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| 266 | elif [ -v n_earth_years ]; then |
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| 267 | ntot_yr_sim=$(echo "$n_earth_years/$r_plnt2earth_yr" | bc -l) |
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| 268 | echo "Number of years to be simulated: $n_earth_years Earth years = $ntot_yr_sim 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 workflow script |
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| 273 | ini_workflow() { |
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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 | convert_earth2plnt_years |
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| 276 | n_yr_sim=0. |
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| 277 | i_pem_run=1 |
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| 278 | i_pcm_run=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 $n_yr_sim $ntot_yr_sim $r_plnt2earth_yr $i_pcm_run $i_pem_run $n_pcm_runs $n_pcm_runs_ini > pem_workflow.sts |
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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: execution mode |
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| 297 | # arg2: number of PCM runs to submit |
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| 298 | # arg3: local number of the PCM run from which to start (optional) |
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| 299 | submit_pcm_phase() { |
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| 300 | find . -type f -name "PCMrun*.job" ! -name "pcm_run.job" -delete |
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| 301 | ii=1 |
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| 302 | if [ ! -z $3 ]; then |
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| 303 | ii=$3 |
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| 304 | fi |
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| 305 | if [ $(echo "$n_yr_sim < $ntot_yr_sim" | bc -l) -eq 1 ]; then |
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| 306 | echo "Run \"PCM $i_pcm_run\" ($ii/$2)" |
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| 307 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 308 | sed -i "s/^k=-\?[0-9]\+$/k=$(echo "$ii - $2 + 2" | bc)/" pcm_run.job |
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| 309 | ./pcm_run.job |
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| 310 | if [ $? -ne 0 ]; then |
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| 311 | abort_workflow |
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| 312 | fi |
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| 313 | else # Mode: submitting jobs |
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| 314 | cp pcm_run.job PCMrun${i_pcm_run}.job |
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| 315 | sed -i -E "/^$job_name/s/(.*[^0-9])([0-9]+)(_[^0-9]*)?$/\1${i_pcm_run}\3/" PCMrun${i_pcm_run}.job |
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| 316 | sed -i "s/^k=-\?[0-9]\+$/k=$(echo "$ii - $2 + 2" | bc)/" PCMrun${i_pcm_run}.job |
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| 317 | if [[ "$job_scheduler" == "SLURM" ]]; then |
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| 318 | jobID=$(sbatch --parsable PCMrun${i_pcm_run}.job) |
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| 319 | elif [[ "$job_scheduler" == "PBS" ]]; then |
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| 320 | jobID=$(qsub PCMrun${i_pcm_run}.job | cut -d. -f1) |
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| 321 | fi |
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| 322 | # Create a file to cancel the dependent jobs of the cycle |
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| 323 | echo "#!/bin/bash" > kill_pem_workflow.sh |
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| 324 | chmod +x kill_pem_workflow.sh |
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| 325 | echo $kill_job $jobID >> kill_pem_workflow.sh |
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| 326 | fi |
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| 327 | ((i_pcm_run++)) |
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| 328 | ((ii++)) |
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| 329 | else |
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| 330 | end_workflow |
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| 331 | fi |
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| 332 | for ((i = $ii; i <= $2; i++)); do |
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| 333 | if [ $(echo "$n_yr_sim < $ntot_yr_sim" | bc -l) -eq 1 ]; then |
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| 334 | echo "Run \"PCM $i_pcm_run\" ($i/$2)" |
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| 335 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 336 | sed -i "s/^k=-\?[0-9]\+$/k=$(echo "$i - $2 + 2" | bc)/" pcm_run.job |
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| 337 | ./pcm_run.job |
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| 338 | if [ $? -ne 0 ]; then |
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| 339 | abort_workflow |
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| 340 | fi |
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| 341 | else # Mode: submitting jobs |
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| 342 | cp pcm_run.job PCMrun${i_pcm_run}.job |
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| 343 | sed -i -E "/^$job_name/s/(.*[^0-9])([0-9]+)(_[^0-9]*)?$/\1${i_pcm_run}\3/" PCMrun${i_pcm_run}.job |
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| 344 | sed -i "s/^k=-\?[0-9]\+$/k=$(echo "$i - $2 + 2" | bc)/" PCMrun${i_pcm_run}.job |
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| 345 | if [[ "$job_scheduler" == "SLURM" ]]; then |
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| 346 | jobID=$(sbatch --parsable --dependency=afterok:${jobID} PCMrun${i_pcm_run}.job) |
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| 347 | elif [[ "$job_scheduler" == "PBS" ]]; then |
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| 348 | jobID=$(qsub -W depend=afterok:${jobID} PCMrun${i_pcm_run}.job | cut -d. -f1) |
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| 349 | fi |
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| 350 | echo $kill_job $jobID >> kill_pem_workflow.sh |
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| 351 | fi |
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| 352 | ((i_pcm_run++)) |
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| 353 | else |
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| 354 | end_workflow |
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| 355 | fi |
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| 356 | done |
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| 357 | } |
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| 358 | |
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| 359 | # To submit the PEM run |
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| 360 | # arg1: execution mode |
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| 361 | submit_pem_phase() { |
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| 362 | if [ $(echo "$n_yr_sim < $ntot_yr_sim" | bc -l) -eq 1 ]; then |
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| 363 | echo "Run \"PEM $i_pem_run\"" |
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| 364 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 365 | ./pem_run.job |
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| 366 | if [ $? -ne 0 ]; then |
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| 367 | abort_workflow |
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| 368 | fi |
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| 369 | else # Mode: submitting jobs |
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| 370 | sed -i -E "/^$job_name/s/(.*[^0-9])([0-9]+)(_[^0-9]*)?$/\1${i_pem_run}\3/" pem_run.job |
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| 371 | if [[ "$job_scheduler" == "SLURM" ]]; then |
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| 372 | jobID=$(sbatch --parsable pem_run.job) |
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| 373 | elif [[ "$job_scheduler" == "PBS" ]]; then |
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| 374 | jobID=$(qsub pem_run.job | cut -d. -f1) |
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| 375 | fi |
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| 376 | # Create a file to cancel the dependent jobs of the cycle |
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| 377 | echo "#!/bin/bash" > kill_pem_workflow.sh |
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| 378 | chmod +x kill_pem_workflow.sh |
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| 379 | echo $kill_job $jobID >> kill_pem_workflow.sh |
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| 380 | fi |
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| 381 | else |
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| 382 | end_workflow |
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| 383 | fi |
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| 384 | } |
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| 385 | |
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| 386 | # To make one cycle of PCM and PEM runs |
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| 387 | # arg1: execution mode |
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| 388 | # arg2: number of PCM runs to submit |
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| 389 | # arg3: local number of the PCM run from which to start (optional) |
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| 390 | submit_cycle() { |
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| 391 | # PCM runs |
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| 392 | submit_pcm_phase $1 $2 $3 |
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| 393 | |
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| 394 | # PEM run |
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| 395 | if [ $(echo "$n_yr_sim < $ntot_yr_sim" | bc -l) -eq 1 ]; then |
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| 396 | echo "Run \"PEM $i_pem_run\"" |
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| 397 | if [ $1 -eq 0 ]; then # Mode: processing scripts |
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| 398 | ./pem_run.job |
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| 399 | if [ $? -ne 0 ]; then |
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| 400 | abort_workflow |
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| 401 | fi |
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| 402 | else # Mode: submitting jobs |
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| 403 | sed -i -E "/^$job_name/s/(.*[^0-9])([0-9]+)(_[^0-9]*)?$/\1${i_pem_run}\3/" pem_run.job |
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| 404 | if [[ "$job_scheduler" == "SLURM" ]]; then |
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| 405 | jobID=$(sbatch --parsable --dependency=afterok:${jobID} pem_run.job) |
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| 406 | elif [[ "$job_scheduler" == "PBS" ]]; then |
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| 407 | jobID=$(qsub -W depend=afterok:${jobID} pem_run.job | cut -d. -f1) |
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| 408 | fi |
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| 409 | echo $kill_job $jobID >> kill_pem_workflow.sh |
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| 410 | fi |
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| 411 | else |
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| 412 | end_workflow |
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| 413 | fi |
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| 414 | } |
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| 415 | |
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| 416 | # To clean-up files after resuming |
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| 417 | # arg1: file name prefix to clean |
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| 418 | # arg2: file name extension to clean |
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| 419 | # arg3: file number from which to clean |
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| 420 | cleanup() { |
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| 421 | prefix=$1 |
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| 422 | extension=$2 |
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| 423 | if [ -z "$extension" ]; then |
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| 424 | for file in ${prefix}*; do |
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| 425 | num=${file#$prefix} |
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| 426 | if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then |
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| 427 | rm $file |
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| 428 | fi |
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| 429 | done |
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| 430 | else |
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| 431 | for file in ${prefix}*${extension}; do |
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| 432 | num=${file#$prefix} |
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| 433 | num=${num%$extension} |
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| 434 | if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then |
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| 435 | rm $file |
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| 436 | fi |
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| 437 | done |
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| 438 | fi |
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| 439 | } |
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| 440 | |
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| 441 | # To resume workflow from PCM run |
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| 442 | # arg1: execution mode |
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| 443 | resume_from_pcm_run() { |
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| 444 | i_pcm_run=$(($i_resume + 1)) |
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| 445 | cleanup diags/diagfi .nc $i_resume |
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| 446 | cleanup diags/diagsoil .nc $i_resume |
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| 447 | cleanup diags/Xoutdaily4pem .nc $i_resume |
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| 448 | cleanup diags/Xoutyearly4pem .nc $i_resume |
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| 449 | cleanup logs/runPCM .log $i_resume |
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| 450 | cleanup starts/restart1D .txt $i_resume |
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| 451 | cleanup starts/restart .nc $i_resume |
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| 452 | cleanup starts/restartfi .nc $i_resume |
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| 453 | cp starts/restartfi${i_resume}.nc startfi.nc |
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| 454 | if [ -f "starts/restart${i_resume}.nc" ]; then |
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| 455 | cp starts/restart${i_resume}.nc start.nc |
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| 456 | elif [ -f "starts/restart1D${i_resume}.txt" ]; then |
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| 457 | cp starts/restart1D${i_resume}.txt start1D.txt |
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| 458 | fi |
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| 459 | if [ $i_resume -le $n_pcm_runs_ini ]; then |
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| 460 | # PCM resumption during the initialization cycle |
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| 461 | i_pem_run=1 |
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| 462 | n_yr_sim=0 |
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| 463 | sed -i "1s/.*/$n_yr_sim $ntot_yr_sim $r_plnt2earth_yr $i_pcm_run $i_pem_run $n_pcm_runs $n_pcm_runs_ini/" pem_workflow.sts |
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| 464 | cleanup diags/diagevol .nc $(($i_pem_run - 1)) |
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| 465 | cleanup diags/diagevol_soil .nc $(($i_pem_run - 1)) |
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| 466 | cleanup logs/runPEM .log $(($i_pem_run - 1)) |
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| 467 | cleanup starts/restart1D_postPEM .txt $(($i_pem_run - 1)) |
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| 468 | cleanup starts/restart_postPEM .nc $(($i_pem_run - 1)) |
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| 469 | cleanup starts/restartfi_postPEM .nc $(($i_pem_run - 1)) |
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| 470 | cleanup starts/restartpem .nc $(($i_pem_run - 1)) |
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| 471 | rm -f startpem.nc |
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| 472 | if [ -f "starts/startpem.nc" ]; then |
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| 473 | cp starts/startpem.nc . |
|---|
| 474 | fi |
|---|
| 475 | if [ $i_resume -eq $(($n_pcm_runs_ini - 1)) ]; then |
|---|
| 476 | cp diags/Xoutdaily4pem${i_resume}.nc Xoutdaily4pem_Y1.nc |
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| 477 | cp diags/Xoutyearly4pem${i_resume}.nc Xoutyearly4pem_Y1.nc |
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| 478 | submit_cycle $1 $n_pcm_runs_ini $i_pcm_run |
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| 479 | elif [ $i_resume -eq $n_pcm_runs_ini ]; then |
|---|
| 480 | cp diags/Xoutdaily4pem$(($i_resume - 1)).nc Xoutdaily4pem_Y1.nc |
|---|
| 481 | cp diags/Xoutyearly4pem$(($i_resume - 1)).nc Xoutyearly4pem_Y1.nc |
|---|
| 482 | cp diags/Xoutdaily4pem${i_resume}.nc Xoutdaily4pem_Y2.nc |
|---|
| 483 | cp diags/Xoutyearly4pem${i_resume}.nc Xoutyearly4pem_Y2.nc |
|---|
| 484 | submit_pem_phase $1 # The next job is a PEM run |
|---|
| 485 | else |
|---|
| 486 | submit_cycle $1 $n_pcm_runs_ini $i_pcm_run |
|---|
| 487 | fi |
|---|
| 488 | else |
|---|
| 489 | # PCM resumption during a cycle |
|---|
| 490 | i_pem_run=$(echo "($i_pcm_run - $n_pcm_runs_ini)/$n_pcm_runs + 1" | bc) |
|---|
| 491 | il=$(echo "($i_resume - $n_pcm_runs_ini + 1)%$n_pcm_runs + 1" | bc) |
|---|
| 492 | n_yr_sim=$(awk "NR==$i_pem_run {printf \"%s\n\", \$3}" "pem_workflow.sts") |
|---|
| 493 | sed -i "1s/.*/$n_yr_sim $ntot_yr_sim $r_plnt2earth_yr $i_pcm_run $i_pem_run $n_pcm_runs $n_pcm_runs_ini/" pem_workflow.sts |
|---|
| 494 | cleanup diags/diagevol .nc $(($i_pem_run - 1)) |
|---|
| 495 | cleanup diags/diagevol_soil .nc $(($i_pem_run - 1)) |
|---|
| 496 | cleanup logs/runPEM .log $(($i_pem_run - 1)) |
|---|
| 497 | cleanup starts/restart1D_postPEM .txt $(($i_pem_run - 1)) |
|---|
| 498 | cleanup starts/restart_postPEM .nc $(($i_pem_run - 1)) |
|---|
| 499 | cleanup starts/restartfi_postPEM .nc $(($i_pem_run - 1)) |
|---|
| 500 | cleanup starts/restartpem .nc $(($i_pem_run - 1)) |
|---|
| 501 | cp starts/restartpem$(($i_pem_run - 1)).nc startpem.nc |
|---|
| 502 | if [ $il -eq $(($n_pcm_runs - 1)) ]; then # Second to last PCM run |
|---|
| 503 | cp diags/Xoutdaily4pem${i_resume}.nc Xoutdaily4pem_Y1.nc |
|---|
| 504 | cp diags/Xoutyearly4pem${i_resume}.nc Xoutyearly4pem_Y1.nc |
|---|
| 505 | submit_cycle $1 $n_pcm_runs $(($il + 1)) |
|---|
| 506 | elif [ $il -eq $n_pcm_runs ]; then # Last PCM run so the next job is a PEM run |
|---|
| 507 | cp diags/Xoutdaily4pem$(($i_resume - 1)).nc Xoutdaily4pem_Y1.nc |
|---|
| 508 | cp diags/Xoutyearly4pem$(($i_resume - 1)).nc Xoutyearly4pem_Y1.nc |
|---|
| 509 | cp diags/Xoutdaily4pem${i_resume}.nc Xoutdaily4pem_Y2.nc |
|---|
| 510 | cp diags/Xoutyearly4pem${i_resume}.nc Xoutyearly4pem_Y2.nc |
|---|
| 511 | submit_pem_phase $1 |
|---|
| 512 | else |
|---|
| 513 | submit_cycle $1 $n_pcm_runs $(($il + 1)) |
|---|
| 514 | fi |
|---|
| 515 | fi |
|---|
| 516 | } |
|---|
| 517 | |
|---|
| 518 | # To resume workflow from PEM run |
|---|
| 519 | # arg1: execution mode |
|---|
| 520 | resume_from_pem_run() { |
|---|
| 521 | i_pem_run=$(echo "$i_resume + 1" | bc) |
|---|
| 522 | i_pcm_run=$(echo "$n_pcm_runs_ini + $n_pcm_runs*($i_resume - 1) + 1" | bc) |
|---|
| 523 | n_yr_sim=$(awk "NR==$i_pem_run {printf \"%s\n\", \$3}" "pem_workflow.sts") |
|---|
| 524 | sed -i "1s/.*/$n_yr_sim $ntot_yr_sim $r_plnt2earth_yr $i_pcm_run $i_pem_run $n_pcm_runs $n_pcm_runs_ini/" pem_workflow.sts |
|---|
| 525 | cleanup diags/diagfi .nc $(($i_pcm_run - 1)) |
|---|
| 526 | cleanup diags/diagsoil .nc $(($i_pcm_run - 1)) |
|---|
| 527 | cleanup logs/runPCM .log $(($i_pcm_run - 1)) |
|---|
| 528 | cleanup starts/restart1D .txt $(($i_pcm_run - 1)) |
|---|
| 529 | cleanup starts/restart .nc $(($i_pcm_run - 1)) |
|---|
| 530 | cleanup starts/restartfi .nc $(($i_pcm_run - 1)) |
|---|
| 531 | cleanup diags/Xoutdaily4pem .nc $(($i_pcm_run - 1)) |
|---|
| 532 | cleanup diags/Xoutyearly4pem .nc $(($i_pcm_run - 1)) |
|---|
| 533 | cleanup diags/diagevol .nc $i_resume |
|---|
| 534 | cleanup diags/diagevol_soil .nc $i_resume |
|---|
| 535 | cleanup logs/runPEM .log $i_resume |
|---|
| 536 | cleanup starts/restart1D_postPEM .txt $i_resume |
|---|
| 537 | cleanup starts/restart_postPEM .nc $i_resume |
|---|
| 538 | cleanup starts/restartfi_postPEM .nc $i_resume |
|---|
| 539 | cleanup starts/restartpem .nc $i_resume |
|---|
| 540 | cp starts/restartpem${i_resume}.nc startpem.nc |
|---|
| 541 | cp starts/restartfi_postPEM${i_resume}.nc startfi.nc |
|---|
| 542 | if [ -f "starts/restart_postPEM${i_resume}.nc" ]; then |
|---|
| 543 | cp starts/restart_postPEM${i_resume}.nc start.nc |
|---|
| 544 | elif [ -f "starts/restart1D_postPEM${i_resume}.txt" ]; then |
|---|
| 545 | cp starts/restart1D_postPEM${i_resume}.txt start1D.txt |
|---|
| 546 | fi |
|---|
| 547 | submit_cycle $1 $n_pcm_runs |
|---|
| 548 | } |
|---|
