1 | #!/bin/bash |
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2 | |
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3 | # This script provides site-specific functions |
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4 | # called by the site-independent scripts |
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5 | # create_runs.sh and submit.sh |
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6 | |
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7 | # NB : we must use the queue 'normal' because there seems to be a limit |
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8 | # on the number of jobs that can be submitted to queue 'test' |
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9 | |
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10 | #----------------------------- split_XXX ---------------------------- |
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11 | |
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12 | function split_mpi_32() { |
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13 | setvar nbp 33 nsplit_i 2 nsplit_j 4 |
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14 | } |
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15 | function split_serial_40() { |
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16 | setvar nbp 41 nsplit_i 2 nsplit_j 2 |
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17 | } |
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18 | function split_mpi_40() { |
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19 | setvar nbp 41 nsplit_i 2 nsplit_j 3 |
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20 | } |
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21 | function split_mpi_80() { |
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22 | setvar nbp 81 nsplit_i 4 nsplit_j 3 |
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23 | } |
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24 | function split_mpi_omp_40() { |
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25 | setvar nbp 41 nsplit_i 2 nsplit_j 2 omp_level_size 4 |
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26 | } |
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27 | |
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28 | #----------------- job submission ------------------ |
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29 | |
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30 | function submit_job_X64_CURIE() # $1=script $* = SLURM OPTIONS |
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31 | { |
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32 | TMP=$(mktemp) |
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33 | ccc_msub $1 > $TMP |
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34 | cat $TMP 1>&2 |
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35 | cat $TMP | awk '{print $NF }' |
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36 | rm -f $TMP |
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37 | } |
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38 | |
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39 | #------------------------------ job_XXX ----------------------------- |
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40 | |
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41 | # Serial jobs |
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42 | function job_serial() { # EXP_NAME |
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43 | job_gen $1 1 1 |
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44 | } |
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45 | function job_serial_40() { # EXP_NAME |
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46 | job_serial $1 |
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47 | } |
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48 | |
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49 | # MPI jobs |
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50 | function job_mpi() { #EXP_NAME NB_MPI |
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51 | job_gen $1 $2 1 |
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52 | } |
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53 | function job_mpi_32() { # EXP_NAME |
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54 | job_mpi $1 80 |
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55 | } |
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56 | function job_mpi_40() { # EXP_NAME |
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57 | job_mpi $1 60 |
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58 | } |
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59 | function job_mpi_80() { # EXP_NAME |
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60 | job_mpi $1 120 |
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61 | } |
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62 | |
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63 | # MPI-OMP jobs |
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64 | function job_mpi_omp() { #EXP_NAME NB_MPI NB_OMP |
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65 | job_gen $1 $2 $3 |
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66 | } |
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67 | function job_mpi_omp_40() { # EXP_NAME |
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68 | job_mpi_omp $1 40 4 |
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69 | } |
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70 | |
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71 | # Generic |
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72 | function job_gen() { # EXP_NAME MPI_TASKS OMP_TASKS MPIRUN |
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73 | MPI=$2 |
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74 | OMP=$3 |
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75 | MPI_OMP=$((MPI*OMP)) |
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76 | NODES=$(((MPI_OMP+63)/64)) |
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77 | VMEM=$((2*MPI_OMP)) |
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78 | cat <<EOF |
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79 | #!/bin/bash |
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80 | #PBS -N $1 |
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81 | #PBS -q std |
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82 | #PBS -n |
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83 | #PBS -l nodes=$NODES:ppn=64 |
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84 | #PBS -l walltime=00:15:00 |
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85 | #PBS -l mem=${VMEM}gb |
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86 | #PBS -l vmem=${VMEM}gb |
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87 | |
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88 | #####comment:PBS -l mem=31922327552,ncpus=60 |
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89 | #Jobs start in the HOME directory, cd to submitted directory |
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90 | cd "\$PBS_O_WORKDIR" |
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91 | |
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92 | ############################################################ |
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93 | NCPU=\$(wc -l < \$PBS_NODEFILE) |
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94 | awk "NR % $OMP == 0" \$PBS_NODEFILE | head -n $MPI > nodelist.txt |
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95 | |
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96 | echo ------------------JOB SUMMARY-------------------------- |
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97 | echo 'PBS OUT: Job allocated on: '\${NCPU}' cpu(s)' |
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98 | echo 'PBS OUT: Job running on the following node(s): ' |
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99 | cat nodelist.txt |
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100 | echo ------------------------------------------------------- |
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101 | echo PBS OUT: Job running on: \$PBS_O_HOST |
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102 | echo PBS OUT: Originating queue: \$PBS_O_QUEUE |
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103 | echo PBS OUT: Executing queue: \$PBS_QUEUE |
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104 | echo PBS OUT: Work directory: \$PBS_O_WORKDIR |
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105 | echo PBS OUT: Execution mode: \$PBS_ENVIRONMENT |
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106 | echo PBS OUT: Job identifier: \$PBS_JOBID |
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107 | echo PBS OUT: Job name: \$PBS_JOBNAME |
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108 | echo PBS OUT: Node file: \$PBS_NODEFILE |
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109 | echo PBS OUT: Current home directory: \$PBS_O_HOME |
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110 | echo PBS OUT: PATH= \$PBS_O_PATH |
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111 | echo ------------------------------------------------------- |
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112 | |
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113 | |
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114 | export OMP_NUM_THREADS=$3 |
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115 | export OMP_STACKSIZE=128M |
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116 | ulimit -s unlimited |
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117 | |
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118 | $(cat $ROOT/DYNAMICO/arch/arch-ifort_CICLAD.env) |
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119 | |
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120 | rm -rf gcm.log logs *.nc netcdf |
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121 | mpirun -np $MPI -cpus-per-proc \$OMP_NUM_THREADS -bycore -bind-to-core -report-bindings ./gcm.exe > gcm.log 2>&1 |
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122 | $4 >> gcm.log |
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123 | date >> gcm.log |
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124 | |
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125 | mkdir -p netcdf |
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126 | cp gcm.log *.def netcdf |
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127 | mv *.nc netcdf |
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128 | |
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129 | mkdir -p logs |
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130 | cp *.xml logs |
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131 | cp -pr $(readlink -e gcm.exe) logs |
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132 | cp -pr $(readlink -e build/src) logs |
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133 | mv xios_client_*.err xios_client_*.out gcm.log logs |
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134 | |
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135 | EOF |
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136 | } |
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137 | |
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138 | #------------------------------ post-processing job ----------------------------- |
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139 | |
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140 | function job_post_X64_CURIE() # LIST |
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141 | { |
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142 | DEPLIST=afterany |
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143 | for ID in $* ; do |
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144 | DEPLIST="$DEPLIST:$ID" |
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145 | done |
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146 | cat <<EOF |
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147 | #!/bin/bash |
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148 | ## Request name |
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149 | #MSUB -r testing |
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150 | #MSUB -q standard |
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151 | #MSUB -A gen7548 |
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152 | #MSUB -E "--dependency=$DEPLIST" |
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153 | ## Number of tasks (=MPI processes) to use |
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154 | #MSUB -n 1 |
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155 | ## Elapsed time limit in seconds |
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156 | #MSUB -T 600 |
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157 | ## Quality of Service required (long [3 days], normal [1 day], test [30 min]) |
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158 | #MSUB -Q normal |
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159 | |
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160 | export OMP_NUM_THREADS=1 |
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161 | # this script is submitted from $ROOT/logs |
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162 | cd \${BRIDGE_MSUB_PWD}/.. |
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163 | |
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164 | $(cat $ROOT/DYNAMICO/arch/arch-X64_CURIE.env) |
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165 | module load python |
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166 | |
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167 | bash/post.sh |
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168 | EOF |
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169 | } |
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