1 | ##################################################### |
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2 | # Author : Simona Flavoni for NEMO |
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3 | # Contact : sflod@locean-ipsl.upmc.fr |
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4 | # |
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5 | # ---------------------------------------------------------------------- |
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6 | # NEMO/SETTE , NEMO Consortium (2010) |
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7 | # Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt) |
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8 | # ---------------------------------------------------------------------- |
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9 | # |
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10 | # Some scripts called by sette.sh |
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11 | # prepare_job.sh : creates the job script for running job |
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12 | ###################################################### |
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13 | #set -x |
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14 | set -o posix |
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15 | #set -u |
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16 | #set -e |
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17 | # |
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18 | # |
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19 | # ================ |
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20 | # prepare_job.sh |
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21 | # ================ |
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22 | # |
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23 | # ------------------------------------------------- |
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24 | # script that creates the job script for NEMO tests |
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25 | # ------------------------------------------------- |
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26 | # |
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27 | # SYNOPSIS |
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28 | # ======== |
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29 | # |
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30 | # :: |
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31 | # |
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32 | # $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_INTERACT MPI_FLAG |
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33 | # |
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34 | # |
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35 | # DESCRIPTION |
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36 | # =========== |
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37 | # |
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38 | # Simple job for SET TESTS for NEMO (SETTE) |
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39 | # |
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40 | # get input files (if needed) : tar file |
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41 | # (note this job needs to have an input_CONFIG.cfg in which can be found input tar file name) |
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42 | # |
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43 | # runs job in interactive or batch mode : all jobs using 1 process are run interactive, and all MPP jobs are |
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44 | # |
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45 | # run in batch (MPI_INTERACT="no") or interactive (MPI_INTERACT="yes") see sette.sh and BATCH_TEMPLATE directory |
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46 | # |
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47 | # and call post_test_tidyup function (that moves in NEMO_VALIDATION_DIR solver.stat, tracer.stat (for LOBSTER & PISCES) & ocean.output) |
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48 | # |
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49 | # EXAMPLES |
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50 | # ======== |
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51 | # |
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52 | # :: |
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53 | # |
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54 | # $ ./fcm_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_INTERACT MPI_FLAG |
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55 | # |
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56 | # run a job of config GYRE with 1 processor SHORT test ( 5 days ) using an interactive run without mpirun |
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57 | # $ ./fcm_job.sh input_GYRE.cfg 1 SHORT yes no |
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58 | # |
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59 | # run a job of config ORCA2_LIM_PISCES with 8 processors test RESTARTABILITY submitting the job to the batch queue system and using mpirun |
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60 | # $ ./fcm_job.sh input_ORCA2_LIM_PISCES.cfg 8 LONG no yes |
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61 | # |
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62 | # |
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63 | # TODO |
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64 | # ==== |
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65 | # |
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66 | # option debug |
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67 | # |
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68 | # |
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69 | # EVOLUTIONS |
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70 | # ========== |
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71 | # |
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72 | # $Id: fcm_job.sh 3050 2011-11-07 14:11:34Z acc $ |
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73 | # |
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74 | # |
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75 | # |
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76 | # * creation |
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77 | # |
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78 | #- |
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79 | # |
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80 | |
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81 | usage=" Usage : ./fcm_job.sh input_CONFIG_NAME.cfg NUMBER_OF_PROCS TEST_NAME INTERACT MPI_FLAG" |
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82 | usage=" example : ./fcm_job.sh input_ORCA2_LIM_PISCES.cfg 8 SHORT no/yes no/yes" |
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83 | |
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84 | |
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85 | minargcount=5 |
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86 | if [ ${#} -lt ${minargcount} ] |
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87 | then |
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88 | echo "not enought arguments for fcm_job.sh script" |
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89 | echo "control number of argument of fcm_job.sh in sette.sh" |
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90 | echo "${usage}" |
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91 | exit 1 |
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92 | fi |
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93 | unset minargcount |
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94 | if [ ! -f ${SETTE_DIR}/output.sette ] ; then |
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95 | touch ${SETTE_DIR}/output.sette |
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96 | fi |
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97 | |
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98 | # |
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99 | # set and export TEST_NAME. It will be used within the post_test_tidyup function |
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100 | # |
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101 | INPUTARFILE=$1 |
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102 | NB_PROC=$2 |
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103 | TEST_NAME=$3 |
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104 | MPI_FLAG=$4 |
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105 | JOB_FILE=$5 |
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106 | |
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107 | # export EXE_DIR. This directory is used to execute model |
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108 | # |
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109 | export EXE_DIR |
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110 | # |
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111 | # |
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112 | echo "date: `date`" >> ${SETTE_DIR}/output.sette |
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113 | echo "" >> ${SETTE_DIR}/output.sette |
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114 | echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette |
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115 | echo "" >> ${SETTE_DIR}/output.sette |
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116 | echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette |
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117 | echo "`more ${SETTE_DIR}/../CONFIG/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette |
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118 | echo "" >> ${SETTE_DIR}/output.sette |
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119 | echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette |
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120 | echo "" >> ${SETTE_DIR}/output.sette |
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121 | echo "executing script : \"fcm_job $@\" " >> ${SETTE_DIR}/output.sette |
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122 | echo " " >> ${SETTE_DIR}/output.sette |
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123 | |
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124 | ################################################################ |
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125 | # SET INPUT |
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126 | # get the input tarfile if needed |
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127 | tar_file=$(sed -ne "1,1p" ${SETTE_DIR}/$INPUTARFILE) |
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128 | if [ "$(cat ${SETTE_DIR}/$INPUTARFILE | grep -c ".tar" )" -ne 0 ] ; then |
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129 | echo "looking for tar file" >> ${SETTE_DIR}/output.sette |
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130 | echo " " >> ${SETTE_DIR}/output.sette |
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131 | cp ${FORCING_DIR}/${tar_file} ${INPUT_DIR}/. |
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132 | echo "file in ${INPUT_DIR}" |
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133 | if [ ! -f ${INPUT_DIR}/${tar_file} ] ; then |
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134 | echo "PROBLEM during copy of tar file" >> ${SETTE_DIR}/output.sette |
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135 | echo "tar file IS NOT present in ${INPUT_DIR} directory " >> ${SETTE_DIR}/output.sette |
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136 | echo " " >> ${SETTE_DIR}/output.sette |
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137 | echo "PROBLEM during copy of tar file" |
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138 | exit 1 |
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139 | else |
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140 | cd ${EXE_DIR} ; tar xvof ${INPUT_DIR}/*.tar ; gunzip -f *gz |
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141 | fi |
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142 | fi |
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143 | |
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144 | if [ ! -f ${EXE_DIR}/namelist_ice ] ; then |
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145 | if [ -f ${EXE_DIR}/namelist_ice_lim2 ] ; then |
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146 | echo "choosing for namelist ice " >> ${SETTE_DIR}/output.sette |
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147 | echo " " >> ${SETTE_DIR}/output.sette |
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148 | cp ${EXE_DIR}/namelist_ice_lim2 ${EXE_DIR}/namelist_ice |
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149 | elif [ -f ${EXE_DIR}/namelist_ice_lim3 ] ; then |
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150 | cp ${EXE_DIR}/namelist_ice_lim3 ${EXE_DIR}/namelist_ice |
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151 | fi |
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152 | fi |
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153 | |
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154 | |
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155 | if [ "$(cat ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "agrif" )" -ne 0 ] ; then |
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156 | #- Namelist for ocean and ice (agrif fine grid) |
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157 | echo "choosing for namelist for AGRIF" >> ${SETTE_DIR}/output.sette |
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158 | echo " " >> ${SETTE_DIR}/output.sette |
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159 | cp ${EXE_DIR}/1_namelist_ice_lim2 ${EXE_DIR}/1_namelist_ice |
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160 | fi |
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161 | ################################################################ |
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162 | |
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163 | ################################################################ |
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164 | # RUN OPA |
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165 | cd ${EXE_DIR} |
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166 | if [ ! -r ${EXE_DIR}/opa ] |
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167 | then |
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168 | echo "executable opa does not exist" |
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169 | echo "executable opa does not exist, exit" >> ${SETTE_DIR}/output.sette |
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170 | exit 1 |
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171 | fi |
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172 | #if [ ${NB_PROC} == 1 ] ; then |
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173 | # echo "running opa" >> ${SETTE_DIR}/output.sette |
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174 | # echo " " >> ${SETTE_DIR}/output.sette |
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175 | # ./opa |
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176 | # |
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177 | # Tidy out output from this test and populate the NEMO_VALIDATION_DIR tree |
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178 | # |
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179 | # post_test_tidyup |
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180 | #else |
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181 | # echo "running opa in MPI" >> ${SETTE_DIR}/output.sette |
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182 | # echo " " >> ${SETTE_DIR}/output.sette |
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183 | |
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184 | # if [ ${MPI_INTERACT} == "yes" ] ; then |
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185 | # # |
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186 | # # example for brodie (NEC SX8) machine |
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187 | # # mpirun -np ${NB_PROC} opa |
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188 | # # example for dedale machine |
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189 | # # mpirun --mca btl self,tcp -np ${NB_PROC} opa |
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190 | # # example for vargas (IBM Power6) machine |
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191 | # mpiexec -n ${NB_PROC} opa |
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192 | # # |
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193 | # post_test_tidyup |
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194 | # fi |
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195 | # |
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196 | # example for NOCS Altix system using PBS batch submission (requires ${SETTE_DIR}/sette_batch_template file) |
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197 | # |
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198 | # if [ ${MPI_INTERACT} == "no" ] ; then |
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199 | case ${COMPILER} in |
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200 | ALTIX_NAUTILUS_MPT) |
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201 | NB_REM=$( echo $NB_PROC | awk '{print $1 % 4}') |
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202 | if [ ${NB_REM} == 0 ] ; then |
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203 | # number of processes required is an integer multiple of 4 |
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204 | # |
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205 | NB_NODES=$( echo $NB_PROC | awk '{print $1 $1 / 4}') |
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206 | else |
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207 | # |
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208 | # number of processes required is not an integer multiple of 4 |
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209 | # round up the number of nodes required. |
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210 | # |
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211 | NB_NODES=$( echo $NB_PROC | awk '{printf("%d",$1 / 4 + 1 )}') |
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212 | fi |
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213 | ;; |
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214 | ifort_MERCATOR_CLUSTER) |
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215 | echo NB_PROCS ${NB_PROC} |
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216 | echo NB_NODES ${NB_NODES} |
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217 | echo NB_PROC ${NB_PROC} |
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218 | if [ ${NB_PROC} -eq 1 ] ; then |
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219 | NB_NODES=1 |
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220 | QUEUE=monoproc |
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221 | NB_PROC_NODE=${NB_PROC} |
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222 | else |
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223 | if [ ${NB_PROC} -le 8 ] ; then |
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224 | NB_NODES=1 |
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225 | QUEUE=mono |
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226 | NB_PROC_NODE=${NB_PROC} |
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227 | else |
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228 | NB_NODES=$( echo $NB_PROC | awk '{print $1 - $1 % 8}' | awk '{print $1 / 8 }') |
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229 | QUEUE=multi |
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230 | NB_PROC_NODE=8 |
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231 | fi |
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232 | fi |
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233 | echo NB_PROCS ${NB_PROC} |
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234 | echo NB_NODES ${NB_NODES} |
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235 | echo NB_PROC_NODE ${NB_PROC_NODE} |
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236 | ;; |
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237 | *) |
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238 | NB_NODES=${NB_PROC} |
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239 | ;; |
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240 | |
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241 | esac |
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242 | # |
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243 | # Pass settings into job file by using sed to edit predefined strings |
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244 | # |
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245 | ((mem=5*NB_PROC)) |
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246 | echo NB_NODES NB_PROC QUEUE ${NB_NODES} ${NB_PROC} ${QUEUE} |
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247 | cat ${SETTE_DIR}/job_batch_template | sed -e"s/NODES/${NB_NODES}/" -e"s/NPROCSNODE/${NB_PROC_NODE}/" \ |
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248 | -e"s/NPROCS/${NB_PROC}/" \ |
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249 | -e"s/QUEUE/${QUEUE}/" -e"s/MEM/${mem}/" \ |
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250 | -e"s/QUEUE/${QUEUE}/" -e"s/MEM/${mem}/" \ |
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251 | -e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \ |
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252 | -e"s:DEF_EXE_DIR:${EXE_DIR}:" \ |
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253 | -e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \ |
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254 | -e"s:MPI_FLAG:${MPI_FLAG}:" \ |
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255 | -e"s:DEF_NEMO_VALIDATION:${NEMO_VALIDATION_DIR}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \ |
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256 | -e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job |
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257 | |
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258 | # |
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259 | # create the unique submission job script |
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260 | # |
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261 | if [ ! -f $JOB_FILE ] ; then |
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262 | mv run_sette_test.job $JOB_FILE |
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263 | else |
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264 | e=`grep -n "# END_BODY" ${JOB_FILE} | cut -d : -f 1` |
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265 | e=$(($e - 1)) |
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266 | head -$e $JOB_FILE > ${JOB_FILE}_new |
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267 | mv ${JOB_FILE}_new ${JOB_FILE} |
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268 | l=`wc -l run_sette_test.job | sed -e "s:run_sette_test.job::"` |
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269 | b=`grep -n "# BODY" run_sette_test.job | cut -d : -f 1` |
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270 | t=$(($l - $b)) |
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271 | tail -$t run_sette_test.job >> $JOB_FILE |
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272 | fi |
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273 | |
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274 | chmod a+x $JOB_FILE |
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275 | |
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276 | #fi |
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