| 89 | | |
| 90 | | ==== 3.1.1 create new experiment folder ==== |
| 91 | | {{{ |
| 92 | | cd ../../config/ORCHIDEE_OL/ |
| 93 | | cp -fr SPINUP_ANALYTIC/ MY_SPINUP_ANALYTIC/ |
| 94 | | cd MY_SPINUP_ANALYTIC/ |
| 95 | | }}} |
| 96 | | ==== 3.1.2 tell libIGCM about the new input files (they are stored on the IMBALANCE-P disk on obelix) ==== |
| 97 | | modify the variable "ListNonDel" in COMP/stomate.card: |
| 98 | | {{{ |
| 99 | | ListNonDel= (${R_IN}/SRF/reftemp.nc, .) \ |
| 100 | | (/home/surface3/common/CNP_files/rev00/USDA_SoilSuborder.nc, .), \ |
| 101 | | (/home/surface3/common/CNP_files/rev00/lithology.nc, .), \ |
| 102 | | (/home/surface3/common/CNP_files/rev00/deposition.nc, .) |
| 103 | | }}} |
| 104 | | |
| 105 | | |
| 106 | | WARNING: the deposition file is a static field at the moment; it does not include N deposition either. At the moment N deposition is set to P deposition in the ORCHIDEE code. Anyway N deposition is not accounted for in the calculations for the N & P cycle for now. |
| 107 | | |
| 108 | | tell that we use the new “soil_param.nc”; in COMP/sechiba.card: |
| 109 | | {{{ |
| 110 | | (/home/surface3/common/CNP_files/rev00/soils_param.nc, .), \ |
| 111 | | }}} |
| 112 | | ==== 3.1.3 adjust the libIGCM ==== |
| 113 | | |
| 114 | | disable XIOS in COMP/orchidee_ol.card |
| 115 | | {{{ |
| 116 | | # Use XIOS as output library instead of IOIPSL |
| 117 | | XIOS=n |
| 118 | | }}} |
| 119 | | disable XIOS in PARAM/run.def |
| 120 | | {{{ |
| 121 | | # Use XIOS for writing diagnostics file |
| 122 | | # defulat = n |
| 123 | | XIOS_ORCHIDEE_OK = n |
| 124 | | }}} |
| 125 | | set the IO frequency to avoid crashes in PARAM/run.def |
| 126 | | {{{ |
| 127 | | # Writefrequency in seconds in sechiba_history.nc |
| 128 | | # default = 86400.0 |
| 129 | | WRITE_STEP = 1800.0 |
| 130 | | |
| 131 | | # Writefrequency in days in stomate_history.nc |
| 132 | | # default = 10. |
| 133 | | STOMATE_HIST_DT = 1 |
| 134 | | }}} |
| 135 | | |
| 136 | | add the new flags for the nutrient cycles in PARAM/run.def: |
| 137 | | {{{ |
| 138 | | # to activate P cycle set =y |
| 139 | | STOMATE_OK_PCYCLE=y |
| 140 | | # to activate N cycle set =y |
| 141 | | STOMATE_OK_NCYCLE=y |
| 142 | | # make sure we dont fake |
| 143 | | LD_FAKE_HEIGHT=n |
| 144 | | # you can enable mass conservation and stoichiometry checks by =y |
| 145 | | STOMATE_MASS_CONSERVATION=y |
| 146 | | STOMATE_DSG_DEBUG=y |
| 147 | | }}} |
| 148 | | in addition you should add all the PFT and soil parameter values as set in |
| 149 | | /home/users/dgoll/ORCHIDEE/DEFS_n_CARDS/run.def_NV2 |
| 150 | | |
| 151 | | disable river routing if you run on non-global scale in run.def |
| 152 | | {{{ |
| 153 | | # Activate river routing |
| 154 | | RIVER_ROUTING = n |
| 155 | | }}} |
| 156 | | |
| 157 | | |
| 158 | | ==== 3.1.4 adjust the job as usual ==== |
| 159 | | modify config.card as usual (see wiki) |
| 160 | | |
| 161 | | modify run.def as usual (see wiki) |
| 162 | | plus |
| 163 | | if you want to archive, for example in the IMBALANCE-P storage; add to config.card: |
| 164 | | {{{ |
| 165 | | ARCHIVE=/home/surface3/dgoll |
| 166 | | }}} |
| 167 | | |
| 168 | | ==== 3.1.5 create job ==== |
| 169 | | {{{ |
| 170 | | ../../../libIGCM/ins_job |
| 171 | | }}} |
| 172 | | |
| 173 | | ==== 3.1.6 adjust job_file (optional) ==== |
| 174 | | |
| 175 | | Header to run a site scale simulation on obelix |
| 176 | | {{{ |
| 177 | | ###################### |
| 178 | | ## OBELIX LSCE ## |
| 179 | | ###################### |
| 180 | | #PBS -N test |
| 181 | | #PBS -m a |
| 182 | | #PBS -j oe |
| 183 | | #PBS -q short |
| 184 | | #PBS -o Script_Output_test.000001 |
| 185 | | #PBS -S /bin/ksh |
| 186 | | #PBS -v BATCH_NUM_PROC_TOT=1 |
| 187 | | #PBS -l nodes=1:ppn=1 |
| 188 | | }}} |
| 189 | | |
| 190 | | to automatically have existing files deleted, set JobType=DEV |
| 191 | | {{{ |
| 192 | | #D- Experience type : DEB(ug), DEV(elopment), RUN (default) |
| 193 | | JobType=DEV |
| 194 | | }}} |
| 195 | | to avoid queuing take full advantage of your job time; the value depends on #PBS -q short and computation time of orchidee |
| 196 | | {{{ |
| 197 | | #D- Number of execution in one job |
| 198 | | PeriodNb=60 |
| 199 | | }}} |
| 200 | | |
| 201 | | to have a temp directory you can access on obelix; exchange dgoll with your ID |
| 202 | | {{{ |
| 203 | | #D- Define running directory |
| 204 | | #D- Default=${TMPDIR} ie temporary batch directory |
| 205 | | #D- |
| 206 | | #RUN_DIR_PATH=/workdir/or/scratchdir/of/this/machine |
| 207 | | RUN_DIR_PATH=/home/scratch01/dgoll/RUN_DIR |
| 208 | | }}} |
| 209 | | ==== 3.1.7 submit the job ==== |
| 210 | | on obelix: |
| 211 | | {{{ |
| 212 | | qsub Job_ID |
| 213 | | }}} |
| 214 | | on curie |
| 215 | | {{{ |
| 216 | | ccc_msub Job_ID |
| 217 | | }}} |
| 218 | | |
| 219 | | --- |
