| 1 | =================================================================== |
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| 2 | LMDZ_Setup is a software suite for installing LMDZ and automatically |
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| 3 | automatically run a number of configurations. |
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| 4 | Authors: Frédéric Hourdin, Adriana Sima, Amaury Baral, Laurent Fairhead (and the LMDZ team) |
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| 5 | |
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| 6 | Last modification : 2024/12/19 |
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| 7 | =================================================================== |
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| 8 | |
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| 9 | Complementary information and FAQ (in French) : |
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| 10 | https://docs.google.com/document/d/1OLZG6e-86NiXuv5-aALxKIh-QPkp4BdCwWtiBFot-6c |
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| 11 | |
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| 12 | |
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| 13 | =================================================================== |
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| 14 | 0. Target platforms |
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| 15 | =================================================================== |
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| 16 | Default gfortran/bash installation on local computers. |
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| 17 | Specific installation on certain computing centers: |
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| 18 | spirit: IPSL cluster |
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| 19 | adastra: Cines supercomputer |
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| 20 | jean-zay: idris supercomputer |
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| 21 | irene: TGCC supercomputer WORK TO BE DONE |
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| 22 | Machine configuration dependency is managed by lmdz_env.sh |
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| 23 | |
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| 24 | |
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| 25 | =================================================================== |
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| 26 | I. What this working environment does and does not |
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| 27 | =================================================================== |
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| 28 | |
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| 29 | This tutorial can only be used on jean-zay computer at idris so far. |
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| 30 | However, extension to ciclad or irene will be done soon. |
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| 31 | |
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| 32 | It proposes a light automatic setup of LMDZ long chained climate simulations |
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| 33 | including installation of the model itself. |
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| 34 | |
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| 35 | It consists in running LMDZ coupled to Orchidee for land surface (optional) |
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| 36 | but with imposed sea surface temperature. |
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| 37 | |
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| 38 | The basic default configuration makes use of the IPSL-CM6A grid configuration |
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| 39 | and tuning, and runs a multi annual simulation on "climatological" |
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| 40 | amip sea surface temperature (with a mean annual cycle) using |
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| 41 | a calendar with 360 days. |
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| 42 | |
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| 43 | Optionally : the configuration includes the ability to use interannually |
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| 44 | varying SST and to activate "nudgning" by reanalysis. |
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| 45 | In both cases, the calendar is then a real one. |
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| 46 | When nudging is activated, the simulation must be run on a monthly |
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| 47 | basis, while otherwise, it can be either monthly or yearly. |
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| 48 | |
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| 49 | Since the tutorial automatically generates its own initial files, it |
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| 50 | can be run with zoom configurations by only changing the number |
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| 51 | of grid points ("resol" in main.sh) and the DEF/gcm.def file (see bellow). |
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| 52 | |
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| 53 | Aerosols can be read for the year 2000 (weighted average over 1999-2001 cf Lurton et al 2020), |
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| 54 | and instantaneous forcing with respect to 1850 can be computed as well. |
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| 55 | NEW (end 2020) : |
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| 56 | tutorial_prod can also run LMDZ coupled with the SPLA model |
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| 57 | (SimPLe Aerosol, activated with option aerosols=spla in setup.sh). |
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| 58 | Emissions of dust and sea salt are then computed interactively. |
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| 59 | 2021-05 : tutorial_prod OK, code LMDZ-SPLA OK, |
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| 60 | regridding SPLA input files : work in progress |
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| 61 | |
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| 62 | A configuration with isotopes is also available since 2023-04. |
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| 63 | |
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| 64 | =================================================================== |
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| 65 | II. Files and scripts |
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| 66 | =================================================================== |
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| 67 | ---------------------------------------------------------------- |
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| 68 | EXPERT : |
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| 69 | If the login groupe and computing allocation groupe are different : |
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| 70 | choose on which STORE space you work (login vs computing allocation); |
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| 71 | edit lmdz_env.sh, and set "groupe", "SCRATCHD" etc. accordingly. |
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| 72 | If you want to install the package in a dedicated folder instead of the root of $STORE: |
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| 73 | set STORED=$STORE/your_folder in lmdz_env.sh |
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| 74 | ---------------------------------------------------------------- |
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| 75 | |
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| 76 | main.sh : a script written to pass options to the main script setup.sh |
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| 77 | |
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| 78 | setup.sh : sets up one (series of) simulation(s) by editing the "job" script_SIMU |
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| 79 | When run with -init 1 options, creates INIT and LIMIT directories |
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| 80 | Run ./setup.sh -h for options |
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| 81 | RECOMMENDATION: do not run it directly, but use main.sh to drive it |
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| 82 | |
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| 83 | script_SIMU : script that is the basis for the job to run the simulations |
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| 84 | Automatically edited by setup.sh |
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| 85 | |
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| 86 | reb.sh : to rebuild splitted outputfiles (parallelism with IOISPL) |
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| 87 | automatically run by script_SIMU |
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| 88 | |
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| 89 | era2gcm_tuto.sh : to interpolate reanalysis onto the GCM grid, for nudging. |
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| 90 | To be run manually after the first use of main.sh |
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| 91 | |
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| 92 | era2gcm_uv10m.nc : for option "aerosols=spla" only : |
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| 93 | to interpolate reanalysis 10m-winds onto the GCM grid, for sea-salt (and dust) emissions. |
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| 94 | To be run manually after the first use of main.sh. |
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| 95 | |
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| 96 | season.sh : computing seasonal means and daily time series |
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| 97 | |
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| 98 | interp_aerosols.sh : interpolating aerosols on the GCM grid. |
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| 99 | Automatically run by setup.sh |
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| 100 | |
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| 101 | post_season.sh : post processing a series of simulations with season.sh |
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| 102 | |
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| 103 | test_ERAfiles_JeanZay.sh : script to test the availability of ERA* files sur Jean-Zay |
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| 104 | In case of nudging, one may use it before running era2gcm.sh |
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| 105 | |
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| 106 | DEF: .def files for simulations |
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| 107 | Some of them are changed by setup.sh or script_SIMU depending on chosen options |
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| 108 | Some others need to be chosen and customized BEFORE RUNNING the scripts (main.sh or setup.sh): |
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| 109 | DEF/config.def (versions *.def_* available): output files, frequencies, levels (see lines phys_out_file*) |
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| 110 | DEF/gcm.def (versions *.def_* available): grid (and grid-related) parameters |
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| 111 | DEF/guide.def : nudging parameters |
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| 112 | |
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| 113 | ============================================================ |
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| 114 | III. Repatriation of input data |
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| 115 | ============================================================ |
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| 116 | |
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| 117 | Installation requires downloading data from |
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| 118 | from http://http://lmdz.lmd.jussieu.fr/pub/3DInputData |
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| 119 | Repatriation is managed by a series of functions found in |
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| 120 | lmdz_env.sh: wget_pub cp_from_pub ln_from_pub get_input_files |
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| 121 | |
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| 122 | In my opinion, LMDZ_Setup's approach to data management is to be able to perform a complete |
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| 123 | installation on any account on any machine, by distributing data from wget http://lmdz.... |
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| 124 | In the new version, you don't duplicate any of the fields you download, and you only download them once to an account. |
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| 125 | This is very small compared to the amount of data generated. |
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| 126 | So I think we're very parsimonious in our use of IT resources. |
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| 127 | Of course, this has to do with the fact that we don't manage a lot of different configurations in terms of boundary conditions, forcing, etc. |
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| 128 | But that's where libiGCM comes in. |
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| 129 | |
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| 130 | |
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| 131 | ============================================================ |
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| 132 | IV. Known problems |
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| 133 | ============================================================ |
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| 134 | |
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| 135 | Running zoomed or coarse grid simulations |
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| 136 | May cause problems with routing and aerosols |
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| 137 | Suggesting to run without aerosols, aerosols="n", in this case |
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| 138 | |
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| 139 | |
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| 140 | ============================================================ |
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| 141 | V. Updates (reverse chronological order) |
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| 142 | ============================================================ |
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| 143 | |
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| 144 | 2024-12 (FH) : retravail de l'accès au données sur http://lmdz... |
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| 145 | |
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| 146 | 2024-11 : Travail de portage multi-machine par Amaury Barral. |
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| 147 | Précédemment sur jean-zay uniquement. |
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| 148 | Porté sur adastra et machines locales. |
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| 149 | |
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| 150 | 2023-07 (AS-FH-LF) : mise sous svn du repertoire TEST_PROD, renommé en "LMDZ_config" |
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| 151 | |
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| 152 | 2023-06 (AS) : Ajout de l'option "veget=7994", pour ORCHIDEE trunk correspondant à la config libIGCM LMDZOR_6.4work |
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| 153 | Le routage (méthode = simple) est désactivé par défaut ; |
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| 154 | il peut être activé comme décrit dans la section "ORCHIDEE-routage". |
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| 155 | Le routage n’a pas été testé avec zoom. |
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| 156 | |
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| 157 | 2023-05 (AS) : optimisation du functionnement de l'option isotopes : tout géré par phys=lmdiso |
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| 158 | |
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| 159 | 2023-04 (S Nguyen) : introducing the option of running with isotopes) |
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| 160 | |
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| 161 | 2021-10 (AS): introducing the option of using the new snow scheme INLANDSIS (setup.sh) |
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| 162 | Option not active yet, E Vignon will take care of that. |
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| 163 | |
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| 164 | 2020 (AS): introducing the possibility to run with SPLA aerosol model |
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| 165 | |
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| 166 | 24/03/2020 (FH): corrections for use with AMIP SSTs and monthly freq |
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| 167 | |
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| 168 | ============================================================ |
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| 169 | VI. TBD |
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| 170 | ============================================================ |
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| 171 | See documentation (link of the shared google doc in the beginning of this Readme) |
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| 172 | |
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| 173 | |
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| 174 | Notes concernant Orchidee |
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| 175 | ------------------------- |
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| 176 | |
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| 177 | Plusieurs versions disponibles via la clé veget |
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| 178 | veget=CMIP6 : version CMIP6 |
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| 179 | veget=XXX : XXX numéro de relase svn d'orchidee |
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| 180 | XXX+:1 |
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| 181 | |
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| 182 | On rapatrie automatiquement des champs nécessaires pour les dernières versions d'orchidee |
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| 183 | PFTmap_IPCC_2000.nc cartepente2d_15min.nc routing.nc routing_simple.nc lai2D.nc \ |
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| 184 | alb_bg_modisopt_2D_ESA_v2.nc reftemp.nc \ |
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| 185 | soils_param.nc woodharvest_2000.nc PFTmap_15PFT.v1_2000.nc soil_bulk_and_ph.nc \ |
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| 186 | |
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| 187 | Les deriners fichiers sont nécessaires seulement |
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| 188 | ndep_nhx.nc ndep_noy.nc nfert_cropland.nc nfert_pasture.nc nmanure_cropland.nc nmanure_pasture.nc bnf.nc" ;; |
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| 189 | |
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| 190 | |
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| 191 | |
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| 192 | Notes concernant la confiugration SPLA |
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| 193 | -------------------------------------- |
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| 194 | Pour l'instant on copie là-dedans de chez Binta les fichiers a la res zoomNaf; |
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| 195 | plus tard on y recupererea des fichiers a haute resolution reguliere depuis http:/LMDZ, |
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| 196 | a regrider ensuite par un script interp_fichiers_spla.sh (comme pour aerosols="clim") |
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| 197 | Les fichiers (regrides, sauf SOILSPEC.data utilise tel quel) seront mis dans $MAINDIR/INPUT_SPLA (equivalent de INPUT_DUST) |
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| 198 | The Path below is for JEANZAY. See with the team how to adapt to your cluster. |
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| 199 | |
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| 200 | #for file in donnees_lisa.nc SOILSPEC.data \ # For Chimere dust emissions |
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| 201 | # cly.dat $( for i in $(seq 1 12 ) ; do echo dust$i.nc ; done ) wth.dat \ # For Inca dust emissions |
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| 202 | # carbon_emissions.nc sulphur_emissions_antro.nc sulphur_emissions_nat.nc \ # For non dust emissions |
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| 203 | |
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| 204 | #Cas particulier des fichiers mensuels dust.nc :A DECIDER : |
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| 205 | #C'est entre le cas des aerosols.clim= 1 seul fichier, annuel, |
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| 206 | # et le cas des vents guidage, pré-interpolés avec era2gcm pour toute la periode, dans MAINDIR/GUIDE. |
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| 207 | # On pourrait (a)demander de precalculer dust.nc aussi, dans MAINDIR/INPUT_SPLA - avec un script à adapter de Jeronimo. Rien a mettre dans SPLA_Init alors. |
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| 208 | # Ou (b) fournir dans SPLA_Init les 12 mois d'un dust.nc climato (an 2006 pour nous ici) à la res EC, et faire juste le regrid vers MAINDIR/INPUT_SPLA |
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| 209 | |
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| 210 | A la fin on doit avoir dans SPLA_Init les fichiers initiaux dans INITIAL plus les repertoires PERIOD00MM contenant dust.nc |
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| 211 | Cela doit se retrouver dans script_SIMU qui les copie dans le repertoire de run sur $SCRATCH |
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| 212 | |
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