source: BOL/LMDZ_Setup_amaury/README0_HowTo.md @ 5214

Last change on this file since 5214 was 4935, checked in by abarral, 7 months ago

mildly refactor main.sh
change README* to .md
(WIP) start refactor setup.sh with sourced install_lmdz

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3Last update : 2023-07-05
4
5Complementary information and FAQ (in French) :
6https://docs.google.com/document/d/1OLZG6e-86NiXuv5-aALxKIh-QPkp4BdCwWtiBFot-6c
7
8I. What this working environment does and does not
9==================================================
10
11This setup can only be used on jean-zay computer at idris so far.
12    However, extension to ciclad or irene will be done soon.
13
14It proposes a light automatic setup of LMDZ long chained climate simulations
15   including installation of the model itself.
16
17It consists in running LMDZ coupled to Orchidee for land surface (optional)
18   but with imposed sea surface temperature.
19
20The basic default configuration makes use of the IPSL-CM6A grid configuration
21   and tuning, and runs a multi annual simulation on "climatological"
22   amip sea surface temperature (with a mean annual cycle) using
23   a calendar with 360 days.
24
25Optionally: the configuration includes the ability to use interannually
26   varying SST and to activate "nudgning" by reanalysis.
27   In both cases, the calendar is then a real one.
28   When nudging is activated, the simulation must be run on a monthly
29   basis, while otherwise, it can be either monthly or yearly.
30
31Since the tutorial automatically generates its own initial files, it
32   can be run with zoom configurations by only changing the number
33   of grid points ("resol" in main.sh) and the DEF/gcm.def file (see bellow).
34
35Aerosols can be read for the year 2000 (weighted average  over 1999-2001 cf Lurton et al 2020),
36  and instantaneous forcing with respect to 1850 can be computed as well.
37  NEW (end 2020) :
38        tutorial_prod can also run LMDZ coupled with the SPLA model
39        (SimPLe Aerosol, activated with option aerosols=spla in setup.sh).
40        Emissions of dust and sea salt are then computed interactively.
41        2021-05 : tutorial_prod OK, code LMDZ-SPLA OK,
42                regridding SPLA input files : work in progress
43
44A configuration with isotopes is also available since 2023-04.
45   
46II. Files and scripts
47===================================================================
48----------------------------------------------------------------
49
50CAREFUL: these scripts MUST be run from $STORE !!!!!
51
52  untar the tutorial_prod.tar file in your $STORE;
53  rename the TEST_PROD directory if you want to;
54  then run everything from this newly created directory
55
56     EXPERT :
57     If the login groupe and computing allocation groupe are different :
58       choose on which STORE space you work (login vs computing allocation);
59       edit lmdz_env.sh, and set "groupe", "SCRATCHD" etc. accordingly.
60     If you want to install the package in a dedicated folder instead of the root of $STORE:
61       set STORED=$STORE/your_folder in lmdz_env.sh
62----------------------------------------------------------------
63
64main.sh : a script written to pass options to the main script setup.sh
65
66setup.sh : sets up one (series of) simulation(s) by editing the "job" script_SIMU
67    When run with -init 1 options, creates INIT and LIMIT directories
68    Run ./setup.sh -h   for options
69    RECOMMENDATION: do not run it directly, but use main.sh to drive it
70   
71script_SIMU : script that is the basis for the job to run the simulations
72    Automatically edited by setup.sh
73
74reb.sh : to rebuild splitted outputfiles (parallelism with IOISPL)
75    automatically run by script_SIMU
76
77era2gcm_tuto.sh : to interpolate reanalysis onto the GCM grid, for nudging.
78   To be run manually after the first use of main.sh
79
80era2gcm_uv10m.nc : for option "aerosols=spla" only :
81     to interpolate reanalysis 10m-winds onto the GCM grid, for sea-salt (and dust) emissions.
82        To be run manually after the first use of main.sh.
83
84season.sh : computing seasonal means and daily time series
85
86interp_aerosols.sh : interpolating aerosols on the GCM grid.
87    Automatically run by setup.sh
88
89post_season.sh : post processing a series of simulations with season.sh
90
91test_ERAfiles_JeanZay.sh : script to test the availability of ERA* files sur Jean-Zay
92    In case of nudging, one may use it before running era2gcm.sh               
93
94DEF: .def files for simulations
95   Some of them are changed by setup.sh or script_SIMU depending on chosen options
96   Some others need to be chosen and customized BEFORE RUNNING the scripts (main.sh or setup.sh):
97     DEF/config.def (versions *.def_* available): output files, frequencies, levels (see lines phys_out_file*)
98     DEF/gcm.def (versions *.def_* available): grid (and grid-related) parameters
99     DEF/guide.def : nudging parameters
100
101III. Known problems
102===================
103
104Running zoomed or coarse grid simulations
105    May cause problems with routing and aerosols
106    Suggesting to put in DEF/config.def
107    ok_cdnc=n
108    ok_ade=n
109    ok_aie=n
110    flag_aerosol=0
111    and in DEF/orchidee*.def
112    RIVER_ROUTING=n : because of this, it is set to n by default
113    Be carefull, depending on the version of orchidee used, the job will
114       choose the corresponding version of DEF/orchidee_6.*.def
115
116IV. Updates (reverse chronological order)
117=========================================
118
1192023-07 (AS-FH-LF) : mise sous svn du repertoire TEST_PROD, renommé en "LMDZ_config"
120
1212023-06 (AS) : Ajout de l'option "veget=7994", pour ORCHIDEE trunk correspondant à la config libIGCM LMDZOR_6.4work
122        Le routage (méthode = simple) est désactivé par défaut ;
123        il peut être activé comme décrit dans la section "ORCHIDEE-routage".
124        Le routage n’a pas été testé avec zoom.
125
1262023-05 (AS) : optimisation du functionnement de l'option isotopes : tout géré par phys=lmdiso
127
1282023-04 (S Nguyen) : introducing the option of running with isotopes)
129       
1302021-10 (AS): introducing the option of using the new snow scheme INLANDSIS (setup.sh)
131        Option not active yet, E Vignon will take care of that.
132
1332020 (AS): introducing the possibility to run with SPLA aerosol model
134
13524/03/2020 (FH): corrections for use with AMIP SSTs and monthly freq
136
137V. TBD
138======
139See documentation (link of the shared google doc in the beginning of this Readme)
140
141
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