Changes between Version 17 and Version 18 of Documentation/UserGuide/TestCase1


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Timestamp:
07/02/19 17:57:41 (2 years ago)
Author:
jgipsl
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  • Documentation/UserGuide/TestCase1

    v17 v18  
    11= How to run a simple test case with ORCHIDEE = 
     2[[PageOutline]] 
    23This page describes how to prepare the run directory and run ORCHIDEE interactively. You can also run using a job and launch on the batch system: [wiki:Documentation/UserGuide/TestCaseBatch].[[BR]] 
    34 
    45You need the following files : 
    5    - forcing_file.nc   (680M) 
    6    - PFTmap.nc         (13M)  
    7    - soils_param.nc    (<1M) 
    8    - reftemp.nc        (<1M) 
    9    - run.def 
    10    - xml files to configure XIOS 
    116   - executable orchidee_ol 
     7   - forcing_file.nc and other netcdf input files 
     8   - run.def parameter file to set up the simulation 
     9   - xml files to configure output using XIOS 
    1210 
    1311Create a directory where you will run the model and copy input files as follow.  
     12== Executable orchidee_ol == 
     13Install and compile the model to get the executable orchidee_ol. Read more here: wiki:Documentation/UserGuide/InstallingORCHIDEEBasic 
    1414 
    15 '''Get the input files :'''  
    16 {{{ 
    17 wget  https://vesg.ipsl.upmc.fr/thredds/catalog/IPSLFS/igcmg/IGCM/SRF/METEO/NCC/ncc_for_1982.nc 
    18 mv ncc_for_1982.nc forcing_file.nc 
    19 wget  https://vesg.ipsl.upmc.fr/thredds/catalog/IPSLFS/igcmg/IGCM/SRF/PFTmap_1850to2005_AR5_LUHa.rc2/PFTmap_IPCC_1982.nc  
    20 mv PFTmap_IPCC_1982.nc PFTmap.nc 
    21 wget  https://vesg.ipsl.upmc.fr/thredds/catalog/IPSLFS/igcmg/IGCM/SRF/soils_param.nc 
    22 wget  https://vesg.ipsl.upmc.fr/thredds/catalog/IPSLFS/igcmg/IGCM/SRF/reftemp.nc 
    23 }}} 
     15== Get the input netcdf files ==  
     16|| '''File in shared repository''' || '''File name expected by ORCHIDEE''' || 
     17|| ${R_IN}/SRF/METEO/CRU-NCEP/v5.3.2/twodeg/cruncep_twodeg_${year}.nc || forcing_file.nc ||  
     18|| ${R_IN}/SRF/PFTmap_1850to2005_AR5_LUHa.rc2/PFTmap_IPCC_${year}.nc  || PFTmap.nc ||  
     19|| ${R_IN}/SRF/WOODHARVEST/LUH2v2/historical4/woodharvest_${year}.nc  || woodharvest.nc ||  
     20|| ${R_IN}/SRF/soils_param.nc || soils_param.nc ||  
     21|| ${R_IN}/SRF/SOIL/soil_bulk_and_ph.nc || soil_bulk_and_ph.nc ||  
     22|| ${R_IN}/SRF/cartepente2d_15min.nc || cartepente2d_15min.nc ||  
     23|| ${R_IN}/SRF/reftemp.nc || reftemp.nc ||  
     24|| ${R_IN}/SRF/albedo/alb_bg_modisopt_2D_ESA_v3.nc || alb_bg.nc ||  
     25|| ${R_IN}/SRF/ROUTING/routing.nc || routing.nc ||  
     26|| ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/synthetic/historical/Nfer_pasture_${year}.nc  || nfert_pasture.nc ||  
     27|| ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/synthetic/historical/Nfer_cropland_${year}.nc || nfert_cropland.nc ||  
     28|| ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/manure/historical/Nmanure_pasture_${year}.nc || nmanure_pasture.nc ||  
     29|| ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/manure/historical/Nmanure_cropland_${year}.nc || nmanure_cropland.nc ||  
     30|| ${R_IN}/SRF/NITROGEN/N_DEPOSITION/CCMI_ndep/historical/CCMI_ndep_nhx_${year}.nc || ndep_nhx.nc ||  
     31|| ${R_IN}/SRF/NITROGEN/N_DEPOSITION/CCMI_ndep/historical/CCMI_ndep_noy_${year}.nc || ndep_noy.nc ||  
     32|| ${R_IN}/SRF/NITROGEN/BNF/bnf_1850.nc || bnf.nc ||  
    2433 
    25 '''Get xml files for running with XIOS:'''[[BR]] 
     34where 
     35* R_IN=/prodigfs/ipslfs/igcmg/IGCM at ciclad/climserv 
     36* R_IN=/home/orchideeshare/igcmg/IGCM at obelix 
     37* IDRIS, TGCC see training courses 
     38* or download using wget, replace R_IN by https://vesg.ipsl.upmc.fr/thredds/catalog/IPSLFS/igcmg/IGCM 
     39 
     40 
     41== Get xml files for running with XIOS == 
    2642''Note: If you do not compile with XIOS, you do not need to copy these files but you need to adapt run.def to activate output with IOIPSL, see further below.''[[BR]] 
    2743 
    28 The xml files controls the output of the model if you use XIOS. XIOS is the default since rev 3115 in the trunk and since rev 3839 only XIOS/trunk revision 965 (XIOS2) or later can be used. Copy the xml files from the "modeles" directory ORCHIDEE/src_xml to your run directory: iodef.xml, context_orchidee.xml, field_def_orchidee.xml and file_def_orchidee.xml. 
     44The xml files controls the output of the model if you use XIOS. XIOS is the default since rev 3115 in the trunk and since rev 3839 only XIOS/trunk revision 965 (XIOS2) or later can be used. Copy all the xml files from the "modeles" directory ORCHIDEE/src_xml to your run directory: iodef.xml, context_orchidee.xml, context_input_orchidee.xml, field_def_orchidee.xml and file_def_orchidee.xml. 
    2945 
    30 Edit file_def_orchidee.xml to change every instance of "_AUTO_" (two for each output file) 
    31  * enabled="_AUTO_" into enabled=".TRUE." or enabled=".FALSE." 
     46Edit file_def_orchidee.xml to change every instance of "_AUTO_" (3 for each output file) 
     47 * output_level="_AUTO_" into output_level=X where X is an integer between 0-11 
    3248 * output_freq="_AUTO_" into output_freq="1mo" or output_freq="1d" par example 
     49 * enabled="_AUTO_" into enabled="true" or enabled="false" 
    3350 * do any other change as you wish to adapt the output to your needs 
    3451 
    3552Edit field_def_orchidee.xml only if you changed the ORCHDEE source code. 
    3653 
    37 '''Save following lines into run.def :''' 
     54== Parameter file run.def == 
     55Save following lines into a file named run.def: 
    3856{{{ 
    39 # Simulation lenght : 
    40 TIME_LENGTH= 365D 
    41 #TIME_LENGTH=31D 
     57# Simulation length 
     58TIME_LENGTH=31D 
    4259 
    4360# Parameters for regional run : 
     
    5774#LIMIT_SOUTH = -90. 
    5875 
    59 VEGET_YEAR=1 
     76# RIVER_ROUTING=n for regional domain 
     77RIVER_ROUTING=n 
    6078 
    61 STOMATE_OK_CO2= y 
    62 STOMATE_OK_STOMATE= y 
     79 
     80# File and variable name for nitrogen input files 
     81#************************************************************************** 
     82Nammonium_FILE = ndep_nhx.nc 
     83Nammonium_VAR = nhx 
     84 
     85Nnitrate_FILE = ndep_noy.nc 
     86Nnitrate_VAR = noy 
     87 
     88Nfert_FILE = NONE 
     89Nfert_VAR = nfer 
     90 
     91Nmanure_FILE = NONE 
     92Nmanure_VAR = Nmanure 
     93 
     94Nfert_cropland_FILE = nfert_cropland.nc 
     95Nfert_cropland_VAR = nfer 
     96 
     97Nmanure_cropland_FILE = nmanure_cropland.nc 
     98Nmanure_cropland_VAR = Nmanure 
     99 
     100Nfert_pasture_FILE = nfert_pasture.nc 
     101Nfert_pasture_VAR = Nfer 
     102 
     103Nmanure_pasture_FILE = nmanure_pasture.nc 
     104Nmanure_pasture_VAR = Nmanure 
     105 
     106Nbnf_FILE= bnf.nc 
     107Nbnf_VAR= BNF_MGN_PERM2_PERYR 
    63108}}} 
    64109 
     
    80125 
    81126 
    82 '''Check you environment:'''[[BR]] 
     127== Check you environment and launch the model == 
    83128To run the model you first need to load the same netcdf library as the one used for the compilation. This depends on the machine you work at.  
    84129 
     
    90135}}} 
    91136 
    92  
    93 '''Once you've get all input files, launch the model in the same directory :'''[[BR]] 
     137Once you've get all input files, launch the model in the same directory : 
    94138{{{ 
    95139./orchidee_ol > out_orchidee_ol 2>&1 
    96140}}} 
    97141 
     142 
     143== Other methods to set up a run directory == 
     144If you run with libIGCM, set up a normal job but add exit in the main Job after following: 
     145{{{ 
     146  echo "#######################################" 
     147  echo "#       DIR AFTER RUN EXECUTION       #" 
     148  echo "#######################################" 
     149 
     150  exit 
     151}}} 
     152Launch the job and the go to the run directory where you'll find all input netcdf files and parameter files. You can work directly in this run directory to make simpler test cases.  
     153 
     154Note: at obelix and ada, set RUN_DIR_PATH in the main job so the run directory will be accessible.    
     155 
     156  
    98157Another way to do it from a run you've already finished with libIGCM is to look at the Script_* output file.  Inside this file libIGCM lists all the files that it copies to the run directory (look for the commands where the commands IGCM_sys_Cp and IGCM_sys_Get appear in the Script_* file).  If you copy those files manually to a new directory, you should be able to launch the exact same simulation. 
    99158