Changes between Version 4 and Version 5 of Projects/INSPECT/ShaCoNEMO-ORCA1-ARCHER


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Timestamp:
22/11/16 17:48:34 (3 years ago)
Author:
annette
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  • Projects/INSPECT/ShaCoNEMO-ORCA1-ARCHER

    v4 v5  
    2525* PISCES is the biogeochemical model  
    2626 
    27 NEMO uses an external library to handle model output diagnostics calkled XIOS, which is documented here:  
     27NEMO uses an external library to handle model output diagnostics called XIOS, which is documented here:  
    2828http://forge.ipsl.jussieu.fr/ioserver/wiki 
    2929 
     
    3434* XIOS-1.0 r703 
    3535* NEMO_3.6_stable r6969 
    36 * ShaCoNEMO r60 
     36* ShaCoNEMO r60   
    3737* ORCA1 input data set v9 
    3838 
    3939Note: Although XIOS-2.0 is now recommended, revision 932 which is suggested for ORCA1 gave a link-time error which was not investigated.  
     40 
     41Note: This is based on the latest version of ShaCoNEMO as of October 2016, and the recommended version of NEMO for this. Both are under active development, so you may wish to use newer versions as they become available.  
    4042 
    4143== Code extract ==  
     
    7577/work/n02/n02/annette/nemo/xios-1.0_r703 
    7678}}} 
    77 To build your own XIOS, see the notes [#BuildingXIOS below].  
    78  
    79 It is advisable to build NEMO with the same key modules as the library:  
     79It is advisable to build NEMO with the same key modules as the library. The above version was built with:  
    8080* `cce/8.4.1` 
    8181* `cray-netcdf-hdf5parallel/4.3.3.1` 
    8282* `cray-mpich/7.2.6` 
     83 
     84(To build your own XIOS, see the notes [#BuildingXIOS below].)  
     85 
     86To build the NEMO code:  
    8387 
    84881. Navigate to the directory holding the build definition files:  
     
    111115qsub build_nemo.pbs 
    112116}}}   
    113 A new directory O1L3P  
     117 This creates a new directory under `CONFIG/` called `O1L3P`. This differentiates between changes made to the original configuration. `O1L3P` will contain the executable plus namelists to be read in by the model.  
    114118 
    115119== Model run ==  
    116120 
    117 1.    
    118  Copy in the XIOS-1 XML files (by default the configuration is set up for XIOS-2):  
     121Once the build has completed successfully, set up the inputs required for the model to run. 
     122 
     1231. Download the ORCA1 input data set, and untar. This needs to go on your work space on ARCHER (`/work/n02/n02/<username>/`):  
    119124{{{ 
    120 cd EXP00 
    121 mv ForXIOS1/* .  
    122 cd ../ 
     125wget http://prodn.idris.fr/thredds/catalog/ipsl_public/romr006/SHACONEMO/eORCA1/catalog.html?dataset=DatasetScanipsl_public/romr006/SHACONEMO/eORCA1/INPUTS_ORCA1_LIM3_PISCES_V9.tar 
     126mkdir INPUTS_ORCA1_LIM3_PISCES_V9 
     127tar -xvf INPUTS_ORCA1_LIM3_PISCES_V9.tar -C INPUTS_ORCA1_LIM3_PISCES_V9 
    123128}}} 
     129 
     1302. Go to the run directory:  
     131{{{ 
     132cd NEMOGCM_3.6_r6969/CONFIG/O1L3P/EXP00 
     133}}} 
     134 NEMO expects the input data in its working directory, so create symlinks:  
     135{{{ 
     136ln -s <path-to-data>/INPUTS_ORCA1_LIM3_PISCES_V9/* .  
     137}}} 
     138 
     1393. In the same directory, copy in the XIOS-1 XML files (by default the configuration is set up for XIOS-2):  
     140{{{ 
     141mv ../../ORCA1_LIM3_PISCES/EXP00/ForXIOS1/* .  
     142}}} 
     143 
     1444. Make namelist changes:  
     145{{{ 
     146 
     147}}} 
     148 
     1495. Copy over to work filesystem  
     150 
     1516. Submit run.  
     152 
     153 
     154 
    124155 
    125156== Working practices ==