Changes between Version 5 and Version 6 of Projects/INSPECT/ShaCoNEMO-ORCA1-ARCHER


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Timestamp:
22/11/16 18:43:26 (3 years ago)
Author:
annette
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  • Projects/INSPECT/ShaCoNEMO-ORCA1-ARCHER

    v5 v6  
    121121Once the build has completed successfully, set up the inputs required for the model to run. 
    122122 
    123 1. Download the ORCA1 input data set, and untar. This needs to go on your work space on ARCHER (`/work/n02/n02/<username>/`):  
     1231. Go to the run directory:  
    124124{{{ 
     125cd NEMOGCM_3.6_r6969/CONFIG/O1L3P/EXP00 
     126}}}  
     127 Copy in the file `EMPave.dat`: 
     128{{{ 
     129cp ../../ORCA1_LIM3_PISCES/EXP00/EMPave_old.dat .  
     130}}} 
     131 
     1322. In the same directory, copy in the XIOS-1 XML files (by default the configuration is set up for XIOS-2):  
     133{{{ 
     134cp -a ../../ORCA1_LIM3_PISCES/EXP00/ForXIOS1/* .  
     135}}} 
     136 
     1373. Then edit the namelist files to make any required changes. For a short test run, edit `namelist_cfg` and set:  
     138 * `nn_itend = 160` : Run length of 5 days.  
     139 * `nn_stock = 160` : Restart file write at 5 days.  
     140 * `jpni = 8`, `jpnj = 12`, `jpnij = 96` : Processor decomposition of 8x12.  
     141 
     1424. Assuming you have been working under your home directory so far, the run directory needs to be copied over to the work filesystem (`/work/n02/n02/<username>/`), as the ARCHER batch nodes cannot see the home filesystem.  
     143 
     144 Create a directory to hold your NEMO run, for example:  
     145{{{ 
     146mkdir -p /work/n02/n02/<username>/nemo/NEMOGCM_3.6_r6969_O1L3P 
     147}}}  
     148 Then copy over the run directory, evaluating any sym-linked files:   
     149{{{ 
     150cd NEMOGCM_3.6_r6969/CONFIG/O1L3P 
     151rsync -arL EXP00 /work/n02/n02/<username>/nemo/NEMOGCM_3.6_r6969 
     152}}} 
     153 If you are on the work filesystem already there is not need to create a new run directory.  
     154 
     1555. Download the ORCA1 input data set, and untar. Again, this needs to go on your work space. To avoid having multiple copies of the data, it is recommended to store this outside of your NEMO run directory.  
     156 
     157 For example:  
     158{{{ 
     159cd /work/n02/n02/<username>/nemo 
    125160wget 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 
    126161mkdir INPUTS_ORCA1_LIM3_PISCES_V9 
    127162tar -xvf INPUTS_ORCA1_LIM3_PISCES_V9.tar -C INPUTS_ORCA1_LIM3_PISCES_V9 
    128163}}} 
    129  
    130 2. Go to the run directory:  
     164 Then create sym-links to the data in your NEMO run directory:  
    131165{{{ 
    132 cd NEMOGCM_3.6_r6969/CONFIG/O1L3P/EXP00 
    133 }}} 
    134  NEMO expects the input data in its working directory, so create symlinks:  
    135 {{{ 
    136 ln -s <path-to-data>/INPUTS_ORCA1_LIM3_PISCES_V9/* .  
     166cd /work/n02/n02/<username>/nemo/NEMOGCM_3.6_r6969_O1L3P/EXP00 
     167ln -s /work/n02/n02/<username>/nemo/INPUTS_ORCA1_LIM3_PISCES_V9/* .  
    137168}}} 
    138169 
    139 3. In the same directory, copy in the XIOS-1 XML files (by default the configuration is set up for XIOS-2):  
    140 {{{ 
    141 mv ../../ORCA1_LIM3_PISCES/EXP00/ForXIOS1/* .  
    142 }}} 
    143  
    144 4. Make namelist changes:  
    145 {{{ 
    146  
    147 }}} 
    148  
    149 5. Copy over to work filesystem  
    150  
    151 6. Submit run.  
    152  
     1706. Create a parallel batch submission file to submit the run,  
    153171 
    154172