Changes between Version 11 and Version 12 of Users/Model Interfacing/Inputs Outputs


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Timestamp:
2017-05-11T12:36:07+02:00 (3 years ago)
Author:
timgraham
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  • Users/Model Interfacing/Inputs Outputs

    v11 v12  
    77 
    88Use of XIOS for diagnostics is activated using the pre-compiler key key_iomput. In nemo_v3_6_STABLE the default version of XIOS is XIOS1.0 but XIOS2.0 can be used by activating key_xios2. '''NB: Due to a change in the XIOS1.0 branch NEMO v3.6 STABLE will only work up to revision 703 of the XIOS1.0 branch without modifying the code manually.''' At the head of the NEMO trunk only XIOS2.0 can be used (XIOS2.0 is the XIOS trunk) and key_xios2 is not required. 
     9 
     10== Extracting and installing XIOS. 
     111) Install the NetCDF4 library. If you want to use single file output you will need to compile the hdf & netcdf libraries to allow parallel IO. 
     12 
     132) Download the version of XIOS that you wish to use. The recommended version is now XIOS2.0: 
     14{{{ 
     15svn co ​http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk xios-2.0 
     16}}} 
     17and follow the instructions here (http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation) to compile it. The latest revision tested by the NEMO systems team is 990 although later revisions should also work correctly. 
     18 
     19[[BR]] 
    920 
    1021== XIOS namelists 
     
    1728An `iodef.xml` file is still required in the run directory. For XIOS2.0 the `field_def.xml` file has been further split into `field_def-opa.xml` (for physics), `field_def-lim.xml` (for ice) and `field_def-bgc.xml` (for biogeochemistry). Also the definition of the output files has been moved from the `iodef.xml` file into separate `file_definition.xml` files which are included in the `iodef.xml` file. Note that the `domain_def.xml` file is also different for XIOS2.0. Examples of these files can be found in the trunk under `NEMOGCM/CONFIG/GYRE_XIOS` in the nemo_v3_6_STABLE branch or in the trunk under `NEMOGCM/CONFIG`. 
    1829 
    19 ---- 
    20  
    21 [[BR]] 
    22 [[BR]] 
    2330[[BR]] 
    2431 
     
    3138In attached mode XIOS runs on each of the cores used by NEMO. This method is less efficient than the detached mode but can be more convenient for testing or with small configurations. To activate this mode simply set `using_server` to false in the `iodef.xml` file and don't allocate any cores to XIOS. Note that due to the different domain decompositions between XIOS and NEMO if the total number of cores is larger than the number of grid points in the j direction then the model run will fail. 
    3239 
    33 == Adding new diagnostics 
     40[[BR]] 
     41 
     42 
     43 
     44== Adding new diagnostics to NEMO 
    3445If you want to add a NEMO diagnostic to the NEMO code you will need to do the following: 
    3546   1) Add any necessary code to calculate you new diagnostic in NEMO