Changes between Version 14 and Version 15 of Users/Model Interfacing/Inputs Outputs


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Timestamp:
2017-05-13T02:44:15+02:00 (3 years ago)
Author:
nicolasmartin
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  • Users/Model Interfacing/Inputs Outputs

    v14 v15  
    44Last edition: '''[[Wikinfo(changed_ts)]]''' by '''[[Wikinfo(changed_by)]]''' 
    55 
    6 Output of diagnostics in NEMO is usually done using XIOS. This is an efficient way of writing diagnostics because the time averaging, file writing and even some simple arithmetic or regridding is carried out in parallel to the NEMO model run. This page gives a basic introduction to using XIOS with NEMO. Much more information is available from the XIOS homepage above and from the NEMO reference manual. 
     6Output of diagnostics in NEMO is usually done using XIOS. This is an efficient way of writing diagnostics because the time averaging, file writing and even some simple arithmetic or regridding is carried out in parallel to the NEMO model run.\\ 
     7This page gives a basic introduction to using XIOS with NEMO. Much more information is available from the XIOS homepage above and from the [/doxygen/index.html?doc=NEMO NEMO reference manual]. 
    78 
    8 Use 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. 
     9Use 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. 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. 
     10 
     11'''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.'''  
    912 
    1013== Extracting and installing XIOS. 
    11 1) 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. 
     141) 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. 
    1215 
    13162) Download the version of XIOS that you wish to use. The recommended version is now XIOS2.0: 
    14 {{{ 
     17{{{#!sh 
    1518svn co ​http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk xios-2.0 
    1619}}} 
    17 and 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. 
     20and follow the instructions in [//ioserver/wiki/documentation XIOS documentation] to compile it. The latest revision tested by the NEMO systems team is 990 although later revisions should also work correctly. 
    1821 
    19 [[BR]] 
     22== Namelists 
    2023 
    21 == XIOS namelists 
    2224XIOS is controlled using xml input files that should be copied to your model run directory before running the model. The exact setup differs slightly between XIOS1.0 and XIOS2.0. 
    2325 
    2426=== XIOS1.0 
     27 
    2528Examples of these files can be found in the reference configurations (`NEMOGCM/CONFIG`) in the nemo_v3_6_STABLE branch. The XIOS executable expects to find a file called `iodef.xml` in the model run directory. In NEMO we have made the decision to use include statements in the `iodef.xml` file to include `field_def.xml` and `domain_def.xml` from the `NEMOGCM/CONFIG/SHARED` directory. Most users will not need to modify `domain_def.xml` or `field_def.xml` unless they want to add new diagnostics to the NEMO code (see below). 
    2629 
    2730=== XIOS2.0 
     31 
    2832An `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`. 
    2933 
    30 [[BR]] 
     34== Modes 
    3135 
    32 == XIOS modes 
    3336=== Detached Mode 
     37 
    3438In detached mode the XIOS executable is executed on separate cores from the NEMO model. This is the recommended method for using XIOS for realistic model runs. To use this mode set `using_server` to `true` at 
    3539the bottom of the `iodef.xml` file: 
    36 {{{ 
     40{{{#!xml 
    3741<variable id="using_server" type="boolean">true</variable> 
    3842}}}  
     
    4044 
    4145=== Attached Mode 
     46 
    4247In 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 
    43 {{{ 
     48{{{#!xml 
    4449<variable id="using_server" type="boolean">true</variable> 
    4550}}}   
    4651and 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. 
    47  
    48 [[BR]] 
    49  
    50  
    5152 
    5253== Adding new diagnostics to NEMO