source: NEMO/trunk/cfgs/SHARED/README.rst @ 10598

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1***********
2Diagnostics
3***********
4
5.. contents::
6           :local:
7
8Output of diagnostics in NEMO is usually done using XIOS.
9This 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.
10This page gives a basic introduction to using XIOS with NEMO.
11Much more information is available from the XIOS homepage above and from the NEMO manual.
12
13Use of XIOS for diagnostics is activated using the pre-compiler key ``key_iomput``.
14
15Extracting and installing XIOS
16------------------------------
17
181. Install the NetCDF4 library.
19   If you want to use single file output you will need to compile the HDF & NetCDF libraries to allow parallel IO.
202. Download the version of XIOS that you wish to use. The recommended version is now XIOS 2.5:
21   
22.. code-block:: console
23
24   $ svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 xios-2.5
25
26and follow the instructions in `XIOS documentation <http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation>`_ to compile it.
27   If you find problems at this stage, support can be found by subscribing to the `XIOS mailing list <http://forge.ipsl.jussieu.fr/mailman/listinfo.cgi/xios-users>`_ and sending a mail message to it.
28
29XIOS Configuration files
30------------------------
31
32XIOS is controlled using xml input files that should be copied to your model run directory before running the model.
33Examples of these files can be found in the reference configurations (``cfgs``). The XIOS executable expects to find a file called ``iodef.xml`` in the model run directory.
34In NEMO we have made the decision to use include statements in the ``iodef.xml`` file to include ``field_def_nemo-oce.xml`` (for physics), ``field_def_nemo-ice.xml`` (for ice), ``field_def_nemo-pisces.xml`` (for biogeochemistry) and ``domain_def.xml`` from the /cfgs/SHARED directory.
35Most users will not need to modify ``domain_def.xml`` or ``field_def_nemo-???.xml`` unless they want to add new diagnostics to the NEMO code.
36The definition of the output files is organized into separate ``file_definition.xml`` files which are included in the ``iodef.xml`` file.
37
38Modes
39-----
40
41Detached Mode
42-------------
43
44In detached mode the XIOS executable is executed on separate cores from the NEMO model.
45This is the recommended method for using XIOS for realistic model runs.
46To use this mode set ``using_server`` to ``true`` at the bottom of the ``iodef.xml`` file:
47
48.. code-block:: xml
49
50   <variable id="using_server" type="boolean">true</variable>
51
52Make sure there is a copy (or link to) your XIOS executable in the working directory and in your job submission script allocate processors to XIOS.
53
54Attached Mode
55-------------
56
57In attached mode XIOS runs on each of the cores used by NEMO.
58This method is less efficient than the detached mode but can be more convenient for testing or with small configurations.
59To activate this mode simply set ``using_server`` to false in the ``iodef.xml`` file
60
61.. code-block:: xml
62
63   <variable id="using_server" type="boolean">false</variable>
64
65and don't allocate any cores to XIOS.
66Note 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.
67
68Adding new diagnostics
69----------------------
70
71If you want to add a NEMO diagnostic to the NEMO code you will need to do the following:
72
731. Add any necessary code to calculate you new diagnostic in NEMO
742. Send the field to XIOS using ``CALL iom_put( 'field_id', variable )`` where ``field_id`` is a unique id for your new diagnostics and variable is the fortran variable containing the data.
75   This should be called at every model timestep regardless of how often you want to output the field. No time averaging should be done in the model code.
763. If it is computationally expensive to calculate your new diagnostic you should also use "iom_use" to determine if it is requested in the current model run. For example,
77   
78.. code-block:: fortran
79
80      IF iom_use('field_id') THEN
81         !Some expensive computation
82         !...
83         !...
84         iom_put('field_id', variable)
85      ENDIF
86
874. Add a variable definition to the ``field_def_nemo-???.xml`` file.
885. Add the variable to the ``iodef.xml`` or ``file_definition.xml`` file.
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