source: NEMO/trunk/cfgs/SHARED/README.rst @ 10562

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1DIAGNOSTICS
2===========
3
4.. contents::
5           :local:
6
7Output of diagnostics in NEMO is usually done using XIOS.
8This 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.
9This page gives a basic introduction to using XIOS with NEMO.
10Much more information is available from the XIOS homepage above and from the NEMO manual.
11
12Use of XIOS for diagnostics is activated using the pre-compiler key ``key_iomput``.
13
14Extracting and installing XIOS
15------------------------------
16
171. Install the NetCDF4 library.
18   If you want to use single file output you will need to compile the HDF & NetCDF libraries to allow parallel IO.
192. Download the version of XIOS that you wish to use. The recommended version is now XIOS 2.5:
20   
21.. code-block:: console
22
23   $ svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 xios-2.5
24
25and follow the instructions in `XIOS documentation <http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation>`_ to compile it.
26   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.
27
28XIOS Configuration files
29------------------------
30
31XIOS is controlled using xml input files that should be copied to your model run directory before running the model.
32Examples 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.
33In 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.
34Most 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.
35The definition of the output files is organized into separate ``file_definition.xml`` files which are included in the ``iodef.xml`` file.
36
37Modes
38-----
39
40Detached Mode
41-------------
42
43In detached mode the XIOS executable is executed on separate cores from the NEMO model.
44This is the recommended method for using XIOS for realistic model runs.
45To use this mode set ``using_server`` to ``true`` at the bottom of the ``iodef.xml`` file:
46
47.. code-block:: xml
48
49   <variable id="using_server" type="boolean">true</variable>
50
51Make 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.
52
53Attached Mode
54-------------
55
56In attached mode XIOS runs on each of the cores used by NEMO.
57This method is less efficient than the detached mode but can be more convenient for testing or with small configurations.
58To activate this mode simply set ``using_server`` to false in the ``iodef.xml`` file
59
60.. code-block:: xml
61
62   <variable id="using_server" type="boolean">false</variable>
63
64and don't allocate any cores to XIOS.
65Note 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.
66
67Adding new diagnostics
68----------------------
69
70If you want to add a NEMO diagnostic to the NEMO code you will need to do the following:
71
721. Add any necessary code to calculate you new diagnostic in NEMO
732. 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.
74   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.
753. 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,
76   
77.. code-block:: fortran
78
79      IF iom_use('field_id') THEN
80         !Some expensive computation
81         !...
82         !...
83         iom_put('field_id', variable)
84      ENDIF
85
864. Add a variable definition to the ``field_def_nemo-???.xml`` file.
875. Add the variable to the ``iodef.xml`` or ``file_definition.xml`` file.
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