Diagnostics

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 manual.

Use of XIOS for diagnostics is activated using the pre-compiler key key_xios.

Extracting and installing XIOS

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.

2. Download the version of XIOS that you wish to use. The recommended version is now XIOS 2.5:

   $ svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5
   

and follow the instructions in XIOS documentation to compile it. If you find problems at this stage, support can be found by subscribing to the XIOS mailing list and sending a mail message to it.

XIOS Configuration files

XIOS is controlled using XML input files that should be copied to your model run directory before running the model. Examples 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. In 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.

Most 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. The definition of the output files is organized into separate file_definition.xml files which are included in the iodef.xml file.

Modes

Detached Mode

In 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 the bottom of the iodef.xml file:

<variable id="using_server" type="boolean">true</variable>

Make 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.

Attached Mode

In 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

<variable id="using_server" type="boolean">false</variable>

and don’t allocate any cores to XIOS.

Note

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.

Adding new diagnostics

If you want to add a NEMO diagnostic to the NEMO code you will need to do the following:

1. Add any necessary code to calculate you new diagnostic in NEMO

2. 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. 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.

3. 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,

   IF iom_use('field_id') THEN
      !Some expensive computation
      !...
      !...
      iom_put('field_id', variable)
   ENDIF
   

4. Add a variable definition to the field_def_nemo-???.xml file.

5. Add the variable to the iodef.xml or file_definition.xml file.