Changeset 11954 for NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/cfgs/SHARED/README.rst
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- 2019-11-22T17:15:18+01:00 (4 years ago)
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NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/cfgs/SHARED/README.rst
r10598 r11954 3 3 *********** 4 4 5 .. todo:: 6 7 8 5 9 .. contents:: 6 10 :local: 7 11 8 12 Output of diagnostics in NEMO is usually done using XIOS. 9 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. 13 This is an efficient way of writing diagnostics because 14 the time averaging, file writing and even some simple arithmetic or regridding is carried out in 15 parallel to the NEMO model run. 10 16 This page gives a basic introduction to using XIOS with NEMO. 11 Much more information is available from the XIOS homepageabove and from the NEMO manual.17 Much more information is available from the :xios:`XIOS homepage<>` above and from the NEMO manual. 12 18 13 Use of XIOS for diagnostics is activated using the pre-compiler key ``key_iomput``. 19 Use of XIOS for diagnostics is activated using the pre-compiler key ``key_iomput``. 14 20 15 21 Extracting and installing XIOS 16 ------------------------------ 22 ============================== 17 23 18 24 1. 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.20 2. Download the version of XIOS that you wish to use. The recommended version is now XIOS 2.5: 21 22 .. code-block:: console 25 If you want to use single file output you will need to compile the HDF & NetCDF libraries to 26 allow parallel IO. 27 2. Download the version of XIOS that you wish to use. 28 The recommended version is now XIOS 2.5: 23 29 24 $ svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 xios-2.5 30 .. code-block:: console 25 31 26 and 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. 32 $ svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 33 34 and follow the instructions in :xios:`XIOS documentation <wiki/documentation>` to compile it. 35 If you find problems at this stage, support can be found by subscribing to 36 the :xios:`XIOS mailing list <../mailman/listinfo.cgi/xios-users>` and sending a mail message to it. 28 37 29 38 XIOS Configuration files 30 39 ------------------------ 31 40 32 XIOS is controlled using xml input files that should be copied to your model run directory before running the model. 33 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. 34 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. 35 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. 36 The definition of the output files is organized into separate ``file_definition.xml`` files which are included in the ``iodef.xml`` file. 41 XIOS is controlled using XML input files that should be copied to 42 your model run directory before running the model. 43 Examples of these files can be found in the reference configurations (:file:`./cfgs`). 44 The XIOS executable expects to find a file called :file:`iodef.xml` in the model run directory. 45 In NEMO we have made the decision to use include statements in the :file:`iodef.xml` file to include: 46 47 - :file:`field_def_nemo-oce.xml` (for physics), 48 - :file:`field_def_nemo-ice.xml` (for ice), 49 - :file:`field_def_nemo-pisces.xml` (for biogeochemistry) and 50 - :file:`domain_def.xml` from the :file:`./cfgs/SHARED` directory. 51 52 Most users will not need to modify :file:`domain_def.xml` or :file:`field_def_nemo-???.xml` unless 53 they want to add new diagnostics to the NEMO code. 54 The definition of the output files is organized into separate :file:`file_definition.xml` files which 55 are included in the :file:`iodef.xml` file. 37 56 38 57 Modes 39 ----- 58 ===== 40 59 41 60 Detached Mode … … 44 63 In detached mode the XIOS executable is executed on separate cores from the NEMO model. 45 64 This is the recommended method for using XIOS for realistic model runs. 46 To use this mode set ``using_server`` to ``true`` at the bottom of the ``iodef.xml`` file:65 To use this mode set ``using_server`` to ``true`` at the bottom of the :file:`iodef.xml` file: 47 66 48 67 .. code-block:: xml 49 68 50 69 <variable id="using_server" type="boolean">true</variable> 51 70 52 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. 71 Make sure there is a copy (or link to) your XIOS executable in the working directory and 72 in your job submission script allocate processors to XIOS. 53 73 54 74 Attached Mode … … 56 76 57 77 In attached mode XIOS runs on each of the cores used by NEMO. 58 This method is less efficient than the detached mode but can be more convenient for testing or with small configurations. 59 To activate this mode simply set ``using_server`` to false in the ``iodef.xml`` file 78 This method is less efficient than the detached mode but can be more convenient for testing or 79 with small configurations. 80 To activate this mode simply set ``using_server`` to false in the :file:`iodef.xml` file 60 81 61 82 .. code-block:: xml 62 83 63 84 <variable id="using_server" type="boolean">false</variable> 64 85 65 86 and don't allocate any cores to XIOS. 66 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. 87 88 .. note:: 89 90 Due to the different domain decompositions between XIOS and NEMO, 91 if the total number of cores is larger than the number of grid points in the ``j`` direction then 92 the model run will fail. 67 93 68 94 Adding new diagnostics 69 ---------------------- 95 ====================== 70 96 71 97 If you want to add a NEMO diagnostic to the NEMO code you will need to do the following: 72 98 73 99 1. Add any necessary code to calculate you new diagnostic in NEMO 74 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. 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. 76 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, 77 78 .. code-block:: fortran 100 2. Send the field to XIOS using ``CALL iom_put( 'field_id', variable )`` where 101 ``field_id`` is a unique id for your new diagnostics and 102 variable is the fortran variable containing the data. 103 This should be called at every model timestep regardless of how often you want to output the field. 104 No time averaging should be done in the model code. 105 3. If it is computationally expensive to calculate your new diagnostic 106 you should also use "iom_use" to determine if it is requested in the current model run. 107 For example, 79 108 80 IF iom_use('field_id') THEN 81 !Some expensive computation 82 !... 83 !... 84 iom_put('field_id', variable) 85 ENDIF 109 .. code-block:: fortran 86 110 87 4. Add a variable definition to the ``field_def_nemo-???.xml`` file. 88 5. Add the variable to the ``iodef.xml`` or ``file_definition.xml`` file. 111 IF iom_use('field_id') THEN 112 !Some expensive computation 113 !... 114 !... 115 iom_put('field_id', variable) 116 ENDIF 117 118 4. Add a variable definition to the :file:`field_def_nemo-???.xml` file. 119 5. Add the variable to the :file:`iodef.xml` or :file:`file_definition.xml` file.
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