Changes between Version 5 and Version 6 of Users/Model Interfacing/Inputs Outputs


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Timestamp:
2017-03-02T09:43:15+01:00 (4 years ago)
Author:
timgraham
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  • Users/Model Interfacing/Inputs Outputs

    v5 v6  
    11= Inputs-Outputs (Using XIOS) 
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    3 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. 
     3Output 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. 
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    5 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.''' 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. 
     5Use 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. 
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    77== XIOS namelists == 
    8 XIOS is controlled using xml input files. Examples of these files can be found in the reference configurations (NEMOGCM/CONFIG). 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. 
     8XIOS is controlled using xml input files. The exact setup differs slightly between XIOS1.0 and XIOS2.0 
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    10 In the nemo trunk 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 outpu 
    11 t files has been moved from the iodef.xml file into separate file_definition.xml files which are included in the iodef.xml file. 
     10=== XIOS1.0 === 
     11Examples 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). 
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     13=== XIOS2.0 === 
     14An 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. 
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