1 | \documentclass[../main/NEMO_manual]{subfiles} |
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2 | |
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3 | \begin{document} |
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4 | \chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)} |
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5 | \label{chap:DIA} |
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6 | |
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7 | \chaptertoc |
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8 | |
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9 | \vfill |
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10 | \begin{figure}[b] |
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11 | \subsubsection*{Changes record} |
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12 | \begin{tabular}{l||l|m{0.65\linewidth}} |
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13 | Release & Author & Modifications \\ |
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14 | {\em 4.0} & {\em Mirek Andrejczuk, Massimiliano Drudi} & {\em } \\ |
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15 | {\em } & {\em Dorotea Iovino, Nicolas Martin} & {\em } \\ |
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16 | {\em 3.6} & {\em Gurvan Madec, Sebastien Masson } & {\em } \\ |
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17 | {\em 3.4} & {\em Gurvan Madec, Rachid Benshila, Andrew Coward } & {\em } \\ |
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18 | {\em } & {\em Christian Ethe, Sebastien Masson } & {\em } \\ |
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19 | \end{tabular} |
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20 | \end{figure} |
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21 | |
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22 | \section{Model output} |
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23 | \label{sec:DIA_io_old} |
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24 | |
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25 | The model outputs are of three types: the restart file, the output listing, and the diagnostic output file(s). |
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26 | The restart file is used internally by the code when the user wants to start the model with |
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27 | initial conditions defined by a previous simulation. |
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28 | It contains all the information that is necessary in order for there to be no changes in the model results |
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29 | (even at the computer precision) between a run performed with several restarts and |
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30 | the same run performed in one step. |
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31 | It should be noted that this requires that the restart file contains two consecutive time steps for |
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32 | all the prognostic variables. |
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33 | |
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34 | The output listing and file(s) are predefined but should be checked and eventually adapted to the user's needs. |
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35 | The output listing is stored in the \textit{ocean.output} file. |
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36 | The information is printed from within the code on the logical unit \texttt{numout}. |
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37 | To locate these prints, use the UNIX command "\textit{grep -i numout}" in the source code directory. |
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38 | |
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39 | By default, diagnostic output files are written in NetCDF format. |
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40 | Since version 3.2, when defining \key{iomput}, an I/O server has been added which |
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41 | provides more flexibility in the choice of the fields to be written as well as how |
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42 | the writing work is distributed over the processors in massively parallel computing. |
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43 | A complete description of the use of this I/O server is presented in the next section. |
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44 | |
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45 | %\gmcomment{ % start of gmcomment |
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46 | |
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47 | \section{Standard model output (IOM)} |
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48 | \label{sec:DIA_iom} |
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49 | |
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50 | Since version 3.2, iomput is the \NEMO\ output interface of choice. |
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51 | It has been designed to be simple to use, flexible and efficient. |
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52 | The two main purposes of iomput are: |
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53 | |
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54 | \begin{enumerate} |
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55 | \item The complete and flexible control of the output files through external XML files adapted by |
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56 | the user from standard templates. |
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57 | \item To achieve high performance and scalable output through the optional distribution of |
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58 | all diagnostic output related tasks to dedicated processes. |
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59 | \end{enumerate} |
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60 | |
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61 | The first functionality allows the user to specify, without code changes or recompilation, |
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62 | aspects of the diagnostic output stream, such as: |
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63 | |
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64 | \begin{itemize} |
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65 | \item The choice of output frequencies that can be different for each file (including real months and years). |
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66 | \item The choice of file contents; includes complete flexibility over which data are written in which files |
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67 | (the same data can be written in different files). |
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68 | \item The possibility to split output files at a chosen frequency. |
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69 | \item The possibility to extract a vertical or an horizontal subdomain. |
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70 | \item The choice of the temporal operation to perform, \eg: average, accumulate, instantaneous, min, max and once. |
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71 | \item Control over metadata via a large XML "database" of possible output fields. |
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72 | \end{itemize} |
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73 | |
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74 | In addition, iomput allows the user to add in the code the output of any new variable (scalar, 2D or 3D) |
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75 | in a very easy way. |
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76 | All details of iomput functionalities are listed in the following subsections. |
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77 | Examples of the XML files that control the outputs can be found in: |
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78 | \path{cfgs/ORCA2_ICE_PISCES/EXPREF/iodef.xml}, |
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79 | \path{cfgs/SHARED/field_def_nemo-oce.xml}, |
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80 | \path{cfgs/SHARED/field_def_nemo-pisces.xml}, |
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81 | \path{cfgs/SHARED/field_def_nemo-ice.xml} and \path{cfgs/SHARED/domain_def_nemo.xml}. \\ |
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82 | |
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83 | The second functionality targets output performance when running in parallel (\key{mpp\_mpi}). |
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84 | Iomput provides the possibility to specify N dedicated I/O processes (in addition to the \NEMO\ processes) |
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85 | to collect and write the outputs. |
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86 | With an appropriate choice of N by the user, the bottleneck associated with the writing of |
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87 | the output files can be greatly reduced. |
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88 | |
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89 | In version 3.6, the \rou{iom\_put} interface depends on |
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90 | an external code called \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS/branchs/xios-2.5}{XIOS-2.5} |
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91 | %(use of revision 618 or higher is required). |
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92 | This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to |
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93 | create a single output file and therefore to bypass the rebuilding phase. |
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94 | Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to |
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95 | an HDF5 library that has been correctly compiled (\ie\ with the configure option $--$enable-parallel). |
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96 | Note that the files created by iomput through XIOS are incompatible with NetCDF3. |
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97 | All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3. |
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98 | |
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99 | Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers, |
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100 | where N is typically much less than the number of \NEMO\ processors, will reduce the number of output files created. |
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101 | This can greatly reduce the post-processing burden usually associated with using large numbers of \NEMO\ processors. |
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102 | Note that for smaller configurations, the rebuilding phase can be avoided, |
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103 | even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server. |
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104 | |
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105 | \subsection{XIOS: Reading and writing restart file} |
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106 | |
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107 | XIOS may be used to read single file restart produced by \NEMO. Currently only the variables written to |
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108 | file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np[=.true. ]{ln_xios_read}{ln\_xios\_read} |
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109 | in \textit{namelist\_cfg}. This setting will be ignored when multiple restart files are present, and default \NEMO |
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110 | functionality will be used for reading. There is no need to change iodef.xml file to use XIOS to read |
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111 | restart, all definitions are done within the \NEMO\ code. For high resolution configuration, however, |
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112 | there may be a need to add the following line in iodef.xml (xios context): |
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113 | |
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114 | \begin{xmllines} |
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115 | <variable id="recv_field_timeout" type="double">1800</variable> |
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116 | \end{xmllines} |
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117 | |
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118 | This variable sets timeout for reading. |
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119 | |
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120 | If XIOS is to be used to read restart from file generated with an earlier \NEMO\ version (3.6 for instance), |
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121 | dimension \forcode{z} defined in restart file must be renamed to \forcode{nav_lev}.\\ |
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122 | |
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123 | XIOS can also be used to write \NEMO\ restart. A namelist parameter \np{nn_wxios}{nn\_wxios} is used to determine the |
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124 | type of restart \NEMO\ will write. If it is set to 0, default \NEMO\ functionality will be used - each |
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125 | processor writes its own restart file; if it is set to 1 XIOS will write restart into a single file; |
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126 | for \np[=2]{nn_wxios}{nn\_wxios} the restart will be written by XIOS into multiple files, one for each XIOS server. |
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127 | Note, however, that \textbf{\NEMO\ will not read restart generated by XIOS when \np[=2]{nn_wxios}{nn\_wxios}}. The restart will |
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128 | have to be rebuild before continuing the run. This option aims to reduce number of restart files generated by \NEMO\ only, |
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129 | and may be useful when there is a need to change number of processors used to run simulation. |
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130 | |
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131 | If an additional variable must be written to a restart file, the following steps are needed: |
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132 | \begin{description} |
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133 | \item [step 1:] add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and |
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134 | define correct grid for the variable (\forcode{grid_N_3D} - 3D variable, \forcode{grid_N} - 2D variable, \forcode{grid_vector} - |
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135 | 1D variable, \forcode{grid_scalar} - scalar), |
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136 | \item [step 2:] add variable to the list of fields written by restart. This can be done either in subroutine |
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137 | \rou{iom\_set\_rstw\_core} (\mdl{iom}) or by calling \rou{iom\_set\_rstw\_active} (\mdl{iom}) with the name of a variable |
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138 | as an argument. This convention follows approach for writing restart using iom, where variables are |
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139 | written either by \rou{rst\_write} or by calling \rou{iom\_rstput} from individual routines. |
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140 | \end{description} |
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141 | |
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142 | An older versions of XIOS do not support reading functionality. It's recommended to use at least XIOS2@1451. |
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143 | |
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144 | \subsection{XIOS: XML Inputs-Outputs Server} |
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145 | |
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146 | \subsubsection{Attached or detached mode?} |
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147 | |
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148 | Iomput is based on \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS}, |
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149 | the io\_server developed by Yann Meurdesoif from IPSL. |
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150 | The behaviour of the I/O subsystem is controlled by settings in the external XML files listed above. |
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151 | Key settings in the iodef.xml file are the tags associated with each defined file. |
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152 | |
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153 | \xmlline|<variable id="using_server" type="bool"></variable>| |
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154 | |
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155 | The \texttt{using\_server} setting determines whether or not the server will be used in |
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156 | \textit{attached mode} |
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157 | (as a library) [\texttt{> false <}] or in \textit{detached mode} |
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158 | (as an external executable on N additional, dedicated cpus) [\texttt{ > true <}]. |
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159 | The \textit{attached mode} is simpler to use but much less efficient for |
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160 | massively parallel applications. |
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161 | The type of each file can be either ''multiple\_file'' or ''one\_file''. |
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162 | |
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163 | In \textit{attached mode} and if the type of file is ''multiple\_file'', |
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164 | then each \NEMO\ process will also act as an IO server and produce its own set of output files. |
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165 | Superficially, this emulates the standard behaviour in previous versions. |
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166 | However, the subdomain written out by each process does not correspond to |
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167 | the \forcode{jpi x jpj x jpk} domain actually computed by the process (although it may if \forcode{jpni=1}). |
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168 | Instead each process will have collected and written out a number of complete longitudinal strips. |
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169 | If the ''one\_file'' option is chosen then all processes will collect their longitudinal strips and |
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170 | write (in parallel) to a single output file. |
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171 | |
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172 | In \textit{detached mode} and if the type of file is ''multiple\_file'', |
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173 | then each stand-alone XIOS process will collect data for a range of complete longitudinal strips and |
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174 | write to its own set of output files. |
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175 | If the ''one\_file'' option is chosen then all XIOS processes will collect their longitudinal strips and |
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176 | write (in parallel) to a single output file. |
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177 | Note running in detached mode requires launching a Multiple Process Multiple Data (MPMD) parallel job. |
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178 | The following subsection provides a typical example but the syntax will vary in different MPP environments. |
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179 | |
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180 | \subsubsection{Number of cpu used by XIOS in detached mode} |
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181 | |
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182 | The number of cores used by the XIOS is specified when launching the model. |
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183 | The number of cores dedicated to XIOS should be from \texttildelow1/10 to \texttildelow1/50 of the number of |
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184 | cores dedicated to \NEMO. |
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185 | Some manufacturers suggest using O($\sqrt{N}$) dedicated IO processors for N processors but |
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186 | this is a general recommendation and not specific to \NEMO. |
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187 | It is difficult to provide precise recommendations because the optimal choice will depend on |
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188 | the particular hardware properties of the target system |
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189 | (parallel filesystem performance, available memory, memory bandwidth etc.) |
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190 | and the volume and frequency of data to be created. |
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191 | Here is an example of 2 cpus for the io\_server and 62 cpu for nemo using mpirun: |
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192 | \cmd|mpirun -np 62 ./nemo.exe : -np 2 ./xios_server.exe| |
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193 | |
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194 | \subsubsection{Control of XIOS: the context in iodef.xml} |
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195 | |
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196 | As well as the \texttt{using\_server} flag, other controls on the use of XIOS are set in |
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197 | the XIOS context in \textit{iodef.xml}. |
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198 | See the XML basics section below for more details on XML syntax and rules. |
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199 | |
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200 | \begin{table} |
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201 | \begin{tabularx}{\textwidth}{|lXl|} |
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202 | \hline |
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203 | variable name & |
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204 | description & |
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205 | example \\ |
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206 | \hline |
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207 | \hline |
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208 | buffer\_size & |
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209 | buffer size used by XIOS to send data from \NEMO\ to XIOS. |
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210 | Larger is more efficient. |
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211 | Note that needed/used buffer sizes are summarized at the end of the job & |
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212 | 25000000 \\ |
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213 | \hline |
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214 | buffer\_server\_factor\_size & |
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215 | ratio between \NEMO\ and XIOS buffer size. |
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216 | Should be 2. & |
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217 | 2 \\ |
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218 | \hline |
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219 | info\_level & |
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220 | verbosity level (0 to 100) & |
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221 | 0 \\ |
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222 | \hline |
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223 | using\_server & |
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224 | activate attached(false) or detached(true) mode & |
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225 | true \\ |
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226 | \hline |
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227 | using\_oasis & |
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228 | XIOS is used with OASIS(true) or not (false) & |
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229 | false \\ |
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230 | \hline |
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231 | oasis\_codes\_id & |
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232 | when using oasis, define the identifier of \NEMO\ in the namcouple. |
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233 | Note that the identifier of XIOS is xios.x & |
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234 | oceanx \\ |
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235 | \hline |
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236 | \end{tabularx} |
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237 | \end{table} |
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238 | |
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239 | \subsection{Practical issues} |
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240 | |
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241 | \subsubsection{Installation} |
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242 | |
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243 | As mentioned, XIOS is supported separately and must be downloaded and compiled before it can be used with \NEMO. |
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244 | See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance. |
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245 | \NEMO\ will need to link to the compiled XIOS library. |
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246 | The \href{https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/guide/html/install.html#extract-and-install-xios} |
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247 | {Extract and install XIOS} guide provides an example illustration of how this can be achieved. |
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248 | |
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249 | \subsubsection{Add your own outputs} |
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250 | |
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251 | It is very easy to add your own outputs with iomput. |
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252 | Many standard fields and diagnostics are already prepared (\ie, steps 1 to 3 below have been done) and |
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253 | simply need to be activated by including the required output in a file definition in iodef.xml (step 4). |
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254 | To add new output variables, all 4 of the following steps must be taken. |
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255 | |
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256 | \begin{enumerate} |
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257 | \item [1.] |
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258 | in \NEMO\ code, add a \forcode{CALL iom_put( 'identifier', array )} where you want to output a 2D or 3D array. |
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259 | \item [2.] |
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260 | If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in |
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261 | the upper part of your module. |
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262 | \item [3.] |
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263 | in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code |
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264 | (see subsequent sections for a details of the XML syntax and rules). |
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265 | For example: |
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266 | |
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267 | \begin{xmllines} |
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268 | <field_definition> |
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269 | <field_group id="grid_T" grid_ref="grid_T_3D"> <!-- T grid --> |
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270 | ... |
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271 | <field id="identifier" long_name="blabla" ... /> |
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272 | ... |
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273 | </field_definition> |
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274 | \end{xmllines} |
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275 | |
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276 | Note your definition must be added to the field\_group whose reference grid is consistent with the size of |
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277 | the array passed to iomput. |
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278 | The grid\_ref attribute refers to definitions set in iodef.xml which, in turn, |
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279 | reference grids and axes either defined in the code |
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280 | (iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) or defined in the domain\_def.xml file. |
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281 | \eg: |
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282 | |
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283 | \begin{xmllines} |
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284 | <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> |
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285 | \end{xmllines} |
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286 | |
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287 | Note, if your array is computed within the surface module each \np{nn_fsbc}{nn\_fsbc} time\_step, |
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288 | add the field definition within the field\_group defined with the id "SBC": |
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289 | \xmlcode{<field_group id="SBC" ...>} which has been defined with the correct frequency of operations |
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290 | (iom\_set\_field\_attr in \mdl{iom}) |
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291 | \item [4.] |
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292 | add your field in one of the output files defined in iodef.xml |
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293 | (again see subsequent sections for syntax and rules) |
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294 | |
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295 | \begin{xmllines} |
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296 | <file id="file1" .../> |
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297 | ... |
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298 | <field field_ref="identifier" /> |
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299 | ... |
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300 | </file> |
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301 | \end{xmllines} |
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302 | |
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303 | \end{enumerate} |
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304 | |
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305 | \subsection{XML fundamentals} |
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306 | |
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307 | \subsubsection{ XML basic rules} |
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308 | |
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309 | XML tags begin with the less-than character ("$<$") and end with the greater-than character ("$>$"). |
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310 | You use tags to mark the start and end of elements, which are the logical units of information in an XML document. |
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311 | In addition to marking the beginning of an element, XML start tags also provide a place to specify attributes. |
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312 | An attribute specifies a single property for an element, using a name/value pair, for example: |
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313 | \xmlcode{<a b="x" c="y" d="z"> ... </a>}. |
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314 | See \href{http://www.xmlnews.org/docs/xml-basics.html}{here} for more details. |
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315 | |
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316 | \subsubsection{Structure of the XML file used in \NEMO} |
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317 | |
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318 | The XML file used in XIOS is structured by 7 families of tags: |
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319 | context, axis, domain, grid, field, file and variable. |
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320 | Each tag family has hierarchy of three flavors (except for context): |
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321 | |
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322 | \begin{table} |
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323 | \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} |
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324 | \hline |
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325 | flavor & description & |
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326 | example \\ |
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327 | \hline |
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328 | \hline |
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329 | root & declaration of the root element that can contain element groups or elements & |
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330 | \xmlcode{<file_definition ... >} \\ |
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331 | \hline |
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332 | group & declaration of a group element that can contain element groups or elements & |
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333 | \xmlcode{<file_group ... >} \\ |
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334 | \hline |
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335 | element & declaration of an element that can contain elements & |
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336 | \xmlcode{<file ... >} \\ |
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337 | \hline |
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338 | \end{tabular*} |
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339 | \end{table} |
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340 | |
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341 | Each element may have several attributes. |
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342 | Some attributes are mandatory, other are optional but have a default value and other are completely optional. |
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343 | Id is a special attribute used to identify an element or a group of elements. |
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344 | It must be unique for a kind of element. |
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345 | It is optional, but no reference to the corresponding element can be done if it is not defined. |
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346 | |
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347 | The XML file is split into context tags that are used to isolate IO definition from |
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348 | different codes or different parts of a code. |
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349 | No interference is possible between 2 different contexts. |
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350 | Each context has its own calendar and an associated timestep. |
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351 | In \NEMO, we used the following contexts (that can be defined in any order): |
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352 | |
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353 | \begin{table} |
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354 | \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} |
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355 | \hline |
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356 | context & description & |
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357 | example \\ |
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358 | \hline |
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359 | \hline |
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360 | context xios & context containing information for XIOS & |
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361 | \xmlcode{<context id="xios" ... >} \\ |
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362 | \hline |
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363 | context nemo & context containing IO information for \NEMO\ (mother grid when using AGRIF) & |
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364 | \xmlcode{<context id="nemo" ... >} \\ |
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365 | \hline |
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366 | context 1\_nemo & context containing IO information for \NEMO\ child grid 1 (when using AGRIF) & |
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367 | \xmlcode{<context id="1_nemo" ... >} \\ |
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368 | \hline |
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369 | context n\_nemo & context containing IO information for \NEMO\ child grid n (when using AGRIF) & |
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370 | \xmlcode{<context id="n_nemo" ... >} \\ |
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371 | \hline |
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372 | \end{tabular} |
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373 | \end{table} |
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374 | |
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375 | \noindent The xios context contains only 1 tag: |
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376 | |
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377 | \begin{table} |
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378 | \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} |
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379 | \hline |
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380 | context tag & |
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381 | description & |
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382 | example \\ |
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383 | \hline |
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384 | \hline |
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385 | variable\_definition & |
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386 | define variables needed by XIOS. |
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387 | This can be seen as a kind of namelist for XIOS. & |
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388 | \xmlcode{<variable_definition ... >} \\ |
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389 | \hline |
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390 | \end{tabular} |
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391 | \end{table} |
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392 | |
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393 | \noindent Each context tag related to \NEMO\ (mother or child grids) is divided into 5 parts |
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394 | (that can be defined in any order): |
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395 | |
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396 | \begin{table} |
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397 | \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} |
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398 | \hline |
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399 | context tag & description & |
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400 | example \\ |
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401 | \hline |
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402 | \hline |
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403 | field\_definition & define all variables that can potentially be outputted & |
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404 | \xmlcode{<field_definition ... >} \\ |
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405 | \hline |
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406 | file\_definition & define the netcdf files to be created and the variables they will contain & |
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407 | \xmlcode{<file_definition ... >} \\ |
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408 | \hline |
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409 | axis\_definition & define vertical axis & |
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410 | \xmlcode{<axis_definition ... >} \\ |
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411 | \hline |
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412 | domain\_definition & define the horizontal grids & |
---|
413 | \xmlcode{<domain_definition ... >} \\ |
---|
414 | \hline |
---|
415 | grid\_definition & define the 2D and 3D grids (association of an axis and a domain) & |
---|
416 | \xmlcode{<grid_definition ... >} \\ |
---|
417 | \hline |
---|
418 | \end{tabular} |
---|
419 | \end{table} |
---|
420 | |
---|
421 | \subsubsection{Nesting XML files} |
---|
422 | |
---|
423 | The XML file can be split in different parts to improve its readability and facilitate its use. |
---|
424 | The inclusion of XML files into the main XML file can be done through the attribute src: |
---|
425 | \xmlline|<context src="./nemo_def.xml" />| |
---|
426 | |
---|
427 | \noindent In \NEMO, by default, the field definition is done in 3 separate files ( |
---|
428 | \path{cfgs/SHARED/field_def_nemo-oce.xml}, |
---|
429 | \path{cfgs/SHARED/field_def_nemo-pisces.xml} and |
---|
430 | \path{cfgs/SHARED/field_def_nemo-ice.xml} ) and the domain definition is done in another file ( \path{cfgs/SHARED/domain_def_nemo.xml} ) |
---|
431 | that |
---|
432 | are included in the main iodef.xml file through the following commands: |
---|
433 | \begin{xmllines} |
---|
434 | <context id="nemo" src="./context_nemo.xml"/> |
---|
435 | \end{xmllines} |
---|
436 | |
---|
437 | \subsubsection{Use of inheritance} |
---|
438 | |
---|
439 | XML extensively uses the concept of inheritance. |
---|
440 | XML has a tree based structure with a parent-child oriented relation: all children inherit attributes from parent, |
---|
441 | but an attribute defined in a child replace the inherited attribute value. |
---|
442 | Note that the special attribute ''id'' is never inherited. |
---|
443 | \\ |
---|
444 | \\ |
---|
445 | example 1: Direct inheritance. |
---|
446 | |
---|
447 | \begin{xmllines} |
---|
448 | <field_definition operation="average" > |
---|
449 | <field id="sst" /> <!-- averaged sst --> |
---|
450 | <field id="sss" operation="instant"/> <!-- instantaneous sss --> |
---|
451 | </field_definition> |
---|
452 | \end{xmllines} |
---|
453 | |
---|
454 | The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average'' of |
---|
455 | the attribute ''operation'' from its parent. |
---|
456 | Note that a child can overwrite the attribute definition inherited from its parents. |
---|
457 | In the example above, the field ''sss'' will for example output instantaneous values instead of average values. |
---|
458 | \\ |
---|
459 | \\ |
---|
460 | example 2: Inheritance by reference. |
---|
461 | |
---|
462 | \begin{xmllines} |
---|
463 | <field_definition> |
---|
464 | <field id="sst" long_name="sea surface temperature" /> |
---|
465 | <field id="sss" long_name="sea surface salinity" /> |
---|
466 | </field_definition> |
---|
467 | <file_definition> |
---|
468 | <file id="myfile" output_freq="1d" /> |
---|
469 | <field field_ref="sst" /> <!-- default def --> |
---|
470 | <field field_ref="sss" long_name="my description" /> <!-- overwrite --> |
---|
471 | </file> |
---|
472 | </file_definition> |
---|
473 | \end{xmllines} |
---|
474 | |
---|
475 | Inherit (and overwrite, if needed) the attributes of a tag you are refering to. |
---|
476 | |
---|
477 | \subsubsection{Use of groups} |
---|
478 | |
---|
479 | Groups can be used for 2 purposes. |
---|
480 | Firstly, the group can be used to define common attributes to be shared by the elements of |
---|
481 | the group through inheritance. |
---|
482 | In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''. |
---|
483 | Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''. |
---|
484 | |
---|
485 | \begin{xmllines} |
---|
486 | <field_group id="grid_T" grid_ref="grid_T_2D"> |
---|
487 | <field id="toce" long_name="temperature" unit="degC" grid_ref="grid_T_3D"/> |
---|
488 | <field id="sst" long_name="sea surface temperature" unit="degC" /> |
---|
489 | <field id="sss" long_name="sea surface salinity" unit="psu" /> |
---|
490 | <field id="ssh" long_name="sea surface height" unit="m" /> |
---|
491 | ... |
---|
492 | \end{xmllines} |
---|
493 | |
---|
494 | Secondly, the group can be used to replace a list of elements. |
---|
495 | Several examples of groups of fields are proposed at the end of the XML field files ( |
---|
496 | \path{cfgs/SHARED/field_def_nemo-oce.xml}, |
---|
497 | \path{cfgs/SHARED/field_def_nemo-pisces.xml} and |
---|
498 | \path{cfgs/SHARED/field_def_nemo-ice.xml} ) . |
---|
499 | For example, a short list of the usual variables related to the U grid: |
---|
500 | |
---|
501 | \begin{xmllines} |
---|
502 | <field_group id="groupU" > |
---|
503 | <field field_ref="uoce" /> |
---|
504 | <field field_ref="ssu" /> |
---|
505 | <field field_ref="utau" /> |
---|
506 | </field_group> |
---|
507 | \end{xmllines} |
---|
508 | |
---|
509 | that can be directly included in a file through the following syntax: |
---|
510 | |
---|
511 | \begin{xmllines} |
---|
512 | <file id="myfile_U" output_freq="1d" /> |
---|
513 | <field_group group_ref="groupU" /> |
---|
514 | <field field_ref="uocetr_eff" /> <!-- add another field --> |
---|
515 | </file> |
---|
516 | \end{xmllines} |
---|
517 | |
---|
518 | \subsection{Detailed functionalities} |
---|
519 | |
---|
520 | The file \path{NEMOGCM/CONFIG/ORCA2_LIM/iodef_demo.xml} provides several examples of the use of |
---|
521 | the new functionalities offered by the XML interface of XIOS. |
---|
522 | |
---|
523 | \subsubsection{Define horizontal subdomains} |
---|
524 | |
---|
525 | Horizontal subdomains are defined through the attributs zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj of |
---|
526 | the tag family domain. |
---|
527 | It must therefore be done in the domain part of the XML file. |
---|
528 | For example, in \path{cfgs/SHARED/domain_def.xml}, we provide the following example of a definition of |
---|
529 | a 5 by 5 box with the bottom left corner at point (10,10). |
---|
530 | |
---|
531 | \begin{xmllines} |
---|
532 | <domain id="myzoomT" domain_ref="grid_T"> |
---|
533 | <zoom_domain ibegin="10" jbegin="10" ni="5" nj="5" /> |
---|
534 | \end{xmllines} |
---|
535 | |
---|
536 | The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. |
---|
537 | For example: |
---|
538 | |
---|
539 | \begin{xmllines} |
---|
540 | <file id="myfile_vzoom" output_freq="1d" > |
---|
541 | <field field_ref="toce" domain_ref="myzoomT"/> |
---|
542 | </file> |
---|
543 | \end{xmllines} |
---|
544 | |
---|
545 | Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain. |
---|
546 | The Equatorial section, the TAO, RAMA and PIRATA moorings are already registered in the code and |
---|
547 | can therefore be outputted without taking care of their (i,j) position in the grid. |
---|
548 | These predefined domains can be activated by the use of specific domain\_ref: |
---|
549 | ''EqT'', ''EqU'' or ''EqW'' for the equatorial sections and |
---|
550 | the mooring position for TAO, RAMA and PIRATA followed by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...) |
---|
551 | |
---|
552 | \begin{xmllines} |
---|
553 | <file id="myfile_vzoom" output_freq="1d" > |
---|
554 | <field field_ref="toce" domain_ref="0n180wT"/> |
---|
555 | </file> |
---|
556 | \end{xmllines} |
---|
557 | |
---|
558 | Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if |
---|
559 | you use the ''multiple\_file'' type for your output files, |
---|
560 | you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat, |
---|
561 | \href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}). |
---|
562 | We are therefore advising to use the ''one\_file'' type in this case. |
---|
563 | |
---|
564 | \subsubsection{Define vertical zooms} |
---|
565 | |
---|
566 | Vertical zooms are defined through the attributs zoom\_begin and zoom\_n of the tag family axis. |
---|
567 | It must therefore be done in the axis part of the XML file. |
---|
568 | For example, in \path{cfgs/ORCA2_ICE_PISCES/EXPREF/iodef_demo.xml}, we provide the following example: |
---|
569 | |
---|
570 | \begin{xmllines} |
---|
571 | <axis_definition> |
---|
572 | <axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" /> |
---|
573 | <axis id="deptht_zoom" azix_ref="deptht" > |
---|
574 | <zoom_axis zoom_begin="1" zoom_n="10" /> |
---|
575 | </axis> |
---|
576 | \end{xmllines} |
---|
577 | |
---|
578 | The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. |
---|
579 | For example: |
---|
580 | |
---|
581 | \begin{xmllines} |
---|
582 | <file id="myfile_hzoom" output_freq="1d" > |
---|
583 | <field field_ref="toce" axis_ref="deptht_myzoom"/> |
---|
584 | </file> |
---|
585 | \end{xmllines} |
---|
586 | |
---|
587 | \subsubsection{Control of the output file names} |
---|
588 | |
---|
589 | The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. |
---|
590 | For example: |
---|
591 | |
---|
592 | \begin{xmllines} |
---|
593 | <file_group id="1d" output_freq="1d" name="myfile_1d" > |
---|
594 | <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA" --> |
---|
595 | ... |
---|
596 | </file> |
---|
597 | <file id="myfileB" name_suffix="_BBB" > <!-- will create file "myfile_1d_BBB" --> |
---|
598 | ... |
---|
599 | </file> |
---|
600 | </file_group> |
---|
601 | \end{xmllines} |
---|
602 | |
---|
603 | However it is often very convienent to define the file name with the name of the experiment, |
---|
604 | the output file frequency and the date of the beginning and the end of the simulation |
---|
605 | (which are informations stored either in the namelist or in the XML file). |
---|
606 | To do so, we added the following rule: |
---|
607 | if the id of the tag file is ''fileN'' (where N = 1 to 999 on 1 to 3 digits) or |
---|
608 | one of the predefined sections or moorings (see next subsection), |
---|
609 | the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by: |
---|
610 | |
---|
611 | \begin{table} |
---|
612 | \begin{tabularx}{\textwidth}{|lX|} |
---|
613 | \hline |
---|
614 | \centering placeholder string & |
---|
615 | automatically replaced by \\ |
---|
616 | \hline |
---|
617 | \hline |
---|
618 | \centering @expname@ & |
---|
619 | the experiment name (from cn\_exp in the namelist) \\ |
---|
620 | \hline |
---|
621 | \centering @freq@ & |
---|
622 | output frequency (from attribute output\_freq) \\ |
---|
623 | \hline |
---|
624 | \centering @startdate@ & |
---|
625 | starting date of the simulation (from nn\_date0 in the restart or the namelist). |
---|
626 | \newline |
---|
627 | \verb?yyyymmdd? format \\ |
---|
628 | \hline |
---|
629 | \centering @startdatefull@ & |
---|
630 | starting date of the simulation (from nn\_date0 in the restart or the namelist). |
---|
631 | \newline |
---|
632 | \verb?yyyymmdd_hh:mm:ss? format \\ |
---|
633 | \hline |
---|
634 | \centering @enddate@ & |
---|
635 | ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). |
---|
636 | \newline |
---|
637 | \verb?yyyymmdd? format \\ |
---|
638 | \hline |
---|
639 | \centering @enddatefull@ & |
---|
640 | ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). |
---|
641 | \newline |
---|
642 | \verb?yyyymmdd_hh:mm:ss? format \\ |
---|
643 | \hline |
---|
644 | \end{tabularx} |
---|
645 | \end{table} |
---|
646 | |
---|
647 | \noindent For example, |
---|
648 | \xmlline|<file id="myfile_hzoom" name="myfile_@expname@_@startdate@_freq@freq@" output_freq="1d" >| |
---|
649 | |
---|
650 | \noindent with the namelist: |
---|
651 | \begin{forlines} |
---|
652 | cn_exp = "ORCA2" |
---|
653 | nn_date0 = 19891231 |
---|
654 | ln_rstart = .false. |
---|
655 | \end{forlines} |
---|
656 | |
---|
657 | \noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d} |
---|
658 | |
---|
659 | \subsubsection{Other controls of the XML attributes from \NEMO} |
---|
660 | |
---|
661 | The values of some attributes are defined by subroutine calls within \NEMO |
---|
662 | (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in \mdl{iom}). |
---|
663 | Any definition given in the XML file will be overwritten. |
---|
664 | By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the XML file |
---|
665 | (but this is not necessary). |
---|
666 | \\ |
---|
667 | |
---|
668 | Here is the list of these attributes: |
---|
669 | \\ |
---|
670 | |
---|
671 | \begin{table} |
---|
672 | \begin{tabular}{|l|c|c|} |
---|
673 | \hline |
---|
674 | tag ids affected by automatic definition of some of their attributes & |
---|
675 | name attribute & |
---|
676 | attribute value \\ |
---|
677 | \hline |
---|
678 | \hline |
---|
679 | field\_definition & |
---|
680 | freq\_op & |
---|
681 | \np{rn_rdt}{rn\_rdt} \\ |
---|
682 | \hline |
---|
683 | SBC & |
---|
684 | freq\_op & |
---|
685 | \np{rn_rdt}{rn\_rdt} $\times$ \np{nn_fsbc}{nn\_fsbc} \\ |
---|
686 | \hline |
---|
687 | ptrc\_T & |
---|
688 | freq\_op & |
---|
689 | \np{rn_rdt}{rn\_rdt} $\times$ \np{nn_dttrc}{nn\_dttrc} \\ |
---|
690 | \hline |
---|
691 | diad\_T & |
---|
692 | freq\_op & |
---|
693 | \np{rn_rdt}{rn\_rdt} $\times$ \np{nn_dttrc}{nn\_dttrc} \\ |
---|
694 | \hline |
---|
695 | EqT, EqU, EqW & |
---|
696 | jbegin, ni, & |
---|
697 | according to the grid \\ |
---|
698 | & |
---|
699 | name\_suffix & |
---|
700 | \\ |
---|
701 | \hline |
---|
702 | TAO, RAMA and PIRATA moorings & |
---|
703 | zoom\_ibegin, zoom\_jbegin, & |
---|
704 | according to the grid \\ |
---|
705 | & |
---|
706 | name\_suffix & |
---|
707 | \\ |
---|
708 | \hline |
---|
709 | \end{tabular} |
---|
710 | \end{table} |
---|
711 | |
---|
712 | \subsubsection{Advanced use of XIOS functionalities} |
---|
713 | |
---|
714 | \subsection{XML reference tables} |
---|
715 | \label{subsec:DIA_IOM_xmlref} |
---|
716 | |
---|
717 | \begin{enumerate} |
---|
718 | \item Simple computation: directly define the computation when refering to the variable in the file definition. |
---|
719 | |
---|
720 | \begin{xmllines} |
---|
721 | <field field_ref="sst" name="tosK" unit="degK" > sst + 273.15 </field> |
---|
722 | <field field_ref="taum" name="taum2" unit="N2/m4" long_name="square of wind stress module" > taum * taum </field> |
---|
723 | <field field_ref="qt" name="stupid_check" > qt - qsr - qns </field> |
---|
724 | \end{xmllines} |
---|
725 | |
---|
726 | \item Simple computation: define a new variable and use it in the file definition. |
---|
727 | |
---|
728 | in field\_definition: |
---|
729 | |
---|
730 | \begin{xmllines} |
---|
731 | <field id="sst2" long_name="square of sea surface temperature" unit="degC2" > sst * sst </field > |
---|
732 | \end{xmllines} |
---|
733 | |
---|
734 | in file\_definition: |
---|
735 | |
---|
736 | \begin{xmllines} |
---|
737 | <field field_ref="sst2" > sst2 </field> |
---|
738 | \end{xmllines} |
---|
739 | |
---|
740 | Note that in this case, the following syntaxe \xmlcode{<field field_ref="sst2" />} is not working as |
---|
741 | sst2 won't be evaluated. |
---|
742 | |
---|
743 | \item Change of variable precision: |
---|
744 | |
---|
745 | \begin{xmllines} |
---|
746 | <!-- force to keep real 8 --> |
---|
747 | <field field_ref="sst" name="tos_r8" prec="8" /> |
---|
748 | <!-- integer 2 with add_offset and scale_factor attributes --> |
---|
749 | <field field_ref="sss" name="sos_i2" prec="2" add_offset="20." scale_factor="1.e-3" /> |
---|
750 | \end{xmllines} |
---|
751 | |
---|
752 | Note that, then the code is crashing, writting real4 variables forces a numerical conversion from |
---|
753 | real8 to real4 which will create an internal error in NetCDF and will avoid the creation of the output files. |
---|
754 | Forcing double precision outputs with prec="8" (for example in the field\_definition) will avoid this problem. |
---|
755 | |
---|
756 | \item add user defined attributes: |
---|
757 | |
---|
758 | \begin{xmllines} |
---|
759 | <file_group id="1d" output_freq="1d" output_level="10" enabled=".true."> <!-- 1d files --> |
---|
760 | <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > |
---|
761 | <field field_ref="sst" name="tos" > |
---|
762 | <variable id="my_attribute1" type="string" > blabla </variable> |
---|
763 | <variable id="my_attribute2" type="integer" > 3 </variable> |
---|
764 | <variable id="my_attribute3" type="float" > 5.0 </variable> |
---|
765 | </field> |
---|
766 | <variable id="my_global_attribute" type="string" > blabla_global </variable> |
---|
767 | </file> |
---|
768 | </file_group> |
---|
769 | \end{xmllines} |
---|
770 | |
---|
771 | \item use of the ``@'' function: example 1, weighted temporal average |
---|
772 | |
---|
773 | - define a new variable in field\_definition |
---|
774 | |
---|
775 | \begin{xmllines} |
---|
776 | <field id="toce_e3t" long_name="temperature * e3t" unit="degC*m" grid_ref="grid_T_3D" >toce * e3t</field> |
---|
777 | \end{xmllines} |
---|
778 | |
---|
779 | - use it when defining your file. |
---|
780 | |
---|
781 | \begin{xmllines} |
---|
782 | <file_group id="5d" output_freq="5d" output_level="10" enabled=".true." > <!-- 5d files --> |
---|
783 | <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > |
---|
784 | <field field_ref="toce" operation="instant" freq_op="5d" > @toce_e3t / @e3t </field> |
---|
785 | </file> |
---|
786 | </file_group> |
---|
787 | \end{xmllines} |
---|
788 | |
---|
789 | The freq\_op="5d" attribute is used to define the operation frequency of the ``@'' function: here 5 day. |
---|
790 | The temporal operation done by the ``@'' is the one defined in the field definition: |
---|
791 | here we use the default, average. |
---|
792 | So, in the above case, @toce\_e3t will do the 5-day mean of toce*e3t. |
---|
793 | Operation="instant" refers to the temporal operation to be performed on the field''@toce\_e3t / @e3t'': |
---|
794 | here the temporal average is alreday done by the ``@'' function so we just use instant to do the ratio of |
---|
795 | the 2 mean values. |
---|
796 | field\_ref="toce" means that attributes not explicitely defined, are inherited from toce field. |
---|
797 | Note that in this case, freq\_op must be equal to the file output\_freq. |
---|
798 | |
---|
799 | \item use of the ``@'' function: example 2, monthly SSH standard deviation |
---|
800 | |
---|
801 | - define a new variable in field\_definition |
---|
802 | |
---|
803 | \begin{xmllines} |
---|
804 | <field id="ssh2" long_name="square of sea surface temperature" unit="degC2" > ssh * ssh </field > |
---|
805 | \end{xmllines} |
---|
806 | |
---|
807 | - use it when defining your file. |
---|
808 | |
---|
809 | \begin{xmllines} |
---|
810 | <file_group id="1m" output_freq="1m" output_level="10" enabled=".true." > <!-- 1m files --> |
---|
811 | <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > |
---|
812 | <field field_ref="ssh" name="sshstd" long_name="sea_surface_temperature_standard_deviation" |
---|
813 | operation="instant" freq_op="1m" > |
---|
814 | sqrt( @ssh2 - @ssh * @ssh ) |
---|
815 | </field> |
---|
816 | </file> |
---|
817 | </file_group> |
---|
818 | \end{xmllines} |
---|
819 | |
---|
820 | The freq\_op="1m" attribute is used to define the operation frequency of the ``@'' function: here 1 month. |
---|
821 | The temporal operation done by the ``@'' is the one defined in the field definition: |
---|
822 | here we use the default, average. |
---|
823 | So, in the above case, @ssh2 will do the monthly mean of ssh*ssh. |
---|
824 | Operation="instant" refers to the temporal operation to be performed on the field ''sqrt( @ssh2 - @ssh * @ssh )'': |
---|
825 | here the temporal average is alreday done by the ``@'' function so we just use instant. |
---|
826 | field\_ref="ssh" means that attributes not explicitely defined, are inherited from ssh field. |
---|
827 | Note that in this case, freq\_op must be equal to the file output\_freq. |
---|
828 | |
---|
829 | \item use of the ``@'' function: example 3, monthly average of SST diurnal cycle |
---|
830 | |
---|
831 | - define 2 new variables in field\_definition |
---|
832 | |
---|
833 | \begin{xmllines} |
---|
834 | <field id="sstmax" field_ref="sst" long_name="max of sea surface temperature" operation="maximum" /> |
---|
835 | <field id="sstmin" field_ref="sst" long_name="min of sea surface temperature" operation="minimum" /> |
---|
836 | \end{xmllines} |
---|
837 | |
---|
838 | - use these 2 new variables when defining your file. |
---|
839 | |
---|
840 | \begin{xmllines} |
---|
841 | <file_group id="1m" output_freq="1m" output_level="10" enabled=".true." > <!-- 1m files --> |
---|
842 | <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" > |
---|
843 | <field field_ref="sst" name="sstdcy" long_name="amplitude of sst diurnal cycle" operation="average" freq_op="1d" > |
---|
844 | @sstmax - @sstmin |
---|
845 | </field> |
---|
846 | </file> |
---|
847 | </file_group> |
---|
848 | \end{xmllines} |
---|
849 | |
---|
850 | \end{enumerate} |
---|
851 | |
---|
852 | The freq\_op="1d" attribute is used to define the operation frequency of the ``@'' function: here 1 day. |
---|
853 | The temporal operation done by the ``@'' is the one defined in the field definition: |
---|
854 | here maximum for sstmax and minimum for sstmin. |
---|
855 | So, in the above case, @sstmax will do the daily max and @sstmin the daily min. |
---|
856 | Operation="average" refers to the temporal operation to be performed on the field ``@sstmax - @sstmin'': |
---|
857 | here monthly mean (of daily max - daily min of the sst). |
---|
858 | field\_ref="sst" means that attributes not explicitely defined, are inherited from sst field. |
---|
859 | |
---|
860 | \subsubsection{Tag list per family} |
---|
861 | |
---|
862 | \begin{table} |
---|
863 | \begin{tabularx}{\textwidth}{|l|X|X|l|X|} |
---|
864 | \hline |
---|
865 | tag name & |
---|
866 | description & |
---|
867 | accepted attribute & |
---|
868 | child of & |
---|
869 | parent of \\ |
---|
870 | \hline |
---|
871 | \hline |
---|
872 | simulation & |
---|
873 | this tag is the root tag which encapsulates all the content of the XML file & |
---|
874 | none & |
---|
875 | none & |
---|
876 | context \\ |
---|
877 | \hline |
---|
878 | context & |
---|
879 | encapsulates parts of the XML file dedicated to different codes or different parts of a code & |
---|
880 | id (''xios'', ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom), src, time\_origin & |
---|
881 | simulation & |
---|
882 | all root tags: ... \_definition \\ |
---|
883 | \hline |
---|
884 | \end{tabularx} |
---|
885 | \caption{XIOS: context tags} |
---|
886 | \end{table} |
---|
887 | |
---|
888 | \begin{table} |
---|
889 | \begin{tabularx}{\textwidth}{|l|X|X|X|l|} |
---|
890 | \hline |
---|
891 | tag name & |
---|
892 | description & |
---|
893 | accepted attribute & |
---|
894 | child of & |
---|
895 | parent of \\ |
---|
896 | \hline |
---|
897 | \hline |
---|
898 | field\_definition & |
---|
899 | encapsulates the definition of all the fields that can potentially be outputted & |
---|
900 | axis\_ref, default\_value, domain\_ref, enabled, grid\_ref, level, operation, prec, src & |
---|
901 | context & |
---|
902 | field or field\_group \\ |
---|
903 | \hline |
---|
904 | field\_group & |
---|
905 | encapsulates a group of fields & |
---|
906 | axis\_ref, default\_value, domain\_ref, enabled, group\_ref, grid\_ref, |
---|
907 | id, level, operation, prec, src & |
---|
908 | field\_definition, field\_group, file & |
---|
909 | field or field\_group \\ |
---|
910 | \hline |
---|
911 | field & |
---|
912 | define a specific field & |
---|
913 | axis\_ref, default\_value, domain\_ref, enabled, field\_ref, grid\_ref, |
---|
914 | id, level, long\_name, name, operation, prec, standard\_name, unit & |
---|
915 | field\_definition, field\_group, file & |
---|
916 | none \\ |
---|
917 | \hline |
---|
918 | \end{tabularx} |
---|
919 | \caption{XIOS: field tags ("\texttt{field\_*}")} |
---|
920 | \end{table} |
---|
921 | |
---|
922 | \begin{table} |
---|
923 | \begin{tabularx}{\textwidth}{|l|X|X|X|l|} |
---|
924 | \hline |
---|
925 | tag name & |
---|
926 | description & |
---|
927 | accepted attribute & |
---|
928 | child of & |
---|
929 | parent of \\ |
---|
930 | \hline |
---|
931 | \hline |
---|
932 | file\_definition & |
---|
933 | encapsulates the definition of all the files that will be outputted & |
---|
934 | enabled, min\_digits, name, name\_suffix, output\_level, |
---|
935 | split\_freq\_format, split\_freq, sync\_freq, type, src & |
---|
936 | context & |
---|
937 | file or file\_group \\ |
---|
938 | \hline |
---|
939 | file\_group & |
---|
940 | encapsulates a group of files that will be outputted & |
---|
941 | enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, |
---|
942 | split\_freq\_format, split\_freq, sync\_freq, type, src & |
---|
943 | file\_definition, file\_group & |
---|
944 | file or file\_group \\ |
---|
945 | \hline |
---|
946 | file & |
---|
947 | define the contents of a file to be outputted & |
---|
948 | enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, |
---|
949 | split\_freq\_format, split\_freq, sync\_freq, type, src & |
---|
950 | file\_definition, file\_group & |
---|
951 | field \\ |
---|
952 | \hline |
---|
953 | \end{tabularx} |
---|
954 | \caption{XIOS: file tags ("\texttt{file\_*}")} |
---|
955 | \end{table} |
---|
956 | |
---|
957 | \begin{table} |
---|
958 | \begin{tabularx}{\textwidth}{|l|X|X|X|X|} |
---|
959 | \hline |
---|
960 | tag name & |
---|
961 | description & |
---|
962 | accepted attribute & |
---|
963 | child of & |
---|
964 | parent of \\ |
---|
965 | \hline |
---|
966 | \hline |
---|
967 | axis\_definition & |
---|
968 | define all the vertical axis potentially used by the variables & |
---|
969 | src & |
---|
970 | context & |
---|
971 | axis\_group, axis \\ |
---|
972 | \hline |
---|
973 | axis\_group & |
---|
974 | encapsulates a group of vertical axis & |
---|
975 | id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size & |
---|
976 | axis\_definition, axis\_group & |
---|
977 | axis\_group, axis \\ |
---|
978 | \hline |
---|
979 | axis & |
---|
980 | define a vertical axis & |
---|
981 | id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size & |
---|
982 | axis\_definition, axis\_group & |
---|
983 | none \\ |
---|
984 | \hline |
---|
985 | \end{tabularx} |
---|
986 | \caption{XIOS: axis tags ("\texttt{axis\_*}")} |
---|
987 | \end{table} |
---|
988 | |
---|
989 | \begin{table} |
---|
990 | \begin{tabularx}{\textwidth}{|l|X|X|X|X|} |
---|
991 | \hline |
---|
992 | tag name & |
---|
993 | description & |
---|
994 | accepted attribute & |
---|
995 | child of & |
---|
996 | parent of \\ |
---|
997 | \hline |
---|
998 | \hline |
---|
999 | domain\_\-definition & |
---|
1000 | define all the horizontal domains potentially used by the variables & |
---|
1001 | src & |
---|
1002 | context & |
---|
1003 | domain\_\-group, domain \\ |
---|
1004 | \hline |
---|
1005 | domain\_group & |
---|
1006 | encapsulates a group of horizontal domains & |
---|
1007 | id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & |
---|
1008 | domain\_\-definition, domain\_group & |
---|
1009 | domain\_\-group, domain \\ |
---|
1010 | \hline |
---|
1011 | domain & |
---|
1012 | define an horizontal domain & |
---|
1013 | id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & |
---|
1014 | domain\_\-definition, domain\_group & |
---|
1015 | none \\ |
---|
1016 | \hline |
---|
1017 | \end{tabularx} |
---|
1018 | \caption{XIOS: domain tags ("\texttt{domain\_*)}"} |
---|
1019 | \end{table} |
---|
1020 | |
---|
1021 | \begin{table} |
---|
1022 | \begin{tabularx}{\textwidth}{|l|X|X|X|X|} |
---|
1023 | \hline |
---|
1024 | tag name & |
---|
1025 | description & |
---|
1026 | accepted attribute & |
---|
1027 | child of & |
---|
1028 | parent of \\ |
---|
1029 | \hline |
---|
1030 | \hline |
---|
1031 | grid\_definition & |
---|
1032 | define all the grid (association of a domain and/or an axis) potentially used by the variables & |
---|
1033 | src & |
---|
1034 | context & |
---|
1035 | grid\_group, grid \\ |
---|
1036 | \hline |
---|
1037 | grid\_group & |
---|
1038 | encapsulates a group of grids & |
---|
1039 | id, domain\_ref,axis\_ref & |
---|
1040 | grid\_definition, grid\_group & |
---|
1041 | grid\_group, grid \\ |
---|
1042 | \hline |
---|
1043 | grid & |
---|
1044 | define a grid & |
---|
1045 | id, domain\_ref,axis\_ref & |
---|
1046 | grid\_definition, grid\_group & |
---|
1047 | none \\ |
---|
1048 | \hline |
---|
1049 | \end{tabularx} |
---|
1050 | \caption{XIOS: grid tags ("\texttt{grid\_*}")} |
---|
1051 | \end{table} |
---|
1052 | |
---|
1053 | \subsubsection{Attributes list per family} |
---|
1054 | |
---|
1055 | \begin{table} |
---|
1056 | \begin{tabularx}{\textwidth}{|l|X|l|l|} |
---|
1057 | \hline |
---|
1058 | attribute name & |
---|
1059 | description & |
---|
1060 | example & |
---|
1061 | accepted by \\ |
---|
1062 | \hline |
---|
1063 | \hline |
---|
1064 | axis\_ref & |
---|
1065 | refers to the id of a vertical axis & |
---|
1066 | axis\_ref="deptht" & |
---|
1067 | field, grid families \\ |
---|
1068 | \hline |
---|
1069 | domain\_ref & |
---|
1070 | refers to the id of a domain & |
---|
1071 | domain\_ref="grid\_T" & |
---|
1072 | field or grid families \\ |
---|
1073 | \hline |
---|
1074 | field\_ref & |
---|
1075 | id of the field we want to add in a file & |
---|
1076 | field\_ref="toce" & |
---|
1077 | field \\ |
---|
1078 | \hline |
---|
1079 | grid\_ref & |
---|
1080 | refers to the id of a grid & |
---|
1081 | grid\_ref="grid\_T\_2D" & |
---|
1082 | field family \\ |
---|
1083 | \hline |
---|
1084 | group\_ref & |
---|
1085 | refer to a group of variables & |
---|
1086 | group\_ref="mooring" & |
---|
1087 | field\_group \\ |
---|
1088 | \hline |
---|
1089 | \end{tabularx} |
---|
1090 | \caption{XIOS: reference attributes ("\texttt{*\_ref}")} |
---|
1091 | \end{table} |
---|
1092 | |
---|
1093 | \begin{table} |
---|
1094 | \begin{tabularx}{\textwidth}{|l|X|l|l|} |
---|
1095 | \hline |
---|
1096 | attribute name & |
---|
1097 | description & |
---|
1098 | example & |
---|
1099 | accepted by \\ |
---|
1100 | \hline |
---|
1101 | \hline |
---|
1102 | zoom\_ibegin & |
---|
1103 | starting point along x direction of the zoom. |
---|
1104 | Automatically defined for TAO/RAMA/PIRATA moorings & |
---|
1105 | zoom\_ibegin="1" & |
---|
1106 | domain family \\ |
---|
1107 | \hline |
---|
1108 | zoom\_jbegin & |
---|
1109 | starting point along y direction of the zoom. |
---|
1110 | Automatically defined for TAO/RAMA/PIRATA moorings & |
---|
1111 | zoom\_jbegin="1" & |
---|
1112 | domain family \\ |
---|
1113 | \hline |
---|
1114 | zoom\_ni & |
---|
1115 | zoom extent along x direction & |
---|
1116 | zoom\_ni="1" & |
---|
1117 | domain family \\ |
---|
1118 | \hline |
---|
1119 | zoom\_nj & |
---|
1120 | zoom extent along y direction & |
---|
1121 | zoom\_nj="1" & |
---|
1122 | domain family \\ |
---|
1123 | \hline |
---|
1124 | \end{tabularx} |
---|
1125 | \caption{XIOS: domain attributes ("\texttt{zoom\_*}")} |
---|
1126 | \end{table} |
---|
1127 | |
---|
1128 | \begin{table} |
---|
1129 | \begin{tabularx}{\textwidth}{|l|X|l|l|} |
---|
1130 | \hline |
---|
1131 | attribute name & |
---|
1132 | description & |
---|
1133 | example & |
---|
1134 | accepted by \\ |
---|
1135 | \hline |
---|
1136 | \hline |
---|
1137 | min\_digits & |
---|
1138 | specify the minimum of digits used in the core number in the name of the NetCDF file & |
---|
1139 | min\_digits="4" & |
---|
1140 | file family \\ |
---|
1141 | \hline |
---|
1142 | name\_suffix & |
---|
1143 | suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file & |
---|
1144 | name\_suffix="\_myzoom" & |
---|
1145 | file family \\ |
---|
1146 | \hline |
---|
1147 | output\_level & |
---|
1148 | output priority of variables in a file: 0 (high) to 10 (low). |
---|
1149 | All variables listed in the file with a level smaller or equal to output\_level will be output. |
---|
1150 | Other variables won't be output even if they are listed in the file. & |
---|
1151 | output\_level="10" & |
---|
1152 | file family \\ |
---|
1153 | \hline |
---|
1154 | split\_freq & |
---|
1155 | frequency at which to temporally split output files. |
---|
1156 | Units can be ts (timestep), y, mo, d, h, mi, s. |
---|
1157 | Useful for long runs to prevent over-sized output files. & |
---|
1158 | split\_freq="1mo" & |
---|
1159 | file family \\ |
---|
1160 | \hline |
---|
1161 | split\_freq\-\_format & |
---|
1162 | date format used in the name of temporally split output files. |
---|
1163 | Can be specified using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s & |
---|
1164 | split\_freq\_format= "\%y\%mo\%d" & |
---|
1165 | file family \\ |
---|
1166 | \hline |
---|
1167 | sync\_freq & |
---|
1168 | NetCDF file synchronization frequency (update of the time\_counter). |
---|
1169 | Units can be ts (timestep), y, mo, d, h, mi, s. & |
---|
1170 | sync\_freq="10d" & |
---|
1171 | file family \\ |
---|
1172 | \hline |
---|
1173 | type (1) & |
---|
1174 | specify if the output files are to be split spatially (multiple\_file) or not (one\_file) & |
---|
1175 | type="multiple\_file" & |
---|
1176 | file familly \\ |
---|
1177 | \hline |
---|
1178 | \end{tabularx} |
---|
1179 | \caption{XIOS: file attributes} |
---|
1180 | \end{table} |
---|
1181 | |
---|
1182 | \begin{table} |
---|
1183 | \begin{tabularx}{\textwidth}{|l|X|l|l|} |
---|
1184 | \hline |
---|
1185 | attribute name & |
---|
1186 | description & |
---|
1187 | example & |
---|
1188 | accepted by \\ |
---|
1189 | \hline |
---|
1190 | \hline |
---|
1191 | default\_value & |
---|
1192 | missing\_value definition & |
---|
1193 | default\_value="1.e20" & |
---|
1194 | field family \\ |
---|
1195 | \hline |
---|
1196 | level & |
---|
1197 | output priority of a field: 0 (high) to 10 (low) & |
---|
1198 | level="1" & |
---|
1199 | field family \\ |
---|
1200 | \hline |
---|
1201 | operation & |
---|
1202 | type of temporal operation: average, accumulate, instantaneous, min, max and once & |
---|
1203 | operation="average" & |
---|
1204 | field family \\ |
---|
1205 | \hline |
---|
1206 | output\_freq & |
---|
1207 | operation frequency. units can be ts (timestep), y, mo, d, h, mi, s. & |
---|
1208 | output\_freq="1d12h" & |
---|
1209 | field family \\ |
---|
1210 | \hline |
---|
1211 | prec & |
---|
1212 | output precision: real 4 or real 8 & |
---|
1213 | prec="4" & |
---|
1214 | field family \\ |
---|
1215 | \hline |
---|
1216 | long\_name & |
---|
1217 | define the long\_name attribute in the NetCDF file & |
---|
1218 | long\_name="Vertical T levels" & |
---|
1219 | field \\ |
---|
1220 | \hline |
---|
1221 | standard\_name & |
---|
1222 | define the standard\_name attribute in the NetCDF file & |
---|
1223 | standard\_name= "Eastward\_Sea\_Ice\_Transport" & |
---|
1224 | field \\ |
---|
1225 | \hline |
---|
1226 | \end{tabularx} |
---|
1227 | \caption{XIOS: field attributes} |
---|
1228 | \end{table} |
---|
1229 | |
---|
1230 | \begin{table} |
---|
1231 | \begin{tabularx}{\textwidth}{|l|X|X|X|} |
---|
1232 | \hline |
---|
1233 | attribute name & |
---|
1234 | description & |
---|
1235 | example & |
---|
1236 | accepted by \\ |
---|
1237 | \hline |
---|
1238 | \hline |
---|
1239 | enabled & |
---|
1240 | switch on/off the output of a field or a file & |
---|
1241 | enabled=".true." & |
---|
1242 | field, file families \\ |
---|
1243 | \hline |
---|
1244 | description & |
---|
1245 | just for information, not used & |
---|
1246 | description="ocean T grid variables" & |
---|
1247 | all tags \\ |
---|
1248 | \hline |
---|
1249 | id & |
---|
1250 | allow to identify a tag & |
---|
1251 | id="nemo" & |
---|
1252 | accepted by all tags except simulation \\ |
---|
1253 | \hline |
---|
1254 | name & |
---|
1255 | name of a variable or a file. If the name of a file is undefined, its id is used as a name & |
---|
1256 | name="tos" & |
---|
1257 | field or file families \\ |
---|
1258 | \hline |
---|
1259 | positive & |
---|
1260 | convention used for the orientation of vertival axis (positive downward in \NEMO). & |
---|
1261 | positive="down" & |
---|
1262 | axis family \\ |
---|
1263 | \hline |
---|
1264 | src & |
---|
1265 | allow to include a file & |
---|
1266 | src="./field\_def.xml" & |
---|
1267 | accepted by all tags except simulation \\ |
---|
1268 | \hline |
---|
1269 | time\_origin & |
---|
1270 | specify the origin of the time counter & |
---|
1271 | time\_origin="1900-01-01 00:00:00" & |
---|
1272 | context \\ |
---|
1273 | \hline |
---|
1274 | type (2) & |
---|
1275 | define the type of a variable tag & |
---|
1276 | type="boolean" & |
---|
1277 | variable \\ |
---|
1278 | \hline |
---|
1279 | unit & |
---|
1280 | unit of a variable or the vertical axis & |
---|
1281 | unit="m" & |
---|
1282 | field and axis families \\ |
---|
1283 | \hline |
---|
1284 | \end{tabularx} |
---|
1285 | \caption{XIOS: miscellaneous attributes} |
---|
1286 | \end{table} |
---|
1287 | |
---|
1288 | \subsection{CF metadata standard compliance} |
---|
1289 | |
---|
1290 | Output from the XIOS IO server is compliant with |
---|
1291 | \href{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.5/build/cf-conventions.html}{version 1.5} of |
---|
1292 | the CF metadata standard. |
---|
1293 | Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of |
---|
1294 | section \autoref{subsec:DIA_IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard. |
---|
1295 | |
---|
1296 | Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by |
---|
1297 | the namelist parameter \np{ln_cfmeta}{ln\_cfmeta} in the \nam{run}{run} namelist. |
---|
1298 | This must be set to true if these metadata are to be included in the output files. |
---|
1299 | |
---|
1300 | \section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})]{NetCDF4 support (\protect\key{netcdf4})} |
---|
1301 | \label{sec:DIA_nc4} |
---|
1302 | |
---|
1303 | Since version 3.3, support for NetCDF4 chunking and (loss-less) compression has been included. |
---|
1304 | These options build on the standard NetCDF output and allow the user control over the size of the chunks via |
---|
1305 | namelist settings. |
---|
1306 | Chunking and compression can lead to significant reductions in file sizes for a small runtime overhead. |
---|
1307 | For a fuller discussion on chunking and other performance issues the reader is referred to |
---|
1308 | the NetCDF4 documentation found \href{https://www.unidata.ucar.edu/software/netcdf/docs/netcdf_perf_chunking.html}{here}. |
---|
1309 | |
---|
1310 | The new features are only available when the code has been linked with a NetCDF4 library |
---|
1311 | (version 4.1 onwards, recommended) which has been built with HDF5 support (version 1.8.4 onwards, recommended). |
---|
1312 | Datasets created with chunking and compression are not backwards compatible with NetCDF3 "classic" format but |
---|
1313 | most analysis codes can be relinked simply with the new libraries and will then read both NetCDF3 and NetCDF4 files. |
---|
1314 | \NEMO\ executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by |
---|
1315 | setting the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4}{nc4} namelist: |
---|
1316 | |
---|
1317 | %------------------------------------------namnc4---------------------------------------------------- |
---|
1318 | |
---|
1319 | \begin{listing} |
---|
1320 | \nlst{namnc4} |
---|
1321 | \caption{\forcode{&namnc4}} |
---|
1322 | \label{lst:namnc4} |
---|
1323 | \end{listing} |
---|
1324 | %------------------------------------------------------------------------------------------------------------- |
---|
1325 | |
---|
1326 | If \key{netcdf4} has not been defined, these namelist parameters are not read. |
---|
1327 | In this case, \np{ln_nc4zip}{ln\_nc4zip} is set false and dummy routines for a few NetCDF4-specific functions are defined. |
---|
1328 | These functions will not be used but need to be included so that compilation is possible with NetCDF3 libraries. |
---|
1329 | |
---|
1330 | When using NetCDF4 libraries, \key{netcdf4} should be defined even if the intention is to |
---|
1331 | create only NetCDF3-compatible files. |
---|
1332 | This is necessary to avoid duplication between the dummy routines and the actual routines present in the library. |
---|
1333 | Most compilers will fail at compile time when faced with such duplication. |
---|
1334 | Thus when linking with NetCDF4 libraries the user must define \key{netcdf4} and |
---|
1335 | control the type of NetCDF file produced via the namelist parameter. |
---|
1336 | |
---|
1337 | Chunking and compression is applied only to 4D fields and |
---|
1338 | there is no advantage in chunking across more than one time dimension since |
---|
1339 | previously written chunks would have to be read back and decompressed before being added to. |
---|
1340 | Therefore, user control over chunk sizes is provided only for the three space dimensions. |
---|
1341 | The user sets an approximate number of chunks along each spatial axis. |
---|
1342 | The actual size of the chunks will depend on global domain size for mono-processors or, more likely, |
---|
1343 | the local processor domain size for distributed processing. |
---|
1344 | The derived values are subject to practical minimum values (to avoid wastefully small chunk sizes) and |
---|
1345 | cannot be greater than the domain size in any dimension. |
---|
1346 | The algorithm used is: |
---|
1347 | |
---|
1348 | \begin{forlines} |
---|
1349 | ichunksz(1) = MIN(idomain_size, MAX((idomain_size-1) / nn_nchunks_i + 1 ,16 )) |
---|
1350 | ichunksz(2) = MIN(jdomain_size, MAX((jdomain_size-1) / nn_nchunks_j + 1 ,16 )) |
---|
1351 | ichunksz(3) = MIN(kdomain_size, MAX((kdomain_size-1) / nn_nchunks_k + 1 , 1 )) |
---|
1352 | ichunksz(4) = 1 |
---|
1353 | \end{forlines} |
---|
1354 | |
---|
1355 | \noindent As an example, setting: |
---|
1356 | |
---|
1357 | \begin{forlines} |
---|
1358 | nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31 |
---|
1359 | \end{forlines} |
---|
1360 | |
---|
1361 | \noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\texttt 46x38x1} respectively in |
---|
1362 | the mono-processor case (\ie\ global domain of {\small\texttt 182x149x31}). |
---|
1363 | An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in |
---|
1364 | table \autoref{tab:DIA_NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with |
---|
1365 | a 4x2 mpi partitioning. |
---|
1366 | Note the variation in the compression ratio achieved which reflects chiefly the dry to wet volume ratio of |
---|
1367 | each processing region. |
---|
1368 | |
---|
1369 | %------------------------------------------TABLE---------------------------------------------------- |
---|
1370 | \begin{table} |
---|
1371 | \centering |
---|
1372 | \begin{tabular}{lrrr} |
---|
1373 | Filename & NetCDF3 & NetCDF4 & Reduction \\ |
---|
1374 | & filesize & filesize & \% \\ |
---|
1375 | & (KB) & (KB) & \\ |
---|
1376 | ORCA2\_restart\_0000.nc & 16420 & 8860 & 47\% \\ |
---|
1377 | ORCA2\_restart\_0001.nc & 16064 & 11456 & 29\% \\ |
---|
1378 | ORCA2\_restart\_0002.nc & 16064 & 9744 & 40\% \\ |
---|
1379 | ORCA2\_restart\_0003.nc & 16420 & 9404 & 43\% \\ |
---|
1380 | ORCA2\_restart\_0004.nc & 16200 & 5844 & 64\% \\ |
---|
1381 | ORCA2\_restart\_0005.nc & 15848 & 8172 & 49\% \\ |
---|
1382 | ORCA2\_restart\_0006.nc & 15848 & 8012 & 50\% \\ |
---|
1383 | ORCA2\_restart\_0007.nc & 16200 & 5148 & 69\% \\ |
---|
1384 | ORCA2\_2d\_grid\_T\_0000.nc & 2200 & 1504 & 32\% \\ |
---|
1385 | ORCA2\_2d\_grid\_T\_0001.nc & 2200 & 1748 & 21\% \\ |
---|
1386 | ORCA2\_2d\_grid\_T\_0002.nc & 2200 & 1592 & 28\% \\ |
---|
1387 | ORCA2\_2d\_grid\_T\_0003.nc & 2200 & 1540 & 30\% \\ |
---|
1388 | ORCA2\_2d\_grid\_T\_0004.nc & 2200 & 1204 & 46\% \\ |
---|
1389 | ORCA2\_2d\_grid\_T\_0005.nc & 2200 & 1444 & 35\% \\ |
---|
1390 | ORCA2\_2d\_grid\_T\_0006.nc & 2200 & 1428 & 36\% \\ |
---|
1391 | ORCA2\_2d\_grid\_T\_0007.nc & 2200 & 1148 & 48\% \\ |
---|
1392 | ... & ... & ... & ... \\ |
---|
1393 | ORCA2\_2d\_grid\_W\_0000.nc & 4416 & 2240 & 50\% \\ |
---|
1394 | ORCA2\_2d\_grid\_W\_0001.nc & 4416 & 2924 & 34\% \\ |
---|
1395 | ORCA2\_2d\_grid\_W\_0002.nc & 4416 & 2512 & 44\% \\ |
---|
1396 | ORCA2\_2d\_grid\_W\_0003.nc & 4416 & 2368 & 47\% \\ |
---|
1397 | ORCA2\_2d\_grid\_W\_0004.nc & 4416 & 1432 & 68\% \\ |
---|
1398 | ORCA2\_2d\_grid\_W\_0005.nc & 4416 & 1972 & 56\% \\ |
---|
1399 | ORCA2\_2d\_grid\_W\_0006.nc & 4416 & 2028 & 55\% \\ |
---|
1400 | ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\% \\ |
---|
1401 | \end{tabular} |
---|
1402 | \caption{Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression} |
---|
1403 | \label{tab:DIA_NC4} |
---|
1404 | \end{table} |
---|
1405 | %---------------------------------------------------------------------------------------------------- |
---|
1406 | |
---|
1407 | When \key{iomput} is activated with \key{netcdf4} chunking and compression parameters for fields produced via |
---|
1408 | \rou{iom\_put} calls are set via an equivalent and identically named namelist to \nam{nc4}{nc4} in |
---|
1409 | \textit{xmlio\_server.def}. |
---|
1410 | Typically this namelist serves the mean files whilst the \nam{nc4}{nc4} in the main namelist file continues to |
---|
1411 | serve the restart files. |
---|
1412 | This duplication is unfortunate but appropriate since, if using io\_servers, the domain sizes of |
---|
1413 | the individual files produced by the io\_server processes may be different to those produced by |
---|
1414 | the invidual processing regions and different chunking choices may be desired. |
---|
1415 | |
---|
1416 | \section[Tracer/Dynamics trends (\forcode{&namtrd})]{Tracer/Dynamics trends (\protect\nam{trd}{trd})} |
---|
1417 | \label{sec:DIA_trd} |
---|
1418 | |
---|
1419 | %------------------------------------------namtrd---------------------------------------------------- |
---|
1420 | |
---|
1421 | \begin{listing} |
---|
1422 | \nlst{namtrd} |
---|
1423 | \caption{\forcode{&namtrd}} |
---|
1424 | \label{lst:namtrd} |
---|
1425 | \end{listing} |
---|
1426 | %------------------------------------------------------------------------------------------------------------- |
---|
1427 | |
---|
1428 | Each trend of the dynamics and/or temperature and salinity time evolution equations can be send to |
---|
1429 | \mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation |
---|
1430 | (\ie\ at the end of each \textit{dyn....F90} and/or \textit{tra....F90} routines). |
---|
1431 | This capability is controlled by options offered in \nam{trd}{trd} namelist. |
---|
1432 | Note that the output are done with XIOS, and therefore the \key{iomput} is required. |
---|
1433 | |
---|
1434 | What is done depends on the \nam{trd}{trd} logical set to \forcode{.true.}: |
---|
1435 | |
---|
1436 | \begin{description} |
---|
1437 | \item [{\np{ln_glo_trd}{ln\_glo\_trd}}]: |
---|
1438 | at each \np{nn_trd}{nn\_trd} time-step a check of the basin averaged properties of |
---|
1439 | the momentum and tracer equations is performed. |
---|
1440 | This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$, |
---|
1441 | and potential energy time evolution equations properties; |
---|
1442 | \item [{\np{ln_dyn_trd}{ln\_dyn\_trd}}]: |
---|
1443 | each 3D trend of the evolution of the two momentum components is output; |
---|
1444 | \item [{\np{ln_dyn_mxl}{ln\_dyn\_mxl}}]: |
---|
1445 | each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output; |
---|
1446 | \item [{\np{ln_vor_trd}{ln\_vor\_trd}}]: |
---|
1447 | a vertical summation of the moment tendencies is performed, |
---|
1448 | then the curl is computed to obtain the barotropic vorticity tendencies which are output; |
---|
1449 | \item [{\np{ln_KE_trd}{ln\_KE\_trd}}] : |
---|
1450 | each 3D trend of the Kinetic Energy equation is output; |
---|
1451 | \item [{\np{ln_tra_trd}{ln\_tra\_trd}}]: |
---|
1452 | each 3D trend of the evolution of temperature and salinity is output; |
---|
1453 | \item [{\np{ln_tra_mxl}{ln\_tra\_mxl}}]: |
---|
1454 | each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output; |
---|
1455 | \end{description} |
---|
1456 | |
---|
1457 | Note that the mixed layer tendency diagnostic can also be used on biogeochemical models via |
---|
1458 | the \key{trdtrc} and \key{trdmxl\_trc} CPP keys. |
---|
1459 | |
---|
1460 | \textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested. |
---|
1461 | In particular, options associated with \np{ln_dyn_mxl}{ln\_dyn\_mxl}, \np{ln_vor_trd}{ln\_vor\_trd}, and \np{ln_tra_mxl}{ln\_tra\_mxl} are not working, |
---|
1462 | and none of the options have been tested with variable volume (\ie\ \np[=.true.]{ln_linssh}{ln\_linssh}). |
---|
1463 | |
---|
1464 | \section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})]{FLO: On-Line Floats trajectories (\protect\key{floats})} |
---|
1465 | \label{sec:DIA_FLO} |
---|
1466 | %--------------------------------------------namflo------------------------------------------------------- |
---|
1467 | |
---|
1468 | \begin{listing} |
---|
1469 | \nlst{namflo} |
---|
1470 | \caption{\forcode{&namflo}} |
---|
1471 | \label{lst:namflo} |
---|
1472 | \end{listing} |
---|
1473 | %-------------------------------------------------------------------------------------------------------------- |
---|
1474 | |
---|
1475 | The on-line computation of floats advected either by the three dimensional velocity field or constraint to |
---|
1476 | remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project. |
---|
1477 | Options are defined by \nam{flo}{flo} namelist variables. |
---|
1478 | The algorithm used is based either on the work of \cite{blanke.raynaud_JPO97} (default option), |
---|
1479 | or on a $4^th$ Runge-Hutta algorithm (\np[=.true.]{ln_flork4}{ln\_flork4}). |
---|
1480 | Note that the \cite{blanke.raynaud_JPO97} algorithm have the advantage of providing trajectories which |
---|
1481 | are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry. |
---|
1482 | |
---|
1483 | \subsubsection{Input data: initial coordinates} |
---|
1484 | |
---|
1485 | Initial coordinates can be given with Ariane Tools convention |
---|
1486 | (IJK coordinates, (\np[=.true.]{ln_ariane}{ln\_ariane}) ) or with longitude and latitude. |
---|
1487 | |
---|
1488 | In case of Ariane convention, input filename is \textit{init\_float\_ariane}. |
---|
1489 | Its format is: \\ |
---|
1490 | { \texttt{I J K nisobfl itrash}} |
---|
1491 | |
---|
1492 | \noindent with: |
---|
1493 | |
---|
1494 | - I,J,K : indexes of initial position |
---|
1495 | |
---|
1496 | - nisobfl: 0 for an isobar float, 1 for a float following the w velocity |
---|
1497 | |
---|
1498 | - itrash : set to zero; it is a dummy variable to respect Ariane Tools convention |
---|
1499 | |
---|
1500 | \noindent Example: \\ |
---|
1501 | \noindent |
---|
1502 | { |
---|
1503 | \texttt{ |
---|
1504 | 100.00000 90.00000 -1.50000 1.00000 0.00000 \\ |
---|
1505 | 102.00000 90.00000 -1.50000 1.00000 0.00000 \\ |
---|
1506 | 104.00000 90.00000 -1.50000 1.00000 0.00000 \\ |
---|
1507 | 106.00000 90.00000 -1.50000 1.00000 0.00000 \\ |
---|
1508 | 108.00000 90.00000 -1.50000 1.00000 0.00000} |
---|
1509 | } \\ |
---|
1510 | |
---|
1511 | In the other case (longitude and latitude), input filename is init\_float. |
---|
1512 | Its format is: \\ |
---|
1513 | { \texttt{Long Lat depth nisobfl ngrpfl itrash}} |
---|
1514 | |
---|
1515 | \noindent with: |
---|
1516 | |
---|
1517 | - Long, Lat, depth : Longitude, latitude, depth |
---|
1518 | |
---|
1519 | - nisobfl: 0 for an isobar float, 1 for a float following the w velocity |
---|
1520 | |
---|
1521 | - ngrpfl : number to identify searcher group |
---|
1522 | |
---|
1523 | - itrash :set to 1; it is a dummy variable. |
---|
1524 | |
---|
1525 | \noindent Example: \\ |
---|
1526 | \noindent |
---|
1527 | { |
---|
1528 | \texttt{ |
---|
1529 | 20.0 0.0 0.0 0 1 1 \\ |
---|
1530 | -21.0 0.0 0.0 0 1 1 \\ |
---|
1531 | -22.0 0.0 0.0 0 1 1 \\ |
---|
1532 | -23.0 0.0 0.0 0 1 1 \\ |
---|
1533 | -24.0 0.0 0.0 0 1 1 } |
---|
1534 | } \\ |
---|
1535 | |
---|
1536 | \np{jpnfl}{jpnfl} is the total number of floats during the run. |
---|
1537 | When initial positions are read in a restart file (\np[=.true.]{ln_rstflo}{ln\_rstflo} ), |
---|
1538 | \np{jpnflnewflo}{jpnflnewflo} can be added in the initialization file. |
---|
1539 | |
---|
1540 | \subsubsection{Output data} |
---|
1541 | |
---|
1542 | \np{nn_writefl}{nn\_writefl} is the frequency of writing in float output file and \np{nn_stockfl}{nn\_stockfl} is the frequency of |
---|
1543 | creation of the float restart file. |
---|
1544 | |
---|
1545 | Output data can be written in ascii files (\np[=.true.]{ln_flo_ascii}{ln\_flo\_ascii}). |
---|
1546 | In that case, output filename is trajec\_float. |
---|
1547 | |
---|
1548 | Another possiblity of writing format is Netcdf (\np[=.false.]{ln_flo_ascii}{ln\_flo\_ascii}) with |
---|
1549 | \key{iomput} and outputs selected in iodef.xml. |
---|
1550 | Here it is an example of specification to put in files description section: |
---|
1551 | |
---|
1552 | \begin{xmllines} |
---|
1553 | <group id="1d_grid_T" name="auto" description="ocean T grid variables" > } |
---|
1554 | <file id="floats" description="floats variables"> } |
---|
1555 | <field ref="traj_lon" name="floats_longitude" freq_op="86400" />} |
---|
1556 | <field ref="traj_lat" name="floats_latitude" freq_op="86400" />} |
---|
1557 | <field ref="traj_dep" name="floats_depth" freq_op="86400" />} |
---|
1558 | <field ref="traj_temp" name="floats_temperature" freq_op="86400" />} |
---|
1559 | <field ref="traj_salt" name="floats_salinity" freq_op="86400" />} |
---|
1560 | <field ref="traj_dens" name="floats_density" freq_op="86400" />} |
---|
1561 | <field ref="traj_group" name="floats_group" freq_op="86400" />} |
---|
1562 | </file>} |
---|
1563 | </group>} |
---|
1564 | \end{xmllines} |
---|
1565 | |
---|
1566 | \section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})]{Harmonic analysis of tidal constituents (\protect\key{diaharm})} |
---|
1567 | \label{sec:DIA_diag_harm} |
---|
1568 | |
---|
1569 | %------------------------------------------nam_diaharm---------------------------------------------------- |
---|
1570 | % |
---|
1571 | \begin{listing} |
---|
1572 | \nlst{nam_diaharm} |
---|
1573 | \caption{\forcode{&nam_diaharm}} |
---|
1574 | \label{lst:nam_diaharm} |
---|
1575 | \end{listing} |
---|
1576 | %---------------------------------------------------------------------------------------------------------- |
---|
1577 | |
---|
1578 | A module is available to compute the amplitude and phase of tidal waves. |
---|
1579 | This on-line Harmonic analysis is actived with \key{diaharm}. |
---|
1580 | |
---|
1581 | Some parameters are available in namelist \nam{_diaharm}{\_diaharm}: |
---|
1582 | |
---|
1583 | - \np{nit000_han}{nit000\_han} is the first time step used for harmonic analysis |
---|
1584 | |
---|
1585 | - \np{nitend_han}{nitend\_han} is the last time step used for harmonic analysis |
---|
1586 | |
---|
1587 | - \np{nstep_han}{nstep\_han} is the time step frequency for harmonic analysis |
---|
1588 | |
---|
1589 | % - \np{nb_ana}{nb\_ana} is the number of harmonics to analyse |
---|
1590 | |
---|
1591 | - \np{tname}{tname} is an array with names of tidal constituents to analyse |
---|
1592 | |
---|
1593 | \np{nit000_han}{nit000\_han} and \np{nitend_han}{nitend\_han} must be between \np{nit000}{nit000} and \np{nitend}{nitend} of the simulation. |
---|
1594 | The restart capability is not implemented. |
---|
1595 | |
---|
1596 | The Harmonic analysis solve the following equation: |
---|
1597 | |
---|
1598 | \[ |
---|
1599 | h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i} |
---|
1600 | \] |
---|
1601 | |
---|
1602 | With $A_{j}$, $\nu_{j}$, $\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error. |
---|
1603 | $h_{i}$ is the sea level for the time $t_{i}$ and $A_{0}$ is the mean sea level. \\ |
---|
1604 | We can rewrite this equation: |
---|
1605 | |
---|
1606 | \[ |
---|
1607 | h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i} |
---|
1608 | \] |
---|
1609 | |
---|
1610 | with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ and $\phi_{j}=arctan(S_{j}/C_{j})$. |
---|
1611 | |
---|
1612 | We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave. |
---|
1613 | |
---|
1614 | \section[Transports across sections (\texttt{\textbf{key\_diadct}})]{Transports across sections (\protect\key{diadct})} |
---|
1615 | \label{sec:DIA_diag_dct} |
---|
1616 | |
---|
1617 | %------------------------------------------nam_diadct---------------------------------------------------- |
---|
1618 | |
---|
1619 | \begin{listing} |
---|
1620 | \nlst{nam_diadct} |
---|
1621 | \caption{\forcode{&nam_diadct}} |
---|
1622 | \label{lst:nam_diadct} |
---|
1623 | \end{listing} |
---|
1624 | %------------------------------------------------------------------------------------------------------------- |
---|
1625 | |
---|
1626 | A module is available to compute the transport of volume, heat and salt through sections. |
---|
1627 | This diagnostic is actived with \key{diadct}. |
---|
1628 | |
---|
1629 | Each section is defined by the coordinates of its 2 extremities. |
---|
1630 | The pathways between them are contructed using tools which can be found in \texttt{tools/SECTIONS\_DIADCT} |
---|
1631 | and are written in a binary file \texttt{section\_ijglobal.diadct} which is later read in by |
---|
1632 | \NEMO\ to compute on-line transports. |
---|
1633 | |
---|
1634 | The on-line transports module creates three output ascii files: |
---|
1635 | |
---|
1636 | - \texttt{volume\_transport} for volume transports (unit: $10^{6} m^{3} s^{-1}$) |
---|
1637 | |
---|
1638 | - \texttt{heat\_transport} for heat transports (unit: $10^{15} W$) |
---|
1639 | |
---|
1640 | - \texttt{salt\_transport} for salt transports (unit: $10^{9}Kg s^{-1}$) \\ |
---|
1641 | |
---|
1642 | Namelist variables in \nam{_diadct}{\_diadct} control how frequently the flows are summed and the time scales over which |
---|
1643 | they are averaged, as well as the level of output for debugging: |
---|
1644 | \np{nn_dct}{nn\_dct} : frequency of instantaneous transports computing |
---|
1645 | \np{nn_dctwri}{nn\_dctwri}: frequency of writing ( mean of instantaneous transports ) |
---|
1646 | \np{nn_debug}{nn\_debug} : debugging of the section |
---|
1647 | |
---|
1648 | \subsubsection{Creating a binary file containing the pathway of each section} |
---|
1649 | |
---|
1650 | In \texttt{tools/SECTIONS\_DIADCT/run}, |
---|
1651 | the file \textit{ {list\_sections.ascii\_global}} contains a list of all the sections that are to be computed |
---|
1652 | (this list of sections is based on MERSEA project metrics). |
---|
1653 | |
---|
1654 | Another file is available for the GYRE configuration (\texttt{ {list\_sections.ascii\_GYRE}}). |
---|
1655 | |
---|
1656 | Each section is defined by: \\ |
---|
1657 | \noindent { \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\ |
---|
1658 | with: |
---|
1659 | |
---|
1660 | - \texttt{long1 lat1}, coordinates of the first extremity of the section; |
---|
1661 | |
---|
1662 | - \texttt{long2 lat2}, coordinates of the second extremity of the section; |
---|
1663 | |
---|
1664 | - \texttt{nclass} the number of bounds of your classes (\eg\ bounds for 2 classes); |
---|
1665 | |
---|
1666 | - \texttt{okstrpond} to compute heat and salt transports, \texttt{nostrpond} if no; |
---|
1667 | |
---|
1668 | - \texttt{ice} to compute surface and volume ice transports, \texttt{noice} if no. \\ |
---|
1669 | |
---|
1670 | \noindent The results of the computing of transports, and the directions of positive and |
---|
1671 | negative flow do not depend on the order of the 2 extremities in this file. \\ |
---|
1672 | |
---|
1673 | \noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\ |
---|
1674 | { |
---|
1675 | \texttt{ |
---|
1676 | long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\ |
---|
1677 | classtype \\ |
---|
1678 | zbound1 \\ |
---|
1679 | zbound2 \\ |
---|
1680 | . \\ |
---|
1681 | . \\ |
---|
1682 | nclass-1 \\ |
---|
1683 | nclass} |
---|
1684 | } |
---|
1685 | |
---|
1686 | \noindent where \texttt{classtype} can be: |
---|
1687 | |
---|
1688 | - \texttt{zsal} for salinity classes |
---|
1689 | |
---|
1690 | - \texttt{ztem} for temperature classes |
---|
1691 | |
---|
1692 | - \texttt{zlay} for depth classes |
---|
1693 | |
---|
1694 | - \texttt{zsigi} for insitu density classes |
---|
1695 | |
---|
1696 | - \texttt{zsigp} for potential density classes \\ |
---|
1697 | |
---|
1698 | The script \texttt{job.ksh} computes the pathway for each section and creates a binary file |
---|
1699 | \texttt{section\_ijglobal.diadct} which is read by \NEMO. \\ |
---|
1700 | |
---|
1701 | It is possible to use this tools for new configuations: \texttt{job.ksh} has to be updated with |
---|
1702 | the coordinates file name and path. \\ |
---|
1703 | |
---|
1704 | Examples of two sections, the ACC\_Drake\_Passage with no classes, |
---|
1705 | and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\ |
---|
1706 | \noindent |
---|
1707 | { |
---|
1708 | \texttt{ |
---|
1709 | -68. -54.5 -60. -64.7 00 okstrpond noice ACC\_Drake\_Passage \\ |
---|
1710 | -80.5 22.5 -80.5 25.5 05 nostrpond noice ATL\_Cuba\_Florida \\ |
---|
1711 | ztem \\ |
---|
1712 | -2.0 \\ |
---|
1713 | 4.5 \\ |
---|
1714 | 7.0 \\ |
---|
1715 | 12.0 \\ |
---|
1716 | 40.0} |
---|
1717 | } |
---|
1718 | |
---|
1719 | \subsubsection{To read the output files} |
---|
1720 | |
---|
1721 | The output format is: \\ |
---|
1722 | { |
---|
1723 | \texttt{ |
---|
1724 | date, time-step number, section number, \\ |
---|
1725 | section name, section slope coefficient, class number, \\ |
---|
1726 | class name, class bound 1 , classe bound2, \\ |
---|
1727 | transport\_direction1, transport\_direction2, \\ |
---|
1728 | transport\_total} |
---|
1729 | } \\ |
---|
1730 | |
---|
1731 | For sections with classes, the first \texttt{nclass-1} lines correspond to the transport for each class and |
---|
1732 | the last line corresponds to the total transport summed over all classes. |
---|
1733 | For sections with no classes, class number \texttt{1} corresponds to \texttt{total class} and |
---|
1734 | this class is called \texttt{N}, meaning \texttt{none}. |
---|
1735 | |
---|
1736 | - \texttt{transport\_direction1} is the positive part of the transport ($\geq$ 0). |
---|
1737 | |
---|
1738 | - \texttt{transport\_direction2} is the negative part of the transport ($\leq$ 0). \\ |
---|
1739 | |
---|
1740 | \noindent The \texttt{section slope coefficient} gives information about the significance of transports signs and |
---|
1741 | direction: \\ |
---|
1742 | |
---|
1743 | \begin{table} |
---|
1744 | \begin{tabular}{|l|l|l|l|l|} |
---|
1745 | \hline |
---|
1746 | section slope coefficient & section type & direction 1 & direction 2 & total transport \\ |
---|
1747 | \hline |
---|
1748 | 0. & horizontal & northward & southward & postive: northward \\ |
---|
1749 | \hline |
---|
1750 | 1000. & vertical & eastward & westward & postive: eastward \\ |
---|
1751 | \hline |
---|
1752 | \texttt{$\neq$ 0, $\neq$ 1000.} & diagonal & eastward & westward & postive: eastward \\ |
---|
1753 | \hline |
---|
1754 | \end{tabular} |
---|
1755 | \end{table} |
---|
1756 | |
---|
1757 | \section{Diagnosing the steric effect in sea surface height} |
---|
1758 | \label{sec:DIA_steric} |
---|
1759 | |
---|
1760 | Changes in steric sea level are caused when changes in the density of the water column imply an expansion or |
---|
1761 | contraction of the column. |
---|
1762 | It is essentially produced through surface heating/cooling and to a lesser extent through non-linear effects of |
---|
1763 | the equation of state (cabbeling, thermobaricity...). |
---|
1764 | Non-Boussinesq models contain all ocean effects within the ocean acting on the sea level. |
---|
1765 | In particular, they include the steric effect. |
---|
1766 | In contrast, Boussinesq models, such as \NEMO, conserve volume, rather than mass, |
---|
1767 | and so do not properly represent expansion or contraction. |
---|
1768 | The steric effect is therefore not explicitely represented. |
---|
1769 | This approximation does not represent a serious error with respect to the flow field calculated by the model |
---|
1770 | \citep{greatbatch_JGR94}, but extra attention is required when investigating sea level, |
---|
1771 | as steric changes are an important contribution to local changes in sea level on seasonal and climatic time scales. |
---|
1772 | This is especially true for investigation into sea level rise due to global warming. |
---|
1773 | |
---|
1774 | Fortunately, the steric contribution to the sea level consists of a spatially uniform component that |
---|
1775 | can be diagnosed by considering the mass budget of the world ocean \citep{greatbatch_JGR94}. |
---|
1776 | In order to better understand how global mean sea level evolves and thus how the steric sea level can be diagnosed, |
---|
1777 | we compare, in the following, the non-Boussinesq and Boussinesq cases. |
---|
1778 | |
---|
1779 | Let denote |
---|
1780 | $\mathcal{M}$ the total mass of liquid seawater ($\mathcal{M} = \int_D \rho dv$), |
---|
1781 | $\mathcal{V}$ the total volume of seawater ($\mathcal{V} = \int_D dv$), |
---|
1782 | $\mathcal{A}$ the total surface of the ocean ($\mathcal{A} = \int_S ds$), |
---|
1783 | $\bar{\rho}$ the global mean seawater (\textit{in situ}) density |
---|
1784 | ($\bar{\rho} = 1/\mathcal{V} \int_D \rho \,dv$), and |
---|
1785 | $\bar{\eta}$ the global mean sea level |
---|
1786 | ($\bar{\eta} = 1/\mathcal{A} \int_S \eta \,ds$). |
---|
1787 | |
---|
1788 | A non-Boussinesq fluid conserves mass. It satisfies the following relations: |
---|
1789 | |
---|
1790 | \begin{equation} |
---|
1791 | \begin{split} |
---|
1792 | \mathcal{M} &= \mathcal{V} \;\bar{\rho} \\ |
---|
1793 | \mathcal{V} &= \mathcal{A} \;\bar{\eta} |
---|
1794 | \end{split} |
---|
1795 | \label{eq:DIA_MV_nBq} |
---|
1796 | \end{equation} |
---|
1797 | |
---|
1798 | Temporal changes in total mass is obtained from the density conservation equation: |
---|
1799 | |
---|
1800 | \begin{equation} |
---|
1801 | \frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} ) |
---|
1802 | = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface} |
---|
1803 | \label{eq:DIA_Co_nBq} |
---|
1804 | \end{equation} |
---|
1805 | |
---|
1806 | where $\rho$ is the \textit{in situ} density, and \textit{emp} the surface mass exchanges with the other media of |
---|
1807 | the Earth system (atmosphere, sea-ice, land). |
---|
1808 | Its global averaged leads to the total mass change |
---|
1809 | |
---|
1810 | \begin{equation} |
---|
1811 | \partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}} |
---|
1812 | \label{eq:DIA_Mass_nBq} |
---|
1813 | \end{equation} |
---|
1814 | |
---|
1815 | where $\overline{\textit{emp}} = \int_S \textit{emp}\,ds$ is the net mass flux through the ocean surface. |
---|
1816 | Bringing \autoref{eq:DIA_Mass_nBq} and the time derivative of \autoref{eq:DIA_MV_nBq} together leads to |
---|
1817 | the evolution equation of the mean sea level |
---|
1818 | |
---|
1819 | \begin{equation} |
---|
1820 | \partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}} |
---|
1821 | - \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}} |
---|
1822 | \label{eq:DIA_ssh_nBq} |
---|
1823 | \end{equation} |
---|
1824 | |
---|
1825 | The first term in equation \autoref{eq:DIA_ssh_nBq} alters sea level by adding or subtracting mass from the ocean. |
---|
1826 | The second term arises from temporal changes in the global mean density; \ie\ from steric effects. |
---|
1827 | |
---|
1828 | In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ appears multiplied by |
---|
1829 | the gravity (\ie\ in the hydrostatic balance of the primitive Equations). |
---|
1830 | In particular, the mass conservation equation, \autoref{eq:DIA_Co_nBq}, degenerates into the incompressibility equation: |
---|
1831 | |
---|
1832 | \[ |
---|
1833 | \frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface} |
---|
1834 | % \label{eq:DIA_Co_Bq} |
---|
1835 | \] |
---|
1836 | |
---|
1837 | and the global average of this equation now gives the temporal change of the total volume, |
---|
1838 | |
---|
1839 | \[ |
---|
1840 | \partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o} |
---|
1841 | % \label{eq:DIA_V_Bq} |
---|
1842 | \] |
---|
1843 | |
---|
1844 | Only the volume is conserved, not mass, or, more precisely, the mass which is conserved is the Boussinesq mass, |
---|
1845 | $\mathcal{M}_o = \rho_o \mathcal{V}$. |
---|
1846 | The total volume (or equivalently the global mean sea level) is altered only by net volume fluxes across |
---|
1847 | the ocean surface, not by changes in mean mass of the ocean: the steric effect is missing in a Boussinesq fluid. |
---|
1848 | |
---|
1849 | Nevertheless, following \citep{greatbatch_JGR94}, the steric effect on the volume can be diagnosed by |
---|
1850 | considering the mass budget of the ocean. |
---|
1851 | The apparent changes in $\mathcal{M}$, mass of the ocean, which are not induced by surface mass flux |
---|
1852 | must be compensated by a spatially uniform change in the mean sea level due to expansion/contraction of the ocean |
---|
1853 | \citep{greatbatch_JGR94}. |
---|
1854 | In others words, the Boussinesq mass, $\mathcal{M}_o$, can be related to $\mathcal{M}$, |
---|
1855 | the total mass of the ocean seen by the Boussinesq model, via the steric contribution to the sea level, |
---|
1856 | $\eta_s$, a spatially uniform variable, as follows: |
---|
1857 | |
---|
1858 | \begin{equation} |
---|
1859 | \mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A} |
---|
1860 | \label{eq:DIA_M_Bq} |
---|
1861 | \end{equation} |
---|
1862 | |
---|
1863 | Any change in $\mathcal{M}$ which cannot be explained by the net mass flux through the ocean surface |
---|
1864 | is converted into a mean change in sea level. |
---|
1865 | Introducing the total density anomaly, $\mathcal{D}= \int_D d_a \,dv$, |
---|
1866 | where $d_a = (\rho -\rho_o ) / \rho_o$ is the density anomaly used in \NEMO\ (cf. \autoref{subsec:TRA_eos}) |
---|
1867 | in \autoref{eq:DIA_M_Bq} leads to a very simple form for the steric height: |
---|
1868 | |
---|
1869 | \begin{equation} |
---|
1870 | \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D} |
---|
1871 | \label{eq:DIA_steric_Bq} |
---|
1872 | \end{equation} |
---|
1873 | |
---|
1874 | The above formulation of the steric height of a Boussinesq ocean requires four remarks. |
---|
1875 | First, one can be tempted to define $\rho_o$ as the initial value of $\mathcal{M}/\mathcal{V}$, |
---|
1876 | \ie\ set $\mathcal{D}_{t=0}=0$, so that the initial steric height is zero. |
---|
1877 | We do not recommend that. |
---|
1878 | Indeed, in this case $\rho_o$ depends on the initial state of the ocean. |
---|
1879 | Since $\rho_o$ has a direct effect on the dynamics of the ocean |
---|
1880 | (it appears in the pressure gradient term of the momentum equation) |
---|
1881 | it is definitively not a good idea when inter-comparing experiments. |
---|
1882 | We better recommend to fixe once for all $\rho_o$ to $1035\;Kg\,m^{-3}$. |
---|
1883 | This value is a sensible choice for the reference density used in a Boussinesq ocean climate model since, |
---|
1884 | with the exception of only a small percentage of the ocean, density in the World Ocean varies by no more than |
---|
1885 | 2$\%$ from this value (\cite{gill_bk82}, page 47). |
---|
1886 | |
---|
1887 | Second, we have assumed here that the total ocean surface, $\mathcal{A}$, |
---|
1888 | does not change when the sea level is changing as it is the case in all global ocean GCMs |
---|
1889 | (wetting and drying of grid point is not allowed). |
---|
1890 | |
---|
1891 | Third, the discretisation of \autoref{eq:DIA_steric_Bq} depends on the type of free surface which is considered. |
---|
1892 | In the non linear free surface case, \ie\ \np[=.true.]{ln_linssh}{ln\_linssh}, it is given by |
---|
1893 | |
---|
1894 | \[ |
---|
1895 | \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} }{ \sum_{i,\,j,\,k} e_{1t} e_{2t} e_{3t} } |
---|
1896 | % \label{eq:DIA_discrete_steric_Bq_nfs} |
---|
1897 | \] |
---|
1898 | |
---|
1899 | whereas in the linear free surface, |
---|
1900 | the volume above the \textit{z=0} surface must be explicitly taken into account to |
---|
1901 | better approximate the total ocean mass and thus the steric sea level: |
---|
1902 | |
---|
1903 | \[ |
---|
1904 | \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta } |
---|
1905 | { \sum_{i,\,j,\,k} e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} e_{1t}e_{2t} \eta } |
---|
1906 | % \label{eq:DIA_discrete_steric_Bq_fs} |
---|
1907 | \] |
---|
1908 | |
---|
1909 | The fourth and last remark concerns the effective sea level and the presence of sea-ice. |
---|
1910 | In the real ocean, sea ice (and snow above it) depresses the liquid seawater through its mass loading. |
---|
1911 | This depression is a result of the mass of sea ice/snow system acting on the liquid ocean. |
---|
1912 | There is, however, no dynamical effect associated with these depressions in the liquid ocean sea level, |
---|
1913 | so that there are no associated ocean currents. |
---|
1914 | Hence, the dynamically relevant sea level is the effective sea level, |
---|
1915 | \ie\ the sea level as if sea ice (and snow) were converted to liquid seawater \citep{campin.marshall.ea_OM08}. |
---|
1916 | However, in the current version of \NEMO\ the sea-ice is levitating above the ocean without mass exchanges between |
---|
1917 | ice and ocean. |
---|
1918 | Therefore the model effective sea level is always given by $\eta + \eta_s$, whether or not there is sea ice present. |
---|
1919 | |
---|
1920 | In AR5 outputs, the thermosteric sea level is demanded. |
---|
1921 | It is steric sea level due to changes in ocean density arising just from changes in temperature. |
---|
1922 | It is given by: |
---|
1923 | |
---|
1924 | \[ |
---|
1925 | \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv |
---|
1926 | % \label{eq:DIA_thermosteric_Bq} |
---|
1927 | \] |
---|
1928 | |
---|
1929 | where $S_o$ and $p_o$ are the initial salinity and pressure, respectively. |
---|
1930 | |
---|
1931 | Both steric and thermosteric sea level are computed in \mdl{diaar5}. |
---|
1932 | |
---|
1933 | \section{Other diagnostics} |
---|
1934 | \label{sec:DIA_diag_others} |
---|
1935 | |
---|
1936 | Aside from the standard model variables, other diagnostics can be computed on-line. |
---|
1937 | The available ready-to-add diagnostics modules can be found in directory DIA. |
---|
1938 | |
---|
1939 | \subsection[Depth of various quantities (\textit{diahth.F90})]{Depth of various quantities (\protect\mdl{diahth})} |
---|
1940 | |
---|
1941 | Among the available diagnostics the following ones are obtained when defining the \key{diahth} CPP key: |
---|
1942 | |
---|
1943 | - the mixed layer depth (based on a density criterion \citep{de-boyer-montegut.madec.ea_JGR04}) (\mdl{diahth}) |
---|
1944 | |
---|
1945 | - the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth}) |
---|
1946 | |
---|
1947 | - the depth of the 20\deg{C} isotherm (\mdl{diahth}) |
---|
1948 | |
---|
1949 | - the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth}) |
---|
1950 | |
---|
1951 | \begin{figure}[!t] |
---|
1952 | \centering |
---|
1953 | \includegraphics[width=0.66\textwidth]{Fig_mask_subasins} |
---|
1954 | \caption[Decomposition of the World Ocean to compute transports as well as |
---|
1955 | the meridional stream-function]{ |
---|
1956 | Decomposition of the World Ocean (here ORCA2) into sub-basin used in to |
---|
1957 | compute the heat and salt transports as well as the meridional stream-function: |
---|
1958 | Atlantic basin (red), Pacific basin (green), |
---|
1959 | Indian basin (blue), Indo-Pacific basin (blue+green). |
---|
1960 | Note that semi-enclosed seas (Red, Med and Baltic seas) as well as |
---|
1961 | Hudson Bay are removed from the sub-basins. |
---|
1962 | Note also that the Arctic Ocean has been split into Atlantic and |
---|
1963 | Pacific basins along the North fold line. |
---|
1964 | } |
---|
1965 | \label{fig:DIA_mask_subasins} |
---|
1966 | \end{figure} |
---|
1967 | |
---|
1968 | % ----------------------------------------------------------- |
---|
1969 | % CMIP specific diagnostics |
---|
1970 | % ----------------------------------------------------------- |
---|
1971 | \subsection[CMIP specific diagnostics (\textit{diaar5.F90}, \textit{diaptr.F90})]{CMIP specific diagnostics (\protect\mdl{diaar5})} |
---|
1972 | |
---|
1973 | A series of diagnostics has been added in the \mdl{diaar5} and \mdl{diaptr}. |
---|
1974 | In \mdl{diaar5} they correspond to outputs that are required for AR5 simulations (CMIP5) |
---|
1975 | (see also \autoref{sec:DIA_steric} for one of them). |
---|
1976 | The module \mdl{diaar5} is active when one of the following outputs is required : |
---|
1977 | global total volume (voltot), global mean ssh (sshtot), global total mass (masstot), global mean temperature (temptot), |
---|
1978 | global mean ssh steric (sshsteric), global mean ssh thermosteric (sshthster), global mean salinity (saltot), |
---|
1979 | sea water pressure at sea floor (botpres), dynamic sea surface height (sshdyn). |
---|
1980 | |
---|
1981 | In \mdl{diaptr} when \np[=.true.]{ln_diaptr}{ln\_diaptr} |
---|
1982 | (see the \nam{ptr}{ptr} namelist below) can be computed on-line the poleward heat and salt transports, |
---|
1983 | their advective and diffusive component, and the meriodional stream function . |
---|
1984 | When \np[=.true.]{ln_subbas}{ln\_subbas}, transports and stream function are computed for the Atlantic, Indian, |
---|
1985 | Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean. |
---|
1986 | The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays, |
---|
1987 | the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:DIA_mask_subasins}). |
---|
1988 | |
---|
1989 | %------------------------------------------namptr----------------------------------------- |
---|
1990 | |
---|
1991 | \begin{listing} |
---|
1992 | \nlst{namptr} |
---|
1993 | \caption{\forcode{&namptr}} |
---|
1994 | \label{lst:namptr} |
---|
1995 | \end{listing} |
---|
1996 | %----------------------------------------------------------------------------------------- |
---|
1997 | |
---|
1998 | % ----------------------------------------------------------- |
---|
1999 | % 25 hour mean and hourly Surface, Mid and Bed |
---|
2000 | % ----------------------------------------------------------- |
---|
2001 | \subsection{25 hour mean output for tidal models} |
---|
2002 | |
---|
2003 | %------------------------------------------nam_dia25h------------------------------------- |
---|
2004 | |
---|
2005 | \begin{listing} |
---|
2006 | \nlst{nam_dia25h} |
---|
2007 | \caption{\forcode{&nam_dia25h}} |
---|
2008 | \label{lst:nam_dia25h} |
---|
2009 | \end{listing} |
---|
2010 | %----------------------------------------------------------------------------------------- |
---|
2011 | |
---|
2012 | A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean. |
---|
2013 | The 25 hour mean is available for daily runs by summing up the 25 hourly instantananeous hourly values from |
---|
2014 | midnight at the start of the day to midight at the day end. |
---|
2015 | This diagnostic is actived with the logical $ln\_dia25h$. |
---|
2016 | |
---|
2017 | % ----------------------------------------------------------- |
---|
2018 | % Top Middle and Bed hourly output |
---|
2019 | % ----------------------------------------------------------- |
---|
2020 | \subsection{Top middle and bed hourly output} |
---|
2021 | |
---|
2022 | %------------------------------------------nam_diatmb----------------------------------------------------- |
---|
2023 | |
---|
2024 | \begin{listing} |
---|
2025 | \nlst{nam_diatmb} |
---|
2026 | \caption{\forcode{&nam_diatmb}} |
---|
2027 | \label{lst:nam_diatmb} |
---|
2028 | \end{listing} |
---|
2029 | %---------------------------------------------------------------------------------------------------------- |
---|
2030 | |
---|
2031 | A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables. |
---|
2032 | This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs. |
---|
2033 | The tidal signal is retained but the overall data usage is cut to just three vertical levels. |
---|
2034 | Also the bottom level is calculated for each cell. |
---|
2035 | This diagnostic is actived with the logical $ln\_diatmb$. |
---|
2036 | |
---|
2037 | % ----------------------------------------------------------- |
---|
2038 | % Courant numbers |
---|
2039 | % ----------------------------------------------------------- |
---|
2040 | \subsection{Courant numbers} |
---|
2041 | |
---|
2042 | Courant numbers provide a theoretical indication of the model's numerical stability. |
---|
2043 | The advective Courant numbers can be calculated according to |
---|
2044 | |
---|
2045 | \[ |
---|
2046 | C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}} |
---|
2047 | % \label{eq:DIA_CFL} |
---|
2048 | \] |
---|
2049 | |
---|
2050 | in the zonal, meridional and vertical directions respectively. |
---|
2051 | The vertical component is included although it is not strictly valid as the vertical velocity is calculated from |
---|
2052 | the continuity equation rather than as a prognostic variable. |
---|
2053 | Physically this represents the rate at which information is propogated across a grid cell. |
---|
2054 | Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step. |
---|
2055 | |
---|
2056 | The variables can be activated by setting the \np{nn_diacfl}{nn\_diacfl} namelist parameter to 1 in the \nam{ctl}{ctl} namelist. |
---|
2057 | The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. |
---|
2058 | In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of |
---|
2059 | where the maximum value occurs. |
---|
2060 | At the end of the model run the maximum value of $C_u$, $C_v$, and $C_w$ for the whole model run is printed along |
---|
2061 | with the coordinates of each. |
---|
2062 | The maximum values from the run are also copied to the ocean.output file. |
---|
2063 | |
---|
2064 | \onlyinsubfile{\input{../../global/epilogue}} |
---|
2065 | |
---|
2066 | \end{document} |
---|