1 | \documentclass[NEMO_book]{subfiles} |
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2 | \begin{document} |
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3 | % ================================================================ |
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4 | % Chapter --- Miscellaneous Topics |
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5 | % ================================================================ |
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6 | \chapter{Miscellaneous Topics} |
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7 | \label{MISC} |
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8 | \minitoc |
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9 | |
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10 | \newpage |
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11 | $\ $\newline % force a new ligne |
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12 | |
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13 | % ================================================================ |
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14 | % Representation of Unresolved Straits |
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15 | % ================================================================ |
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16 | \section{Representation of Unresolved Straits} |
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17 | \label{MISC_strait} |
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18 | |
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19 | In climate modeling, it often occurs that a crucial connections between water masses |
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20 | is broken as the grid mesh is too coarse to resolve narrow straits. For example, coarse |
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21 | grid spacing typically closes off the Mediterranean from the Atlantic at the Strait of |
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22 | Gibraltar. In this case, it is important for climate models to include the effects of salty |
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23 | water entering the Atlantic from the Mediterranean. Likewise, it is important for the |
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24 | Mediterranean to replenish its supply of water from the Atlantic to balance the net |
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25 | evaporation occurring over the Mediterranean region. This problem occurs even in |
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26 | eddy permitting simulations. For example, in ORCA 1/4\deg several straits of the Indonesian |
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27 | archipelago (Ombai, Lombok...) are much narrow than even a single ocean grid-point. |
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28 | |
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29 | We describe briefly here the three methods that can be used in \NEMO to handle |
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30 | such improperly resolved straits. The first two consist of opening the strait by hand |
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31 | while ensuring that the mass exchanges through the strait are not too large by |
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32 | either artificially reducing the surface of the strait grid-cells or, locally increasing |
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33 | the lateral friction. In the third one, the strait is closed but exchanges of mass, |
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34 | heat and salt across the land are allowed. |
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35 | Note that such modifications are so specific to a given configuration that no attempt |
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36 | has been made to set them in a generic way. However, examples of how |
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37 | they can be set up is given in the ORCA 2\deg and 0.5\deg configurations. For example, |
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38 | for details of implementation in ORCA2, search: |
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39 | \texttt{ IF( cp\_cfg == "orca" .AND. jp\_cfg == 2 ) } |
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40 | |
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41 | % ------------------------------------------------------------------------------------------------------------- |
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42 | % Hand made geometry changes |
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43 | % ------------------------------------------------------------------------------------------------------------- |
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44 | \subsection{Hand made geometry changes} |
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45 | \label{MISC_strait_hand} |
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46 | |
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47 | $\bullet$ reduced scale factor in the cross-strait direction to a value in better agreement |
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48 | with the true mean width of the strait. (Fig.~\ref{Fig_MISC_strait_hand}). |
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49 | This technique is sometime called "partially open face" or "partially closed cells". |
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50 | The key issue here is only to reduce the faces of $T$-cell ($i.e.$ change the value |
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51 | of the horizontal scale factors at $u$- or $v$-point) but not the volume of the $T$-cell. |
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52 | Indeed, reducing the volume of strait $T$-cell can easily produce a numerical |
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53 | instability at that grid point that would require a reduction of the model time step. |
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54 | The changes associated with strait management are done in \mdl{domhgr}, |
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55 | just after the definition or reading of the horizontal scale factors. |
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56 | |
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57 | $\bullet$ increase of the viscous boundary layer thickness by local increase of the |
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58 | fmask value at the coast (Fig.~\ref{Fig_MISC_strait_hand}). This is done in |
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59 | \mdl{dommsk} together with the setting of the coastal value of fmask |
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60 | (see Section \ref{LBC_coast}) |
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61 | |
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62 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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63 | \begin{figure}[!tbp] \begin{center} |
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64 | \includegraphics[width=0.80\textwidth]{Fig_Gibraltar} |
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65 | \includegraphics[width=0.80\textwidth]{Fig_Gibraltar2} |
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66 | \caption{ \protect\label{Fig_MISC_strait_hand} |
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67 | Example of the Gibraltar strait defined in a $1^{\circ} \times 1^{\circ}$ mesh. |
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68 | \textit{Top}: using partially open cells. The meridional scale factor at $v$-point |
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69 | is reduced on both sides of the strait to account for the real width of the strait |
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70 | (about 20 km). Note that the scale factors of the strait $T$-point remains unchanged. |
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71 | \textit{Bottom}: using viscous boundary layers. The four fmask parameters |
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72 | along the strait coastlines are set to a value larger than 4, $i.e.$ "strong" no-slip |
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73 | case (see Fig.\ref{Fig_LBC_shlat}) creating a large viscous boundary layer |
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74 | that allows a reduced transport through the strait.} |
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75 | \end{center} \end{figure} |
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76 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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77 | |
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78 | |
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79 | % ================================================================ |
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80 | % Closed seas |
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81 | % ================================================================ |
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82 | \section{Closed seas (\protect\mdl{closea})} |
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83 | \label{MISC_closea} |
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84 | |
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85 | \colorbox{yellow}{Add here a short description of the way closed seas are managed} |
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86 | |
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87 | |
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88 | % ================================================================ |
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89 | % Sub-Domain Functionality |
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90 | % ================================================================ |
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91 | \section{Sub-Domain Functionality} |
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92 | \label{MISC_zoom} |
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93 | |
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94 | \subsection{Simple subsetting of input files via netCDF attributes} |
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95 | |
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96 | The extended grids for use with the under-shelf ice cavities will result in redundant rows |
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97 | around Antarctica if the ice cavities are not active. A simple mechanism for subsetting |
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98 | input files associated with the extended domains has been implemented to avoid the need to |
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99 | maintain different sets of input fields for use with or without active ice cavities. The |
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100 | existing 'zoom' options are overly complex for this task and marked for deletion anyway. |
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101 | This alternative subsetting operates for the j-direction only and works by optionally |
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102 | looking for and using a global file attribute (named: \np{open\_ocean\_jstart}) to |
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103 | determine the starting j-row for input. The use of this option is best explained with an |
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104 | example: Consider an ORCA1 configuration using the extended grid bathymetry and coordinate |
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105 | files: |
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106 | \vspace{-10pt} |
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107 | \begin{alltt} |
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108 | \tiny |
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109 | \begin{verbatim} |
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110 | eORCA1_bathymetry_v2.nc |
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111 | eORCA1_coordinates.nc |
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112 | \end{verbatim} |
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113 | \end{alltt} |
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114 | \noindent These files define a horizontal domain of 362x332. Assuming the first row with |
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115 | open ocean wet points in the non-isf bathymetry for this set is row 42 (Fortran indexing) |
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116 | then the formally correct setting for \np{open\_ocean\_jstart} is 41. Using this value as the |
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117 | first row to be read will result in a 362x292 domain which is the same size as the original |
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118 | ORCA1 domain. Thus the extended coordinates and bathymetry files can be used with all the |
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119 | original input files for ORCA1 if the ice cavities are not active (\np{ln\_isfcav = |
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120 | .false.}). Full instructions for achieving this are: |
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121 | |
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122 | \noindent Add the new attribute to any input files requiring a j-row offset, i.e: |
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123 | \vspace{-10pt} |
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124 | \begin{alltt} |
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125 | \tiny |
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126 | \begin{verbatim} |
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127 | ncatted -a open_ocean_jstart,global,a,d,41 eORCA1_coordinates.nc |
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128 | ncatted -a open_ocean_jstart,global,a,d,41 eORCA1_bathymetry_v2.nc |
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129 | \end{verbatim} |
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130 | \end{alltt} |
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131 | |
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132 | \noindent Add the logical switch to \ngn{namcfg} in the configuration namelist and set true: |
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133 | %--------------------------------------------namcfg-------------------------------------------------------- |
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134 | \namdisplay{namcfg} |
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135 | %-------------------------------------------------------------------------------------------------------------- |
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136 | |
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137 | \noindent Note the j-size of the global domain is the (extended j-size minus |
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138 | \np{open\_ocean\_jstart} + 1 ) and this must match the size of all datasets other than |
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139 | bathymetry and coordinates currently. However the option can be extended to any global, 2D |
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140 | and 3D, netcdf, input field by adding the: |
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141 | \vspace{-10pt} |
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142 | \begin{alltt} |
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143 | \tiny |
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144 | \begin{verbatim} |
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145 | lrowattr=ln_use_jattr |
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146 | \end{verbatim} |
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147 | \end{alltt} |
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148 | optional argument to the appropriate \np{iom\_get} call and the \np{open\_ocean\_jstart} attribute to the corresponding input files. It remains the users responsibility to set \np{jpjdta} and \np{jpjglo} values in the \np{namelist\_cfg} file according to their needs. |
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149 | |
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150 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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151 | \begin{figure}[!ht] \begin{center} |
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152 | \includegraphics[width=0.90\textwidth]{Fig_LBC_zoom} |
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153 | \caption{ \protect\label{Fig_LBC_zoom} |
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154 | Position of a model domain compared to the data input domain when the zoom functionality is used.} |
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155 | \end{center} \end{figure} |
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156 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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157 | |
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158 | |
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159 | % ================================================================ |
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160 | % Accuracy and Reproducibility |
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161 | % ================================================================ |
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162 | \section{Accuracy and Reproducibility (\protect\mdl{lib\_fortran})} |
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163 | \label{MISC_fortran} |
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164 | |
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165 | \subsection{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})} |
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166 | \label{MISC_sign} |
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167 | |
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168 | The SIGN(A, B) is the \textsc {Fortran} intrinsic function delivers the magnitude |
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169 | of A with the sign of B. For example, SIGN(-3.0,2.0) has the value 3.0. |
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170 | The problematic case is when the second argument is zero, because, on platforms |
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171 | that support IEEE arithmetic, zero is actually a signed number. |
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172 | There is a positive zero and a negative zero. |
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173 | |
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174 | In \textsc{Fortran}~90, the processor was required always to deliver a positive result for SIGN(A, B) |
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175 | if B was zero. Nevertheless, in \textsc{Fortran}~95, the processor is allowed to do the correct thing |
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176 | and deliver ABS(A) when B is a positive zero and -ABS(A) when B is a negative zero. |
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177 | This change in the specification becomes apparent only when B is of type real, and is zero, |
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178 | and the processor is capable of distinguishing between positive and negative zero, |
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179 | and B is negative real zero. Then SIGN delivers a negative result where, under \textsc{Fortran}~90 |
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180 | rules, it used to return a positive result. |
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181 | This change may be especially sensitive for the ice model, so we overwrite the intrinsinc |
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182 | function with our own function simply performing : \\ |
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183 | \verb? IF( B >= 0.e0 ) THEN ; SIGN(A,B) = ABS(A) ? \\ |
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184 | \verb? ELSE ; SIGN(A,B) =-ABS(A) ? \\ |
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185 | \verb? ENDIF ? \\ |
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186 | This feature can be found in \mdl{lib\_fortran} module and is effective when \key{nosignedzero} |
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187 | is defined. We use a CPP key as the overwritting of a intrinsic function can present |
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188 | performance issues with some computers/compilers. |
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189 | |
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190 | |
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191 | \subsection{MPP reproducibility} |
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192 | \label{MISC_glosum} |
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193 | |
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194 | The numerical reproducibility of simulations on distributed memory parallel computers |
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195 | is a critical issue. In particular, within NEMO global summation of distributed arrays |
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196 | is most susceptible to rounding errors, and their propagation and accumulation cause |
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197 | uncertainty in final simulation reproducibility on different numbers of processors. |
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198 | To avoid so, based on \citet{He_Ding_JSC01} review of different technics, |
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199 | we use a so called self-compensated summation method. The idea is to estimate |
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200 | the roundoff error, store it in a buffer, and then add it back in the next addition. |
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201 | |
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202 | Suppose we need to calculate $b = a_1 + a_2 + a_3$. The following algorithm |
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203 | will allow to split the sum in two ($sum_1 = a_{1} + a_{2}$ and $b = sum_2 = sum_1 + a_3$) |
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204 | with exactly the same rounding errors as the sum performed all at once. |
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205 | \begin{align*} |
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206 | sum_1 \ \ &= a_1 + a_2 \\ |
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207 | error_1 &= a_2 + ( a_1 - sum_1 ) \\ |
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208 | sum_2 \ \ &= sum_1 + a_3 + error_1 \\ |
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209 | error_2 &= a_3 + error_1 + ( sum_1 - sum_2 ) \\ |
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210 | b \qquad \ &= sum_2 \\ |
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211 | \end{align*} |
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212 | An example of this feature can be found in \mdl{lib\_fortran} module. |
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213 | It is systematicallt used in glob\_sum function (summation over the entire basin excluding |
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214 | duplicated rows and columns due to cyclic or north fold boundary condition as well as |
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215 | overlap MPP areas). The self-compensated summation method should be used in all summation |
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216 | in i- and/or j-direction. See closea.F90 module for an example. |
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217 | Note also that this implementation may be sensitive to the optimization level. |
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218 | |
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219 | \subsection{MPP scalability} |
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220 | \label{MISC_mppsca} |
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221 | |
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222 | The default method of communicating values across the north-fold in distributed memory applications |
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223 | (\key{mpp\_mpi}) uses a \textsc{MPI\_ALLGATHER} function to exchange values from each processing |
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224 | region in the northern row with every other processing region in the northern row. This enables a |
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225 | global width array containing the top 4 rows to be collated on every northern row processor and then |
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226 | folded with a simple algorithm. Although conceptually simple, this "All to All" communication will |
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227 | hamper performance scalability for large numbers of northern row processors. From version 3.4 |
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228 | onwards an alternative method is available which only performs direct "Peer to Peer" communications |
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229 | between each processor and its immediate "neighbours" across the fold line. This is achieved by |
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230 | using the default \textsc{MPI\_ALLGATHER} method during initialisation to help identify the "active" |
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231 | neighbours. Stored lists of these neighbours are then used in all subsequent north-fold exchanges to |
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232 | restrict exchanges to those between associated regions. The collated global width array for each |
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233 | region is thus only partially filled but is guaranteed to be set at all the locations actually |
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234 | required by each individual for the fold operation. This alternative method should give identical |
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235 | results to the default \textsc{ALLGATHER} method and is recommended for large values of \np{jpni}. |
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236 | The new method is activated by setting \np{ln\_nnogather} to be true ({\bf nammpp}). The |
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237 | reproducibility of results using the two methods should be confirmed for each new, non-reference |
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238 | configuration. |
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239 | |
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240 | % ================================================================ |
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241 | % Model optimisation, Control Print and Benchmark |
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242 | % ================================================================ |
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243 | \section{Model Optimisation, Control Print and Benchmark} |
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244 | \label{MISC_opt} |
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245 | %--------------------------------------------namctl------------------------------------------------------- |
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246 | \namdisplay{namctl} |
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247 | %-------------------------------------------------------------------------------------------------------------- |
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248 | |
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249 | \gmcomment{why not make these bullets into subsections?} |
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250 | Options are defined through the \ngn{namctl} namelist variables. |
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251 | |
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252 | $\bullet$ Vector optimisation: |
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253 | |
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254 | \key{vectopt\_loop} enables the internal loops to collapse. This is very |
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255 | a very efficient way to increase the length of vector calculations and thus |
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256 | to speed up the model on vector computers. |
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257 | |
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258 | % Add here also one word on NPROMA technique that has been found useless, since compiler have made significant progress during the last decade. |
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259 | |
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260 | % Add also one word on NEC specific optimisation (Novercheck option for example) |
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261 | |
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262 | $\bullet$ Control print %: describe here 4 things: |
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263 | |
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264 | 1- \np{ln\_ctl} : compute and print the trends averaged over the interior domain |
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265 | in all TRA, DYN, LDF and ZDF modules. This option is very helpful when |
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266 | diagnosing the origin of an undesired change in model results. |
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267 | |
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268 | 2- also \np{ln\_ctl} but using the nictl and njctl namelist parameters to check |
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269 | the source of differences between mono and multi processor runs. |
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270 | |
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271 | %%gm to be removed both here and in the code |
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272 | 3- last digit comparison (\np{nn\_bit\_cmp}). In an MPP simulation, the computation of |
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273 | a sum over the whole domain is performed as the summation over all processors of |
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274 | each of their sums over their interior domains. This double sum never gives exactly |
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275 | the same result as a single sum over the whole domain, due to truncation differences. |
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276 | The "bit comparison" option has been introduced in order to be able to check that |
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277 | mono-processor and multi-processor runs give exactly the same results. |
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278 | %THIS is to be updated with the mpp_sum_glo introduced in v3.3 |
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279 | % nn_bit_cmp today only check that the nn_cla = 0 (no cross land advection) |
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280 | %%gm end |
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281 | |
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282 | $\bullet$ Benchmark (\np{nn\_bench}). This option defines a benchmark run based on |
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283 | a GYRE configuration (see \S\ref{CFG_gyre}) in which the resolution remains the same |
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284 | whatever the domain size. This allows a very large model domain to be used, just by |
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285 | changing the domain size (\jp{jpiglo}, \jp{jpjglo}) and without adjusting either the time-step |
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286 | or the physical parameterisations. |
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287 | |
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288 | % ================================================================ |
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289 | \end{document} |
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290 | |
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291 | |
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292 | |
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293 | |
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