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chap_misc.tex in NEMO/trunk/doc/latex/NEMO/subfiles – NEMO

source: NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex @ 11567

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1\documentclass[../main/NEMO_manual]{subfiles}
2
3\begin{document}
4% ================================================================
5% Chapter --- Miscellaneous Topics
6% ================================================================
7\chapter{Miscellaneous Topics}
8\label{chap:MISC}
9
10\chaptertoc
11
12\newpage
13
14% ================================================================
15% Representation of Unresolved Straits
16% ================================================================
17\section{Representation of unresolved straits}
18\label{sec:MISC_strait}
19
20In climate modeling, it often occurs that a crucial connections between water masses is broken as
21the grid mesh is too coarse to resolve narrow straits.
22For example, coarse grid spacing typically closes off the Mediterranean from the Atlantic at
23the Strait of Gibraltar.
24In this case, it is important for climate models to include the effects of salty water entering the Atlantic from
25the Mediterranean.
26Likewise, it is important for the Mediterranean to replenish its supply of water from the Atlantic to
27balance the net evaporation occurring over the Mediterranean region.
28This problem occurs even in eddy permitting simulations.
29For example, in ORCA 1/4\deg\ several straits of the Indonesian archipelago (Ombai, Lombok...)
30are much narrow than even a single ocean grid-point.
31
32We describe briefly here the two methods that can be used in \NEMO\ to handle such
33improperly resolved straits. The methods consist of opening the strait while ensuring
34that the mass exchanges through the strait are not too large by either artificially
35reducing the cross-sectional area of the strait grid-cells or, locally increasing the
36lateral friction.
37
38% -------------------------------------------------------------------------------------------------------------
39%       Hand made geometry changes
40% -------------------------------------------------------------------------------------------------------------
41\subsection{Hand made geometry changes}
42\label{subsec:MISC_strait_hand}
43
44The first method involves reducing the scale factor in the cross-strait direction to a
45value in better agreement with the true mean width of the strait
46(\autoref{fig:MISC_strait_hand}).  This technique is sometime called "partially open face"
47or "partially closed cells".  The key issue here is only to reduce the faces of $T$-cell
48(\ie\ change the value of the horizontal scale factors at $u$- or $v$-point) but not the
49volume of the $T$-cell.  Indeed, reducing the volume of strait $T$-cell can easily produce
50a numerical instability at that grid point which would require a reduction of the model
51time step.  Thus to instigate a local change in the width of a Strait requires two steps:
52
53\begin{itemize}
54
55\item Add \texttt{e1e2u} and \texttt{e1e2v} arrays to the \np{cn\_domcfg} file. These 2D
56arrays should contain the products of the unaltered values of: $\texttt{e1u}*\texttt{e2u}$
57and $\texttt{e1u}*\texttt{e2v}$ respectively. That is the original surface areas of $u$-
58and $v$- cells respectively.  These areas are usually defined by the corresponding product
59within the \NEMO\ code but the presence of \texttt{e1e2u} and \texttt{e1e2v} in the
60\np{cn\_domcfg} file will suppress this calculation and use the supplied fields instead.
61If the model domain is provided by user-supplied code in \mdl{usrdef\_hgr}, then this
62routine should also return \texttt{e1e2u} and \texttt{e1e2v} and set the integer return
63argument \texttt{ie1e2u\_v} to a non-zero value. Values other than 0 for this argument
64will suppress the calculation of the areas.
65
66\item Change values of \texttt{e2u} or \texttt{e1v} (either in the \np{cn\_domcfg} file or
67via code in  \mdl{usrdef\_hgr}), whereever a Strait reduction is required. The choice of
68whether to alter \texttt{e2u} or \texttt{e1v} depends. respectively,  on whether the
69Strait in question is North-South orientated (\eg\ Gibraltar) or East-West orientated (\eg
70Lombok).
71
72\end{itemize}
73
74The second method is to increase the viscous boundary layer thickness by a local increase
75of the fmask value at the coast. This method can also be effective in wider passages.  The
76concept is illustarted in the second part of  \autoref{fig:MISC_strait_hand} and changes
77to specific locations can be coded in \mdl{usrdef\_fmask}. The \forcode{usr_def_fmask}
78routine is always called after \texttt{fmask} has been defined according to the choice of
79lateral boundary condition as discussed in \autoref{sec:LBC_coast}. The default version of
80\mdl{usrdef\_fmask} contains settings specific to ORCA2 and ORCA1 configurations. These are
81meant as examples only; it is up to the user to verify settings and provide alternatives
82for their own configurations. The default \forcode{usr_def_fmask} makes no changes to
83\texttt{fmask} for any other configuration.
84
85%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
86\begin{figure}[!tbp]
87  \centering
88  \includegraphics[width=0.66\textwidth]{Fig_Gibraltar}
89  \includegraphics[width=0.66\textwidth]{Fig_Gibraltar2}
90  \caption[Two methods to defined the Gibraltar strait]{
91    Example of the Gibraltar strait defined in a 1\deg\ $\times$ 1\deg\ mesh.
92    \textit{Top}: using partially open cells.
93    The meridional scale factor at $v$-point is reduced on both sides of the strait to
94    account for the real width of the strait (about 20 km).
95    Note that the scale factors of the strait $T$-point remains unchanged.
96    \textit{Bottom}: using viscous boundary layers.
97    The four fmask parameters along the strait coastlines are set to a value larger than 4,
98    \ie\ "strong" no-slip case (see \autoref{fig:LBC_shlat}) creating a large viscous boundary layer
99    that allows a reduced transport through the strait.}
100  \label{fig:MISC_strait_hand}
101\end{figure}
102%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
103
104%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
105\begin{figure}[!tbp]
106  \centering
107  \includegraphics[width=0.66\textwidth]{Fig_closea_mask_example}
108  \caption[Mask fields for the \protect\mdl{closea} module]{
109    Example of mask fields for the \protect\mdl{closea} module.
110    \textit{Left}: a closea\_mask field;
111    \textit{Right}: a closea\_mask\_rnf field.
112    In this example, if \protect\np{ln\_closea} is set to \forcode{.true.},
113    the mean freshwater flux over each of the American Great Lakes will be set to zero,
114    and the total residual for all the lakes, if negative, will be put into
115    the St Laurence Seaway in the area shown.}
116  \label{fig:MISC_closea_mask_example}
117\end{figure}
118%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
119
120% ================================================================
121% Closed seas
122% ================================================================
123\section[Closed seas (\textit{closea.F90})]
124{Closed seas (\protect\mdl{closea})}
125\label{sec:MISC_closea}
126
127Some configurations include inland seas and lakes as ocean
128points. This is particularly the case for configurations that are
129coupled to an atmosphere model where one might want to include inland
130seas and lakes as ocean model points in order to provide a better
131bottom boundary condition for the atmosphere. However there is no
132route for freshwater to run off from the lakes to the ocean and this
133can lead to large drifts in the sea surface height over the lakes. The
134closea module provides options to either fill in closed seas and lakes
135at run time, or to set the net surface freshwater flux for each lake
136to zero and put the residual flux into the ocean.
137
138Prior to \NEMO\ 4 the locations of inland seas and lakes was set via
139hardcoded indices for various ORCA configurations. From \NEMO\ 4 onwards
140the inland seas and lakes are defined using mask fields in the
141domain configuration file. The options are as follows.
142
143\begin{enumerate}
144\item{{\bfseries No ``closea\_mask'' field is included in domain configuration
145  file.} In this case the closea module does nothing.}
146
147\item{{\bfseries A field called closea\_mask is included in the domain
148configuration file and ln\_closea=.false. in namelist namcfg.} In this
149case the inland seas defined by the closea\_mask field are filled in
150(turned to land points) at run time. That is every point in
151closea\_mask that is nonzero is set to be a land point.}
152
153\item{{\bfseries A field called closea\_mask is included in the domain
154configuration file and ln\_closea=.true. in namelist namcfg.} Each
155inland sea or group of inland seas is set to a positive integer value
156in the closea\_mask field (see \autoref{fig:MISC_closea_mask_example}
157for an example). The net surface flux over each inland sea or group of
158inland seas is set to zero each timestep and the residual flux is
159distributed over the global ocean (ie. all ocean points where
160closea\_mask is zero).}
161
162\item{{\bfseries Fields called closea\_mask and closea\_mask\_rnf are
163included in the domain configuration file and ln\_closea=.true. in
164namelist namcfg.} This option works as for option 3, except that if
165the net surface flux over an inland sea is negative (net
166precipitation) it is put into the ocean at specified runoff points. A
167net positive surface flux (net evaporation) is still spread over the
168global ocean. The mapping from inland seas to runoff points is defined
169by the closea\_mask\_rnf field. Each mapping is defined by a positive
170integer value for the inland sea(s) and the corresponding runoff
171points. An example is given in
172\autoref{fig:MISC_closea_mask_example}. If no mapping is provided for a
173particular inland sea then the residual is spread over the global
174ocean.}
175
176\item{{\bfseries Fields called closea\_mask and closea\_mask\_emp are
177included in the domain configuration file and ln\_closea=.true. in
178namelist namcfg.} This option works the same as option 4 except that
179the nonzero net surface flux is sent to the ocean at the specified
180runoff points regardless of whether it is positive or negative. The
181mapping from inland seas to runoff points in this case is defined by
182the closea\_mask\_emp field.}
183\end{enumerate}
184
185There is a python routine to create the closea\_mask fields and append
186them to the domain configuration file in the utils/tools/DOMAINcfg directory.
187
188% ================================================================
189% Sub-Domain Functionality
190% ================================================================
191\section{Sub-domain functionality}
192\label{sec:MISC_zoom}
193
194\subsection{Simple subsetting of input files via NetCDF attributes}
195
196The extended grids for use with the under-shelf ice cavities will result in redundant rows
197around Antarctica if the ice cavities are not active.  A simple mechanism for subsetting
198input files associated with the extended domains has been implemented to avoid the need to
199maintain different sets of input fields for use with or without active ice cavities.  This
200subsetting operates for the j-direction only and works by optionally looking for and using
201a global file attribute (named: \np{open\_ocean\_jstart}) to determine the starting j-row
202for input.  The use of this option is best explained with an example:
203\medskip
204
205\noindent Consider an ORCA1
206configuration using the extended grid domain configuration file: \ifile{eORCA1\_domcfg.nc}
207This file define a horizontal domain of 362x332.  The first row with
208open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran\ indexing)
209then the formally correct setting for \np{open\_ocean\_jstart} is 41.  Using this value as
210the first row to be read will result in a 362x292 domain which is the same size as the
211original ORCA1 domain.  Thus the extended domain configuration file can be used with all
212the original input files for ORCA1 if the ice cavities are not active (\np{ln\_isfcav =
213.false.}).  Full instructions for achieving this are:
214
215\begin{itemize}
216\item  Add the new attribute to any input files requiring a j-row offset, i.e:
217\begin{cmds}
218ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_domcfg.nc
219\end{cmds}
220
221\item Add the logical switch \np{ln\_use\_jattr} to \nam{cfg} in the configuration
222namelist (if it is not already there) and set \np{.true.}
223\end{itemize}
224
225\noindent Note that with this option, the j-size of the global domain is (extended
226j-size minus \np{open\_ocean\_jstart} + 1 ) and this must match the \texttt{jpjglo} value
227for the configuration. This means an alternative version of \ifile{eORCA1\_domcfg.nc} must
228be created for when \np{ln\_use\_jattr} is active. The \texttt{ncap2} tool provides a
229convenient way of achieving this:
230
231\begin{cmds}
232ncap2 -s 'jpjglo=292' eORCA1_domcfg.nc nORCA1_domcfg.nc
233\end{cmds}
234
235The domain configuration file is unique in this respect since it also contains the value of \jp{jpjglo}
236that is read and used by the model.
237Any other global, 2D and 3D, netcdf, input field can be prepared for use in a reduced domain by adding the
238\texttt{open\_ocean\_jstart} attribute to the file's global attributes.
239In particular this is true for any field that is read by \NEMO\ using the following optional argument to
240the appropriate call to \np{iom\_get}.
241
242\begin{forlines}
243lrowattr=ln_use_jattr
244\end{forlines}
245
246Currently, only the domain configuration variables make use of this optional argument so
247this facility is of little practical use except for tests where no other external input
248files are needed or you wish to use an extended domain configuration with inputs from
249earlier, non-extended configurations. Alternatively, it should be possible to exclude
250empty rows for extended domain, forced ocean runs using interpolation on the fly, by
251adding the optional argument to \texttt{iom\_get} calls for the weights and initial
252conditions. Experimenting with this remains an exercise for the user.
253
254% ================================================================
255% Accuracy and Reproducibility
256% ================================================================
257\section[Accuracy and reproducibility (\textit{lib\_fortran.F90})]
258{Accuracy and reproducibility (\protect\mdl{lib\_fortran})}
259\label{sec:MISC_fortran}
260
261\subsection[Issues with intrinsinc SIGN function (\texttt{\textbf{key\_nosignedzero}})]
262{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})}
263\label{subsec:MISC_sign}
264
265The SIGN(A, B) is the \fortran\ intrinsic function delivers the magnitude of A with the sign of B.
266For example, SIGN(-3.0,2.0) has the value 3.0.
267The problematic case is when the second argument is zero, because, on platforms that support IEEE arithmetic,
268zero is actually a signed number.
269There is a positive zero and a negative zero.
270
271In \fninety, the processor was required always to deliver a positive result for SIGN(A, B) if B was zero.
272Nevertheless, in \fninety, the processor is allowed to do the correct thing and deliver ABS(A) when
273B is a positive zero and -ABS(A) when B is a negative zero.
274This change in the specification becomes apparent only when B is of type real, and is zero,
275and the processor is capable of distinguishing between positive and negative zero,
276and B is negative real zero.
277Then SIGN delivers a negative result where, under \fninety\ rules, it used to return a positive result.
278This change may be especially sensitive for the ice model,
279so we overwrite the intrinsinc function with our own function simply performing :   \\
280\verb?   IF( B >= 0.e0 ) THEN   ;   SIGN(A,B) = ABS(A)  ?    \\
281\verb?   ELSE                   ;   SIGN(A,B) =-ABS(A)     ?  \\
282\verb?   ENDIF    ? \\
283This feature can be found in \mdl{lib\_fortran} module and is effective when \key{nosignedzero} is defined.
284We use a CPP key as the overwritting of a intrinsic function can present performance issues with
285some computers/compilers.
286
287
288\subsection{MPP reproducibility}
289\label{subsec:MISC_glosum}
290
291The numerical reproducibility of simulations on distributed memory parallel computers is a critical issue.
292In particular, within \NEMO\ global summation of distributed arrays is most susceptible to rounding errors,
293and their propagation and accumulation cause uncertainty in final simulation reproducibility on
294different numbers of processors.
295To avoid so, based on \citet{he.ding_JS01} review of different technics,
296we use a so called self-compensated summation method.
297The idea is to estimate the roundoff error, store it in a buffer, and then add it back in the next addition.
298
299Suppose we need to calculate $b = a_1 + a_2 + a_3$.
300The following algorithm will allow to split the sum in two
301($sum_1 = a_{1} + a_{2}$ and $b = sum_2 = sum_1 + a_3$) with exactly the same rounding errors as
302the sum performed all at once.
303\begin{align*}
304   sum_1 \ \  &= a_1 + a_2 \\
305   error_1     &= a_2 + ( a_1 - sum_1 ) \\
306   sum_2 \ \  &= sum_1 + a_3 + error_1 \\
307   error_2     &= a_3 + error_1 + ( sum_1 - sum_2 ) \\
308   b \qquad \ &= sum_2 \\
309\end{align*}
310An example of this feature can be found in \mdl{lib\_fortran} module.
311It is systematicallt used in glob\_sum function (summation over the entire basin excluding duplicated rows and
312columns due to cyclic or north fold boundary condition as well as overlap MPP areas).
313The self-compensated summation method should be used in all summation in i- and/or j-direction.
314See \mdl{closea} module for an example.
315Note also that this implementation may be sensitive to the optimization level.
316
317\subsection{MPP scalability}
318\label{subsec:MISC_mppsca}
319
320The default method of communicating values across the north-fold in distributed memory applications (\key{mpp\_mpi})
321uses a \textsc{MPI\_ALLGATHER} function to exchange values from each processing region in
322the northern row with every other processing region in the northern row.
323This enables a global width array containing the top 4 rows to be collated on every northern row processor and then
324folded with a simple algorithm.
325Although conceptually simple, this "All to All" communication will hamper performance scalability for
326large numbers of northern row processors.
327From version 3.4 onwards an alternative method is available which only performs direct "Peer to Peer" communications
328between each processor and its immediate "neighbours" across the fold line.
329This is achieved by using the default \textsc{MPI\_ALLGATHER} method during initialisation to
330help identify the "active" neighbours.
331Stored lists of these neighbours are then used in all subsequent north-fold exchanges to
332restrict exchanges to those between associated regions.
333The collated global width array for each region is thus only partially filled but is guaranteed to
334be set at all the locations actually required by each individual for the fold operation.
335This alternative method should give identical results to the default \textsc{ALLGATHER} method and
336is recommended for large values of \np{jpni}.
337The new method is activated by setting \np{ln\_nnogather} to be true (\nam{mpp}).
338The reproducibility of results using the two methods should be confirmed for each new,
339non-reference configuration.
340
341% ================================================================
342% Model optimisation, Control Print and Benchmark
343% ================================================================
344\section{Model optimisation, control print and benchmark}
345\label{sec:MISC_opt}
346%--------------------------------------------namctl-------------------------------------------------------
347
348\begin{listing}
349  \nlst{namctl}
350  \caption{\forcode{&namctl}}
351  \label{lst:namctl}
352\end{listing}
353%--------------------------------------------------------------------------------------------------------------
354
355Options are defined through the  \nam{ctl} namelist variables.
356
357\subsection{Vector optimisation}
358
359\key{vectopt\_loop} enables the internal loops to collapse.
360This is very a very efficient way to increase the length of vector calculations and thus
361to speed up the model on vector computers.
362
363% Add here also one word on NPROMA technique that has been found useless, since compiler have made significant progress during the last decade.
364
365% Add also one word on NEC specific optimisation (Novercheck option for example)
366
367\subsection{Control print}
368
369The \np{ln\_ctl} switch was originally used as a debugging option in two modes:
370
371\begin{enumerate}
372\item{\np{ln\_ctl}: compute and print the trends averaged over the interior domain in all TRA, DYN, LDF and
373ZDF modules.
374This option is very helpful when diagnosing the origin of an undesired change in model results. }
375
376\item{also \np{ln\_ctl} but using the nictl and njctl namelist parameters to check the source of differences between
377mono and multi processor runs.}
378\end{enumerate}
379
380However, in recent versions it has also been used to force all processors to assume the
381reporting role. Thus when \np{ln\_ctl} is true all processors produce their own versions
382of files such as: ocean.output, layout.dat, etc.  All such files, beyond the the normal
383reporting processor (narea == 1), are named with a \_XXXX extension to their name, where
384XXXX is a 4-digit area number (with leading zeros, if required). Other reporting files
385such as run.stat (and its netCDF counterpart: run.stat.nc) and tracer.stat contain global
386information and are only ever produced by the reporting master (narea == 1). For version
3874.0 a start has been made to return \np{ln\_ctl} to its original function by introducing
388a new control structure which allows finer control over which files are produced. This
389feature is still evolving but it does already allow the user to: select individually the
390production of run.stat and tracer.stat files and to toggle the production of other files
391on processors other than the reporting master. These other reporters can be a simple
392subset of processors as defined by a minimum, maximum and incremental processor number.
393
394Note, that production of the run.stat and tracer.stat files require global communications.
395For run.stat, these are global min and max operations to find metrics such as the gloabl
396maximum velocity. For tracer.stat these are global sums of tracer fields. To improve model
397performance these operations are disabled by default and, where necessary, any use of the
398global values have been replaced with local calculations. For example, checks on the CFL
399criterion are now done on the local domain and only reported if a breach is detected.
400
401Experienced users may wish to still monitor this information as a check on model progress.
402If so, the best compromise will be to activate the files with:
403
404\begin{verbatim}
405     sn_cfctl%l_config = .TRUE.
406       sn_cfctl%l_runstat = .TRUE.
407       sn_cfctl%l_trcstat = .TRUE.
408\end{verbatim}
409
410and to use the new time increment setting to ensure the values are collected and reported
411at a suitably long interval. For example:
412
413\begin{verbatim}
414       sn_cfctl%ptimincr  = 25
415\end{verbatim}
416
417will carry out the global communications and write the information every 25 timesteps. This
418increment also applies to the time.step file which is otherwise updated every timestep.
419
420% ================================================================
421\biblio
422
423\pindex
424
425\end{document}
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