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5\chapter{Miscellaneous Topics}
12\paragraph{Changes record} ~\\
15  \begin{tabularx}{\textwidth}{l||X|X}
16    Release & Author(s) & Modifications \\
17    \hline
18    {\em   4.0} & {\em ...} & {\em ...} \\
19    {\em   3.6} & {\em ...} & {\em ...} \\
20    {\em   3.4} & {\em ...} & {\em ...} \\
21    {\em <=3.4} & {\em ...} & {\em ...}
22  \end{tabularx}
27%% =================================================================================================
28\section{Representation of unresolved straits}
31In climate modeling, it often occurs that a crucial connections between water masses is broken as
32the grid mesh is too coarse to resolve narrow straits.
33For example, coarse grid spacing typically closes off the Mediterranean from the Atlantic at
34the Strait of Gibraltar.
35In this case, it is important for climate models to include the effects of salty water entering the Atlantic from
36the Mediterranean.
37Likewise, it is important for the Mediterranean to replenish its supply of water from the Atlantic to
38balance the net evaporation occurring over the Mediterranean region.
39This problem occurs even in eddy permitting simulations.
40For example, in ORCA 1/4\deg\ several straits of the Indonesian archipelago (Ombai, Lombok...)
41are much narrow than even a single ocean grid-point.
43We describe briefly here the two methods that can be used in \NEMO\ to handle such
44improperly resolved straits. The methods consist of opening the strait while ensuring
45that the mass exchanges through the strait are not too large by either artificially
46reducing the cross-sectional area of the strait grid-cells or, locally increasing the
47lateral friction.
49%% =================================================================================================
50\subsection{Hand made geometry changes}
53The first method involves reducing the scale factor in the cross-strait direction to a
54value in better agreement with the true mean width of the strait
55(\autoref{fig:MISC_strait_hand}).  This technique is sometime called "partially open face"
56or "partially closed cells".  The key issue here is only to reduce the faces of $T$-cell
57(\ie\ change the value of the horizontal scale factors at $u$- or $v$-point) but not the
58volume of the $T$-cell.  Indeed, reducing the volume of strait $T$-cell can easily produce
59a numerical instability at that grid point which would require a reduction of the model
60time step.  Thus to instigate a local change in the width of a Strait requires two steps:
64\item Add \texttt{e1e2u} and \texttt{e1e2v} arrays to the \np{cn_domcfg}{cn\_domcfg} file. These 2D
65arrays should contain the products of the unaltered values of: $\texttt{e1u}*\texttt{e2u}$
66and $\texttt{e1u}*\texttt{e2v}$ respectively. That is the original surface areas of $u$-
67and $v$- cells respectively.  These areas are usually defined by the corresponding product
68within the \NEMO\ code but the presence of \texttt{e1e2u} and \texttt{e1e2v} in the
69\np{cn_domcfg}{cn\_domcfg} file will suppress this calculation and use the supplied fields instead.
70If the model domain is provided by user-supplied code in \mdl{usrdef\_hgr}, then this
71routine should also return \texttt{e1e2u} and \texttt{e1e2v} and set the integer return
72argument \texttt{ie1e2u\_v} to a non-zero value. Values other than 0 for this argument
73will suppress the calculation of the areas.
75\item Change values of \texttt{e2u} or \texttt{e1v} (either in the \np{cn_domcfg}{cn\_domcfg} file or
76via code in  \mdl{usrdef\_hgr}), whereever a Strait reduction is required. The choice of
77whether to alter \texttt{e2u} or \texttt{e1v} depends. respectively,  on whether the
78Strait in question is North-South orientated (\eg\ Gibraltar) or East-West orientated (\eg
83The second method is to increase the viscous boundary layer thickness by a local increase
84of the fmask value at the coast. This method can also be effective in wider passages.  The
85concept is illustarted in the second part of  \autoref{fig:MISC_strait_hand} and changes
86to specific locations can be coded in \mdl{usrdef\_fmask}. The \forcode{usr_def_fmask}
87routine is always called after \texttt{fmask} has been defined according to the choice of
88lateral boundary condition as discussed in \autoref{sec:LBC_coast}. The default version of
89\mdl{usrdef\_fmask} contains settings specific to ORCA2 and ORCA1 configurations. These are
90meant as examples only; it is up to the user to verify settings and provide alternatives
91for their own configurations. The default \forcode{usr_def_fmask} makes no changes to
92\texttt{fmask} for any other configuration.
95  \centering
96  \includegraphics[width=0.66\textwidth]{MISC_Gibraltar}
97  \includegraphics[width=0.66\textwidth]{MISC_Gibraltar2}
98  \caption[Two methods to defined the Gibraltar strait]{
99    Example of the Gibraltar strait defined in a 1\deg\ $\times$ 1\deg\ mesh.
100    \textit{Top}: using partially open cells.
101    The meridional scale factor at $v$-point is reduced on both sides of the strait to
102    account for the real width of the strait (about 20 km).
103    Note that the scale factors of the strait $T$-point remains unchanged.
104    \textit{Bottom}: using viscous boundary layers.
105    The four fmask parameters along the strait coastlines are set to a value larger than 4,
106    \ie\ "strong" no-slip case (see \autoref{fig:LBC_shlat}) creating a large viscous boundary layer
107    that allows a reduced transport through the strait.}
108  \label{fig:MISC_strait_hand}
112  \centering
113  \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example}
114  \caption[Mask fields for the \protect\mdl{closea} module]{
115    Example of mask fields for the \protect\mdl{closea} module.
116    \textit{Left}: a closea\_mask field;
117    \textit{Right}: a closea\_mask\_rnf field.
118    In this example, if \protect\np{ln_closea}{ln\_closea} is set to \forcode{.true.},
119    the mean freshwater flux over each of the American Great Lakes will be set to zero,
120    and the total residual for all the lakes, if negative, will be put into
121    the St Laurence Seaway in the area shown.}
122  \label{fig:MISC_closea_mask_example}
125%% =================================================================================================
126\section[Closed seas (\textit{closea.F90})]{Closed seas (\protect\mdl{closea})}
129Some configurations include inland seas and lakes as ocean
130points. This is particularly the case for configurations that are
131coupled to an atmosphere model where one might want to include inland
132seas and lakes as ocean model points in order to provide a better
133bottom boundary condition for the atmosphere. However there is no
134route for freshwater to run off from the lakes to the ocean and this
135can lead to large drifts in the sea surface height over the lakes. The
136closea module provides options to either fill in closed seas and lakes
137at run time, or to set the net surface freshwater flux for each lake
138to zero and put the residual flux into the ocean.
140Prior to \NEMO\ 4 the locations of inland seas and lakes was set via
141hardcoded indices for various ORCA configurations. From \NEMO\ 4 onwards
142the inland seas and lakes are defined using mask fields in the
143domain configuration file. The options are as follows.
146\item {{\bfseries No ``closea\_mask'' field is included in domain configuration
147  file.} In this case the closea module does nothing.}
149\item {{\bfseries A field called closea\_mask is included in the domain
150configuration file and ln\_closea=.false. in namelist namcfg.} In this
151case the inland seas defined by the closea\_mask field are filled in
152(turned to land points) at run time. That is every point in
153closea\_mask that is nonzero is set to be a land point.}
155\item {{\bfseries A field called closea\_mask is included in the domain
156configuration file and ln\_closea=.true. in namelist namcfg.} Each
157inland sea or group of inland seas is set to a positive integer value
158in the closea\_mask field (see \autoref{fig:MISC_closea_mask_example}
159for an example). The net surface flux over each inland sea or group of
160inland seas is set to zero each timestep and the residual flux is
161distributed over the global ocean (ie. all ocean points where
162closea\_mask is zero).}
164\item {{\bfseries Fields called closea\_mask and closea\_mask\_rnf are
165included in the domain configuration file and ln\_closea=.true. in
166namelist namcfg.} This option works as for option 3, except that if
167the net surface flux over an inland sea is negative (net
168precipitation) it is put into the ocean at specified runoff points. A
169net positive surface flux (net evaporation) is still spread over the
170global ocean. The mapping from inland seas to runoff points is defined
171by the closea\_mask\_rnf field. Each mapping is defined by a positive
172integer value for the inland sea(s) and the corresponding runoff
173points. An example is given in
174\autoref{fig:MISC_closea_mask_example}. If no mapping is provided for a
175particular inland sea then the residual is spread over the global
178\item {{\bfseries Fields called closea\_mask and closea\_mask\_emp are
179included in the domain configuration file and ln\_closea=.true. in
180namelist namcfg.} This option works the same as option 4 except that
181the nonzero net surface flux is sent to the ocean at the specified
182runoff points regardless of whether it is positive or negative. The
183mapping from inland seas to runoff points in this case is defined by
184the closea\_mask\_emp field.}
187There is a python routine to create the closea\_mask fields and append
188them to the domain configuration file in the utils/tools/DOMAINcfg directory.
190%% =================================================================================================
191\section{Sub-domain functionality}
194%% =================================================================================================
195\subsection{Simple subsetting of input files via NetCDF attributes}
197The extended grids for use with the under-shelf ice cavities will result in redundant rows
198around Antarctica if the ice cavities are not active.  A simple mechanism for subsetting
199input files associated with the extended domains has been implemented to avoid the need to
200maintain different sets of input fields for use with or without active ice cavities.  This
201subsetting operates for the j-direction only and works by optionally looking for and using
202a global file attribute (named: \np{open_ocean_jstart}{open\_ocean\_jstart}) to determine the starting j-row
203for input.  The use of this option is best explained with an example:
206\noindent Consider an ORCA1
207configuration using the extended grid domain configuration file: \ifile{eORCA1\}
208This file define a horizontal domain of 362x332.  The first row with
209open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran\ indexing)
210then the formally correct setting for \np{open_ocean_jstart}{open\_ocean\_jstart} is 41.  Using this value as
211the first row to be read will result in a 362x292 domain which is the same size as the
212original ORCA1 domain.  Thus the extended domain configuration file can be used with all
213the original input files for ORCA1 if the ice cavities are not active (\np{ln\_isfcav =
214.false.}).  Full instructions for achieving this are:
217\item Add the new attribute to any input files requiring a j-row offset, i.e:
219ncatted  -a open_ocean_jstart,global,a,d,41
222\item Add the logical switch \np{ln_use_jattr}{ln\_use\_jattr} to \nam{cfg}{cfg} in the configuration
223namelist (if it is not already there) and set \forcode{.true.}
226\noindent Note that with this option, the j-size of the global domain is (extended
227j-size minus \np{open_ocean_jstart}{open\_ocean\_jstart} + 1 ) and this must match the \texttt{jpjglo} value
228for the configuration. This means an alternative version of \ifile{eORCA1\} must
229be created for when \np{ln_use_jattr}{ln\_use\_jattr} is active. The \texttt{ncap2} tool provides a
230convenient way of achieving this:
233ncap2 -s 'jpjglo=292'
236The domain configuration file is unique in this respect since it also contains the value of \jp{jpjglo}
237that is read and used by the model.
238Any other global, 2D and 3D, netcdf, input field can be prepared for use in a reduced domain by adding the
239\texttt{open\_ocean\_jstart} attribute to the file's global attributes.
240In particular this is true for any field that is read by \NEMO\ using the following optional argument to
241the appropriate call to \np{iom_get}{iom\_get}.
247Currently, only the domain configuration variables make use of this optional argument so
248this facility is of little practical use except for tests where no other external input
249files are needed or you wish to use an extended domain configuration with inputs from
250earlier, non-extended configurations. Alternatively, it should be possible to exclude
251empty rows for extended domain, forced ocean runs using interpolation on the fly, by
252adding the optional argument to \texttt{iom\_get} calls for the weights and initial
253conditions. Experimenting with this remains an exercise for the user.
255%% =================================================================================================
256\section[Accuracy and reproducibility (\textit{lib\_fortran.F90})]{Accuracy and reproducibility (\protect\mdl{lib\_fortran})}
259%% =================================================================================================
260\subsection[Issues with intrinsinc SIGN function (\texttt{\textbf{key\_nosignedzero}})]{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})}
263The SIGN(A, B) is the \fortran\ intrinsic function delivers the magnitude of A with the sign of B.
264For example, SIGN(-3.0,2.0) has the value 3.0.
265The problematic case is when the second argument is zero, because, on platforms that support IEEE arithmetic,
266zero is actually a signed number.
267There is a positive zero and a negative zero.
269In \fninety, the processor was required always to deliver a positive result for SIGN(A, B) if B was zero.
270Nevertheless, in \fninety, the processor is allowed to do the correct thing and deliver ABS(A) when
271B is a positive zero and -ABS(A) when B is a negative zero.
272This change in the specification becomes apparent only when B is of type real, and is zero,
273and the processor is capable of distinguishing between positive and negative zero,
274and B is negative real zero.
275Then SIGN delivers a negative result where, under \fninety\ rules, it used to return a positive result.
276This change may be especially sensitive for the ice model,
277so we overwrite the intrinsinc function with our own function simply performing :   \\
278\verb?   IF( B >= 0.e0 ) THEN   ;   SIGN(A,B) = ABS(A)  ?    \\
279\verb?   ELSE                   ;   SIGN(A,B) =-ABS(A)     ?  \\
280\verb?   ENDIF    ? \\
281This feature can be found in \mdl{lib\_fortran} module and is effective when \key{nosignedzero} is defined.
282We use a CPP key as the overwritting of a intrinsic function can present performance issues with
283some computers/compilers.
285%% =================================================================================================
286\subsection{MPP reproducibility}
289The numerical reproducibility of simulations on distributed memory parallel computers is a critical issue.
290In particular, within \NEMO\ global summation of distributed arrays is most susceptible to rounding errors,
291and their propagation and accumulation cause uncertainty in final simulation reproducibility on
292different numbers of processors.
293To avoid so, based on \citet{he.ding_JS01} review of different technics,
294we use a so called self-compensated summation method.
295The idea is to estimate the roundoff error, store it in a buffer, and then add it back in the next addition.
297Suppose we need to calculate $b = a_1 + a_2 + a_3$.
298The following algorithm will allow to split the sum in two
299($sum_1 = a_{1} + a_{2}$ and $b = sum_2 = sum_1 + a_3$) with exactly the same rounding errors as
300the sum performed all at once.
302   sum_1 \ \  &= a_1 + a_2 \\
303   error_1     &= a_2 + ( a_1 - sum_1 ) \\
304   sum_2 \ \  &= sum_1 + a_3 + error_1 \\
305   error_2     &= a_3 + error_1 + ( sum_1 - sum_2 ) \\
306   b \qquad \ &= sum_2 \\
308An example of this feature can be found in \mdl{lib\_fortran} module.
309It is systematicallt used in glob\_sum function (summation over the entire basin excluding duplicated rows and
310columns due to cyclic or north fold boundary condition as well as overlap MPP areas).
311The self-compensated summation method should be used in all summation in i- and/or j-direction.
312See \mdl{closea} module for an example.
313Note also that this implementation may be sensitive to the optimization level.
315%% =================================================================================================
316\subsection{MPP scalability}
319The default method of communicating values across the north-fold in distributed memory applications (\key{mpp\_mpi})
320uses a \textsc{MPI\_ALLGATHER} function to exchange values from each processing region in
321the northern row with every other processing region in the northern row.
322This enables a global width array containing the top 4 rows to be collated on every northern row processor and then
323folded with a simple algorithm.
324Although conceptually simple, this "All to All" communication will hamper performance scalability for
325large numbers of northern row processors.
326From version 3.4 onwards an alternative method is available which only performs direct "Peer to Peer" communications
327between each processor and its immediate "neighbours" across the fold line.
328This is achieved by using the default \textsc{MPI\_ALLGATHER} method during initialisation to
329help identify the "active" neighbours.
330Stored lists of these neighbours are then used in all subsequent north-fold exchanges to
331restrict exchanges to those between associated regions.
332The collated global width array for each region is thus only partially filled but is guaranteed to
333be set at all the locations actually required by each individual for the fold operation.
334This alternative method should give identical results to the default \textsc{ALLGATHER} method and
335is recommended for large values of \np{jpni}{jpni}.
336The new method is activated by setting \np{ln_nnogather}{ln\_nnogather} to be true (\nam{mpp}{mpp}).
337The reproducibility of results using the two methods should be confirmed for each new,
338non-reference configuration.
340%% =================================================================================================
341\section{Model optimisation, control print and benchmark}
345  \nlst{namctl}
346  \caption{\forcode{&namctl}}
347  \label{lst:namctl}
350Options are defined through the  \nam{ctl}{ctl} namelist variables.
352%% =================================================================================================
353\subsection{Vector optimisation}
355\key{vectopt\_loop} enables the internal loops to collapse.
356This is very a very efficient way to increase the length of vector calculations and thus
357to speed up the model on vector computers.
359% Add here also one word on NPROMA technique that has been found useless, since compiler have made significant progress during the last decade.
361% Add also one word on NEC specific optimisation (Novercheck option for example)
363%% =================================================================================================
364\subsection{Status and debugging information output}
367NEMO can produce a range of text information output either: in the main output
368file (ocean.output) written by the normal reporting processor (narea == 1) or various
369specialist output files (e.g. layout.dat, run.stat, tracer.stat etc.). Some, for example
370run.stat and tracer.stat, contain globally collected values for which a single file is
371sufficient. Others, however, contain information that could, potentially, be different
372for each processing region. For computational efficiency, the default volume of text
373information produced is reduced to just a few files from the narea=1 processor.
375When more information is required for monitoring or debugging purposes, the various
376forms of output can be selected via the \np{sn\_cfctl} structure. As well as simple
377on-off switches this structure also allows selection of a range of processors for
378individual reporting (where appropriate) and a time-increment option to restrict
379globally collected values to specified time-step increments.
381Most options within the structure are influenced by the top-level switches shown here
382with their default settings:
385   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T
386     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following
389The first switch is a convenience option which can be used to switch on and off all
390sub-options. However, if it is false then switching off all sub-options is only done
391if \texttt{sn_cfctl%l\_config} is also false. Specifically, the logic is:
394  IF ( sn_cfctl%l_allon ) THEN
395    set all suboptions .TRUE.
396    and set procmin, procmax and procincr so that all regions are selected ([0,10000000,1], respectively)
397  ELSEIF ( sn_cfctl%l_config ) THEN
398    honour individual settings of the suboptions from the namelist
399  ELSE
400    set all suboptions .FALSE.
401  ENDIF
404Details of the suboptions follow but first an explanation of the stand-alone option:
405\texttt{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks
406carried out in \textt{stpctl.F90}. These checks detect probable numerical instabilites
407by searching for excessive sea surface heights or velocities and salinity values
408outside a sensible physical range. If breaches are detected then the default behaviour
409is to locate and report the local indices of the grid-point in breach. These indices
410are included in the error message that precedes the model shutdown. When true,
411\texttt{sn_cfctl%l_glochk} modifies this action by performing a global location of
412the various minimum and maximum values and the global indices are reported. This has
413some value in locating the most severe error in cases where the first detected error
414may not be the worst culprit.
416\subsubsection{Control print suboptions}
418The options that can be individually selected fall into three categories:
420\begin{enumerate} \item{Time step progress information} This category includes
421\texttt{run.stat} and \texttt{tracer.stat} files which record certain physical and
422passive tracer metrics (respectively). Typical contents of \texttt{run.stat} include
423global maximums of ssh, velocity; and global minimums and maximums of temperature
424and salinity.  A netCDF version of \texttt{run.stat} (\texttt{}) is also
425produced with the same time-series data and this can easily be expanded to include
426extra monitoring information.  \texttt{tracer.stat} contains the volume-weighted
427average tracer value for each passive tracer. Collecting these metrics involves
428global communications and will impact on model efficiency so both these options are
429disabled by default by setting the respective options, \texttt{sn\_cfctl%runstat} and
430\texttt{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or
431both of these options and setting the \texttt{sn\_cfctl%timincr} entry to an integer
432value greater than one. This increment determines the time-step frequency at which
433the global metrics are collected and reported.  This increment also applies to the
434time.step file which is otherwise updated every timestep.
435\item{One-time configuration information/progress logs}
437Some run-time configuration information and limited progress information is always
438produced by the first ocean process. This includes the \texttt{ocean.output} file
439which reports on all the namelist options read by the model and remains open to catch
440any warning or error messages generated during execution. A \texttt{layout.dat}
441file is also produced which details the MPI-decomposition used by the model. The
442suboptions: \texttt{sn\_cfctl%oceout} and \texttt{sn\_cfctl%layout} can be used
443to activate the creation of these files by all ocean processes.  For example,
444when \texttt{sn\_cfctl%oceout} is true all processors produce their own version of
445\texttt{ocean.output}.  All files, beyond the the normal reporting processor (narea == 1), are
446named with a \_XXXX extension to their name, where XXXX is a 4-digit area number (with
447leading zeros, if required). This is useful as a debugging aid since all processes can
448report their local conditions. Note though that these files are buffered on most UNIX
449systems so bug-hunting efforts using this facility should also utilise the \fortran:
452   CALL FLUSH(numout)
455statement after any additional write statements to ensure that file contents reflect
456the last model state. Associated with the \texttt{sn\_cfctl%oceout} option is the
457additional \texttt{sn\_cfctl%oasout} suboption. This does not activate its own output
458file but rather activates the writing of addition information regarding the OASIS
459configuration when coupling via oasis and the sbccpl routine. This information is
460written to any active \texttt{ocean.output} files.
461\item{Control sums of trends for debugging}
463NEMO includes an option for debugging reproducibility differences between
464a MPP and mono-processor runs.  This is somewhat dated and clearly only
465useful for this purpose when dealing with configurations that can be run
466on a single processor. The full details can be found in this report: \href{
468control print option in NEMO} The switches to activate production of the control sums
469of trends for either the physics or passive tracers are the \texttt{sn\_cfctl%prtctl}
470and \texttt{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its
471original intention, the ability to produce these control sums of trends in specific
472areas provides another tool for diagnosing model behaviour.  If only the output from a
473select few regions is required then additional options are available to activate options
474for only a simple subset of processing regions. These are: \texttt{sn\_cfctl%procmin},
475\texttt{sn\_cfctl%procmax} and \texttt{sn\_cfctl%procincr} which can be used to specify
476the minimum and maximum active areas and the increment. The default values are set
477such that all regions will be active. Note this subsetting can also be used to limit
478which additional \texttt{ocean.output} and \texttt{layout.dat} files are produced if
479those suboptions are active.
484   sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only
485   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T
486     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following
487       sn_cfctl%l_runstat = .FALSE. ! switches and which areas produce reports with the proc integer settings.
488       sn_cfctl%l_trcstat = .FALSE. ! The default settings for the proc integers should ensure
489       sn_cfctl%l_oceout  = .FALSE. ! that  all areas report.
490       sn_cfctl%l_layout  = .FALSE. !
491       sn_cfctl%l_prtctl  = .FALSE. !
492       sn_cfctl%l_prttrc  = .FALSE. !
493       sn_cfctl%l_oasout  = .FALSE. !
494       sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0]
495       sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000]
496       sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1]
497       sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info
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