10 |
%% o automatically inserted at \section{Reference} |
%% o automatically inserted at \section{Reference} |
11 |
|
|
12 |
|
|
13 |
\section{exch2: Extended Cubed Sphere \mbox{Topology}} |
\subsection{exch2: Extended Cubed Sphere \mbox{Topology}} |
14 |
\label{sec:exch2} |
\label{sec:exch2} |
15 |
|
|
16 |
|
|
17 |
\subsection{Introduction} |
\subsubsection{Introduction} |
18 |
|
|
19 |
The \texttt{exch2} package extends the original cubed sphere topology |
The \texttt{exch2} package extends the original cubed sphere topology |
20 |
configuration to allow more flexible domain decomposition and |
configuration to allow more flexible domain decomposition and |
23 |
dimensions of the subdomain. Furthermore, the tiles can run on |
dimensions of the subdomain. Furthermore, the tiles can run on |
24 |
separate processors individually or in groups, which provides for |
separate processors individually or in groups, which provides for |
25 |
manual compile-time load balancing across a relatively arbitrary |
manual compile-time load balancing across a relatively arbitrary |
26 |
number of processors. \\ |
number of processors. |
27 |
|
|
28 |
The exchange parameters are declared in |
The exchange parameters are declared in |
29 |
\filelink{pkg/exch2/W2\_EXCH2\_TOPOLOGY.h}{pkg-exch2-W2_EXCH2_TOPOLOGY.h} |
\filelink{pkg/exch2/W2\_EXCH2\_TOPOLOGY.h}{pkg-exch2-W2_EXCH2_TOPOLOGY.h} |
32 |
validity of the cube topology depends on the \file{SIZE.h} file as |
validity of the cube topology depends on the \file{SIZE.h} file as |
33 |
detailed below. The default files provided in the release configure a |
detailed below. The default files provided in the release configure a |
34 |
cubed sphere topology of six tiles, one per subdomain, each with |
cubed sphere topology of six tiles, one per subdomain, each with |
35 |
32$\times$32 grid points, all running on a single processor. Both |
32$\times$32 grid points, with all tiles running on a single processor. Both |
36 |
files are generated by Matlab scripts in |
files are generated by Matlab scripts in |
37 |
\file{utils/exch2/matlab-topology-generator}; see Section |
\file{utils/exch2/matlab-topology-generator}; see Section |
38 |
\ref{sec:topogen} \sectiontitle{Generating Topology Files for exch2} |
\ref{sec:topogen} \sectiontitle{Generating Topology Files for exch2} |
41 |
\file{utils/exch2/code-mods} along with the appropriate \file{SIZE.h} |
\file{utils/exch2/code-mods} along with the appropriate \file{SIZE.h} |
42 |
file for single-processor execution. |
file for single-processor execution. |
43 |
|
|
44 |
\subsection{Invoking exch2} |
\subsubsection{Invoking exch2} |
45 |
|
|
46 |
To use exch2 with the cubed sphere, the following conditions must be |
To use exch2 with the cubed sphere, the following conditions must be |
47 |
met: \\ |
met: |
48 |
|
|
49 |
$\bullet$ The exch2 package is included when \file{genmake2} is run. |
\begin{itemize} |
50 |
The easiest way to do this is to add the line \code{exch2} to the |
\item The exch2 package is included when \file{genmake2} is run. The |
51 |
\file{profile.conf} file -- see Section |
easiest way to do this is to add the line \code{exch2} to the |
52 |
\ref{sect:buildingCode} \sectiontitle{Building the code} for general |
\file{packages.conf} file -- see Section \ref{sect:buildingCode} |
53 |
details. \\ |
\sectiontitle{Building the code} for general |
54 |
|
details. |
55 |
|
|
56 |
$\bullet$ An example of \file{W2\_EXCH2\_TOPOLOGY.h} and |
\item An example of \file{W2\_EXCH2\_TOPOLOGY.h} and |
57 |
\file{w2\_e2setup.F} must reside in a directory containing files |
\file{w2\_e2setup.F} must reside in a directory containing files |
58 |
symbolically linked when \file{genmake2} runs. The safest place to |
symbolically linked by the \file{genmake2} script. The safest place |
59 |
put these is the directory indicated in the \code{-mods=DIR} command |
to put these is the directory indicated in the \code{-mods=DIR} |
60 |
line modifier (typically \file{../code}), or the build directory. |
command line modifier (typically \file{../code}), or the build |
61 |
The default versions of these files reside in \file{pkg/exch2} and |
directory. The default versions of these files reside in |
62 |
are linked automatically if no other versions exist elsewhere in the |
\file{pkg/exch2} and are linked automatically if no other versions |
63 |
build path, but they should be left untouched to avoid breaking |
exist elsewhere in the build path, but they should be left untouched |
64 |
configurations other than the one you intend to modify.\\ |
to avoid breaking configurations other than the one you intend to |
65 |
|
modify. |
66 |
$\bullet$ Files containing grid parameters, named |
|
67 |
\file{tile00$n$.mitgrid} where $n$=\code{(1:6)} (one per subdomain), |
\item Files containing grid parameters, named \file{tile00$n$.mitgrid} |
68 |
must be in the working directory when the MITgcm executable is run. |
where $n$=\code{(1:6)} (one per subdomain), must be in the working |
69 |
These files are provided in the example experiments for cubed sphere |
directory when the MITgcm executable is run. These files are |
70 |
configurations with 32$\times$32 cube sides and are non-trivial to |
provided in the example experiments for cubed sphere configurations |
71 |
generate -- please contact MITgcm support if you want to generate |
with 32$\times$32 cube sides -- please contact MITgcm support if you |
72 |
files for other configurations. \\ |
want to generate files for other configurations. |
73 |
|
|
74 |
$\bullet$ As always when compiling MITgcm, the file \file{SIZE.h} must |
\item As always when compiling MITgcm, the file \file{SIZE.h} must be |
75 |
be placed where \file{genmake2} will find it. In particular for |
placed where \file{genmake2} will find it. In particular for exch2, |
76 |
exch2, the domain decomposition specified in \file{SIZE.h} must |
the domain decomposition specified in \file{SIZE.h} must correspond |
77 |
correspond with the particular configuration's topology specified in |
with the particular configuration's topology specified in |
78 |
\file{W2\_EXCH2\_TOPOLOGY.h} and \file{w2\_e2setup.F}. Domain |
\file{W2\_EXCH2\_TOPOLOGY.h} and \file{w2\_e2setup.F}. Domain |
79 |
decomposition issues particular to exch2 are addressed in Section |
decomposition issues particular to exch2 are addressed in Section |
80 |
\ref{sec:topogen} \sectiontitle{Generating Topology Files for exch2} |
\ref{sec:topogen} \sectiontitle{Generating Topology Files for exch2} |
81 |
and \ref{sec:exch2mpi} \sectiontitle{exch2, SIZE.h, and MPI}; a more |
and \ref{sec:exch2mpi} \sectiontitle{exch2, SIZE.h, and |
82 |
general background on the subject relevant to MITgcm is presented in |
Multiprocessing}; a more general background on the subject |
83 |
Section \ref{sect:specifying_a_decomposition} |
relevant to MITgcm is presented in Section |
84 |
\sectiontitle{Specifying a decomposition}.\\ |
\ref{sect:specifying_a_decomposition} |
85 |
|
\sectiontitle{Specifying a decomposition}. |
86 |
|
\end{itemize} |
87 |
|
|
88 |
At the time of this writing the following examples use exch2 and may |
At the time of this writing the following examples use exch2 and may |
89 |
be used for guidance: |
be used for guidance: |
99 |
|
|
100 |
|
|
101 |
|
|
102 |
\subsection{Generating Topology Files for exch2} |
\subsubsection{Generating Topology Files for exch2} |
103 |
\label{sec:topogen} |
\label{sec:topogen} |
104 |
|
|
105 |
Alternate cubed sphere topologies may be created using the Matlab |
Alternate cubed sphere topologies may be created using the Matlab |
109 |
from the Matlab prompt (there are no parameters to pass) generates |
from the Matlab prompt (there are no parameters to pass) generates |
110 |
exch2 topology files \file{W2\_EXCH2\_TOPOLOGY.h} and |
exch2 topology files \file{W2\_EXCH2\_TOPOLOGY.h} and |
111 |
\file{w2\_e2setup.F} in the working directory and displays a figure of |
\file{w2\_e2setup.F} in the working directory and displays a figure of |
112 |
the topology via Matlab. The other m-files in the directory are |
the topology via Matlab -- figures \ref{fig:6tile}, \ref{fig:18tile}, |
113 |
subroutines of \file{driver.m} and should not be run ``bare'' except |
and \ref{fig:48tile} are examples of the generated diagrams. The other |
114 |
|
m-files in the directory are |
115 |
|
subroutines called from \file{driver.m} and should not be run ``bare'' except |
116 |
for development purposes. \\ |
for development purposes. \\ |
117 |
|
|
118 |
The parameters that determine the dimensions and topology of the |
The parameters that determine the dimensions and topology of the |
119 |
generated configuration are \code{nr}, \code{nb}, \code{ng}, |
generated configuration are \code{nr}, \code{nb}, \code{ng}, |
120 |
\code{tnx} and \code{tny}, and all are assigned early in the script. \\ |
\code{tnx} and \code{tny}, and all are assigned early in the script. \\ |
121 |
|
|
122 |
The first three determine the size of the subdomains and |
The first three determine the height and width of the subdomains and |
123 |
hence the size of the overall domain. Each one determines the number |
hence the size of the overall domain. Each one determines the number |
124 |
of grid points, and therefore the resolution, along the subdomain |
of grid points, and therefore the resolution, along the subdomain |
125 |
sides in a ``great circle'' around an axis of the cube. At the time |
sides in a ``great circle'' around each the three spatial axes of the cube. At the time |
126 |
of this writing MITgcm requires these three parameters to be equal, |
of this writing MITgcm requires these three parameters to be equal, |
127 |
but they provide for future releases to accomodate different |
but they provide for future releases to accomodate different |
128 |
resolutions around the axes to allow (for example) greater resolution |
resolutions around the axes to allow subdomains with differing resolutions.\\ |
|
around the equator.\\ |
|
129 |
|
|
130 |
The parameters \code{tnx} and \code{tny} determine the dimensions of |
The parameters \code{tnx} and \code{tny} determine the width and height of |
131 |
the tiles into which the subdomains are decomposed, and must evenly |
the tiles into which the subdomains are decomposed, and must evenly |
132 |
divide the integer assigned to \code{nr}, \code{nb} and \code{ng}. |
divide the integer assigned to \code{nr}, \code{nb} and \code{ng}. |
133 |
The result is a rectangular tiling of the subdomain. Figure |
The result is a rectangular tiling of the subdomain. Figure |
134 |
\ref{fig:24tile} shows one possible topology for a twenty-four-tile |
\ref{fig:48tile} shows one possible topology for a twenty-four-tile |
135 |
cube, and figure \ref{fig:12tile} shows one for twelve tiles. \\ |
cube, and figure \ref{fig:6tile} shows one for six tiles. \\ |
136 |
|
|
137 |
\begin{figure} |
\begin{figure} |
138 |
\begin{center} |
\begin{center} |
139 |
\resizebox{4in}{!}{ |
\resizebox{6in}{!}{ |
140 |
\includegraphics{part6/s24t_16x16.ps} |
% \includegraphics{part6/s24t_16x16.ps} |
141 |
|
\includegraphics{part6/adjust_cs.ps} |
142 |
} |
} |
143 |
\end{center} |
\end{center} |
144 |
|
|
145 |
\caption{Plot of a cubed sphere topology with a 32$\times$192 domain |
\caption{Plot of a cubed sphere topology with a 32$\times$192 domain |
146 |
divided into six 32$\times$32 subdomains, each of which is divided |
divided into six 32$\times$32 subdomains, each of which is divided |
147 |
into four tiles (\code{tnx=16, tny=16}) for a total of twenty-four |
into eight tiles of width \code{tnx=16} and height \code{tny=8} for a |
148 |
tiles. } \label{fig:24tile} |
total of forty-eight tiles. The colored borders of the subdomains |
149 |
|
represent the parameters \code{nr} (red), \code{ng} (green), and |
150 |
|
\code{nb} (blue). |
151 |
|
This tiling is used in the example |
152 |
|
verification/adjustment.cs-32x32x1/ |
153 |
|
with the option (blanklist.txt) to remove the land-only 4 tiles |
154 |
|
(11,12,13,14) which are filled in red on the plot. |
155 |
|
} \label{fig:48tile} |
156 |
\end{figure} |
\end{figure} |
157 |
|
|
158 |
\begin{figure} |
\begin{figure} |
159 |
\begin{center} |
\begin{center} |
160 |
\resizebox{4in}{!}{ |
\resizebox{6in}{!}{ |
161 |
\includegraphics{part6/s12t_16x32.ps} |
% \includegraphics{part6/s12t_16x32.ps} |
162 |
|
\includegraphics{part6/polarcap.ps} |
163 |
} |
} |
164 |
\end{center} |
\end{center} |
165 |
\caption{Plot of a cubed sphere topology with a 32$\times$192 domain |
\caption{Plot of a non-square cubed sphere topology with |
166 |
divided into six 32$\times$32 subdomains of two tiles each |
6 subdomains of different size (nr=90,ng=360,nb=90), |
167 |
(\code{tnx=16, tny=32}). |
divided into one to four tiles each |
168 |
} \label{fig:12tile} |
(\code{tnx=90, tny=90}), resulting in a total of 18 tiles. |
169 |
|
} \label{fig:18tile} |
170 |
\end{figure} |
\end{figure} |
171 |
|
|
172 |
\begin{figure} |
\begin{figure} |
173 |
\begin{center} |
\begin{center} |
174 |
\resizebox{4in}{!}{ |
\resizebox{4in}{!}{ |
175 |
|
% \includegraphics{part6/s6t_32x32.ps} |
176 |
\includegraphics{part6/s6t_32x32.ps} |
\includegraphics{part6/s6t_32x32.ps} |
177 |
} |
} |
178 |
\end{center} |
\end{center} |
194 |
|
|
195 |
|
|
196 |
|
|
197 |
\subsection{exch2, SIZE.h, and multiprocessing} |
\subsubsection{exch2, SIZE.h, and Multiprocessing} |
198 |
\label{sec:exch2mpi} |
\label{sec:exch2mpi} |
199 |
|
|
200 |
Once the topology configuration files are created, the Fortran |
Once the topology configuration files are created, the Fortran |
201 |
\code{PARAMETER}s in \file{SIZE.h} must be configured to match. |
\code{PARAMETER}s in \file{SIZE.h} must be configured to match. |
202 |
Section \ref{sect:specifying_a_decomposition} \sectiontitle{Specifying |
Section \ref{sect:specifying_a_decomposition} \sectiontitle{Specifying |
203 |
a decomposition} provides a general description of domain |
a decomposition} provides a general description of domain |
204 |
decomposition within MITgcm and its relation to \file{SIZE.h}. The |
decomposition within MITgcm and its relation to \file{SIZE.h}. The |
205 |
current section specifies certain constraints the exch2 package |
current section specifies constraints that the exch2 package imposes |
206 |
imposes as well as describes how to enable parallel execution with |
and describes how to enable parallel execution with MPI. |
|
MPI. \\ |
|
207 |
|
|
208 |
As in the general case, the parameters \varlink{sNx}{sNx} and |
As in the general case, the parameters \varlink{sNx}{sNx} and |
209 |
\varlink{sNy}{sNy} define the size of the individual tiles, and so |
\varlink{sNy}{sNy} define the size of the individual tiles, and so |
210 |
must be assigned the same respective values as \code{tnx} and |
must be assigned the same respective values as \code{tnx} and |
211 |
\code{tny} in \file{driver.m}.\\ |
\code{tny} in \file{driver.m}. |
212 |
|
|
213 |
The halo width parameters \varlink{OLx}{OLx} and \varlink{OLy}{OLy} |
The halo width parameters \varlink{OLx}{OLx} and \varlink{OLy}{OLy} |
214 |
have no special bearing on exch2 and may be assigned as in the general |
have no special bearing on exch2 and may be assigned as in the general |
215 |
case. The same holds for \varlink{Nr}{Nr}, the number of vertical |
case. The same holds for \varlink{Nr}{Nr}, the number of vertical |
216 |
levels in the model.\\ |
levels in the model. |
217 |
|
|
218 |
The parameters \varlink{nSx}{nSx}, \varlink{nSy}{nSy}, |
The parameters \varlink{nSx}{nSx}, \varlink{nSy}{nSy}, |
219 |
\varlink{nPx}{nPx}, and \varlink{nPy}{nPy} relate to the number of |
\varlink{nPx}{nPx}, and \varlink{nPy}{nPy} relate to the number of |
220 |
tiles and how they are distributed on processors. When using exch2, |
tiles and how they are distributed on processors. When using exch2, |
221 |
the tiles are stored in a single dimension, and so |
the tiles are stored in the $x$ dimension, and so |
222 |
\code{\varlink{nSy}{nSy}=1} in all cases. Since the tiles as |
\code{\varlink{nSy}{nSy}=1} in all cases. Since the tiles as |
223 |
configured by exch2 cannot be split up accross processors without |
configured by exch2 cannot be split up accross processors without |
224 |
regenerating the topology, \code{\varlink{nPy}{nPy}=1} as well. \\ |
regenerating the topology, \code{\varlink{nPy}{nPy}=1} as well. |
225 |
|
|
226 |
The number of tiles MITgcm allocates and how they are distributed |
The number of tiles MITgcm allocates and how they are distributed |
227 |
between processors depends on \varlink{nPx}{nPx} and |
between processors depends on \varlink{nPx}{nPx} and |
228 |
\varlink{nSx}{nSx}. \varlink{nSx}{nSx} is the number of tiles per |
\varlink{nSx}{nSx}. \varlink{nSx}{nSx} is the number of tiles per |
229 |
processor and \varlink{nPx}{nPx} the number of processors. The total |
processor and \varlink{nPx}{nPx} is the number of processors. The |
230 |
number of tiles in the topology minus those listed in |
total number of tiles in the topology minus those listed in |
231 |
\file{blanklist.txt} must equal \code{nSx*nPx}. \\ |
\file{blanklist.txt} must equal \code{nSx*nPx}. Note that in order to |
232 |
|
obtain maximum usage from a given number of processors in some cases, |
233 |
The following is an example of \file{SIZE.h} for the twelve-tile |
this restriction might entail sharing a processor with a tile that |
234 |
configuration illustrated in figure \ref{fig:12tile} running on |
would otherwise be excluded because it is topographically outside of |
235 |
one processor: \\ |
the domain and therefore in \file{blanklist.txt}. For example, |
236 |
|
suppose you have five processors and a domain decomposition of |
237 |
|
thirty-six tiles that allows you to exclude seven tiles. To evenly |
238 |
|
distribute the remaining twenty-nine tiles among five processors, you |
239 |
|
would have to run one ``dummy'' tile to make an even six tiles per |
240 |
|
processor. Such dummy tiles are \emph{not} listed in |
241 |
|
\file{blanklist.txt}. |
242 |
|
|
243 |
|
The following is an example of \file{SIZE.h} for the six-tile |
244 |
|
configuration illustrated in figure \ref{fig:6tile} |
245 |
|
running on one processor: |
246 |
|
|
247 |
\begin{verbatim} |
\begin{verbatim} |
248 |
PARAMETER ( |
PARAMETER ( |
249 |
& sNx = 16, |
& sNx = 32, |
250 |
& sNy = 32, |
& sNy = 32, |
251 |
& OLx = 2, |
& OLx = 2, |
252 |
& OLy = 2, |
& OLy = 2, |
253 |
& nSx = 12, |
& nSx = 6, |
254 |
& nSy = 1, |
& nSy = 1, |
255 |
& nPx = 1, |
& nPx = 1, |
256 |
& nPy = 1, |
& nPy = 1, |
259 |
& Nr = 5) |
& Nr = 5) |
260 |
\end{verbatim} |
\end{verbatim} |
261 |
|
|
262 |
The following is an example for the twenty-four-tile topology in |
The following is an example for the forty-eight-tile topology in |
263 |
figure \ref{fig:24tile} running on six processors: |
figure \ref{fig:48tile} running on six processors: |
264 |
|
|
265 |
\begin{verbatim} |
\begin{verbatim} |
266 |
PARAMETER ( |
PARAMETER ( |
267 |
& sNx = 16, |
& sNx = 16, |
268 |
& sNy = 16, |
& sNy = 8, |
269 |
& OLx = 2, |
& OLx = 2, |
270 |
& OLy = 2, |
& OLy = 2, |
271 |
& nSx = 4, |
& nSx = 8, |
272 |
& nSy = 1, |
& nSy = 1, |
273 |
& nPx = 6, |
& nPx = 6, |
274 |
& nPy = 1, |
& nPy = 1, |
278 |
\end{verbatim} |
\end{verbatim} |
279 |
|
|
280 |
|
|
281 |
|
\subsubsection{Key Variables} |
|
|
|
|
|
|
|
\subsection{Key Variables} |
|
282 |
|
|
283 |
The descriptions of the variables are divided up into scalars, |
The descriptions of the variables are divided up into scalars, |
284 |
one-dimensional arrays indexed to the tile number, and two and |
one-dimensional arrays indexed to the tile number, and two and |
288 |
arrays to individual tiles, and the arrays indexed by tile and |
arrays to individual tiles, and the arrays indexed by tile and |
289 |
neighbor to relationships between tiles and their neighbors. \\ |
neighbor to relationships between tiles and their neighbors. \\ |
290 |
|
|
291 |
\subsubsection{Scalars} |
Scalars: |
292 |
|
|
293 |
The number of tiles in a particular topology is set with the parameter |
The number of tiles in a particular topology is set with the parameter |
294 |
\code{NTILES}, and the maximum number of neighbors of any tiles by |
\code{NTILES}, and the maximum number of neighbors of any tiles by |
302 |
of tiles in the $x$ and $y$ global indices. For example, the default |
of tiles in the $x$ and $y$ global indices. For example, the default |
303 |
setup of six tiles (Fig. \ref{fig:6tile}) has |
setup of six tiles (Fig. \ref{fig:6tile}) has |
304 |
\code{exch2\_domain\_nxt=6} and \code{exch2\_domain\_nyt=1}. A |
\code{exch2\_domain\_nxt=6} and \code{exch2\_domain\_nyt=1}. A |
305 |
topology of twenty-four square tiles, four per subdomain (as in figure |
topology of forty-eight tiles, eight per subdomain (as in figure |
306 |
\ref{fig:24tile}), will have \code{exch2\_domain\_nxt=12} and |
\ref{fig:48tile}), will have \code{exch2\_domain\_nxt=12} and |
307 |
\code{exch2\_domain\_nyt=2}. Note that these parameters express the |
\code{exch2\_domain\_nyt=4}. Note that these parameters express the |
308 |
tile layout to allow global data files that are tile-layout-neutral |
tile layout in order to allow global data files that are tile-layout-neutral. |
309 |
and have no bearing on the internal storage of the arrays. The tiles |
They have no bearing on the internal storage of the arrays. The tiles |
310 |
are stored internally in a range from \code{(1:\varlink{bi}{bi})} the |
are stored internally in a range from \code{\varlink{bi}{bi}=(1:NTILES)} in the |
311 |
$x$ axis, and the $y$ axis variable \varlink{bj}{bj} generally is |
$x$ axis, and the $y$ axis variable \varlink{bj}{bj} is assumed to |
312 |
ignored within the package. \\ |
equal \code{1} throughout the package. \\ |
313 |
|
|
314 |
\subsubsection{Arrays Indexed to Tile Number} |
Arrays indexed to tile number: |
315 |
|
|
316 |
The following arrays are of length \code{NTILES} and are indexed to |
The following arrays are of length \code{NTILES} and are indexed to |
317 |
the tile number, which is indicated in the diagrams with the notation |
the tile number, which is indicated in the diagrams with the notation |
321 |
\varlink{exch2\_tny}{exch2_tny} express the $x$ and $y$ dimensions of |
\varlink{exch2\_tny}{exch2_tny} express the $x$ and $y$ dimensions of |
322 |
each tile. At present for each tile \texttt{exch2\_tnx=sNx} and |
each tile. At present for each tile \texttt{exch2\_tnx=sNx} and |
323 |
\texttt{exch2\_tny=sNy}, as assigned in \file{SIZE.h} and described in |
\texttt{exch2\_tny=sNy}, as assigned in \file{SIZE.h} and described in |
324 |
section \ref{sec:exch2mpi} \sectiontitle{exch2, SIZE.h, and |
Section \ref{sec:exch2mpi} \sectiontitle{exch2, SIZE.h, and |
325 |
multiprocessing}. Future releases of MITgcm are to allow varying tile |
Multiprocessing}. Future releases of MITgcm may allow varying tile |
326 |
sizes. \\ |
sizes. \\ |
327 |
|
|
328 |
The location of the tiles' Cartesian origin within a subdomain are |
The arrays \varlink{exch2\_tbasex}{exch2_tbasex} and |
329 |
determined by the arrays \varlink{exch2\_tbasex}{exch2_tbasex} and |
\varlink{exch2\_tbasey}{exch2_tbasey} determine the tiles' |
330 |
\varlink{exch2\_tbasey}{exch2_tbasey}. These variables are used to |
Cartesian origin within a subdomain |
331 |
relate the location of the edges of different tiles to each other. As |
and locate the edges of different tiles relative to each other. As |
332 |
an example, in the default six-tile topology (Fig. \ref{fig:6tile}) |
an example, in the default six-tile topology (Fig. \ref{fig:6tile}) |
333 |
each index in these arrays is set to \code{0} since a tile occupies |
each index in these arrays is set to \code{0} since a tile occupies |
334 |
its entire subdomain. The twenty-four-tile case discussed above will |
its entire subdomain. The twenty-four-tile case discussed above will |
335 |
have values of \code{0} or \code{16}, depending on the quadrant the |
have values of \code{0} or \code{16}, depending on the quadrant of the |
336 |
tile falls within the subdomain. The elements of the arrays |
tile within the subdomain. The elements of the arrays |
337 |
\varlink{exch2\_txglobalo}{exch2_txglobalo} and |
\varlink{exch2\_txglobalo}{exch2_txglobalo} and |
338 |
\varlink{exch2\_txglobalo}{exch2_txglobalo} are similar to |
\varlink{exch2\_txglobalo}{exch2_txglobalo} are similar to |
339 |
\varlink{exch2\_tbasex}{exch2_tbasex} and |
\varlink{exch2\_tbasex}{exch2_tbasex} and |
340 |
\varlink{exch2\_tbasey}{exch2_tbasey}, but locate the tiles within the |
\varlink{exch2\_tbasey}{exch2_tbasey}, but locate the tile edges within the |
341 |
global address space, similar to that used by global output and input |
global address space, similar to that used by global output and input |
342 |
files. \\ |
files. \\ |
343 |
|
|
344 |
The array \varlink{exch2\_myFace}{exch2_myFace} contains the number of |
The array \varlink{exch2\_myFace}{exch2_myFace} contains the number of |
345 |
the subdomain of each tile, in a range \code{(1:6)} in the case of the |
the subdomain of each tile, in a range \code{(1:6)} in the case of the |
346 |
standard cube topology and indicated by \textbf{\textsf{f}}$n$ in |
standard cube topology and indicated by \textbf{\textsf{f}}$n$ in |
347 |
figures \ref{fig:12tile} and |
figures \ref{fig:6tile} and |
348 |
\ref{fig:24tile}. \varlink{exch2\_nNeighbours}{exch2_nNeighbours} |
\ref{fig:48tile}. \varlink{exch2\_nNeighbours}{exch2_nNeighbours} |
349 |
contains a count of the neighboring tiles each tile has, and is used |
contains a count of the neighboring tiles each tile has, and sets |
350 |
for setting bounds for looping over neighboring tiles. |
the bounds for looping over neighboring tiles. |
351 |
\varlink{exch2\_tProc}{exch2_tProc} holds the process rank of each |
\varlink{exch2\_tProc}{exch2_tProc} holds the process rank of each |
352 |
tile, and is used in interprocess communication. \\ |
tile, and is used in interprocess communication. \\ |
353 |
|
|
356 |
\varlink{exch2\_isEedge}{exch2_isEedge}, |
\varlink{exch2\_isEedge}{exch2_isEedge}, |
357 |
\varlink{exch2\_isSedge}{exch2_isSedge}, and |
\varlink{exch2\_isSedge}{exch2_isSedge}, and |
358 |
\varlink{exch2\_isNedge}{exch2_isNedge} are set to \code{1} if the |
\varlink{exch2\_isNedge}{exch2_isNedge} are set to \code{1} if the |
359 |
indexed tile lies on the respective edge of a subdomain, \code{0} if |
indexed tile lies on the edge of its subdomain, \code{0} if |
360 |
not. The values are used within the topology generator to determine |
not. The values are used within the topology generator to determine |
361 |
the orientation of neighboring tiles, and to indicate whether a tile |
the orientation of neighboring tiles, and to indicate whether a tile |
362 |
lies on the corner of a subdomain. The latter case requires special |
lies on the corner of a subdomain. The latter case requires special |
364 |
corners of the cube. \\ |
corners of the cube. \\ |
365 |
|
|
366 |
|
|
367 |
\subsubsection{Arrays Indexed to Tile Number and Neighbor} |
Arrays Indexed to Tile Number and Neighbor: |
368 |
|
|
369 |
The following arrays have vectors of length \code{MAX\_NEIGHBOURS} and |
The following arrays have vectors of length \code{MAX\_NEIGHBOURS} and |
370 |
\code{NTILES} and describe the orientations between the the tiles. \\ |
\code{NTILES} and describe the orientations between the the tiles. \\ |
389 |
The arrays \varlink{exch2\_pi}{exch2_pi} and |
The arrays \varlink{exch2\_pi}{exch2_pi} and |
390 |
\varlink{exch2\_pj}{exch2_pj} specify the transformations of indices |
\varlink{exch2\_pj}{exch2_pj} specify the transformations of indices |
391 |
in exchanges between the neighboring tiles. These transformations are |
in exchanges between the neighboring tiles. These transformations are |
392 |
necessary in exchanges between subdomains because the array index in |
necessary in exchanges between subdomains because a horizontal dimension |
393 |
one dimension may map to the other index in an adjacent subdomain, and |
in one subdomain |
394 |
may be have its indexing reversed. This swapping arises from the |
may map to other horizonal dimension in an adjacent subdomain, and |
395 |
|
may also have its indexing reversed. This swapping arises from the |
396 |
``folding'' of two-dimensional arrays into a three-dimensional |
``folding'' of two-dimensional arrays into a three-dimensional |
397 |
cube. \\ |
cube. \\ |
398 |
|
|
400 |
are the neighbor ID \code{N} and the tile number \code{T} as explained |
are the neighbor ID \code{N} and the tile number \code{T} as explained |
401 |
above, plus a vector of length \code{2} containing transformation |
above, plus a vector of length \code{2} containing transformation |
402 |
factors \code{t}. The first element of the transformation vector |
factors \code{t}. The first element of the transformation vector |
403 |
holds the factor to multiply the index in the same axis, and the |
holds the factor to multiply the index in the same dimension, and the |
404 |
second element holds the the same for the orthogonal index. To |
second element holds the the same for the orthogonal dimension. To |
405 |
clarify, \code{exch2\_pi(1,N,T)} holds the mapping of the $x$ axis |
clarify, \code{exch2\_pi(1,N,T)} holds the mapping of the $x$ axis |
406 |
index of tile \code{T} to the $x$ axis of tile \code{T}'s neighbor |
index of tile \code{T} to the $x$ axis of tile \code{T}'s neighbor |
407 |
\code{N}, and \code{exch2\_pi(2,N,T)} holds the mapping of \code{T}'s |
\code{N}, and \code{exch2\_pi(2,N,T)} holds the mapping of \code{T}'s |
416 |
\code{(1,0)}, since all tiles on the same subdomain are oriented |
\code{(1,0)}, since all tiles on the same subdomain are oriented |
417 |
identically. An axis that corresponds to the orthogonal dimension |
identically. An axis that corresponds to the orthogonal dimension |
418 |
with the same index direction in a particular tile-neighbor |
with the same index direction in a particular tile-neighbor |
419 |
orientation will have \code{(0,1)}. Those in the opposite index |
orientation will have \code{(0,1)}. Those with the opposite index |
420 |
direction will have \code{(0,-1)} in order to reverse the ordering. \\ |
direction will have \code{(0,-1)} in order to reverse the ordering. \\ |
421 |
|
|
422 |
The arrays \varlink{exch2\_oi}{exch2_oi}, |
The arrays \varlink{exch2\_oi}{exch2_oi}, |
467 |
\varlink{exch2\_jthi\_c}{exch2_jthi_c} hold the location and index |
\varlink{exch2\_jthi\_c}{exch2_jthi_c} hold the location and index |
468 |
bounds of the edge segment of the neighbor tile \code{N}'s subdomain |
bounds of the edge segment of the neighbor tile \code{N}'s subdomain |
469 |
that gets exchanged with the local tile \code{T}. To take the example |
that gets exchanged with the local tile \code{T}. To take the example |
470 |
of tile \code{T=2} in the twelve-tile topology |
of tile \code{T=2} in the forty-eight-tile topology |
471 |
(Fig. \ref{fig:12tile}): \\ |
(Fig. \ref{fig:48tile}): \\ |
472 |
|
|
473 |
\begin{verbatim} |
\begin{verbatim} |
474 |
exch2_itlo_c(4,2)=17 |
exch2_itlo_c(4,2)=17 |
502 |
\code{Tn}'s $y$ axis corresponds to \code{T}'s $x$ axis, \code{T}'s |
\code{Tn}'s $y$ axis corresponds to \code{T}'s $x$ axis, \code{T}'s |
503 |
northern edge exchanges with \code{Tn}'s western edge. The western |
northern edge exchanges with \code{Tn}'s western edge. The western |
504 |
edge of the tiles corresponds to the lower bound of the $x$ axis, so |
edge of the tiles corresponds to the lower bound of the $x$ axis, so |
505 |
\code{exch2\_itlo\_c} \code{exch2\_ithi\_c} are \code{0}. The range of |
\code{exch2\_itlo\_c} and \code{exch2\_ithi\_c} are \code{0}, in the |
506 |
|
western halo region of \code{Tn}. The range of |
507 |
\code{exch2\_jtlo\_c} and \code{exch2\_jthi\_c} correspond to the |
\code{exch2\_jtlo\_c} and \code{exch2\_jthi\_c} correspond to the |
508 |
width of \code{T}'s northern edge, plus the halo. \\ |
width of \code{T}'s northern edge, expanded by one into the halo. \\ |
509 |
|
|
510 |
|
|
511 |
\subsection{Key Routines} |
\subsubsection{Key Routines} |
512 |
|
|
513 |
Most of the subroutines particular to exch2 handle the exchanges |
Most of the subroutines particular to exch2 handle the exchanges |
514 |
themselves and are of the same format as those described in |
themselves and are of the same format as those described in |
515 |
\ref{sect:cube_sphere_communication} \sectiontitle{Cube sphere |
\ref{sect:cube_sphere_communication} \sectiontitle{Cube sphere |
516 |
communication}. Like the original routines, they are written as |
communication}. Like the original routines, they are written as |
517 |
templates which the local Makefile converts from RX into RL and RS |
templates which the local Makefile converts from \code{RX} into |
518 |
forms. \\ |
\code{RL} and \code{RS} forms. \\ |
519 |
|
|
520 |
The interfaces with the core model subroutines are |
The interfaces with the core model subroutines are |
521 |
\code{EXCH\_UV\_XY\_RX}, \code{EXCH\_UV\_XYZ\_RX} and |
\code{EXCH\_UV\_XY\_RX}, \code{EXCH\_UV\_XYZ\_RX} and |
530 |
the singularities at the cube corners. \\ |
the singularities at the cube corners. \\ |
531 |
|
|
532 |
The separate scalar and vector forms of \code{EXCH2\_RX1\_CUBE} and |
The separate scalar and vector forms of \code{EXCH2\_RX1\_CUBE} and |
533 |
\code{EXCH2\_RX2\_CUBE} reflect that the vector-handling subrouine |
\code{EXCH2\_RX2\_CUBE} reflect that the vector-handling subroutine |
534 |
needs to pass both the $u$ and $v$ components of the phsical vectors. |
needs to pass both the $u$ and $v$ components of the physical vectors. |
535 |
This arises from the topological folding discussed above, where the |
This swapping arises from the topological folding discussed above, where the |
536 |
$x$ and $y$ axes get swapped in some cases. This swapping is not an |
$x$ and $y$ axes get swapped in some cases, and is not an |
537 |
issue with the scalar version. These subroutines call |
issue with the scalar case. These subroutines call |
538 |
\code{EXCH2\_SEND\_RX1} and \code{EXCH2\_SEND\_RX2}, which do most of |
\code{EXCH2\_SEND\_RX1} and \code{EXCH2\_SEND\_RX2}, which do most of |
539 |
the work using the variables discussed above. \\ |
the work using the variables discussed above. \\ |
540 |
|
|
541 |
|
\subsubsection{Experiments and tutorials that use exch2} |
542 |
|
\label{sec:pkg:exch2:experiments} |
543 |
|
|
544 |
|
\begin{itemize} |
545 |
|
\item{Held Suarez tutorial, in tutorial\_held\_suarez\_cs verification directory, |
546 |
|
described in section \ref{sect:eg-hs} } |
547 |
|
\end{itemize} |