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revision 1.18 by afe, Thu May 6 15:21:01 2004 UTC revision 1.22 by edhill, Tue Oct 12 18:16:03 2004 UTC
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12    
13  \section{exch2: Extended Cubed Sphere \mbox{Topology}}  \section{exch2: Extended Cubed Sphere \mbox{Topology}}
14  \label{sec:exch2}  \label{sec:exch2}
15    \label{sec:pkg:exch2}
16    \begin{rawhtml}
17    <!-- CMIREDIR:package_exch2: -->
18    \end{rawhtml}
19    
20    
21  \subsection{Introduction}  \subsection{Introduction}
# Line 44  file for single-processor execution. Line 48  file for single-processor execution.
48  \subsection{Invoking exch2}  \subsection{Invoking exch2}
49    
50  To use exch2 with the cubed sphere, the following conditions must be  To use exch2 with the cubed sphere, the following conditions must be
51  met: \\  met:
52    
53  $\bullet$ The exch2 package is included when \file{genmake2} is run.  \begin{itemize}
54    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
55    \file{profile.conf} file -- see Section    easiest way to do this is to add the line \code{exch2} to the
56    \ref{sect:buildingCode} \sectiontitle{Building the code} for general    \file{profile.conf} file -- see Section \ref{sect:buildingCode}
57    details. \\    \sectiontitle{Building the code} for general details.
58      
59  $\bullet$ An example of \file{W2\_EXCH2\_TOPOLOGY.h} and  \item An example of \file{W2\_EXCH2\_TOPOLOGY.h} and
60    \file{w2\_e2setup.F} must reside in a directory containing files    \file{w2\_e2setup.F} must reside in a directory containing files
61    symbolically linked when \file{genmake2} runs.  The safest place to    symbolically linked by the \file{genmake2} script.  The safest place
62    put these is the directory indicated in the \code{-mods=DIR} command    to put these is the directory indicated in the \code{-mods=DIR}
63    line modifier (typically \file{../code}), or the build directory.    command line modifier (typically \file{../code}), or the build
64    The default versions of these files reside in \file{pkg/exch2} and    directory.  The default versions of these files reside in
65    are linked automatically if no other versions exist elsewhere in the    \file{pkg/exch2} and are linked automatically if no other versions
66    build path, but they should be left untouched to avoid breaking    exist elsewhere in the build path, but they should be left untouched
67    configurations other than the one you intend to modify.\\    to avoid breaking configurations other than the one you intend to
68      modify.
69  $\bullet$ Files containing grid parameters, named    
70    \file{tile00$n$.mitgrid} where $n$=\code{(1:6)} (one per subdomain),  \item Files containing grid parameters, named \file{tile00$n$.mitgrid}
71    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
72    These files are provided in the example experiments for cubed sphere    directory when the MITgcm executable is run.  These files are
73    configurations with 32$\times$32 cube sides    provided in the example experiments for cubed sphere configurations
74    -- please contact MITgcm support if you want to generate    with 32$\times$32 cube sides -- please contact
75    files for other configurations. \\    \begin{rawhtml}
76        <A href="mailto:mitgcm-support@dev.mitgcm.org">
77  $\bullet$ As always when compiling MITgcm, the file \file{SIZE.h} must    \end{rawhtml}
78    be placed where \file{genmake2} will find it.  In particular for  \begin{verbatim}
79    exch2, the domain decomposition specified in \file{SIZE.h} must  MITgcm-support@mitgcm.org
80    correspond with the particular configuration's topology specified in  \end{verbatim}
81      \begin{rawhtml} </A> \end{rawhtml}
82      if you want to generate files for other configurations.
83      
84    \item As always when compiling MITgcm, the file \file{SIZE.h} must be
85      placed where \file{genmake2} will find it.  In particular for exch2,
86      the domain decomposition specified in \file{SIZE.h} must correspond
87      with the particular configuration's topology specified in
88    \file{W2\_EXCH2\_TOPOLOGY.h} and \file{w2\_e2setup.F}.  Domain    \file{W2\_EXCH2\_TOPOLOGY.h} and \file{w2\_e2setup.F}.  Domain
89    decomposition issues particular to exch2 are addressed in Section    decomposition issues particular to exch2 are addressed in Section
90    \ref{sec:topogen} \sectiontitle{Generating Topology Files for exch2}    \ref{sec:topogen} \sectiontitle{Generating Topology Files for exch2}
91    and \ref{sec:exch2mpi} \sectiontitle{exch2, SIZE.h, and MPI}; a more    and \ref{sec:exch2mpi} \sectiontitle{exch2, SIZE.h, and
92    general background on the subject relevant to MITgcm is presented in      Multiprocessing}; a more general background on the subject
93    Section \ref{sect:specifying_a_decomposition}    relevant to MITgcm is presented in Section
94    \sectiontitle{Specifying a decomposition}.\\    \ref{sect:specifying_a_decomposition} \sectiontitle{Specifying a
95        decomposition}.
96    \end{itemize}
97    
98    
99    
100  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
101  be used for guidance:  be used for guidance:
# Line 107  from the Matlab prompt (there are no par Line 122  from the Matlab prompt (there are no par
122  exch2 topology files \file{W2\_EXCH2\_TOPOLOGY.h} and  exch2 topology files \file{W2\_EXCH2\_TOPOLOGY.h} and
123  \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
124  the topology via Matlab -- figures \ref{fig:6tile}, \ref{fig:12tile},  the topology via Matlab -- figures \ref{fig:6tile}, \ref{fig:12tile},
125  and \ref{fig:24tile} are examples.  The other m-files in the directory are  and \ref{fig:24tile} are examples of the generated diagrams.  The other
126  subroutines of \file{driver.m} and should not be run ``bare'' except  m-files in the directory are
127    subroutines called from \file{driver.m} and should not be run ``bare'' except
128  for development purposes. \\  for development purposes. \\
129    
130  The parameters that determine the dimensions and topology of the  The parameters that determine the dimensions and topology of the
131  generated configuration are \code{nr}, \code{nb}, \code{ng},  generated configuration are \code{nr}, \code{nb}, \code{ng},
132  \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. \\
133    
134  The first three determine the size of the subdomains and  The first three determine the height and width of the subdomains and
135  hence the size of the overall domain.  Each one determines the number  hence the size of the overall domain.  Each one determines the number
136  of grid points, and therefore the resolution, along the subdomain  of grid points, and therefore the resolution, along the subdomain
137  sides in a ``great circle'' around each the three spatial axes of the cube.  At the time  sides in a ``great circle'' around each the three spatial axes of the cube.  At the time
138  of this writing MITgcm requires these three parameters to be equal,  of this writing MITgcm requires these three parameters to be equal,
139  but they provide for future releases  to accomodate different  but they provide for future releases  to accomodate different
140  resolutions around the axes to allow (for example) greater resolution  resolutions around the axes to allow subdomains with differing resolutions.\\
 around the equator.\\  
141    
142  The parameters \code{tnx} and \code{tny} determine the width and height of  The parameters \code{tnx} and \code{tny} determine the width and height of
143  the tiles into which the subdomains are decomposed, and must evenly  the tiles into which the subdomains are decomposed, and must evenly
# Line 182  by their tile number in the topology, se Line 197  by their tile number in the topology, se
197    
198    
199    
200  \subsection{exch2, SIZE.h, and multiprocessing}  \subsection{exch2, SIZE.h, and Multiprocessing}
201  \label{sec:exch2mpi}  \label{sec:exch2mpi}
202    
203  Once the topology configuration files are created, the Fortran  Once the topology configuration files are created, the Fortran
# Line 190  Once the topology configuration files ar Line 205  Once the topology configuration files ar
205  Section \ref{sect:specifying_a_decomposition} \sectiontitle{Specifying  Section \ref{sect:specifying_a_decomposition} \sectiontitle{Specifying
206  a decomposition} provides a general description of domain  a decomposition} provides a general description of domain
207  decomposition within MITgcm and its relation to \file{SIZE.h}. The  decomposition within MITgcm and its relation to \file{SIZE.h}. The
208  current section specifies certain constraints the exch2 package  current section specifies constraints that the exch2 package
209  imposes as well as describes how to enable parallel execution with  imposes and describes how to enable parallel execution with
210  MPI. \\  MPI. \\
211    
212  As in the general case, the parameters \varlink{sNx}{sNx} and  As in the general case, the parameters \varlink{sNx}{sNx} and
# Line 207  levels in the model.\\ Line 222  levels in the model.\\
222  The parameters \varlink{nSx}{nSx}, \varlink{nSy}{nSy},  The parameters \varlink{nSx}{nSx}, \varlink{nSy}{nSy},
223  \varlink{nPx}{nPx}, and \varlink{nPy}{nPy} relate to the number of  \varlink{nPx}{nPx}, and \varlink{nPy}{nPy} relate to the number of
224  tiles and how they are distributed on processors.  When using exch2,  tiles and how they are distributed on processors.  When using exch2,
225  the tiles are stored in a single dimension, and so  the tiles are stored in the $x$ dimension, and so
226  \code{\varlink{nSy}{nSy}=1} in all cases.  Since the tiles as  \code{\varlink{nSy}{nSy}=1} in all cases.  Since the tiles as
227  configured by exch2 cannot be split up accross processors without  configured by exch2 cannot be split up accross processors without
228  regenerating the topology, \code{\varlink{nPy}{nPy}=1} as well. \\  regenerating the topology, \code{\varlink{nPy}{nPy}=1} as well. \\
# Line 215  regenerating the topology, \code{\varlin Line 230  regenerating the topology, \code{\varlin
230  The number of tiles MITgcm allocates and how they are distributed  The number of tiles MITgcm allocates and how they are distributed
231  between processors depends on \varlink{nPx}{nPx} and  between processors depends on \varlink{nPx}{nPx} and
232  \varlink{nSx}{nSx}.  \varlink{nSx}{nSx} is the number of tiles per  \varlink{nSx}{nSx}.  \varlink{nSx}{nSx} is the number of tiles per
233  processor and \varlink{nPx}{nPx} the number of processors.  The total  processor and \varlink{nPx}{nPx} is the number of processors.  The total
234  number of tiles in the topology minus those listed in  number of tiles in the topology minus those listed in
235  \file{blanklist.txt} must equal \code{nSx*nPx}. \\  \file{blanklist.txt} must equal \code{nSx*nPx}.  Note that in order to
236    obtain maximum usage from a given number of processors in some cases,
237    this restriction might entail sharing a processor with a tile that would
238    otherwise be excluded. \\
239    
240  The following is an example of \file{SIZE.h} for the twelve-tile  The following is an example of \file{SIZE.h} for the twelve-tile
241  configuration illustrated in figure \ref{fig:12tile} running on  configuration illustrated in figure \ref{fig:12tile} running on
# Line 287  setup of six tiles (Fig. \ref{fig:6tile} Line 305  setup of six tiles (Fig. \ref{fig:6tile}
305  topology of twenty-four square tiles, four per subdomain (as in figure  topology of twenty-four square tiles, four per subdomain (as in figure
306  \ref{fig:24tile}), will have \code{exch2\_domain\_nxt=12} and  \ref{fig:24tile}), will have \code{exch2\_domain\_nxt=12} and
307  \code{exch2\_domain\_nyt=2}.  Note that these parameters express the  \code{exch2\_domain\_nyt=2}.  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} is assumed to  $x$ axis, and the $y$ axis variable \varlink{bj}{bj} is assumed to
312  equal \code{1} throughout the package. \\  equal \code{1} throughout the package. \\
313    
314  \subsubsection{Arrays Indexed to Tile Number}  \subsubsection{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
318  \textsf{t}$n$.  The indices are omitted in the descriptions. \\  \code{tn}.  The indices are omitted in the descriptions. \\
319    
320  The arrays \varlink{exch2\_tnx}{exch2_tnx} and  The arrays \varlink{exch2\_tnx}{exch2_tnx} and
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 may 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{fn}} in
347  figures \ref{fig:12tile} and  figures \ref{fig:12tile} and \ref{fig:24tile}. The
348  \ref{fig:24tile}. \varlink{exch2\_nNeighbours}{exch2_nNeighbours}  \varlink{exch2\_nNeighbours}{exch2_nNeighbours} variable contains a
349  contains a count of the neighboring tiles each tile has, and is used  count of the neighboring tiles each tile has, and sets the bounds for
350  for setting bounds for looping over neighboring tiles.  looping over neighboring tiles.  And
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    
# Line 338  The arrays \varlink{exch2\_isWedge}{exch Line 356  The arrays \varlink{exch2\_isWedge}{exch
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
# Line 371  This provides a back-reference from the Line 389  This provides a back-reference from the
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    
# Line 381  The dimensions of \code{exch2\_pi(t,N,T) Line 400  The dimensions of \code{exch2\_pi(t,N,T)
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
# Line 397  the arrays for all tile neighbors on the Line 416  the arrays for all tile neighbors on the
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},
# Line 483  the neighbor tile is \code{Tn=5}: Line 502  the neighbor tile is \code{Tn=5}:
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}  \subsection{Key Routines}
# Line 494  Most of the subroutines particular to ex Line 514  Most of the subroutines particular to ex
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
# Line 510  for scalars and \code{EXCH2\_RX2\_CUBE} Line 530  for scalars and \code{EXCH2\_RX2\_CUBE}
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    
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