.. _sub_phys_pkg_exch2: exch2: Extended Cubed Sphere Topology ------------------------------------- (in directory: :filelink:`pkg/exch2/`) Introduction ++++++++++++ The ``exch2`` package extends the original cubed sphere topology configuration to allow more flexible domain decomposition and parallelization. Cube faces (also called subdomains) may be divided into any number of tiles that divide evenly into the grid point dimensions of the subdomain. Furthermore, the tiles can run on separate processors individually or in groups, which provides for manual compile-time load balancing across a relatively arbitrary number of processors. The exchange parameters are declared in :filelink:`W2_EXCH_TOPOLOGY.h ` and assigned in :filelink:`w2_e2setup.F `. The validity of the cube topology depends on the ``SIZE.h`` file as detailed below. The default files provided in the release configure a cubed sphere topology of six tiles, one per subdomain, each with 32 :math:`\times` 32 grid points, with all tiles running on a single processor. Both files are generated by Matlab scripts in :filelink:`utils/exch2/matlab-topology-generator`; see :numref:`ssub_exch2_topogen` for details on creating alternate topologies. Pregenerated examples of these files with alternate topologies are provided under :filelink:`utils/exch2/code-mods` along with the appropriate ``SIZE.h`` file for single-processor execution. Invoking exch2 ++++++++++++++ To use exch2 with the cubed sphere, the following conditions must be met: - The exch2 package is included when ``genmake2`` is run. The easiest way to do this is to add the line ``exch2`` to the ``packages.conf`` file -- see Section :ref:`building_code` for general details. - An example of :code:`W2_EXCH2_TOPOLOGY.h` and ``w2_e2setup.F`` must reside in a directory containing files symbolically linked by the ``genmake2`` script. The safest place to put these is the directory indicated in the :code:`-mods=DIR` command line modifier (typically ``../code``), or the build directory. The default versions of these files reside in :filelink:`pkg/exch2` and are linked automatically if no other versions exist elsewhere in the build path, but they should be left untouched to avoid breaking configurations other than the one you intend to modify. - Files containing grid parameters, named ``tile00$n$.mitgrid`` where n=(1:6) (one per subdomain), must be in the working directory when the MITgcm executable is run. These files are provided in the example experiments for cubed sphere configurations with 32 :math:`\times` 32 cube sides -- please contact MITgcm support if you want to generate files for other configurations. - As always when compiling MITgcm, the file ``SIZE.h`` must be placed where ``genmake2`` will find it. In particular for exch2, the domain decomposition specified in ``SIZE.h`` must correspond with the particular configuration's topology specified in ``W2_EXCH2_TOPOLOGY.h`` and ``w2_e2setup.F``. Domain decomposition issues particular to exch2 are addressed in Section :ref:`ssub_exch2_topogen` and :ref:`ssub_exch2mpi` a more general background on the subject relevant to MITgcm is presented in Section :ref:`using_wrapper`. At the time of this writing the following examples use exch2 and may be used for guidance: - :filelink:`verification/adjust_nlfs.cs-32x32x1` - :filelink:`verification/adjustment.cs-32x32x1` - :filelink:`verification/aim.5l_cs` - :filelink:`verification/global_ocean.cs32x15` - :filelink:`verification/hs94.cs-32x32x5` .. _ssub_exch2_topogen: Generating Topology Files for exch2 +++++++++++++++++++++++++++++++++++ Alternate cubed sphere topologies may be created using the Matlab scripts in :filelink:`utils/exch2/matlab-topology-generator`. Running the m-file :filelink:`driver.m ` from the Matlab prompt (there are no parameters to pass) generates exch2 topology files ``W2_EXCH2_TOPOLOGY.h`` and ``w2_e2setup.F`` in the working directory and displays a figure of the topology via Matlab -- :numref:`fig_6tile`, :numref:`fig_18tile`, and :numref:`fig_48tile` are examples of the generated diagrams. The other m-files in the directory are subroutines called from :filelink:`driver.m ` and should not be run ''bare'' except for development purposes. The parameters that determine the dimensions and topology of the generated configuration are :code:`nr`, :code:`nb`, :code:`ng`, :code:`tnx` and :code:`tny`, and all are assigned early in the script. The first three determine the height and width of the subdomains and hence the size of the overall domain. Each one determines the number of grid points, and therefore the resolution, along the subdomain sides in a ''great circle'' around each the three spatial axes of the cube. At the time of this writing MITgcm requires these three parameters to be equal, but they provide for future releases to accomodate different resolutions around the axes to allow subdomains with differing resolutions. The parameters :code:`tnx` and :code:`tny` determine the width and height of the tiles into which the subdomains are decomposed, and must evenly divide the integer assigned to :code:`nr`, :code:`nb` and :code:`ng`. The result is a rectangular tiling of the subdomain. :numref:`fig_48tile` shows one possible topology for a twenty-four-tile cube, and :numref:`fig_6tile` shows one for six tiles. .. figure:: figs/adjust_cs.* :width: 70% :align: center :alt: cube sphere topology :name: fig_48tile Plot of a cubed sphere topology with a 32 :math:`\times` 192 domain divided into six 32 :math:`\times` 32 subdomains, each of which is divided into eight tiles of width :code:`tnx=16` and height :code:`tny=8` for a total of forty-eight tiles. The colored borders of the subdomains represent the parameters :code:`nr` (red), :code:`ng` (green), and :code:`nb` (blue). This tiling is used in the example verification/adjustment.cs-32x32x1/ with the option (blanklist.txt) to remove the land-only 4 tiles (11,12,13,14) which are filled in red on the plot. .. figure:: figs/polarcap.* :width: 70% :align: center :alt: polar cap topology :name: fig_18tile Plot of a non-square cubed sphere topology with 6 subdomains of different size (nr=90,ng=360,nb=90), divided into one to four tiles each (:code:`tnx=90, tny=90`), resulting in a total of 18 tiles. .. figure:: figs/s6t_32x32.* :width: 70% :align: center :alt: default cubed sphere topology :name: fig_6tile Plot of a cubed sphere topology with a 32 :math:`\times` 192 domain divided into six 32 :math:`\times` 32 subdomains with one tile each (:code:`tnx=32, tny=32`). This is the default configuration. Tiles can be selected from the topology to be omitted from being allocated memory and processors. This tuning is useful in ocean modeling for omitting tiles that fall entirely on land. The tiles omitted are specified in the file blanklist.txt by their tile number in the topology, separated by a newline. .. _ssub_exch2mpi: exch2, SIZE.h, and Multiprocessing ++++++++++++++++++++++++++++++++++ Once the topology configuration files are created, each Fortran ``PARAMETER`` in ``SIZE.h`` must be configured to match. :numref:`using_wrapper` povides a general description of domain decomposition within MITgcm and its relation to ``SIZE.h``. The current section specifies constraints that the exch2 package imposes and describes how to enable parallel execution with MPI. As in the general case, the parameters :varlink:`sNx` and :varlink:`sNy` define the size of the individual tiles, and so must be assigned the same respective values as ``tnx`` and ``tny`` in :filelink:`driver.m `. The halo width parameters :varlink:`OLx` and :varlink:`OLy` have no special bearing on exch2 and may be assigned as in the general case. The same holds for :varlink:`Nr`, the number of vertical levels in the model. The parameters :varlink:`nSx`, :varlink:`nSy`, :varlink:`nPx`, and :varlink:`nPy` relate to the number of tiles and how they are distributed on processors. When using exch2, the tiles are stored in the ``x`` dimension, and so :varlink:`nSy` =1 in all cases. Since the tiles as configured by exch2 cannot be split up accross processors without regenerating the topology, :varlink:`nPy` = 1 as well. The number of tiles MITgcm allocates and how they are distributed between processors depends on :varlink:`nPx` and :varlink:`nSx`. :varlink:`nSx` is the number of tiles per processor and :varlink:`nPx` is the number of processors. The total number of tiles in the topology minus those listed in ``blanklist.txt`` must equal :code:`nSx*nPx`. Note that in order to obtain maximum usage from a given number of processors in some cases, this restriction might entail sharing a processor with a tile that would otherwise be excluded because it is topographically outside of the domain and therefore in ``blanklist.txt``. For example, suppose you have five processors and a domain decomposition of thirty-six tiles that allows you to exclude seven tiles. To evenly distribute the remaining twenty-nine tiles among five processors, you would have to run one ''dummy'' tile to make an even six tiles per processor. Such dummy tiles are *not* listed in ``blanklist.txt``. The following is an example of ``SIZE.h`` for the six-tile configuration illustrated in :numref:`fig_6tile` running on one processor: :: PARAMETER ( & sNx = 32, & sNy = 32, & OLx = 2, & OLy = 2, & nSx = 6, & nSy = 1, & nPx = 1, & nPy = 1, & Nx = sNx*nSx*nPx, & Ny = sNy*nSy*nPy, & Nr = 5) The following is an example for the forty-eight-tile topology in :numref:`fig_48tile` running on six processors: :: PARAMETER ( & sNx = 16, & sNy = 8, & OLx = 2, & OLy = 2, & nSx = 8, & nSy = 1, & nPx = 6, & nPy = 1, & Nx = sNx*nSx*nPx, & Ny = sNy*nSy*nPy, & Nr = 5) .. _ssub_exch2_key_variables: Key Variables +++++++++++++ The descriptions of the variables are divided up into scalars, one-dimensional arrays indexed to the tile number, and two and three-dimensional arrays indexed to tile number and neighboring tile. This division reflects the functionality of these variables: The scalars are common to every part of the topology, the tile-indexed arrays to individual tiles, and the arrays indexed by tile and neighbor to relationships between tiles and their neighbors. Scalars: ~~~~~~~~ The number of tiles in a particular topology is set with the parameter :varlink:`exch2_nTiles`, and the maximum number of neighbors of any tiles by :varlink:`W2_maxNeighbours`. These parameters are used for defining the size of the various one and two dimensional arrays that store tile parameters indexed to the tile number and are assigned in the files generated by :filelink:`driver.m `. The scalar parameters :code:`exch2_domain_nxt` and :code:`exch2_domain_nyt` express the number of tiles in the ``x`` and ``y`` global indices. For example, the default setup of six tiles (:numref:`fig_6tile`) has :code:`exch2_domain_nxt=6` and :code:`exch2_domain_nyt=1`. A topology of forty-eight tiles, eight per subdomain (as in :numref:`fig_48tile`), will have :code:`exch2_domain_nxt=12` and :code:`exch2_domain_nyt=4`. Note that these parameters express the tile layout in order to allow global data files that are tile-layout-neutral. They have no bearing on the internal storage of the arrays. The tiles are stored internally in a range from ``bi`` = ``(1:exch2_nTiles)`` in the ``x`` axis, and the ``y`` axis variable ``bj`` is assumed to equal 1 throughout the package. Arrays indexed to tile number: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The following arrays are of length :code:`exch2_nTiles` and are indexed to the tile number, which is indicated in the diagrams with the notation ``tn``. The indices are omitted in the descriptions. The arrays :varlink:`exch2_tnx` and :varlink:`exch2_tny` express the ``x`` and ``y`` dimensions of each tile. At present for each tile :code:`exch2_tnx`=``sNx`` and :code:`exch2_tny` = :code:`sNy`, as assigned in ``SIZE.h`` and described in :numref:`ssub_exch2mpi`. Future releases of MITgcm may allow varying tile sizes. The arrays :varlink:`exch2_tbasex` and :varlink:`exch2_tbasey` determine the tiles' Cartesian origin within a subdomain and locate the edges of different tiles relative to each other. As an example, in the default six-tile topology (:numref:`fig_6tile`) each index in these arrays is set to 0 since a tile occupies its entire subdomain. The twenty-four-tile case discussed above will have values of 0 or 16, depending on the quadrant of the tile within the subdomain. The elements of the arrays :varlink:`exch2_txglobalo` and :varlink:`exch2_txglobalo` are similar to :varlink:`exch2_tbasex` and :varlink:`exch2_tbasey`, but locate the tile edges within the global address space, similar to that used by global output and input files. The array :varlink:`exch2_myFace` contains the number of the subdomain of each tile, in a range ``(1:6)`` in the case of the standard cube topology and indicated by **fn** in :numref:`fig_6tile` and :numref:`fig_48tile`. :varlink:`exch2_nNeighbours` contains a count of the neighboring tiles each tile has, and sets the bounds for looping over neighboring tiles. :varlink:`exch2_tProc` holds the process rank of each tile, and is used in interprocess communication. The arrays :varlink:`exch2_isWedge`, :varlink:`exch2_isEedge`, :varlink:`exch2_isSedge`, and :varlink:`exch2_isNedge` are set to 1 if the indexed tile lies on the edge of its subdomain, 0 if not. The values are used within the topology generator to determine the orientation of neighboring tiles, and to indicate whether a tile lies on the corner of a subdomain. The latter case requires special exchange and numerical handling for the singularities at the eight corners of the cube. Arrays Indexed to Tile Number and Neighbor: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The following arrays have vectors of length :varlink:`W2_maxNeighbours` and :varlink:`exch2_nTiles` and describe the orientations between the the tiles. The array :code:`exch2_neighbourId(a,T)` holds the tile number :code:`Tn` for each of the tile number :code:`T`'s neighboring tiles :code:`a`. The neighbor tiles are indexed :code:`1:exch2_nNeighbours(T)` in the order right to left on the north then south edges, and then top to bottom on the east then west edges. The :code:`exch2_opposingSend_record(a,T)` array holds the index :code:`b` of the element in :code:`exch2_neighbourId(b,Tn)` that holds the tile number :code:`T`, given :code:`Tn=exch2_neighborId(a,T)`. In other words, :: exch2_neighbourId( exch2_opposingSend_record(a,T), exch2_neighbourId(a,T) ) = T This provides a back-reference from the neighbor tiles. The arrays :varlink:`exch2_pi` and :varlink:`exch2_pj` specify the transformations of indices in exchanges between the neighboring tiles. These transformations are necessary in exchanges between subdomains because a horizontal dimension in one subdomain may map to other horizonal dimension in an adjacent subdomain, and may also have its indexing reversed. This swapping arises from the ''folding'' of two-dimensional arrays into a three-dimensional cube. The dimensions of :code:`exch2_pi(t,N,T)` and :code:`exch2_pj(t,N,T)` are the neighbor ID :code:`N` and the tile number :code:`T` as explained above, plus a vector of length 2 containing transformation factors :code:`t`. The first element of the transformation vector holds the factor to multiply the index in the same dimension, and the second element holds the the same for the orthogonal dimension. To clarify, :code:`exch2_pi(1,N,T)` holds the mapping of the ``x`` axis index of tile :code:`T` to the ``x`` axis of tile :code:`T`'s neighbor :code:`N`, and :code:`exch2_pi(2,N,T)` holds the mapping of :code:`T`'s ``x`` index to the neighbor :code:`N`'s ``y`` index. One of the two elements of :code:`exch2_pi` or :code:`exch2_pj` for a given tile :code:`T` and neighbor :code:`N` will be 0, reflecting the fact that the two axes are orthogonal. The other element will be 1 or -1, depending on whether the axes are indexed in the same or opposite directions. For example, the transform vector of the arrays for all tile neighbors on the same subdomain will be ``(1,0)``, since all tiles on the same subdomain are oriented identically. An axis that corresponds to the orthogonal dimension with the same index direction in a particular tile-neighbor orientation will have ``(0,1)``. Those with the opposite index direction will have ``(0,-1)`` in order to reverse the ordering. The arrays :varlink:`exch2_oi`, :varlink:`exch2_oj`, :varlink:`exch2_oi_f`, and :varlink:`exch2_oj_f` are indexed to tile number and neighbor and specify the relative offset within the subdomain of the array index of a variable going from a neighboring tile :code:`N` to a local tile :code:`T`. Consider :code:`T=1` in the six-tile topology (:numref:`fig_6tile`), where :: exch2_oi(1,1)=33 exch2_oi(2,1)=0 exch2_oi(3,1)=32 exch2_oi(4,1)=-32 The simplest case is :code:`exch2_oi(2,1)`, the southern neighbor, which is :code:`Tn=6`. The axes of :code:`T` and :code:`Tn` have the same orientation and their ``x`` axes have the same origin, and so an exchange between the two requires no changes to the ``x`` index. For the western neighbor (:code:`Tn=5`), :code:`code_oi(3,1)=32` since the :code:`x=0` vector on :code:`T` corresponds to the :code:`y=32` vector on :code:`Tn`. The eastern edge of :code:`T` shows the reverse case (:code:`exch2_oi(4,1)=-32)`), where :code:`x=32` on :code:`T` exchanges with :code:`x=0` on :code:`Tn=2`. The most interesting case, where :code:`exch2_oi(1,1)=33` and :code:`Tn=3`, involves a reversal of indices. As in every case, the offset :code:`exch2_oi` is added to the original ``x`` index of :code:`T` multiplied by the transformation factor :code:`exch2_pi(t,N,T)`. Here :code:`exch2_pi(1,1,1)=0` since the ``x`` axis of :code:`T` is orthogonal to the ``x`` axis of :code:`Tn`. :code:`exch2_pi(2,1,1)=-1` since the ``x`` axis of :code:`T` corresponds to the ``y`` axis of :code:`Tn`, but the index is reversed. The result is that the index of the northern edge of :code:`T`, which runs :code:`(1:32)`, is transformed to :code:`(-1:-32)`. :code:`exch2_oi(1,1)` is then added to this range to get back :code:`(32:1)` -- the index of the ``y`` axis of :code:`Tn` relative to :code:`T`. This transformation may seem overly convoluted for the six-tile case, but it is necessary to provide a general solution for various topologies. Finally, :varlink:`exch2_itlo_c`, :varlink:`exch2_ithi_c`, :varlink:`exch2_jtlo_c` and :varlink:`exch2_jthi_c` hold the location and index bounds of the edge segment of the neighbor tile :code:`N`'s subdomain that gets exchanged with the local tile :code:`T`. To take the example of tile :code:`T=2` in the forty-eight-tile topology (:numref:`fig_48tile`): :: exch2_itlo_c(4,2)=17 exch2_ithi_c(4,2)=17 exch2_jtlo_c(4,2)=0 exch2_jthi_c(4,2)=33 Here :code:`N=4`, indicating the western neighbor, which is :code:`Tn=1`. :code:`Tn` resides on the same subdomain as :code:`T`, so the tiles have the same orientation and the same ``x`` and ``y`` axes. The ``x`` axis is orthogonal to the western edge and the tile is 16 points wide, so :code:`exch2_itlo_c` and :code:`exch2_ithi_c` indicate the column beyond :code:`Tn`'s eastern edge, in that tile's halo region. Since the border of the tiles extends through the entire height of the subdomain, the ``y`` axis bounds :code:`exch2_jtlo_c` to :code:`exch2_jthi_c` cover the height of :code:`(1:32)`, plus 1 in either direction to cover part of the halo. For the north edge of the same tile :code:`T=2` where :code:`N=1` and the neighbor tile is :code:`Tn=5`: :: exch2_itlo_c(1,2)=0 exch2_ithi_c(1,2)=0 exch2_jtlo_c(1,2)=0 exch2_jthi_c(1,2)=17 :code:`T`'s northern edge is parallel to the ``x`` axis, but since :code:`Tn`'s ``y`` axis corresponds to :code:`T`'s ``x`` axis, :code:`T`'s northern edge exchanges with :code:`Tn`'s western edge. The western edge of the tiles corresponds to the lower bound of the ``x`` axis, so :code:`exch2_itlo_c` and :code:`exch2_ithi_c` are 0, in the western halo region of :code:`Tn`. The range of :code:`exch2_jtlo_c` and :code:`exch2_jthi_c` correspond to the width of :code:`T`'s northern edge, expanded by one into the halo. Key Routines ++++++++++++ Most of the subroutines particular to exch2 handle the exchanges themselves and are of the same format as those described in :ref:`cubed_sphere_comm`. Like the original routines, they are written as templates which the local Makefile converts from :code:`RX` into :code:`RL` and :code:`RS` forms. The interfaces with the core model subroutines are :code:`EXCH_UV_XY_RX`, :code:`EXCH_UV_XYZ_RX` and :code:`EXCH_XY_RX`. They override the standard exchange routines when :code:`genmake2` is run with :code:`exch2` option. They in turn call the local exch2 subroutines :code:`EXCH2_UV_XY_RX` and :code:`EXCH2_UV_XYZ_RX` for two and three-dimensional vector quantities, and :code:`EXCH2_XY_RX` and :code:`EXCH2_XYZ_RX` for two and three-dimensional scalar quantities. These subroutines set the dimensions of the area to be exchanged, call :code:`EXCH2_RX1_CUBE` for scalars and :code:`EXCH2_RX2_CUBE` for vectors, and then handle the singularities at the cube corners. The separate scalar and vector forms of :code:`EXCH2_RX1_CUBE` and :code:`EXCH2_RX2_CUBE` reflect that the vector-handling subroutine needs to pass both the $u$ and $v$ components of the physical vectors. This swapping arises from the topological folding discussed above, where the ``x`` and ``y`` axes get swapped in some cases, and is not an issue with the scalar case. These subroutines call :code:`EXCH2_SEND_RX1` and :code:`EXCH2_SEND_RX2`, which do most of the work using the variables discussed above. .. _ssub_exch2_experiments: Experiments and tutorials that use exch2 ++++++++++++++++++++++++++++++++++++++++ - Held Suarez tutorial, in :filelink:`verification/tutorial_held_suarez_cs` verification directory.