/[MITgcm]/manual/s_software/text/sarch.tex

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-revision 1.2 by adcroft,
Thu Oct 11 19:12:38 2001 UTC
+revision 1.4 by cnh,
Thu Oct 25 18:36:55 2001 UTC
 Line 41 
 packages operate.
  This chapter focuses on describing the {\bf WRAPPER} environment under which
  both the core numerics and the pluggable packages function. The description
- presented here is intended to be a detailed exposistion and contains significant
+ presented here is intended to be a detailed exposition and contains significant
  background material, as well as advanced details on working with the WRAPPER.
  The examples section of this manual (part \ref{part:example}) contains more
  succinct, step-by-step instructions on running basic numerical
 Line 89 
 and operating systems. This allows numer
  \caption{
  Numerical code is written too fit within a software support
  infrastructure called WRAPPER. The WRAPPER is portable and
- can be sepcialized for a wide range of specific target hardware and
+ can be specialized for a wide range of specific target hardware and
  programming environments, without impacting numerical code that fits
  within the WRAPPER. Codes that fit within the WRAPPER can generally be
  made to run as fast on a particular platform as codes specially
 Line 166 
 Computationally, associated with each re
  space allocated to a particular logical processor, there will be data
  structures (arrays, scalar variables etc...) that hold the simulated state of
  that region. We refer to these data structures as being {\bf owned} by the
- pprocessor to which their
+ processor to which their
  associated region of physical space has been allocated. Individual
  regions that are allocated to processors are called {\bf tiles}. A
  processor can own more
 Line 789 
 thirty-two grid points, and x and y over
  There are six tiles allocated to six separate logical processors ({\em nSx=6}).
  This set of values can be used for a cube sphere calculation.
  Each tile of size $32 \times 32$ represents a face of the
- cube. Initialising the tile connectivity correctly ( see section
+ cube. Initializing the tile connectivity correctly ( see section
  \ref{sec:cube_sphere_communication}. allows the rotations associated with
  moving between the six cube faces to be embedded within the
  tile-tile communication code.
 Line 842 
 occurs through the procedure {\em THE\_M
  \end{figure}
  \subsubsection{Multi-threaded execution}
+ \label{sec:multi-threaded-execution}
  Prior to transferring control to the procedure {\em THE\_MODEL\_MAIN()} the
  WRAPPER may cause several coarse grain threads to be initialized. The routine
  {\em THE\_MODEL\_MAIN()} is called once for each thread and is passed a single
-Line 929 
 Parameter:  {\em nTy}
+Line 930 
 Parameter:  {\em nTy}
  } \\
  \subsubsection{Multi-process execution}
+ \label{sec:multi-process-execution}
  Despite its appealing programming model, multi-threaded execution remains
  less common then multi-process execution. One major reason for this
-Line 940 
 models varies between systems.
+Line 942 
 models varies between systems.
  Multi-process execution is more ubiquitous.
  In order to run code in a multi-process configuration a decomposition
- specification is given ( in which the at least one of the
+ specification ( see section \ref{sec:specifying_a_decomposition})
+ is given ( in which the at least one of the
  parameters {\em nPx} or {\em nPy} will be greater than one)
  and then, as for multi-threaded operation,
  appropriate compile time and run time steps must be taken.
-Line 1106 
 This information is held in the variable
+Line 1109 
 This information is held in the variable
  This latter set of variables can take one of the following values
  {\em COMM\_NONE}, {\em COMM\_MSG}, {\em COMM\_PUT} and {\em COMM\_GET}.
  A value of {\em COMM\_NONE} is used to indicate that a tile has no
- neighbor to cummnicate with on a particular face. A value
+ neighbor to communicate with on a particular face. A value
  of {\em COMM\_MSG} is used to indicated that some form of distributed
  memory communication is required to communicate between
  these tile faces ( see section \ref{sec:distributed_memory_communication}).
-Line 1163 
 the product of the parameters {\em nTx}
+Line 1166 
 the product of the parameters {\em nTx}
  are read from the file {\em eedata}. If the value of {\em nThreads}
  is inconsistent with the number of threads requested from the
  operating system (for example by using an environment
- varialble as described in section \ref{sec:multi_threaded_execution})
+ variable as described in section \ref{sec:multi_threaded_execution})
  then usually an error will be reported by the routine
  {\em CHECK\_THREADS}.\\
-Line 1197 
 For an Ultra Sparc system the following
+Line 1200 
 For an Ultra Sparc system the following
  \begin{verbatim}
  asm("membar #LoadStore|#StoreStore");
  \end{verbatim}
- for an Alpha based sytem the euivalent code reads
+ for an Alpha based system the equivalent code reads
  \begin{verbatim}
  asm("mb");
  \end{verbatim}
-Line 1364 
 communications library ( see {\em ini\_j
+Line 1367 
 communications library ( see {\em ini\_j
  \item The {\em \_GSUM} and {\em \_EXCH} macro definitions are replaced
  with calls to custom routines ( see {\em gsum\_jam.F} and {\em exch\_jam.F})
  \item a highly specialized form of the exchange operator (optimized
- for overlap regions of width one) is substitued into the elliptic
+ for overlap regions of width one) is substituted into the elliptic
  solver routine {\em cg2d.F}.
  \end{itemize}
  Developing specialized code for other libraries follows a similar
-Line 1376 
 Actual {\em \_EXCH} routine code is gene
+Line 1379 
 Actual {\em \_EXCH} routine code is gene
  a series of template files, for example {\em exch\_rx.template}.
  This is done to allow a large number of variations on the exchange
  process to be maintained. One set of variations supports the
- cube sphere grid. Support for a cube sphere gris in MITgcm is based
+ cube sphere grid. Support for a cube sphere grid in MITgcm is based
  on having each face of the cube as a separate tile (or tiles).
- The exchage routines are then able to absorb much of the
+ The exchange routines are then able to absorb much of the
  detailed rotation and reorientation required when moving around the
  cube grid. The set of {\em \_EXCH} routines that contain the
  word cube in their name perform these transformations.
  They are invoked when the run-time logical parameter
  {\em useCubedSphereExchange} is set true. To facilitate the
  transformations on a staggered C-grid, exchange operations are defined
- separately for both vector and scalar quantitities and for
+ separately for both vector and scalar quantities and for
  grid-centered and for grid-face and corner quantities.
  Three sets of exchange routines are defined. Routines
  with names of the form {\em exch\_rx} are used to exchange
-Line 1450 
 C  :
+Line 1453 
 C  :
  C  |
  C  |-THE_MODEL_MAIN :: Primary driver for the MITgcm algorithm
  C    |              :: Called from WRAPPER level numerical
- C    |              :: code innvocation routine. On entry
+ C    |              :: code invocation routine. On entry
  C    |              :: to THE_MODEL_MAIN separate thread and
  C    |              :: separate processes will have been established.
  C    |              :: Each thread and process will have a unique ID
-Line 1464 
 C    | |-INI_PARMS :: Routine to set ker
+Line 1467 
 C    | |-INI_PARMS :: Routine to set ker
  C    | |           :: By default kernel parameters are read from file
  C    | |           :: "data" in directory in which code executes.
  C    | |
- C    | |-MON_INIT :: Initialises monitor pacakge ( see pkg/monitor )
+ C    | |-MON_INIT :: Initializes monitor package ( see pkg/monitor )
  C    | |
- C    | |-INI_GRID :: Control grid array (vert. and hori.) initialisation.
+ C    | |-INI_GRID :: Control grid array (vert. and hori.) initialization.
  C    | | |        :: Grid arrays are held and described in GRID.h.
  C    | | |
- C    | | |-INI_VERTICAL_GRID        :: Initialise vertical grid arrays.
+ C    | | |-INI_VERTICAL_GRID        :: Initialize vertical grid arrays.
  C    | | |
- C    | | |-INI_CARTESIAN_GRID       :: Cartesian horiz. grid initialisation
+ C    | | |-INI_CARTESIAN_GRID       :: Cartesian horiz. grid initialization
  C    | | |                          :: (calculate grid from kernel parameters).
  C    | | |
  C    | | |-INI_SPHERICAL_POLAR_GRID :: Spherical polar horiz. grid
- C    | | |                          :: initialisation (calculate grid from
+ C    | | |                          :: initialization (calculate grid from
  C    | | |                          :: kernel parameters).
  C    | | |
  C    | | |-INI_CURVILINEAR_GRID     :: General orthogonal, structured horiz.
- C    | |                            :: grid initialisations. ( input from raw
+ C    | |                            :: grid initializations. ( input from raw
  C    | |                            :: grid files, LONC.bin, DXF.bin etc... )
  C    | |
  C    | |-INI_DEPTHS    :: Read (from "bathyFile") or set bathymetry/orgography.
-Line 1490 
 C    | |
+Line 1493 
 C    | |
  C    | |-INI_LINEAR_PHSURF :: Set ref. surface Bo_surf
  C    | |
  C    | |-INI_CORI          :: Set coriolis term. zero, f-plane, beta-plane,
- C    | |                   :: sphere optins are coded.
+ C    | |                   :: sphere options are coded.
  C    | |
  C    | |-PACAKGES_BOOT      :: Start up the optional package environment.
  C    | |                    :: Runtime selection of active packages.
-Line 1511 
 C    | |
+Line 1514 
 C    | |
  C    | |-PACKAGES_CHECK
  C    | | |
  C    | | |-KPP_CHECK           :: KPP Package. pkg/kpp
- C    | | |-OBCS_CHECK          :: Open bndy Pacakge. pkg/obcs
+ C    | | |-OBCS_CHECK          :: Open bndy Package. pkg/obcs
  C    | | |-GMREDI_CHECK        :: GM Package. pkg/gmredi
  C    | |
  C    | |-PACKAGES_INIT_FIXED
-Line 1531 
 C    |
+Line 1534 
 C    |
  C    |-CTRL_UNPACK :: Control vector support package. see pkg/ctrl
  C    |
  C    |-ADTHE_MAIN_LOOP :: Derivative evaluating form of main time stepping loop
- C    !                 :: Auotmatically gerenrated by TAMC/TAF.
+ C    !                 :: Auotmatically generated by TAMC/TAF.
  C    |
  C    |-CTRL_PACK   :: Control vector support package. see pkg/ctrl
  C    |
-Line 1545 
 C    | | |
+Line 1548 
 C    | | |
  C    | | |-INI_LINEAR_PHISURF :: Set ref. surface Bo_surf
  C    | | |
  C    | | |-INI_CORI     :: Set coriolis term. zero, f-plane, beta-plane,
- C    | | |              :: sphere optins are coded.
+ C    | | |              :: sphere options are coded.
  C    | | |
  C    | | |-INI_CG2D     :: 2d con. grad solver initialisation.
  C    | | |-INI_CG3D     :: 3d con. grad solver initialisation.
-Line 1553 
 C    | | |-INI_MIXING   :: Initialise di
+Line 1556 
 C    | | |-INI_MIXING   :: Initialise di
  C    | | |-INI_DYNVARS  :: Initialise to zero all DYNVARS.h arrays (dynamical
  C    | | |              :: fields).
  C    | | |
- C    | | |-INI_FIELDS   :: Control initialising model fields to non-zero
+ C    | | |-INI_FIELDS   :: Control initializing model fields to non-zero
  C    | | | |-INI_VEL    :: Initialize 3D flow field.
  C    | | | |-INI_THETA  :: Set model initial temperature field.
  C    | | | |-INI_SALT   :: Set model initial salinity field.
-Line 1631 
 C/\  | | |-CALC_EXACT_ETA :: Change SSH
+Line 1634 
 C/\  | | |-CALC_EXACT_ETA :: Change SSH
  C/\  | | |-CALC_SURF_DR   :: Calculate the new surface level thickness.
  C/\  | | |-EXF_GETFORCING :: External forcing package. ( pkg/exf )
  C/\  | | |-EXTERNAL_FIELDS_LOAD :: Control loading time dep. external data.
- C/\  | | | |                    :: Simple interpolcation between end-points
+ C/\  | | | |                    :: Simple interpolation between end-points
  C/\  | | | |                    :: for forcing datasets.
  C/\  | | | |
  C/\  | | | |-EXCH :: Sync forcing. in overlap regions.

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