--- manual/s_software/text/sarch.tex 2001/10/11 19:12:38 1.2 +++ manual/s_software/text/sarch.tex 2001/11/13 18:32:33 1.5 @@ -1,4 +1,4 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.2 2001/10/11 19:12:38 adcroft Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.5 2001/11/13 18:32:33 cnh Exp $ In this chapter we describe the software architecture and implementation strategy for the MITgcm code. The first part of this @@ -41,7 +41,7 @@ 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 @@ -89,7 +89,7 @@ \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 @@ -136,14 +136,14 @@ class of machines (for example Parallel Vector Processor Systems). Instead the WRAPPER provides applications with an abstract {\it machine model}. The machine model is very general, however, it can -easily be specialized to fit, in a computationally effificent manner, any +easily be specialized to fit, in a computationally efficient manner, any computer architecture currently available to the scientific computing community. \subsection{Machine model parallelism} Codes operating under the WRAPPER target an abstract machine that is assumed to consist of one or more logical processors that can compute concurrently. -Computational work is divided amongst the logical +Computational work is divided among the logical processors by allocating ``ownership'' to each processor of a certain set (or sets) of calculations. Each set of calculations owned by a particular processor is associated with a specific @@ -166,7 +166,7 @@ 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 @@ -402,8 +402,8 @@ \includegraphics{part4/comm-primm.eps} } \end{center} -\caption{Three performance critical parallel primititives are provided -by the WRAPPER. These primititives are always used to communicate data +\caption{Three performance critical parallel primitives are provided +by the WRAPPER. These primitives are always used to communicate data between tiles. The figure shows four tiles. The curved arrows indicate exchange primitives which transfer data between the overlap regions at tile edges and interior regions for nearest-neighbor tiles. @@ -789,7 +789,7 @@ 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. @@ -842,6 +842,7 @@ \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 @@ -929,6 +930,7 @@ } \\ \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 @@ -940,7 +942,8 @@ 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. @@ -1003,7 +1006,7 @@ \begin{verbatim} mpirun -np 64 -machinefile mf ./mitgcmuv \end{verbatim} -In this example the text {\em -np 64} specifices the number of processes +In this example the text {\em -np 64} specifies the number of processes that will be created. The numeric value {\em 64} must be equal to the product of the processor grid settings of {\em nPx} and {\em nPy} in the file {\em SIZE.h}. The parameter {\em mf} specifies that a text file @@ -1106,7 +1109,7 @@ 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}). @@ -1163,7 +1166,7 @@ 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}.\\ @@ -1197,7 +1200,7 @@ \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} @@ -1209,7 +1212,7 @@ \item {\bf Cache line size} As discussed in section \ref{sec:cache_effects_and_false_sharing}, milti-threaded codes explicitly avoid penalties associated with excessive -coherence traffic on an SMP system. To do this the sgared memory data structures +coherence traffic on an SMP system. To do this the shared memory data structures used by the {\em GLOBAL\_SUM}, {\em GLOBAL\_MAX} and {\em BARRIER} routines are padded. The variables that control the padding are set in the header file {\em EEPARAMS.h}. These variables are called @@ -1217,7 +1220,7 @@ {\em lShare8}. The default values should not normally need changing. \item {\bf \_BARRIER} This is a CPP macro that is expanded to a call to a routine -which synchronises all the logical processors running under the +which synchronizes all the logical processors running under the WRAPPER. Using a macro here preserves flexibility to insert a specialized call in-line into application code. By default this resolves to calling the procedure {\em BARRIER()}. The default @@ -1225,13 +1228,13 @@ \item {\bf \_GSUM} This is a CPP macro that is expanded to a call to a routine -which sums up a floating point numner +which sums up a floating point number over all the logical processors running under the WRAPPER. Using a macro here provides extra flexibility to insert a specialized call in-line into application code. By default this -resolves to calling the procedure {\em GLOBAL\_SOM\_R8()} ( for -84=bit floating point operands) -or {\em GLOBAL\_SOM\_R4()} (for 32-bit floating point operands). The default +resolves to calling the procedure {\em GLOBAL\_SUM\_R8()} ( for +64-bit floating point operands) +or {\em GLOBAL\_SUM\_R4()} (for 32-bit floating point operands). The default setting for the \_GSUM macro is given in the file {\em CPP\_EEMACROS.h}. The \_GSUM macro is a performance critical operation, especially for large processor count, small tile size configurations. @@ -1250,23 +1253,23 @@ \_EXCH operation plays a crucial role in scaling to small tile, large logical and physical processor count configurations. The example in section \ref{sec:jam_example} discusses defining an -optimised and specialized form on the \_EXCH operation. +optimized and specialized form on the \_EXCH operation. The \_EXCH operation is also central to supporting grids such as the cube-sphere grid. In this class of grid a rotation may be required between tiles. Aligning the coordinate requiring rotation with the -tile decomposistion, allows the coordinate transformation to +tile decomposition, allows the coordinate transformation to be embedded within a custom form of the \_EXCH primitive. \item {\bf Reverse Mode} The communication primitives \_EXCH and \_GSUM both employ hand-written adjoint forms (or reverse mode) forms. These reverse mode forms can be found in the -sourc code directory {\em pkg/autodiff}. +source code directory {\em pkg/autodiff}. For the global sum primitive the reverse mode form calls are to {\em GLOBAL\_ADSUM\_R4} and {\em GLOBAL\_ADSUM\_R8}. The reverse mode form of the -exchamge primitives are found in routines +exchange primitives are found in routines prefixed {\em ADEXCH}. The exchange routines make calls to the same low-level communication primitives as the forward mode operations. However, the routine argument {\em simulationMode} @@ -1278,7 +1281,7 @@ maximum number of OS threads that a code will use. This value defaults to thirty-two and is set in the file {\em EEPARAMS.h}. For single threaded execution it can be reduced to one if required. -The va;lue is largely private to the WRAPPER and application code +The value; is largely private to the WRAPPER and application code will nor normally reference the value, except in the following scenario. For certain physical parametrization schemes it is necessary to have @@ -1293,8 +1296,8 @@ being specified involves many more tiles than OS threads then it can save memory resources to reduce the variable {\em MAX\_NO\_THREADS} to be equal to the actual number of threads that -will be used and to declare the physical parameterisation -work arrays with a sinble {\em MAX\_NO\_THREADS} extra dimension. +will be used and to declare the physical parameterization +work arrays with a single {\em MAX\_NO\_THREADS} extra dimension. An example of this is given in the verification experiment {\em aim.5l\_cs}. Here the default setting of {\em MAX\_NO\_THREADS} is altered to @@ -1307,12 +1310,12 @@ \begin{verbatim} common /FORCIN/ sst1(ngp,MAX_NO_THREADS) \end{verbatim} -This declaration scheme is not used widely, becuase most global data +This declaration scheme is not used widely, because most global data is used for permanent not temporary storage of state information. In the case of permanent state information this approach cannot be used because there has to be enough storage allocated for all tiles. However, the technique can sometimes be a useful scheme for reducing memory -requirements in complex physical paramterisations. +requirements in complex physical parameterizations. \end{enumerate} \begin{figure} @@ -1345,7 +1348,7 @@ The isolation of performance critical communication primitives and the sub-division of the simulation domain into tiles is a powerful tool. Here we show how it can be used to improve application performance and -how it can be used to adapt to new gridding approaches. +how it can be used to adapt to new griding approaches. \subsubsection{JAM example} \label{sec:jam_example} @@ -1364,7 +1367,7 @@ \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 @@ -1376,16 +1379,16 @@ 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 @@ -1450,7 +1453,7 @@ 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 @@ -1464,22 +1467,22 @@ 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. @@ -1490,7 +1493,7 @@ 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. @@ -1511,7 +1514,7 @@ 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 @@ -1531,7 +1534,7 @@ 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 | @@ -1545,7 +1548,7 @@ 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. @@ -1553,7 +1556,7 @@ 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. @@ -1631,7 +1634,7 @@ 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.