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

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-revision 1.21 by edhill,
Tue Apr  4 15:54:55 2006 UTC
+revision 1.23 by edhill,
Tue Apr  4 19:14:14 2006 UTC
 Line 1
  % $Header$
- This chapter focuses on describing the {\bf WRAPPER} environment within which
+ This chapter focuses on describing the {\bf WRAPPER} environment
- both the core numerics and the pluggable packages operate. The description
+ within which both the core numerics and the pluggable packages
- presented here is intended to be a detailed exposition and contains significant
+ operate. The description presented here is intended to be a detailed
- background material, as well as advanced details on working with the WRAPPER.
+ exposition and contains significant background material, as well as
- The tutorial sections of this manual (see sections
+ advanced details on working with the WRAPPER.  The tutorial sections
- \ref{sect:tutorials}  and \ref{sect:tutorialIII})
+ of this manual (see sections \ref{sect:tutorials} and
- contain more succinct, step-by-step instructions on running basic numerical
+ \ref{sect:tutorialIII}) contain more succinct, step-by-step
- experiments, of varous types, both sequentially and in parallel. For many
+ instructions on running basic numerical experiments, of varous types,
- projects simply starting from an example code and adapting it to suit a
+ both sequentially and in parallel. For many projects simply starting
- particular situation
+ from an example code and adapting it to suit a particular situation
- will be all that is required.
+ will be all that is required.  The first part of this chapter
- The first part of this chapter discusses the MITgcm architecture at an
+ discusses the MITgcm architecture at an abstract level. In the second
- abstract level. In the second part of the chapter we described practical
+ part of the chapter we described practical details of the MITgcm
- details of the MITgcm implementation and of current tools and operating system
+ implementation and of current tools and operating system features that
- features that are employed.
+ are employed.
  \section{Overall architectural goals}
  \begin{rawhtml}
 Line 25 
 Broadly, the goals of the software archi
  three-fold
  \begin{itemize}
- \item We wish to be able to study a very broad range
+ \item We wish to be able to study a very broad range of interesting
- of interesting and challenging rotating fluids problems.
+   and challenging rotating fluids problems.
- \item We wish the model code to be readily targeted to
+ \item We wish the model code to be readily targeted to a wide range of
- a wide range of platforms
+   platforms
- \item On any given platform we would like to be
+ \item On any given platform we would like to be able to achieve
- able to achieve performance comparable to an implementation
+   performance comparable to an implementation developed and
- developed and specialized specifically for that platform.
+   specialized specifically for that platform.
  \end{itemize}
- These points are summarized in figure \ref{fig:mitgcm_architecture_goals}
+ These points are summarized in figure
- which conveys the goals of the MITgcm design. The goals lead to
+ \ref{fig:mitgcm_architecture_goals} which conveys the goals of the
- a software architecture which at the high-level can be viewed as consisting
+ MITgcm design. The goals lead to a software architecture which at the
- of
+ high-level can be viewed as consisting of
  \begin{enumerate}
  \item A core set of numerical and support code. This is discussed in
 Line 71 
 is required.
  \begin{center}
  \resizebox{!}{2.5in}{\includegraphics{part4/mitgcm_goals.eps}}
  \end{center}
- \caption{
+ \caption{ The MITgcm architecture is designed to allow simulation of a
- The MITgcm architecture is designed to allow simulation of a wide
+   wide range of physical problems on a wide range of hardware. The
- range of physical problems on a wide range of hardware. The computational
+   computational resource requirements of the applications targeted
- resource requirements of the applications targeted range from around
+   range from around $10^7$ bytes ($\approx 10$ megabytes) of memory to
- $10^7$ bytes ( $\approx 10$ megabytes ) of memory to $10^{11}$ bytes
+   $10^{11}$ bytes ($\approx 100$ gigabytes). Arithmetic operation
- ( $\approx 100$ gigabytes). Arithmetic operation counts for the applications of
+   counts for the applications of interest range from $10^{9}$ floating
- interest range from $10^{9}$ floating point operations to more than $10^{17}$
+   point operations to more than $10^{17}$ floating point operations.}
- floating point operations.}
  \label{fig:mitgcm_architecture_goals}
  \end{figure}
-Line 87 
 floating point operations.}
+Line 86 
 floating point operations.}
  <!-- CMIREDIR:wrapper: -->
  \end{rawhtml}
- A significant element of the software architecture utilized in
+ A significant element of the software architecture utilized in MITgcm
- MITgcm is a software superstructure and substructure collectively
+ is a software superstructure and substructure collectively called the
- called the WRAPPER (Wrappable Application Parallel Programming
+ WRAPPER (Wrappable Application Parallel Programming Environment
- Environment Resource). All numerical and support code in MITgcm is written
+ Resource). All numerical and support code in MITgcm is written to
- to ``fit'' within the WRAPPER infrastructure. Writing code to ``fit'' within
+ ``fit'' within the WRAPPER infrastructure. Writing code to ``fit''
- the WRAPPER means that coding has to follow certain, relatively
+ within the WRAPPER means that coding has to follow certain, relatively
  straightforward, rules and conventions (these are discussed further in
  section \ref{sect:specifying_a_decomposition}).
  The approach taken by the WRAPPER is illustrated in figure
- \ref{fig:fit_in_wrapper} which shows how the WRAPPER serves to insulate code
+ \ref{fig:fit_in_wrapper} which shows how the WRAPPER serves to
- that fits within it from architectural differences between hardware platforms
+ insulate code that fits within it from architectural differences
- and operating systems. This allows numerical code to be easily retargetted.
+ between hardware platforms and operating systems. This allows
+ numerical code to be easily retargetted.
  \begin{figure}
 Line 416 
 default WRAPPER sources, because of thei
  \subsection{Distributed memory communication}
  \label{sect:distributed_memory_communication}
  Many parallel systems are not constructed in a way where it is
- possible or practical for an application to use shared memory
+ possible or practical for an application to use shared memory for
- for communication. For example cluster systems consist of individual computers
+ communication. For example cluster systems consist of individual
- connected by a fast network. On such systems there is no notion of shared memory
+ computers connected by a fast network. On such systems there is no
- at the system level. For this sort of system the WRAPPER provides support
+ notion of shared memory at the system level. For this sort of system
- for communication based on a bespoke communication library
+ the WRAPPER provides support for communication based on a bespoke
- (see figure \ref{fig:comm_msg}).  The default communication library used is MPI
+ communication library (see figure \ref{fig:comm_msg}).  The default
- \ref{mpi}. However, it is relatively straightforward to implement bindings to
+ communication library used is MPI \cite{MPI-std-20}. However, it is
- optimized platform specific communication libraries. For example the work
+ relatively straightforward to implement bindings to optimized platform
- described in \ref{hoe-hill:99} substituted standard MPI communication for a
+ specific communication libraries. For example the work described in
- highly optimized library.
+ \ref{hoe-hill:99} substituted standard MPI communication for a highly
+ optimized library.
  \subsection{Communication primitives}
  \label{sect:communication_primitives}
-Line 1480 
 Core equations plus packages.
+Line 1481 
 Core equations plus packages.
  {\footnotesize
  \begin{verbatim}
  C
- C
  C Invocation from WRAPPER level...
  C  :
  C  :
 Line 1544 
 C    | | |-CTRL_INIT           :: Contro
  C    | | |-OPTIM_READPARMS     :: Optimisation support package. see pkg/ctrl
  C    | | |-GRDCHK_READPARMS    :: Gradient check package. see pkg/grdchk
  C    | | |-ECCO_READPARMS      :: ECCO Support Package. see pkg/ecco
+ C    | | |-PTRACERS_READPARMS  :: multiple tracer package, see pkg/ptracers
+ C    | | |-GCHEM_READPARMS     :: tracer interface package, see pkg/gchem
  C    | |
  C    | |-PACKAGES_CHECK
  C    | | |
  C    | | |-KPP_CHECK           :: KPP Package. pkg/kpp
- C    | | |-OBCS_CHECK          :: Open bndy Package. pkg/obcs
+ C    | | |-OBCS_CHECK          :: Open bndy Pacakge. pkg/obcs
  C    | | |-GMREDI_CHECK        :: GM Package. pkg/gmredi
  C    | |
  C    | |-PACKAGES_INIT_FIXED
  C    | | |-OBCS_INIT_FIXED     :: Open bndy Package. see pkg/obcs
  C    | | |-FLT_INIT            :: Floats Package. see pkg/flt
+ C    | | |-GCHEM_INIT_FIXED    :: tracer interface pachage, see pkg/gchem
  C    | |
  C    | |-ZONAL_FILT_INIT       :: FFT filter Package. see pkg/zonal_filt
  C    | |
- C    | |-INI_CG2D              :: 2d con. grad solver initialisation.
+ C    | |-INI_CG2D              :: 2d con. grad solver initialization.
  C    | |
- C    | |-INI_CG3D              :: 3d con. grad solver initialisation.
+ C    | |-INI_CG3D              :: 3d con. grad solver initialization.
  C    | |
  C    | |-CONFIG_SUMMARY        :: Provide synopsis of kernel setup.
  C    |                         :: Includes annotated table of kernel
-Line 1584 
 C    | | |
+Line 1587 
 C    | | |
  C    | | |-INI_CORI     :: Set coriolis term. zero, f-plane, beta-plane,
  C    | | |              :: sphere options are coded.
  C    | | |
- C    | | |-INI_CG2D     :: 2d con. grad solver initialisation.
+ C    | | |-INI_CG2D     :: 2d con. grad solver initialization.
- C    | | |-INI_CG3D     :: 3d con. grad solver initialisation.
+ C    | | |-INI_CG3D     :: 3d con. grad solver initialization.
- C    | | |-INI_MIXING   :: Initialise diapycnal diffusivity.
+ C    | | |-INI_MIXING   :: Initialize diapycnal diffusivity.
- C    | | |-INI_DYNVARS  :: Initialise to zero all DYNVARS.h arrays (dynamical
+ C    | | |-INI_DYNVARS  :: Initialize to zero all DYNVARS.h arrays (dynamical
  C    | | |              :: fields).
  C    | | |
  C    | | |-INI_FIELDS   :: Control initializing model fields to non-zero
-Line 1595 
 C    | | | |-INI_VEL    :: Initialize 3D
+Line 1598 
 C    | | | |-INI_VEL    :: Initialize 3D
  C    | | | |-INI_THETA  :: Set model initial temperature field.
  C    | | | |-INI_SALT   :: Set model initial salinity field.
  C    | | | |-INI_PSURF  :: Set model initial free-surface height/pressure.
- C    | | |
+ C    | | | |-INI_PRESSURE :: Compute model initial hydrostatic pressure
- C    | | |-INI_TR1      :: Set initial tracer 1 distribution.
+ C    | | | |-READ_CHECKPOINT :: Read the checkpoint
  C    | | |
  C    | | |-THE_CORRECTION_STEP :: Step forward to next time step.
  C    | | | |                   :: Here applied to move restart conditions
-Line 1623 
 C    | | | |-FIND_RHO  :: Find adjacent
+Line 1626 
 C    | | | |-FIND_RHO  :: Find adjacent
  C    | | | |-CONVECT   :: Mix static instability.
  C    | | | |-TIMEAVE_CUMULATE :: Update convection statistics.
  C    | | |
- C    | | |-PACKAGES_INIT_VARIABLES :: Does initialisation of time evolving
+ C    | | |-PACKAGES_INIT_VARIABLES :: Does initialization of time evolving
  C    | | | |                       :: package data.
  C    | | | |
  C    | | | |-GMREDI_INIT          :: GM package. ( see pkg/gmredi )
  C    | | | |-KPP_INIT             :: KPP package. ( see pkg/kpp )
  C    | | | |-KPP_OPEN_DIAGS
  C    | | | |-OBCS_INIT_VARIABLES  :: Open bndy. package. ( see pkg/obcs )
+ C    | | | |-PTRACERS_INIT        :: multi. tracer package,(see pkg/ptracers)
+ C    | | | |-GCHEM_INIT           :: tracer interface pkg (see pkh/gchem)
  C    | | | |-AIM_INIT             :: Interm. atmos package. ( see pkg/aim )
  C    | | | |-CTRL_MAP_INI         :: Control vector package.( see pkg/ctrl )
  C    | | | |-COST_INIT            :: Cost function package. ( see pkg/cost )
-Line 1672 
 C/\  | | | |                    :: Simpl
+Line 1677 
 C/\  | | | |                    :: Simpl
  C/\  | | | |                    :: for forcing datasets.
  C/\  | | | |
  C/\  | | | |-EXCH :: Sync forcing. in overlap regions.
+ C/\  | | |-SEAICE_MODEL   :: Compute sea-ice terms. ( pkg/seaice )
+ C/\  | | |-FREEZE         :: Limit surface temperature.
+ C/\  | | |-GCHEM_FIELD_LOAD :: load tracer forcing fields (pkg/gchem)
  C/\  | | |
  C/\  | | |-THERMODYNAMICS :: theta, salt + tracer equations driver.
  C/\  | | | |
  C/\  | | | |-INTEGRATE_FOR_W :: Integrate for vertical velocity.
  C/\  | | | |-OBCS_APPLY_W    :: Open bndy. package ( see pkg/obcs ).
- C/\  | | | |-FIND_RHO        :: Calculates [rho(S,T,z)-Rhonil] of a slice
+ C/\  | | | |-FIND_RHO        :: Calculates [rho(S,T,z)-RhoConst] of a slice
  C/\  | | | |-GRAD_SIGMA      :: Calculate isoneutral gradients
  C/\  | | | |-CALC_IVDC       :: Set Implicit Vertical Diffusivity for Convection
  C/\  | | | |
  C/\  | | | |-OBCS_CALC            :: Open bndy. package ( see pkg/obcs ).
  C/\  | | | |-EXTERNAL_FORCING_SURF:: Accumulates appropriately dimensioned
- C/\  | | | |                      :: forcing terms.
+ C/\  | | | | |                    :: forcing terms.
+ C/\  | | | | |-PTRACERS_FORCING_SURF :: Tracer package ( see pkg/ptracers ).
  C/\  | | | |
  C/\  | | | |-GMREDI_CALC_TENSOR   :: GM package ( see pkg/gmredi ).
  C/\  | | | |-GMREDI_CALC_TENSOR_DUMMY :: GM package ( see pkg/gmredi ).
-Line 1701 
 C/\  | | | |
+Line 1710 
 C/\  | | | |
  C/\  | | | |-CALC_GT              :: Calculate the temperature tendency terms
  C/\  | | | | |
  C/\  | | | | |-GAD_CALC_RHS       :: Generalised advection package
- C/\  | | | | |                    :: ( see pkg/gad )
+ C/\  | | | | | |                  :: ( see pkg/gad )
+ C/\  | | | | | |-KPP_TRANSPORT_T  :: KPP non-local transport ( see pkg/kpp ).
+ C/\  | | | | |
  C/\  | | | | |-EXTERNAL_FORCING_T :: Problem specific forcing for temperature.
  C/\  | | | | |-ADAMS_BASHFORTH2   :: Extrapolate tendencies forward in time.
  C/\  | | | | |-FREESURF_RESCALE_G :: Re-scale Gt for free-surface height.
-Line 1711 
 C/\  | | | |
+Line 1722 
 C/\  | | | |
  C/\  | | | |-CALC_GS              :: Calculate the salinity tendency terms
  C/\  | | | | |
  C/\  | | | | |-GAD_CALC_RHS       :: Generalised advection package
- C/\  | | | | |                    :: ( see pkg/gad )
+ C/\  | | | | | |                  :: ( see pkg/gad )
+ C/\  | | | | | |-KPP_TRANSPORT_S  :: KPP non-local transport ( see pkg/kpp ).
+ C/\  | | | | |
  C/\  | | | | |-EXTERNAL_FORCING_S :: Problem specific forcing for salt.
  C/\  | | | | |-ADAMS_BASHFORTH2   :: Extrapolate tendencies forward in time.
  C/\  | | | | |-FREESURF_RESCALE_G :: Re-scale Gs for free-surface height.
  C/\  | | | |
  C/\  | | | |-TIMESTEP_TRACER      :: Step tracer field forward in time
  C/\  | | | |
- C/\  | | | |-CALC_GTR1            :: Calculate other tracer(s) tendency terms
+ C/\  | | | |-TIMESTEP_TRACER      :: Step tracer field forward in time
+ C/\  | | | |
+ C/\  | | | |-PTRACERS_INTEGRATE   :: Integrate other tracer(s) (see pkg/ptracers).
  C/\  | | | | |
  C/\  | | | | |-GAD_CALC_RHS       :: Generalised advection package
- C/\  | | | | |                    :: ( see pkg/gad )
+ C/\  | | | | | |                  :: ( see pkg/gad )
- C/\  | | | | |-EXTERNAL_FORCING_TR:: Problem specific forcing for tracer.
+ C/\  | | | | | |-KPP_TRANSPORT_PTR:: KPP non-local transport ( see pkg/kpp ).
+ C/\  | | | | |
+ C/\  | | | | |-PTRACERS_FORCING   :: Problem specific forcing for tracer.
+ C/\  | | | | |-GCHEM_FORCING_INT  :: tracer forcing for gchem pkg (if all
+ C/\  | | | | |                       tendancy terms calcualted together)
  C/\  | | | | |-ADAMS_BASHFORTH2   :: Extrapolate tendencies forward in time.
  C/\  | | | | |-FREESURF_RESCALE_G :: Re-scale Gs for free-surface height.
+ C/\  | | | | |-TIMESTEP_TRACER    :: Step tracer field forward in time
  C/\  | | | |
- C/\  | | | |-TIMESTEP_TRACER      :: Step tracer field forward in time
  C/\  | | | |-OBCS_APPLY_TS        :: Open bndy. package (see pkg/obcs ).
- C/\  | | | |-FREEZE               :: Limit range of temperature.
  C/\  | | | |
  C/\  | | | |-IMPLDIFF             :: Solve vertical implicit diffusion equation.
  C/\  | | | |-OBCS_APPLY_TS        :: Open bndy. package (see pkg/obcs ).
-Line 1787 
 C/\  | | |
+Line 1805 
 C/\  | | |
  C/\  | | |-DO_FIELDS_BLOCKING_EXCHANGES :: Sync up overlap regions.
  C/\  | | | |-EXCH
  C/\  | | |
+ C/\  | | |-GCHEM_FORCING_SEP :: tracer forcing for gchem pkg (if
+ C/\  | | |                      tracer dependent tendencies calculated
+ C/\  | | |                      separatly)
+ C/\  | | |
  C/\  | | |-FLT_MAIN         :: Float package ( pkg/flt ).
  C/\  | | |
  C/\  | | |-MONITOR          :: Monitor package ( pkg/monitor ).
-Line 1797 
 C/\  | | | |-TIMEAVE_STATV_WRITE :: Time
+Line 1819 
 C/\  | | | |-TIMEAVE_STATV_WRITE :: Time
  C/\  | | | |-AIM_WRITE_DIAGS     :: Intermed. atmos diags. see pkg/aim
  C/\  | | | |-GMREDI_DIAGS        :: GM diags. see pkg/gmredi
  C/\  | | | |-KPP_DO_DIAGS        :: KPP diags. see pkg/kpp
+ C/\  | | | |-SBO_CALC            :: SBO diags. see pkg/sbo
+ C/\  | | | |-SBO_DIAGS           :: SBO diags. see pkg/sbo
+ C/\  | | | |-SEAICE_DO_DIAGS     :: SEAICE diags. see pkg/seaice
+ C/\  | | | |-GCHEM_DIAGS         :: gchem diags. see pkg/gchem
  C/\  | | |
  C/\  | | |-WRITE_CHECKPOINT :: Do I/O for restart files.
  C/\  | |
-Line 1814 
 C    |-TIMER_PRINTALL :: Computational t
+Line 1840 
 C    |-TIMER_PRINTALL :: Computational t
  C    |
  C    |-COMM_STATS     :: Summarise inter-proc and inter-thread communication
  C                     :: events.
  C
  \end{verbatim}
  }

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