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revision 1.22 by edhill, Tue Apr 4 18:33:52 2006 UTC revision 1.24 by jmc, Wed Apr 5 01:12:02 2006 UTC
# Line 165  manner, any computer architecture curren Line 165  manner, any computer architecture curren
165  scientific computing community.  scientific computing community.
166    
167  \subsection{Machine model parallelism}  \subsection{Machine model parallelism}
168    \label{sect:domain_decomposition}
169  \begin{rawhtml}  \begin{rawhtml}
170  <!-- CMIREDIR:domain_decomp: -->  <!-- CMIREDIR:domain_decomp: -->
171  \end{rawhtml}  \end{rawhtml}
# Line 1481  Core equations plus packages. Line 1482  Core equations plus packages.
1482  {\footnotesize  {\footnotesize
1483  \begin{verbatim}  \begin{verbatim}
1484  C  C
 C  
1485  C Invocation from WRAPPER level...  C Invocation from WRAPPER level...
1486  C  :  C  :
1487  C  :  C  :
# Line 1545  C    | | |-CTRL_INIT           :: Contro Line 1545  C    | | |-CTRL_INIT           :: Contro
1545  C    | | |-OPTIM_READPARMS     :: Optimisation support package. see pkg/ctrl  C    | | |-OPTIM_READPARMS     :: Optimisation support package. see pkg/ctrl
1546  C    | | |-GRDCHK_READPARMS    :: Gradient check package. see pkg/grdchk  C    | | |-GRDCHK_READPARMS    :: Gradient check package. see pkg/grdchk
1547  C    | | |-ECCO_READPARMS      :: ECCO Support Package. see pkg/ecco  C    | | |-ECCO_READPARMS      :: ECCO Support Package. see pkg/ecco
1548    C    | | |-PTRACERS_READPARMS  :: multiple tracer package, see pkg/ptracers
1549    C    | | |-GCHEM_READPARMS     :: tracer interface package, see pkg/gchem
1550  C    | |  C    | |
1551  C    | |-PACKAGES_CHECK  C    | |-PACKAGES_CHECK
1552  C    | | |  C    | | |
1553  C    | | |-KPP_CHECK           :: KPP Package. pkg/kpp  C    | | |-KPP_CHECK           :: KPP Package. pkg/kpp
1554  C    | | |-OBCS_CHECK          :: Open bndy Package. pkg/obcs  C    | | |-OBCS_CHECK          :: Open bndy Pacakge. pkg/obcs
1555  C    | | |-GMREDI_CHECK        :: GM Package. pkg/gmredi  C    | | |-GMREDI_CHECK        :: GM Package. pkg/gmredi
1556  C    | |  C    | |
1557  C    | |-PACKAGES_INIT_FIXED  C    | |-PACKAGES_INIT_FIXED
1558  C    | | |-OBCS_INIT_FIXED     :: Open bndy Package. see pkg/obcs  C    | | |-OBCS_INIT_FIXED     :: Open bndy Package. see pkg/obcs
1559  C    | | |-FLT_INIT            :: Floats Package. see pkg/flt  C    | | |-FLT_INIT            :: Floats Package. see pkg/flt
1560    C    | | |-GCHEM_INIT_FIXED    :: tracer interface pachage, see pkg/gchem
1561  C    | |  C    | |
1562  C    | |-ZONAL_FILT_INIT       :: FFT filter Package. see pkg/zonal_filt  C    | |-ZONAL_FILT_INIT       :: FFT filter Package. see pkg/zonal_filt
1563  C    | |  C    | |
1564  C    | |-INI_CG2D              :: 2d con. grad solver initialisation.  C    | |-INI_CG2D              :: 2d con. grad solver initialization.
1565  C    | |  C    | |
1566  C    | |-INI_CG3D              :: 3d con. grad solver initialisation.  C    | |-INI_CG3D              :: 3d con. grad solver initialization.
1567  C    | |  C    | |
1568  C    | |-CONFIG_SUMMARY        :: Provide synopsis of kernel setup.  C    | |-CONFIG_SUMMARY        :: Provide synopsis of kernel setup.
1569  C    |                         :: Includes annotated table of kernel  C    |                         :: Includes annotated table of kernel
# Line 1585  C    | | | Line 1588  C    | | |
1588  C    | | |-INI_CORI     :: Set coriolis term. zero, f-plane, beta-plane,  C    | | |-INI_CORI     :: Set coriolis term. zero, f-plane, beta-plane,
1589  C    | | |              :: sphere options are coded.  C    | | |              :: sphere options are coded.
1590  C    | | |  C    | | |
1591  C    | | |-INI_CG2D     :: 2d con. grad solver initialisation.  C    | | |-INI_CG2D     :: 2d con. grad solver initialization.
1592  C    | | |-INI_CG3D     :: 3d con. grad solver initialisation.  C    | | |-INI_CG3D     :: 3d con. grad solver initialization.
1593  C    | | |-INI_MIXING   :: Initialise diapycnal diffusivity.  C    | | |-INI_MIXING   :: Initialize diapycnal diffusivity.
1594  C    | | |-INI_DYNVARS  :: Initialise to zero all DYNVARS.h arrays (dynamical  C    | | |-INI_DYNVARS  :: Initialize to zero all DYNVARS.h arrays (dynamical
1595  C    | | |              :: fields).  C    | | |              :: fields).
1596  C    | | |  C    | | |
1597  C    | | |-INI_FIELDS   :: Control initializing model fields to non-zero  C    | | |-INI_FIELDS   :: Control initializing model fields to non-zero
# Line 1596  C    | | | |-INI_VEL    :: Initialize 3D Line 1599  C    | | | |-INI_VEL    :: Initialize 3D
1599  C    | | | |-INI_THETA  :: Set model initial temperature field.  C    | | | |-INI_THETA  :: Set model initial temperature field.
1600  C    | | | |-INI_SALT   :: Set model initial salinity field.  C    | | | |-INI_SALT   :: Set model initial salinity field.
1601  C    | | | |-INI_PSURF  :: Set model initial free-surface height/pressure.  C    | | | |-INI_PSURF  :: Set model initial free-surface height/pressure.
1602  C    | | |  C    | | | |-INI_PRESSURE :: Compute model initial hydrostatic pressure
1603  C    | | |-INI_TR1      :: Set initial tracer 1 distribution.  C    | | | |-READ_CHECKPOINT :: Read the checkpoint
1604  C    | | |  C    | | |
1605  C    | | |-THE_CORRECTION_STEP :: Step forward to next time step.  C    | | |-THE_CORRECTION_STEP :: Step forward to next time step.
1606  C    | | | |                   :: Here applied to move restart conditions  C    | | | |                   :: Here applied to move restart conditions
# Line 1624  C    | | | |-FIND_RHO  :: Find adjacent Line 1627  C    | | | |-FIND_RHO  :: Find adjacent
1627  C    | | | |-CONVECT   :: Mix static instability.  C    | | | |-CONVECT   :: Mix static instability.
1628  C    | | | |-TIMEAVE_CUMULATE :: Update convection statistics.  C    | | | |-TIMEAVE_CUMULATE :: Update convection statistics.
1629  C    | | |  C    | | |
1630  C    | | |-PACKAGES_INIT_VARIABLES :: Does initialisation of time evolving  C    | | |-PACKAGES_INIT_VARIABLES :: Does initialization of time evolving
1631  C    | | | |                       :: package data.  C    | | | |                       :: package data.
1632  C    | | | |  C    | | | |
1633  C    | | | |-GMREDI_INIT          :: GM package. ( see pkg/gmredi )  C    | | | |-GMREDI_INIT          :: GM package. ( see pkg/gmredi )
1634  C    | | | |-KPP_INIT             :: KPP package. ( see pkg/kpp )  C    | | | |-KPP_INIT             :: KPP package. ( see pkg/kpp )
1635  C    | | | |-KPP_OPEN_DIAGS      C    | | | |-KPP_OPEN_DIAGS    
1636  C    | | | |-OBCS_INIT_VARIABLES  :: Open bndy. package. ( see pkg/obcs )  C    | | | |-OBCS_INIT_VARIABLES  :: Open bndy. package. ( see pkg/obcs )
1637    C    | | | |-PTRACERS_INIT        :: multi. tracer package,(see pkg/ptracers)
1638    C    | | | |-GCHEM_INIT           :: tracer interface pkg (see pkh/gchem)
1639  C    | | | |-AIM_INIT             :: Interm. atmos package. ( see pkg/aim )  C    | | | |-AIM_INIT             :: Interm. atmos package. ( see pkg/aim )
1640  C    | | | |-CTRL_MAP_INI         :: Control vector package.( see pkg/ctrl )  C    | | | |-CTRL_MAP_INI         :: Control vector package.( see pkg/ctrl )
1641  C    | | | |-COST_INIT            :: Cost function package. ( see pkg/cost )  C    | | | |-COST_INIT            :: Cost function package. ( see pkg/cost )
# Line 1673  C/\  | | | |                    :: Simpl Line 1678  C/\  | | | |                    :: Simpl
1678  C/\  | | | |                    :: for forcing datasets.  C/\  | | | |                    :: for forcing datasets.
1679  C/\  | | | |                    C/\  | | | |                  
1680  C/\  | | | |-EXCH :: Sync forcing. in overlap regions.  C/\  | | | |-EXCH :: Sync forcing. in overlap regions.
1681    C/\  | | |-SEAICE_MODEL   :: Compute sea-ice terms. ( pkg/seaice )
1682    C/\  | | |-FREEZE         :: Limit surface temperature.
1683    C/\  | | |-GCHEM_FIELD_LOAD :: load tracer forcing fields (pkg/gchem)
1684  C/\  | | |  C/\  | | |
1685  C/\  | | |-THERMODYNAMICS :: theta, salt + tracer equations driver.  C/\  | | |-THERMODYNAMICS :: theta, salt + tracer equations driver.
1686  C/\  | | | |  C/\  | | | |
1687  C/\  | | | |-INTEGRATE_FOR_W :: Integrate for vertical velocity.  C/\  | | | |-INTEGRATE_FOR_W :: Integrate for vertical velocity.
1688  C/\  | | | |-OBCS_APPLY_W    :: Open bndy. package ( see pkg/obcs ).  C/\  | | | |-OBCS_APPLY_W    :: Open bndy. package ( see pkg/obcs ).
1689  C/\  | | | |-FIND_RHO        :: Calculates [rho(S,T,z)-Rhonil] of a slice  C/\  | | | |-FIND_RHO        :: Calculates [rho(S,T,z)-RhoConst] of a slice
1690  C/\  | | | |-GRAD_SIGMA      :: Calculate isoneutral gradients  C/\  | | | |-GRAD_SIGMA      :: Calculate isoneutral gradients
1691  C/\  | | | |-CALC_IVDC       :: Set Implicit Vertical Diffusivity for Convection  C/\  | | | |-CALC_IVDC       :: Set Implicit Vertical Diffusivity for Convection
1692  C/\  | | | |  C/\  | | | |
1693  C/\  | | | |-OBCS_CALC            :: Open bndy. package ( see pkg/obcs ).  C/\  | | | |-OBCS_CALC            :: Open bndy. package ( see pkg/obcs ).
1694  C/\  | | | |-EXTERNAL_FORCING_SURF:: Accumulates appropriately dimensioned  C/\  | | | |-EXTERNAL_FORCING_SURF:: Accumulates appropriately dimensioned
1695  C/\  | | | |                      :: forcing terms.  C/\  | | | | |                    :: forcing terms.
1696    C/\  | | | | |-PTRACERS_FORCING_SURF :: Tracer package ( see pkg/ptracers ).
1697  C/\  | | | |  C/\  | | | |
1698  C/\  | | | |-GMREDI_CALC_TENSOR   :: GM package ( see pkg/gmredi ).  C/\  | | | |-GMREDI_CALC_TENSOR   :: GM package ( see pkg/gmredi ).
1699  C/\  | | | |-GMREDI_CALC_TENSOR_DUMMY :: GM package ( see pkg/gmredi ).  C/\  | | | |-GMREDI_CALC_TENSOR_DUMMY :: GM package ( see pkg/gmredi ).
# Line 1702  C/\  | | | | Line 1711  C/\  | | | |
1711  C/\  | | | |-CALC_GT              :: Calculate the temperature tendency terms  C/\  | | | |-CALC_GT              :: Calculate the temperature tendency terms
1712  C/\  | | | | |  C/\  | | | | |
1713  C/\  | | | | |-GAD_CALC_RHS       :: Generalised advection package  C/\  | | | | |-GAD_CALC_RHS       :: Generalised advection package
1714  C/\  | | | | |                    :: ( see pkg/gad )  C/\  | | | | | |                  :: ( see pkg/gad )
1715    C/\  | | | | | |-KPP_TRANSPORT_T  :: KPP non-local transport ( see pkg/kpp ).
1716    C/\  | | | | |
1717  C/\  | | | | |-EXTERNAL_FORCING_T :: Problem specific forcing for temperature.  C/\  | | | | |-EXTERNAL_FORCING_T :: Problem specific forcing for temperature.
1718  C/\  | | | | |-ADAMS_BASHFORTH2   :: Extrapolate tendencies forward in time.  C/\  | | | | |-ADAMS_BASHFORTH2   :: Extrapolate tendencies forward in time.
1719  C/\  | | | | |-FREESURF_RESCALE_G :: Re-scale Gt for free-surface height.  C/\  | | | | |-FREESURF_RESCALE_G :: Re-scale Gt for free-surface height.
# Line 1712  C/\  | | | | Line 1723  C/\  | | | |
1723  C/\  | | | |-CALC_GS              :: Calculate the salinity tendency terms  C/\  | | | |-CALC_GS              :: Calculate the salinity tendency terms
1724  C/\  | | | | |  C/\  | | | | |
1725  C/\  | | | | |-GAD_CALC_RHS       :: Generalised advection package  C/\  | | | | |-GAD_CALC_RHS       :: Generalised advection package
1726  C/\  | | | | |                    :: ( see pkg/gad )  C/\  | | | | | |                  :: ( see pkg/gad )
1727    C/\  | | | | | |-KPP_TRANSPORT_S  :: KPP non-local transport ( see pkg/kpp ).
1728    C/\  | | | | |
1729  C/\  | | | | |-EXTERNAL_FORCING_S :: Problem specific forcing for salt.  C/\  | | | | |-EXTERNAL_FORCING_S :: Problem specific forcing for salt.
1730  C/\  | | | | |-ADAMS_BASHFORTH2   :: Extrapolate tendencies forward in time.  C/\  | | | | |-ADAMS_BASHFORTH2   :: Extrapolate tendencies forward in time.
1731  C/\  | | | | |-FREESURF_RESCALE_G :: Re-scale Gs for free-surface height.  C/\  | | | | |-FREESURF_RESCALE_G :: Re-scale Gs for free-surface height.
1732  C/\  | | | |  C/\  | | | |
1733  C/\  | | | |-TIMESTEP_TRACER      :: Step tracer field forward in time  C/\  | | | |-TIMESTEP_TRACER      :: Step tracer field forward in time
1734  C/\  | | | |  C/\  | | | |
1735  C/\  | | | |-CALC_GTR1            :: Calculate other tracer(s) tendency terms  C/\  | | | |-TIMESTEP_TRACER      :: Step tracer field forward in time
1736    C/\  | | | |
1737    C/\  | | | |-PTRACERS_INTEGRATE   :: Integrate other tracer(s) (see pkg/ptracers).
1738  C/\  | | | | |  C/\  | | | | |
1739  C/\  | | | | |-GAD_CALC_RHS       :: Generalised advection package  C/\  | | | | |-GAD_CALC_RHS       :: Generalised advection package
1740  C/\  | | | | |                    :: ( see pkg/gad )  C/\  | | | | | |                  :: ( see pkg/gad )
1741  C/\  | | | | |-EXTERNAL_FORCING_TR:: Problem specific forcing for tracer.  C/\  | | | | | |-KPP_TRANSPORT_PTR:: KPP non-local transport ( see pkg/kpp ).
1742    C/\  | | | | |
1743    C/\  | | | | |-PTRACERS_FORCING   :: Problem specific forcing for tracer.
1744    C/\  | | | | |-GCHEM_FORCING_INT  :: tracer forcing for gchem pkg (if all
1745    C/\  | | | | |                       tendancy terms calcualted together)
1746  C/\  | | | | |-ADAMS_BASHFORTH2   :: Extrapolate tendencies forward in time.  C/\  | | | | |-ADAMS_BASHFORTH2   :: Extrapolate tendencies forward in time.
1747  C/\  | | | | |-FREESURF_RESCALE_G :: Re-scale Gs for free-surface height.  C/\  | | | | |-FREESURF_RESCALE_G :: Re-scale Gs for free-surface height.
1748    C/\  | | | | |-TIMESTEP_TRACER    :: Step tracer field forward in time
1749  C/\  | | | |  C/\  | | | |
 C/\  | | | |-TIMESTEP_TRACER      :: Step tracer field forward in time  
1750  C/\  | | | |-OBCS_APPLY_TS        :: Open bndy. package (see pkg/obcs ).  C/\  | | | |-OBCS_APPLY_TS        :: Open bndy. package (see pkg/obcs ).
 C/\  | | | |-FREEZE               :: Limit range of temperature.  
1751  C/\  | | | |  C/\  | | | |
1752  C/\  | | | |-IMPLDIFF             :: Solve vertical implicit diffusion equation.  C/\  | | | |-IMPLDIFF             :: Solve vertical implicit diffusion equation.
1753  C/\  | | | |-OBCS_APPLY_TS        :: Open bndy. package (see pkg/obcs ).  C/\  | | | |-OBCS_APPLY_TS        :: Open bndy. package (see pkg/obcs ).
# Line 1788  C/\  | | | Line 1806  C/\  | | |
1806  C/\  | | |-DO_FIELDS_BLOCKING_EXCHANGES :: Sync up overlap regions.  C/\  | | |-DO_FIELDS_BLOCKING_EXCHANGES :: Sync up overlap regions.
1807  C/\  | | | |-EXCH                                                    C/\  | | | |-EXCH                                                  
1808  C/\  | | |  C/\  | | |
1809    C/\  | | |-GCHEM_FORCING_SEP :: tracer forcing for gchem pkg (if
1810    C/\  | | |                      tracer dependent tendencies calculated
1811    C/\  | | |                      separatly)
1812    C/\  | | |
1813  C/\  | | |-FLT_MAIN         :: Float package ( pkg/flt ).  C/\  | | |-FLT_MAIN         :: Float package ( pkg/flt ).
1814  C/\  | | |  C/\  | | |
1815  C/\  | | |-MONITOR          :: Monitor package ( pkg/monitor ).  C/\  | | |-MONITOR          :: Monitor package ( pkg/monitor ).
# Line 1798  C/\  | | | |-TIMEAVE_STATV_WRITE :: Time Line 1820  C/\  | | | |-TIMEAVE_STATV_WRITE :: Time
1820  C/\  | | | |-AIM_WRITE_DIAGS     :: Intermed. atmos diags. see pkg/aim  C/\  | | | |-AIM_WRITE_DIAGS     :: Intermed. atmos diags. see pkg/aim
1821  C/\  | | | |-GMREDI_DIAGS        :: GM diags. see pkg/gmredi  C/\  | | | |-GMREDI_DIAGS        :: GM diags. see pkg/gmredi
1822  C/\  | | | |-KPP_DO_DIAGS        :: KPP diags. see pkg/kpp  C/\  | | | |-KPP_DO_DIAGS        :: KPP diags. see pkg/kpp
1823    C/\  | | | |-SBO_CALC            :: SBO diags. see pkg/sbo
1824    C/\  | | | |-SBO_DIAGS           :: SBO diags. see pkg/sbo
1825    C/\  | | | |-SEAICE_DO_DIAGS     :: SEAICE diags. see pkg/seaice
1826    C/\  | | | |-GCHEM_DIAGS         :: gchem diags. see pkg/gchem
1827  C/\  | | |  C/\  | | |
1828  C/\  | | |-WRITE_CHECKPOINT :: Do I/O for restart files.  C/\  | | |-WRITE_CHECKPOINT :: Do I/O for restart files.
1829  C/\  | |  C/\  | |
# Line 1815  C    |-TIMER_PRINTALL :: Computational t Line 1841  C    |-TIMER_PRINTALL :: Computational t
1841  C    |  C    |
1842  C    |-COMM_STATS     :: Summarise inter-proc and inter-thread communication  C    |-COMM_STATS     :: Summarise inter-proc and inter-thread communication
1843  C                     :: events.  C                     :: events.
1844  C  C
1845  \end{verbatim}  \end{verbatim}
1846  }  }
1847    
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