/[MITgcm]/manual/s_autodiff/text/doc_ad_2.tex

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-revision 1.15 by heimbach,
Wed Apr 24 11:01:46 2002 UTC
+revision 1.17 by edhill,
Sat Oct 16 03:40:17 2004 UTC
 Line 42 
 Jacobian matrices of the forward code's
  %**********************************************************************
  \section{Some basic algebra}
  \label{sec_ad_algebra}
+ \begin{rawhtml}
+ <!-- CMIREDIR:sec_ad_algebra: -->
+ \end{rawhtml}
  %**********************************************************************
  Let $ \cal{M} $ be a general nonlinear, model, i.e. a
-Line 676 
 Schematic view of intermediate dump and
+Line 679 
 Schematic view of intermediate dump and
  %**********************************************************************
  \section{TLM and ADM generation in general}
  \label{sec_ad_setup_gen}
+ \begin{rawhtml}
+ <!-- CMIREDIR:sec_ad_setup_gen: -->
+ \end{rawhtml}
  %**********************************************************************
  In this section we describe in a general fashion
  the parts of the code that are relevant for automatic
- differentiation using the software tool TAMC.
+ differentiation using the software tool TAF.
  \input{part5/doc_ad_the_model}
  The basic flow is depicted in \ref{fig:adthemodel}.
- If the option {\tt ALLOW\_AUTODIFF\_TAMC} is defined, the driver routine
+ If CPP option {\tt ALLOW\_AUTODIFF\_TAMC} is defined, the driver routine
  {\it the\_model\_main}, instead of calling {\it the\_main\_loop},
  invokes the adjoint of this routine, {\it adthe\_main\_loop},
- which is the toplevel routine in terms of reverse mode computation.
+ which is the toplevel routine in terms of automatic differentiation.
- The routine {\it adthe\_main\_loop} has been generated by TAMC.
+ The routine {\it adthe\_main\_loop} has been generated by TAF.
- It contains both the forward integration of the full model,
+ It contains both the forward integration of the full model, the
+ cost function calculation,
  any additional storing that is required for efficient checkpointing,
  and the reverse integration of the adjoint model.
- The structure of {\it adthe\_main\_loop} has been strongly
- simplified for clarification; in particular, no checkpointing
+ [DESCRIBE IN A SEPARATE SECTION THE WORKING OF THE TLM]
+ In Fig. \ref{fig:adthemodel}
+ the structure of {\it adthe\_main\_loop} has been strongly
+ simplified to focus on the essentials; in particular, no checkpointing
  procedures are shown here.
  Prior to the call of {\it adthe\_main\_loop}, the routine
  {\it ctrl\_unpack} is invoked to unpack the control vector
-Line 709 
 the driver routine {\it grdchk\_main} is
+Line 720 
 the driver routine {\it grdchk\_main} is
  the gradient has been computed via the adjoint
  (cf. Section \ref{section_grdchk}).
+ %------------------------------------------------------------------
+ \subsection{General setup
+ \label{section_ad_setup}}
+ In order to configure AD-related setups the following packages need
+ to be enabled:
+ {\it
+ \begin{table}[h!]
+ \begin{tabular}{l}
+ autodiff \\
+ ctrl \\
+ cost \\
+ grdchk \\
+ \end{tabular}
+ \end{table}
+ }
+ The packages are enabled by adding them to your experiment-specific
+ configuration file
+ {\it packages.conf} (see Section ???).
+ The following AD-specific CPP option files need to be customized:
+ %
+ \begin{itemize}
+ %
+ \item {\it ECCO\_CPPOPTIONS.h} \\
+ This header file collects CPP options for the packages
+ {\it autodiff, cost, ctrl} as well as AD-unrelated options for
+ the external forcing package {\it exf}.
+ \footnote{NOTE: These options are not set in their package-specific
+ headers such as {\it COST\_CPPOPTIONS.h}, but are instead collected
+ in the single header file {\it ECCO\_CPPOPTIONS.h}.
+ The package-specific header files serve as simple
+ placeholders at this point.}
+ %
+ \item {\it tamc.h} \\
+ This header configures the splitting of the time stepping loop
+ w.r.t. the 3-level checkpointing (see section ???).
+ %
+ \end{itemize}
+ %------------------------------------------------------------------
+ \subsection{Building the AD code
+ \label{section_ad_build}}
+ The build process of an AD code is very similar to building
+ the forward model. However, depending on which AD code one wishes
+ to generate, and on which AD tool is available (TAF or TAMC),
+ the following {\tt make} targets are available:
+ \begin{table}[h!]
+ {\footnotesize
+ \begin{tabular}{ccll}
+ ~ & {\it AD-target} & {\it output} & {\it description} \\
+ \hline
+ \hline
+ (1) & {\tt <MODE><TOOL>only} & {\tt <MODE>\_<TOOL>\_output.f}  &
+ generates code for $<$MODE$>$ using $<$TOOL$>$ \\
+ ~ & ~ & ~ & no {\tt make} dependencies on {\tt .F .h} \\
+ ~ & ~ & ~ & useful for compiling on remote platforms \\
+ \hline
+ (2) & {\tt <MODE><TOOL>} & {\tt <MODE>\_<TOOL>\_output.f}  &
+ generates code for $<$MODE$>$ using $<$TOOL$>$ \\
+ ~ & ~ & ~ & includes {\tt make} dependencies on {\tt .F .h} \\
+ ~ & ~ & ~ & i.e. input for $<$TOOL$>$ may be re-generated \\
+ \hline
+ (3) & {\tt <MODE>all} & {\tt mitgcmuv\_<MODE>}  &
+ generates code for $<$MODE$>$ using $<$TOOL$>$ \\
+ ~ & ~ & ~ & and compiles all code \\
+ ~ & ~ & ~ & (use of TAF is set as default) \\
+ \hline
+ \hline
+ \end{tabular}
+ }
+ \end{table}
+ %
+ Here, the following placeholders are used
+ %
+ \begin{itemize}
+ %
+ \item [$<$TOOL$>$]
+ %
+ \begin{itemize}
+ %
+ \item {\tt TAF}
+ \item {\tt TAMC}
+ %
+ \end{itemize}
+ %
+ \item [$<$MODE$>$]
+ %
+ \begin{itemize}
+ %
+ \item {\tt ad} generates the adjoint model (ADM)
+ \item {\tt ftl} generates the tangent linear model (TLM)
+ \item {\tt svd} generates both ADM and TLM for \\
+ singular value decomposition (SVD) type calculations
+ %
+ \end{itemize}
+ %
+ \end{itemize}
+ For example, to generate the adjoint model using TAF after routines ({\tt .F})
+ or headers ({\tt .h}) have been modified, but without compilation,
+ type {\tt make adtaf};
+ or, to generate the tangent linear model using TAMC without
+ re-generating the input code, type {\tt make ftltamconly}.
+ A typical full build process to generate the ADM via TAF would
+ look like follows:
+ \begin{verbatim}
+ % mkdir build
+ % cd build
+ % ../../../tools/genmake2 -mods=../code_ad
+ % make depend
+ % make adall
+ \end{verbatim}
+ %------------------------------------------------------------------
+ \subsection{The AD build process in detail
+ \label{section_ad_build_detail}}
+ The {\tt make <MODE>all} target consists of the following procedures:
+ \begin{enumerate}
+ %
+ \item
+ A header file {\tt AD\_CONFIG.h} is generated which contains a CPP option
+ on which code ought to be generated. Depending on the {\tt make} target,
+ the contents is
+ \begin{itemize}
+ \item
+ {\tt \#define ALLOW\_ADJOINT\_RUN}
+ \item
+ {\tt \#define ALLOW\_TANGENTLINEAR\_RUN}
+ \item
+ {\tt \#define ALLOW\_ECCO\_OPTIMIZATION}
+ \end{itemize}
+ %
+ \item
+ A single file {\tt <MODE>\_input\_code.f} is concatenated
+ consisting of all {\tt .f} files that are part of the list {\bf AD\_FILES}
+ and all {\tt .flow} files that are part of the list {\bf AD\_FLOW\_FILES}.
+ %
+ \item
+ The AD tool is invoked with the {\bf <MODE>\_<TOOL>\_FLAGS}.
+ The default AD tool flags in {\tt genmake2} can be overrwritten by
+ an {\tt adjoint\_options} file (similar to the platform-specific
+ {\tt build\_options}, see Section ???.
+ The AD tool writes the resulting AD code into the file
+ {\tt <MODE>\_input\_code\_ad.f}
+ %
+ \item
+ A short sed script {\tt adjoint\_sed} is applied to
+ {\tt <MODE>\_input\_code\_ad.f}
+ to reinstate {\bf myThid} into the CALL argument list of active file I/O.
+ The result is written to file {\tt <MODE>\_<TOOL>\_output.f}.
+ %
+ \item
+ All routines are compiled and an executable is generated
+ (see Table ???).
+ %
+ \end{enumerate}
+ \subsubsection{The list AD\_FILES and {\tt .list} files}
+ Not all routines are presented to the AD tool.
+ Routines typically hidden are diagnostics routines which
+ do not influence the cost function, but may create
+ artificial flow dependencies such as I/O of active variables.
+ {\tt genmake2} generates a list (or variable) {\bf AD\_FILES}
+ which contains all routines that are shown to the AD tool.
+ This list is put together from all files with suffix {\tt .list}
+ that {\tt genmake2} finds in its search directories.
+ The list file for the core MITgcm routines is in {\tt model/src/}
+ is called {\tt model\_ad\_diff.list}.
+ Note that no wrapper routine is shown to TAF. These are either
+ not visible at all to the AD code, or hand-written AD code
+ is available (see next section).
+ Each package directory contains its package-specific
+ list file {\tt <PKG>\_ad\_diff.list}. For example,
+ {\tt pkg/ptracers/} contains the file {\tt ptracers\_ad\_diff.list}.
+ Thus, enabling a package will automatically extend the
+ {\bf AD\_FILES} list of {\tt genmake2} to incorporate the
+ package-specific routines.
+ Note that you will need to regenerate the {\tt Makefile} if
+ you enable a package (e.g. by adding it to {\tt packages.conf})
+ and a {\tt Makefile} already exists.
+ \subsubsection{The list AD\_FLOW\_FILES and {\tt .flow} files}
+ TAMC and TAF can evaluate user-specified directives
+ that start with a specific syntax ({\tt CADJ}, {\tt C\$TAF}, {\tt !\$TAF}).
+ The main categories of directives are STORE directives and
+ FLOW directives. Here, we are concerned with flow directives,
+ store directives are treated elsewhere.
+ Flow directives enable the AD tool to evaluate how it should treat
+ routines that are 'hidden' by the user, i.e. routines which are
+ not contained in the {\bf AD\_FILES} list (see previous section),
+ but which are called in part of the code that the AD tool does see.
+ The flow directive tell the AD tool
+ %
+ \begin{itemize}
+ %
+ \item which subroutine arguments are input/output
+ \item which subroutine arguments are active
+ \item which subroutine arguments are required to compute the cost
+ \item which subroutine arguments are dependent
+ %
+ \end{itemize}
+ %
+ The syntax for the flow directives can be found in the
+ AD tool manuals.
+ {\tt genmake2} generates a list (or variable) {\bf AD\_FLOW\_FILES}
+ which contains all files with suffix{\tt .flow} that it finds
+ in its search directories.
+ The flow directives for the core MITgcm routines of
+ {\tt eesupp/src/} and {\tt model/src/}
+ reside in {\tt pkg/autodiff/}.
+ This directory also contains hand-written adjoint code
+ for the MITgcm WRAPPER (see Section ???).
+ Flow directives for package-specific routines are contained in
+ the corresponding package directories in the file
+ {\tt <PKG>\_ad.flow}, e.g. ptracers-specific directives are in
+ {\tt ptracers\_ad.flow}.
+ \subsubsection{Store directives for 3-level checkpointing}
+ The storing that is required at each period of the
+-level checkpointing is controled by three
+ top-level headers.
+ \begin{verbatim}
+ do ilev_3 = 1, nchklev_3
+ #  include ``checkpoint_lev3.h''
+    do ilev_2 = 1, nchklev_2
+ #     include ``checkpoint_lev2.h''
+       do ilev_1 = 1, nchklev_1
+ #        include ``checkpoint_lev1.h''
+ ...
+       end do
+    end do
+ end do
+ \end{verbatim}
+ All files {\tt checkpoint\_lev?.h} are contained in directory
+ {\tt pkg/autodiff/}.
+ \subsubsection{Changing the default AD tool flags: ad\_options files}
+ \subsubsection{Hand-written adjoint code}
+ %------------------------------------------------------------------
  \subsection{The cost function (dependent variable)
  \label{section_cost}}
-Line 726 
 in the next section.
+Line 1004 
 in the next section.
  \input{part5/doc_cost_flow}
- \subsubsection{genmake and CPP options}
+ \subsubsection{Enabling the package}
- %
- \begin{itemize}
- %
- \item
  \fbox{
  \begin{minipage}{12cm}
- {\it genmake}, {\it CPP\_OPTIONS.h}, {\it ECCO\_CPPOPTIONS.h}
+ {\it packages.conf}, {\it ECCO\_CPPOPTIONS.h}
  \end{minipage}
  }
- \end{itemize}
+ \begin{itemize}
- %
- The directory {\it pkg/cost} can be included to the
- compile list in 3 different ways (cf. Section \ref{???}):
  %
- \begin{enumerate}
+ \item
+ The package is enabled by adding {\it cost} to your file {\it packages.conf}
+ (see Section ???)
  %
- \item {\it genmake}: \\
+ \item
- Change the default settings in the file {\it genmake} by adding
- {\bf cost} to the {\bf enable} list (not recommended).
- %
+ \end{itemize}
- \item {\it .genmakerc}: \\
- Customize the settings of {\bf enable}, {\bf disable} which are
- appropriate for your experiment in the file {\it .genmakerc}
- and add the file to your compile directory.
- %
- \item genmake-options: \\
- Call {\it genmake} with the option
- {\tt genmake -enable=cost}.
  %
- \end{enumerate}
  N.B.: In general the following packages ought to be enabled
  simultaneously: {\it autodiff, cost, ctrl}.
  The basic CPP option to enable the cost function is {\bf ALLOW\_COST}.

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