/[MITgcm]/manual/s_examples/tracer_adjsens/doc_ad_examples.tex
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revision 1.2 by jmc, Tue Jan 15 20:16:44 2008 UTC revision 1.3 by jmc, Mon Aug 30 23:09:20 2010 UTC
# Line 3  Line 3 
3    
4  %**********************************************************************  %**********************************************************************
5  \section{Sensitivity of Air-Sea Exchange to Tracer Injection Site }  \section{Sensitivity of Air-Sea Exchange to Tracer Injection Site }
6  \label{www:tutorials}  %\label{www:tutorials}
7  \label{sect:eg-simple-tracer-adjoint}  \label{sec:eg-simple-tracer-adjoint}
8  \label{sec_ad_setup_ex}  \label{sec_ad_setup_ex}
9  \label{sect:tutorialIII}  \label{sec:tutorialIII}
10  \begin{rawhtml}  \begin{rawhtml}
11  <!-- CMIREDIR:sec_ad_setup_ex: -->  <!-- CMIREDIR:sec_ad_setup_ex: -->
12  \end{rawhtml}  \end{rawhtml}
# Line 14  Line 14 
14  (in directory: {\it verification/tutorial\_tracer\_adjsens/})  (in directory: {\it verification/tutorial\_tracer\_adjsens/})
15  \end{center}  \end{center}
16  %**********************************************************************  %**********************************************************************
17    \label{ask_the_author:tracer_adjsens:doc_ad_examples}
18    
19  MITgcm has been adapted to enable AD using TAMC or TAF.  MITgcm has been adapted to enable AD using TAMC or TAF.
20  The present description, therefore, is specific to the  The present description, therefore, is specific to the
# Line 26  The AD-relevant hooks in the code are sk Line 27  The AD-relevant hooks in the code are sk
27  \ref{fig:adthemodel}, \ref{fig:adthemain}.  \ref{fig:adthemodel}, \ref{fig:adthemain}.
28    
29  \subsection{Overview of the experiment}  \subsection{Overview of the experiment}
30  \label{www:tutorials}  %\label{www:tutorials}
31    
32  We describe an adjoint sensitivity analysis of out-gassing from  We describe an adjoint sensitivity analysis of out-gassing from
33  the ocean into the atmosphere of a carbon-like tracer injected  the ocean into the atmosphere of a carbon-like tracer injected
34  into the ocean interior (see \cite{hil-eta:01}).  into the ocean interior (see \cite{hil-eta:01}).
35    
36  \subsubsection{Passive tracer equation}  \subsubsection{Passive tracer equation}
37  \label{www:tutorials}  %\label{www:tutorials}
38    
39  For this work MITgcm was augmented with a thermodynamically  For this work MITgcm was augmented with a thermodynamically
40  inactive tracer, $C$. Tracer residing in the ocean  inactive tracer, $C$. Tracer residing in the ocean
# Line 68  As source we choose a constant in time i Line 69  As source we choose a constant in time i
69  $ S = 1 \,\, {\rm mol / s}$.  $ S = 1 \,\, {\rm mol / s}$.
70    
71  \subsubsection{Model configuration}  \subsubsection{Model configuration}
72  \label{www:tutorials}  %\label{www:tutorials}
73    
74  The model configuration employed has a constant  The model configuration employed has a constant
75  $4^\circ \times 4^\circ$ resolution horizontal grid and realistic  $4^\circ \times 4^\circ$ resolution horizontal grid and realistic
# Line 80  fresh-water forcing the model reproduces Line 81  fresh-water forcing the model reproduces
81  features of the ocean general circulation.  features of the ocean general circulation.
82    
83  \subsubsection{Out-gassing cost function}  \subsubsection{Out-gassing cost function}
84  \label{www:tutorials}  %\label{www:tutorials}
85    
86  To quantify and understand out-gassing due to injections of $C$  To quantify and understand out-gassing due to injections of $C$
87  in eqn. (\ref{carbon_ddt}),  in eqn. (\ref{carbon_ddt}),
# Line 107  and regions in which $CO_2$ injections w Line 108  and regions in which $CO_2$ injections w
108  sequestered within the ocean.  sequestered within the ocean.
109    
110  \subsection{Code configuration}  \subsection{Code configuration}
111  \label{www:tutorials}  %\label{www:tutorials}
112    
113  The model configuration for this experiment resides under the  The model configuration for this experiment resides under the
114  directory {\it verification/carbon/}.  directory {\it verification/carbon/}.
# Line 183  Below we describe the customizations of Line 184  Below we describe the customizations of
184  specific to this experiment.  specific to this experiment.
185    
186  \subsubsection{File {\it .genmakerc}}  \subsubsection{File {\it .genmakerc}}
187  \label{www:tutorials}  %\label{www:tutorials}
188  This file overwrites default settings of {\it genmake}.  This file overwrites default settings of {\it genmake}.
189  In the present example it is used to switch on the following  In the present example it is used to switch on the following
190  packages which are related to automatic differentiation  packages which are related to automatic differentiation
# Line 193  Other packages which are not needed are Line 194  Other packages which are not needed are
194  \hspace*{4ex} {\tt set DISABLE=( aim obcs zonal\_filt shap\_filt cal exf )}  \hspace*{4ex} {\tt set DISABLE=( aim obcs zonal\_filt shap\_filt cal exf )}
195    
196  \subsubsection{File {\it COST\_CPPOPTIONS.h,  CTRL\_OPTIONS.h}}  \subsubsection{File {\it COST\_CPPOPTIONS.h,  CTRL\_OPTIONS.h}}
197  \label{www:tutorials}  %\label{www:tutorials}
198    
199  These files used to contain package-specific CPP-options  These files used to contain package-specific CPP-options
200  (see Section \ref{???}).  (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
201  For technical reasons those options have been grouped together  For technical reasons those options have been grouped together
202  in the file {\it ECCO\_OPTIONS.h}.  in the file {\it ECCO\_OPTIONS.h}.
203  To retain the modularity, the files have been kept and contain  To retain the modularity, the files have been kept and contain
204  the standard include of the {\it CPP\_OPTIONS.h} file.  the standard include of the {\it CPP\_OPTIONS.h} file.
205    
206  \subsubsection{File {\it CPP\_EEOPTIONS.h}}  \subsubsection{File {\it CPP\_EEOPTIONS.h}}
207  \label{www:tutorials}  %\label{www:tutorials}
208    
209  This file contains 'wrapper'-specific CPP options.  This file contains 'wrapper'-specific CPP options.
210  It only needs to be changed if the code is to be run  It only needs to be changed if the code is to be run
211  in a parallel environment (see Section \ref{???}).  in a parallel environment (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
212    
213  \subsubsection{File {\it CPP\_OPTIONS.h}}  \subsubsection{File {\it CPP\_OPTIONS.h}}
214  \label{www:tutorials}  %\label{www:tutorials}
215    
216  This file contains model-specific CPP options  This file contains model-specific CPP options
217  (see Section \ref{???}).  (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
218  Most options are related to the forward model setup.  Most options are related to the forward model setup.
219  They are identical to the global steady circulation setup of  They are identical to the global steady circulation setup of
220  {\it verification/global\_ocean.90x40x15/}.  {\it verification/global\_ocean.90x40x15/}.
# Line 242  adjoint-generated gradient. Line 243  adjoint-generated gradient.
243  The gradient check package is further described in Section ???.  The gradient check package is further described in Section ???.
244    
245  \subsubsection{File {\it ECCO\_OPTIONS.h}}  \subsubsection{File {\it ECCO\_OPTIONS.h}}
246  \label{www:tutorials}  %\label{www:tutorials}
247    
248  The CPP options of several AD-related packages are grouped  The CPP options of several AD-related packages are grouped
249  in this file:  in this file:
# Line 266  defines TAMC-related features in the cod Line 267  defines TAMC-related features in the cod
267  %  %
268  \hspace*{4ex} {\tt \#define ALLOW\_TAMC\_CHECKPOINTING} \\  \hspace*{4ex} {\tt \#define ALLOW\_TAMC\_CHECKPOINTING} \\
269  enables the checkpointing feature of TAMC  enables the checkpointing feature of TAMC
270  (see Section \ref{???}).  (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
271  In the present example a 3-level checkpointing is implemented.  In the present example a 3-level checkpointing is implemented.
272  The code contains the relevant store directives, common block  The code contains the relevant store directives, common block
273  and tape initializations, storing key computation,  and tape initializations, storing key computation,
# Line 279  in the files {\it checkpoint\_lev3\_dire Line 280  in the files {\it checkpoint\_lev3\_dire
280  %  %
281  \hspace*{4ex} {\tt \#define ALLOW\_AUTODIFF\_MONITOOR} \\  \hspace*{4ex} {\tt \#define ALLOW\_AUTODIFF\_MONITOOR} \\
282  enables the monitoring of intermediate adjoint variables  enables the monitoring of intermediate adjoint variables
283  (see Section \ref{???}). \\  (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}). \\
284  %  %
285  \hspace*{4ex} {\tt \#define ALLOW\_DIVIDED\_ADJOINT} \\  \hspace*{4ex} {\tt \#define ALLOW\_DIVIDED\_ADJOINT} \\
286  enables adjoint dump and restart  enables adjoint dump and restart
287  (see Section \ref{???}).  (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
288  %  %
289  \item Cost function package: {\it pkg/cost/} \\  \item Cost function package: {\it pkg/cost/} \\
290  This package contains all relevant routines for  This package contains all relevant routines for
291  initializing, accumulating and finalizing the cost function  initializing, accumulating and finalizing the cost function
292  (see Section \ref{???}). \\  (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}). \\
293  \hspace*{4ex} {\tt \#define ALLOW\_COST} \\  \hspace*{4ex} {\tt \#define ALLOW\_COST} \\
294  enables all general aspects of the cost function handling,  enables all general aspects of the cost function handling,
295  in particular the hooks in the forward code for  in particular the hooks in the forward code for
# Line 325  isopycnal diffusivity \\ Line 326  isopycnal diffusivity \\
326  \end{itemize}  \end{itemize}
327    
328  \subsubsection{File {\it SIZE.h}}  \subsubsection{File {\it SIZE.h}}
329  \label{www:tutorials}  %\label{www:tutorials}
330    
331  The file contains the grid point dimensions of the forward  The file contains the grid point dimensions of the forward
332  model. It is identical to the {\it verification/exp2/}: \\  model. It is identical to the {\it verification/exp2/}: \\
# Line 338  with standard overlap dimensioning Line 339  with standard overlap dimensioning
339  {\tt OLx = OLy = 3}.  {\tt OLx = OLy = 3}.
340    
341  \subsubsection{File {\it adcommon.h}}  \subsubsection{File {\it adcommon.h}}
342  \label{www:tutorials}  %\label{www:tutorials}
343    
344  This file contains common blocks of some adjoint variables  This file contains common blocks of some adjoint variables
345  that are generated by TAMC.  that are generated by TAMC.
# Line 371  The header file is enabled via the CPP-o Line 372  The header file is enabled via the CPP-o
372  {\bf ALLOW\_AUTODIFF\_MONITOR}.  {\bf ALLOW\_AUTODIFF\_MONITOR}.
373    
374  \subsubsection{File {\it tamc.h}}  \subsubsection{File {\it tamc.h}}
375  \label{www:tutorials}  %\label{www:tutorials}
376    
377  This routine contains the dimensions for TAMC checkpointing  This routine contains the dimensions for TAMC checkpointing
378  and some indices relevant for storing ky computations.  and some indices relevant for storing ky computations.
# Line 380  and some indices relevant for storing ky Line 381  and some indices relevant for storing ky
381  %  %
382  \item {\tt \#ifdef ALLOW\_TAMC\_CHECKPOINTING} \\  \item {\tt \#ifdef ALLOW\_TAMC\_CHECKPOINTING} \\
383  3-level checkpointing is enabled, i.e. the timestepping  3-level checkpointing is enabled, i.e. the timestepping
384  is divided into three different levels (see Section \ref{???}).  is divided into three different levels (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
385  The model state of the outermost ({\tt nchklev\_3}) and the  The model state of the outermost ({\tt nchklev\_3}) and the
386  intermediate ({\tt nchklev\_2}) timestepping loop are stored to file  intermediate ({\tt nchklev\_2}) timestepping loop are stored to file
387  (handled in {\it the\_main\_loop}).  (handled in {\it the\_main\_loop}).
# Line 415  The following parameters may be worth de Line 416  The following parameters may be worth de
416  ~  ~
417    
418  \subsubsection{File {\it makefile}}  \subsubsection{File {\it makefile}}
419  \label{www:tutorials}  %\label{www:tutorials}
420    
421  This file contains all relevant parameter flags and  This file contains all relevant parameter flags and
422  lists to run TAMC or TAF.  lists to run TAMC or TAF.
# Line 499  adjoint routines refer to the TAMC defau Line 500  adjoint routines refer to the TAMC defau
500    
501    
502  \subsubsection{The input parameter files}  \subsubsection{The input parameter files}
503  \label{www:tutorials}  %\label{www:tutorials}
504    
505  \paragraph{File {\it data}}  \paragraph{File {\it data}}
506    
# Line 535  surface boundary values (surface wind st Line 536  surface boundary values (surface wind st
536  Contains model state after model spinup.  Contains model state after model spinup.
537    
538  \subsection{Compiling the model and its adjoint}  \subsection{Compiling the model and its adjoint}
539  \label{www:tutorials}  %\label{www:tutorials}
540    
541  The built process of the adjoint model is slightly more  The built process of the adjoint model is slightly more
542  complex than that of compiling the forward code.  complex than that of compiling the forward code.
# Line 657  a more straightforward build process. Line 658  a more straightforward build process.
658  {\small  {\small
659  \[  \[
660  \boxed{  \boxed{
661  \begin{split}  \begin{aligned}
662   ~ & \mbox{\tt cd bin} \\   ~ & \mbox{\tt cd bin} \\
663   ~ & \mbox{\tt ln -s ../verification/my\_experiment/code/.genmakerc .} \\   ~ & \mbox{\tt ln -s ../verification/my\_experiment/code/.genmakerc .} \\
664   ~ & \mbox{\tt ln -s ../verification/my\_experiment/code/*.[Fh] .} \\   ~ & \mbox{\tt ln -s ../verification/my\_experiment/code/*.[Fh] .} \\
# Line 669  a more straightforward build process. Line 670  a more straightforward build process.
670   ~ & \hspace*{6ex} \mbox{\tt                 adrestore small\_f allcode admodeltaf/admodeltamc adchange} \\   ~ & \hspace*{6ex} \mbox{\tt                 adrestore small\_f allcode admodeltaf/admodeltamc adchange} \\
671   ~ & \mbox{\tt cd ../bin} \\   ~ & \mbox{\tt cd ../bin} \\
672   ~ & \mbox{\tt make} \\   ~ & \mbox{\tt make} \\
673  \end{split}  \end{aligned}
674  }  }
675  \]  \]
676  }  }
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