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revision 1.29 by edhill, Thu Oct 14 19:11:47 2004 UTC revision 1.34 by edhill, Sat Apr 8 15:29:05 2006 UTC
# Line 15  structure are described more fully in ch Line 15  structure are described more fully in ch
15  this section, we provide information on how to customize the code when  this section, we provide information on how to customize the code when
16  you are ready to try implementing the configuration you have in mind.  you are ready to try implementing the configuration you have in mind.
17    
18    
19  \section{Where to find information}  \section{Where to find information}
20  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
21    \begin{rawhtml}
22    <!-- CMIREDIR:whereToFindInfo: -->
23    \end{rawhtml}
24    
25  A web site is maintained for release 2 (``Pelican'') of MITgcm:  A web site is maintained for release 2 (``Pelican'') of MITgcm:
26  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
# Line 50  http://mitgcm.org/htdig/ Line 54  http://mitgcm.org/htdig/
54    
55  \section{Obtaining the code}  \section{Obtaining the code}
56  \label{sect:obtainingCode}  \label{sect:obtainingCode}
57    \begin{rawhtml}
58    <!-- CMIREDIR:obtainingCode: -->
59    \end{rawhtml}
60    
61  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
62  the instructions below. As a courtesy we ask that you send e-mail to us at  the instructions below. As a courtesy we ask that you send e-mail to us at
# Line 92  be set within your shell.  For a csh or Line 99  be set within your shell.  For a csh or
99  \begin{verbatim}  \begin{verbatim}
100  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
101  \end{verbatim}  \end{verbatim}
102  in your .cshrc or .tcshrc file.  For bash or sh shells, put:  in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
103    shells, put:
104  \begin{verbatim}  \begin{verbatim}
105  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
106  \end{verbatim}  \end{verbatim}
# Line 118  The MITgcm web site contains further dir Line 126  The MITgcm web site contains further dir
126  code and CVS.  It also contains a web interface to our CVS archive so  code and CVS.  It also contains a web interface to our CVS archive so
127  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
128  development milestones:  development milestones:
129  \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
130  \begin{verbatim}  \begin{verbatim}
131  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
132  \end{verbatim}  \end{verbatim}
# Line 147  of CVS aliases Line 155  of CVS aliases
155    \label{tab:cvsModules}    \label{tab:cvsModules}
156  \end{table}  \end{table}
157    
158  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
159  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
160  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
161  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
162  track of your file versions with respect to the repository. Don't edit  track of your file versions with respect to the repository. Don't edit
163  the files in \textit{CVS}!  You can also use CVS to download code  the files in \texttt{CVS}!  You can also use CVS to download code
164  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
165  MITgcm code can be found  MITgcm code can be found
166  \begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/usingcvstoget.html" target="idontexist"> \end{rawhtml}
167  here  here
168  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
169  .  .
# Line 184  delete; even if you do not use CVS yours Line 192  delete; even if you do not use CVS yours
192  us if you should need to send us your copy of the code.  If a recent  us if you should need to send us your copy of the code.  If a recent
193  tar file does not exist, then please contact the developers through  tar file does not exist, then please contact the developers through
194  the  the
195  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
196  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
197  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
198  mailing list.  mailing list.
# Line 256  also means we can't tell what version of Line 264  also means we can't tell what version of
264  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
265    
266  \section{Model and directory structure}  \section{Model and directory structure}
267    \begin{rawhtml}
268    <!-- CMIREDIR:directory_structure: -->
269    \end{rawhtml}
270    
271  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
272  support wrapper. This wrapper is designed to provide a general  support wrapper. This wrapper is designed to provide a general
# Line 263  framework for grid-point models. MITgcmU Line 274  framework for grid-point models. MITgcmU
274  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
275  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
276  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
277  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
278  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
279  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
280  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
281  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
282  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
283  part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is  part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is
284  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
285  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
286  structure).  structure).
287    
288  \begin{itemize}  \begin{itemize}
289    
290  \item \textit{bin}: this directory is initially empty. It is the  \item \texttt{bin}: this directory is initially empty. It is the
291    default directory in which to compile the code.    default directory in which to compile the code.
292        
293  \item \textit{diags}: contains the code relative to time-averaged  \item \texttt{diags}: contains the code relative to time-averaged
294    diagnostics. It is subdivided into two subdirectories \textit{inc}    diagnostics. It is subdivided into two subdirectories \texttt{inc}
295    and \textit{src} that contain include files (*.\textit{h} files) and    and \texttt{src} that contain include files (\texttt{*.h} files) and
296    Fortran subroutines (*.\textit{F} files), respectively.    Fortran subroutines (\texttt{*.F} files), respectively.
297    
298  \item \textit{doc}: contains brief documentation notes.  \item \texttt{doc}: contains brief documentation notes.
299        
300  \item \textit{eesupp}: contains the execution environment source code.  \item \texttt{eesupp}: contains the execution environment source code.
301    Also subdivided into two subdirectories \textit{inc} and    Also subdivided into two subdirectories \texttt{inc} and
302    \textit{src}.    \texttt{src}.
303        
304  \item \textit{exe}: this directory is initially empty. It is the  \item \texttt{exe}: this directory is initially empty. It is the
305    default directory in which to execute the code.    default directory in which to execute the code.
306        
307  \item \textit{model}: this directory contains the main source code.  \item \texttt{model}: this directory contains the main source code.
308    Also subdivided into two subdirectories \textit{inc} and    Also subdivided into two subdirectories \texttt{inc} and
309    \textit{src}.    \texttt{src}.
310        
311  \item \textit{pkg}: contains the source code for the packages. Each  \item \texttt{pkg}: contains the source code for the packages. Each
312    package corresponds to a subdirectory. For example, \textit{gmredi}    package corresponds to a subdirectory. For example, \texttt{gmredi}
313    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
314    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
315    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in section 3.
316        
317  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
318    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
319    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
320    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
321    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
322    The latter is described in details in part V.    The latter is described in details in part V.
323        
324  \item \textit{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
325    subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
326    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
327    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
328    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
329    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
330    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
331    model output.    model output.
332        
333  \item \textit{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
334    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sect:modelExamples}.
335    
336  \end{itemize}  \end{itemize}
337    
338  \section[MITgcm Example Experiments]{Example experiments}  \section[MITgcm Example Experiments]{Example experiments}
339  \label{sect:modelExamples}  \label{sect:modelExamples}
340    \begin{rawhtml}
341    <!-- CMIREDIR:modelExamples: -->
342    \end{rawhtml}
343    
344  %% a set of twenty-four pre-configured numerical experiments  %% a set of twenty-four pre-configured numerical experiments
345    
346  The MITgcm distribution comes with more than a dozen pre-configured  The full MITgcm distribution comes with more than a dozen
347  numerical experiments. Some of these example experiments are tests of  pre-configured numerical experiments. Some of these example
348  individual parts of the model code, but many are fully fledged  experiments are tests of individual parts of the model code, but many
349  numerical simulations. A few of the examples are used for tutorial  are fully fledged numerical simulations. A few of the examples are
350  documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.  used for tutorial documentation in sections \ref{sect:eg-baro} -
351  The other examples follow the same general structure as the tutorial  \ref{sect:eg-global}.  The other examples follow the same general
352  examples. However, they only include brief instructions in a text file  structure as the tutorial examples. However, they only include brief
353  called {\it README}.  The examples are located in subdirectories under  instructions in a text file called {\it README}.  The examples are
354  the directory \textit{verification}. Each example is briefly described  located in subdirectories under the directory \texttt{verification}.
355  below.  Each example is briefly described below.
356    
357  \subsection{Full list of model examples}  \subsection{Full list of model examples}
358    
359  \begin{enumerate}  \begin{enumerate}
360        
361  \item \textit{exp0} - single layer, ocean double gyre (barotropic with  \item \texttt{exp0} - single layer, ocean double gyre (barotropic with
362    free-surface). This experiment is described in detail in section    free-surface). This experiment is described in detail in section
363    \ref{sect:eg-baro}.    \ref{sect:eg-baro}.
364    
365  \item \textit{exp1} - Four layer, ocean double gyre. This experiment  \item \texttt{exp1} - Four layer, ocean double gyre. This experiment
366    is described in detail in section \ref{sect:eg-baroc}.    is described in detail in section \ref{sect:eg-baroc}.
367        
368  \item \textit{exp2} - 4x4 degree global ocean simulation with steady  \item \texttt{exp2} - 4x4 degree global ocean simulation with steady
369    climatological forcing. This experiment is described in detail in    climatological forcing. This experiment is described in detail in
370    section \ref{sect:eg-global}.    section \ref{sect:eg-global}.
371        
372  \item \textit{exp4} - Flow over a Gaussian bump in open-water or  \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
373    channel with open boundaries.    channel with open boundaries.
374        
375  \item \textit{exp5} - Inhomogenously forced ocean convection in a  \item \texttt{exp5} - Inhomogenously forced ocean convection in a
376    doubly periodic box.    doubly periodic box.
377    
378  \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  \item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for
379  Gent/McWilliams scheme). 2D (Y-Z).  Gent/McWilliams scheme). 2D (Y-Z).
380    
381  \item \textit{internal wave} - Ocean internal wave forced by open  \item \texttt{internal wave} - Ocean internal wave forced by open
382    boundary conditions.    boundary conditions.
383        
384  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
385    scheme; 1 month integration    scheme; 1 month integration
386        
387  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and  \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
388    Suarez '94 forcing.    Suarez '94 forcing.
389        
390  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and  \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
391    Suarez '94 forcing.    Suarez '94 forcing.
392        
393  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
394    Suarez '94 forcing on the cubed sphere.    Suarez '94 forcing on the cubed sphere.
395        
396  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
397    Global Zonal Mean configuration, 1x64x5 resolution.    Global Zonal Mean configuration, 1x64x5 resolution.
398        
399  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
400    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
401        
402  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
403    physics. 3D Equatorial Channel configuration.    physics. 3D Equatorial Channel configuration.
404        
405  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.
406    Global configuration, on latitude longitude grid with 128x64x5 grid    Global configuration, on latitude longitude grid with 128x64x5 grid
407    points ($2.8^\circ{\rm degree}$ resolution).    points ($2.8^\circ$ resolution).
408        
409  \item \textit{adjustment.128x64x1} Barotropic adjustment problem on  \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
410    latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
     degree}$ resolution).  
411        
412  \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on  \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
413    cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm    cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
414      degree}$ resolution).    resolution).
415        
416  \item \textit{advect\_cs} Two-dimensional passive advection test on  \item \texttt{advect\_cs} Two-dimensional passive advection test on
417    cube sphere grid.    cube sphere grid.
418        
419  \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive  \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
420    advection test on Cartesian grid.    advection test on Cartesian grid.
421        
422  \item \textit{advect\_yz} Two-dimensional (vertical plane) passive  \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
423    advection test on Cartesian grid.    advection test on Cartesian grid.
424        
425  \item \textit{carbon} Simple passive tracer experiment. Includes  \item \texttt{carbon} Simple passive tracer experiment. Includes
426    derivative calculation. Described in detail in section    derivative calculation. Described in detail in section
427    \ref{sect:eg-carbon-ad}.    \ref{sect:eg-carbon-ad}.
428    
429  \item \textit{flt\_example} Example of using float package.  \item \texttt{flt\_example} Example of using float package.
430        
431  \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
432    boundary conditions and poles.    boundary conditions and poles.
433    
434  \item \textit{global\_ocean\_pressure} Global circulation in pressure  \item \texttt{global\_ocean\_pressure} Global circulation in pressure
435    coordinate (non-Boussinesq ocean model). Described in detail in    coordinate (non-Boussinesq ocean model). Described in detail in
436    section \ref{sect:eg-globalpressure}.    section \ref{sect:eg-globalpressure}.
437        
438  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube  \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
439    sphere grid.    sphere grid.
440    
441  \end{enumerate}  \end{enumerate}
# Line 432  Gent/McWilliams scheme). 2D (Y-Z). Line 445  Gent/McWilliams scheme). 2D (Y-Z).
445  Each example directory has the following subdirectories:  Each example directory has the following subdirectories:
446    
447  \begin{itemize}  \begin{itemize}
448  \item \textit{code}: contains the code particular to the example. At a  \item \texttt{code}: contains the code particular to the example. At a
449    minimum, this directory includes the following files:    minimum, this directory includes the following files:
450    
451    \begin{itemize}    \begin{itemize}
452    \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to    \item \texttt{code/packages.conf}: declares the list of packages or
453        package groups to be used.  If not included, the default version
454        is located in \texttt{pkg/pkg\_default}.  Package groups are
455        simply convenient collections of commonly used packages which are
456        defined in \texttt{pkg/pkg\_default}.  Some packages may require
457        other packages or may require their absence (that is, they are
458        incompatible) and these package dependencies are listed in
459        \texttt{pkg/pkg\_depend}.
460    
461      \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
462      the ``execution environment'' part of the code. The default      the ``execution environment'' part of the code. The default
463      version is located in \textit{eesupp/inc}.      version is located in \texttt{eesupp/inc}.
464        
465    \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to    \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
466      the ``numerical model'' part of the code. The default version is      the ``numerical model'' part of the code. The default version is
467      located in \textit{model/inc}.      located in \texttt{model/inc}.
468        
469    \item \textit{code/SIZE.h}: declares size of underlying    \item \texttt{code/SIZE.h}: declares size of underlying
470      computational grid.  The default version is located in      computational grid.  The default version is located in
471      \textit{model/inc}.      \texttt{model/inc}.
472    \end{itemize}    \end{itemize}
473        
474    In addition, other include files and subroutines might be present in    In addition, other include files and subroutines might be present in
475    \textit{code} depending on the particular experiment. See Section 2    \texttt{code} depending on the particular experiment. See Section 2
476    for more details.    for more details.
477        
478  \item \textit{input}: contains the input data files required to run  \item \texttt{input}: contains the input data files required to run
479    the example. At a minimum, the \textit{input} directory contains the    the example. At a minimum, the \texttt{input} directory contains the
480    following files:    following files:
481    
482    \begin{itemize}    \begin{itemize}
483    \item \textit{input/data}: this file, written as a namelist,    \item \texttt{input/data}: this file, written as a namelist,
484      specifies the main parameters for the experiment.      specifies the main parameters for the experiment.
485        
486    \item \textit{input/data.pkg}: contains parameters relative to the    \item \texttt{input/data.pkg}: contains parameters relative to the
487      packages used in the experiment.      packages used in the experiment.
488        
489    \item \textit{input/eedata}: this file contains ``execution    \item \texttt{input/eedata}: this file contains ``execution
490      environment'' data. At present, this consists of a specification      environment'' data. At present, this consists of a specification
491      of the number of threads to use in $X$ and $Y$ under multithreaded      of the number of threads to use in $X$ and $Y$ under multithreaded
492      execution.      execution.
# Line 475  Each example directory has the following Line 497  Each example directory has the following
497    of the experiment.  This varies from experiment to experiment. See    of the experiment.  This varies from experiment to experiment. See
498    section 2 for more details.    section 2 for more details.
499    
500  \item \textit{results}: this directory contains the output file  \item \texttt{results}: this directory contains the output file
501    \textit{output.txt} produced by the simulation example. This file is    \texttt{output.txt} produced by the simulation example. This file is
502    useful for comparison with your own output when you run the    useful for comparison with your own output when you run the
503    experiment.    experiment.
504  \end{itemize}  \end{itemize}
# Line 486  compile the code. Line 508  compile the code.
508    
509  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
510  \label{sect:buildingCode}  \label{sect:buildingCode}
511    \begin{rawhtml}
512  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
513  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
514  compiler and optimization options and also figures out any file  
515  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
516  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
517    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
518    file dependencies. We supply a script (\texttt{genmake2}), described
519    in section \ref{sect:genmake}, that automatically creates the
520    \texttt{Makefile} for you. You then need to build the dependencies and
521  compile the code.  compile the code.
522    
523  As an example, let's assume that you want to build and run experiment  As an example, assume that you want to build and run experiment
524  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
525  actually do this but here let's build the code in  actually do this but here let's build the code in
526  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
527  \begin{verbatim}  \begin{verbatim}
528  % cd verification/exp2/input  % cd verification/exp2/build
529  \end{verbatim}  \end{verbatim}
530  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
531  \begin{verbatim}  \begin{verbatim}
532  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
533  \end{verbatim}  \end{verbatim}
534  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
535  code with any files in the directory {\em ../code/}.  code with any files in the directory \texttt{../code/}.
536    
537  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
538  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
539  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
540  appropriate set of options from the files (``optfiles'') contained in  appropriate set of options from the files (``optfiles'') contained in
541  the {\em tools/build\_options} directory.  Under some circumstances, a  the \texttt{tools/build\_options} directory.  Under some
542  user may have to create a new ``optfile'' in order to specify the  circumstances, a user may have to create a new ``optfile'' in order to
543  exact combination of compiler, compiler flags, libraries, and other  specify the exact combination of compiler, compiler flags, libraries,
544  options necessary to build a particular configuration of MITgcm.  In  and other options necessary to build a particular configuration of
545  such cases, it is generally helpful to read the existing ``optfiles''  MITgcm.  In such cases, it is generally helpful to read the existing
546  and mimic their syntax.  ``optfiles'' and mimic their syntax.
547    
548  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
549  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
550  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
551  architectures) to the  architectures) to the
552  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
553  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
554  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
555  list.  list.
556    
557  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
558  \begin{verbatim}  \begin{verbatim}
559  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
560  \end{verbatim}  \end{verbatim}
561    
562  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
563    dependencies with the command:
564  \begin{verbatim}  \begin{verbatim}
565  % make depend  % make depend
566  \end{verbatim}  \end{verbatim}
567  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
568  upon which other files depend. The purpose of this is to reduce  list of files upon which other files depend. The purpose of this is to
569  re-compilation if and when you start to modify the code. The {\tt make  reduce re-compilation if and when you start to modify the code. The
570    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
571  directory.  It is important to note that the {\tt make depend} stage  this directory.  It is important to note that the {\tt make depend}
572  will occasionally produce warnings or errors since the dependency  stage will occasionally produce warnings or errors since the
573  parsing tool is unable to find all of the necessary header files  dependency parsing tool is unable to find all of the necessary header
574  (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it is  files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
575  usually OK to ignore the warnings/errors and proceed to the next step.  is usually OK to ignore the warnings/errors and proceed to the next
576    step.
577    
578  Next compile the code:  Next one can compile the code using:
579  \begin{verbatim}  \begin{verbatim}
580  % make  % make
581  \end{verbatim}  \end{verbatim}
582  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
583  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
584  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
585    (shared multi-processor) systems, the build process can often be sped
586    up appreciably using the command:
587    \begin{verbatim}
588    % make -j 2
589    \end{verbatim}
590    where the ``2'' can be replaced with a number that corresponds to the
591    number of CPUs available.
592    
593  Now you are ready to run the model. General instructions for doing so are  Now you are ready to run the model. General instructions for doing so are
594  given in section \ref{sect:runModel}. Here, we can run the model with:  given in section \ref{sect:runModel}. Here, we can run the model by
595    first creating links to all the input files:
596    \begin{verbatim}
597    ln -s ../input/* .
598    \end{verbatim}
599    and then calling the executable with:
600  \begin{verbatim}  \begin{verbatim}
601  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
602  \end{verbatim}  \end{verbatim}
603  where we are re-directing the stream of text output to the file {\em  where we are re-directing the stream of text output to the file
604  output.txt}.  \texttt{output.txt}.
605    
606    
607  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
608  \label{sect:runModel}  \label{sect:runModel}
609    \begin{rawhtml}
610    <!-- CMIREDIR:runModel: -->
611    \end{rawhtml}
612    
613  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sect:buildingCode})
614  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
615  local directory.  local directory.
616    
# Line 583  do!). The above command will spew out ma Line 625  do!). The above command will spew out ma
625  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
626  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
627  etc. It is worth keeping this text output with the binary output so we  etc. It is worth keeping this text output with the binary output so we
628  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
629  \begin{verbatim}  \begin{verbatim}
630  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
631  \end{verbatim}  \end{verbatim}
# Line 591  In the event that the model encounters a Line 633  In the event that the model encounters a
633  helpful to include the last few line of this \texttt{output.txt} file  helpful to include the last few line of this \texttt{output.txt} file
634  along with the (\texttt{stderr}) error message within any bug reports.  along with the (\texttt{stderr}) error message within any bug reports.
635    
636  For the example experiments in {\em verification}, an example of the  For the example experiments in \texttt{verification}, an example of the
637  output is kept in {\em results/output.txt} for comparison. You can  output is kept in \texttt{results/output.txt} for comparison. You can
638  compare your {\em output.txt} with the corresponding one for that  compare your \texttt{output.txt} with the corresponding one for that
639  experiment to check that the set-up works.  experiment to check that the set-up works.
640    
641    
642    
643  \subsection{Output files}  \subsection{Output files}
644    
645  The model produces various output files.  Depending upon the I/O  The model produces various output files and, when using \texttt{mnc},
646  package selected (either \texttt{mdsio} or \texttt{mnc} or both as  sometimes even directories.  Depending upon the I/O package(s)
647  determined by both the compile-time settings and the run-time flags in  selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
648  \texttt{data.pkg}), the following output may appear.  both as determined by \texttt{code/packages.conf}) and the run-time
649    flags set (in \texttt{input/data.pkg}), the following output may
650    appear.
651    
652    
653  \subsubsection{MDSIO output files}  \subsubsection{MDSIO output files}
# Line 613  package.  At a minimum, the instantaneou Line 657  package.  At a minimum, the instantaneou
657  written out, which is made of the following files:  written out, which is made of the following files:
658    
659  \begin{itemize}  \begin{itemize}
660  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
661  0 $ eastward).    and positive eastward).
662    
663  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
664  and $> 0$ northward).    (m/s and positive northward).
665    
666  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
667  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
668  i.e. downward).    towards increasing pressure i.e. downward).
669    
670  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
671  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
672    
673  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
674  (g/kg).    vapor (g/kg).
675    
676  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
677  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
678  \end{itemize}  \end{itemize}
679    
680  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
681  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
682  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
683    
684  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
685    
686  \begin{itemize}  \begin{itemize}
687  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
688  \end{itemize}  \end{itemize}
689    
690  is written out. This file represents the state of the model in a condensed  is written out. This file represents the state of the model in a condensed
# Line 648  form and is used for restarting the inte Line 692  form and is used for restarting the inte
692  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
693    
694  \begin{itemize}  \begin{itemize}
695  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
696  \end{itemize}  \end{itemize}
697    
698  containing the D-grid velocity data and that has to be written out as well  containing the D-grid velocity data and that has to be written out as well
699  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
700  as the pickup files but are named differently. Their name contain the chain  as the pickup files but are named differently. Their name contain the chain
701  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
702  used to restart the model but are overwritten every other time they are  used to restart the model but are overwritten every other time they are
703  output to save disk space during long integrations.  output to save disk space during long integrations.
704    
# Line 668  a name such as \texttt{mnc\_test\_\${DAT Line 712  a name such as \texttt{mnc\_test\_\${DAT
712  within this subdirectory are all in the ``self-describing'' netCDF  within this subdirectory are all in the ``self-describing'' netCDF
713  format and can thus be browsed and/or plotted using tools such as:  format and can thus be browsed and/or plotted using tools such as:
714  \begin{itemize}  \begin{itemize}
715  \item At a minimum, the \texttt{ncdump} utility is typically included  \item \texttt{ncdump} is a utility which is typically included
716    with every netCDF install:    with every netCDF install:
717    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
718  \begin{verbatim}  \begin{verbatim}
719  http://www.unidata.ucar.edu/packages/netcdf/  http://www.unidata.ucar.edu/packages/netcdf/
720  \end{verbatim}  \end{verbatim}
721    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
722      binaries into formatted ASCII text files.
723    
724  \item The \texttt{ncview} utility is a very convenient and quick way  \item \texttt{ncview} utility is a very convenient and quick way
725    to plot netCDF data and it runs on most OSes:    to plot netCDF data and it runs on most OSes:
726    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
727  \begin{verbatim}  \begin{verbatim}
# Line 686  http://meteora.ucsd.edu/~pierce/ncview_h Line 731  http://meteora.ucsd.edu/~pierce/ncview_h
731        
732  \item MatLAB(c) and other common post-processing environments provide  \item MatLAB(c) and other common post-processing environments provide
733    various netCDF interfaces including:    various netCDF interfaces including:
734      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
735    \begin{verbatim}
736    http://mexcdf.sourceforge.net/
737    \end{verbatim}
738      \begin{rawhtml} </A> \end{rawhtml}
739    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
740  \begin{verbatim}  \begin{verbatim}
741  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
742  \end{verbatim}  \end{verbatim}
743    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
   
744  \end{itemize}  \end{itemize}
745    
746    
# Line 699  http://woodshole.er.usgs.gov/staffpages/ Line 748  http://woodshole.er.usgs.gov/staffpages/
748    
749  The ``traditional'' or mdsio model data are written according to a  The ``traditional'' or mdsio model data are written according to a
750  ``meta/data'' file format.  Each variable is associated with two files  ``meta/data'' file format.  Each variable is associated with two files
751  with suffix names \textit{.data} and \textit{.meta}. The  with suffix names \texttt{.data} and \texttt{.meta}. The
752  \textit{.data} file contains the data written in binary form  \texttt{.data} file contains the data written in binary form
753  (big\_endian by default). The \textit{.meta} file is a ``header'' file  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
754  that contains information about the size and the structure of the  that contains information about the size and the structure of the
755  \textit{.data} file. This way of organizing the output is particularly  \texttt{.data} file. This way of organizing the output is particularly
756  useful when running multi-processors calculations. The base version of  useful when running multi-processors calculations. The base version of
757  the model includes a few matlab utilities to read output files written  the model includes a few matlab utilities to read output files written
758  in this format. The matlab scripts are located in the directory  in this format. The matlab scripts are located in the directory
759  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m}  \texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
760  reads the data. Look at the comments inside the script to see how to  reads the data. Look at the comments inside the script to see how to
761  use it.  use it.
762    
# Line 726  Some examples of reading and visualizing Line 775  Some examples of reading and visualizing
775  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
776  \end{verbatim}  \end{verbatim}
777    
778  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available.  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
779    they are described in Section \ref{sec:pkg:mnc}.
780    
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