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revision 1.27 by cnh, Thu Oct 14 14:24:28 2004 UTC revision 1.35 by molod, Thu Apr 20 22:09:08 2006 UTC
# Line 17  you are ready to try implementing the co Line 17  you are ready to try implementing the co
17    
18  \section{Where to find information}  \section{Where to find information}
19  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
20    \begin{rawhtml}
21    <!-- CMIREDIR:whereToFindInfo: -->
22    \end{rawhtml}
23    
24  A web site is maintained for release 2 (``Pelican'') of MITgcm:  A web site is maintained for release 2 (``Pelican'') of MITgcm:
25  \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 53  http://mitgcm.org/htdig/
53    
54  \section{Obtaining the code}  \section{Obtaining the code}
55  \label{sect:obtainingCode}  \label{sect:obtainingCode}
56    \begin{rawhtml}
57    <!-- CMIREDIR:obtainingCode: -->
58    \end{rawhtml}
59    
60  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
61  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 98  be set within your shell.  For a csh or
98  \begin{verbatim}  \begin{verbatim}
99  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
100  \end{verbatim}  \end{verbatim}
101  in your .cshrc or .tcshrc file.  For bash or sh shells, put:  in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
102    shells, put:
103  \begin{verbatim}  \begin{verbatim}
104  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
105  \end{verbatim}  \end{verbatim}
# Line 118  The MITgcm web site contains further dir Line 125  The MITgcm web site contains further dir
125  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
126  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
127  development milestones:  development milestones:
128  \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
129  \begin{verbatim}  \begin{verbatim}
130  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
131  \end{verbatim}  \end{verbatim}
# Line 147  of CVS aliases Line 154  of CVS aliases
154    \label{tab:cvsModules}    \label{tab:cvsModules}
155  \end{table}  \end{table}
156    
157  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
158  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
159  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
160  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
161  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
162  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
163  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
164  MITgcm code can be found  MITgcm code can be found
165  \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}
166  here  here
167  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
168  .  .
# Line 184  delete; even if you do not use CVS yours Line 191  delete; even if you do not use CVS yours
191  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
192  tar file does not exist, then please contact the developers through  tar file does not exist, then please contact the developers through
193  the  the
194  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
195  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
196  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
197  mailing list.  mailing list.
# Line 256  also means we can't tell what version of Line 263  also means we can't tell what version of
263  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
264    
265  \section{Model and directory structure}  \section{Model and directory structure}
266    \begin{rawhtml}
267    <!-- CMIREDIR:directory_structure: -->
268    \end{rawhtml}
269    
270  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
271  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 273  framework for grid-point models. MITgcmU
273  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
274  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
275  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
276  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
277  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
278  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
279  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
280  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
281  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
282  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
283  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
284  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
285  structure).  structure).
286    
287  \begin{itemize}  \begin{itemize}
288    
289  \item \textit{bin}: this directory is initially empty. It is the  \item \texttt{bin}: this directory is initially empty. It is the
290    default directory in which to compile the code.    default directory in which to compile the code.
291        
292  \item \textit{diags}: contains the code relative to time-averaged  \item \texttt{diags}: contains the code relative to time-averaged
293    diagnostics. It is subdivided into two subdirectories \textit{inc}    diagnostics. It is subdivided into two subdirectories \texttt{inc}
294    and \textit{src} that contain include files (*.\textit{h} files) and    and \texttt{src} that contain include files (\texttt{*.h} files) and
295    Fortran subroutines (*.\textit{F} files), respectively.    Fortran subroutines (\texttt{*.F} files), respectively.
296    
297  \item \textit{doc}: contains brief documentation notes.  \item \texttt{doc}: contains brief documentation notes.
298        
299  \item \textit{eesupp}: contains the execution environment source code.  \item \texttt{eesupp}: contains the execution environment source code.
300    Also subdivided into two subdirectories \textit{inc} and    Also subdivided into two subdirectories \texttt{inc} and
301    \textit{src}.    \texttt{src}.
302        
303  \item \textit{exe}: this directory is initially empty. It is the  \item \texttt{exe}: this directory is initially empty. It is the
304    default directory in which to execute the code.    default directory in which to execute the code.
305        
306  \item \textit{model}: this directory contains the main source code.  \item \texttt{model}: this directory contains the main source code.
307    Also subdivided into two subdirectories \textit{inc} and    Also subdivided into two subdirectories \texttt{inc} and
308    \textit{src}.    \texttt{src}.
309        
310  \item \textit{pkg}: contains the source code for the packages. Each  \item \texttt{pkg}: contains the source code for the packages. Each
311    package corresponds to a subdirectory. For example, \textit{gmredi}    package corresponds to a subdirectory. For example, \texttt{gmredi}
312    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
313    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
314    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in section 3.
315        
316  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
317    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
318    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
319    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
320    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
321    The latter is described in details in part V.    The latter is described in details in part V.
322        
323  \item \textit{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
324    subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
325    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
326    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
327    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
328    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
329    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
330    model output.    model output.
331        
332  \item \textit{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
333    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sect:modelExamples}.
334    
335  \end{itemize}  \end{itemize}
336    
337  \section[MITgcm Example Experiments]{Example experiments}  \section[MITgcm Example Experiments]{Example experiments}
338  \label{sect:modelExamples}  \label{sect:modelExamples}
339    \begin{rawhtml}
340    <!-- CMIREDIR:modelExamples: -->
341    \end{rawhtml}
342    
343  %% a set of twenty-four pre-configured numerical experiments  %% a set of twenty-four pre-configured numerical experiments
344    
345  The MITgcm distribution comes with more than a dozen pre-configured  The full MITgcm distribution comes with more than a dozen
346  numerical experiments. Some of these example experiments are tests of  pre-configured numerical experiments. Some of these example
347  individual parts of the model code, but many are fully fledged  experiments are tests of individual parts of the model code, but many
348  numerical simulations. A few of the examples are used for tutorial  are fully fledged numerical simulations. A few of the examples are
349  documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.  used for tutorial documentation in sections \ref{sect:eg-baro} -
350  The other examples follow the same general structure as the tutorial  \ref{sect:eg-global}.  The other examples follow the same general
351  examples. However, they only include brief instructions in a text file  structure as the tutorial examples. However, they only include brief
352  called {\it README}.  The examples are located in subdirectories under  instructions in a text file called {\it README}.  The examples are
353  the directory \textit{verification}. Each example is briefly described  located in subdirectories under the directory \texttt{verification}.
354  below.  Each example is briefly described below.
355    
356  \subsection{Full list of model examples}  \subsection{Full list of model examples}
357    
358  \begin{enumerate}  \begin{enumerate}
359        
360  \item \textit{exp0} - single layer, ocean double gyre (barotropic with  \item \texttt{exp0} - single layer, ocean double gyre (barotropic with
361    free-surface). This experiment is described in detail in section    free-surface). This experiment is described in detail in section
362    \ref{sect:eg-baro}.    \ref{sect:eg-baro}.
363    
364  \item \textit{exp1} - Four layer, ocean double gyre. This experiment  \item \texttt{exp1} - Four layer, ocean double gyre. This experiment
365    is described in detail in section \ref{sect:eg-baroc}.    is described in detail in section \ref{sect:eg-baroc}.
366        
367  \item \textit{exp2} - 4x4 degree global ocean simulation with steady  \item \texttt{exp2} - 4x4 degree global ocean simulation with steady
368    climatological forcing. This experiment is described in detail in    climatological forcing. This experiment is described in detail in
369    section \ref{sect:eg-global}.    section \ref{sect:eg-global}.
370        
371  \item \textit{exp4} - Flow over a Gaussian bump in open-water or  \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
372    channel with open boundaries.    channel with open boundaries.
373        
374  \item \textit{exp5} - Inhomogenously forced ocean convection in a  \item \texttt{exp5} - Inhomogenously forced ocean convection in a
375    doubly periodic box.    doubly periodic box.
376    
377  \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  \item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for
378  Gent/McWilliams scheme). 2D (Y-Z).  Gent/McWilliams scheme). 2D (Y-Z).
379    
380  \item \textit{internal wave} - Ocean internal wave forced by open  \item \texttt{internal wave} - Ocean internal wave forced by open
381    boundary conditions.    boundary conditions.
382        
383  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
384    scheme; 1 month integration    scheme; 1 month integration
385        
386  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and  \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
387    Suarez '94 forcing.    Suarez '94 forcing.
388        
389  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and  \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
390    Suarez '94 forcing.    Suarez '94 forcing.
391        
392  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
393    Suarez '94 forcing on the cubed sphere.    Suarez '94 forcing on the cubed sphere.
394        
395  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
396    Global Zonal Mean configuration, 1x64x5 resolution.    Global Zonal Mean configuration, 1x64x5 resolution.
397        
398  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
399    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
400        
401  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
402    physics. 3D Equatorial Channel configuration.    physics. 3D Equatorial Channel configuration.
403        
404  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.
405    Global configuration, on latitude longitude grid with 128x64x5 grid    Global configuration, on latitude longitude grid with 128x64x5 grid
406    points ($2.8^\circ{\rm degree}$ resolution).    points ($2.8^\circ$ resolution).
407        
408  \item \textit{adjustment.128x64x1} Barotropic adjustment problem on  \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
409    latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
     degree}$ resolution).  
410        
411  \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on  \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
412    cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm    cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
413      degree}$ resolution).    resolution).
414        
415  \item \textit{advect\_cs} Two-dimensional passive advection test on  \item \texttt{advect\_cs} Two-dimensional passive advection test on
416    cube sphere grid.    cube sphere grid.
417        
418  \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive  \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
419    advection test on Cartesian grid.    advection test on Cartesian grid.
420        
421  \item \textit{advect\_yz} Two-dimensional (vertical plane) passive  \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
422    advection test on Cartesian grid.    advection test on Cartesian grid.
423        
424  \item \textit{carbon} Simple passive tracer experiment. Includes  \item \texttt{carbon} Simple passive tracer experiment. Includes
425    derivative calculation. Described in detail in section    derivative calculation. Described in detail in section
426    \ref{sect:eg-carbon-ad}.    \ref{sect:eg-carbon-ad}.
427    
428  \item \textit{flt\_example} Example of using float package.  \item \texttt{flt\_example} Example of using float package.
429        
430  \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
431    boundary conditions and poles.    boundary conditions and poles.
432    
433  \item \textit{global\_ocean\_pressure} Global circulation in pressure  \item \texttt{global\_ocean\_pressure} Global circulation in pressure
434    coordinate (non-Boussinesq ocean model). Described in detail in    coordinate (non-Boussinesq ocean model). Described in detail in
435    section \ref{sect:eg-globalpressure}.    section \ref{sect:eg-globalpressure}.
436        
437  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube  \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
438    sphere grid.    sphere grid.
439    
440  \end{enumerate}  \end{enumerate}
# Line 432  Gent/McWilliams scheme). 2D (Y-Z). Line 444  Gent/McWilliams scheme). 2D (Y-Z).
444  Each example directory has the following subdirectories:  Each example directory has the following subdirectories:
445    
446  \begin{itemize}  \begin{itemize}
447  \item \textit{code}: contains the code particular to the example. At a  \item \texttt{code}: contains the code particular to the example. At a
448    minimum, this directory includes the following files:    minimum, this directory includes the following files:
449    
450    \begin{itemize}    \begin{itemize}
451    \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to    \item \texttt{code/packages.conf}: declares the list of packages or
452        package groups to be used.  If not included, the default version
453        is located in \texttt{pkg/pkg\_default}.  Package groups are
454        simply convenient collections of commonly used packages which are
455        defined in \texttt{pkg/pkg\_default}.  Some packages may require
456        other packages or may require their absence (that is, they are
457        incompatible) and these package dependencies are listed in
458        \texttt{pkg/pkg\_depend}.
459    
460      \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
461      the ``execution environment'' part of the code. The default      the ``execution environment'' part of the code. The default
462      version is located in \textit{eesupp/inc}.      version is located in \texttt{eesupp/inc}.
463        
464    \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to    \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
465      the ``numerical model'' part of the code. The default version is      the ``numerical model'' part of the code. The default version is
466      located in \textit{model/inc}.      located in \texttt{model/inc}.
467        
468    \item \textit{code/SIZE.h}: declares size of underlying    \item \texttt{code/SIZE.h}: declares size of underlying
469      computational grid.  The default version is located in      computational grid.  The default version is located in
470      \textit{model/inc}.      \texttt{model/inc}.
471    \end{itemize}    \end{itemize}
472        
473    In addition, other include files and subroutines might be present in    In addition, other include files and subroutines might be present in
474    \textit{code} depending on the particular experiment. See Section 2    \texttt{code} depending on the particular experiment. See Section 2
475    for more details.    for more details.
476        
477  \item \textit{input}: contains the input data files required to run  \item \texttt{input}: contains the input data files required to run
478    the example. At a minimum, the \textit{input} directory contains the    the example. At a minimum, the \texttt{input} directory contains the
479    following files:    following files:
480    
481    \begin{itemize}    \begin{itemize}
482    \item \textit{input/data}: this file, written as a namelist,    \item \texttt{input/data}: this file, written as a namelist,
483      specifies the main parameters for the experiment.      specifies the main parameters for the experiment.
484        
485    \item \textit{input/data.pkg}: contains parameters relative to the    \item \texttt{input/data.pkg}: contains parameters relative to the
486      packages used in the experiment.      packages used in the experiment.
487        
488    \item \textit{input/eedata}: this file contains ``execution    \item \texttt{input/eedata}: this file contains ``execution
489      environment'' data. At present, this consists of a specification      environment'' data. At present, this consists of a specification
490      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
491      execution.      execution.
# Line 475  Each example directory has the following Line 496  Each example directory has the following
496    of the experiment.  This varies from experiment to experiment. See    of the experiment.  This varies from experiment to experiment. See
497    section 2 for more details.    section 2 for more details.
498    
499  \item \textit{results}: this directory contains the output file  \item \texttt{results}: this directory contains the output file
500    \textit{output.txt} produced by the simulation example. This file is    \texttt{output.txt} produced by the simulation example. This file is
501    useful for comparison with your own output when you run the    useful for comparison with your own output when you run the
502    experiment.    experiment.
503  \end{itemize}  \end{itemize}
# Line 486  compile the code. Line 507  compile the code.
507    
508  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
509  \label{sect:buildingCode}  \label{sect:buildingCode}
510    \begin{rawhtml}
511  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
512  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
513  compiler and optimization options and also figures out any file  
514  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
515  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
516    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
517    file dependencies. We supply a script (\texttt{genmake2}), described
518    in section \ref{sect:genmake}, that automatically creates the
519    \texttt{Makefile} for you. You then need to build the dependencies and
520  compile the code.  compile the code.
521    
522  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
523  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
524  actually do this but here let's build the code in  actually do this but here let's build the code in
525  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
526  \begin{verbatim}  \begin{verbatim}
527  % cd verification/exp2/input  % cd verification/exp2/build
528  \end{verbatim}  \end{verbatim}
529  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
530  \begin{verbatim}  \begin{verbatim}
531  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
532  \end{verbatim}  \end{verbatim}
533  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
534  code with any files in the directory {\em ./code/}.  code with any files in the directory \texttt{../code/}.
535    
536  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
537  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
538  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
539  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
540    tools/build\_options} directory.  Under some circumstances, a user  the \texttt{tools/build\_options} directory.  Under some
541  may have to create a new ``optfile'' in order to specify the exact  circumstances, a user may have to create a new ``optfile'' in order to
542  combination of compiler, compiler flags, libraries, and other options  specify the exact combination of compiler, compiler flags, libraries,
543  necessary to build a particular configuration of MITgcm.  In such  and other options necessary to build a particular configuration of
544  cases, it is generally helpful to read the existing ``optfiles'' and  MITgcm.  In such cases, it is generally helpful to read the existing
545  mimic their syntax.  ``optfiles'' and mimic their syntax.
546    
547  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
548  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
549  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
550  architectures) to the  architectures) to the
551  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
552  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
553  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
554  list.  list.
555    
556  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
557  \begin{verbatim}  \begin{verbatim}
558  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
559  \end{verbatim}  \end{verbatim}
560    
561  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
562    dependencies with the command:
563  \begin{verbatim}  \begin{verbatim}
564  % make depend  % make depend
565  \end{verbatim}  \end{verbatim}
566  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
567  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
568  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
569    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
570  directory.  this directory.  It is important to note that the {\tt make depend}
571    stage will occasionally produce warnings or errors since the
572    dependency parsing tool is unable to find all of the necessary header
573    files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
574    is usually OK to ignore the warnings/errors and proceed to the next
575    step.
576    
577  Next compile the code:  Next one can compile the code using:
578  \begin{verbatim}  \begin{verbatim}
579  % make  % make
580  \end{verbatim}  \end{verbatim}
581  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
582  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
583  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
584    (shared multi-processor) systems, the build process can often be sped
585    up appreciably using the command:
586    \begin{verbatim}
587    % make -j 2
588    \end{verbatim}
589    where the ``2'' can be replaced with a number that corresponds to the
590    number of CPUs available.
591    
592  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
593  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
594    first creating links to all the input files:
595    \begin{verbatim}
596    ln -s ../input/* .
597    \end{verbatim}
598    and then calling the executable with:
599  \begin{verbatim}  \begin{verbatim}
600  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
601  \end{verbatim}  \end{verbatim}
602  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
603  output.txt}.  \texttt{output.txt}.
   
604    
605  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
606    
# Line 948  the GNU g77 compiler and the mpich MPI l Line 989  the GNU g77 compiler and the mpich MPI l
989         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
990  \end{verbatim} }  \end{verbatim} }
991    
   
   
992  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
993  \label{sect:runModel}  \label{sect:runModel}
994    \begin{rawhtml}
995    <!-- CMIREDIR:runModel: -->
996    \end{rawhtml}
997    
998  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sect:buildingCode})
999  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
1000  local directory.  local directory.
1001    
1002  To run the model as a single process (ie. not in parallel) simply  To run the model as a single process (\textit{ie.} not in parallel)
1003  type:  simply type:
1004  \begin{verbatim}  \begin{verbatim}
1005  % ./mitgcmuv  % ./mitgcmuv
1006  \end{verbatim}  \end{verbatim}
# Line 968  do!). The above command will spew out ma Line 1010  do!). The above command will spew out ma
1010  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
1011  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
1012  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
1013  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
1014  \begin{verbatim}  \begin{verbatim}
1015  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
1016  \end{verbatim}  \end{verbatim}
1017    In the event that the model encounters an error and stops, it is very
1018  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
1019  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
1020  your {\em output.txt} with this one to check that the set-up works.  
1021    For the example experiments in \texttt{verification}, an example of the
1022    output is kept in \texttt{results/output.txt} for comparison. You can
1023    compare your \texttt{output.txt} with the corresponding one for that
1024    experiment to check that the set-up works.
1025    
1026    
1027    
1028  \subsection{Output files}  \subsection{Output files}
1029    
1030  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
1031  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
1032    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
1033    both as determined by \texttt{code/packages.conf}) and the run-time
1034    flags set (in \texttt{input/data.pkg}), the following output may
1035    appear.
1036    
1037    
1038    \subsubsection{MDSIO output files}
1039    
1040    The ``traditional'' output files are generated by the \texttt{mdsio}
1041    package.  At a minimum, the instantaneous ``state'' of the model is
1042    written out, which is made of the following files:
1043    
1044  \begin{itemize}  \begin{itemize}
1045  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
1046  0 $ eastward).    and positive eastward).
1047    
1048  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
1049  and $> 0$ northward).    (m/s and positive northward).
1050    
1051  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
1052  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
1053  i.e. downward).    towards increasing pressure i.e. downward).
1054    
1055  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
1056  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
1057    
1058  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
1059  (g/kg).    vapor (g/kg).
1060    
1061  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
1062  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
1063  \end{itemize}  \end{itemize}
1064    
1065  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
1066  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
1067  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
1068    
1069  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
1070    
1071  \begin{itemize}  \begin{itemize}
1072  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
1073  \end{itemize}  \end{itemize}
1074    
1075  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 1020  form and is used for restarting the inte Line 1077  form and is used for restarting the inte
1077  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
1078    
1079  \begin{itemize}  \begin{itemize}
1080  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
1081  \end{itemize}  \end{itemize}
1082    
1083  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
1084  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
1085  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
1086  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
1087  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
1088  output to save disk space during long integrations.  output to save disk space during long integrations.
1089    
1090    
1091    
1092    \subsubsection{MNC output files}
1093    
1094    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
1095    is usually (though not necessarily) placed within a subdirectory with
1096    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files
1097    within this subdirectory are all in the ``self-describing'' netCDF
1098    format and can thus be browsed and/or plotted using tools such as:
1099    \begin{itemize}
1100    \item \texttt{ncdump} is a utility which is typically included
1101      with every netCDF install:
1102      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
1103    \begin{verbatim}
1104    http://www.unidata.ucar.edu/packages/netcdf/
1105    \end{verbatim}
1106      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
1107      binaries into formatted ASCII text files.
1108    
1109    \item \texttt{ncview} utility is a very convenient and quick way
1110      to plot netCDF data and it runs on most OSes:
1111      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
1112    \begin{verbatim}
1113    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
1114    \end{verbatim}
1115      \begin{rawhtml} </A> \end{rawhtml}
1116      
1117    \item MatLAB(c) and other common post-processing environments provide
1118      various netCDF interfaces including:
1119      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
1120    \begin{verbatim}
1121    http://mexcdf.sourceforge.net/
1122    \end{verbatim}
1123      \begin{rawhtml} </A> \end{rawhtml}
1124      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
1125    \begin{verbatim}
1126    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
1127    \end{verbatim}
1128      \begin{rawhtml} </A> \end{rawhtml}
1129    \end{itemize}
1130    
1131    
1132  \subsection{Looking at the output}  \subsection{Looking at the output}
1133    
1134  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
1135  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
1136  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
1137  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
1138  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
1139  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
1140  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
1141  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
1142  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
1143  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
1144  the data. Look at the comments inside the script to see how to use it.  \texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
1145    reads the data. Look at the comments inside the script to see how to
1146    use it.
1147    
1148  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
1149  \begin{verbatim}  \begin{verbatim}
# Line 1059  Some examples of reading and visualizing Line 1160  Some examples of reading and visualizing
1160  >> 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
1161  \end{verbatim}  \end{verbatim}
1162    
1163    Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
1164    they are described in Section \ref{sec:pkg:mnc}.
1165    
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