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revision 1.14 by edhill, Wed Jul 30 13:42:52 2003 UTC revision 1.15 by edhill, Wed Jan 28 20:50:14 2004 UTC
# Line 18  you are ready to try implementing the co Line 18  you are ready to try implementing the co
18  \section{Where to find information}  \section{Where to find information}
19  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
20    
21  A web site is maintained for release 1 (Sealion) of MITgcm:  A web site is maintained for release 2 (``Pelican'') of MITgcm:
22    \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
23  \begin{verbatim}  \begin{verbatim}
24  http://mitgcm.org/sealion  http://mitgcm.org/pelican
25  \end{verbatim}  \end{verbatim}
26    \begin{rawhtml} </A> \end{rawhtml}
27  Here you will find an on-line version of this document, a  Here you will find an on-line version of this document, a
28  ``browsable'' copy of the code and a searchable database of the model  ``browsable'' copy of the code and a searchable database of the model
29  and site, as well as links for downloading the model and  and site, as well as links for downloading the model and
30  documentation, to data-sources and other related sites.  documentation, to data-sources, and other related sites.
31    
32  There is also a support news group for the model that you can email at  There is also a web-archived support mailing list for the model that
33  \texttt{MITgcm-support@mitgcm.org} or browse at:  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
34    \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
35    \begin{verbatim}
36    http://mitgcm.org/mailman/listinfo/mitgcm-support/
37    http://mitgcm.org/pipermail/mitgcm-support/
38    \end{verbatim}
39    \begin{rawhtml} </A> \end{rawhtml}
40    Essentially all of the MITgcm web pages can be searched using a
41    popular web crawler such as Google or through our own search facility:
42  \begin{verbatim}  \begin{verbatim}
43  news://mitgcm.org/mitgcm.support  http://mitgcm.org/htdig/
44  \end{verbatim}  \end{verbatim}
45  A mail to the email list will reach all the developers and be archived  \begin{rawhtml} </A> \end{rawhtml}
46  on the newsgroup. A users email list will be established at some time  %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
47  in the future.  
48    
49    
50  \section{Obtaining the code}  \section{Obtaining the code}
51  \label{sect:obtainingCode}  \label{sect:obtainingCode}
# Line 72  provides an efficient and elegant way of Line 83  provides an efficient and elegant way of
83  track of your changes. If CVS is not available on your machine, you can also  track of your changes. If CVS is not available on your machine, you can also
84  download a tar file.  download a tar file.
85    
86  Before you can use CVS, the following environment variable has to be set in  Before you can use CVS, the following environment variable(s) should
87  your .cshrc or .tcshrc:  be set within your shell.  For a csh or tcsh shell, put the following
88    \begin{verbatim}
89    % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
90    \end{verbatim}
91    in your .cshrc or .tcshrc file.  For bash or sh shells, put:
92  \begin{verbatim}  \begin{verbatim}
93  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
94  \end{verbatim}  \end{verbatim}
95    in your .profile or .bashrc file.
96    
97  To start using CVS, register with the MITgcm CVS server using command:  
98    To get MITgcm through CVS, first register with the MITgcm CVS server
99    using command:
100  \begin{verbatim}  \begin{verbatim}
101  % cvs login ( CVS password: cvsanon )  % cvs login ( CVS password: cvsanon )
102  \end{verbatim}  \end{verbatim}
103  You only need to do ``cvs login'' once.  You only need to do a ``cvs login'' once.
104    
105  To obtain the sources for release1 type:  To obtain the latest sources type:
106    \begin{verbatim}
107    % cvs co MITgcm
108    \end{verbatim}
109    or to get a specific release type:
110  \begin{verbatim}  \begin{verbatim}
111  % cvs co -d directory -P -r release1_beta1 MITgcm  % cvs co -d directory -P -r release1_beta1 MITgcm
112  \end{verbatim}  \end{verbatim}
113    The MITgcm web site contains further directions concerning the source
114    code and CVS.  It also contains a web interface to our CVS archive so
115    that one may easily view the state of files, revisions, and other
116    development milestones:
117    \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
118    \begin{verbatim}
119    http://mitgcm.org/source_code.html
120    \end{verbatim}
121    \begin{rawhtml} </A> \end{rawhtml}
122    
123  This creates a directory called \textit{directory}. If \textit{directory}  
124  exists this command updates your code based on the repository. Each  The checkout process creates a directory called \textit{MITgcm}. If
125  directory in the source tree contains a directory \textit{CVS}. This  the directory \textit{MITgcm} exists this command updates your code
126  information is required by CVS to keep track of your file versions with  based on the repository. Each directory in the source tree contains a
127  respect to the repository. Don't edit the files in \textit{CVS}!  directory \textit{CVS}. This information is required by CVS to keep
128  You can also use CVS to download code updates.  More extensive  track of your file versions with respect to the repository. Don't edit
129  information on using CVS for maintaining MITgcm code can be found  the files in \textit{CVS}!  You can also use CVS to download code
130    updates.  More extensive information on using CVS for maintaining
131    MITgcm code can be found
132  \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}
133  here  here
134  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
# Line 106  here Line 139  here
139  \label{sect:conventionalDownload}  \label{sect:conventionalDownload}
140    
141  If you do not have CVS on your system, you can download the model as a  If you do not have CVS on your system, you can download the model as a
142  tar file from the reference web site at:  tar file from the web site at:
143  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
144  \begin{verbatim}  \begin{verbatim}
145  http://mitgcm.org/download/  http://mitgcm.org/download/
# Line 114  http://mitgcm.org/download/ Line 147  http://mitgcm.org/download/
147  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
148  The tar file still contains CVS information which we urge you not to  The tar file still contains CVS information which we urge you not to
149  delete; even if you do not use CVS yourself the information can help  delete; even if you do not use CVS yourself the information can help
150  us if you should need to send us your copy of the code.  us if you should need to send us your copy of the code.  If a recent
151    tar file does not exist, then please contact the developers through
152    the MITgcm-support list.
153    
154  \paragraph*{Upgrading from an earlier version}  \paragraph*{Upgrading from an earlier version}
155    
# Line 124  your copy instead of downloading the ent Line 159  your copy instead of downloading the ent
159  \begin{verbatim}  \begin{verbatim}
160  % cd MITgcm  % cd MITgcm
161  \end{verbatim}  \end{verbatim}
162  and then issue the cvs update command:  and then issue the cvs update command such as:
163  \begin{verbatim}  \begin{verbatim}
164  % cvs -q update -r release1_beta1 -d -P  % cvs -q update -r release1_beta1 -d -P
165  \end{verbatim}  \end{verbatim}
# Line 140  C model/src/ini_parms.F Line 175  C model/src/ini_parms.F
175  \end{verbatim}  \end{verbatim}
176  If the list of conflicts scrolled off the screen, you can re-issue the  If the list of conflicts scrolled off the screen, you can re-issue the
177  cvs update command and it will report the conflicts. Conflicts are  cvs update command and it will report the conflicts. Conflicts are
178  indicated in the code by the delimites ``<<<<<<<'', ``======='' and  indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and
179  ``>>>>>>>''. For example,  ``$>>>>>>>$''. For example,
180  \begin{verbatim}  \begin{verbatim}
181  <<<<<<< ini_parms.F  <<<<<<< ini_parms.F
182       & bottomDragLinear,myOwnBottomDragCoefficient,       & bottomDragLinear,myOwnBottomDragCoefficient,
# Line 156  changed to: Line 191  changed to:
191  \begin{verbatim}  \begin{verbatim}
192       & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,       & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
193  \end{verbatim}  \end{verbatim}
194  and the lines with the delimiters (<<<<<<,======,>>>>>>) be deleted.  and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted.
195  Unless you are making modifications which exactly parallel  Unless you are making modifications which exactly parallel
196  developments we make, these types of conflicts should be rare.  developments we make, these types of conflicts should be rare.
197    
# Line 223  relative to the atmospheric intermediate Line 258  relative to the atmospheric intermediate
258  in detail in section 3.  in detail in section 3.
259    
260  \item \textit{tools}: this directory contains various useful tools. For  \item \textit{tools}: this directory contains various useful tools. For
261  example, \textit{genmake} is a script written in csh (C-shell) that should  example, \textit{genmake2} is a script written in csh (C-shell) that should
262  be used to generate your makefile. The directory \textit{adjoint} contains  be used to generate your makefile. The directory \textit{adjoint} contains
263  the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that  the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that
264  generates the adjoint code. The latter is described in details in part V.  generates the adjoint code. The latter is described in details in part V.
# Line 243  section \ref{sect:modelExamples}. Line 278  section \ref{sect:modelExamples}.
278  \section{Example experiments}  \section{Example experiments}
279  \label{sect:modelExamples}  \label{sect:modelExamples}
280    
281  The MITgcm distribution comes with a set of twenty-four pre-configured  %% a set of twenty-four pre-configured numerical experiments
282  numerical experiments. Some of these examples experiments are tests of  
283  individual parts of the model code, but many are fully fledged numerical  The MITgcm distribution comes with more than a dozen pre-configured
284  simulations. A few of the examples are used for tutorial documentation  numerical experiments. Some of these example experiments are tests of
285  in sections \ref{sect:eg-baro} - \ref{sect:eg-global}. The other examples  individual parts of the model code, but many are fully fledged
286  follow the same general structure as the tutorial examples. However,  numerical simulations. A few of the examples are used for tutorial
287  they only include brief instructions in a text file called {\it README}.  documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.
288  The examples are located in subdirectories under  The other examples follow the same general structure as the tutorial
289  the directory \textit{verification}. Each  examples. However, they only include brief instructions in a text file
290  example is briefly described below.  called {\it README}.  The examples are located in subdirectories under
291    the directory \textit{verification}. Each example is briefly described
292    below.
293    
294  \subsection{Full list of model examples}  \subsection{Full list of model examples}
295    
296  \begin{enumerate}  \begin{enumerate}
297  \item \textit{exp0} - single layer, ocean double gyre (barotropic with  \item \textit{exp0} - single layer, ocean double gyre (barotropic with
298  free-surface). This experiment is described in detail in section    free-surface). This experiment is described in detail in section
299  \ref{sect:eg-baro}.    \ref{sect:eg-baro}.
   
 \item \textit{exp1} - Four layer, ocean double gyre. This experiment is described in detail in section  
 \ref{sect:eg-baroc}.  
300    
301    \item \textit{exp1} - Four layer, ocean double gyre. This experiment
302      is described in detail in section \ref{sect:eg-baroc}.
303      
304  \item \textit{exp2} - 4x4 degree global ocean simulation with steady  \item \textit{exp2} - 4x4 degree global ocean simulation with steady
305  climatological forcing. This experiment is described in detail in section    climatological forcing. This experiment is described in detail in
306  \ref{sect:eg-global}.    section \ref{sect:eg-global}.
307      
308  \item \textit{exp4} - Flow over a Gaussian bump in open-water or channel  \item \textit{exp4} - Flow over a Gaussian bump in open-water or
309  with open boundaries.    channel with open boundaries.
310      
311  \item \textit{exp5} - Inhomogenously forced ocean convection in a doubly  \item \textit{exp5} - Inhomogenously forced ocean convection in a
312  periodic box.    doubly periodic box.
313    
314  \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
315  Gent/McWilliams scheme). 2D (Y-Z).  Gent/McWilliams scheme). 2D (Y-Z).
316    
317  \item \textit{internal wave} - Ocean internal wave forced by open boundary  \item \textit{internal wave} - Ocean internal wave forced by open
318  conditions.    boundary conditions.
319      
320  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
321  scheme; 1 month integration    scheme; 1 month integration
322      
323  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and Suarez  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and
324  '94 forcing.    Suarez '94 forcing.
325      
326  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
327  '94 forcing.    Suarez '94 forcing.
328      
329  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
330  Suarez '94 forcing on the cubed sphere.    Suarez '94 forcing on the cubed sphere.
331      
332  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics. Global  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
333  Zonal Mean configuration, 1x64x5 resolution.    Global Zonal Mean configuration, 1x64x5 resolution.
334      
335  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
336  physics, equatorial Slice configuration.    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
337  2D (X-Z).    
   
338  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
339  physics. 3D Equatorial Channel configuration.    physics. 3D Equatorial Channel configuration.
340      
341  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
342  Global configuration, on latitude longitude grid with 128x64x5 grid points    Global configuration, on latitude longitude grid with 128x64x5 grid
343  ($2.8^\circ{\rm degree}$ resolution).    points ($2.8^\circ{\rm degree}$ resolution).
344      
345  \item \textit{adjustment.128x64x1} Barotropic adjustment  \item \textit{adjustment.128x64x1} Barotropic adjustment problem on
346  problem on latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm degree}$ resolution).    latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
347        degree}$ resolution).
348  \item \textit{adjustment.cs-32x32x1}    
349  Barotropic adjustment  \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on
350  problem on cube sphere grid with 32x32 points per face ( roughly    cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
351  $2.8^\circ{\rm degree}$ resolution).      degree}$ resolution).
352      
353  \item \textit{advect\_cs} Two-dimensional passive advection test on  \item \textit{advect\_cs} Two-dimensional passive advection test on
354  cube sphere grid.    cube sphere grid.
355      
356  \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive advection  \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive
357  test on Cartesian grid.    advection test on Cartesian grid.
358      
359  \item \textit{advect\_yz} Two-dimensional (vertical plane) passive advection test on Cartesian grid.  \item \textit{advect\_yz} Two-dimensional (vertical plane) passive
360      advection test on Cartesian grid.
361  \item \textit{carbon} Simple passive tracer experiment. Includes derivative    
362  calculation. Described in detail in section \ref{sect:eg-carbon-ad}.  \item \textit{carbon} Simple passive tracer experiment. Includes
363      derivative calculation. Described in detail in section
364      \ref{sect:eg-carbon-ad}.
365    
366  \item \textit{flt\_example} Example of using float package.  \item \textit{flt\_example} Example of using float package.
367      
368  \item \textit{global\_ocean.90x40x15} Global circulation with  \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
369  GM, flux boundary conditions and poles.    boundary conditions and poles.
370    
371  \item \textit{global\_ocean\_pressure} Global circulation in pressure  \item \textit{global\_ocean\_pressure} Global circulation in pressure
372    coordinate (non-Boussinesq ocean model). Described in detail in    coordinate (non-Boussinesq ocean model). Described in detail in
373    section \ref{sect:eg-globalpressure}.    section \ref{sect:eg-globalpressure}.
374      
375  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube sphere  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube
376  grid.    sphere grid.
377    
378  \end{enumerate}  \end{enumerate}
379    
# Line 348  Each example directory has the following Line 386  Each example directory has the following
386  minimum, this directory includes the following files:  minimum, this directory includes the following files:
387    
388  \begin{itemize}  \begin{itemize}
389  \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the  \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
390  ``execution environment'' part of the code. The default version is located    the ``execution environment'' part of the code. The default version
391  in \textit{eesupp/inc}.    is located in \textit{eesupp/inc}.
392      
393  \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the  \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the
394  ``numerical model'' part of the code. The default version is located in    ``numerical model'' part of the code. The default version is located
395  \textit{model/inc}.    in \textit{model/inc}.
396      
397  \item \textit{code/SIZE.h}: declares size of underlying computational grid.  \item \textit{code/SIZE.h}: declares size of underlying computational
398  The default version is located in \textit{model/inc}.    grid.  The default version is located in \textit{model/inc}.
399  \end{itemize}  \end{itemize}
400    
401  In addition, other include files and subroutines might be present in \textit{%  In addition, other include files and subroutines might be present in
402  code} depending on the particular experiment. See section 2 for more details.  \textit{code} depending on the particular experiment. See Section 2
403    for more details.
404  \item \textit{input}: contains the input data files required to run the  
405  example. At a minimum, the \textit{input} directory contains the following  \item \textit{input}: contains the input data files required to run
406  files:    the example. At a minimum, the \textit{input} directory contains the
407      following files:
408    
409  \begin{itemize}  \begin{itemize}
410  \item \textit{input/data}: this file, written as a namelist, specifies the  \item \textit{input/data}: this file, written as a namelist, specifies
411  main parameters for the experiment.    the main parameters for the experiment.
412      
413  \item \textit{input/data.pkg}: contains parameters relative to the packages  \item \textit{input/data.pkg}: contains parameters relative to the
414  used in the experiment.    packages used in the experiment.
415      
416  \item \textit{input/eedata}: this file contains ``execution environment''  \item \textit{input/eedata}: this file contains ``execution
417  data. At present, this consists of a specification of the number of threads    environment'' data. At present, this consists of a specification of
418  to use in $X$ and $Y$ under multithreaded execution.    the number of threads to use in $X$ and $Y$ under multithreaded
419      execution.
420  \end{itemize}  \end{itemize}
421    
422  In addition, you will also find in this directory the forcing and topography  In addition, you will also find in this directory the forcing and topography
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