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revision 1.27 by cnh, Thu Oct 14 14:24:28 2004 UTC revision 1.32 by edhill, Wed Apr 5 02:27:33 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 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}
# 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 ($2.8^\circ{\rm degree}$ 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 ($2.8^\circ{\rm
411      degree}$ resolution).      degree}$ resolution).
412        
413  \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on  \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
414    cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm    cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
415      degree}$ resolution).      degree}$ resolution).
416        
417  \item \textit{advect\_cs} Two-dimensional passive advection test on  \item \texttt{advect\_cs} Two-dimensional passive advection test on
418    cube sphere grid.    cube sphere grid.
419        
420  \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive  \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
421    advection test on Cartesian grid.    advection test on Cartesian grid.
422        
423  \item \textit{advect\_yz} Two-dimensional (vertical plane) passive  \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
424    advection test on Cartesian grid.    advection test on Cartesian grid.
425        
426  \item \textit{carbon} Simple passive tracer experiment. Includes  \item \texttt{carbon} Simple passive tracer experiment. Includes
427    derivative calculation. Described in detail in section    derivative calculation. Described in detail in section
428    \ref{sect:eg-carbon-ad}.    \ref{sect:eg-carbon-ad}.
429    
430  \item \textit{flt\_example} Example of using float package.  \item \texttt{flt\_example} Example of using float package.
431        
432  \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
433    boundary conditions and poles.    boundary conditions and poles.
434    
435  \item \textit{global\_ocean\_pressure} Global circulation in pressure  \item \texttt{global\_ocean\_pressure} Global circulation in pressure
436    coordinate (non-Boussinesq ocean model). Described in detail in    coordinate (non-Boussinesq ocean model). Described in detail in
437    section \ref{sect:eg-globalpressure}.    section \ref{sect:eg-globalpressure}.
438        
439  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube  \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
440    sphere grid.    sphere grid.
441    
442  \end{enumerate}  \end{enumerate}
# Line 432  Gent/McWilliams scheme). 2D (Y-Z). Line 446  Gent/McWilliams scheme). 2D (Y-Z).
446  Each example directory has the following subdirectories:  Each example directory has the following subdirectories:
447    
448  \begin{itemize}  \begin{itemize}
449  \item \textit{code}: contains the code particular to the example. At a  \item \texttt{code}: contains the code particular to the example. At a
450    minimum, this directory includes the following files:    minimum, this directory includes the following files:
451    
452    \begin{itemize}    \begin{itemize}
453    \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to    \item \texttt{code/packages.conf}: declares the list of packages or
454        package groups to be used.  If not included, the default version
455        is located in \texttt{pkg/pkg\_default}.  Package groups are
456        simply convenient collections of commonly used packages which are
457        defined in \texttt{pkg/pkg\_default}.  Some packages may require
458        other packages or may require their absence (that is, they are
459        incompatible) and these package dependencies are listed in
460        \texttt{pkg/pkg\_depend}.
461    
462      \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
463      the ``execution environment'' part of the code. The default      the ``execution environment'' part of the code. The default
464      version is located in \textit{eesupp/inc}.      version is located in \texttt{eesupp/inc}.
465        
466    \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to    \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
467      the ``numerical model'' part of the code. The default version is      the ``numerical model'' part of the code. The default version is
468      located in \textit{model/inc}.      located in \texttt{model/inc}.
469        
470    \item \textit{code/SIZE.h}: declares size of underlying    \item \texttt{code/SIZE.h}: declares size of underlying
471      computational grid.  The default version is located in      computational grid.  The default version is located in
472      \textit{model/inc}.      \texttt{model/inc}.
473    \end{itemize}    \end{itemize}
474        
475    In addition, other include files and subroutines might be present in    In addition, other include files and subroutines might be present in
476    \textit{code} depending on the particular experiment. See Section 2    \texttt{code} depending on the particular experiment. See Section 2
477    for more details.    for more details.
478        
479  \item \textit{input}: contains the input data files required to run  \item \texttt{input}: contains the input data files required to run
480    the example. At a minimum, the \textit{input} directory contains the    the example. At a minimum, the \texttt{input} directory contains the
481    following files:    following files:
482    
483    \begin{itemize}    \begin{itemize}
484    \item \textit{input/data}: this file, written as a namelist,    \item \texttt{input/data}: this file, written as a namelist,
485      specifies the main parameters for the experiment.      specifies the main parameters for the experiment.
486        
487    \item \textit{input/data.pkg}: contains parameters relative to the    \item \texttt{input/data.pkg}: contains parameters relative to the
488      packages used in the experiment.      packages used in the experiment.
489        
490    \item \textit{input/eedata}: this file contains ``execution    \item \texttt{input/eedata}: this file contains ``execution
491      environment'' data. At present, this consists of a specification      environment'' data. At present, this consists of a specification
492      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
493      execution.      execution.
# Line 475  Each example directory has the following Line 498  Each example directory has the following
498    of the experiment.  This varies from experiment to experiment. See    of the experiment.  This varies from experiment to experiment. See
499    section 2 for more details.    section 2 for more details.
500    
501  \item \textit{results}: this directory contains the output file  \item \texttt{results}: this directory contains the output file
502    \textit{output.txt} produced by the simulation example. This file is    \texttt{output.txt} produced by the simulation example. This file is
503    useful for comparison with your own output when you run the    useful for comparison with your own output when you run the
504    experiment.    experiment.
505  \end{itemize}  \end{itemize}
# Line 486  compile the code. Line 509  compile the code.
509    
510  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
511  \label{sect:buildingCode}  \label{sect:buildingCode}
512    \begin{rawhtml}
513  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
514  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
515  compiler and optimization options and also figures out any file  
516  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
517  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
518    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
519    file dependencies. We supply a script (\texttt{genmake2}), described
520    in section \ref{sect:genmake}, that automatically creates the
521    \texttt{Makefile} for you. You then need to build the dependencies and
522  compile the code.  compile the code.
523    
524  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
525  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
526  actually do this but here let's build the code in  actually do this but here let's build the code in
527  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
528  \begin{verbatim}  \begin{verbatim}
529  % cd verification/exp2/input  % cd verification/exp2/build
530  \end{verbatim}  \end{verbatim}
531  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
532  \begin{verbatim}  \begin{verbatim}
533  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
534  \end{verbatim}  \end{verbatim}
535  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
536  code with any files in the directory {\em ./code/}.  code with any files in the directory \texttt{../code/}.
537    
538  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
539  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
540  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
541  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
542    tools/build\_options} directory.  Under some circumstances, a user  the \texttt{tools/build\_options} directory.  Under some
543  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
544  combination of compiler, compiler flags, libraries, and other options  specify the exact combination of compiler, compiler flags, libraries,
545  necessary to build a particular configuration of MITgcm.  In such  and other options necessary to build a particular configuration of
546  cases, it is generally helpful to read the existing ``optfiles'' and  MITgcm.  In such cases, it is generally helpful to read the existing
547  mimic their syntax.  ``optfiles'' and mimic their syntax.
548    
549  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
550  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
# Line 529  MITgcm-support@mitgcm.org Line 555  MITgcm-support@mitgcm.org
555  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
556  list.  list.
557    
558  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
559  \begin{verbatim}  \begin{verbatim}
560  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
561  \end{verbatim}  \end{verbatim}
562    
563  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
564    dependencies with the command:
565  \begin{verbatim}  \begin{verbatim}
566  % make depend  % make depend
567  \end{verbatim}  \end{verbatim}
568  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
569  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
570  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
571    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
572  directory.  this directory.  It is important to note that the {\tt make depend}
573    stage will occasionally produce warnings or errors since the
574    dependency parsing tool is unable to find all of the necessary header
575    files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
576    is usually OK to ignore the warnings/errors and proceed to the next
577    step.
578    
579  Next compile the code:  Next one can compile the code using:
580  \begin{verbatim}  \begin{verbatim}
581  % make  % make
582  \end{verbatim}  \end{verbatim}
583  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
584  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
585  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
586    (shared multi-processor) systems, the build process can often be sped
587  Now you are ready to run the model. General instructions for doing so are  up appreciably using the command:
 given in section \ref{sect:runModel}. Here, we can run the model with:  
588  \begin{verbatim}  \begin{verbatim}
589  ./mitgcmuv > output.txt  % make -j 2
590  \end{verbatim}  \end{verbatim}
591  where we are re-directing the stream of text output to the file {\em  where the ``2'' can be replaced with a number that corresponds to the
592  output.txt}.  number of CPUs available.
   
   
 \subsection{Building/compiling the code elsewhere}  
   
 In the example above (section \ref{sect:buildingCode}) we built the  
 executable in the {\em input} directory of the experiment for  
 convenience. You can also configure and compile the code in other  
 locations, for example on a scratch disk with out having to copy the  
 entire source tree. The only requirement to do so is you have {\tt  
   genmake2} in your path or you know the absolute path to {\tt  
   genmake2}.  
   
 The following sections outline some possible methods of organizing  
 your source and data.  
   
 \subsubsection{Building from the {\em ../code directory}}  
   
 This is just as simple as building in the {\em input/} directory:  
 \begin{verbatim}  
 % cd verification/exp2/code  
 % ../../../tools/genmake2  
 % make depend  
 % make  
 \end{verbatim}  
 However, to run the model the executable ({\em mitgcmuv}) and input  
 files must be in the same place. If you only have one calculation to make:  
 \begin{verbatim}  
 % cd ../input  
 % cp ../code/mitgcmuv ./  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
 or if you will be making multiple runs with the same executable:  
 \begin{verbatim}  
 % cd ../  
 % cp -r input run1  
 % cp code/mitgcmuv run1  
 % cd run1  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
   
 \subsubsection{Building from a new directory}  
593    
594  Since the {\em input} directory contains input files it is often more  Now you are ready to run the model. General instructions for doing so are
595  useful to keep {\em input} pristine and build in a new directory  given in section \ref{sect:runModel}. Here, we can run the model by
596  within {\em verification/exp2/}:  first creating links to all the input files:
 \begin{verbatim}  
 % cd verification/exp2  
 % mkdir build  
 % cd build  
 % ../../../tools/genmake2 -mods=../code  
 % make depend  
 % make  
 \end{verbatim}  
 This builds the code exactly as before but this time you need to copy  
 either the executable or the input files or both in order to run the  
 model. For example,  
 \begin{verbatim}  
 % cp ../input/* ./  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
 or if you tend to make multiple runs with the same executable then  
 running in a new directory each time might be more appropriate:  
 \begin{verbatim}  
 % cd ../  
 % mkdir run1  
 % cp build/mitgcmuv run1/  
 % cp input/* run1/  
 % cd run1  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
   
 \subsubsection{Building on a scratch disk}  
   
 Model object files and output data can use up large amounts of disk  
 space so it is often the case that you will be operating on a large  
 scratch disk. Assuming the model source is in {\em ~/MITgcm} then the  
 following commands will build the model in {\em /scratch/exp2-run1}:  
 \begin{verbatim}  
 % cd /scratch/exp2-run1  
 % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \  
   -mods=~/MITgcm/verification/exp2/code  
 % make depend  
 % make  
 \end{verbatim}  
 To run the model here, you'll need the input files:  
597  \begin{verbatim}  \begin{verbatim}
598  % cp ~/MITgcm/verification/exp2/input/* ./  ln -s ../input/* .
 % ./mitgcmuv > output.txt  
599  \end{verbatim}  \end{verbatim}
600    and then calling the executable with:
 As before, you could build in one directory and make multiple runs of  
 the one experiment:  
601  \begin{verbatim}  \begin{verbatim}
602  % cd /scratch/exp2  ./mitgcmuv > output.txt
 % mkdir build  
 % cd build  
 % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \  
   -mods=~/MITgcm/verification/exp2/code  
 % make depend  
 % make  
 % cd ../  
 % cp -r ~/MITgcm/verification/exp2/input run2  
 % cd run2  
 % ./mitgcmuv > output.txt  
603  \end{verbatim}  \end{verbatim}
604    where we are re-directing the stream of text output to the file
605    \texttt{output.txt}.
 \subsection{Using \texttt{genmake2}}  
 \label{sect:genmake}  
   
 To compile the code, first use the program \texttt{genmake2} (located  
 in the \texttt{tools} directory) to generate a Makefile.  
 \texttt{genmake2} is a shell script written to work with all  
 ``sh''--compatible shells including bash v1, bash v2, and Bourne.  
 Internally, \texttt{genmake2} determines the locations of needed  
 files, the compiler, compiler options, libraries, and Unix tools.  It  
 relies upon a number of ``optfiles'' located in the  
 \texttt{tools/build\_options} directory.  
   
 The purpose of the optfiles is to provide all the compilation options  
 for particular ``platforms'' (where ``platform'' roughly means the  
 combination of the hardware and the compiler) and code configurations.  
 Given the combinations of possible compilers and library dependencies  
 ({\it eg.}  MPI and NetCDF) there may be numerous optfiles available  
 for a single machine.  The naming scheme for the majority of the  
 optfiles shipped with the code is  
 \begin{center}  
   {\bf OS\_HARDWARE\_COMPILER }  
 \end{center}  
 where  
 \begin{description}  
 \item[OS] is the name of the operating system (generally the  
   lower-case output of the {\tt 'uname'} command)  
 \item[HARDWARE] is a string that describes the CPU type and  
   corresponds to output from the  {\tt 'uname -m'} command:  
   \begin{description}  
   \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,  
     and athlon  
   \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)  
   \item[amd64] is AMD x86\_64 systems  
   \item[ppc] is for Mac PowerPC systems  
   \end{description}  
 \item[COMPILER] is the compiler name (generally, the name of the  
   FORTRAN executable)  
 \end{description}  
   
 In many cases, the default optfiles are sufficient and will result in  
 usable Makefiles.  However, for some machines or code configurations,  
 new ``optfiles'' must be written. To create a new optfile, it is  
 generally best to start with one of the defaults and modify it to suit  
 your needs.  Like \texttt{genmake2}, the optfiles are all written  
 using a simple ``sh''--compatible syntax.  While nearly all variables  
 used within \texttt{genmake2} may be specified in the optfiles, the  
 critical ones that should be defined are:  
   
 \begin{description}  
 \item[FC] the FORTRAN compiler (executable) to use  
 \item[DEFINES] the command-line DEFINE options passed to the compiler  
 \item[CPP] the C pre-processor to use  
 \item[NOOPTFLAGS] options flags for special files that should not be  
   optimized  
 \end{description}  
   
 For example, the optfile for a typical Red Hat Linux machine (``ia32''  
 architecture) using the GCC (g77) compiler is  
 \begin{verbatim}  
 FC=g77  
 DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'  
 CPP='cpp  -traditional -P'  
 NOOPTFLAGS='-O0'  
 #  For IEEE, use the "-ffloat-store" option  
 if test "x$IEEE" = x ; then  
     FFLAGS='-Wimplicit -Wunused -Wuninitialized'  
     FOPTIM='-O3 -malign-double -funroll-loops'  
 else  
     FFLAGS='-Wimplicit -Wunused -ffloat-store'  
     FOPTIM='-O0 -malign-double'  
 fi  
 \end{verbatim}  
   
 If you write an optfile for an unrepresented machine or compiler, you  
 are strongly encouraged to submit the optfile to the MITgcm project  
 for inclusion.  Please send the file to the  
 \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}  
 \begin{center}  
   MITgcm-support@mitgcm.org  
 \end{center}  
 \begin{rawhtml} </A> \end{rawhtml}  
 mailing list.  
   
 In addition to the optfiles, \texttt{genmake2} supports a number of  
 helpful command-line options.  A complete list of these options can be  
 obtained from:  
 \begin{verbatim}  
 % genmake2 -h  
 \end{verbatim}  
   
 The most important command-line options are:  
 \begin{description}  
     
 \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that  
   should be used for a particular build.  
     
   If no "optfile" is specified (either through the command line or the  
   MITGCM\_OPTFILE environment variable), genmake2 will try to make a  
   reasonable guess from the list provided in {\em  
     tools/build\_options}.  The method used for making this guess is  
   to first determine the combination of operating system and hardware  
   (eg. "linux\_ia32") and then find a working FORTRAN compiler within  
   the user's path.  When these three items have been identified,  
   genmake2 will try to find an optfile that has a matching name.  
     
 \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  
   set of packages to be used.  The normal order of precedence for  
   packages is as follows:  
   \begin{enumerate}  
   \item If available, the command line (\texttt{--pdefault}) settings  
     over-rule any others.  
   
   \item Next, \texttt{genmake2} will look for a file named  
     ``\texttt{packages.conf}'' in the local directory or in any of the  
     directories specified with the \texttt{--mods} option.  
       
   \item Finally, if neither of the above are available,  
     \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.  
   \end{enumerate}  
     
 \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  
   used for packages.  
     
   If not specified, the default dependency file {\em pkg/pkg\_depend}  
   is used.  The syntax for this file is parsed on a line-by-line basis  
   where each line containes either a comment ("\#") or a simple  
   "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol  
   specifies a "must be used with" or a "must not be used with"  
   relationship, respectively.  If no rule is specified, then it is  
   assumed that the two packages are compatible and will function  
   either with or without each other.  
     
 \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or  
   automatic differentiation options file to be used.  The file is  
   analogous to the ``optfile'' defined above but it specifies  
   information for the AD build process.  
     
   The default file is located in {\em  
     tools/adjoint\_options/adjoint\_default} and it defines the "TAF"  
   and "TAMC" compilers.  An alternate version is also available at  
   {\em tools/adjoint\_options/adjoint\_staf} that selects the newer  
   "STAF" compiler.  As with any compilers, it is helpful to have their  
   directories listed in your {\tt \$PATH} environment variable.  
     
 \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of  
   directories containing ``modifications''.  These directories contain  
   files with names that may (or may not) exist in the main MITgcm  
   source tree but will be overridden by any identically-named sources  
   within the ``MODS'' directories.  
     
   The order of precedence for this "name-hiding" is as follows:  
   \begin{itemize}  
   \item ``MODS'' directories (in the order given)  
   \item Packages either explicitly specified or provided by default  
     (in the order given)  
   \item Packages included due to package dependencies (in the order  
     that that package dependencies are parsed)  
   \item The "standard dirs" (which may have been specified by the  
     ``-standarddirs'' option)  
   \end{itemize}  
     
 \item[\texttt{--mpi}] This option enables certain MPI features (using  
   CPP \texttt{\#define}s) within the code and is necessary for MPI  
   builds (see Section \ref{sect:mpi-build}).  
     
 \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of  
   soft-links and other bugs common with the \texttt{make} versions  
   provided by commercial Unix vendors, GNU \texttt{make} (sometimes  
   called \texttt{gmake}) should be preferred.  This option provides a  
   means for specifying the make executable to be used.  
     
 \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)  
   machines, the ``bash'' shell is unavailable.  To run on these  
   systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,  
   a Bourne, POSIX, or compatible) shell.  The syntax in these  
   circumstances is:  
   \begin{center}  
     \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}  
   \end{center}  
   where \texttt{/bin/sh} can be replaced with the full path and name  
   of the desired shell.  
   
 \end{description}  
   
   
 \subsection{Building with MPI}  
 \label{sect:mpi-build}  
   
 Building MITgcm to use MPI libraries can be complicated due to the  
 variety of different MPI implementations available, their dependencies  
 or interactions with different compilers, and their often ad-hoc  
 locations within file systems.  For these reasons, its generally a  
 good idea to start by finding and reading the documentation for your  
 machine(s) and, if necessary, seeking help from your local systems  
 administrator.  
   
 The steps for building MITgcm with MPI support are:  
 \begin{enumerate}  
     
 \item Determine the locations of your MPI-enabled compiler and/or MPI  
   libraries and put them into an options file as described in Section  
   \ref{sect:genmake}.  One can start with one of the examples in:  
   \begin{rawhtml} <A  
     href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">  
   \end{rawhtml}  
   \begin{center}  
     \texttt{MITgcm/tools/build\_options/}  
   \end{center}  
   \begin{rawhtml} </A> \end{rawhtml}  
   such as \texttt{linux\_ia32\_g77+mpi\_cg01} or  
   \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at  
   hand.  You may need help from your user guide or local systems  
   administrator to determine the exact location of the MPI libraries.  
   If libraries are not installed, MPI implementations and related  
   tools are available including:  
   \begin{itemize}  
   \item \begin{rawhtml} <A  
       href="http://www-unix.mcs.anl.gov/mpi/mpich/">  
     \end{rawhtml}  
     MPICH  
     \begin{rawhtml} </A> \end{rawhtml}  
   
   \item \begin{rawhtml} <A  
       href="http://www.lam-mpi.org/">  
     \end{rawhtml}  
     LAM/MPI  
     \begin{rawhtml} </A> \end{rawhtml}  
   
   \item \begin{rawhtml} <A  
       href="http://www.osc.edu/~pw/mpiexec/">  
     \end{rawhtml}  
     MPIexec  
     \begin{rawhtml} </A> \end{rawhtml}  
   \end{itemize}  
     
 \item Build the code with the \texttt{genmake2} \texttt{-mpi} option  
   (see Section \ref{sect:genmake}) using commands such as:  
 {\footnotesize \begin{verbatim}  
   %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE  
   %  make depend  
   %  make  
 \end{verbatim} }  
     
 \item Run the code with the appropriate MPI ``run'' or ``exec''  
   program provided with your particular implementation of MPI.  
   Typical MPI packages such as MPICH will use something like:  
 \begin{verbatim}  
   %  mpirun -np 4 -machinefile mf ./mitgcmuv  
 \end{verbatim}  
   Sightly more complicated scripts may be needed for many machines  
   since execution of the code may be controlled by both the MPI  
   library and a job scheduling and queueing system such as PBS,  
   LoadLeveller, Condor, or any of a number of similar tools.  A few  
   example scripts (those used for our \begin{rawhtml} <A  
     href="http://mitgcm.org/testing.html"> \end{rawhtml}regular  
   verification runs\begin{rawhtml} </A> \end{rawhtml}) are available  
   at:  
   \begin{rawhtml} <A  
     href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">  
   \end{rawhtml}  
   {\footnotesize \tt  
     http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }  
   \begin{rawhtml} </A> \end{rawhtml}  
   
 \end{enumerate}  
   
 An example of the above process on the MITgcm cluster (``cg01'') using  
 the GNU g77 compiler and the mpich MPI library is:  
   
 {\footnotesize \begin{verbatim}  
   %  cd MITgcm/verification/exp5  
   %  mkdir build  
   %  cd build  
   %  ../../../tools/genmake2 -mpi -mods=../code \  
        -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01  
   %  make depend  
   %  make  
   %  cd ../input  
   %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \  
        -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv  
 \end{verbatim} }  
   
606    
607    
608  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
609  \label{sect:runModel}  \label{sect:runModel}
610    \begin{rawhtml}
611    <!-- CMIREDIR:runModel: -->
612    \end{rawhtml}
613    
614  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sect:buildingCode})
615  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
616  local directory.  local directory.
617    
618  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)
619  type:  simply type:
620  \begin{verbatim}  \begin{verbatim}
621  % ./mitgcmuv  % ./mitgcmuv
622  \end{verbatim}  \end{verbatim}
# Line 968  do!). The above command will spew out ma Line 626  do!). The above command will spew out ma
626  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
627  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
628  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
629  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
630  \begin{verbatim}  \begin{verbatim}
631  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
632  \end{verbatim}  \end{verbatim}
633    In the event that the model encounters an error and stops, it is very
634  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
635  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
636  your {\em output.txt} with this one to check that the set-up works.  
637    For the example experiments in \texttt{verification}, an example of the
638    output is kept in \texttt{results/output.txt} for comparison. You can
639    compare your \texttt{output.txt} with the corresponding one for that
640    experiment to check that the set-up works.
641    
642    
643    
644  \subsection{Output files}  \subsection{Output files}
645    
646  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
647  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
648    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
649    both as determined by \texttt{code/packages.conf}) and the run-time
650    flags set (in \texttt{input/data.pkg}), the following output may
651    appear.
652    
653    
654    \subsubsection{MDSIO output files}
655    
656    The ``traditional'' output files are generated by the \texttt{mdsio}
657    package.  At a minimum, the instantaneous ``state'' of the model is
658    written out, which is made of the following files:
659    
660  \begin{itemize}  \begin{itemize}
661  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s and $>
662  0 $ eastward).  0 $ eastward).
663    
664  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field (m/s
665  and $> 0$ northward).  and $> 0$ northward).
666    
667  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field (ocean:
668  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure
669  i.e. downward).  i.e. downward).
670    
671  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean: $^{0}$C,
672  atmosphere: $^{0}$K).  atmosphere: $^{0}$K).
673    
674  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor
675  (g/kg).  (g/kg).
676    
677  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:
678  surface pressure anomaly (Pa).  surface pressure anomaly (Pa).
679  \end{itemize}  \end{itemize}
680    
681  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
682  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example, \texttt{%
683  U.0000000300} is the zonal velocity at iteration 300.  U.0000000300} is the zonal velocity at iteration 300.
684    
685  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
686    
687  \begin{itemize}  \begin{itemize}
688  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
689  \end{itemize}  \end{itemize}
690    
691  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 693  form and is used for restarting the inte
693  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
694    
695  \begin{itemize}  \begin{itemize}
696  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
697  \end{itemize}  \end{itemize}
698    
699  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
700  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
701  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
702  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
703  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
704  output to save disk space during long integrations.  output to save disk space during long integrations.
705    
706    
707    
708    \subsubsection{MNC output files}
709    
710    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
711    is usually (though not necessarily) placed within a subdirectory with
712    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files
713    within this subdirectory are all in the ``self-describing'' netCDF
714    format and can thus be browsed and/or plotted using tools such as:
715    \begin{itemize}
716    \item \texttt{ncdump} is a utility which is typically included
717      with every netCDF install:
718      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
719    \begin{verbatim}
720         http://www.unidata.ucar.edu/packages/netcdf/
721    \end{verbatim}
722      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
723      binaries into formatted ASCII text files.
724    
725    \item \texttt{ncview} utility is a very convenient and quick way
726      to plot netCDF data and it runs on most OSes:
727      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
728    \begin{verbatim}
729         http://meteora.ucsd.edu/~pierce/ncview_home_page.html
730    \end{verbatim}
731      \begin{rawhtml} </A> \end{rawhtml}
732      
733    \item MatLAB(c) and other common post-processing environments provide
734      various netCDF interfaces including:
735      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
736    \begin{verbatim}
737    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
738    \end{verbatim}
739      \begin{rawhtml} </A> \end{rawhtml}
740    \end{itemize}
741    
742    
743  \subsection{Looking at the output}  \subsection{Looking at the output}
744    
745  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
746  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
747  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
748  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
749  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
750  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
751  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
752  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
753  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
754  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
755  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}
756    reads the data. Look at the comments inside the script to see how to
757    use it.
758    
759  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
760  \begin{verbatim}  \begin{verbatim}
# Line 1059  Some examples of reading and visualizing Line 771  Some examples of reading and visualizing
771  >> 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
772  \end{verbatim}  \end{verbatim}
773    
774    Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
775    they are described in Section \ref{sec:pkg:mnc}.
776    
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