/[MITgcm]/manual/s_getstarted/text/getting_started.tex
ViewVC logotype

Diff of /manual/s_getstarted/text/getting_started.tex

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.30 by edhill, Sat Oct 16 03:40:13 2004 UTC revision 1.31 by edhill, Tue Aug 9 21:52:09 2005 UTC
# Line 99  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 154  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 273  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}
# Line 350  documentation in sections \ref{sect:eg-b Line 351  documentation in sections \ref{sect:eg-b
351  The other examples follow the same general structure as the tutorial  The other examples follow the same general structure as the tutorial
352  examples. However, they only include brief instructions in a text file  examples. However, they only include brief instructions in a text file
353  called {\it README}.  The examples are located in subdirectories under  called {\it README}.  The examples are located in subdirectories under
354  the directory \textit{verification}. Each example is briefly described  the directory \texttt{verification}. Each example is briefly described
355  below.  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 445  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 488  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 503  compile the code. Line 513  compile the code.
513  <!-- CMIREDIR:buildingCode: -->  <!-- CMIREDIR:buildingCode: -->
514  \end{rawhtml}  \end{rawhtml}
515    
516  To compile the code, we use the {\em make} program. This uses a file  To compile the code, we use the \texttt{make} program. This uses a
517  ({\em Makefile}) that allows us to pre-process source files, specify  file (\texttt{Makefile}) that allows us to pre-process source files,
518  compiler and optimization options and also figures out any file  specify compiler and optimization options and also figures out any
519  dependencies. We supply a script ({\em genmake2}), described in  file dependencies. We supply a script (\texttt{genmake2}), described
520  section \ref{sect:genmake}, that automatically creates the {\em  in section \ref{sect:genmake}, that automatically creates the
521    Makefile} for you. You then need to build the dependencies and  \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 (``optfiles'') contained in  appropriate set of options from the files (``optfiles'') contained in
542  the {\em tools/build\_options} directory.  Under some circumstances, a  the \texttt{tools/build\_options} directory.  Under some
543  user may have to create a new ``optfile'' in order to specify the  circumstances, a user may have to create a new ``optfile'' in order to
544  exact combination of compiler, compiler flags, libraries, and other  specify the exact combination of compiler, compiler flags, libraries,
545  options necessary to build a particular configuration of MITgcm.  In  and other options necessary to build a particular configuration of
546  such cases, it is generally helpful to read the existing ``optfiles''  MITgcm.  In such cases, it is generally helpful to read the existing
547  and 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 545  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.  It is important to note that the {\tt make depend} stage  this directory.  It is important to note that the {\tt make depend}
573  will occasionally produce warnings or errors since the dependency  stage will occasionally produce warnings or errors since the
574  parsing tool is unable to find all of the necessary header files  dependency parsing tool is unable to find all of the necessary header
575  (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it is  files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
576  usually OK to ignore the warnings/errors and proceed to the next step.  is usually OK to ignore the warnings/errors and proceed to the next
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    up appreciably using the command:
588    \begin{verbatim}
589    % make -j 2
590    \end{verbatim}
591    where the ``2'' can be replaced with a number that corresponds to the
592    number of CPUs available.
593    
594  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
595  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
596    first creating links to all the input files:
597    \begin{verbatim}
598    ln -s ../input/* .
599    \end{verbatim}
600    and then calling the executable with:
601  \begin{verbatim}  \begin{verbatim}
602  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
603  \end{verbatim}  \end{verbatim}
604  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
605  output.txt}.  \texttt{output.txt}.
606    
607    
608  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
# Line 587  output.txt}. Line 611  output.txt}.
611  <!-- CMIREDIR:runModel: -->  <!-- CMIREDIR:runModel: -->
612  \end{rawhtml}  \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    
# Line 602  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}
# Line 610  In the event that the model encounters a Line 634  In the event that the model encounters a
634  helpful to include the last few line of this \texttt{output.txt} file  helpful to include the last few line of this \texttt{output.txt} file
635  along with the (\texttt{stderr}) error message within any bug reports.  along with the (\texttt{stderr}) error message within any bug reports.
636    
637  For the example experiments in {\em verification}, an example of the  For the example experiments in \texttt{verification}, an example of the
638  output is kept in {\em results/output.txt} for comparison. You can  output is kept in \texttt{results/output.txt} for comparison. You can
639  compare your {\em output.txt} with the corresponding one for that  compare your \texttt{output.txt} with the corresponding one for that
640  experiment to check that the set-up works.  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.  Depending upon the I/O  The model produces various output files and, when using \texttt{mnc},
647  package selected (either \texttt{mdsio} or \texttt{mnc} or both as  sometimes even directories.  Depending upon the I/O package(s)
648  determined by both the compile-time settings and the run-time flags in  selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
649  \texttt{data.pkg}), the following output may appear.  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}  \subsubsection{MDSIO output files}
# Line 632  package.  At a minimum, the instantaneou Line 658  package.  At a minimum, the instantaneou
658  written out, which is made of the following files:  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 667  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    
# Line 687  a name such as \texttt{mnc\_test\_\${DAT Line 713  a name such as \texttt{mnc\_test\_\${DAT
713  within this subdirectory are all in the ``self-describing'' netCDF  within this subdirectory are all in the ``self-describing'' netCDF
714  format and can thus be browsed and/or plotted using tools such as:  format and can thus be browsed and/or plotted using tools such as:
715  \begin{itemize}  \begin{itemize}
716  \item At a minimum, the \texttt{ncdump} utility is typically included  \item \texttt{ncdump} is a utility which is typically included
717    with every netCDF install:    with every netCDF install:
718    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
719  \begin{verbatim}  \begin{verbatim}
720  http://www.unidata.ucar.edu/packages/netcdf/       http://www.unidata.ucar.edu/packages/netcdf/
721  \end{verbatim}  \end{verbatim}
722    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
723      binaries into formatted ASCII text files.
724    
725  \item The \texttt{ncview} utility is a very convenient and quick way  \item \texttt{ncview} utility is a very convenient and quick way
726    to plot netCDF data and it runs on most OSes:    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}    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
728  \begin{verbatim}  \begin{verbatim}
729  http://meteora.ucsd.edu/~pierce/ncview_home_page.html       http://meteora.ucsd.edu/~pierce/ncview_home_page.html
730  \end{verbatim}  \end{verbatim}
731    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
732        
# Line 710  http://meteora.ucsd.edu/~pierce/ncview_h Line 737  http://meteora.ucsd.edu/~pierce/ncview_h
737  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
738  \end{verbatim}  \end{verbatim}
739    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
   
740  \end{itemize}  \end{itemize}
741    
742    
# Line 718  http://woodshole.er.usgs.gov/staffpages/ Line 744  http://woodshole.er.usgs.gov/staffpages/
744    
745  The ``traditional'' or mdsio model data are written according to a  The ``traditional'' or mdsio model data are written according to a
746  ``meta/data'' file format.  Each variable is associated with two files  ``meta/data'' file format.  Each variable is associated with two files
747  with suffix names \textit{.data} and \textit{.meta}. The  with suffix names \texttt{.data} and \texttt{.meta}. The
748  \textit{.data} file contains the data written in binary form  \texttt{.data} file contains the data written in binary form
749  (big\_endian by default). The \textit{.meta} file is a ``header'' file  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
750  that contains information about the size and the structure of the  that contains information about the size and the structure of the
751  \textit{.data} file. This way of organizing the output is particularly  \texttt{.data} file. This way of organizing the output is particularly
752  useful when running multi-processors calculations. The base version of  useful when running multi-processors calculations. The base version of
753  the model includes a few matlab utilities to read output files written  the model includes a few matlab utilities to read output files written
754  in this format. The matlab scripts are located in the directory  in this format. The matlab scripts are located in the directory
755  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m}  \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  reads the data. Look at the comments inside the script to see how to
757  use it.  use it.
758    
# Line 745  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.  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
775    they are described in Section \ref{sec:pkg:mnc}.
776    
Legend:
Removed from v.1.30  
changed lines
  Added in v.1.31
  ViewVC Help
Powered by ViewVC 1.1.22