/[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 1.29 by edhill, Thu Oct 14 19:11:47 2004 UTC revision 1.35 by molod, Thu Apr 20 22:09:08 2006 UTC
# Line 17  you are ready to try implementing the co Line 17  you are ready to try implementing the co
17    
18  \section{Where to find information}  \section{Where to find information}
19  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
20    \begin{rawhtml}
21    <!-- CMIREDIR:whereToFindInfo: -->
22    \end{rawhtml}
23    
24  A web site is maintained for release 2 (``Pelican'') of MITgcm:  A web site is maintained for release 2 (``Pelican'') of MITgcm:
25  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
# Line 50  http://mitgcm.org/htdig/ Line 53  http://mitgcm.org/htdig/
53    
54  \section{Obtaining the code}  \section{Obtaining the code}
55  \label{sect:obtainingCode}  \label{sect:obtainingCode}
56    \begin{rawhtml}
57    <!-- CMIREDIR:obtainingCode: -->
58    \end{rawhtml}
59    
60  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
61  the instructions below. As a courtesy we ask that you send e-mail to us at  the instructions below. As a courtesy we ask that you send e-mail to us at
# Line 92  be set within your shell.  For a csh or Line 98  be set within your shell.  For a csh or
98  \begin{verbatim}  \begin{verbatim}
99  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
100  \end{verbatim}  \end{verbatim}
101  in your .cshrc or .tcshrc file.  For bash or sh shells, put:  in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
102    shells, put:
103  \begin{verbatim}  \begin{verbatim}
104  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
105  \end{verbatim}  \end{verbatim}
# Line 118  The MITgcm web site contains further dir Line 125  The MITgcm web site contains further dir
125  code and CVS.  It also contains a web interface to our CVS archive so  code and CVS.  It also contains a web interface to our CVS archive so
126  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
127  development milestones:  development milestones:
128  \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
129  \begin{verbatim}  \begin{verbatim}
130  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
131  \end{verbatim}  \end{verbatim}
# Line 147  of CVS aliases Line 154  of CVS aliases
154    \label{tab:cvsModules}    \label{tab:cvsModules}
155  \end{table}  \end{table}
156    
157  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
158  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
159  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
160  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
161  track of your file versions with respect to the repository. Don't edit  track of your file versions with respect to the repository. Don't edit
162  the files in \textit{CVS}!  You can also use CVS to download code  the files in \texttt{CVS}!  You can also use CVS to download code
163  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
164  MITgcm code can be found  MITgcm code can be found
165  \begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/usingcvstoget.html" target="idontexist"> \end{rawhtml}
166  here  here
167  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
168  .  .
# Line 184  delete; even if you do not use CVS yours Line 191  delete; even if you do not use CVS yours
191  us if you should need to send us your copy of the code.  If a recent  us if you should need to send us your copy of the code.  If a recent
192  tar file does not exist, then please contact the developers through  tar file does not exist, then please contact the developers through
193  the  the
194  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
195  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
196  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
197  mailing list.  mailing list.
# Line 256  also means we can't tell what version of Line 263  also means we can't tell what version of
263  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
264    
265  \section{Model and directory structure}  \section{Model and directory structure}
266    \begin{rawhtml}
267    <!-- CMIREDIR:directory_structure: -->
268    \end{rawhtml}
269    
270  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
271  support wrapper. This wrapper is designed to provide a general  support wrapper. This wrapper is designed to provide a general
# Line 263  framework for grid-point models. MITgcmU Line 273  framework for grid-point models. MITgcmU
273  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
274  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
275  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
276  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
277  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
278  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
279  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
280  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
281  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
282  part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is  part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is
283  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
284  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
285  structure).  structure).
286    
287  \begin{itemize}  \begin{itemize}
288    
289  \item \textit{bin}: this directory is initially empty. It is the  \item \texttt{bin}: this directory is initially empty. It is the
290    default directory in which to compile the code.    default directory in which to compile the code.
291        
292  \item \textit{diags}: contains the code relative to time-averaged  \item \texttt{diags}: contains the code relative to time-averaged
293    diagnostics. It is subdivided into two subdirectories \textit{inc}    diagnostics. It is subdivided into two subdirectories \texttt{inc}
294    and \textit{src} that contain include files (*.\textit{h} files) and    and \texttt{src} that contain include files (\texttt{*.h} files) and
295    Fortran subroutines (*.\textit{F} files), respectively.    Fortran subroutines (\texttt{*.F} files), respectively.
296    
297  \item \textit{doc}: contains brief documentation notes.  \item \texttt{doc}: contains brief documentation notes.
298        
299  \item \textit{eesupp}: contains the execution environment source code.  \item \texttt{eesupp}: contains the execution environment source code.
300    Also subdivided into two subdirectories \textit{inc} and    Also subdivided into two subdirectories \texttt{inc} and
301    \textit{src}.    \texttt{src}.
302        
303  \item \textit{exe}: this directory is initially empty. It is the  \item \texttt{exe}: this directory is initially empty. It is the
304    default directory in which to execute the code.    default directory in which to execute the code.
305        
306  \item \textit{model}: this directory contains the main source code.  \item \texttt{model}: this directory contains the main source code.
307    Also subdivided into two subdirectories \textit{inc} and    Also subdivided into two subdirectories \texttt{inc} and
308    \textit{src}.    \texttt{src}.
309        
310  \item \textit{pkg}: contains the source code for the packages. Each  \item \texttt{pkg}: contains the source code for the packages. Each
311    package corresponds to a subdirectory. For example, \textit{gmredi}    package corresponds to a subdirectory. For example, \texttt{gmredi}
312    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
313    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
314    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in section 3.
315        
316  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
317    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
318    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
319    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
320    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
321    The latter is described in details in part V.    The latter is described in details in part V.
322        
323  \item \textit{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
324    subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
325    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
326    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
327    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
328    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
329    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
330    model output.    model output.
331        
332  \item \textit{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
333    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sect:modelExamples}.
334    
335  \end{itemize}  \end{itemize}
336    
337  \section[MITgcm Example Experiments]{Example experiments}  \section[MITgcm Example Experiments]{Example experiments}
338  \label{sect:modelExamples}  \label{sect:modelExamples}
339    \begin{rawhtml}
340    <!-- CMIREDIR:modelExamples: -->
341    \end{rawhtml}
342    
343  %% a set of twenty-four pre-configured numerical experiments  %% a set of twenty-four pre-configured numerical experiments
344    
345  The MITgcm distribution comes with more than a dozen pre-configured  The full MITgcm distribution comes with more than a dozen
346  numerical experiments. Some of these example experiments are tests of  pre-configured numerical experiments. Some of these example
347  individual parts of the model code, but many are fully fledged  experiments are tests of individual parts of the model code, but many
348  numerical simulations. A few of the examples are used for tutorial  are fully fledged numerical simulations. A few of the examples are
349  documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.  used for tutorial documentation in sections \ref{sect:eg-baro} -
350  The other examples follow the same general structure as the tutorial  \ref{sect:eg-global}.  The other examples follow the same general
351  examples. However, they only include brief instructions in a text file  structure as the tutorial examples. However, they only include brief
352  called {\it README}.  The examples are located in subdirectories under  instructions in a text file called {\it README}.  The examples are
353  the directory \textit{verification}. Each example is briefly described  located in subdirectories under the directory \texttt{verification}.
354  below.  Each example is briefly described below.
355    
356  \subsection{Full list of model examples}  \subsection{Full list of model examples}
357    
358  \begin{enumerate}  \begin{enumerate}
359        
360  \item \textit{exp0} - single layer, ocean double gyre (barotropic with  \item \texttt{exp0} - single layer, ocean double gyre (barotropic with
361    free-surface). This experiment is described in detail in section    free-surface). This experiment is described in detail in section
362    \ref{sect:eg-baro}.    \ref{sect:eg-baro}.
363    
364  \item \textit{exp1} - Four layer, ocean double gyre. This experiment  \item \texttt{exp1} - Four layer, ocean double gyre. This experiment
365    is described in detail in section \ref{sect:eg-baroc}.    is described in detail in section \ref{sect:eg-baroc}.
366        
367  \item \textit{exp2} - 4x4 degree global ocean simulation with steady  \item \texttt{exp2} - 4x4 degree global ocean simulation with steady
368    climatological forcing. This experiment is described in detail in    climatological forcing. This experiment is described in detail in
369    section \ref{sect:eg-global}.    section \ref{sect:eg-global}.
370        
371  \item \textit{exp4} - Flow over a Gaussian bump in open-water or  \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
372    channel with open boundaries.    channel with open boundaries.
373        
374  \item \textit{exp5} - Inhomogenously forced ocean convection in a  \item \texttt{exp5} - Inhomogenously forced ocean convection in a
375    doubly periodic box.    doubly periodic box.
376    
377  \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  \item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for
378  Gent/McWilliams scheme). 2D (Y-Z).  Gent/McWilliams scheme). 2D (Y-Z).
379    
380  \item \textit{internal wave} - Ocean internal wave forced by open  \item \texttt{internal wave} - Ocean internal wave forced by open
381    boundary conditions.    boundary conditions.
382        
383  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
384    scheme; 1 month integration    scheme; 1 month integration
385        
386  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and  \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
387    Suarez '94 forcing.    Suarez '94 forcing.
388        
389  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and  \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
390    Suarez '94 forcing.    Suarez '94 forcing.
391        
392  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
393    Suarez '94 forcing on the cubed sphere.    Suarez '94 forcing on the cubed sphere.
394        
395  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
396    Global Zonal Mean configuration, 1x64x5 resolution.    Global Zonal Mean configuration, 1x64x5 resolution.
397        
398  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
399    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
400        
401  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
402    physics. 3D Equatorial Channel configuration.    physics. 3D Equatorial Channel configuration.
403        
404  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.
405    Global configuration, on latitude longitude grid with 128x64x5 grid    Global configuration, on latitude longitude grid with 128x64x5 grid
406    points ($2.8^\circ{\rm degree}$ resolution).    points ($2.8^\circ$ resolution).
407        
408  \item \textit{adjustment.128x64x1} Barotropic adjustment problem on  \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
409    latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
     degree}$ resolution).  
410        
411  \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on  \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
412    cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm    cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
413      degree}$ resolution).    resolution).
414        
415  \item \textit{advect\_cs} Two-dimensional passive advection test on  \item \texttt{advect\_cs} Two-dimensional passive advection test on
416    cube sphere grid.    cube sphere grid.
417        
418  \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive  \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
419    advection test on Cartesian grid.    advection test on Cartesian grid.
420        
421  \item \textit{advect\_yz} Two-dimensional (vertical plane) passive  \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
422    advection test on Cartesian grid.    advection test on Cartesian grid.
423        
424  \item \textit{carbon} Simple passive tracer experiment. Includes  \item \texttt{carbon} Simple passive tracer experiment. Includes
425    derivative calculation. Described in detail in section    derivative calculation. Described in detail in section
426    \ref{sect:eg-carbon-ad}.    \ref{sect:eg-carbon-ad}.
427    
428  \item \textit{flt\_example} Example of using float package.  \item \texttt{flt\_example} Example of using float package.
429        
430  \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
431    boundary conditions and poles.    boundary conditions and poles.
432    
433  \item \textit{global\_ocean\_pressure} Global circulation in pressure  \item \texttt{global\_ocean\_pressure} Global circulation in pressure
434    coordinate (non-Boussinesq ocean model). Described in detail in    coordinate (non-Boussinesq ocean model). Described in detail in
435    section \ref{sect:eg-globalpressure}.    section \ref{sect:eg-globalpressure}.
436        
437  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube  \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
438    sphere grid.    sphere grid.
439    
440  \end{enumerate}  \end{enumerate}
# Line 432  Gent/McWilliams scheme). 2D (Y-Z). Line 444  Gent/McWilliams scheme). 2D (Y-Z).
444  Each example directory has the following subdirectories:  Each example directory has the following subdirectories:
445    
446  \begin{itemize}  \begin{itemize}
447  \item \textit{code}: contains the code particular to the example. At a  \item \texttt{code}: contains the code particular to the example. At a
448    minimum, this directory includes the following files:    minimum, this directory includes the following files:
449    
450    \begin{itemize}    \begin{itemize}
451    \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to    \item \texttt{code/packages.conf}: declares the list of packages or
452        package groups to be used.  If not included, the default version
453        is located in \texttt{pkg/pkg\_default}.  Package groups are
454        simply convenient collections of commonly used packages which are
455        defined in \texttt{pkg/pkg\_default}.  Some packages may require
456        other packages or may require their absence (that is, they are
457        incompatible) and these package dependencies are listed in
458        \texttt{pkg/pkg\_depend}.
459    
460      \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
461      the ``execution environment'' part of the code. The default      the ``execution environment'' part of the code. The default
462      version is located in \textit{eesupp/inc}.      version is located in \texttt{eesupp/inc}.
463        
464    \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to    \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
465      the ``numerical model'' part of the code. The default version is      the ``numerical model'' part of the code. The default version is
466      located in \textit{model/inc}.      located in \texttt{model/inc}.
467        
468    \item \textit{code/SIZE.h}: declares size of underlying    \item \texttt{code/SIZE.h}: declares size of underlying
469      computational grid.  The default version is located in      computational grid.  The default version is located in
470      \textit{model/inc}.      \texttt{model/inc}.
471    \end{itemize}    \end{itemize}
472        
473    In addition, other include files and subroutines might be present in    In addition, other include files and subroutines might be present in
474    \textit{code} depending on the particular experiment. See Section 2    \texttt{code} depending on the particular experiment. See Section 2
475    for more details.    for more details.
476        
477  \item \textit{input}: contains the input data files required to run  \item \texttt{input}: contains the input data files required to run
478    the example. At a minimum, the \textit{input} directory contains the    the example. At a minimum, the \texttt{input} directory contains the
479    following files:    following files:
480    
481    \begin{itemize}    \begin{itemize}
482    \item \textit{input/data}: this file, written as a namelist,    \item \texttt{input/data}: this file, written as a namelist,
483      specifies the main parameters for the experiment.      specifies the main parameters for the experiment.
484        
485    \item \textit{input/data.pkg}: contains parameters relative to the    \item \texttt{input/data.pkg}: contains parameters relative to the
486      packages used in the experiment.      packages used in the experiment.
487        
488    \item \textit{input/eedata}: this file contains ``execution    \item \texttt{input/eedata}: this file contains ``execution
489      environment'' data. At present, this consists of a specification      environment'' data. At present, this consists of a specification
490      of the number of threads to use in $X$ and $Y$ under multithreaded      of the number of threads to use in $X$ and $Y$ under multithreaded
491      execution.      execution.
# Line 475  Each example directory has the following Line 496  Each example directory has the following
496    of the experiment.  This varies from experiment to experiment. See    of the experiment.  This varies from experiment to experiment. See
497    section 2 for more details.    section 2 for more details.
498    
499  \item \textit{results}: this directory contains the output file  \item \texttt{results}: this directory contains the output file
500    \textit{output.txt} produced by the simulation example. This file is    \texttt{output.txt} produced by the simulation example. This file is
501    useful for comparison with your own output when you run the    useful for comparison with your own output when you run the
502    experiment.    experiment.
503  \end{itemize}  \end{itemize}
# Line 486  compile the code. Line 507  compile the code.
507    
508  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
509  \label{sect:buildingCode}  \label{sect:buildingCode}
510    \begin{rawhtml}
511  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
512  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
513  compiler and optimization options and also figures out any file  
514  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
515  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
516    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
517    file dependencies. We supply a script (\texttt{genmake2}), described
518    in section \ref{sect:genmake}, that automatically creates the
519    \texttt{Makefile} for you. You then need to build the dependencies and
520  compile the code.  compile the code.
521    
522  As an example, let's assume that you want to build and run experiment  As an example, assume that you want to build and run experiment
523  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
524  actually do this but here let's build the code in  actually do this but here let's build the code in
525  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
526  \begin{verbatim}  \begin{verbatim}
527  % cd verification/exp2/input  % cd verification/exp2/build
528  \end{verbatim}  \end{verbatim}
529  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
530  \begin{verbatim}  \begin{verbatim}
531  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
532  \end{verbatim}  \end{verbatim}
533  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
534  code with any files in the directory {\em ../code/}.  code with any files in the directory \texttt{../code/}.
535    
536  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
537  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
538  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
539  appropriate set of options from the files (``optfiles'') contained in  appropriate set of options from the files (``optfiles'') contained in
540  the {\em tools/build\_options} directory.  Under some circumstances, a  the \texttt{tools/build\_options} directory.  Under some
541  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
542  exact combination of compiler, compiler flags, libraries, and other  specify the exact combination of compiler, compiler flags, libraries,
543  options necessary to build a particular configuration of MITgcm.  In  and other options necessary to build a particular configuration of
544  such cases, it is generally helpful to read the existing ``optfiles''  MITgcm.  In such cases, it is generally helpful to read the existing
545  and mimic their syntax.  ``optfiles'' and mimic their syntax.
546    
547  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
548  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
549  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
550  architectures) to the  architectures) to the
551  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
552  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
553  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
554  list.  list.
555    
556  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
557  \begin{verbatim}  \begin{verbatim}
558  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
559  \end{verbatim}  \end{verbatim}
560    
561  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
562    dependencies with the command:
563  \begin{verbatim}  \begin{verbatim}
564  % make depend  % make depend
565  \end{verbatim}  \end{verbatim}
566  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
567  upon which other files depend. The purpose of this is to reduce  list of files upon which other files depend. The purpose of this is to
568  re-compilation if and when you start to modify the code. The {\tt make  reduce re-compilation if and when you start to modify the code. The
569    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
570  directory.  It is important to note that the {\tt make depend} stage  this directory.  It is important to note that the {\tt make depend}
571  will occasionally produce warnings or errors since the dependency  stage will occasionally produce warnings or errors since the
572  parsing tool is unable to find all of the necessary header files  dependency parsing tool is unable to find all of the necessary header
573  (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it is  files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
574  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
575    step.
576    
577  Next compile the code:  Next one can compile the code using:
578  \begin{verbatim}  \begin{verbatim}
579  % make  % make
580  \end{verbatim}  \end{verbatim}
581  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
582  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
583  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
584    (shared multi-processor) systems, the build process can often be sped
585    up appreciably using the command:
586    \begin{verbatim}
587    % make -j 2
588    \end{verbatim}
589    where the ``2'' can be replaced with a number that corresponds to the
590    number of CPUs available.
591    
592  Now you are ready to run the model. General instructions for doing so are  Now you are ready to run the model. General instructions for doing so are
593  given in section \ref{sect:runModel}. Here, we can run the model with:  given in section \ref{sect:runModel}. Here, we can run the model by
594    first creating links to all the input files:
595    \begin{verbatim}
596    ln -s ../input/* .
597    \end{verbatim}
598    and then calling the executable with:
599  \begin{verbatim}  \begin{verbatim}
600  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
601  \end{verbatim}  \end{verbatim}
602  where we are re-directing the stream of text output to the file {\em  where we are re-directing the stream of text output to the file
603  output.txt}.  \texttt{output.txt}.
604    
605    \subsection{Building/compiling the code elsewhere}
606    
607    In the example above (section \ref{sect:buildingCode}) we built the
608    executable in the {\em input} directory of the experiment for
609    convenience. You can also configure and compile the code in other
610    locations, for example on a scratch disk with out having to copy the
611    entire source tree. The only requirement to do so is you have {\tt
612      genmake2} in your path or you know the absolute path to {\tt
613      genmake2}.
614    
615    The following sections outline some possible methods of organizing
616    your source and data.
617    
618    \subsubsection{Building from the {\em ../code directory}}
619    
620    This is just as simple as building in the {\em input/} directory:
621    \begin{verbatim}
622    % cd verification/exp2/code
623    % ../../../tools/genmake2
624    % make depend
625    % make
626    \end{verbatim}
627    However, to run the model the executable ({\em mitgcmuv}) and input
628    files must be in the same place. If you only have one calculation to make:
629    \begin{verbatim}
630    % cd ../input
631    % cp ../code/mitgcmuv ./
632    % ./mitgcmuv > output.txt
633    \end{verbatim}
634    or if you will be making multiple runs with the same executable:
635    \begin{verbatim}
636    % cd ../
637    % cp -r input run1
638    % cp code/mitgcmuv run1
639    % cd run1
640    % ./mitgcmuv > output.txt
641    \end{verbatim}
642    
643    \subsubsection{Building from a new directory}
644    
645    Since the {\em input} directory contains input files it is often more
646    useful to keep {\em input} pristine and build in a new directory
647    within {\em verification/exp2/}:
648    \begin{verbatim}
649    % cd verification/exp2
650    % mkdir build
651    % cd build
652    % ../../../tools/genmake2 -mods=../code
653    % make depend
654    % make
655    \end{verbatim}
656    This builds the code exactly as before but this time you need to copy
657    either the executable or the input files or both in order to run the
658    model. For example,
659    \begin{verbatim}
660    % cp ../input/* ./
661    % ./mitgcmuv > output.txt
662    \end{verbatim}
663    or if you tend to make multiple runs with the same executable then
664    running in a new directory each time might be more appropriate:
665    \begin{verbatim}
666    % cd ../
667    % mkdir run1
668    % cp build/mitgcmuv run1/
669    % cp input/* run1/
670    % cd run1
671    % ./mitgcmuv > output.txt
672    \end{verbatim}
673    
674    \subsubsection{Building on a scratch disk}
675    
676    Model object files and output data can use up large amounts of disk
677    space so it is often the case that you will be operating on a large
678    scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
679    following commands will build the model in {\em /scratch/exp2-run1}:
680    \begin{verbatim}
681    % cd /scratch/exp2-run1
682    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
683      -mods=~/MITgcm/verification/exp2/code
684    % make depend
685    % make
686    \end{verbatim}
687    To run the model here, you'll need the input files:
688    \begin{verbatim}
689    % cp ~/MITgcm/verification/exp2/input/* ./
690    % ./mitgcmuv > output.txt
691    \end{verbatim}
692    
693    As before, you could build in one directory and make multiple runs of
694    the one experiment:
695    \begin{verbatim}
696    % cd /scratch/exp2
697    % mkdir build
698    % cd build
699    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
700      -mods=~/MITgcm/verification/exp2/code
701    % make depend
702    % make
703    % cd ../
704    % cp -r ~/MITgcm/verification/exp2/input run2
705    % cd run2
706    % ./mitgcmuv > output.txt
707    \end{verbatim}
708    
709    
710    \subsection{Using \texttt{genmake2}}
711    \label{sect:genmake}
712    
713    To compile the code, first use the program \texttt{genmake2} (located
714    in the \texttt{tools} directory) to generate a Makefile.
715    \texttt{genmake2} is a shell script written to work with all
716    ``sh''--compatible shells including bash v1, bash v2, and Bourne.
717    Internally, \texttt{genmake2} determines the locations of needed
718    files, the compiler, compiler options, libraries, and Unix tools.  It
719    relies upon a number of ``optfiles'' located in the
720    \texttt{tools/build\_options} directory.
721    
722    The purpose of the optfiles is to provide all the compilation options
723    for particular ``platforms'' (where ``platform'' roughly means the
724    combination of the hardware and the compiler) and code configurations.
725    Given the combinations of possible compilers and library dependencies
726    ({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
727    for a single machine.  The naming scheme for the majority of the
728    optfiles shipped with the code is
729    \begin{center}
730      {\bf OS\_HARDWARE\_COMPILER }
731    \end{center}
732    where
733    \begin{description}
734    \item[OS] is the name of the operating system (generally the
735      lower-case output of the {\tt 'uname'} command)
736    \item[HARDWARE] is a string that describes the CPU type and
737      corresponds to output from the  {\tt 'uname -m'} command:
738      \begin{description}
739      \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
740        and athlon
741      \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
742      \item[amd64] is AMD x86\_64 systems
743      \item[ppc] is for Mac PowerPC systems
744      \end{description}
745    \item[COMPILER] is the compiler name (generally, the name of the
746      FORTRAN executable)
747    \end{description}
748    
749    In many cases, the default optfiles are sufficient and will result in
750    usable Makefiles.  However, for some machines or code configurations,
751    new ``optfiles'' must be written. To create a new optfile, it is
752    generally best to start with one of the defaults and modify it to suit
753    your needs.  Like \texttt{genmake2}, the optfiles are all written
754    using a simple ``sh''--compatible syntax.  While nearly all variables
755    used within \texttt{genmake2} may be specified in the optfiles, the
756    critical ones that should be defined are:
757    
758    \begin{description}
759    \item[FC] the FORTRAN compiler (executable) to use
760    \item[DEFINES] the command-line DEFINE options passed to the compiler
761    \item[CPP] the C pre-processor to use
762    \item[NOOPTFLAGS] options flags for special files that should not be
763      optimized
764    \end{description}
765    
766    For example, the optfile for a typical Red Hat Linux machine (``ia32''
767    architecture) using the GCC (g77) compiler is
768    \begin{verbatim}
769    FC=g77
770    DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
771    CPP='cpp  -traditional -P'
772    NOOPTFLAGS='-O0'
773    #  For IEEE, use the "-ffloat-store" option
774    if test "x$IEEE" = x ; then
775        FFLAGS='-Wimplicit -Wunused -Wuninitialized'
776        FOPTIM='-O3 -malign-double -funroll-loops'
777    else
778        FFLAGS='-Wimplicit -Wunused -ffloat-store'
779        FOPTIM='-O0 -malign-double'
780    fi
781    \end{verbatim}
782    
783    If you write an optfile for an unrepresented machine or compiler, you
784    are strongly encouraged to submit the optfile to the MITgcm project
785    for inclusion.  Please send the file to the
786    \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
787    \begin{center}
788      MITgcm-support@mitgcm.org
789    \end{center}
790    \begin{rawhtml} </A> \end{rawhtml}
791    mailing list.
792    
793    In addition to the optfiles, \texttt{genmake2} supports a number of
794    helpful command-line options.  A complete list of these options can be
795    obtained from:
796    \begin{verbatim}
797    % genmake2 -h
798    \end{verbatim}
799    
800    The most important command-line options are:
801    \begin{description}
802      
803    \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
804      should be used for a particular build.
805      
806      If no "optfile" is specified (either through the command line or the
807      MITGCM\_OPTFILE environment variable), genmake2 will try to make a
808      reasonable guess from the list provided in {\em
809        tools/build\_options}.  The method used for making this guess is
810      to first determine the combination of operating system and hardware
811      (eg. "linux\_ia32") and then find a working FORTRAN compiler within
812      the user's path.  When these three items have been identified,
813      genmake2 will try to find an optfile that has a matching name.
814      
815    \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
816      set of packages to be used.  The normal order of precedence for
817      packages is as follows:
818      \begin{enumerate}
819      \item If available, the command line (\texttt{--pdefault}) settings
820        over-rule any others.
821    
822      \item Next, \texttt{genmake2} will look for a file named
823        ``\texttt{packages.conf}'' in the local directory or in any of the
824        directories specified with the \texttt{--mods} option.
825        
826      \item Finally, if neither of the above are available,
827        \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
828      \end{enumerate}
829      
830    \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
831      used for packages.
832      
833      If not specified, the default dependency file {\em pkg/pkg\_depend}
834      is used.  The syntax for this file is parsed on a line-by-line basis
835      where each line containes either a comment ("\#") or a simple
836      "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
837      specifies a "must be used with" or a "must not be used with"
838      relationship, respectively.  If no rule is specified, then it is
839      assumed that the two packages are compatible and will function
840      either with or without each other.
841      
842    \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
843      automatic differentiation options file to be used.  The file is
844      analogous to the ``optfile'' defined above but it specifies
845      information for the AD build process.
846      
847      The default file is located in {\em
848        tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
849      and "TAMC" compilers.  An alternate version is also available at
850      {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
851      "STAF" compiler.  As with any compilers, it is helpful to have their
852      directories listed in your {\tt \$PATH} environment variable.
853      
854    \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
855      directories containing ``modifications''.  These directories contain
856      files with names that may (or may not) exist in the main MITgcm
857      source tree but will be overridden by any identically-named sources
858      within the ``MODS'' directories.
859      
860      The order of precedence for this "name-hiding" is as follows:
861      \begin{itemize}
862      \item ``MODS'' directories (in the order given)
863      \item Packages either explicitly specified or provided by default
864        (in the order given)
865      \item Packages included due to package dependencies (in the order
866        that that package dependencies are parsed)
867      \item The "standard dirs" (which may have been specified by the
868        ``-standarddirs'' option)
869      \end{itemize}
870      
871    \item[\texttt{--mpi}] This option enables certain MPI features (using
872      CPP \texttt{\#define}s) within the code and is necessary for MPI
873      builds (see Section \ref{sect:mpi-build}).
874      
875    \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
876      soft-links and other bugs common with the \texttt{make} versions
877      provided by commercial Unix vendors, GNU \texttt{make} (sometimes
878      called \texttt{gmake}) should be preferred.  This option provides a
879      means for specifying the make executable to be used.
880      
881    \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
882      machines, the ``bash'' shell is unavailable.  To run on these
883      systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
884      a Bourne, POSIX, or compatible) shell.  The syntax in these
885      circumstances is:
886      \begin{center}
887        \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
888      \end{center}
889      where \texttt{/bin/sh} can be replaced with the full path and name
890      of the desired shell.
891    
892    \end{description}
893    
894    
895    \subsection{Building with MPI}
896    \label{sect:mpi-build}
897    
898    Building MITgcm to use MPI libraries can be complicated due to the
899    variety of different MPI implementations available, their dependencies
900    or interactions with different compilers, and their often ad-hoc
901    locations within file systems.  For these reasons, its generally a
902    good idea to start by finding and reading the documentation for your
903    machine(s) and, if necessary, seeking help from your local systems
904    administrator.
905    
906    The steps for building MITgcm with MPI support are:
907    \begin{enumerate}
908      
909    \item Determine the locations of your MPI-enabled compiler and/or MPI
910      libraries and put them into an options file as described in Section
911      \ref{sect:genmake}.  One can start with one of the examples in:
912      \begin{rawhtml} <A
913        href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
914      \end{rawhtml}
915      \begin{center}
916        \texttt{MITgcm/tools/build\_options/}
917      \end{center}
918      \begin{rawhtml} </A> \end{rawhtml}
919      such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
920      \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
921      hand.  You may need help from your user guide or local systems
922      administrator to determine the exact location of the MPI libraries.
923      If libraries are not installed, MPI implementations and related
924      tools are available including:
925      \begin{itemize}
926      \item \begin{rawhtml} <A
927          href="http://www-unix.mcs.anl.gov/mpi/mpich/">
928        \end{rawhtml}
929        MPICH
930        \begin{rawhtml} </A> \end{rawhtml}
931    
932      \item \begin{rawhtml} <A
933          href="http://www.lam-mpi.org/">
934        \end{rawhtml}
935        LAM/MPI
936        \begin{rawhtml} </A> \end{rawhtml}
937    
938      \item \begin{rawhtml} <A
939          href="http://www.osc.edu/~pw/mpiexec/">
940        \end{rawhtml}
941        MPIexec
942        \begin{rawhtml} </A> \end{rawhtml}
943      \end{itemize}
944      
945    \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
946      (see Section \ref{sect:genmake}) using commands such as:
947    {\footnotesize \begin{verbatim}
948      %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
949      %  make depend
950      %  make
951    \end{verbatim} }
952      
953    \item Run the code with the appropriate MPI ``run'' or ``exec''
954      program provided with your particular implementation of MPI.
955      Typical MPI packages such as MPICH will use something like:
956    \begin{verbatim}
957      %  mpirun -np 4 -machinefile mf ./mitgcmuv
958    \end{verbatim}
959      Sightly more complicated scripts may be needed for many machines
960      since execution of the code may be controlled by both the MPI
961      library and a job scheduling and queueing system such as PBS,
962      LoadLeveller, Condor, or any of a number of similar tools.  A few
963      example scripts (those used for our \begin{rawhtml} <A
964        href="http://mitgcm.org/testing.html"> \end{rawhtml}regular
965      verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
966      at:
967      \begin{rawhtml} <A
968        href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
969      \end{rawhtml}
970      {\footnotesize \tt
971        http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
972      \begin{rawhtml} </A> \end{rawhtml}
973    
974    \end{enumerate}
975    
976    An example of the above process on the MITgcm cluster (``cg01'') using
977    the GNU g77 compiler and the mpich MPI library is:
978    
979    {\footnotesize \begin{verbatim}
980      %  cd MITgcm/verification/exp5
981      %  mkdir build
982      %  cd build
983      %  ../../../tools/genmake2 -mpi -mods=../code \
984           -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
985      %  make depend
986      %  make
987      %  cd ../input
988      %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
989           -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
990    \end{verbatim} }
991    
992  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
993  \label{sect:runModel}  \label{sect:runModel}
994    \begin{rawhtml}
995    <!-- CMIREDIR:runModel: -->
996    \end{rawhtml}
997    
998  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sect:buildingCode})
999  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
1000  local directory.  local directory.
1001    
# Line 583  do!). The above command will spew out ma Line 1010  do!). The above command will spew out ma
1010  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
1011  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
1012  etc. It is worth keeping this text output with the binary output so we  etc. It is worth keeping this text output with the binary output so we
1013  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
1014  \begin{verbatim}  \begin{verbatim}
1015  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
1016  \end{verbatim}  \end{verbatim}
# Line 591  In the event that the model encounters a Line 1018  In the event that the model encounters a
1018  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
1019  along with the (\texttt{stderr}) error message within any bug reports.  along with the (\texttt{stderr}) error message within any bug reports.
1020    
1021  For the example experiments in {\em verification}, an example of the  For the example experiments in \texttt{verification}, an example of the
1022  output is kept in {\em results/output.txt} for comparison. You can  output is kept in \texttt{results/output.txt} for comparison. You can
1023  compare your {\em output.txt} with the corresponding one for that  compare your \texttt{output.txt} with the corresponding one for that
1024  experiment to check that the set-up works.  experiment to check that the set-up works.
1025    
1026    
1027    
1028  \subsection{Output files}  \subsection{Output files}
1029    
1030  The model produces various output files.  Depending upon the I/O  The model produces various output files and, when using \texttt{mnc},
1031  package selected (either \texttt{mdsio} or \texttt{mnc} or both as  sometimes even directories.  Depending upon the I/O package(s)
1032  determined by both the compile-time settings and the run-time flags in  selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
1033  \texttt{data.pkg}), the following output may appear.  both as determined by \texttt{code/packages.conf}) and the run-time
1034    flags set (in \texttt{input/data.pkg}), the following output may
1035    appear.
1036    
1037    
1038  \subsubsection{MDSIO output files}  \subsubsection{MDSIO output files}
# Line 613  package.  At a minimum, the instantaneou Line 1042  package.  At a minimum, the instantaneou
1042  written out, which is made of the following files:  written out, which is made of the following files:
1043    
1044  \begin{itemize}  \begin{itemize}
1045  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
1046  0 $ eastward).    and positive eastward).
1047    
1048  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
1049  and $> 0$ northward).    (m/s and positive northward).
1050    
1051  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
1052  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
1053  i.e. downward).    towards increasing pressure i.e. downward).
1054    
1055  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
1056  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
1057    
1058  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
1059  (g/kg).    vapor (g/kg).
1060    
1061  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
1062  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
1063  \end{itemize}  \end{itemize}
1064    
1065  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
1066  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
1067  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
1068    
1069  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
1070    
1071  \begin{itemize}  \begin{itemize}
1072  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
1073  \end{itemize}  \end{itemize}
1074    
1075  is written out. This file represents the state of the model in a condensed  is written out. This file represents the state of the model in a condensed
# Line 648  form and is used for restarting the inte Line 1077  form and is used for restarting the inte
1077  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
1078    
1079  \begin{itemize}  \begin{itemize}
1080  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
1081  \end{itemize}  \end{itemize}
1082    
1083  containing the D-grid velocity data and that has to be written out as well  containing the D-grid velocity data and that has to be written out as well
1084  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
1085  as the pickup files but are named differently. Their name contain the chain  as the pickup files but are named differently. Their name contain the chain
1086  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
1087  used to restart the model but are overwritten every other time they are  used to restart the model but are overwritten every other time they are
1088  output to save disk space during long integrations.  output to save disk space during long integrations.
1089    
# Line 668  a name such as \texttt{mnc\_test\_\${DAT Line 1097  a name such as \texttt{mnc\_test\_\${DAT
1097  within this subdirectory are all in the ``self-describing'' netCDF  within this subdirectory are all in the ``self-describing'' netCDF
1098  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:
1099  \begin{itemize}  \begin{itemize}
1100  \item At a minimum, the \texttt{ncdump} utility is typically included  \item \texttt{ncdump} is a utility which is typically included
1101    with every netCDF install:    with every netCDF install:
1102    \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}
1103  \begin{verbatim}  \begin{verbatim}
1104  http://www.unidata.ucar.edu/packages/netcdf/  http://www.unidata.ucar.edu/packages/netcdf/
1105  \end{verbatim}  \end{verbatim}
1106    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
1107      binaries into formatted ASCII text files.
1108    
1109  \item The \texttt{ncview} utility is a very convenient and quick way  \item \texttt{ncview} utility is a very convenient and quick way
1110    to plot netCDF data and it runs on most OSes:    to plot netCDF data and it runs on most OSes:
1111    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
1112  \begin{verbatim}  \begin{verbatim}
# Line 686  http://meteora.ucsd.edu/~pierce/ncview_h Line 1116  http://meteora.ucsd.edu/~pierce/ncview_h
1116        
1117  \item MatLAB(c) and other common post-processing environments provide  \item MatLAB(c) and other common post-processing environments provide
1118    various netCDF interfaces including:    various netCDF interfaces including:
1119      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
1120    \begin{verbatim}
1121    http://mexcdf.sourceforge.net/
1122    \end{verbatim}
1123      \begin{rawhtml} </A> \end{rawhtml}
1124    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
1125  \begin{verbatim}  \begin{verbatim}
1126  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
1127  \end{verbatim}  \end{verbatim}
1128    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
   
1129  \end{itemize}  \end{itemize}
1130    
1131    
# Line 699  http://woodshole.er.usgs.gov/staffpages/ Line 1133  http://woodshole.er.usgs.gov/staffpages/
1133    
1134  The ``traditional'' or mdsio model data are written according to a  The ``traditional'' or mdsio model data are written according to a
1135  ``meta/data'' file format.  Each variable is associated with two files  ``meta/data'' file format.  Each variable is associated with two files
1136  with suffix names \textit{.data} and \textit{.meta}. The  with suffix names \texttt{.data} and \texttt{.meta}. The
1137  \textit{.data} file contains the data written in binary form  \texttt{.data} file contains the data written in binary form
1138  (big\_endian by default). The \textit{.meta} file is a ``header'' file  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
1139  that contains information about the size and the structure of the  that contains information about the size and the structure of the
1140  \textit{.data} file. This way of organizing the output is particularly  \texttt{.data} file. This way of organizing the output is particularly
1141  useful when running multi-processors calculations. The base version of  useful when running multi-processors calculations. The base version of
1142  the model includes a few matlab utilities to read output files written  the model includes a few matlab utilities to read output files written
1143  in this format. The matlab scripts are located in the directory  in this format. The matlab scripts are located in the directory
1144  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m}  \texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
1145  reads the data. Look at the comments inside the script to see how to  reads the data. Look at the comments inside the script to see how to
1146  use it.  use it.
1147    
# Line 726  Some examples of reading and visualizing Line 1160  Some examples of reading and visualizing
1160  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
1161  \end{verbatim}  \end{verbatim}
1162    
1163  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available.  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
1164    they are described in Section \ref{sec:pkg:mnc}.
1165    
Legend:
Removed from v.1.29  
changed lines
  Added in v.1.35
  ViewVC Help
Powered by ViewVC 1.1.22