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<!-- CMIREDIR:packages: --> |
<!-- CMIREDIR:packages: --> |
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\end{rawhtml} |
\end{rawhtml} |
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In this chapter and in the following chapter, the MITgcm ``packages'' are |
In this chapter and in the following chapter, the MITgcm ``packages'' are |
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described. While you can carry out many experiments with MITgcm by starting |
described. While you can carry out many experiments with MITgcm by starting |
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from case studies in section \ref{sec:modelExamples}, configuring |
from case studies in section \ref{sec:modelExamples}, configuring |
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a brand new experiment or making major changes to an experimental configuration |
a brand new experiment or making major changes to an experimental configuration |
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requires some knowledge of the {\it packages} |
requires some knowledge of the {\it packages} |
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that make up the full MITgcm code. Packages are used in MITgcm to |
that make up the full MITgcm code. Packages are used in MITgcm to |
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help organize and layer various code building blocks that are assembled |
help organize and layer various code building blocks that are assembled |
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and selected to perform a specific experiment. Each of the specific experiments |
and selected to perform a specific experiment. Each of the specific experiments |
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described in section \ref{sec:modelExamples} uses a particular combination |
described in section \ref{sec:modelExamples} uses a particular combination |
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of packages. |
of packages. |
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Figure \ref{fig:package_organigramme} shows the full set of packages that |
Figure \ref{fig:package_organigramme} shows the full set of packages that |
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are available. As shown in the figure packages are classified into different |
are available. As shown in the figure packages are classified into different |
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groupings that layer on top of each other. The top layer packages are |
groupings that layer on top of each other. The top layer packages are |
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generally specialized to specific simulation types. In this layer there are |
generally specialized to specific simulation types. In this layer there are |
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packages that deal with biogeochemical processes, ocean interior |
packages that deal with biogeochemical processes, ocean interior |
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and boundary layer processes, atmospheric processes, sea-ice, coupled |
and boundary layer processes, atmospheric processes, sea-ice, coupled |
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simulations and state estimation. |
simulations and state estimation. |
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Below this layer are a set of general purpose |
Below this layer are a set of general purpose |
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numerical and computational packages. The general purpose numerical packages |
numerical and computational packages. The general purpose numerical packages |
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provide code for kernel numerical alogorithms |
provide code for kernel numerical alogorithms |
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that apply to |
that apply to |
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many different simulation types. Similarly, the general purpose computational |
many different simulation types. Similarly, the general purpose computational |
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packages implement non-numerical alogorithms that provide parallelism, |
packages implement non-numerical alogorithms that provide parallelism, |
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I/O and time-keeping functions that are used in many different scenarios. |
I/O and time-keeping functions that are used in many different scenarios. |
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\begin{figure} |
\begin{figure} |
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%%\begin{minipage}{12cm} |
%%\begin{minipage}{12cm} |
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%%\marginsize{0cm}{0cm}{0cm}{0cm} |
%%\marginsize{0cm}{0cm}{0cm}{0cm} |
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%% \epsfbox{s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps} |
%% \epsfbox{s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps} |
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%%\epsfig{file=s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm} |
%%\epsfig{file=s_phys_pkgs/figs/organigramme_mitgcm_pkg.eps, angle=-90, scale=0.85, width=17cm} |
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%%\end{minipage} |
%%\end{minipage} |
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\resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/organigramme_mitgcm_pkg2.eps}} |
%\resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/organigramme_mitgcm_pkg2.eps}} |
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|
\resizebox{5.5in}{!}{\includegraphics{s_phys_pkgs/figs/mitgcm_package_organisation.eps}} |
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\\ |
\\ |
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\caption{ Hierarchy of code layers that are assembled to make up an MITgcm |
\caption{ Hierarchy of code layers that are assembled to make up an MITgcm |
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simulation. Conceptually (and in terms of code organization) MITgcm consists |
simulation. Conceptually (and in terms of code organization) MITgcm consists |
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of several layers. At the base is a layer of core software that provides a |
of several layers. At the base is a layer of core software that provides a |
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basic numerical and computational foundation for MITgcm simulations. This |
basic numerical and computational foundation for MITgcm simulations. This |
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layer is shown marked {\bf Foundation Code} at the bottom of the figure |
layer is shown marked {\bf Foundation Code} at the bottom of the figure |
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and corresponds to code in the italicised subdirectories on the figure. |
and corresponds to code in the italicised subdirectories on the figure. |
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This layer is not organized into packages. All code above the foundation layer |
This layer is not organized into packages. All code above the foundation layer |
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is organized as packages. Much of the code in MITgcm is contained in packages |
is organized as packages. Much of the code in MITgcm is contained in packages |
| 54 |
which serve as a useful way of organizing and layering the different levels of |
which serve as a useful way of organizing and layering the different levels of |
| 55 |
functionality that make up the full MITgcm software distribution. |
functionality that make up the full MITgcm software distribution. |
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The figure shows the different packages in MITgcm as boxes containing bold |
The figure shows the different packages in MITgcm as boxes containing bold |
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face upper case names. Directly above the foundation layer are two layers of |
face upper case names. Directly above the foundation layer are two layers of |
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general purpose infrastructure software that consist of computational and |
general purpose infrastructure software that consist of computational and |
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numerical packages. These general purpose packages can be applied to both |
numerical packages. These general purpose packages can be applied to both |
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online and offline simulations and are used in many different physical |
online and offline simulations and are used in many different physical |
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simulation types. Above these layers are more specialized packages. } |
simulation types. Above these layers are more specialized packages. } |
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\label{fig:package_organigramme} |
\label{fig:package_organigramme} |
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\end{figure} |
\end{figure} |
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The following sections describe the packages shown in |
The following sections describe the packages shown in |
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figure \ref{fig:package_organigramme}. Section \ref{sec:pkg:using} |
figure \ref{fig:package_organigramme}. Section \ref{sec:pkg:using} |
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describes the general procedure for using any package in MITgcm. |
describes the general procedure for using any package in MITgcm. |
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Following that sections \ref{sec:pkg:gad}-\ref{sec:pkg:monitor} |
Following that sections \ref{sec:pkg:gad}-\ref{sec:pkg:monitor} |
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layout the algorithms implemented in specific packages |
layout the algorithms implemented in specific packages |
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and describe how to use the individual packages. A brief synopsis of the |
and describe how to use the individual packages. A brief synopsis of the |
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function of each package is given in table \ref{tab:package_summary_tab}. |
function of each package is given in table \ref{tab:package_summary_tab}. |
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Organizationally package code is assigned a |
Organizationally package code is assigned a |
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separate subdirectory in the MITgcm code distribution |
separate subdirectory in the MITgcm code distribution |
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\input{s_phys_pkgs/text/opps.tex} |
\input{s_phys_pkgs/text/opps.tex} |
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\newpage |
\newpage |
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\input{s_phys_pkgs/text/kl10.tex} |
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\newpage |
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\input{s_phys_pkgs/text/bulk_force.tex} |
\input{s_phys_pkgs/text/bulk_force.tex} |
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\newpage |
\newpage |
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