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% *======================================================================*
% Cactus Thorn template for ThornGuide documentation
% Author: Ian Kelley
% Date: Sun Jun 02, 2002
% $Header: /home/eschnett/C/carpet/Carpet/Carpet/CarpetIOHDF5/doc/documentation.tex,v 1.2 2004/03/18 18:17:21 cott Exp $
%
% Thorn documentation in the latex file doc/documentation.tex
% will be included in ThornGuides built with the Cactus make system.
% The scripts employed by the make system automatically include
% pages about variables, parameters and scheduling parsed from the
% relevent thorn CCL files.
%
% This template contains guidelines which help to assure that your
% documentation will be correctly added to ThornGuides. More
% information is available in the Cactus UsersGuide.
%
% Guidelines:
% - Do not change anything before the line
% % START CACTUS THORNGUIDE",
% except for filling in the title, author, date etc. fields.
% - Each of these fields should only be on ONE line.
% - Author names should be sparated with a \\ or a comma
% - You can define your own macros are OK, but they must appear after
% the START CACTUS THORNGUIDE line, and do not redefine standard
% latex commands.
% - To avoid name clashes with other thorns, 'labels', 'citations',
% 'references', and 'image' names should conform to the following
% convention:
% ARRANGEMENT_THORN_LABEL
% For example, an image wave.eps in the arrangement CactusWave and
% thorn WaveToyC should be renamed to CactusWave_WaveToyC_wave.eps
% - Graphics should only be included using the graphix package.
% More specifically, with the "includegraphics" command. Do
% not specify any graphic file extensions in your .tex file. This
% will allow us (later) to create a PDF version of the ThornGuide
% via pdflatex. |
% - References should be included with the latex "bibitem" command.
% - use \begin{abstract}...\end{abstract} instead of \abstract{...}
% - For the benefit of our Perl scripts, and for future extensions,
% please use simple latex.
%
% *======================================================================*
%
% Example of including a graphic image:
% \begin{figure}[ht]
% \begin{center}
% \includegraphics[width=6cm]{MyArrangement_MyThorn_MyFigure}
% \end{center}
% \caption{Illustration of this and that}
% \label{MyArrangement_MyThorn_MyLabel}
% \end{figure}
%
% Example of using a label:
% \label{MyArrangement_MyThorn_MyLabel}
%
% Example of a citation:
% \cite{MyArrangement_MyThorn_Author99}
%
% Example of including a reference
% \bibitem{MyArrangement_MyThorn_Author99}
% {J. Author, {\em The Title of the Book, Journal, or periodical}, 1 (1999),
% 1--16. {\tt http://www.nowhere.com/}}
%
% *======================================================================*
% If you are using CVS use this line to give version information
% $Header: /home/eschnett/C/carpet/Carpet/Carpet/CarpetIOHDF5/doc/documentation.tex,v 1.2 2004/03/18 18:17:21 cott Exp $
\documentclass{article}
% Use the Cactus ThornGuide style file
% (Automatically used from Cactus distribution, if you have a
% thorn without the Cactus Flesh download this from the Cactus
% homepage at www.cactuscode.org)
\usepackage{../../../../doc/ThornGuide/cactus}
\begin{document}
% The author of the documentation
\author{Erik Schnetter $<$schnetter@uni-tuebingen.de$>$, Christian D. Ott $<$cott@aei.mpg.de$>$}
% The title of the document (not necessarily the name of the Thorn)
\title{CarpetIOHDF5}
% the date your document was last changed, if your document is in CVS,
% please use:
% \date{$ $Date: 2004/03/18 18:17:21 $ $}
\date{March 18, 2004}
\maketitle
% Do not delete next line
% START CACTUS THORNGUIDE
% Add all definitions used in this documentation here
% \def\mydef etc
% Add an abstract for this thorn's documentation
\begin{abstract}
CarpetIOHDF5 provides HDF5 based 3-D output to the Cactus mesh refinement driver Carpet.
This document explains CarpetIOHDF5's usage and contains a specification of the
CarpetIOHDF5 file format that was adapted from John Shalf's FlexIO library.
\end{abstract}
% The following sections are suggestive only.
% Remove them or add your own.
\section{Introduction}
Having encountered various problems with CarpetIOFlexIO and the underlying FlexIO library,
Erik Schnetter decided to create CarpetIOHDF5. CarpetIOHDF5 provides 3-D output for the
Carpet Mesh Refinement driver within the Cactus Code. Christian D. Ott added
file reader (analogous to Erik Schnetter's implementation present in CarpetIOFlexIO)
and checkpoint/recovery features to CarpetIOHDF5.
Right now, CarpetIOHDF5 only uses serial I/O - all data are copied to processor 0 for I/O.
This document aims at giving the user a first handle on how to use
CarpetIOHDF5. It also documents the HDF5 file layout used.
\section{Using This Thorn}
\subsection{Obtaining This Thorn}
You can get a checkout from
{\tt cvs.carpetcode.org:/home/cvs Carpet/CarpetIOHDF5}
\subsection{Basic Usage}
First, you have to activate the thorn in your Cactus parameter file:
{\tt ActiveThorns = "CarpetIOHDF5"}
\subsubsection{3-D Output}
\begin{itemize}
\item {\tt iohdf5::out3D\_vars = "your list of Cactus grid functions to output"}
\item {\tt iohdf5::out3D\_every = n} : Output every {\tt n} time steps
\item {\tt iohdf5::out3D\_dir = "your preferred 3-D output directory"}
\end{itemize}
\subsubsection{Checkpointing}
CarpetIOHDF5 uses the Cactus checkpoint/recovery infrastructure provided by
CactusBase/IOUtil.
\begin{itemize}
\item {\tt iohdf5::checkpoint = "yes"} : Turns on checkpointing
\item {\tt iohdf5::checkpoint\_every = n} : Checkpointing every {\tt n} time steps
\item {\tt iohdf5::checkpoint\_ID = "yes"} : Turns on checkpointing after initial data
\item {\tt io::checkpoint\_dir = "your preferred checkpoint directory"}
\item {\tt iohdf5::checkpoint\_keep = n} : Keep {\tt n} checkpoint files around
\end{itemize}
\subsubsection{Recover}
CarpetIOHDF5 uses the Cactus checkpoint/recovery infrastructure provided by
CactusBase/IOUtil. Currently all the checkpoint information is copied onto processor 0 and
written into a single file whose name is invented by IOUtil. Unfortunately, single cpu
checkpoint files have a different name (a missing \_file\_0 tag) than checkpoint
files from multi-cpu runs. Somebody should tweek IOBase...
In principle, CarpetIOHDF5 is able to restart on any number
of cpus from a checkpoint file of a run using any (other or same) number of cpus.
\begin{itemize}
\item {\tt iohdf5::recover = "auto"} : Recover from the most recent Checkpoint file. This bombs,
if no checkpoint file is found.
\item {\tt iohdf5::recover = "autoprobe"} : Recover from the most recent Checkpoint file. This continues
without recovering if no checkpoint file is found.
\item {\tt iohdf5::recover\_dir = "directory containing the checkpoint file"}
\item {\tt iohdf5::recover = "manual"} : Recover from a file specified by {\tt iohdf5::recover\_file}. This
bombs if the file is not found.
\item {\tt iohdf5::recover\_file = "file you want to recover from"} : Only needs to be set if
{\tt iohdf5::recover = "manual"}.
\end{itemize}
\subsection{Special Behaviour}
\begin{itemize}
\item {\tt iohdf5::h5verbose = "yes"} : Makes CarpetIOHDF5 very talkative.
\end{itemize}
%\subsection{Interaction With Other Thorns}
%
%\subsection{Support and Feedback}
%
%\section{History}
%
%\subsection{Thorn Source Code}
%
%\subsection{Thorn Documentation}
%
%\subsection{Acknowledgements}
%
%
%\begin{thebibliography}{9}
%
%\end{thebibliography}
%
% Do not delete next line
% END CACTUS THORNGUIDE
\end{document}
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