From c498272ac2003153d912bfa6ff75ae9b08e89fca Mon Sep 17 00:00:00 2001 From: eschnett Date: Sun, 21 Oct 2012 03:22:54 +0000 Subject: Remove appendices from reference manual These appendices are already in the users' guide. Also re-instate references that were commented out. git-svn-id: http://svn.cactuscode.org/flesh/trunk@4880 17b73243-c579-4c4c-a9d2-2d5706c11dac --- doc/ReferenceManual.pdf | Bin 923722 -> 771464 bytes doc/ReferenceManual/Preface.tex | 5 -- doc/ReferenceManual/ReferenceManual.tex | 2 - doc/UsersGuide.pdf | Bin 713494 -> 716136 bytes doc/UsersGuide/Appendices.tex | 112 +++++++++++++++----------------- 5 files changed, 53 insertions(+), 66 deletions(-) (limited to 'doc') diff --git a/doc/ReferenceManual.pdf b/doc/ReferenceManual.pdf index ed680a1c..d511d43e 100644 Binary files a/doc/ReferenceManual.pdf and b/doc/ReferenceManual.pdf differ diff --git a/doc/ReferenceManual/Preface.tex b/doc/ReferenceManual/Preface.tex index 9334d6eb..98539d40 100644 --- a/doc/ReferenceManual/Preface.tex +++ b/doc/ReferenceManual/Preface.tex @@ -42,11 +42,6 @@ This guide covers the following topics Here all the \verb|Util_*()| Cactus flesh functions which are available to thorn writers are described. -\item [\bf Part~\ref{part:Appendices}: Appendices.] - These contain a description of the Cactus Configuration Language, - a glossary, - and other odds and ends, such as how to use GNATS or TAGS. - \end{Lentry} Other topics to be discussed in separate documents include: diff --git a/doc/ReferenceManual/ReferenceManual.tex b/doc/ReferenceManual/ReferenceManual.tex index a4a8cbae..228d1ceb 100644 --- a/doc/ReferenceManual/ReferenceManual.tex +++ b/doc/ReferenceManual/ReferenceManual.tex @@ -87,8 +87,6 @@ urlcolor=blue \input UtilReference.tex -\input ../UsersGuide/Appendices.tex - %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% diff --git a/doc/UsersGuide.pdf b/doc/UsersGuide.pdf index 91f8bb15..32bd597d 100644 Binary files a/doc/UsersGuide.pdf and b/doc/UsersGuide.pdf differ diff --git a/doc/UsersGuide/Appendices.tex b/doc/UsersGuide/Appendices.tex index 759f7555..126c65a8 100644 --- a/doc/UsersGuide/Appendices.tex +++ b/doc/UsersGuide/Appendices.tex @@ -12,9 +12,6 @@ \label{part:Appendices} \renewcommand{\thepage}{\Alph{part}\arabic{page}} -Note that these appendices appear (identically) in both the -Cactus Users' Guide and the Cactus Reference Manual. - %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% @@ -37,7 +34,7 @@ Cactus Users' Guide and the Cactus Reference Manual. The Cactus Reference Manual documents most of the Cactus flesh APIs. \item[arrangement] A collection of thorns, stored in a subdirectory of the Cactus - \verb|arrangements| directory.% See Section~\ref{sec:arrangements}. + \verb|arrangements| directory. See Section~\ref{sec:arrangements}. \item[autoconf] A GNU program which builds a configuration script which can be used to make a Makefile. @@ -67,13 +64,13 @@ http://en.wikipedia.org/wiki/Cactus configuration (these flags change what binary is produced), but the Cactus \verb|VERBOSE| and \verb|WARN| configure options aren't part of a configuration (they don't change what binary will be produced). -% See Section~\ref{sec:configurations}. + See Section~\ref{sec:configurations}. \item[checkout] - Get a copy of source code from SVN.% See Section~\ref{sec:checkout}. + Get a copy of source code from SVN. See Section~\ref{sec:checkout}. \item[checkpoint] Save the entire state of a Cactus run to a file, so that the run can be restarted at a later time. -% See Sections~\ref{sec:checkpointing}, \ref{chap:cp_recovery_methods}. + See Sections~\ref{sec:checkpointing}, \ref{chap:cp_recovery_methods}. \item[computational grid] A discrete finite set of spatial points in $\Re^n$ (typically, $1 \le n \le 3$). @@ -94,8 +91,7 @@ http://en.wikipedia.org/wiki/Cactus \item[SVN] \textit{Subversion} is the favoured code distribution system for Cactus. - See Section %s~\ref{sec:checkout}, - \ref{sec:Appendix.svn}. + See Sections~\ref{sec:checkout},\ref{sec:Appendix.svn}. \item[domain decomposition] The technique of breaking up a large computational problem into parts that are easier to solve. In Cactus, it refers especially to a decomposition @@ -103,8 +99,10 @@ http://en.wikipedia.org/wiki/Cactus \item[driver] A special kind of thorn which creates and handles grid hierarchies and grid variables. -%Drivers are responsible for memory management for grid variables, and for all parallel operations, in response to requests from the scheduler. -% See Section~\ref{sec:parallelisation}. + Drivers are responsible for memory management for grid variables, + and for all parallel operations, in response to requests from the + scheduler. + See Section~\ref{sec:parallelisation}. \item[evolution] An iteration interpreted as a step through time. Also, a particular Cactus schedule bin for executing routines when evolution occurs. @@ -114,12 +112,12 @@ http://en.wikipedia.org/wiki/Cactus get if you check out Cactus from our SVN repository. \item[friend] Interfaces that are \textit{friends}, share their collective set of protected grid variables. - See Section~\ref{sec:Appendix.interface}. %%~\ref{subsec:interface_ccl}. + See Section~\ref{sec:Appendix.interface}~\ref{subsec:interface_ccl}. \item[function aliasing] The process of referring to a function to be provided by an interface independently of which thorn actually contains the function, or what language the function is written in. The function is called an - \textit{alias function}.%% See Section~\ref{sec:function_aliasing}, + \textit{alias function}. See Section~\ref{sec:function_aliasing}, \ref{subsec:Appendix.interface.function_aliasing}. \item[GA] Shorthand for a \textit{grid array}. @@ -136,7 +134,7 @@ http://en.wikipedia.org/wiki/Cactus to the corresponding ghost zone of the other block, and vice versa. In single processor runs there are no ghost zones. Contrast with symmetry or boundary zones. - %See Section~\ref{sec:ghost_size}. + See Section~\ref{sec:ghost_size}. \item[grid] Short for \textit{computational grid}. \item[grid array] @@ -148,7 +146,7 @@ http://en.wikipedia.org/wiki/Cactus computational grid. (See also \textit{local array}.) From another perspective, \textit{grid functions} are functions (of any of the Cactus - data types% (see Section~\ref{sect-ThornWriting/DataTypes}) + data types (see Section~\ref{sect-ThornWriting/DataTypes}) defined on the domain of grid points. Typically, grid functions are used to discretely approximate functions defined on the domain $\Re^n$, with \textit{finite differencing} @@ -168,7 +166,7 @@ http://en.wikipedia.org/wiki/Cactus to being an internal variable of the thorn or one of its routines. \textit{grid scalar}, \textit{grid function}, and \textit{grid array} are all examples of \textit{grid variables}. - %See Sections~\ref{sec:cactus_variables-groups}, + See Sections~\ref{sec:cactus_variables-groups}, \ref{subsec:Appendix.interface-variables} \item[GNATS] The GNU program we use for reporting and tracking bugs, comments and @@ -187,15 +185,14 @@ http://en.wikipedia.org/wiki/Cactus store both data (for example, Cactus grid variables), and meta data (data describing the other data, for example, Cactus coordinate systems). - See %Section~\ref{subsec:hdf5}, also + See Section~\ref{subsec:hdf5}, also \url{http://hdf.ncsa.uiuc.edu/HDF5/}. \item[implementation] Defines the interface that a thorn presents to the rest of a Cactus program. - % See Section~\ref{sec:implementations}. + See Section~\ref{sec:implementations}. \item[inherit] A thorn that \textit{inherits} from another implementation can access all the other implementation's public variables. - See Section~\ref{sec:Appendix.interface}. - %\ref{subsec:interface_ccl}. + See Section~\ref{sec:Appendix.interface}, \ref{subsec:interface_ccl}. \item[interface] \item[interpolation] Given a set of grid variables and interpolation points (points in the @@ -222,8 +219,8 @@ http://en.wikipedia.org/wiki/Cactus \item[MPI] \textit{Message Passing Interface}, an API and software library for sending messages between processors in a multiprocessor system. -% See Sections~\ref{subsec:Compilation-Available_Options}, -% \ref{subsubsec:Compiling-MPI}. + See Sections~\ref{subsec:Compilation-Available_Options}, + \ref{subsubsec:Compiling-MPI}. \item[multi-patch] \item[mutual recursion] See \textit{recursion, mutual}. @@ -269,21 +266,21 @@ http://en.wikipedia.org/wiki/Cactus \item[parameter] A variable that controls the run time behaviour of the Cactus executable. Parameters have default values which can be set in a - \textit{parameter file}.% (See Chapter~\ref{chap:Cactus_parameters}). + \textit{parameter file}. (See Chapter~\ref{chap:Cactus_parameters}). The flesh has parameters; thorn parameters are made available to the rest of Cactus by describing them in the thorn's {\tt param.ccl} file (See Appendix~\ref{sec:Appendix.param}). \item[parameter file] (Also called \textit{par file}.) A text file used as the input of a Cactus program, specifying initial values of thorn parameters. - % See Section~\ref{sec:Parameter_File}. + See Section~\ref{sec:Parameter_File}. \item[processor topology] \item[PUGH] The default driver thorn for Cactus which uses MPI. - %See Section~\ref{sec:required_software}. + See Section~\ref{sec:required_software}. \item[PVM] \textit{Parallel Virtual Machine}, provides interprocessor communication. - %See Section~\ref{sec:required_software}. + See Section~\ref{sec:required_software}. \item[recursion, mutual] See \textit{mutual recursion}. \item[reduction] @@ -296,8 +293,7 @@ http://en.wikipedia.org/wiki/Cactus are registered with the flesh via the thorn's {\tt schedule.ccl} file to be executed in a certain schedule bin, before or after another function or group executes, and so forth. - See section~\ref{sec:Appendix.schedule}. - %~\ref{chap:scheduling}, + See section~\ref{sec:Appendix.schedule}~\ref{chap:scheduling}, \item[schedule bin] One of a set of special timebins pre-defined by Cactus. See Section \ref{sec:Appendix.schedule_bins} for a list. @@ -306,16 +302,15 @@ http://en.wikipedia.org/wiki/Cactus Appendix \ref{sec:Appendix.schedule}). Each schedule group must be defined to occur in a Cactus schedule bin or another schedule group. - %See Chapter~\ref{chap:scheduling}, \ref{scheduling:schedule_bins}. + See Chapter~\ref{chap:scheduling}, \ref{scheduling:schedule_bins}. \item[shares] An implementation may \textit{share} restricted parameters with another implementation, which means the other implementation can get the parameter values, and if the parameters are steerable, it can change them. - See Section~\ref{sec:Appendix.param}. - %\ref{subsec:param_ccl}. + See Section~\ref{sec:Appendix.param} \ref{subsec:param_ccl}. \item[steerable parameter] A parameter which can be changed at any time after the program has been - initialised.% See Section~\ref{sec:Cactus_parameters.steerable}. + initialised. See Section~\ref{sec:Cactus_parameters.steerable}. \item[symmetry operation] A grid operation that is a manifestation of a geometrical symmetry, especially rotation or reflection. @@ -329,7 +324,7 @@ http://en.wikipedia.org/wiki/Cactus computational interior on one processor to the corresponding ghost zone (see) on another processor. Also refers to a special Cactus timebin corresponding to the occurrence of this process. - %See Section~\ref{sec:ghost_size}. + See Section~\ref{sec:ghost_size}. \item[TAGS] See Section~\ref{sec:Appendix.tags}. \item[target] @@ -338,16 +333,16 @@ http://en.wikipedia.org/wiki/Cactus command line for \texttt{make}, the rules are executed, usually to build some software. \item[test suite] - %See Sections~\ref{sec:testing}, \ref{sec:adding_test_suite}. + See Sections~\ref{sec:testing}, \ref{sec:adding_test_suite}. \item[thorn] A collection of subroutines defining a Cactus interface. - %See Chapters~\ref{chap:thorn_concepts}, \ref{chap:thorn_anatomy}. + See Chapters~\ref{chap:thorn_concepts}, \ref{chap:thorn_anatomy}. \item[ThornList] A file used by the Cactus CST to determine which thorns to compile into a Cactus executable - %(see Section~\ref{sec:gmtafobuanadco}, \ref{sec:cointh}). + (see Section~\ref{sec:gmtafobuanadco}, \ref{sec:cointh}). Can also be used to determine which thorns - to check out from SVN.% (see Section~\ref{sec:checkout}). + to check out from SVN. (see Section~\ref{sec:checkout}). A ThornList for each Cactus configuration lies in the configuration subdirectory of the Cactus {\tt configs} directory. \item[time bin] @@ -355,13 +350,13 @@ http://en.wikipedia.org/wiki/Cactus runs specified routines. See \textit{scheduler}, \textit{schedule bin}. \item[time level] \item[timer] - A Cactus API for reporting time.% See Section~\ref{sec:timers}. + A Cactus API for reporting time. See Section~\ref{sec:timers}. \item[trigger] \item[unigrid] \item[WMPI] \textit{Win32 Message Passing Interface}. - %See Sections~\ref{subsec:Compilation-Available_Options}, - %\ref{subsubsec:Compiling-MPI}. + See Sections~\ref{subsec:Compilation-Available_Options}, + \ref{subsubsec:Compiling-MPI}. \item[wrapper] \end{Lentry} @@ -404,8 +399,8 @@ thorns, and which include files are provided by this thorn. \item Blocks detailing aliased functions provided or used by this thorn. \item A series of blocks listing the thorn's global variables. \end{itemize} -%(For a more extensive discussion of Cactus variables, see Chapter -%\ref{chap:cactus_variables}.) +(For a more extensive discussion of Cactus variables, see Chapter +\ref{chap:cactus_variables}.) \subsection{Header Block} The header block has the form: @@ -570,8 +565,7 @@ optional, with the default variable type being {\t SCALAR}. {\tt SIZE} grid-points should be allocated on each processor. The default value is {\tt DISTRIB=DEFAULT}. \item{} {\t GHOSTSIZE} defines number of ghost zones in each dimension -of an {\tt ARRAY}. -%Does GHOSTSIZE default to one for a GF and zero for a GA? +of an {\tt ARRAY}. It defaults to zero. \item{} {\t TAGS} defines an optional string which is used to create a set of key-value pairs associated with the group. The keys are case independent. The string (which must be deliminated by single or @@ -586,9 +580,9 @@ of an {\tt ARRAY}. (see the ReferenceManual for detailed descriptions).\\ For a list of currently supported {\t TAGS} key-value table information, please refer to the corresponding chapter in the documentation of the - \verb|CactusDoc| arrangement.% (Section \ref{sec:OtherGmakeTargetsDoc} on -% page \pageref{sec:OtherGmakeTargetsDoc} explains how to build this -% documentation). + \verb|CactusDoc| arrangement. (Section \ref{sec:OtherGmakeTargetsDoc} on + page \pageref{sec:OtherGmakeTargetsDoc} explains how to build this + documentation). \item{} The (optional) block following the group declaration line, contains a list of variables contained in the group. All variables in a group have the same data type, variable type, dimension and @@ -604,9 +598,9 @@ line. If the variable block is omitted, this description can be given at the end of the declaration line. \end{itemize} -%The process of sharing code among thorns using include files is -%discussed in Section~\ref{sec:includefiles}. -% +The process of sharing code among thorns using include files is +discussed in Section~\ref{sec:includefiles}. + \section{param.ccl} \label{sec:Appendix.param} @@ -614,8 +608,8 @@ The parameter configuration file consists of a list of \textit{parameter object specification items} (OSIs) giving the type and range of the parameter separated by optional \textit{parameter data scoping items} (DSIs), which detail access to the -parameter.% (For a more extensive discussion of Cactus parameters, see Chapter -%\ref{chap:Cactus_parameters}.) +parameter. (For a more extensive discussion of Cactus parameters, see Chapter +\ref{chap:Cactus_parameters}.) \subsection{Parameter Data Scoping Items} @@ -796,8 +790,8 @@ beginning of a line followed by \var{} on that same line. \section{schedule.ccl} \label{sec:Appendix.schedule} -%(A more extensive discussion of Cactus scheduling is provided in Chapter -%\ref{chap:scheduling}.) +(A more extensive discussion of Cactus scheduling is provided in Chapter +\ref{chap:scheduling}.) A schedule configuration file consists of: \begin{itemize} @@ -903,9 +897,9 @@ schedule [GROUP] <\var{function name}|\var{group name}> AT|IN <\var{time}> \verb list of these. (Any names that are not provided by an active thorn are ignored.) Note that a single schedule block may have multiple {\tt BEFORE/AFTER} clauses. - %See Section~\ref{chap:scheduling} - %(``Scheduling'') in the Cactus Users' Guide for more information - %about {\tt BEFORE/AFTER} clauses. + See Section~\ref{chap:scheduling} + (``Scheduling'') in the Cactus Users' Guide for more information + about {\tt BEFORE/AFTER} clauses. \item[{\tt LANG}] The code language for the function (either {\tt C} or {\tt FORTRAN}). No language should be specified for a schedule group. @@ -1301,8 +1295,8 @@ character `{\tt /}' reserved for future expansion.%%% tree-like data structures.%%% }%%% -Values are 1-dimensional arrays of any of the usual Cactus data types. -%described in Section~\ref{sect-ThornWriting/DataTypes}. +Values are 1-dimensional arrays of any of the usual Cactus data types, +described in Section~\ref{sect-ThornWriting/DataTypes}. A string can be stored by treating it as a 1-dimensional array of \verb|CCTK_CHAR| (there's an example of this below). -- cgit v1.2.3