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author | knarf <knarf@17b73243-c579-4c4c-a9d2-2d5706c11dac> | 2009-01-22 22:31:43 +0000 |
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committer | knarf <knarf@17b73243-c579-4c4c-a9d2-2d5706c11dac> | 2009-01-22 22:31:43 +0000 |
commit | 6c48d35c2ab7e3a00851bcb90a76da5c129a5c4f (patch) | |
tree | d1578841124bcb85e8054c9d31b8b109793437f7 /doc/UsersGuide | |
parent | 7f9059691119315cf7354bafddcc647a8075c0f2 (diff) |
remove (comment) broken references
git-svn-id: http://svn.cactuscode.org/flesh/trunk@4514 17b73243-c579-4c4c-a9d2-2d5706c11dac
Diffstat (limited to 'doc/UsersGuide')
-rw-r--r-- | doc/UsersGuide/Appendices.tex | 105 |
1 files changed, 56 insertions, 49 deletions
diff --git a/doc/UsersGuide/Appendices.tex b/doc/UsersGuide/Appendices.tex index fbc8938c..8df62632 100644 --- a/doc/UsersGuide/Appendices.tex +++ b/doc/UsersGuide/Appendices.tex @@ -37,7 +37,7 @@ 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. @@ -66,13 +66,13 @@ Cactus Users' Guide and the Cactus Reference Manual. configuration (these flags change what binary is produced), but the Cactus \verb|SILENT| 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 CVS. See Section~\ref{sec:checkout}. + Get a copy of source code from CVS.% 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 $1 \le n \le 3$). @@ -92,7 +92,8 @@ Cactus Users' Guide and the Cactus Reference Manual. code that binds the thorn source files with the Flesh. \item[CVS] The \textit{Concurrent Versions System} is the favoured code - distribution system for Cactus. See Sections~\ref{sec:checkout}, + distribution system for Cactus. + See Section %s~\ref{sec:checkout}, \ref{sec:Appendix.cvs}. \item[domain decomposition] The technique of breaking up a large computational problem into parts @@ -102,7 +103,7 @@ Cactus Users' Guide and the Cactus Reference Manual. 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}. +% 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. @@ -112,12 +113,12 @@ Cactus Users' Guide and the Cactus Reference Manual. get if you check out Cactus from our CVS repository. \item[friend] Interfaces that are \textit{friends} share their collective set of protected grid variables. - See Section~\ref{subsec:interface_ccl}. \ref{sec:Appendix.interface}. + 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}. @@ -134,7 +135,7 @@ Cactus Users' Guide and the Cactus Reference Manual. 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] @@ -146,7 +147,7 @@ Cactus Users' Guide and the Cactus Reference Manual. 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} @@ -166,7 +167,7 @@ Cactus Users' Guide and the Cactus Reference Manual. 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 @@ -185,13 +186,15 @@ Cactus Users' Guide and the Cactus Reference Manual. 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 \url{http://hdf.ncsa.uiuc.edu/HDF5/}. + 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{subsec:interface_ccl}. \ref{sec:Appendix.interface}. + 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 @@ -218,8 +221,8 @@ Cactus Users' Guide and the Cactus Reference Manual. \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}. @@ -265,21 +268,21 @@ Cactus Users' Guide and the Cactus Reference Manual. \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] @@ -291,8 +294,9 @@ Cactus Users' Guide and the Cactus Reference Manual. in which to execute Cactus routines. Thorn functions and schedule groups 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 Chapter~\ref{chap:scheduling}, - and Section \ref{sec:Appendix.schedule}. + or group executes, and so forth. + 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. @@ -301,17 +305,18 @@ Cactus Users' Guide and the Cactus Reference Manual. 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{subsec:param_ccl}. \ref{sec:Appendix.param}. + See Section~\ref{sec:Appendix.param}. + %\ref{subsec:param_ccl}. \item[staggering] - See Section~\ref{sec:staggering}. + %See Section~\ref{sec:staggering}. \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. @@ -325,7 +330,7 @@ Cactus Users' Guide and the Cactus Reference Manual. 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] @@ -334,16 +339,16 @@ Cactus Users' Guide and the Cactus Reference Manual. 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 CVS (see Section~\ref{sec:checkout}). + to check out from CVS.% (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] @@ -351,13 +356,13 @@ Cactus Users' Guide and the Cactus Reference Manual. 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} @@ -400,8 +405,8 @@ 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: @@ -587,9 +592,9 @@ 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 @@ -605,9 +610,9 @@ 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} @@ -615,8 +620,8 @@ 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} @@ -797,8 +802,9 @@ beginning of a line followed by \var{<default value>} 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 schedule configuration file consists of +%(A more extensive discussion of Cactus scheduling is provided in Chapter +%\ref{chap:scheduling}.) +A schedule configuration file consists of \begin{itemize} \item{} \textit{assignment statements} to switch on storage for @@ -893,9 +899,10 @@ schedule [GROUP] <\var{function name}|\var{group name}> AT|IN <\var{time}> \verb a schedule group name, or a parentheses-enclosed whitespace-separated 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. + {\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. |