From 934c58a18098245b57324649e0e5606e64f2c589 Mon Sep 17 00:00:00 2001 From: schnetter Date: Wed, 6 Nov 2002 13:55:24 +0000 Subject: Added thorn documentation. Added option table argument. Added copyright statement. git-svn-id: http://svn.cactuscode.org/arrangements/CactusNumerical/Slab/trunk@9 2e825fa2-fb71-486d-8b7f-a5ff3f0f6cb8 --- COPYING | 340 +++++++++++++++++++++++++++++++++++++++++ doc/documentation.tex | 409 ++++++++++++++++++++++++++++++++++++++++++++++---- src/slab.c | 17 +-- src/slab.h | 29 ++-- 4 files changed, 737 insertions(+), 58 deletions(-) create mode 100644 COPYING diff --git a/COPYING b/COPYING new file mode 100644 index 0000000..5b6e7c6 --- /dev/null +++ b/COPYING @@ -0,0 +1,340 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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If this is what you want to do, use the GNU Library General +Public License instead of this License. diff --git a/doc/documentation.tex b/doc/documentation.tex index 7ccf999..d08f29c 100644 --- a/doc/documentation.tex +++ b/doc/documentation.tex @@ -97,12 +97,13 @@ % Add an abstract for this thorn's documentation \begin{abstract} The Slab thorn provides generic slabbing facilities. A slab is a -sub-array of another array. Both can be multidimensional, and the -slab can have a non-unit stride. The Slab thorn provides a routine to -copy a slab from one array into a slab of another array, while -possibly transposing or inverting the slab. The distribution of the -arrays can be specified freely, so that the Slab thorn can also be -used to interface to non-Cactus libraries with different data layouts. +sub-array of another array. Both the array and the slab can be +multidimensional, and the slab can have a non-unit stride. The Slab +thorn provides a routine to copy a slab from one array into a slab of +another array, while possibly transposing or mirroring the slab. The +processor distribution of the arrays can be specified freely, so that +the Slab thorn can be used to interface to non-Cactus libraries with +different data layouts. The Slab thorn is driver independent, i.e.\ not tied to PUGH or Carpet, and does not require MPI for single-processor configurations. @@ -111,40 +112,386 @@ Carpet, and does not require MPI for single-processor configurations. % The following sections are suggestive only. % Remove them or add your own. + + \section{Introduction} A \emph{Slab} is a subarray of another array. This concept is used in many places with many different names. Fortran has so-called ``array -subscript triplets'', which are the same thing. - -\section{Physical System} - -\section{Numerical Implementation} - -\section{Using This Thorn} - -\subsection{Obtaining This Thorn} +subscript triplets'', which represent the same thing. In BLAS, the +``leading dimension'' arguments are used to described slabs. Slabs +are sometimes also called ``array views'' in object oriented +applications. Slabs are rectangular in shape, and can be rotated with +regard to their containing array by multiples of 90 degrees. They can +also be mirrored, i.e.\ the direction of axes can be inverted. -\subsection{Basic Usage} +It is often necessary to copy slabs from one array into other arrays, +or to copy one slab of an array to another slab of the same array. +This can be used to change the processor distribution of some data, or +to apply symmetry or periodicity boundary conditions, or to collect +data onto a single processor to process it more easily. -\subsection{Special Behaviour} -\subsection{Interaction With Other Thorns} -\subsection{Support and Feedback} - -\section{History} - -\subsection{Thorn Source Code} - -\subsection{Thorn Documentation} - -\subsection{Acknowledgements} - - -\begin{thebibliography}{9} +\section{Using This Thorn} -\end{thebibliography} +\begin{FunctionDescription}{Slab\_Transfer}{} +Transfer a slab contained in one array to a (possibly different) slab +of another (possibly the same) array + +\begin{SynopsisSection} +\begin{Synopsis}{C} +\begin{verbatim} +INHERITS: Slab + +#include "cctk.h" +#include "Slab.h" + +struct slabinfo { + int gsh; + int lbnd, lsh; + int lbbox, ubbox, nghostzones; + int off, str, len; +}; + +struct xferinfo { + struct slabinfo src, dst; + int xpose; + int flip; +}; + +int Slab_Transfer (cGH * restrict const cctkGH, + int const dim, + struct xferinfo const * restrict const xferinfo, + int const options, + int const srctype, + void const * const srcptr, + int const dsttype, + void * const dstptr); +\end{verbatim} +\end{Synopsis} +\end{SynopsisSection} + +\begin{ResultSection} +\begin{Result}{0} +Success +\end{Result} +\begin{Result}{nonzero} +Failure +\end{Result} +\end{ResultSection} + +\begin{ParameterSection} +\begin{Parameter}{cctkGH} +Pointer to the CCTK grid hierarchy +\end{Parameter} + +\begin{parameter}{dim} +Number of dimensions of the arrays and slabs. Must be nonnegative. +\end{Parameter} + +\begin{parameter}{xferinfo[dim]} +Describes the layout of the slab transfer, i.e.\ the shape and +distribution of the source and destination arrays, and the locations +of the source and destination slabs, and a possible transformation +between the slabs. Each dimension is described separately. See the +entries \texttt{xferinfo[d].*} below. +\end{Parameter} + +\begin{parameter}{xferinfo[d].src} +Describes the source array and source slab. See the \textit{slabinfo} +entries below. +\end{Parameter} + +\begin{parameter}{xferinfo[d].dst} +Describes the destination array and destination slab. See the +\textit{slabinfo} entries below. +\end{Parameter} + +\begin{parameter}{xferinfo[d].xpose} +Describes how to transpose the slab, i.e.\ possibly permuting the slab +axes, as in $(x,y) \rightarrow (y,x)$. \texttt{xferinfo[d].xpose} +contains an integer value in the range \texttt{0\ldots dim-1}, +specifying the source axis corresponding to the destination axis +\texttt{d}. Specify \texttt{xferinfo[d].xpose = d} for no +transposition. No two values of \texttt{xferinfo[*].xpose} may be the +same. +\end{Parameter} + +\begin{parameter}{xferinfo[d].flip} +Describes how to mirror the slab, i.e.\ possibly inverting the slab +axes, as in $(x) \rightarrow (-x)$. \texttt{xferinfo[d].flip} +containes a boolean value specifying whether the axis in direction +\texttt{d} should be inverted, i.e.\ either \texttt{0} or \texttt{1}, +where \texttt{0} indicates no inversion, and \texttt{1} indicates +inversion. + +When axes are both transposed and inverted while a slab is copied, +then the transposing happens first, and the axis inversion later. +That is, the sequence of ``actions'' is: extract slab, transpose, +invert, insert slab. For example, when transposing the $x$ and $z$ +axes and inverting the $x$ axis, then the destination slab's $x$ axis +is the source slab's flipped $z$ axis, while the destination $z$ axis +is the unflipped source $x$ axis. +\end{Parameter} + +\begin{parameter}{\textit{slab}} +Describes the shape and processor distribution of one dimension of an +array, and the location of this dimension of a slab. The shape and +distribution is specified in the same manner as in the \texttt{cGH} +structure. See the entries \texttt{\textit{slab}.*} below. +\end{Parameter} + +\begin{parameter}{\textit{slab}.gsh} +Global shape of the array; the overall number of grid points +\end{Parameter} + +\begin{parameter}{\textit{slab}.lbnd} +Lower boundary of the array; the global index of the lower boundary of +the processor-local part of the array +\end{Parameter} + +\begin{parameter}{\textit{slab}.lsh} +Local shape of the array; the number of grid points on this processor +\end{Parameter} + +\begin{parameter}{\textit{slab}.lbbox} +Lower bounding box of the array; whether the lower boundary of the +array is an outer boundary. This corresponds to the even entries in +Cactus' \texttt{bbox} array. Must be \texttt{0} or \texttt{1}. +\end{Parameter} + +\begin{parameter}{\textit{slab}.ubbox} +Upper bounding box of the array; whether the upper boundary of the +array is an outer boundary. This corresponds to the odd entries in +Cactus' \texttt{bbox} array. Must be \texttt{0} or \texttt{1}. +\end{Parameter} + +\begin{parameter}{\textit{slab}.nghostzones} +Number of ghost zones of the array; the number of grid points on this +processor that are only copied from neighbouring processors +\end{Parameter} + +\begin{parameter}{\textit{slab}.off} +Slab offset; the global index of the lowest grid point of the slab +\end{Parameter} + +\begin{parameter}{\textit{slab}.str} +Slab stride; the distance between two grid points making up the slab. +Specify \texttt{\textit{slab}.str = 1} for a unit stride. Must be +positive. +\end{Parameter} + +\begin{parameter}{\textit{slab}.len} +Slab length; the number of grid points that make up the slab. This +does not count the grid points that are skipped if the slab has a +non-unit stride. Must be nonnegative. +\end{Parameter} + +\begin{parameter}{options} +Handle of an option table. Currently there are no options defined. +Pass either $-1$ or a handle to an empty table. +\end{Parameter} + +\begin{parameter}{srctype} +Type of the source array. Pass the corresponding +\texttt{CCTK\_VARIABLE\_*} constant. +\end{Parameter} + +\begin{parameter}{srcptr} +Pointer to the source array +\end{Parameter} + +\begin{parameter}{dsttype} +Type of the destination array. Pass the corresponding +\texttt{CCTK\_VARIABLE\_*} constant. +\end{Parameter} + +\begin{parameter}{dstptr} +Pointer to the destination array +\end{Parameter} +\end{ParameterSection} + +\begin{Discussion} +\texttt{Slab\_Transfer} copies one slab from one array onto a possibly +different slab in possibly the same array. The shape and processor +distribution of the arrays can be specified freely, as long as each +processor holds a rectangular subset of grid points. The location of +the slab can also be specified freely, and the slab can be rotated (by +multiples of 90 degrees) or inverted before it is copied. The source +and destination slab are allowed to overlap. + +\texttt{Slab\_Transfer} is conservative with regard to +synchronisation. It assumes that the ghost zones of the source array +are not valid, but will correctly fill in the ghost zones in the +destination slab. + +There are currently some restrictions, which can be remedied if the +need arises: The datatype of the arrays must be CCTK\_REAL. The +dimension must be 3 (lower dimensions can easily be padded). The +communication schedule is set up for every slab transfer, which is +expensive. The number of ghost zones along the lower and upper +boundary is assumed to be the same. There is no Fortran interface. +\end{Discussion} + +\begin{SeeAlsoSection} +\begin{SeeAlso}{CarpetSlab} +The hyperslabbing thorn of the driver Carpet. +\end{SeeAlso} +\begin{SeeAlso}{PUGHSlab} +The hyperslabbing thorn of the driver CactusPUGH. +\end{SeeAlso} +\begin{SeeAlso}{New hyperslabbing API} +The web page \href{http://www.cactuscode.org/Development/Current.html} +{http://www.cactuscode.org/Development/Current.html} contains a +hyperlink to the new proposed hyperslabbing API. This API is slightly +different from the one used here. +\end{SeeAlso} +\end{SeeAlsoSection} + +\begin{ExampleSection} +\begin{Example}{C} +The identity transfer: copy a whole 3D grid function without +transforming it + +\begin{verbatim} +#include +#include "cctk.h" +#include "cctk_Arguments.h" + +#include "Slab.h" + +DECLARE_CCTK_ARGUMENTS; + +struct xferinfo info[3]; +int d; +int ierr; + +/* Set up the array descriptors */ +assert (cctk_dim <= 3); +for (d=0; d +#include "cctk.h" +#include "cctk_Arguments.h" + +#include "Slab.h" + +DECLARE_CCTK_ARGUMENTS; + +struct xferinfo info[3]; +int d; +int ierr; + +/* Set up the array descriptors (same as above) */ +assert (cctk_dim <= 3); +for (d=0; d y ? x : y; -} - static inline int roundup (int const x, int const y) { assert (x >= 0); @@ -363,7 +354,8 @@ static void bbox_xform (struct bbox * restrict const ydst, int Slab_Transfer (cGH * restrict const cctkGH, int const dim, - struct xferinfo const * const xferinfo, + struct xferinfo const * restrict const xferinfo, + int const options, int const srctype, void const * const srcptr, int const dsttype, @@ -663,7 +655,6 @@ int Slab_Transfer (cGH * restrict const cctkGH, && srcipos[c] < info[c].src.local.off + info[c].src.local.len); if (! (srcipos[c] >= allinfo[n*dim+c].src.slab.off && srcipos[c] <= allinfo[n*dim+c].src.slab.off + (allinfo[n*dim+c].src.slab.len - 1) * allinfo[n*dim+c].src.slab.str)) { - printf ("ssc n=%d ipos=[%d,%d,%d] d=%d srcipos=%d slab.off=%d slab.len=%d\n", n, i, j, k, d, srcipos[c], allinfo[n*dim+c].src.slab.off, allinfo[n*dim+c].src.slab.len); } assert (srcipos[c] >= allinfo[n*dim+c].src.slab.off && srcipos[c] <= allinfo[n*dim+c].src.slab.off + (allinfo[n*dim+c].src.slab.len - 1) * allinfo[n*dim+c].src.slab.str); diff --git a/src/slab.h b/src/slab.h index b79af0a..2aa32bc 100644 --- a/src/slab.h +++ b/src/slab.h @@ -5,19 +5,6 @@ #include "cctk.h" -struct slabinfo { - int gsh; - int lbnd, lsh; - int lbbox, ubbox, nghostzones; - int off, str, len; -}; - -struct xferinfo { - struct slabinfo src, dst; - int xpose; - int flip; -}; - /* Slab_Transfer copies a slab from one array into a slab of another array. @@ -83,9 +70,23 @@ struct xferinfo { The source and the destination arrays may be the same. */ +struct slabinfo { + int gsh; + int lbnd, lsh; + int lbbox, ubbox, nghostzones; + int off, str, len; +}; + +struct xferinfo { + struct slabinfo src, dst; + int xpose; + int flip; +}; + int Slab_Transfer (cGH * restrict const cctkGH, int const dim, - struct xferinfo const * const xferinfo, + struct xferinfo const * restrict const xferinfo, + int const options, int const srctype, void const * const srcptr, int const dsttype, -- cgit v1.2.3