Docs updates.

This commit is contained in:
sfilippone
2025-12-23 15:07:22 +01:00
parent 5eb4f55406
commit 7e0347281e
34 changed files with 6974 additions and 6974 deletions
+4 -4
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@@ -26,7 +26,7 @@ defined in the library as follows:
\item[psb\_mpk\_] Kind parameter for 4-bytes integer data, as is
always used by MPI;
\item[psb\_epk\_] Kind parameter for 8-bytes integer data, as is
always used by the \fortinline|sizeof| methods;
always returned by the \fortinline|sizeof| methods;
\item[psb\_ipk\_] Kind parameter for ``local'' integer indices and data;
with default build options this is a 4 bytes integer;
\item[psb\_lpk\_] Kind parameter for ``global'' integer indices and data;
@@ -47,9 +47,9 @@ developer's documentation.
\subsection{Descriptor data structure}
\label{sec:desc}
All the general matrix informations and elements to be
exchanged among processes are stored within a data structure of the
type \hypertarget{descdata}{{\tt psb\_desc\_type}}.
All the general matrix information and the identification of elements
to be exchanged among processes are stored within a data structure of
the type \hypertarget{descdata}{{\tt psb\_desc\_type}}.
Every structure of this type is associated with a discretization
pattern and enables data communications and other operations that are
necessary for implementing the various algorithms of interest to us.
+8 -8
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@@ -2,11 +2,11 @@
\section{Error handling\label{sec:errors}}
The PSBLAS library error handling policy has been completely rewritten
in version 2.0. The idea behind the design of this new error handling
strategy is to keep error messages on a stack allowing the user to
trace back up to the point where the first error message has been
generated. Every routine in the PSBLAS-2.0 library has, as last
The PSBLAS library error handling policy has been defined at the time
version 2.0 was written. The idea behind the design of error
handling strategy is to keep error messages on a stack allowing the
user to trace back up to the point where the first error message has
been generated. Every routine in the PSBLAS library has, as last
non-optional argument, an integer \verb|info| variable; whenever,
inside the routine, an error is detected, this variable is set to a
value corresponding to a specific error code. Then this error code is
@@ -21,7 +21,7 @@ levels of nested calls until the level where the user decides to abort
the program execution.
Figure~\ref{fig:routerr} shows the layout of a generic \verb|psb_foo|
routine with respect to the PSBLAS-2.0 error handling policy. It is
routine with respect to the PSBLAS error handling policy. It is
possible to see how, whenever an error condition is detected, the
\verb|info| variable is set to the corresponding error code which is,
then, pushed on top of the stack by means of the
@@ -110,7 +110,7 @@ end subroutine psb_foo
Figure~\ref{fig:errormsg} reports a sample error message generated by
the PSBLAS-2.0 library. This error has been generated by the fact that
the PSBLAS library. This error has been generated by the fact that
the user has chosen the invalid ``FOO'' storage format to represent
the sparse matrix. From this error message it is possible to see that
the error has been detected inside the \verb|psb_cest| subroutine
@@ -161,7 +161,7 @@ Aborting...
\fbox{\TheSbox}
\end{center}
\fi
\caption{\label{fig:errormsg}A sample PSBLAS-3.0 error
\caption{\label{fig:errormsg}A sample PSBLAS error
message. Process 0 detected an error condition inside the {\textrm
psb\_cest} subroutine}
\end{listing}
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@@ -1,10 +1,9 @@
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+44 -45
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@@ -21,12 +21,13 @@ The software architecture allows us to offer support for many
alternatives in the implementation, including usage of
heterogeneous platforms, and computations performed on GPUs throuh
CUDA.
There is support for GPU computations through OpenACC, but it is at
this time a highly experimental version; we plan to also look at using
accelerators through OpenMP as support from compilers improves.
There is also support for GPU computations through OpenACC, but it is
at this time a highly experimental version; we plan to also look at
using accelerators through OpenMP as support from compilers improves.
The project is lead by Salvatore Filippone; a number of people have been contributing to this package over the
years; contributors in roughly reverse chronological order:
The project is lead by Salvatore Filippone; a number of people have
been contributing to this package over the years; contributors in
roughly reverse chronological order:
\begin{obeylines}
Luca Pepè Sciarria
Theophane Loloum
@@ -81,18 +82,19 @@ works discussing advanced programming in Fortran~2008
include~\cite{DesPat:11,RouXiaXu:11}; sufficient support for
Fortran~2008 is now available from many compilers, including recent
versions of the GNU Fortran compiler from the Free Software
Foundation, and the FLANG compiler from the LLVM project.
Foundation, the FLANG compiler from the LLVM project, and the Intel
OneAPI compiler.
The README file contains a list of compilers against which we have
successfully tested the current release.
Previous approaches have been based on mixing Fortran~95, with its
support for object-based design, with other languages; these have
been advocated by a number of authors,
e.g.~\cite{machiels}. Moreover, the Fortran~95 facilities for dynamic
memory management and interface overloading greatly enhance the
usability of the PSBLAS
subroutines. In this way, the library can take care of runtime memory
requirements that are quite difficult or even impossible to predict at
implementation or compilation time.
e.g.~\cite{machiels}. The Fortran~95 facilities for dynamic
memory management and interface overloading ensure that the library
can take care of runtime memory requirements that are quite difficult
or even impossible to predict at implementation or compilation time.
The presentation of the
PSBLAS library follows the general structure of the proposal for
@@ -101,13 +103,13 @@ proposal for BLAS on dense matrices~\cite{BLAS1,BLAS2,BLAS3}.
The applicability of sparse iterative solvers to many different areas
causes some terminology problems because the same concept may be
denoted through different names depending on the application area. The
PSBLAS features presented in this document will be discussed referring
to a finite difference discretization of a Partial Differential
Equation (PDE). However, the scope of the library is wider than
that: for example, it can be applied to finite element discretizations
of PDEs, and even to different classes of problems such as nonlinear
optimization, for example in optimal control problems.
denoted by different names depending on the application area. The
PSBLAS features presented in this document will be discussed taking as
a reference a finite difference discretization of a Partial
Differential Equation (PDE). However, the scope of the library is
wider than that: it can be applied to finite element and other
discretizations of PDEs, and even to different classes of problems
such as nonlinear optimization, for example in optimal control problems.
The design of a solver for sparse linear systems is driven by many
conflicting objectives, such as limiting occupation of storage
@@ -145,7 +147,7 @@ application layer.
The serial parts of the computation on each process are executed through
calls to the serial sparse BLAS subroutines.
In a similar way, the inter-process message exchanges are encapsulated
in an applicaiton layer that has been strongly inspired by the Basic
in an application layer that has been strongly inspired by the Basic
Linear Algebra Communication Subroutines (BLACS) library~\cite{BLACS}.
Usually there is no need to deal directly with MPI; however, in some
cases, MPI routines are used directly to improve efficiency. For
@@ -184,10 +186,9 @@ the variable associated to each mesh point is assigned to a process
that will own the corresponding row in the coefficient matrix and
will carry out all related computations. This allocation strategy
is equivalent to a partition of the discretization mesh into {\em
sub-domains}.
Our library supports any distribution that keeps together
the coefficients of each matrix row; there are no other constraints on
the variable assignment.
sub-domains}; our library supports any distribution that keeps
together the coefficients of each matrix row; there are no other
constraints on the variable assignment.
This choice is consistent with simple data distributions
%commonly used in ScaLAPACK
such as \verb|CYCLIC(N)| and \verb|BLOCK|,
@@ -201,8 +202,8 @@ matrices, that is, the entries of a vector follow the same distribution
of the matrix rows.
We assume that the sparse matrix is built in parallel, where each
process generates its own portion. We never require that the entire
matrix be available on a single node. However, it is possible
process generates its own portion: we never \emph{require} that the
entire matrix be available on a single node. However, it is possible
to hold the entire matrix in one process and distribute it
explicitly\footnote{In our prototype implementation we provide
sample scatter/gather routines.}, even though the resulting memory
@@ -227,33 +228,31 @@ assigned to the parallel processes,
we classify the points of a given sub-domain as following.
\begin{description}
\item[Internal.] An internal point of
a given domain {\em depends} only on points of the
same domain.
If all points of a domain are assigned to one
process, then a computational step (e.g., a
matrix-vector product) of the
equations associated with the internal points requires no data
items from other domains and no communications.
a given sub-domain {\em depends} only on points of the
same sub-domain.
If all points of a sub-domain are assigned to one
process, then a computational step (e.g., a matrix-vector product) of
the equations associated with the internal points requires no data
items from other sub-domains and no communications.
\item[Boundary.] A point of
a given domain is a boundary point if it {\em depends} on points
belonging to other domains.
\item[Boundary.] A point of a given sub-domain is a boundary point if
it {\em depends} on points belonging to other sub-domains.
\item[Halo.] A halo point for a given domain is a point belonging to
another domain such that there is a boundary point which {\em depends\/}
\item[Halo.] A halo point for a given sub-domain is a point belonging to
another sub-domain such that there is a boundary point which {\em depends\/}
on it. Whenever performing a computational step, such as a
matrix-vector product, the values associated with halo points are
requested from other domains. A boundary point of a given
domain is usually a halo point for some other domain\footnote{This is
requested from other sub-domains. A boundary point of a given
sub-domain is usually a halo point for some other sub-domain\footnote{This is
the normal situation when the pattern of the sparse matrix is
symmetric, which is equivalent to say that the interaction between
two variables is reciprocal. If the matrix pattern is non-symmetric
we may have one-way interactions, and these could cause a situation
in which a boundary point is not a halo point for its neighbour.}; therefore
the cardinality of the boundary points set determines the amount of data
sent to other domains.
sent to other sub-domains.
\item[Overlap.] An overlap point is a boundary point assigned to
multiple domains. Any operation that involves an overlap point
multiple sub-domains. Any operation that involves an overlap point
has to be replicated for each assignment.
\end{description}
Overlap points do not usually exist in the basic data
@@ -378,7 +377,7 @@ $1\dots n_{\hbox{row}_i}$, each element of which corresponds to a certain
element of $1\dots n$. The user does not set explicitly this mapping;
when the application needs to indicate to which element of the index
space a certain item is related, such as the row and column index of a
matrix coefficient, it does so in the ``global'' numbering, and the
matrix coefficient, it usually does so in the ``global'' numbering, and the
library will translate into the appropriate ``local'' numbering.
For a given index space $1\dots n$ there are many possible associated
@@ -390,7 +389,7 @@ with a call to \verb|psb_cdasb| and a sparse matrix with a call to
\verb|psb_spasb|. After \verb|psb_cdasb| each process $i$ will have
defined a set of ``halo'' (or ``ghost'') indices
$n_{\hbox{row}_i}+1\dots n_{\hbox{col}_i}$, denoting elements of the index
space that are \emph{not} assigned to process $i$; however the
space that are \emph{not} assigned to process $i$; the
variables associated with them are needed to complete computations
associated with the sparse matrix $A$, and thus they have to be
fetched from (neighbouring) processes. The descriptor of the index
@@ -521,7 +520,7 @@ computation. This is certainly true for the data allocation and
assembly routines, for all the computational routines and for some of
the tools routines.
However there are many cases where no synchronization, and indeed no
However there are cases where no synchronization, and indeed no
communication among processes, is implied; for instance, all the routines in
sec.~\ref{sec:datastruct} are only acting on the local data structures,
and thus may be called independently. The most important case is that
+2 -2
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@@ -156,8 +156,8 @@ An integer value; 0 means no error has been detected.
Richardson Iteration Driver Routine}
This subroutine is a driver implementig a Richardson iteration
\[ x_{k+1} = M^-1 (b-Ax_k) +x_k,\]
with the preconditioner operator $M$ defined in the previous section.
\[ x_{k+1} = M^{-1} (b-Ax_k) +x_k,\]
with the preconditioner operator $M$ defined in section~\ref{sec:precs}.
The stopping criterion can take the following values:
\begin{description}
+5 -4
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@@ -94,12 +94,12 @@ Specified as: an integer variable.
Scope: {\bf local}.\\
Type: {\bf required}.\\
Intent: {\bf out}.\\
Specified as: an integer value. $-1 \le iam \le np-1$\
Returned as: an integer value. $-1 \le iam \le np-1$\
\item[np] Number of processes in the PSBLAS virtual parallel machine.\\
Scope: {\bf global}.\\
Type: {\bf required}.\\
Intent: {\bf out}.\\
Specified as: an integer variable. \
Returned as: an integer variable. \
\end{description}
@@ -153,8 +153,9 @@ Specified as: a logical variable, default value: true.
same program, or to enter and exit multiple times into the parallel
environment, this routine may be called to
selectively close the contexts with \verb|close=.false.|, while on
the last call it should be called with \verb|close=.true.| to
shutdown in a clean way the entire parallel environment.
the last instance it should close in a clean way the entire
parallel environment with \verb|close=.true.|
\end{enumerate}
+3 -3
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@@ -1246,7 +1246,7 @@ An integer value; 0 means no error has been detected.
This function computes the entrywise product between two vectors $x$ and
$y$
\[dot \leftarrow x(i) y(i).\]
\[y(i) \leftarrow x(i) y(i).\]
\fortinline|psb_gemlt(x, y, desc_a, info)|
@@ -1313,7 +1313,7 @@ $y$
This function computes the entrywise division between two vectors $x$ and
$y$
\[/ \leftarrow x(i)/y(i).\]
\[y(i) \leftarrow x(i)/y(i).\]
\fortinline|psb_gediv(x, y, desc_a, info, [flag)|
@@ -1385,7 +1385,7 @@ $y$
This function computes the entrywise inverse of a vector $x$ and puts it into
$y$
\[/ \leftarrow 1/x(i).\]
\[y(i) \leftarrow 1/x(i).\]
\fortinline|psb_geinv(x, y, desc_a, info, [flag)|
+18 -16
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@@ -598,7 +598,7 @@ An integer value; 0 means no error has been detected.
state.
\item The descriptor may be in either the build or assembled state.
\item Providing a good estimate for the number of nonzeroes $nnz$ in
the assembled matrix may substantially improve performance in the
the assembled matrix may improve performance in the
matrix build phase, as it will reduce or eliminate the need for
(potentially multiple) data reallocations;
\item Using \verb|psb_matbld_remote_| is likely to cause a runtime overhead at
@@ -722,7 +722,7 @@ An integer value; 0 means no error has been detected.
entirety to a single call to this routine: the buildup of a row
may be split into as many calls as desired (even in the CSR format);
\item Coefficients from different rows may also be mixed up freely
in a single call, according to the application needs;
in a single call (in COO format), according to the application needs;
\item Coefficients from matrix rows not owned by the calling
process are treated according to the value of \verb|bldmode|
specified at allocation time; if
@@ -1246,7 +1246,7 @@ An integer value; 0 means no error has been detected.
%% psb_glob_to_loc %%
%
\clearpage\subsection{psb\_glob\_to\_loc --- Global to local indices
convertion}
conversion}
%\addcontentsline{toc}{subsection}{psb\_glob\_to\_loc}
\begin{verbatim}
@@ -1261,7 +1261,7 @@ call psb_glob_to_loc(x, desc_a, info, iact,owned)
Scope: {\bf local} \\
Type: {\bf required}\\
Intent: {\bf in, inout}.\\
Specified as: a rank one integer array.\\
Specified as: a rank one integer array of global indices, i.e. \verb|psb_lpk_|.\\
\item[desc\_a] the communication descriptor.\\
Scope:{\bf local}.\\
Type:{\bf required}.\\
@@ -1292,7 +1292,7 @@ Intent: {\bf inout}.\\
Specified as: a rank one integer array.
\item[y] If $y$ is present,
then $y$ is overwritten with the translated integer indices, and $x$
is left unchanged.
is left unchanged; since $y$ contains local indices it should use \verb|psb_ipk_|.
Scope: {\bf global} \\
Type: {\bf optional}\\
Intent: {\bf out}.\\
@@ -1325,7 +1325,8 @@ call psb_loc_to_glob(x, desc_a, info, iact)
\begin{description}
\item[Type:] Asynchronous.
\item[\bf On Entry]
\item[x] An integer vector of indices to be converted.\\
\item[x] An integer vector of indices to be converted; if $y$ is present,
they are local indices, i.e. \verb|psb_ipk_| \\
Scope: {\bf local} \\
Type: {\bf required}\\
Intent: {\bf in, inout}.\\
@@ -1346,14 +1347,14 @@ Specified as: a character variable \verb|I|gnore, \verb|W|arning or
\begin{description}
\item[\bf On Return]
\item[x] If $y$ is not present,
then $x$ is overwritten with the translated integer indices.
then $x$ is overwritten with the translated integer global indices, i.e. \verb|psb_lpk_|
Scope: {\bf global} \\
Type: {\bf required}\\
Intent: {\bf inout}.\\
Specified as: a rank one integer array.
\item[y] If $y$ is not present,
then $y$ is overwritten with the translated integer indices, and $x$
is left unchanged.
\item[y] If $y$ not present,
then $y$ is overwritten with the translated global
indices i.e. \verb|psb_lpk_|, and $x$ is left unchanged.
Scope: {\bf global} \\
Type: {\bf optional}\\
Intent: {\bf out}.\\
@@ -1773,7 +1774,7 @@ Specified as: a preconditioner data structure \precdata.
\item[Function value] The memory occupation of the object specified in
the calling sequence, in bytes.\\
Scope: {\bf local} \\
Returned as: an \verb|integer(psb_long_int_k_)| number.
Returned as: an \verb|integer(psb_lpk_)| number.
\end{description}
@@ -1873,9 +1874,10 @@ the (sorted) value of $x$ in the original sequence.
$O(n^2)$; of the other three, in the average case quicksort will be the
fastest and merge-sort the slowest. However note that:
\begin{enumerate}
\item The the best case running time for insertion sort is $\Omega(n)$ while the average
and worst case are $O(n^2)$; however for very short input sequences this is
likely to be the fastest method;
\item The best case running time for insertion sort is $\Omega(n)$
while the average and worst case are $O(n^2)$; moreover, for
very short input sequences this is likely to be the fastest
method;
\item The worst case running time for quicksort is $O(n^2)$; the algorithm
implemented here follows the well-known median-of-three heuristics,
but the worst case may still apply;
@@ -1885,8 +1887,8 @@ the (sorted) value of $x$ in the original sequence.
subsequences that may be already in the desired ordering prior to
the subroutine call; this situation is relatively common when
dealing with groups of indices of sparse matrix entries, thus
merge-sort is the preferred choice when a sorting is needed
by other routines in the library.
merge-sort is the preferred choice when a sorting routine is needed
for preprocessing matrix data.
\end{enumerate}
\end{enumerate}
+1 -1
View File
@@ -136,7 +136,7 @@
by Salvatore Filippone\\
Alfredo Buttari \\
Fabio Durastante}\\
June 9th, 2025
December 23rd, 2025
\end{minipage}}
}
%\addtolength{\textwidth}{\centeroffset}
+1 -1
View File
@@ -106,7 +106,7 @@ Fabio Durastante } \\
%\today
Software version: 3.9.0\\
%\today
June 9th, 2025
December 23rd, 2025
\cleardoublepage
\begingroup
\renewcommand*{\thepage}{toc}