Docs updates.
@@ -23,7 +23,7 @@ class="pplb7t-">Alfredo Buttari </span><br
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class="newline" /><span
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class="pplb7t-">Fabio Durastante </span><br
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class="newline" />Software version: 3.9.0<br
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class="newline" />June 9th, 2025
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class="newline" />December 23rd, 2025
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@@ -23,7 +23,7 @@ class="pplb7t-">Alfredo Buttari </span><br
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class="newline" /><span
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class="pplb7t-">Fabio Durastante </span><br
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class="newline" />Software version: 3.9.0<br
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class="newline" />June 9th, 2025
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class="newline" />December 23rd, 2025
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@@ -11,7 +11,7 @@
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</head><body
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>
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<div class="footnote-text">
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<!--l. 208--><p class="indent" > <span class="footnote-mark"><a
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<!--l. 209--><p class="indent" > <span class="footnote-mark"><a
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id="fn1x0"><a
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id="x6-4003x2"></a> <sup class="textsuperscript">1</sup></a></span><span
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class="pplr7t-x-x-80">In our prototype implementation we provide sample scatter/gather routines.</span></div>
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@@ -11,7 +11,7 @@
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</head><body
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>
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<div class="footnote-text">
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<!--l. 252--><p class="noindent" ><span class="footnote-mark"><a
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<!--l. 251--><p class="noindent" ><span class="footnote-mark"><a
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id="fn2x0"><a
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id="x7-5002x2.1"></a> <sup class="textsuperscript">2</sup></a></span><span
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class="pplr7t-x-x-80">This is the normal situation when the pattern of the sparse matrix is symmetric, which is equivalent to</span>
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@@ -11,7 +11,7 @@
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</head><body
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>
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<div class="footnote-text">
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<!--l. 420--><p class="noindent" ><span class="footnote-mark"><a
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<!--l. 419--><p class="noindent" ><span class="footnote-mark"><a
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id="fn3x0"><a
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id="x8-7020x3"></a> <sup class="textsuperscript">3</sup></a></span><span
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class="pplr7t-x-x-80">The subroutine style </span><span
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@@ -210,7 +210,7 @@ href="userhtmlse6.html#x12-930006.15" id="QQ2-12-122">psb_gefree — Frees a
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<br />   <span class="subsectionToc" >6.16 <a
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href="userhtmlse6.html#x12-940006.16" id="QQ2-12-123">psb_gelp — Applies a left permutation to a dense matrix</a></span>
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<br />   <span class="subsectionToc" >6.17 <a
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href="userhtmlse6.html#x12-950006.17" id="QQ2-12-124">psb_glob_to_loc — Global to local indices convertion</a></span>
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href="userhtmlse6.html#x12-950006.17" id="QQ2-12-124">psb_glob_to_loc — Global to local indices conversion</a></span>
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<br />   <span class="subsectionToc" >6.18 <a
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href="userhtmlse6.html#x12-960006.18" id="QQ2-12-125">psb_loc_to_glob — Local to global indices conversion</a></span>
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<br />   <span class="subsectionToc" >6.19 <a
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@@ -34,8 +34,8 @@ base toolkit to build much more sophisticated preconditioners which can be plugg
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seamlessly into the base solvers.
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<!--l. 20--><p class="indent" > The software architecture allows us to offer support for many alternatives in the
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implementation, including usage of heterogeneous platforms, and computations
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performed on GPUs throuh CUDA. There is support for GPU computations through
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OpenACC, but it is at this time a highly experimental version; we plan to
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performed on GPUs throuh CUDA. There is also support for GPU computations
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through OpenACC, but it is at this time a highly experimental version; we plan to
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also look at using accelerators through OpenMP as support from compilers
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improves.
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<!--l. 28--><p class="indent" > The project is lead by Salvatore Filippone; a number of people have been
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@@ -58,7 +58,7 @@ chronological order: <span class="obeylines-h">
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<br />Dario Pascucci</span>
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<div class="flushright"
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>
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<!--l. 48--><p class="noindent" >
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<!--l. 49--><p class="noindent" >
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Salvatore Filippone<br />
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@@ -71,12 +71,12 @@ Fabio Durastante</div>
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<!--l. 57--><div class="crosslinks"><p class="noindent">[<a
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<!--l. 58--><div class="crosslinks"><p class="noindent">[<a
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href="userhtmlse1.html" >next</a>] [<a
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href="userhtmlli1.html" >prev</a>] [<a
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href="userhtmlli1.html#tailuserhtmlli1.html" >prev-tail</a>] [<a
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href="userhtmlli2.html" >front</a>] [<a
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href="userhtml.html#userhtmlli2.html" >up</a>] </p></div>
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<!--l. 57--><p class="indent" > <a
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<!--l. 58--><p class="indent" > <a
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id="tailuserhtmlli2.html"></a>
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</body></html>
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@@ -10,7 +10,7 @@
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<link rel="stylesheet" type="text/css" href="userhtml.css">
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</head><body
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>
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<!--l. 57--><div class="crosslinks"><p class="noindent">[<a
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<!--l. 58--><div class="crosslinks"><p class="noindent">[<a
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href="userhtmlse2.html" >next</a>] [<a
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href="userhtmlli2.html" >prev</a>] [<a
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href="userhtmlli2.html#tailuserhtmlli2.html" >prev-tail</a>] [<a
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@@ -18,7 +18,7 @@ href="#tailuserhtmlse1.html">tail</a>] [<a
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href="userhtml.html#userhtmlse1.html" >up</a>] </p></div>
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<h3 class="sectionHead"><span class="titlemark">1 </span> <a
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id="x4-30001"></a>Introduction</h3>
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<!--l. 59--><p class="noindent" >The PSBLAS library, developed with the aim to facilitate the parallelization of
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<!--l. 60--><p class="noindent" >The PSBLAS library, developed with the aim to facilitate the parallelization of
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computationally intensive scientific applications, is designed to address parallel
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implementation of iterative solvers for sparse linear systems through the
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distributed memory paradigm. It includes routines for multiplying sparse
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@@ -27,30 +27,31 @@ diagonal entries, preprocessing sparse matrices, and contains additional
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routines for dense matrix operations. The current implementation of PSBLAS
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addresses a distributed memory execution model operating with message
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passing.
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<!--l. 70--><p class="indent" > The PSBLAS library version 3 is implemented in the Fortran 2008 <span class="cite">[<a
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<!--l. 71--><p class="indent" > The PSBLAS library version 3 is implemented in the Fortran 2008 <span class="cite">[<a
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href="userhtmlli3.html#Xmetcalf">17</a>]</span>
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programming language, with reuse and/or adaptation of existing Fortran 77 and
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Fortran 95 software, plus a handful of C routines.
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<!--l. 75--><p class="indent" > The use of Fortran 2008 offers a number of advantages over Fortran 95, mostly
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<!--l. 76--><p class="indent" > The use of Fortran 2008 offers a number of advantages over Fortran 95, mostly
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in the handling of requirements for evolution and adaptation of the library to new
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||||
computing architectures and integration of new algorithms. For a detailed
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||||
discussion of our design see <span class="cite">[<a
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||||
href="userhtmlli3.html#XSparse03">11</a>]</span>; other works discussing advanced programming in
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||||
Fortran 2008 include <span class="cite">[<a
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||||
href="userhtmlli3.html#XDesPat:11">21</a>, <a
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||||
href="userhtmlli3.html#XRouXiaXu:11">19</a>]</span>; sufficient support for Fortran 2008 is now available
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||||
from many compilers, including recent versions of the GNU Fortran compiler from
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||||
the Free Software Foundation, and the FLANG compiler from the LLVM
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||||
project.
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||||
<!--l. 87--><p class="indent" > Previous approaches have been based on mixing Fortran 95, with its support for
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||||
href="userhtmlli3.html#XRouXiaXu:11">19</a>]</span>; sufficient support for Fortran 2008 is now
|
||||
available from many compilers, including recent versions of the GNU Fortran
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||||
compiler from the Free Software Foundation, the FLANG compiler from the
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LLVM project, and the Intel OneAPI compiler. The README file contains
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||||
a list of compilers against which we have successfully tested the current
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release.
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||||
<!--l. 91--><p class="indent" > Previous approaches have been based on mixing Fortran 95, with its support for
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object-based design, with other languages; these have been advocated by a number
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of authors, e.g. <span class="cite">[<a
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href="userhtmlli3.html#Xmachiels">16</a>]</span>. Moreover, the Fortran 95 facilities for dynamic memory
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management and interface overloading greatly enhance the usability of the PSBLAS
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subroutines. In this way, the library can take care of runtime memory requirements
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that are quite difficult or even impossible to predict at implementation or
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compilation time.
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<!--l. 97--><p class="indent" > The presentation of the PSBLAS library follows the general structure of the
|
||||
href="userhtmlli3.html#Xmachiels">16</a>]</span>. The Fortran 95 facilities for dynamic memory management and
|
||||
interface overloading ensure that the library can take care of runtime memory
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requirements that are quite difficult or even impossible to predict at implementation
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or compilation time.
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<!--l. 99--><p class="indent" > The presentation of the PSBLAS library follows the general structure of the
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||||
proposal for serial Sparse BLAS <span class="cite">[<a
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||||
href="userhtmlli3.html#Xsblas97">8</a>, <a
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||||
href="userhtmlli3.html#Xsblas02">9</a>]</span>, which in its turn is based on the proposal for
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@@ -58,16 +59,15 @@ BLAS on dense matrices <span class="cite">[<a
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href="userhtmlli3.html#XBLAS1">15</a>, <a
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href="userhtmlli3.html#XBLAS2">5</a>, <a
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||||
href="userhtmlli3.html#XBLAS3">6</a>]</span>.
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<!--l. 102--><p class="indent" > The applicability of sparse iterative solvers to many different areas causes
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some terminology problems because the same concept may be denoted
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||||
through different names depending on the application area. The PSBLAS
|
||||
features presented in this document will be discussed referring to a finite
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||||
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
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||||
problems such as nonlinear optimization, for example in optimal control
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||||
problems.
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||||
<!--l. 112--><p class="indent" > The design of a solver for sparse linear systems is driven by many conflicting
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<!--l. 104--><p class="indent" > The applicability of sparse iterative solvers to many different areas causes some
|
||||
terminology problems because the same concept may be 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
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||||
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
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||||
control problems.
|
||||
<!--l. 114--><p class="indent" > The design of a solver for sparse linear systems is driven by many conflicting
|
||||
objectives, such as limiting occupation of storage resources, exploiting regularities in
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||||
the input data, exploiting hardware characteristics of the parallel platform. To
|
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|
||||
@@ -88,12 +88,12 @@ applications.
|
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|
||||
|
||||
|
||||
<!--l. 129--><div class="crosslinks"><p class="noindent">[<a
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||||
<!--l. 131--><div class="crosslinks"><p class="noindent">[<a
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||||
href="userhtmlse2.html" >next</a>] [<a
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href="userhtmlli2.html" >prev</a>] [<a
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href="userhtmlli2.html#tailuserhtmlli2.html" >prev-tail</a>] [<a
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||||
href="userhtmlse1.html" >front</a>] [<a
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||||
href="userhtml.html#userhtmlse1.html" >up</a>] </p></div>
|
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<!--l. 129--><p class="indent" > <a
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<!--l. 131--><p class="indent" > <a
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id="tailuserhtmlse1.html"></a>
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</body></html>
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@@ -464,11 +464,12 @@ class="newline" />An integer value; 0 means no error has been detected.</dd></dl
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<!--l. 158--><p class="noindent" >This subroutine is a driver implementig a Richardson iteration
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||||
<div class="math-display" >
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||||
<img
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||||
src="userhtml33x.png" alt="x = M - 1(b - Ax )+ x ,
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||||
src="userhtml33x.png" alt="x = M - 1(b- Ax )+ x ,
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k+1 k k
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" class="math-display" ></div>
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<!--l. 159--><p class="nopar" > with the preconditioner operator <span
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||||
class="zplmr7m-">M </span>defined in the previous section.
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class="zplmr7m-">M </span>defined in section <a
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href="userhtmlse10.html#x16-13600010">10<!--tex4ht:ref: sec:precs --></a>.
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<!--l. 162--><p class="indent" > The stopping criterion can take the following values:
|
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<dl class="description"><dt class="description">
|
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<!--l. 164--><p class="noindent" >
|
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|
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@@ -10,7 +10,7 @@
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<link rel="stylesheet" type="text/css" href="userhtml.css">
|
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</head><body
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||||
>
|
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<!--l. 129--><div class="crosslinks"><p class="noindent">[<a
|
||||
<!--l. 131--><div class="crosslinks"><p class="noindent">[<a
|
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href="userhtmlse6.html" >next</a>] [<a
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href="userhtmlse1.html" >prev</a>] [<a
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href="userhtmlse1.html#tailuserhtmlse1.html" >prev-tail</a>] [<a
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@@ -18,7 +18,7 @@ href="#tailuserhtmlse2.html">tail</a>] [<a
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href="userhtml.html#userhtmlse2.html" >up</a>] </p></div>
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<h3 class="sectionHead"><span class="titlemark">2 </span> <a
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||||
id="x5-40002"></a>General overview</h3>
|
||||
<!--l. 131--><p class="noindent" >The PSBLAS library is designed to handle the implementation of iterative solvers for
|
||||
<!--l. 133--><p class="noindent" >The PSBLAS library is designed to handle the implementation of iterative solvers for
|
||||
sparse linear systems on distributed memory parallel computers. The system
|
||||
coefficient matrix <span
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||||
class="zplmr7m-">A </span>must be square; it may be real or complex, nonsymmetric, and
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||||
@@ -33,14 +33,14 @@ The ongoing discussion focuses on the Fortran 2008 layer immediately
|
||||
below the 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 Linear Algebra
|
||||
application layer that has been strongly inspired by the Basic Linear Algebra
|
||||
Communication Subroutines (BLACS) library <span class="cite">[<a
|
||||
href="userhtmlli3.html#XBLACS">7</a>]</span>. Usually there is no need to deal
|
||||
directly with MPI; however, in some cases, MPI routines are used directly
|
||||
to improve efficiency. For further details on our communication layer see
|
||||
Sec. <a
|
||||
href="userhtmlse7.html#x13-1060007">7<!--tex4ht:ref: sec:parenv --></a>.
|
||||
<!--l. 158--><p class="indent" > <hr class="figure"><div class="figure"
|
||||
<!--l. 160--><p class="indent" > <hr class="figure"><div class="figure"
|
||||
>
|
||||
|
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|
||||
@@ -52,8 +52,8 @@ href="userhtmlse7.html#x13-1060007">7<!--tex4ht:ref: sec:parenv --></a>.
|
||||
|
||||
<div class="center"
|
||||
>
|
||||
<!--l. 159--><p class="noindent" >
|
||||
<!--l. 161--><p class="noindent" ><img
|
||||
<!--l. 161--><p class="noindent" >
|
||||
<!--l. 163--><p class="noindent" ><img
|
||||
src="psblas.png" alt="PIC"
|
||||
width="46" height="46" ></div>
|
||||
<br /> <div class="caption"
|
||||
@@ -62,8 +62,8 @@ class="content">PSBLAS library components hierarchy.</span></div><!--tex4ht:labe
|
||||
|
||||
|
||||
|
||||
<!--l. 167--><p class="indent" > </div><hr class="endfigure">
|
||||
<!--l. 170--><p class="indent" > The type of linear system matrices that we address typically arise in
|
||||
<!--l. 169--><p class="indent" > </div><hr class="endfigure">
|
||||
<!--l. 172--><p class="indent" > The type of linear system matrices that we address typically arise in
|
||||
the numerical solution of PDEs; in such a context, it is necessary to pay
|
||||
special attention to the structure of the problem from which the application
|
||||
originates. The nonzero pattern of a matrix arising from the discretization of a
|
||||
@@ -71,12 +71,12 @@ PDE is influenced by various factors, such as the shape of the domain, the
|
||||
discretization strategy, and the equation/unknown ordering. The matrix itself can be
|
||||
interpreted as the adjacency matrix of the graph associated with the discretization
|
||||
mesh.
|
||||
<!--l. 181--><p class="indent" > The distribution of the coefficient matrix for the linear system is based on the
|
||||
<!--l. 183--><p class="indent" > The distribution of the coefficient matrix for the linear system is based on the
|
||||
“owner computes” rule: 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 <span
|
||||
class="pplri7t-">sub-domains</span>. Our library supports any
|
||||
class="pplri7t-">sub-domains</span>; 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 such as <span class="obeylines-h"><span class="verb"><span
|
||||
@@ -88,9 +88,10 @@ the literature, e.g. METIS <span class="cite">[<a
|
||||
href="userhtmlli3.html#XMETIS">14</a>]</span>. Dense vectors conform to sparse matrices,
|
||||
that is, the entries of a vector follow the same distribution of the matrix
|
||||
rows.
|
||||
<!--l. 203--><p class="indent" > 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 to hold the entire matrix in one process and distribute it
|
||||
<!--l. 204--><p class="indent" > We assume that the sparse matrix is built in parallel, where each process generates
|
||||
its own portion: we never <span
|
||||
class="pplri7t-">require </span>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<span class="footnote-mark"><a
|
||||
href="userhtml6.html#fn1x0"><sup class="textsuperscript">1</sup></a></span><a
|
||||
id="x5-4002f1"></a> ,
|
||||
@@ -98,10 +99,10 @@ even though the resulting memory bottleneck would make this option unattractive
|
||||
in most cases.
|
||||
<h4 class="subsectionHead"><span class="titlemark">2.1 </span> <a
|
||||
id="x5-50002.1"></a>Basic Nomenclature</h4>
|
||||
<!--l. 215--><p class="noindent" >Our computational model implies that the data allocation on the parallel distributed
|
||||
<!--l. 216--><p class="noindent" >Our computational model implies that the data allocation on the parallel distributed
|
||||
memory machine is guided by the structure of the physical model, and specifically
|
||||
by the discretization mesh of the PDE.
|
||||
<!--l. 220--><p class="indent" > Each point of the discretization mesh will have (at least) one associated
|
||||
<!--l. 221--><p class="indent" > Each point of the discretization mesh will have (at least) one associated
|
||||
equation/variable, and therefore one index. We say that point <span
|
||||
class="zplmr7m-">i </span><span
|
||||
class="pplri7t-">depends </span>on point <span
|
||||
@@ -117,56 +118,57 @@ class="pplri7t-">sub-domains </span>assigned
|
||||
to the parallel processes, we classify the points of a given sub-domain as
|
||||
following.
|
||||
<dl class="description"><dt class="description">
|
||||
<!--l. 229--><p class="noindent" >
|
||||
<!--l. 230--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Internal.</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 229--><p class="noindent" >An internal point of a given domain <span
|
||||
class="pplri7t-">depends </span>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
|
||||
<!--l. 230--><p class="noindent" >An internal point of a given sub-domain <span
|
||||
class="pplri7t-">depends </span>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
|
||||
|
||||
|
||||
|
||||
associated with the internal points requires no data items from other
|
||||
domains and no communications.
|
||||
equations associated with the internal points requires no data items from
|
||||
other sub-domains and no communications.
|
||||
</dd><dt class="description">
|
||||
<!--l. 238--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Boundary.</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 238--><p class="noindent" >A point of a given domain is a boundary point if it <span
|
||||
class="pplri7t-">depends </span>on points
|
||||
belonging to other domains.
|
||||
<!--l. 238--><p class="noindent" >A point of a given sub-domain is a boundary point if it <span
|
||||
class="pplri7t-">depends </span>on points
|
||||
belonging to other sub-domains.
|
||||
</dd><dt class="description">
|
||||
<!--l. 242--><p class="noindent" >
|
||||
<!--l. 241--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Halo.</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 242--><p class="noindent" >A halo point for a given domain is a point belonging to another domain
|
||||
such that there is a boundary point which <span
|
||||
class="pplri7t-">depends </span>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<span class="footnote-mark"><a
|
||||
<!--l. 241--><p class="noindent" >A halo point for a given sub-domain is a point belonging to another
|
||||
sub-domain such that there is a boundary point which <span
|
||||
class="pplri7t-">depends </span>on it.
|
||||
Whenever performing a computational step, such as a matrix-vector product,
|
||||
the values associated with halo points are requested from other sub-domains.
|
||||
A boundary point of a given sub-domain is usually a halo point for some
|
||||
other sub-domain<span class="footnote-mark"><a
|
||||
href="userhtml7.html#fn2x0"><sup class="textsuperscript">2</sup></a></span><a
|
||||
id="x5-5001f2"></a> ;
|
||||
therefore the cardinality of the boundary points set determines the amount
|
||||
of data sent to other domains.
|
||||
of data sent to other sub-domains.
|
||||
</dd><dt class="description">
|
||||
<!--l. 255--><p class="noindent" >
|
||||
<!--l. 254--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Overlap.</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 255--><p class="noindent" >An overlap point is a boundary point assigned to multiple domains. Any
|
||||
operation that involves an overlap point has to be replicated for each
|
||||
<!--l. 254--><p class="noindent" >An overlap point is a boundary point assigned to multiple sub-domains.
|
||||
Any operation that involves an overlap point has to be replicated for each
|
||||
assignment.</dd></dl>
|
||||
<!--l. 259--><p class="noindent" >Overlap points do not usually exist in the basic data distributions; however they are a
|
||||
<!--l. 258--><p class="noindent" >Overlap points do not usually exist in the basic data distributions; however they are a
|
||||
feature of Domain Decomposition Schwarz preconditioners which are the subject of
|
||||
related research work <span class="cite">[<a
|
||||
href="userhtmlli3.html#X2007c">4</a>, <a
|
||||
href="userhtmlli3.html#X2007d">3</a>]</span>.
|
||||
<!--l. 264--><p class="indent" > We denote the sets of internal, boundary and halo points for a given subdomain
|
||||
<!--l. 263--><p class="indent" > We denote the sets of internal, boundary and halo points for a given subdomain
|
||||
by <span
|
||||
class="zplmr7y-"><img
|
||||
src="zplmr7y-49.png" alt="I" class="x-x-49" /></span>, <span
|
||||
@@ -203,7 +205,7 @@ class="zplmr7y-">|<img
|
||||
src="zplmr7y-48.png" alt="H" class="x-x-48" /></span><sub><span
|
||||
class="zplmr7m-x-x-76">i</span></sub><span
|
||||
class="zplmr7y-">|</span>.
|
||||
<!--l. 274--><p class="indent" > <hr class="figure"><div class="figure"
|
||||
<!--l. 273--><p class="indent" > <hr class="figure"><div class="figure"
|
||||
>
|
||||
|
||||
|
||||
@@ -215,8 +217,8 @@ class="zplmr7y-">|</span>.
|
||||
|
||||
<div class="center"
|
||||
>
|
||||
<!--l. 275--><p class="noindent" >
|
||||
<!--l. 278--><p class="noindent" ><img
|
||||
<!--l. 274--><p class="noindent" >
|
||||
<!--l. 277--><p class="noindent" ><img
|
||||
src="points.png" alt="PIC"
|
||||
width="46" height="46" ></div>
|
||||
<br /> <div class="caption"
|
||||
@@ -225,113 +227,113 @@ class="content">Point classfication.</span></div><!--tex4ht:label?: x5-5003r2 --
|
||||
|
||||
|
||||
|
||||
<!--l. 284--><p class="indent" > </div><hr class="endfigure">
|
||||
<!--l. 286--><p class="indent" > This classification of mesh points guides the naming scheme that we adopted in
|
||||
<!--l. 283--><p class="indent" > </div><hr class="endfigure">
|
||||
<!--l. 285--><p class="indent" > This classification of mesh points guides the naming scheme that we adopted in
|
||||
the library internals and in the data structures. We explicitly note that “Halo” points
|
||||
are also often called “ghost” points in the literature.
|
||||
<h4 class="subsectionHead"><span class="titlemark">2.2 </span> <a
|
||||
id="x5-60002.2"></a>Library contents</h4>
|
||||
<!--l. 295--><p class="noindent" >The PSBLAS library consists of various classes of subroutines:
|
||||
<!--l. 294--><p class="noindent" >The PSBLAS library consists of various classes of subroutines:
|
||||
<dl class="description"><dt class="description">
|
||||
<!--l. 297--><p class="noindent" >
|
||||
<!--l. 296--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Computational routines</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 297--><p class="noindent" >comprising:
|
||||
<!--l. 296--><p class="noindent" >comprising:
|
||||
<ul class="itemize1">
|
||||
<li class="itemize">
|
||||
<!--l. 299--><p class="noindent" >Sparse matrix by dense matrix product;
|
||||
<!--l. 298--><p class="noindent" >Sparse matrix by dense matrix product;
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 300--><p class="noindent" >Sparse triangular systems solution for block diagonal matrices;
|
||||
<!--l. 299--><p class="noindent" >Sparse triangular systems solution for block diagonal matrices;
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 302--><p class="noindent" >Vector and matrix norms;
|
||||
<!--l. 301--><p class="noindent" >Vector and matrix norms;
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 303--><p class="noindent" >Dense matrix sums;
|
||||
<!--l. 302--><p class="noindent" >Dense matrix sums;
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 304--><p class="noindent" >Dot products.</li></ul>
|
||||
<!--l. 303--><p class="noindent" >Dot products.</li></ul>
|
||||
</dd><dt class="description">
|
||||
<!--l. 306--><p class="noindent" >
|
||||
<!--l. 305--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Communication routines</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 306--><p class="noindent" >handling halo and overlap communications;
|
||||
<!--l. 305--><p class="noindent" >handling halo and overlap communications;
|
||||
</dd><dt class="description">
|
||||
<!--l. 308--><p class="noindent" >
|
||||
<!--l. 307--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Data management and auxiliary routines</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 308--><p class="noindent" >including:
|
||||
<!--l. 307--><p class="noindent" >including:
|
||||
<ul class="itemize1">
|
||||
<li class="itemize">
|
||||
<!--l. 310--><p class="noindent" >Parallel environment management
|
||||
<!--l. 309--><p class="noindent" >Parallel environment management
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 311--><p class="noindent" >Communication descriptors allocation;
|
||||
<!--l. 310--><p class="noindent" >Communication descriptors allocation;
|
||||
|
||||
|
||||
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 312--><p class="noindent" >Dense and sparse matrix allocation;
|
||||
<!--l. 311--><p class="noindent" >Dense and sparse matrix allocation;
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 313--><p class="noindent" >Dense and sparse matrix build and update;
|
||||
<!--l. 312--><p class="noindent" >Dense and sparse matrix build and update;
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 314--><p class="noindent" >Sparse matrix and data distribution preprocessing.</li></ul>
|
||||
<!--l. 313--><p class="noindent" >Sparse matrix and data distribution preprocessing.</li></ul>
|
||||
</dd><dt class="description">
|
||||
<!--l. 316--><p class="noindent" >
|
||||
<!--l. 315--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Preconditioner routines</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 316--><p class="noindent" >
|
||||
<!--l. 315--><p class="noindent" >
|
||||
</dd><dt class="description">
|
||||
<!--l. 317--><p class="noindent" >
|
||||
<!--l. 316--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Iterative methods</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 317--><p class="noindent" >a subset of classical and Krylov subspace iterative methods</dd></dl>
|
||||
<!--l. 320--><p class="noindent" >The following naming scheme has been adopted for all the symbols internally defined
|
||||
<!--l. 316--><p class="noindent" >a subset of classical and Krylov subspace iterative methods</dd></dl>
|
||||
<!--l. 319--><p class="noindent" >The following naming scheme has been adopted for all the symbols internally defined
|
||||
in the PSBLAS software package:
|
||||
<ul class="itemize1">
|
||||
<li class="itemize">
|
||||
<!--l. 323--><p class="noindent" >all symbols (i.e. subroutine names, data types...) are prefixed by <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 322--><p class="noindent" >all symbols (i.e. subroutine names, data types...) are prefixed by <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_</span></span></span>
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 325--><p class="noindent" >all data type names are suffixed by <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 324--><p class="noindent" >all data type names are suffixed by <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">_type</span></span></span>
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 326--><p class="noindent" >all constants are suffixed by <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 325--><p class="noindent" >all constants are suffixed by <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">_</span></span></span>
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 327--><p class="noindent" >all top-level subroutine names follow the rule <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 326--><p class="noindent" >all top-level subroutine names follow the rule <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_xxname</span></span></span> where <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">xx</span></span></span> can be
|
||||
either:
|
||||
<ul class="itemize2">
|
||||
<li class="itemize">
|
||||
<!--l. 330--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 329--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">ge</span></span></span>: the routine is related to dense data,
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 331--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 330--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">sp</span></span></span>: the routine is related to sparse data,
|
||||
</li>
|
||||
<li class="itemize">
|
||||
<!--l. 332--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 331--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">cd</span></span></span>: the routine is related to communication descriptor (see <a
|
||||
href="userhtmlse3.html#x9-100003">3<!--tex4ht:ref: sec:datastruct --></a>).</li></ul>
|
||||
|
||||
|
||||
|
||||
<!--l. 335--><p class="noindent" >For example the <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 334--><p class="noindent" >For example the <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_geins</span></span></span>, <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spins</span></span></span> and <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cdins</span></span></span> perform the same
|
||||
@@ -339,33 +341,33 @@ class="cmtt-10">psb_cdins</span></span></span> perform the same
|
||||
href="userhtmlse6.html#x12-780006">6<!--tex4ht:ref: sec:toolsrout --></a>) on dense matrices, sparse matrices and communication
|
||||
descriptors respectively. Interface overloading allows the usage of the same
|
||||
subroutine names for both real and complex data.</li></ul>
|
||||
<!--l. 342--><p class="noindent" >In the description of the subroutines, arguments or argument entries are classified
|
||||
<!--l. 341--><p class="noindent" >In the description of the subroutines, arguments or argument entries are classified
|
||||
as:
|
||||
<dl class="description"><dt class="description">
|
||||
<!--l. 345--><p class="noindent" >
|
||||
<!--l. 344--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">global</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 345--><p class="noindent" >For input arguments, the value must be the same on all processes
|
||||
<!--l. 344--><p class="noindent" >For input arguments, the value must be the same on all processes
|
||||
participating in the subroutine call; for output arguments the value is
|
||||
guaranteed to be the same.
|
||||
</dd><dt class="description">
|
||||
<!--l. 348--><p class="noindent" >
|
||||
<!--l. 347--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">local</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 348--><p class="noindent" >Each process has its own value(s) independently.</dd></dl>
|
||||
<!--l. 350--><p class="noindent" >To finish our general description, we define a version string with the constant
|
||||
<!--l. 347--><p class="noindent" >Each process has its own value(s) independently.</dd></dl>
|
||||
<!--l. 349--><p class="noindent" >To finish our general description, we define a version string with the constant
|
||||
<div class="math-display" >
|
||||
<img
|
||||
src="userhtml0x.png" alt="psb_version_string_
|
||||
" class="math-display" ></div>
|
||||
<!--l. 352--><p class="nopar" > whose current value is <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 351--><p class="nopar" > whose current value is <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">3.9.0</span></span></span>
|
||||
<!--l. 355--><p class="noindent" >
|
||||
<!--l. 354--><p class="noindent" >
|
||||
<h4 class="subsectionHead"><span class="titlemark">2.3 </span> <a
|
||||
id="x5-70002.3"></a>Application structure</h4>
|
||||
<!--l. 358--><p class="noindent" >The main underlying principle of the PSBLAS library is that the library objects are
|
||||
<!--l. 357--><p class="noindent" >The main underlying principle of the PSBLAS library is that the library objects are
|
||||
created and exist with reference to a discretized space to which there corresponds
|
||||
an index space and a matrix sparsity pattern. As an example, consider a
|
||||
cell-centered finite-volume discretization of the Navier-Stokes equations on a
|
||||
@@ -375,13 +377,13 @@ class="zplmr7m-">n </span>is isomorphic to the set of cell centers,
|
||||
whereas the pattern of the associated linear system matrix is isomorphic to the
|
||||
adjacency graph imposed on the discretization mesh by the discretization
|
||||
stencil.
|
||||
<!--l. 368--><p class="indent" > Thus the first order of business is to establish an index space, and this is done
|
||||
<!--l. 367--><p class="indent" > Thus the first order of business is to establish an index space, and this is done
|
||||
with a call to <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cdall</span></span></span> in which we specify the size of the index space <span
|
||||
class="zplmr7m-">n </span>and the
|
||||
allocation of the elements of the index space to the various processes making up the
|
||||
MPI (virtual) parallel machine.
|
||||
<!--l. 374--><p class="indent" > The index space is partitioned among processes, and this creates a mapping from
|
||||
<!--l. 373--><p class="indent" > The index space is partitioned among processes, and this creates a mapping from
|
||||
the “global” numbering 1<span
|
||||
class="zplmr7m-">…</span><span
|
||||
class="zplmr7m-">n </span>to a numbering “local” to each process; each process <span
|
||||
@@ -393,14 +395,14 @@ class="zplmr7m-x-x-60">i</span></sub></sub>, each element of which corresponds t
|
||||
element of 1<span
|
||||
class="zplmr7m-">…</span><span
|
||||
class="zplmr7m-">n</span>. 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
|
||||
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 usually does so in the
|
||||
“global” numbering, and the library will translate into the appropriate “local”
|
||||
numbering.
|
||||
|
||||
|
||||
|
||||
<!--l. 384--><p class="indent" > For a given index space 1<span
|
||||
<!--l. 383--><p class="indent" > For a given index space 1<span
|
||||
class="zplmr7m-">…</span><span
|
||||
class="zplmr7m-">n </span>there are many possible associated topologies, i.e.
|
||||
many different discretization stencils; thus the description of the index space is not
|
||||
@@ -423,51 +425,51 @@ class="zplmr7m-">n</span><sub>col<sub>
|
||||
class="zplmr7m-x-x-60">i</span></sub></sub>,
|
||||
denoting elements of the index space that are <span
|
||||
class="pplri7t-">not </span>assigned to process <span
|
||||
class="zplmr7m-">i</span>; however the
|
||||
variables associated with them are needed to complete computations associated with
|
||||
class="zplmr7m-">i</span>; the variables
|
||||
associated with them are needed to complete computations associated with
|
||||
the sparse matrix <span
|
||||
class="zplmr7m-">A</span>, and thus they have to be fetched from (neighbouring)
|
||||
processes. The descriptor of the index space is built exactly for the purpose
|
||||
of properly sequencing the communication steps required to achieve this
|
||||
objective.
|
||||
<!--l. 400--><p class="indent" > A simple application structure will walk through the index space allocation,
|
||||
<!--l. 399--><p class="indent" > A simple application structure will walk through the index space allocation,
|
||||
matrix/vector creation and linear system solution as follows:
|
||||
<ol class="enumerate1" >
|
||||
<li
|
||||
class="enumerate" id="x5-7002x1">
|
||||
<!--l. 404--><p class="noindent" >Initialize parallel environment with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 403--><p class="noindent" >Initialize parallel environment with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_init</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7004x2">
|
||||
<!--l. 405--><p class="noindent" >Initialize index space with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 404--><p class="noindent" >Initialize index space with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cdall</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7006x3">
|
||||
<!--l. 406--><p class="noindent" >Allocate sparse matrix and dense vectors with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 405--><p class="noindent" >Allocate sparse matrix and dense vectors with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spall</span></span></span> and <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_geall</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7008x4">
|
||||
<!--l. 408--><p class="noindent" >Loop over all local rows, generate matrix and vector entries, and insert
|
||||
<!--l. 407--><p class="noindent" >Loop over all local rows, generate matrix and vector entries, and insert
|
||||
them with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spins</span></span></span> and <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_geins</span></span></span>
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7010x5">
|
||||
<!--l. 410--><p class="noindent" >Assemble the various entities:
|
||||
<!--l. 409--><p class="noindent" >Assemble the various entities:
|
||||
<ol class="enumerate2" >
|
||||
<li
|
||||
class="enumerate" id="x5-7012x1">
|
||||
<!--l. 412--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 411--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cdasb</span></span></span>,
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7014x2">
|
||||
<!--l. 413--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 412--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spasb</span></span></span>,
|
||||
|
||||
|
||||
@@ -475,12 +477,12 @@ class="cmtt-10">psb_spasb</span></span></span>,
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7016x3">
|
||||
<!--l. 414--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 413--><p class="noindent" ><span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_geasb</span></span></span>;</li></ol>
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7018x6">
|
||||
<!--l. 416--><p class="noindent" >Choose the preconditioner to be used with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 415--><p class="noindent" >Choose the preconditioner to be used with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">prec%init</span></span></span> and <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">prec%set</span></span></span>, and build it with
|
||||
<span class="obeylines-h"><span class="verb"><span
|
||||
@@ -490,39 +492,39 @@ href="userhtml8.html#fn3x0"><sup class="textsuperscript">3</sup></a></span><a
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7022x7">
|
||||
<!--l. 421--><p class="noindent" >Call one of the iterative drivers with the method of choice, e.g. <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 420--><p class="noindent" >Call one of the iterative drivers with the method of choice, e.g. <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_krylov</span></span></span>
|
||||
with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">bicgstab</span></span></span>.</li></ol>
|
||||
<!--l. 424--><p class="noindent" >This is the structure of the sample programs in the directory <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 423--><p class="noindent" >This is the structure of the sample programs in the directory <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">test/pargen/</span></span></span>.
|
||||
<!--l. 427--><p class="indent" > For a simulation in which the same discretization mesh is used over multiple
|
||||
<!--l. 426--><p class="indent" > For a simulation in which the same discretization mesh is used over multiple
|
||||
time steps, the following structure may be more appropriate:
|
||||
<ol class="enumerate1" >
|
||||
<li
|
||||
class="enumerate" id="x5-7024x1">
|
||||
<!--l. 430--><p class="noindent" >Initialize parallel environment with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 429--><p class="noindent" >Initialize parallel environment with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_init</span></span></span>
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7026x2">
|
||||
<!--l. 431--><p class="noindent" >Initialize index space with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 430--><p class="noindent" >Initialize index space with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cdall</span></span></span>
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7028x3">
|
||||
<!--l. 432--><p class="noindent" >Loop over the topology of the discretization mesh and build the
|
||||
<!--l. 431--><p class="noindent" >Loop over the topology of the discretization mesh and build the
|
||||
descriptor with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cdins</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7030x4">
|
||||
<!--l. 434--><p class="noindent" >Assemble the descriptor with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 433--><p class="noindent" >Assemble the descriptor with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cdasb</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7032x5">
|
||||
<!--l. 435--><p class="noindent" >Allocate the sparse matrices and dense vectors with; <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 434--><p class="noindent" >Allocate the sparse matrices and dense vectors with; <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spall</span></span></span> and
|
||||
<span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_geall</span></span></span>;
|
||||
@@ -532,34 +534,34 @@ class="cmtt-10">psb_geall</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7034x6">
|
||||
<!--l. 437--><p class="noindent" >Loop over the time steps:
|
||||
<!--l. 436--><p class="noindent" >Loop over the time steps:
|
||||
<ol class="enumerate2" >
|
||||
<li
|
||||
class="enumerate" id="x5-7036x1">
|
||||
<!--l. 439--><p class="noindent" >If after first time step, reinitialize the sparse matrix with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 438--><p class="noindent" >If after first time step, reinitialize the sparse matrix with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_sprn</span></span></span>;
|
||||
also zero out the dense vectors;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7038x2">
|
||||
<!--l. 442--><p class="noindent" >Loop over the mesh, generate the coefficients and insert/update
|
||||
<!--l. 441--><p class="noindent" >Loop over the mesh, generate the coefficients and insert/update
|
||||
them with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spins</span></span></span> and <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_geins</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7040x3">
|
||||
<!--l. 444--><p class="noindent" >Assemble with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 443--><p class="noindent" >Assemble with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spasb</span></span></span> and <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_geasb</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7042x4">
|
||||
<!--l. 445--><p class="noindent" >
|
||||
<!--l. 444--><p class="noindent" >
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7044x5">
|
||||
<!--l. 445--><p class="noindent" >Choose the preconditioner to be used with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 444--><p class="noindent" >Choose the preconditioner to be used with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">prec%init</span></span></span> and
|
||||
<span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">prec%set</span></span></span>, and build it with <span class="obeylines-h"><span class="verb"><span
|
||||
@@ -567,21 +569,21 @@ class="cmtt-10">prec%build</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-7046x6">
|
||||
<!--l. 448--><p class="noindent" >Call one of the iterative drivers with the method of choice, e.g.
|
||||
<!--l. 447--><p class="noindent" >Call one of the iterative drivers with the method of choice, e.g.
|
||||
<span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_krylov</span></span></span> with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">bicgstab</span></span></span>.</li></ol>
|
||||
</li></ol>
|
||||
<!--l. 452--><p class="noindent" >The insertion routines will be called as many times as needed; they only need to be
|
||||
<!--l. 451--><p class="noindent" >The insertion routines will be called as many times as needed; they only need to be
|
||||
called on the data that is actually allocated to the current process, i.e. each process
|
||||
generates its own data.
|
||||
<!--l. 457--><p class="indent" > In principle there is no specific order in the calls to <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 456--><p class="indent" > In principle there is no specific order in the calls to <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spins</span></span></span>, nor is there a
|
||||
requirement to build a matrix row in its entirety before calling the routine; this
|
||||
allows the application programmer to walk through the discretization mesh element
|
||||
by element, generating the main part of a given matrix row but also contributions to
|
||||
the rows corresponding to neighbouring elements.
|
||||
<!--l. 464--><p class="indent" > From a functional point of view it is even possible to execute one call for each
|
||||
<!--l. 463--><p class="indent" > From a functional point of view it is even possible to execute one call for each
|
||||
nonzero coefficient; however this would have a substantial computational
|
||||
overhead. It is therefore advisable to pack a certain amount of data into each
|
||||
call to the insertion routine, say touching on a few tens of rows; the best
|
||||
@@ -595,23 +597,23 @@ process and pass it in a single call to <span class="obeylines-h"><span class="v
|
||||
class="cmtt-10">psb_spins</span></span></span>; this, however, would entail a
|
||||
doubling of memory occupation, and thus would be almost always far from
|
||||
optimal.
|
||||
<!--l. 477--><p class="noindent" >
|
||||
<!--l. 476--><p class="noindent" >
|
||||
<h5 class="subsubsectionHead"><span class="titlemark">2.3.1 </span> <a
|
||||
id="x5-80002.3.1"></a>User-defined index mappings</h5>
|
||||
<!--l. 479--><p class="noindent" >PSBLAS supports user-defined global to local index mappings, subject to the
|
||||
<!--l. 478--><p class="noindent" >PSBLAS supports user-defined global to local index mappings, subject to the
|
||||
constraints outlined in sec. <a
|
||||
href="#x5-70002.3">2.3<!--tex4ht:ref: sec:appstruct --></a>:
|
||||
<ol class="enumerate1" >
|
||||
<li
|
||||
class="enumerate" id="x5-8002x1">
|
||||
<!--l. 482--><p class="noindent" >The set of indices owned locally must be mapped to the set 1<span
|
||||
<!--l. 481--><p class="noindent" >The set of indices owned locally must be mapped to the set 1<span
|
||||
class="zplmr7m-">…</span><span
|
||||
class="zplmr7m-">n</span><sub>row<sub><span
|
||||
class="zplmr7m-x-x-60">i</span></sub></sub>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-8004x2">
|
||||
<!--l. 484--><p class="noindent" >The set of halo points must be mapped to the set <span
|
||||
<!--l. 483--><p class="noindent" >The set of halo points must be mapped to the set <span
|
||||
class="zplmr7m-">n</span><sub>row<sub><span
|
||||
class="zplmr7m-x-x-60">i</span></sub></sub> <span
|
||||
class="zplmr7t-">+ </span>1<span
|
||||
@@ -619,14 +621,14 @@ class="zplmr7m-">…</span><span
|
||||
class="zplmr7m-">n</span><sub>col<sub>
|
||||
<span
|
||||
class="zplmr7m-x-x-60">i</span></sub></sub>;</li></ol>
|
||||
<!--l. 487--><p class="noindent" >but otherwise the mapping is arbitrary. The user application is responsible to ensure
|
||||
<!--l. 486--><p class="noindent" >but otherwise the mapping is arbitrary. The user application is responsible to ensure
|
||||
consistency of this mapping; some errors may be caught by the library, but
|
||||
this is not guaranteed. The application structure to support this usage is as
|
||||
follows:
|
||||
<ol class="enumerate1" >
|
||||
<li
|
||||
class="enumerate" id="x5-8006x1">
|
||||
<!--l. 493--><p class="noindent" >Initialize index
|
||||
<!--l. 492--><p class="noindent" >Initialize index
|
||||
space with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cdall(ictx,desc,info,vl=vl,lidx=lidx)</span></span></span> passing the
|
||||
vectors <span class="obeylines-h"><span class="verb"><span
|
||||
@@ -636,7 +638,7 @@ class="cmtt-10">lidx(:)</span></span></span> containing the corresponding local
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-8008x2">
|
||||
<!--l. 498--><p class="noindent" >Add the halo points <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 497--><p class="noindent" >Add the halo points <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">ja(:)</span></span></span> and their associated local indices <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">lidx(:)</span></span></span>
|
||||
with a(some) call(s) to <span class="obeylines-h"><span class="verb"><span
|
||||
@@ -644,7 +646,7 @@ class="cmtt-10">psb_cdins(nz,ja,desc,info,lidx=lidx)</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
class="enumerate" id="x5-8010x3">
|
||||
<!--l. 501--><p class="noindent" >Assemble the descriptor with <span class="obeylines-h"><span class="verb"><span
|
||||
<!--l. 500--><p class="noindent" >Assemble the descriptor with <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cdasb</span></span></span>;
|
||||
</li>
|
||||
<li
|
||||
@@ -652,7 +654,7 @@ class="cmtt-10">psb_cdasb</span></span></span>;
|
||||
|
||||
|
||||
|
||||
<!--l. 502--><p class="noindent" >Build the sparse matrices and vectors, optionally making use in
|
||||
<!--l. 501--><p class="noindent" >Build the sparse matrices and vectors, optionally making use in
|
||||
<span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spins</span></span></span> and <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_geins</span></span></span> of the <span class="obeylines-h"><span class="verb"><span
|
||||
@@ -661,41 +663,41 @@ class="cmtt-10">local</span></span></span> argument specifying that the
|
||||
class="cmtt-10">ia</span></span></span>, <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">ja</span></span></span> and <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">irw</span></span></span>, respectively, are already local indices.</li></ol>
|
||||
<!--l. 509--><p class="noindent" >
|
||||
<!--l. 508--><p class="noindent" >
|
||||
<h4 class="subsectionHead"><span class="titlemark">2.4 </span> <a
|
||||
id="x5-90002.4"></a>Programming model</h4>
|
||||
<!--l. 511--><p class="noindent" >The PSBLAS librarary is based on the Single Program Multiple Data (SPMD)
|
||||
<!--l. 510--><p class="noindent" >The PSBLAS librarary is based on the Single Program Multiple Data (SPMD)
|
||||
programming model: each process participating in the computation performs the
|
||||
same actions on a chunk of data. Parallelism is thus data-driven.
|
||||
<!--l. 516--><p class="indent" > Because of this structure, many subroutines coordinate their action across the
|
||||
<!--l. 515--><p class="indent" > Because of this structure, many subroutines coordinate their action across the
|
||||
various processes, thus providing an implicit synchronization point, and therefore
|
||||
<span
|
||||
class="pplri7t-">must </span>be called simultaneously by all processes participating in the computation. This
|
||||
is certainly true for the data allocation and assembly routines, for all the
|
||||
computational routines and for some of the tools routines.
|
||||
<!--l. 524--><p class="indent" > However there are many cases where no synchronization, and indeed no
|
||||
communication among processes, is implied; for instance, all the routines in sec. <a
|
||||
href="userhtmlse3.html#x9-100003">3<!--tex4ht:ref: sec:datastruct --></a>
|
||||
are only acting on the local data structures, and thus may be called independently.
|
||||
The most important case is that of the coefficient insertion routines: since the number
|
||||
of coefficients in the sparse and dense matrices varies among the processors, and
|
||||
since the user is free to choose an arbitrary order in builiding the matrix entries,
|
||||
these routines cannot imply a synchronization.
|
||||
<!--l. 534--><p class="indent" > Throughout this user’s guide each subroutine will be clearly indicated
|
||||
<!--l. 523--><p class="indent" > However there are cases where no synchronization, and indeed no communication
|
||||
among processes, is implied; for instance, all the routines in sec. <a
|
||||
href="userhtmlse3.html#x9-100003">3<!--tex4ht:ref: sec:datastruct --></a> are only acting on
|
||||
the local data structures, and thus may be called independently. The most important
|
||||
case is that of the coefficient insertion routines: since the number of coefficients in the
|
||||
sparse and dense matrices varies among the processors, and since the user is free to
|
||||
choose an arbitrary order in builiding the matrix entries, these routines cannot imply
|
||||
a synchronization.
|
||||
<!--l. 533--><p class="indent" > Throughout this user’s guide each subroutine will be clearly indicated
|
||||
as:
|
||||
<dl class="description"><dt class="description">
|
||||
<!--l. 537--><p class="noindent" >
|
||||
<!--l. 536--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Synchronous:</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 537--><p class="noindent" >must be called simultaneously by all the processes in the relevant
|
||||
<!--l. 536--><p class="noindent" >must be called simultaneously by all the processes in the relevant
|
||||
communication context;
|
||||
</dd><dt class="description">
|
||||
<!--l. 539--><p class="noindent" >
|
||||
<!--l. 538--><p class="noindent" >
|
||||
<span
|
||||
class="pplb7t-">Asynchronous:</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 539--><p class="noindent" >may be called in a totally independent manner.</dd></dl>
|
||||
<!--l. 538--><p class="noindent" >may be called in a totally independent manner.</dd></dl>
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -60,8 +60,8 @@ class="pplb7t-">psb</span><span
|
||||
class="pplb7t-">_epk</span><span
|
||||
class="pplb7t-">_</span> </dt><dd
|
||||
class="description">
|
||||
<!--l. 28--><p class="noindent" >Kind parameter for 8-bytes integer data, as is always used by the <code class="lstinline"><span style="color:#000000">sizeof</span></code>
|
||||
methods;
|
||||
<!--l. 28--><p class="noindent" >Kind parameter for 8-bytes integer data, as is always returned by the
|
||||
<code class="lstinline"><span style="color:#000000">sizeof</span></code> methods;
|
||||
</dd><dt class="description">
|
||||
<!--l. 30--><p class="noindent" >
|
||||
<span
|
||||
@@ -94,15 +94,15 @@ documentation.
|
||||
<!--l. 48--><p class="noindent" >
|
||||
<h4 class="subsectionHead"><span class="titlemark">3.1 </span> <a
|
||||
id="x9-110003.1"></a>Descriptor data structure</h4>
|
||||
<!--l. 50--><p class="noindent" >All the general matrix informations and elements to be exchanged among processes
|
||||
are stored within a data structure of the type <a
|
||||
<!--l. 50--><p class="noindent" >All the general matrix information and the identification of elements to be
|
||||
exchanged among processes are stored within a data structure of the type
|
||||
<a
|
||||
id="descdata"></a><span
|
||||
class="cmtt-10">psb</span><span
|
||||
class="cmtt-10">_desc</span><span
|
||||
class="cmtt-10">_type</span>. 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.
|
||||
class="cmtt-10">_type</span>. 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.
|
||||
<!--l. 57--><p class="indent" > The data structure itself <code class="lstinline"><span style="color:#000000">psb_desc_type</span></code> can be treated as an opaque object
|
||||
handled via the tools routines of Sec. <a
|
||||
href="userhtmlse6.html#x12-780006">6<!--tex4ht:ref: sec:toolsrout --></a> or the query routines detailed below;
|
||||
|
||||
@@ -3129,7 +3129,7 @@ class="zplmr7m-">x </span>and
|
||||
class="zplmr7m-">y</span>
|
||||
<div class="math-display" >
|
||||
<img
|
||||
src="userhtml22x.png" alt="dot ← x(i)y(i).
|
||||
src="userhtml22x.png" alt="y(i) ← x(i)y(i).
|
||||
" class="math-display" ></div>
|
||||
<!--l. 1249--><p class="nopar" >
|
||||
<!--l. 1251--><p class="indent" > <code class="lstinline"><span style="color:#000000">psb_gemlt</span><span style="color:#000000">(</span><span style="color:#000000">x</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">y</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">desc_a</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">info</span><span style="color:#000000">)</span></code>
|
||||
@@ -3314,7 +3314,7 @@ class="zplmr7m-">x </span>and
|
||||
class="zplmr7m-">y</span>
|
||||
<div class="math-display" >
|
||||
<img
|
||||
src="userhtml23x.png" alt="/ ← x(i)/y(i).
|
||||
src="userhtml23x.png" alt="y(i) ← x(i)/y(i).
|
||||
" class="math-display" ></div>
|
||||
<!--l. 1316--><p class="nopar" >
|
||||
<!--l. 1318--><p class="indent" > <code class="lstinline"><span style="color:#000000">psb_gediv</span><span style="color:#000000">(</span><span style="color:#000000">x</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">y</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">desc_a</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">info</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">[</span><span style="color:#000000">flag</span><span style="color:#000000">)</span></code>
|
||||
@@ -3516,7 +3516,7 @@ class="zplmr7m-">x </span>and puts it into
|
||||
class="zplmr7m-">y</span>
|
||||
<div class="math-display" >
|
||||
<img
|
||||
src="userhtml24x.png" alt="/ ← 1/x(i).
|
||||
src="userhtml24x.png" alt="y(i) ← 1/x(i).
|
||||
" class="math-display" ></div>
|
||||
<!--l. 1388--><p class="nopar" >
|
||||
<!--l. 1390--><p class="indent" > <code class="lstinline"><span style="color:#000000">psb_geinv</span><span style="color:#000000">(</span><span style="color:#000000">x</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">y</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">desc_a</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">info</span><span style="color:#000000">,</span><span style="color:#000000"> </span><span style="color:#000000">[</span><span style="color:#000000">flag</span><span style="color:#000000">)</span></code>
|
||||
|
||||
@@ -18,10 +18,10 @@ href="userhtmlse5.html#tailuserhtmlse8.html">tail</a>] [<a
|
||||
href="userhtml.html#userhtmlse11.html" >up</a>] </p></div>
|
||||
<h3 class="sectionHead"><span class="titlemark">8 </span> <a
|
||||
id="x14-1240008"></a>Error handling</h3>
|
||||
<!--l. 5--><p class="noindent" >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
|
||||
<!--l. 5--><p class="noindent" >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-2.0 library has, as
|
||||
error message has been generated. Every routine in the PSBLAS library has, as
|
||||
last non-optional argument, an integer <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">info</span></span></span> variable; whenever, inside the
|
||||
routine, an error is detected, this variable is set to a value corresponding to a
|
||||
@@ -38,16 +38,16 @@ execution.
|
||||
<!--l. 23--><p class="indent" > Figure <a
|
||||
href="#x14-124025r5">5<!--tex4ht:ref: fig:routerr --></a> shows the layout of a generic <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_foo</span></span></span> routine with respect to the
|
||||
PSBLAS-2.0 error handling policy. It is possible to see how, whenever an error
|
||||
condition is detected, the <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">info</span></span></span> variable is set to the corresponding error code which
|
||||
is, then, pushed on top of the stack by means of the <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_errpush</span></span></span>. An error condition
|
||||
may be directly detected inside a routine or indirectly checking the error code
|
||||
returned returned by a called routine. Whenever an error is encountered, after it has
|
||||
been pushed on stack, the program execution skips to a point where the error
|
||||
condition is handled; the error condition is handled either by returning control to the
|
||||
caller routine or by calling the <span class="obeylines-h"><span class="verb"><span
|
||||
PSBLAS error handling policy. It is possible to see how, whenever an error condition
|
||||
is detected, the <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">info</span></span></span> variable is set to the corresponding error code which is, then,
|
||||
pushed on top of the stack by means of the <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_errpush</span></span></span>. An error condition may be
|
||||
directly detected inside a routine or indirectly checking the error code returned
|
||||
returned by a called routine. Whenever an error is encountered, after it has been
|
||||
pushed on stack, the program execution skips to a point where the error condition is
|
||||
handled; the error condition is handled either by returning control to the caller
|
||||
routine or by calling the <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb\_error</span></span></span> routine which prints the content of
|
||||
the error stack and aborts the program execution, according to the choice
|
||||
made by the user with <span class="obeylines-h"><span class="verb"><span
|
||||
@@ -292,14 +292,13 @@ error handling policy.</span></div><!--tex4ht:label?: x14-124025r5 -->
|
||||
|
||||
</div><hr class="endfloat" />
|
||||
<!--l. 112--><p class="indent" > Figure <a
|
||||
href="#x14-124026r6">6<!--tex4ht:ref: fig:errormsg --></a> reports a sample error message generated by the PSBLAS-2.0
|
||||
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 <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cest</span></span></span> subroutine called by <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spasb</span></span></span> ... by process 0 (i.e. the root
|
||||
process).
|
||||
href="#x14-124026r6">6<!--tex4ht:ref: fig:errormsg --></a> reports a sample error message generated by 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 <span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_cest</span></span></span> subroutine called by
|
||||
<span class="obeylines-h"><span class="verb"><span
|
||||
class="cmtt-10">psb_spasb</span></span></span> ... by process 0 (i.e. the root process).
|
||||
|
||||
|
||||
|
||||
@@ -331,8 +330,8 @@ Aborting...
|
||||
<!--l. 156--><p class="nopar" > </div></div>
|
||||
</div>
|
||||
<br /> <div class="caption"
|
||||
><span class="id">Listing 6: </span><span
|
||||
class="content">A sample PSBLAS-3.0 error message. Process 0 detected an error
|
||||
><span class="id">Listing 6: </span><span
|
||||
class="content">A sample PSBLAS error message. Process 0 detected an error
|
||||
condition inside the psb_cest subroutine</span></div><!--tex4ht:label?: x14-124026r6 -->
|
||||
|
||||
|
||||
|
||||