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<h4 class="subsectionHead"><span class="titlemark">2.3 </span> <a
id="x9-60002.3"></a>Application structure</h4>
<!--l. 301--><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
simulation domain; the index space 1<span
class="cmmi-10">&#x2026;</span><span
class="cmmi-10">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. 311--><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="cmmi-10">n </span>and the
allocation of the elements of the index space to the various processes making up the
MPI (virtual) parallel machine.
<!--l. 317--><p class="indent" > The index space is partitioned among processes, and this creates a mapping from
the &#8220;global&#8221; numbering 1<span
class="cmmi-10">&#x2026;</span><span
class="cmmi-10">n </span>to a numbering &#8220;local&#8221; to each process; each process <span
class="cmmi-10">i</span>
will own a certain subset 1<span
class="cmmi-10">&#x2026;</span><span
class="cmmi-10">n</span><sub>row<sub><span
class="cmmi-5">i</span></sub></sub>, each element of which corresponds to a certain
element of 1<span
class="cmmi-10">&#x2026;</span><span
class="cmmi-10">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
&#8220;global&#8221; numbering, and the library will translate into the appropriate &#8220;local&#8221;
numbering.
<!--l. 327--><p class="indent" > For a given index space 1<span
class="cmmi-10">&#x2026;</span><span
class="cmmi-10">n </span>there are many possible associated topologies, i.e.
many different discretization stencils; thus the description of the index space is not
completed until the user has defined a sparsity pattern, either explicitly through
<span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_cdins</span></span></span> or implicitly through <span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_spins</span></span></span>. The descriptor is finalized with a call to
<span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_cdasb</span></span></span> and a sparse matrix with a call to <span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_spasb</span></span></span>. After <span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_cdasb</span></span></span> each
process <span
class="cmmi-10">i </span>will have defined a set of &#8220;halo&#8221; (or &#8220;ghost&#8221;) indices <span
class="cmmi-10">n</span><sub>row<sub><span
class="cmmi-5">i</span></sub></sub> + 1<span
class="cmmi-10">&#x2026;</span><span
class="cmmi-10">n</span><sub>col<sub>
<span
class="cmmi-5">i</span></sub></sub>,
denoting elements of the index space that are <span
class="cmti-10">not </span>assigned to process <span
class="cmmi-10">i</span>; however the
variables associated with them are needed to complete computations associated with
the sparse matrix <span
class="cmmi-10">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. 343--><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="x9-6002x1">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="x9-6004x2">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="x9-6006x3">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="x9-6008x4">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="x9-6010x5">Assemble the various entities:
<ol class="enumerate2" >
<li
class="enumerate" id="x9-6012x1"><span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_cdasb</span></span></span>
</li>
<li
class="enumerate" id="x9-6014x2"><span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_spasb</span></span></span>
</li>
<li
class="enumerate" id="x9-6016x3"><span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_geasb</span></span></span></li></ol>
</li>
<li
class="enumerate" id="x9-6018x6">Choose the preconditioner to be used with <span class="obeylines-h"><span class="verb"><span
class="cmtt-10">prec%init</span></span></span> and build it with
<span class="obeylines-h"><span class="verb"><span
class="cmtt-10">prec%build</span></span></span><span class="footnote-mark"><a
href="userhtml10.html#fn3x0"><sup class="textsuperscript">3</sup></a></span><a
id="x9-6019f3"></a> .
</li>
<li
5 years ago
class="enumerate" id="x9-6021x7">Call the iterative driver <span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_krylov</span></span></span> with the method of choice, e.g.
<span class="obeylines-h"><span class="verb"><span
class="cmtt-10">bicgstab</span></span></span>.</li></ol>
<!--l. 366--><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>.
5 years ago
<!--l. 369--><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="x9-6023x1">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="x9-6025x2">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="x9-6027x3">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="x9-6029x4">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="x9-6031x5">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>
</li>
<li
class="enumerate" id="x9-6033x6">Loop over the time steps:
<ol class="enumerate2" >
<li
class="enumerate" id="x9-6035x1">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="x9-6037x2">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="x9-6039x3">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="x9-6041x4">Choose and build preconditioner 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%build</span></span></span>
</li>
<li
class="enumerate" id="x9-6043x5">Call the iterative method of choice, e.g. <span class="obeylines-h"><span class="verb"><span
class="cmtt-10">psb_bicgstab</span></span></span></li></ol>
</li></ol>
5 years ago
<!--l. 392--><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.
5 years ago
<!--l. 397--><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.
5 years ago
<!--l. 404--><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
performng value would depend on both the architecture of the computer being
used and on the problem structure. At the opposite extreme, it would be
possible to generate the entire part of a coefficient matrix residing on a
process and pass it in a single call to <span class="obeylines-h"><span class="verb"><span
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.
5 years ago
<!--l. 417--><p class="noindent" >
<h5 class="subsubsectionHead"><span class="titlemark">2.3.1 </span> <a
id="x9-70002.3.1"></a>User-defined index mappings</h5>
5 years ago
<!--l. 419--><p class="noindent" >PSBLAS supports user-defined global to local index mappings, subject to the
constraints outlined in sec.&#x00A0;<a
href="#x9-60002.3">2.3<!--tex4ht:ref: sec:appstruct --></a>:
<ol class="enumerate1" >
<li
class="enumerate" id="x9-7002x1">The set of indices owned locally must be mapped to the set 1<span
class="cmmi-10">&#x2026;</span><span
class="cmmi-10">n</span><sub>row<sub><span
class="cmmi-5">i</span></sub></sub>;
</li>
<li
class="enumerate" id="x9-7004x2">The set of halo points must be mapped to the set <span
class="cmmi-10">n</span><sub>row<sub><span
class="cmmi-5">i</span></sub></sub> + 1<span
class="cmmi-10">&#x2026;</span><span
class="cmmi-10">n</span><sub>col<sub>
<span
class="cmmi-5">i</span></sub></sub>;</li></ol>
5 years ago
<!--l. 427--><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="x9-7006x1">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
class="cmtt-10">vl(:)</span></span></span> containing the set of global indices owned by the current
process and <span class="obeylines-h"><span class="verb"><span
class="cmtt-10">lidx(:)</span></span></span> containing the corresponding local indices;
</li>
<li
class="enumerate" id="x9-7008x2">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
class="cmtt-10">psb_cdins(nz,ja,desc,info,lidx=lidx)</span></span></span>;
</li>
<li
class="enumerate" id="x9-7010x3">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="x9-7012x4">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
class="cmtt-10">local</span></span></span> argument specifying that the indices in <span class="obeylines-h"><span class="verb"><span
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>
5 years ago
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5 years ago
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