[cig-commits] r3914 - short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog

baagaard at geodynamics.org baagaard at geodynamics.org
Mon Jul 3 14:02:23 PDT 2006


Author: baagaard
Date: 2006-07-03 14:02:23 -0700 (Mon, 03 Jul 2006)
New Revision: 3914

Added:
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/reversenog.xml
Removed:
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/tutorialbm5.xml
Log:
User guide. Changed name of tutorial.

Copied: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/reversenog.xml (from rev 3913, short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/tutorialbm5.xml)

Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/tutorialbm5.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/tutorialbm5.xml	2006-07-03 21:01:53 UTC (rev 3913)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/tutorialbm5.xml	2006-07-03 21:02:23 UTC (rev 3914)
@@ -1,711 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
-  "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="tutorial_scecbm5">
-  <title>Tutorial Using SCEC Benchmark 5</title>
-
-  <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
-  <section>
-    <title>Overview</title>
-    <para>
-      In this tutorial, we will walk through the steps necessary to
-      construct, run, and view the results of a benchmark problem
-      (SCEC Benchmark 5). This problem examines the viscoelastic
-      (Maxwell) relaxation of stress from a single, finite, dip-slip
-      earthquake in 3-D without body forces. 
-    </para>
-
-    <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++ -->
-    <section>
-      <title>Problem Description</title>
-      <para>
-        The model domain is a cube with edges 24 km long (0 km &le; x
-        &le; 24 km; 0 km &le; y &le; 24 km; -24 km &le; z &le; 0) and
-        is composed of two materials. One material occupies the
-        top-half of the domain, -12 km &le; z &le; 0 km, while the other
-        occupies the lower half, -24 km &le; z &lt; 12 km. Both
-        materials are Poisson solids with Lame's constants (&mgr; and
-        &lgr;) equal to 30 GPa and Maxwell viscoelastic
-        properties. The top layer has a viscosity of
-        10<superscript>25</superscript> Pa-s (and is essentially
-        elastic) while the bottom layer has a viscosity of
-        10<superscript>18</superscript> Pa-s.
-      </para>
-      <para>
-        The reverse fault dips at an angle of 45 degrees. The top of the
-        fault sits at x = 4 km with the bottom of the fault at x = 20
-        km. The fault surface is confined to the region 0 km &le; y
-        &le; 16 km and -16 km &le; z &le; 0 km. The slip distribution
-        is 1.0 m of uniform thrust motion for -12 km &le; z with a
-        linear taper to 0 at z = -16 km.
-      </para>
-      <para>
-        The plane y=0 is a plane of symmetry, so the y-DOF
-        displacements on this face are zero. The boundary conditions
-        on the other lateral faces and bottom of the mesh are the
-        displacements from the analytical elastic solution. These
-        displacements are held fixed through time.
-      </para>
-
-      <figure id="figure_bm5_geometry">
-	<title>Geometry of model domain for SCEC Benchmark 5.</title>
-	<mediaobject>
-          <imageobject role="fo">
-	    <imagedata fileref="figs/geometry.eps" format="EPS" />
-	  </imageobject>
-          <imageobject role="xhtml,html">
-	    <imagedata fileref="figs/geometry.png" format="PNG" />
-	  </imageobject>
-	</mediaobject>
-      </figure>
-    </section>
-
-    <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++ -->
-    <section>
-      <title>Prerequisites</title>
-      <para>
-        You should have already installed PyLith following the
-        instructions in <xref linkend="install" />. In order to work
-        through the full tutorial, in addition to
-        <application>PyLith</application> you will need <ulink
-        url="http://www.hpfem.jku.at/netgen/">
-        <application>NetGen</application></ulink> to generate the mesh
-        and <ulink url="http://www.paraview.org"> ParaView</ulink> to
-        view simulation results. You may use other packages, but some
-        adaption from what is described here will be
-        necessary. Alternatively, you can just complete a subset of
-        the tutorial using files provided (as described below),
-        skipping the steps for which you do not have the proper
-        software packages installed.
-      </para>
-    </section>
-  </section>
-
-  <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
-  <section>
-    <title>Download and unpack</title>
-    <para>
-      We will start by downloading the tutorial tarball and unpacking
-      it.
-    </para>
-
-    <orderedlist numeration="arabic">
-      <listitem>
-	<para>
-          Download the <ulink
-          url="http://www.geodynamics.org:8080/cig/Members/willic3/pylithusers/pylith0.8/pylith-0.8_tutorials.tgz">tutorial
-          tarball</ulink> and unpack it in a location of your
-          choosing.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>tar -zxvf pylith-0.8_tutorials.tgz</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-	<para>
-          Go to the <filename
-          class="directory">tutorials/scecbm5</filename>
-          directory. The <filename
-          class="directory">archive</filename> directory contains all
-          of the input and output files associated with this
-          tutorial. We will copy input files from this directory into
-          the <filename class="directory">workarea</filename>
-          directory. At each step, you can check to make sure your
-          input and output agree with the files in the <filename
-          class="directory">archive</filename> directory. These files
-          also allow you to start at an intermediate step as described
-          in the next section.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>cd tutorials/scecbm5</userinput>
-        </screen>
-	
-      </listitem>
-    </orderedlist>
-
-    <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++ -->
-    <section>
-      <title>Tutor</title>
-      <para>
-        Copy the <filename>tutor.sh</filename> script from the
-        <filename class="directory">archive</filename> directory into
-        the <filename class="directory">workarea</filename>
-        directory. This script can (1) check to make sure the files
-        necessary for a given step in the tutorial exist, (2) retrieve
-        any missing files from the <filename
-        class="directory">archive</filename> directory that are needed
-        for a given step, or (3) prepare the work area for a given
-        step by removing old files that would otherwise be
-        overwritten. Run <command>tutor.sh</command> without any
-        arguments for more information. We will use this script at the
-        beginning of each step to retrieve files as necessary from the
-        archive.
-      </para>
-      <tip>
-	<para>
-          When retrieving files from the <filename
-          classname="directory">archive</filename> directory,
-          <command>tutor.sh</command> will not overwrite files that
-          already exist in the <filename
-          class="directory">workarea</filename> directory. This means
-          that if you mangle files in the working area, you should
-          remove them and let the tutor retrieve clean copies.
-        </para>
-      </tip>
-      <tip>
-	<para>
-          If you have run this tutorial previously, you may want to
-          run <command>tutor.sh</command> in mode "clean" with step
-          "all" to clear out all old tutorial files.
-        </para>
-      </tip>
-      <screen>
-<prompt>bash$ </prompt><userinput>cd workarea</userinput>
-<prompt>bash$ </prompt><userinput>cp ../archive/tutor.sh .</userinput>
-<prompt>bash$ </prompt><userinput>./tutor.sh clean all</userinput>
-      </screen>
-    </section>
-
-  </section>
-
-  <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
-  <section>
-    <title>Generate the mesh</title>
-    <para>
-      In this step we will generate the finite-element mesh for the
-      benchmark problem using <application>NetGen</application>.
-    </para>
-
-    <orderedlist numeration="arabic">
-      <listitem>
-	<para>
-          In the <filename class="directory">scecbm5/workarea</filename>
-          directory, run <command>tutor.sh</command> for step "mesh"
-          with mode "retrieve" to fetch the geometry file for
-          <application>NetGen</application>. You may also want to run
-          <command>tutor.sh</command> for this step with mode "clean"
-          to clean out old files.
-        </para>
-      <screen>
-<prompt>bash$ </prompt><userinput>./tutor.sh retrieve mesh</userinput>
-<prompt>bash$ </prompt><userinput>./tutor.sh clean mesh</userinput>
-      </screen>
-      </listitem>
-      <listitem>
-	<para>
-          Examine the <filename>bm5.geo</filename> file to see how the
-          geometry for the problem is defined. Notice that the
-          different planes have been flagged with different boundary
-          condition codes. These will be used to associate boundary
-          conditions with surfaces and element nodes.
-        </para>
-      </listitem>
-      <listitem>
-	<para>
-          Start up <application>NetGen</application> by running
-          <command>ng</command>.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>ng</userinput>
-      </screen>
-      </listitem>
-      <listitem>
-	<para>
-          Select <menuchoice><guimenu>File</guimenu><guimenuitem>Load
-          Geometry</guimenuitem></menuchoice> and select
-          <filename>bm5.geo</filename>.
-        </para>
-      </listitem>
-      <listitem>
-	<para>
-          Click on <guibutton>Generate Mesh</guibutton>.
-        </para>
-      </listitem>
-      <listitem>
-	<para>
-          Export the mesh to a file named
-          <filename>bm5.netgen</filename>, making sure the export
-          filetype is "Neutral format".
-        </para>
-      </listitem>
-      <listitem>
-	<para>
-          You can now exit <application>NetGen</application>.
-        </para>
-      </listitem>
-    </orderedlist>
-  </section>
-          
-  <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
-  <section>
-    <title>Setup simulation input files</title>
-    <para>
-      In this step we will setup the PyLith input files for the mesh
-      and boundary conditions.
-    </para>
-    
-    <orderedlist numeration="arabic">
-      <listitem>
-	<para>
-          Run <command>tutor.sh</command> for step "setup" with mode
-          "retrieve" to fetch files from the archive.
-        </para>
-      <screen>
-<prompt>bash$ </prompt><userinput>./tutor.sh retrieve setup</userinput>
-      </screen>
-      </listitem>
-      <listitem>
-	<para>
-          First, we need to build two simple Fortran utilities that we
-          will use to generate PyLith input files from the
-          <application>NetGen</application> output.
-        </para>
-        <orderedlist numeration="lowerroman">
-	  <listitem>
-	    <para>
-              Return to the top-level <filename
-              class="directory">tutorials</filename> directory and go
-              to the <filename class="directory">utils</filename>
-              sub-directory.
-            </para>
-	    <screen>
-<prompt>bash$ </prompt><userinput>cd ../../utils</userinput>
-            </screen>
-	  </listitem>
-	  <listitem>
-	    <para>
-              Edit the <filename>Makefile</filename> as appropriate
-              (it is presently setup for g77).
-            </para>
-	  </listitem>
-	  <listitem>
-	    <para>
-              Run <command>make</command> to build the two utilities:
-            </para>
-	    <variablelist>
-	      <varlistentry>
-		<term><command>readnetgen</command></term>
-		<listitem>
-		  <para>
-                    A Fortran program to read
-                    <application>NetGen</application> neutral format
-                    and create several of the input files needed by
-                    PyLith.
-                  </para>
-		</listitem>
-	      </varlistentry>
-	      <varlistentry>
-		<term><command>faultcalc</command></term>
-		<listitem>
-		  <para>
-                    A Fortran program to compute split node
-                    displacements using second order polynomials over
-                    specified regions.
-                  </para>
-		</listitem>
-	      </varlistentry>
-	    </variablelist>
-	    <screen>
-<prompt>bash$ </prompt><userinput>make</userinput>
-            </screen>
-	    <tip>
-	    <para>
-              If you plan to use <application>NetGen</application> to
-              generate meshes, you may want to copy these utilities to
-              a location in your <envar>PATH</envar> or update your
-              <envar>PATH</envar> to include the <filename
-              class="directory">utils</filename> directory.
-            </para>
-	    </tip>
-	  </listitem>
-	  <listitem>
-	    <para>
-              Return to the <filename
-              class="directory">workarea</filename> directory.
-            </para>
-	    <screen>
-<prompt>bash$ </prompt><userinput>cd ../scecbm5/workarea</userinput>
-            </screen>
-	  </listitem>
-	</orderedlist>
-      </listitem>
-      <listitem>
-	<para>
-          Run the utility program <command>readnetgen</command> to
-          process the <application>NetGen</application> output file
-          into PyLith compatible input files. It will ask for a root
-          filename, enter <filename>bm5</filename>. This utilitiy will
-          generate the following files:
-          <filename>bm5.w01.wink</filename>,
-          <filename>bm5.coord</filename>,
-          <filename>bm5.connect</filename>,
-          <filename>bm5.bc</filename>,
-          <filename>bm5.1.fcoord</filename>,
-          <filename>bm5.1.fbc</filename>.
-         </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>../../utils/readnetgen</userinput>
-<prompt> Enter root name for all files.  Both input and</prompt>
-<prompt> output files will all have this prefix:</prompt>
-<userinput>bm5</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-        <para>
-          The boundary conditions on the fault for this benchmark are
-          somewhat complex. The utility program
-          <command>faultcalc</command> creates split node boundary
-          conditions over specified regions, using functions based on
-          second degree polynomials. The <command>readnetgen</command>
-          program has already produced the main input for
-          <command>faultcalc</command> &mdash; split node definitions
-          in <filename>bm5.1.fbc</filename> and nodal coordinates in
-          <filename>bm5.coord</filename>. The file
-          <filename>bm5.fault.par</filename> contains the polynomial
-          coefficients for this benchmark problem. Run
-          <command>faultcalc</command> to get the
-          <filename>bm5.split</filename> file that PyLith needs as
-          input.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>../../utils/faultcalc p=bm5.fault.par n=bm5.coord \
-i=bm5.1.fbc o=bm5.split</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-        <para>
-          The external boundary conditions for this benchmark are also
-          complicated and require computing the displacements for the
-          analytical elastic solution at each finite element node on
-          the external boundaries. The file specifying these boundary
-          conditions, <filename>bm5.bc</filename>, was produced with
-          <command>readnetgen</command> using the
-          <filename>bm5.aux</filename> file (which contains
-          precomputed displacements for the external boundaries for
-          the mesh produced from the <filename>bm5.geo</filename>
-          geometry).
-        </para>
-	<warning>
-          <para>
-            If you make any changes to <filename>bm5.geo</filename> or
-            change the geometry within
-            <application>NetGen</application>, the boundary condition
-            file <filename>bm5.bc</filename> will no longer be
-            correct and you will have to generate one yourself.
-	    Note that it is also possible that a different version
-	    of <application>NetGen</application> may provide a slightly
-	    different mesh, which would also be incompatible with the
-	    provided boundary conditions.
-          </para>
-	</warning>
-      </listitem>
-    </orderedlist>
-  </section>
-
-
-  <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
-  <section>
-    <title>Run the simulation on one processor</title>
-    <para>
-      In this step we will run the simulation on a single processor.
-    </para>
-    
-    <orderedlist numeration="arabic">
-      <listitem>
-	<para>
-          Run <command>tutor.sh</command> for step "run1" with mode
-          "retrieve" to fetch some parameter files from the archive.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>./tutor.sh retrieve run1</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-	<para>
-          In <filename>bm5.fuldat</filename>, we have specified
-          that we want full output at time steps 10, 50, and 100. We
-          define six materials with both elastic and viscoelastic
-          behavior in <filename>bm5.prop</filename>. In
-          <filename>bm5.statevar</filename> we choose to include total
-          stress, total strain, incremental stress, and incremental
-          strain in the output. As defined in
-          <filename>bm5.time</filename>, the simulation will have 100
-          time steps of 0.1 year each.
-        </para>
-      </listitem>
-      <listitem>
-        <para>
-          Run the simulation by executing <userinput>runbm5.sh
-          1</userinput>, where the 1 refers to the number of processors.
-        </para>
-	<tip>
-          <para>
-            All of the input is echoed in the file
-            <filename>bm5.ascii</filename>. You can check to make sure
-            your input is digested correctly by examining this
-            file. For large problems, this file can be quite
-            large. You can suppress creation of this file using the
-            command line argument
-            <option>--scanner.asciiOutput=none</option> flag. On the
-            other hand, for debugging purposes in small problems, you
-            may wish to output everything, including the computed
-            results, in this file using
-            <option>--scanner.asciiOutput=full</option>.
-          </para>
-        </tip>
-	<screen>
-<prompt>bash$ </prompt><userinput>./runbm5.sh 1</userinput>
-        </screen>
-      </listitem>
-    </orderedlist>
-  </section>
-
-  <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
-  <section>
-    <title>Visualize the single processor run</title>
-    <para>
-      Now it is time to visualize the results of the simulation. By
-      default, PyLith writes simulation output using <ulink
-      url="http://help.avs.com/Express/doc/help/reference/dvmac/UCD_Form.htm">
-      <application>AVS</application> <acronym>UCD</acronym>
-      files</ulink>. These can be read by several other
-      visualization tools besides <application>AVS</application>,
-      e.g., <application>ParaView</application> and <application>Iris
-      Explorer</application>. We will use the open-source application
-      <application>ParaView</application> to visualize the results.
-    </para>
-    
-    <orderedlist numeration="arabic">
-      <listitem>
-	<para>
-          If necessary, run <command>tutor.sh</command> for step
-          "viz1" with mode "retrieve" to fetch the simulation output
-          from the archive.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>./tutor.sh retrieve viz1</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-	<para>
-          PyLith does not write complete <acronym>UCD</acronym>
-          files. So the first step is to combine the mesh topology
-          information with the output at a given time step into a
-          complete <acronym>UCD</acronym> file. For example, use
-          <command>cat</command> to merge the nodal coordinates file
-          (<filename>bm5_1.0.mesh.inp</filename>) and the nodal
-          displacements at time step 10 file
-          (<filename>bm5_1.0.mesh.time.00010.inp</filename>) into
-          <filename>bm5_1.0.mesh.t00010.inp</filename>.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>cat bm5_1.0.mesh.inp bm5_1.0.mesh.time.00010.inp \
-> bm5_1.0.mesh.t00010.inp</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-	<para>
-          Start <application>ParaView</application> by executing
-          <command>paraview</command>.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>paraview</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-	<para>
-          Load the <acronym>UCD</acronym> file that you just created
-          by selecting
-          <menuchoice><guimenu>File</guimenu><guimenuitem>Open
-          Data</guimenuitem></menuchoice>. Select the file in the
-          dialog box and the click the <guibutton>Open</guibutton>
-          button. Click the <guibutton>Accept</guibutton> button. You
-          should see a color rendering of the x displacements. You can
-          use the mouse to rotate, translate, and zoom. Your image
-          should look similar to the one in <xref
-          linkend="figure_bm5_xdisp_t10" />.
-        </para>
-	
-	<figure id="figure_bm5_xdisp_t10">
-	  <title>ParaView rendering of displacement in x-direction at
-	  time step 10 (10 yrs after imposed dislocation) for SCEC
-	  Benchmark 5.</title>
-	  <mediaobject>
-	    <imageobject role="fo">
-	      <imagedata fileref="figs/xdisp_t10.eps" format="EPS" />
-	    </imageobject>
-	    <imageobject role="xhtml,html">
-	      <imagedata fileref="figs/xdisp_t10.png" format="PNG" />
-	    </imageobject>
-	  </mediaobject>
-	</figure>
-
-      </listitem>
-      <listitem>
-	<para>
-          In the <guibutton>Display</guibutton> tab, you can change
-          several options, such as including a color bar, coloring a
-          different component, interpolating colors, and changing the
-          color map.
-        </para>
-      </listitem>
-      <listitem>
-        <para>
-          Let's show the displacements as vectors. Click on the
-          calculator icon, and add the three displacement components
-          together. Enter "XDispl*iHat+YDispl*jHat+ZDispl*kHat" in the
-          <guilabel>Calculator</guilabel> box. Note the variable names
-          are available by clicking on the
-          <guibutton>scalars</guibutton> button and the
-          <guibutton>iHat</guibutton>, <guibutton>jHat</guibutton>,
-          <guibutton>kHat</guibutton> buttons are on the right side of
-          the top row. Click on the <guibutton>Accept</guibutton>
-          button. To show the dataset as vectors, click on the
-          <guibutton>glyph</guibutton> button (looks like several
-          dots) in the toolbar. After clicking the
-          <guibutton>Accept</guibutton> button, you should have a
-          vector plot. You can turn on/off other datasets by clicking
-          on the eye icon to the left of the dataset name. If you
-          color the surfaces using the x-displacements field while
-          also making the displacement vectors visible (colored using
-          <literal>property</literal>), you should see an image
-          similar to the one in <xref
-          linkend="figure_bm5_xdisp_vec_t10" />.
-        </para>
-
-	<figure id="figure_bm5_xdisp_vec_t10">
-	  <title>ParaView rendering of displacement in x-direction and
-	  displacement vectors at time step 10 (10 yrs after imposed
-	  dislocation) for SCEC Benchmark 5.</title>
-	  <mediaobject>
-	    <imageobject role="fo">
-	      <imagedata fileref="figs/xdisp_vec_t10.eps" format="EPS" />
-	    </imageobject>
-	    <imageobject role="xhtml,html">
-	      <imagedata fileref="figs/xdisp_vec_t10.png" format="PNG" />
-	    </imageobject>
-	  </mediaobject>
-	</figure>
-
-      </listitem>
-    </orderedlist>
-  </section>
-
-  <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
-  <section>
-    <title>Run the simulation on two processors</title>
-    <para>
-      In this step we will run the simulation on two processors. Even
-      if your machine only has one processor, a "multprocessor" job
-      will run as multiple processes on the single processor. In such
-      cases, the job will run slightly slower than the single
-      processor run, but the two processes will behave independently
-      as if they are on different processors.
-    </para>
-    
-    <orderedlist numeration="arabic">
-      <listitem>
-	<para>
-          Run <command>tutor.sh</command> for step "run2" with mode
-          "retrieve" to make sure all parameter files are available.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>./tutor.sh retrieve run2</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-	<para>
-          The parameter files are the same as those in the single
-          processor run. The <command>runbm5</command> script will
-          automatically take care of duplicating these files so that
-          there is one for each processor.
-        </para>
-      </listitem>
-      <listitem>
-        <para>
-          Run the simulation by executing <command>runbm5.sh
-          2</command>, where the 2 refers to the number of processors.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>./runbm5.sh 2</userinput>
-        </screen>
-      </listitem>
-    </orderedlist>
-  </section>
-
-  <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
-  <section>
-    <title>Visualize the two processor run</title>
-
-    <para>
-      PyLith does not currently support parallel output, so each
-      processor writes its <acronym>UCD</acronym> output to a
-      different file. This means that you need to form complete
-      <acronym>UCD</acronym> files for each processor and then load
-      each one into <application>ParaView</application>. 
-    </para>
-    
-    <orderedlist numeration="arabic">
-      <listitem>
-	<para>
-          If necessary, run <command>tutor.sh</command> for step
-          "viz2" with mode "retrieve" to fetch the simulation output
-          from the archive.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>./tutor.sh retrieve viz2</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-	<para>
-          As in the case of the single processor run, the first step
-          is to combine the mesh topology information with the output
-          at a given time step into a complete <acronym>UCD</acronym>
-          file. Because PyLith writes the output from each processor
-          into a different file, we must run <command>cat</command>
-          twice to create <acronym>UCD</acronym> files for each
-          processor.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>cat bm5_2.0.mesh.inp bm5_2.0.mesh.time.00010.inp
-> bm5_2.0.mesh.t00010.inp</userinput>
-<prompt>bash$ </prompt><userinput>cat bm5_2.1.mesh.inp bm5_2.1.mesh.time.00010.inp
-> bm5_2.1.mesh.t00010.inp</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-	<para>
-          Start <application>ParaView</application> by executing
-          <command>paraview</command>.
-        </para>
-	<screen>
-<prompt>bash$ </prompt><userinput>paraview</userinput>
-        </screen>
-      </listitem>
-      <listitem>
-	<para>
-          Load the <acronym>UCD</acronym> files that you just created
-          by selecting
-          <menuchoice><guimenu>File</guimenu><guimenuitem>Open
-          Data</guimenuitem></menuchoice>. Select the file in the
-          dialog box and the click the <guibutton>Open</guibutton>
-          button. Click the <guibutton>Accept</guibutton> button. You
-          can now visualize the datasets just like you did for the
-          single processor case.
-        </para>
-      </listitem>
-      <listitem>
-        <para>
-          You can merge the datasets from the different processors by
-          selecting
-          <menuchoice><guimenu>Filter</guimenu><guimenuitem>Append</guimenuitem></menuchoice>. Doing
-          so will allow you to operate on the data from all of the
-          processors simultaneously instead of having to repeat any
-          processing for every processor.
-        </para>
-      </listitem>
-    </orderedlist>
-  </section>
-
-
-</section>



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