[cig-commits] r3826 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide: runpylith
tutorials
baagaard at geodynamics.org
baagaard at geodynamics.org
Tue Jun 20 15:03:22 PDT 2006
Author: baagaard
Date: 2006-06-20 15:03:21 -0700 (Tue, 20 Jun 2006)
New Revision: 3826
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5.xml
Log:
Worked on documentation of command-line arguments.
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml 2006-06-20 19:04:01 UTC (rev 3825)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml 2006-06-20 22:03:21 UTC (rev 3826)
@@ -190,12 +190,21 @@
<section>
<title>Command-line Arguments</title>
<para>
- PyLith's command-line arguments fall into two categories: Pyre
- properties and facilities, and PETSc settings.
+ Command-line arugments associated with running PyLith fall into
+ three categories: MPI settings, Pyre properties and facilities,
+ and PETSc settings.
</para>
<!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
<section>
+ <title>MPI Settings</title>
+ <para>
+
+ </para>
+ </section>
+
+ <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
+ <section>
<title>Properties and Facilities</title>
<para>
PyLith gathers many simulation parameters and settings using
@@ -211,27 +220,100 @@
<para>
In the current version of PyLith, all of the properties are
associated with the "scanner" component. You can get a list of
- all of these properties by running PyLith with the
- "--scanner.help-properties" command-line argument.
+ all of these properties along with a description of what they
+ do by running PyLith with the
+ <option>--scanner.help-properties</option> command-line
+ argument.
</para>
- <para>
- ADD SOME EXAMPLES HERE
- </para>
- <para>
- CHARLES- ADD DOCUMENTATION FOR EACH OF THE SCANNER PROPERTIES
- BY ADDING A LINES IN THE INVENTORY OF THE FORM
- property.meta['tip']="yada yada yada."
- </para>
+
+ <example id="example_pylith_properties">
+ <title>Setting scanner properties from the command line.</title>
+ <screen>
+ <cmdsynopsis>
+ <command>mpirun</command>
+ <arg choice="plain">-np <replaceable>1</replaceable></arg>
+ <arg choice="plain">pylith3dapp.py</arg>
+ <arg>--scanner.help-properties</arg><sbr/>
+ <arg>--scanner.asciiOutput=<replaceable>none</replaceable></arg>
+ <arg>--scanner.title=<replaceable>"My simulation"</replaceable></arg>
+ </cmdsynopsis>
+ </screen>
+ </example>
+
</section>
<!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
<section>
<title>PETSc Settings</title>
<para>
- ADD STUFF HERE
+ PyLith relies on PETSc for the linear algebra
+ computations. Many of PETSc options can be set using
+ command-line arguments. The ones of primary interest in the
+ case of PyLith are shown in <xref
+ linkend="table_petsc_options" />.
</para>
+
+ <table id="table_petsc_options">
+ <title>Useful command-line arguments for setting PETSc options.</title>
+
+ <tgroup cols="2" align="left">
+ <thead>
+ <row>
+ <entry>Argument</entry>
+ <entry>Description</entry>
+ </row>
+ </thead>
+ <tbody>
+ <row>
+ <entry><cmdsynopsis>
+ <arg choice="plain">-log_summary</arg>
+ </cmdsynopsis></entry>
+ <entry>Print logging objects and events.</entry>
+ </row>
+ <row>
+ <entry><cmdsynopsis>
+ <arg choice="plain">-sub_pc_type
+ <replaceable>ilu</replaceable></arg>
+ </cmdsynopsis></entry>
+ <entry>Set preconditioner to incomplete factorization. See
+ PETSc documentation for a list of all preconditioners.</entry>
+ </row>
+ <row>
+ <entry><cmdsynopsis>
+ <arg choice="plain">-ksp_monitor</arg>
+ </cmdsynopsis></entry>
+ <entry>Dump preconditioned residual norm to stdout.</entry>
+ </row>
+ <row>
+ <entry><cmdsynopsis>
+ <arg choice="plain">-ksp_view</arg>
+ </cmdsynopsis></entry>
+ <entry>Print linear solver parameters.</entry>
+ </row>
+ <row>
+ <entry><cmdsynopsis>
+ <arg choice="plain">-ksp_rtol
+ <replaceable>1.0e-09</replaceable></arg>
+ </cmdsynopsis></entry>
+ <entry>Relative decrease in residual norm</entry>
+ </row>
+ </tbody>
+ </tgroup>
+ </table>
+
</section>
</section>
+ <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
+ <section>
+ <title>Setting Pyre properties using pml files</title>
+ <para>
+ PyLith's Pyre properties can also be set using
+ <filename>pml</filename> files. These are <acronym>XML</acronym>
+ files that follow a special Pyre schema. ADD STUFF HERE
+ </para>
+
+ </section>
+
</chapter>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5.xml 2006-06-20 19:04:01 UTC (rev 3825)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5.xml 2006-06-20 22:03:21 UTC (rev 3826)
@@ -160,7 +160,7 @@
<listitem>
<para>
Return to the <filename>scecbm5/workarea</filename>
- directory. Run <command>tutor.py</command> for step "mesh"
+ 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"
@@ -220,7 +220,7 @@
<orderedlist numeration="arabic">
<listitem>
<para>
- Run <command>tutor.py</command> for step "setup" with mode
+ Run <command>tutor.sh</command> for step "setup" with mode
"retrieve" to fetch files from the archive.
</para>
</listitem>
@@ -310,8 +310,8 @@
<filename>bm5.coord</filename>. The file
<filename>bm5-fault.par</filename> contains the polynomial
coefficients for this benchmark problem. Execute the command
- <command>faultcalc p=bm5-fault.par n=bm5.coord i=bm5.1.fbc
- o=bm5.split</command>. This will give you the
+ <userinput>faultcalc p=bm5-fault.par n=bm5.coord i=bm5.1.fbc
+ o=bm5.split</userinput>. This will give you the
<filename>bm5.split</filename> file that PyLith needs as
input.
</para>
@@ -372,8 +372,8 @@
</listitem>
<listitem>
<para>
- Run the simulation by executing <command>runbm5.sh
- 1</command>, where the 1 refers to the number of processors.
+ Run the simulation by executing <userinput>runbm5.sh
+ 1</userinput>, where the 1 refers to the number of processors.
</para>
<tip>
<para>
@@ -383,11 +383,11 @@
file. For large problems, this file can be quite
large. You can suppress creation of this file using the
command line argument
- <option>-pl3dscan.asciiOutput=none</option> flag. On the
+ <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>-pl3dscan.asciiOutput=full</option>.
+ <option>--scanner.asciiOutput=full</option>.
</para>
</tip>
</listitem>
@@ -426,9 +426,9 @@
(<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>, <command>cat
+ <filename>bm5_1.0.mesh.t00010.inp</filename>, <userinput>cat
bm5_1.0.mesh.inp bm5_1.0.mesh.time.00010.inp >
- bm5_1.0.mesh.t00010.inp</command>.
+ bm5_1.0.mesh.t00010.inp</userinput>.
</para>
</listitem>
<listitem>
@@ -545,11 +545,11 @@
(<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>, <command>cat
+ <filename>bm5_1.0.mesh.t00010.inp</filename>, <userinput>cat
bm5_1.0.mesh.inp bm5_1.0.mesh.time.00010.inp >
- bm5_1.0.mesh.t00010.inp</command>. Repeat this for processor
- 1, <command>cat bm5_1.1.mesh.inp bm5_1.1.mesh.time.00010.inp
- > bm5_1.1.mesh.t00010.inp</command>.
+ bm5_1.0.mesh.t00010.inp</userinput>. Repeat this for processor
+ 1, <userinput>cat bm5_1.1.mesh.inp bm5_1.1.mesh.time.00010.inp
+ > bm5_1.1.mesh.t00010.inp</userinput>.
</para>
</listitem>
<listitem>
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