[cig-commits] r3850 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide: . install
tutorials/tutorialbm5
baagaard at geodynamics.org
baagaard at geodynamics.org
Thu Jun 22 10:38:21 PDT 2006
Author: baagaard
Date: 2006-06-22 10:38:20 -0700 (Thu, 22 Jun 2006)
New Revision: 3850
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/license.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml
Log:
User guide. Added license text provided by Charles. Fixed some more typos in tutorial.
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml 2006-06-22 16:52:53 UTC (rev 3849)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml 2006-06-22 17:38:20 UTC (rev 3850)
@@ -94,7 +94,7 @@
location.
</para>
<screen>
-<prompt>bash$ </prompt>tar -zxvf pylith-0.8-linux-x86.tar.gz
+<prompt>bash$ </prompt><userinput>tar -zxvf pylith-0.8-linux-x86.tar.gz</userinput>
</screen>
</listitem>
<listitem>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/license.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/license.xml 2006-06-22 16:52:53 UTC (rev 3849)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/license.xml 2006-06-22 17:38:20 UTC (rev 3850)
@@ -5,35 +5,33 @@
<title>PyLith Software License</title>
<para>
- ADD LICENSE TEXT HERE
+ Copyright (C) 2004-2006 Rensselaer Polytechnic Institute
</para>
-<!--
-Should 2004 be replaced with 2004-2006?
+ <para>
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without
+ restriction, including without limitation the rights to use, copy,
+ modify, merge, publish, distribute, sublicense, and/or sell copies
+ of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ </para>
-License info currently in source code:
+ <para>
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ </para>
-Copyright 2004 Rensselaer Polytechnic Institute.
-All worldwide rights reserved. A license to use, copy, modify and
-distribute this software for non-commercial research purposes only
-is hereby granted, provided that this copyright notice and
-accompanying disclaimer is not modified or removed from the software.
+ <para>
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
+ </para>
-DISCLAIMER: The software is distributed "AS IS" without any express
-or implied warranty, including but not limited to, any implied
-warranties of merchantability or fitness for a particular purpose
-or any warranty of non-infringement of any current or pending patent
-rights. The authors of the software make no representations about
-the suitability of this software for any particular purpose. The
-entire risk as to the quality and performance of the software is with
-the user. Should the software prove defective, the user assumes the
-cost of all necessary servicing, repair or correction. In
-particular, neither Rensselaer Polytechnic Institute, nor the authors
-of the software are liable for any indirect, special, consequential,
-or incidental damages related to the software, to the maximum extent
-the law permits.
-
--->
-
-
</chapter>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml 2006-06-22 16:52:53 UTC (rev 3849)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml 2006-06-22 17:38:20 UTC (rev 3850)
@@ -98,7 +98,7 @@
choosing.
</para>
<screen>
-<prompt>bash$ </prompt>tar -zxvf pylith-0.8_tutorials.tgz
+<prompt>bash$ </prompt><userinput>tar -zxvf pylith-0.8_tutorials.tgz</userinput>
</screen>
</listitem>
<listitem>
@@ -117,7 +117,7 @@
in the next section.
</para>
<screen>
-<prompt>bash$ </prompt>cd tutorials/scecbm5
+<prompt>bash$ </prompt><userinput>cd tutorials/scecbm5</userinput>
</screen>
</listitem>
@@ -160,9 +160,9 @@
</para>
</tip>
<screen>
-<prompt>bash$ </prompt>cd workarea
-<prompt>bash$ </prompt>cp ../archive/tutor.sh .
-<prompt>bash$ </prompt>./tutor.sh clean all
+<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>
@@ -187,8 +187,8 @@
to clean out old files.
</para>
<screen>
-<prompt>bash$ </prompt>./tutor.sh retrieve mesh
-<prompt>bash$ </prompt>./tutor.sh clean mesh
+<prompt>bash$ </prompt><userinput>./tutor.sh retrieve mesh</userinput>
+<prompt>bash$ </prompt><userinput>./tutor.sh clean mesh</userinput>
</screen>
</listitem>
<listitem>
@@ -206,7 +206,7 @@
<command>ng</command>.
</para>
<screen>
-<prompt>bash$ </prompt>ng
+<prompt>bash$ </prompt><userinput>ng</userinput>
</screen>
</listitem>
<listitem>
@@ -251,7 +251,7 @@
"retrieve" to fetch files from the archive.
</para>
<screen>
-<prompt>bash$ </prompt>./tutor.sh retrieve setup
+<prompt>bash$ </prompt><userinput>./tutor.sh retrieve setup</userinput>
</screen>
</listitem>
<listitem>
@@ -269,7 +269,7 @@
sub-directory.
</para>
<screen>
-<prompt>bash$ </prompt>cd ../../utils
+<prompt>bash$ </prompt><userinput>cd ../../utils</userinput>
</screen>
</listitem>
<listitem>
@@ -306,7 +306,7 @@
</varlistentry>
</variablelist>
<screen>
-<prompt>bash$ </prompt>make
+<prompt>bash$ </prompt><userinput>make</userinput>
</screen>
<tip>
<para>
@@ -318,6 +318,15 @@
</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>
@@ -335,10 +344,10 @@
<filename>bm5.1.fbc</filename>.
</para>
<screen>
-<prompt>bash$ </prompt>../../utils/readnetgen
-<prompt>ADD CORRECT PROMPT HERE</prompt>
-<prompt></prompt>
-<prompt></prompt>bm5
+<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>
@@ -352,14 +361,14 @@
<command>faultcalc</command> — 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
+ <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>../../utils/faultcalc p=bm5-fault.par n=bm5.coord i=bm5.1.fbc o=bm5.split
+<prompt>bash$ </prompt><userinput>../../utils/faultcalc p=bm5.fault.par n=bm5.coord i=bm5.1.fbc o=bm5.split</userinput>
</screen>
</listitem>
<listitem>
@@ -403,7 +412,7 @@
"retrieve" to fetch some parameter files from the archive.
</para>
<screen>
-<prompt>bash$ </prompt>./tutor.sh retrieve run1
+<prompt>bash$ </prompt><userinput>./tutor.sh retrieve run1</userinput>
</screen>
</listitem>
<listitem>
@@ -440,7 +449,7 @@
</para>
</tip>
<screen>
-<prompt>bash$ </prompt>./runbm5.sh 1
+<prompt>bash$ </prompt><userinput>./runbm5.sh 1</userinput>
</screen>
</listitem>
</orderedlist>
@@ -469,7 +478,7 @@
from the archive.
</para>
<screen>
-<prompt>bash$ </prompt>./tutor.sh retrieve viz1
+<prompt>bash$ </prompt><userinput>./tutor.sh retrieve viz1</userinput>
</screen>
</listitem>
<listitem>
@@ -485,7 +494,7 @@
<filename>bm5_1.0.mesh.t00010.inp</filename>.
</para>
<screen>
-<prompt>bash$ </prompt>cat bm5_1.0.mesh.inp bm5_1.0.mesh.time.00010.inp > bm5_1.0.mesh.t00010.inp
+<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>
@@ -494,7 +503,7 @@
<command>paraview</command>.
</para>
<screen>
-<prompt>bash$ </prompt>paraview
+<prompt>bash$ </prompt><userinput>paraview</userinput>
</screen>
</listitem>
<listitem>
@@ -558,7 +567,7 @@
"retrieve" to make sure all parameter files are available.
</para>
<screen>
-<prompt>bash$ </prompt>./tutor.sh retrieve run2
+<prompt>bash$ </prompt><userinput>./tutor.sh retrieve run2</userinput>
</screen>
</listitem>
<listitem>
@@ -575,7 +584,7 @@
2</command>, where the 2 refers to the number of processors.
</para>
<screen>
-<prompt>bash$ </prompt>./runbm5.sh 2
+<prompt>bash$ </prompt><userinput>./runbm5.sh 2</userinput>
</screen>
</listitem>
</orderedlist>
@@ -601,7 +610,7 @@
from the archive.
</para>
<screen>
-<prompt>bash$ </prompt>./tutor.sh retrieve viz2
+<prompt>bash$ </prompt><userinput>./tutor.sh retrieve viz2</userinput>
</screen>
</listitem>
<listitem>
@@ -615,8 +624,10 @@
processor.
</para>
<screen>
-<prompt>bash$ </prompt>cat bm5_1.0.mesh.inp bm5_1.0.mesh.time.00010.inp > bm5_1.0.mesh.t00010.inp
-<prompt>bash$ </prompt>cat bm5_1.1.mesh.inp bm5_1.1.mesh.time.00010.inp > bm5_1.1.mesh.t00010.inp
+<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>
@@ -625,7 +636,7 @@
<command>paraview</command>.
</para>
<screen>
-<prompt>bash$ </prompt>paraview
+<prompt>bash$ </prompt><userinput>paraview</userinput>
</screen>
</listitem>
<listitem>
@@ -637,11 +648,19 @@
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. By making the datasets from the
- different processors all visible you can examine the
- aggregate output.
+ 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>
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