[cig-commits] r7995 - in short/3D/PyLith/trunk: doc/userguide doc/userguide/runpylith examples/3d/hex8 examples/3d/tet4 tests/2d/quad4b tests/3d/tet4

brad at geodynamics.org brad at geodynamics.org
Thu Sep 20 16:25:28 PDT 2007 

Author: brad
Date: 2007-09-20 16:25:28 -0700 (Thu, 20 Sep 2007)
New Revision: 7995

Modified:
   short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
   short/3D/PyLith/trunk/doc/userguide/userguide.lyx
   short/3D/PyLith/trunk/examples/3d/hex8/pylithapp.cfg
   short/3D/PyLith/trunk/examples/3d/tet4/pylithapp.cfg
   short/3D/PyLith/trunk/tests/2d/quad4b/dislocation.cfg
   short/3D/PyLith/trunk/tests/3d/tet4/dislocation.cfg
Log:
Reduced gmres_max_it to reasonable number to prevent using lots of extra memory. Added table to user guide with recommended PETSc options for quasi-static simulations.

Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx	2007-09-20 21:24:47 UTC (rev 7994)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx	2007-09-20 23:25:28 UTC (rev 7995)
@@ -1,5 +1,5 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 245
+#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
 \begin_document
 \begin_header
 \textclass book
@@ -8,13 +8,21 @@
 \end_preamble
 \language english
 \inputencoding latin1
-\fontscheme default
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
 \graphics default
 \paperfontsize default
 \spacing single
 \papersize default
 \use_geometry true
 \use_amsmath 1
+\use_esint 0
 \cite_engine basic
 \use_bibtopic false
 \paperorientation portrait
@@ -32,6 +40,7 @@
 \paperpagestyle default
 \tracking_changes false
 \output_changes false
+\author "" 
 \end_header
 
 \begin_body
@@ -67,12 +76,14 @@
  faults, and output (for subsets of the mesh).
  This information can be provided using the PyLith mesh ASCII format (See
  Chapter 
-\begin_inset LatexCommand \ref{cha:Tutorials}
+\begin_inset LatexCommand ref
+reference "cha:Tutorials"
 
 \end_inset
 
  for examples and Section 
-\begin_inset LatexCommand \ref{sec:MeshIOAscii}
+\begin_inset LatexCommand ref
+reference "sec:MeshIOAscii"
 
 \end_inset
 
@@ -94,12 +105,14 @@
  Arbitrarily complex spatial variations in boundary and fault conditions
  and material properties may be given in the spatial database (See Chapter
  
-\begin_inset LatexCommand \ref{cha:Tutorials}
+\begin_inset LatexCommand ref
+reference "cha:Tutorials"
 
 \end_inset
 
  for examples and Appendix 
-\begin_inset LatexCommand \ref{sec:Spatialdata:SimpleIOAscii}
+\begin_inset LatexCommand ref
+reference "sec:Spatialdata:SimpleIOAscii"
 
 \end_inset
 
@@ -111,7 +124,8 @@
 \end_layout
 
 \begin_layout Standard
-\begin_inset LatexCommand \label{sec:setting:parameters}
+\begin_inset LatexCommand label
+name "sec:setting:parameters"
 
 \end_inset
 
@@ -421,11 +435,22 @@
 .
  The ones of primary interest in the case of PyLith are shown in Table\InsetSpace ~
 
-\begin_inset LatexCommand \ref{tab:Useful-command-line-arguments}
+\begin_inset LatexCommand ref
+reference "tab:petsc:options:defaults"
 
 \end_inset
 
 .
+ In many quasi-static simulations, runtime can be reduced by replacing the
+ Jacobi preconditioner with Additive Schwarz with Gram-Schmidt orthogonalization
+ (see Table\InsetSpace ~
+
+\begin_inset LatexCommand ref
+reference "tab:petsc:options:quasistatic"
+
+\end_inset
+
+).
 \end_layout
 
 \begin_layout Standard
@@ -651,9 +676,13 @@
 
 \end_layout
 
-\begin_layout Caption
-\begin_inset LatexCommand \label{tab:Useful-command-line-arguments}
+\begin_layout Standard
+\begin_inset Caption
 
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:petsc:options:defaults"
+
 \end_inset
 
 Useful command-line arguments for setting PETSc options.
@@ -664,6 +693,218 @@
 
 \end_layout
 
+\end_inset
+
+
+\begin_inset Float table
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align center
+\begin_inset Tabular
+<lyxtabular version="3" rows="5" columns="3">
+<features>
+<column alignment="left" valignment="top" leftline="true" width="0.9in">
+<column alignment="center" valignment="middle" leftline="true" width="0.8in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="4in">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\series bold
+Property
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\series bold
+Value
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\series bold
+Description
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+pc_type
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\shape italic
+asm
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Additive Schwarz method
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+ksp_max_it
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\emph on
+100
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Maximum number of iterations.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+ksp_gmres_restart
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+50
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Number of iterations after which Gram-Schmidt orthogonalization is restarted
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\family typewriter
+ksp_rtol
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+
+\shape italic
+1.0e-08
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Convergence tolerance for relative decrease in residual norm.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:petsc:options:quasistatic"
+
+\end_inset
+
+PETSc options that often result in improved performance in quasi-static
+ problems.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
 \begin_layout Section
 Mesh Information
 \end_layout
@@ -674,7 +915,8 @@
  a GMV file and an accompanying Pset file from LaGriT, or by specifying
  the information in PyLith mesh ASCII format.
  See Chapter 
-\begin_inset LatexCommand \ref{cha:Tutorials}
+\begin_inset LatexCommand ref
+reference "cha:Tutorials"
 
 \end_inset
 
@@ -683,28 +925,33 @@
 
 \begin_layout Standard
 PyLith supports linear cells in 1D (Figure 
-\begin_inset LatexCommand \ref{fig:1D-linear-elements}
+\begin_inset LatexCommand ref
+reference "fig:1D-linear-elements"
 
 \end_inset
 
 ), 2D (Figure 
-\begin_inset LatexCommand \ref{fig:2D-linear-elements}
+\begin_inset LatexCommand ref
+reference "fig:2D-linear-elements"
 
 \end_inset
 
 ), and 3D (Figure 
-\begin_inset LatexCommand \ref{fig:3D-linear-elements}
+\begin_inset LatexCommand ref
+reference "fig:3D-linear-elements"
 
 \end_inset
 
 ).
  The vertex ordering must follow the convention shown in Figures 
-\begin_inset LatexCommand \ref{fig:1D-linear-elements}
+\begin_inset LatexCommand ref
+reference "fig:1D-linear-elements"
 
 \end_inset
 
 -
-\begin_inset LatexCommand \ref{fig:3D-linear-elements}
+\begin_inset LatexCommand ref
+reference "fig:3D-linear-elements"
 
 \end_inset
 
@@ -731,12 +978,14 @@
  For a mesh with a single material type, there will only be a single label
  for every cell in the mesh.
  See Chapters 
-\begin_inset LatexCommand \ref{cha:material:models}
+\begin_inset LatexCommand ref
+reference "cha:material:models"
 
 \end_inset
 
  and 
-\begin_inset LatexCommand \ref{cha:boundary:interface:conditions}
+\begin_inset LatexCommand ref
+reference "cha:boundary:interface:conditions"
 
 \end_inset
 
@@ -763,12 +1012,21 @@
  
 \end_layout
 
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
 Linear bar cell available for 1D problems.
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
-\begin_inset LatexCommand \label{fig:1D-linear-elements}
+\begin_inset LatexCommand label
+name "fig:1D-linear-elements"
 
 \end_inset
 
@@ -825,13 +1083,22 @@
 
 \end_layout
 
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
 Linear cells available for 2D problems are the triangle (left) and the quadrilat
 eral (right).
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
-\begin_inset LatexCommand \label{fig:2D-linear-elements}
+\begin_inset LatexCommand label
+name "fig:2D-linear-elements"
 
 \end_inset
 
@@ -888,10 +1155,14 @@
 
 \end_layout
 
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
 Linear cells available for 3D problems are the tetrahedron (left) and the
  hexahedron (right).
-\begin_inset LatexCommand \label{fig:3D-linear-elements}
+\begin_inset LatexCommand label
+name "fig:3D-linear-elements"
 
 \end_inset
 
@@ -903,6 +1174,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Section
 Databases for Boundaries, Interfaces, and Material Properties
 \end_layout
@@ -920,7 +1196,8 @@
 \family default
  file is used to associate boundary condition types and spatial databases
  with each vertex group (see Chapter 
-\begin_inset LatexCommand \ref{cha:boundary:interface:conditions}
+\begin_inset LatexCommand ref
+reference "cha:boundary:interface:conditions"
 
 \end_inset
 
@@ -931,7 +1208,8 @@
 \family default
  file is used to associate material types and spatial databases with cells
  identified by the material identifier (see Figure 
-\begin_inset LatexCommand \ref{fig:Material-models}
+\begin_inset LatexCommand ref
+reference "fig:Material-models"
 
 \end_inset
 
@@ -974,7 +1252,8 @@
  This might be the case, for example, if the material properties are provided
  by a database of seismic velocities and densities.
  See Section 
-\begin_inset LatexCommand \ref{sec:Spatialdata:SimpleIOAscii}
+\begin_inset LatexCommand ref
+reference "sec:Spatialdata:SimpleIOAscii"
 
 \end_inset
 
@@ -1002,7 +1281,8 @@
  This sort of condition might be used, for example, to specify the variation
  of slip on a fault plane.
  The examples discussed in Chapter 
-\begin_inset LatexCommand \ref{cha:Tutorials}
+\begin_inset LatexCommand ref
+reference "cha:Tutorials"
 
 \end_inset
 

Modified: short/3D/PyLith/trunk/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/userguide.lyx	2007-09-20 21:24:47 UTC (rev 7994)
+++ short/3D/PyLith/trunk/doc/userguide/userguide.lyx	2007-09-20 23:25:28 UTC (rev 7995)
@@ -1,5 +1,5 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 245
+#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
 \begin_document
 \begin_header
 \textclass book
@@ -12,13 +12,21 @@
 \end_preamble
 \language english
 \inputencoding latin1
-\fontscheme default
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
 \graphics default
 \paperfontsize default
 \spacing single
 \papersize default
 \use_geometry true
 \use_amsmath 1
+\use_esint 0
 \cite_engine natbib_authoryear
 \use_bibtopic false
 \paperorientation portrait
@@ -36,6 +44,7 @@
 \paperpagestyle plain
 \tracking_changes false
 \output_changes false
+\author "" 
 \end_header
 
 \begin_body
@@ -91,7 +100,7 @@
 \end_layout
 
 \begin_layout Author
-© California Institute of Technology
+© California Institute of Technology
 \newline
 Version 1.0
 \end_layout
@@ -127,7 +136,7 @@
 \end_inset
 
 
-\begin_inset LatexCommand \tableofcontents{}
+\begin_inset LatexCommand tableofcontents
 
 \end_inset
 
@@ -269,8 +278,11 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Williams:etal:2005"
 
-\bibitem {Williams:etal:2005}
+\end_inset
+
 Williams, C.A., B.
  Aagaard, M.G.
  Knepley (2005), Development of software for studying earthquakes across
@@ -285,8 +297,11 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Williams:2006"
 
-\bibitem {Williams:2006}
+\end_inset
+
 Williams, C.A.
  (2006), Development of a package for modeling stress in the lithosphere,
  
@@ -304,8 +319,11 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Aagaard:etal:2001a"
 
-\bibitem {Aagaard:etal:2001a}
+\end_inset
+
 Aagaard, B.T., J.F.
  Hall, and T.H.
  Heaton (2001), Characterization of near-source ground motions with earthquake
@@ -317,8 +335,11 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Aagaard:etal:2001b"
 
-\bibitem {Aagaard:etal:2001b}
+\end_inset
+
 Aagaard, B.T., T.H.
  Heaton, and J.F.
  Hall (2001), Dynamic earthquake ruptures in the presence of lithostatic
@@ -331,8 +352,11 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Brune:1970"
 
-\bibitem {Brune:1970}
+\end_inset
+
 Brune, J.N.
  (1970), Tectonic stress and spectra of seismic shear waves from earthquakes,
  
@@ -343,8 +367,11 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+key "Kojic:Bathe:1987"
 
-\bibitem {Kojic:Bathe:1987}
+\end_inset
+
 Kojic, M.
  and K.-J.
  Bathe (1987), The `Effective Stress-Function' Algorithm for Thermo-Elasto-Plast
@@ -364,8 +391,12 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "7"
+key "Zienkiewicz:Taylor:2000"
 
-\bibitem [7]{Zienkiewicz:Taylor:2000}
+\end_inset
+
 Zienkiewicz, O.C.
  and R.L.
  Taylor (2000), 
@@ -376,8 +407,12 @@
 \end_layout
 
 \begin_layout Bibliography
+\begin_inset LatexCommand bibitem
+label "8"
+key "Taylor:2003"
 
-\bibitem [8]{Taylor:2003}
+\end_inset
+
 Taylor, R.L.
  (2003), `FEAP--A Finite Element Analysis Program', 
 \shape italic

Modified: short/3D/PyLith/trunk/examples/3d/hex8/pylithapp.cfg
===================================================================
--- short/3D/PyLith/trunk/examples/3d/hex8/pylithapp.cfg	2007-09-20 21:24:47 UTC (rev 7994)
+++ short/3D/PyLith/trunk/examples/3d/hex8/pylithapp.cfg	2007-09-20 23:25:28 UTC (rev 7995)
@@ -88,5 +88,5 @@
 ksp_monitor = true
 ksp_view = true
 #log_summary = true
-ksp_max_it = 500
-ksp_gmres_restart = 5000
+ksp_max_it = 100
+ksp_gmres_restart = 50

Modified: short/3D/PyLith/trunk/examples/3d/tet4/pylithapp.cfg
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/pylithapp.cfg	2007-09-20 21:24:47 UTC (rev 7994)
+++ short/3D/PyLith/trunk/examples/3d/tet4/pylithapp.cfg	2007-09-20 23:25:28 UTC (rev 7995)
@@ -93,5 +93,5 @@
 ksp_monitor = true
 ksp_view = true
 #log_summary = true
-ksp_max_it = 500
-ksp_gmres_restart = 5000
+ksp_max_it = 100
+ksp_gmres_restart = 50

Modified: short/3D/PyLith/trunk/tests/2d/quad4b/dislocation.cfg
===================================================================
--- short/3D/PyLith/trunk/tests/2d/quad4b/dislocation.cfg	2007-09-20 21:24:47 UTC (rev 7994)
+++ short/3D/PyLith/trunk/tests/2d/quad4b/dislocation.cfg	2007-09-20 23:25:28 UTC (rev 7995)
@@ -114,7 +114,7 @@
 [pylithapp.petsc]
 pc_type = asm
 ksp_rtol = 1.0e-8
-ksp_gmres_restart = 5000
+ksp_gmres_restart = 50
 
 # ----------------------------------------------------------------------
 # output

Modified: short/3D/PyLith/trunk/tests/3d/tet4/dislocation.cfg
===================================================================
--- short/3D/PyLith/trunk/tests/3d/tet4/dislocation.cfg	2007-09-20 21:24:47 UTC (rev 7994)
+++ short/3D/PyLith/trunk/tests/3d/tet4/dislocation.cfg	2007-09-20 23:25:28 UTC (rev 7995)
@@ -93,8 +93,8 @@
 ksp_monitor = true
 ksp_view = true
 log_summary = true
-ksp_max_it = 500
-ksp_gmres_restart = 5000
+ksp_max_it = 100
+ksp_gmres_restart = 50
 
 # ----------------------------------------------------------------------
 # output

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