[cig-commits] r13472 - in doc/snac: . figures

echoi at geodynamics.org echoi at geodynamics.org
Mon Dec 8 05:31:14 PST 2008 

Author: echoi
Date: 2008-12-08 05:31:14 -0800 (Mon, 08 Dec 2008)
New Revision: 13472

Added:
   doc/snac/figures/EP_hierarchy_StG.pdf
Modified:
   doc/snac/snac.lyx
Log:
1. Added a new figure to Sec. 1.2.3.
2. Some work on Ch. 2 and Sec. 3.1.



Added: doc/snac/figures/EP_hierarchy_StG.pdf
===================================================================
--- doc/snac/figures/EP_hierarchy_StG.pdf	                        (rev 0)
+++ doc/snac/figures/EP_hierarchy_StG.pdf	2008-12-08 13:31:14 UTC (rev 13472)
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Modified: doc/snac/snac.lyx
===================================================================
--- doc/snac/snac.lyx	2008-12-08 12:22:56 UTC (rev 13471)
+++ doc/snac/snac.lyx	2008-12-08 13:31:14 UTC (rev 13472)
@@ -1649,10 +1649,17 @@
 \end_layout
 
 \begin_layout Standard
-The two diagrams below outline the entry points set up in SNAC.
+The diagram below (Fig.
+ 
+\begin_inset LatexCommand ref
+reference "fig:EP_hierarchy"
+
+\end_inset
+
+) outlines the entry points set up in SNAC.
  It is represented as a tree-like hierarchy: if a ``hook'' calls other entry
  points, either in its own function or other normal functions it calls,
- the called entry points are below and offset to the right of that hook.
+ the called entry points are offset to the right of that hook.
  
 \end_layout
 
@@ -1666,12 +1673,24 @@
 
 \begin_layout Standard
 \begin_inset Graphics
-	filename figures/EntryPointHierarchyinStGermain.png
+	filename figures/EP_hierarchy_StG.pdf
 	lyxscale 40
 
 \end_inset
 
 
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "fig:EP_hierarchy"
+
+\end_inset
+
+A tree-like diagram showing the hierarchy of entry points set up in SNAC
+ together with hooked-up functions in each entry point.
+ The functions defined by StGermain are marked in blue while those defined
+ in SNAC are in red.
 \end_layout
 
 \end_inset
@@ -1679,6 +1698,11 @@
 
 \end_layout
 
+\end_inset
+
+
+\end_layout
+
 \begin_layout Section
 \begin_inset LatexCommand label
 name "sec:StGermain"
@@ -1758,7 +1782,7 @@
 \end_inset
 
 .
- First, you will need to have MPI available on your machine.
+ First, you will need to have MPI and Python available on your machine.
  
 \end_layout
 
@@ -1775,8 +1799,7 @@
 \end_layout
 
 \begin_layout Standard
-SNAC has been tested on [TODO -- is this an accurate list?] Linux and Mac
- OS X platforms.
+SNAC has been tested on Linux and Mac OS X platforms.
  
 \end_layout
 
@@ -1803,19 +1826,84 @@
 
 \begin_layout Standard
 This is done by setting following environment variables so the VMake build
- system knows where to find MPICH: 
+ system knows where to find MPICH.
 \end_layout
 
+\begin_layout Standard
+In bash,
+\end_layout
+
 \begin_layout LyX-Code
-In bash: export MPI_DIR="/usr/local/mpich" 
+export CXX=g++ 
 \end_layout
 
 \begin_layout LyX-Code
-In tcsh: setenv MPI_DIR /usr/local/mpich 
+export MPI_DIR=${HOME}/opt/mpich-1.2.7p1 
 \end_layout
 
+\begin_layout LyX-Code
+export MPI_BINDIR=${MPI_DIR}/bin 
+\end_layout
+
+\begin_layout LyX-Code
+export MPI_LIBDIR=${MPI_DIR}/lib 
+\end_layout
+
+\begin_layout LyX-Code
+export MPI_INCDIR=${MPI_DIR}/include 
+\end_layout
+
+\begin_layout LyX-Code
+export MPI_RUN=${MPI_BINDIR}/mpirun 
+\end_layout
+
+\begin_layout LyX-Code
+export PATH=${MPI_BINDIR}:${PATH} 
+\end_layout
+
+\begin_layout LyX-Code
+export LD_LIBRATY_PATH=${MPI_LIBDIR}:${LD_LIBRATY_PATH}
+\end_layout
+
 \begin_layout Standard
-Again, where /usr/local/mpich is the path where mpich was installed.
+In tcsh,
+\end_layout
+
+\begin_layout LyX-Code
+setenv CXX g++ 
+\end_layout
+
+\begin_layout LyX-Code
+setenv MPI_DIR ${HOME}/opt/mpich-1.2.7p1 
+\end_layout
+
+\begin_layout LyX-Code
+setenv MPI_BINDIR ${MPI_DIR}/bin 
+\end_layout
+
+\begin_layout LyX-Code
+setenv MPI_LIBDIR ${MPI_DIR}/lib 
+\end_layout
+
+\begin_layout LyX-Code
+setenv MPI_INCDIR ${MPI_DIR}/include 
+\end_layout
+
+\begin_layout LyX-Code
+setenv MPI_RUN ${MPI_BINDIR}/mpirun 
+\end_layout
+
+\begin_layout LyX-Code
+setenv PATH ${MPI_BINDIR}:${PATH} 
+\end_layout
+
+\begin_layout LyX-Code
+setenv LD_LIBRATY_PATH ${MPI_LIBDIR}:${LD_LIBRATY_PATH}
+\end_layout
+
+\begin_layout Standard
+${HOME}/opt/mpich-1.2.7p1 should be appropriately replaced with the actual
+ path where mpich is installed.
  
 \end_layout
 
@@ -1839,7 +1927,14 @@
 \end_layout
 
 \begin_layout Enumerate
-Tell the build system where libraries are 
+Tell the build system where libraries are.
+ See the suggested environmental variables below (Box 
+\begin_inset LatexCommand ref
+reference "box:VMakeEnvVars"
+
+\end_inset
+
+).
 \end_layout
 
 \begin_layout Enumerate
@@ -1909,10 +2004,19 @@
 Using SNAC
 \end_layout
 
+\begin_layout LyX-Code
+Snac input.xml
+\end_layout
+
 \begin_layout Standard
-[TODO -- note: Nothing was under this section head.]
+Running SNAC in parallel depends on the system configuration, but here is
+ an example
 \end_layout
 
+\begin_layout LyX-Code
+mpirun `which Snac` ./input.xml > log.stdout
+\end_layout
+
 \begin_layout Section
 Changing Parameters 
 \end_layout
@@ -3445,8 +3549,12 @@
 \end_layout
 
 \begin_layout Standard
-To visualize your results, it is recommended that you use the open source
- Open Visualization Data Explorer, better known as OpenDX.
+SNAC writes binary output files and it is necessary to convert them to a
+ VTK file format to visualize them.
+ Two such converting programs are provided.
+ One is for the open source Open Visualization Data Explorer, better known
+ as OpenDX.
+ The other is used to generate VTK files.
  Both the software and tutorials are available from the 
 \begin_inset LatexCommand htmlurl
 name "OpenDX website"

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