[cig-commits] r4715 - mc/3D/CitcomS/trunk/doc/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Fri Oct 6 10:17:19 PDT 2006
Author: tan2
Date: 2006-10-06 10:17:18 -0700 (Fri, 06 Oct 2006)
New Revision: 4715
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
Some minor edits
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-06 01:19:57 UTC (rev 4714)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-06 17:17:18 UTC (rev 4715)
@@ -2462,12 +2462,12 @@
can be executed without any command line options and will run a regional
model with default parameters.
It can also run a full spherical model if correct parameters are set (see
-
+ Section
\begin_inset LatexCommand \vref{sec:Cookbook-1:-Global}
\end_inset
-for an example).
+ for an example).
\end_layout
\begin_layout Standard
@@ -2489,7 +2489,7 @@
\begin_layout Standard
Most of the properties you will set using CitComS.py have identical names
- as the parameters for the old CitComS, which is described in
+ as the parameters for the old CitComS, which is described in Appendix
\begin_inset LatexCommand \vref{cha:Appendix-A:-Facilities,}
\end_inset
@@ -2628,8 +2628,8 @@
\begin_layout Description
\begin_inset Graphics
filename graphics/c_fig3.jpg
+ lyxscale 75
width 75page%
- keepAspectRatio
\end_inset
@@ -3263,8 +3263,8 @@
\end_layout
\begin_layout Standard
-Once you have run CitComS, you should have a series of output files (potentially
- spread throughout the file systems of your Beowulf).
+Once you have run CitComS.py, you should have a series of output files (potential
+ly spread throughout the file systems of your Beowulf).
You will have to retrieve and combine the data for the time step (or age)
of interest.
To visualize your results, it is recommended that you use the open source
@@ -3275,20 +3275,21 @@
\end_inset
.
+ If you are uisng Linux, OpenDX is usually avaiable as package
+\family typewriter
+dx
+\family default
+ or
+\family typewriter
+opendx
+\family default
+ in your distribution.
If you are using Mac OS X, OpenDX is available via
\begin_inset LatexCommand \htmlurl[Fink]{http://fink.sourceforge.net/}
\end_inset
.
- However, if the installation proves to be difficult, a binary version is
- available (for a fee) from
-\begin_inset LatexCommand \htmlurl[VIS Inc.]{http://www.vizsolutions.com/macdx.html}
-
-\end_inset
-
-.
-
\end_layout
\begin_layout Section
@@ -3296,7 +3297,7 @@
\end_layout
\begin_layout Standard
-Generally, the results from your CitComS run will be distributed on disks
+Generally, the results from your CitComS.py run will be distributed on disks
attached to individual nodes of your Beowulf cluster.
The output files are written in each node under the directory that you
specified as the
@@ -3364,13 +3365,17 @@
field that lists the time step numbers and their corresponding times.
The time step value you selected is what will be exported for postprocessing.
The time file contains the non-dimensional model time.
- The format of the time file can be found in Appendix C.
-
+ The format of the time file can be found in Appendix
+\begin_inset LatexCommand \vref{cha:Appendix-C:-CitComS,}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
-When you execute a CitComS run, your input parameters will be saved in a
- file
+When you execute a CitComS.py run, your input parameters will be saved in
+ a file
\family typewriter
pidxxxxx.cfg
\family default
@@ -3381,18 +3386,22 @@
is usually a five-digit number for the process ID.
This file contains most of the input parameters, which can be useful for
archiving and post-processing.
- (XXX: TODO)
+ This file will be referred as the
+\family typewriter
+pidfile
+\family default
+ in the chapter.
\end_layout
\begin_layout Standard
-These output files need to be post-processed before you can do the visualization.
- There is a script that can post-process (retrieve and combine) CitComS
+These output files need to be postprocessed before you can do the visualization.
+ There is a script that can postprocess (retrieve and combine) CitComS.py
output:
\family typewriter
autocombine.py
\family default
.
- The script will retrieve CitComS data to the current directory and combine
+ The script will retrieve CitComS.py data to the current directory and combine
the output into a few files.
\end_layout
@@ -3405,7 +3414,7 @@
\end_layout
\begin_layout LyX-Code
-$ autocombine.py mpirun.nodes PID.parameters 10
+$ autocombine.py mpirun.nodes pid12345.cfg 10
\end_layout
\begin_layout Standard
@@ -3413,11 +3422,11 @@
\family typewriter
mpirun.nodes
\family default
-) and CitComS.py input parameters (
+) and CitComS.py pidfile (
\family typewriter
-PID.param
+pid12345.cfg
\family default
-eters), then calls other scripts to do the actual job.
+), then calls other scripts to do the actual job.
The general usage for
\family typewriter
autocombine.py
@@ -3426,7 +3435,7 @@
\end_layout
\begin_layout LyX-Code
-$ autocombine.py [machinefile] [input_param]
+$ autocombine.py [machinefile] [pidfile]
\backslash
\end_layout
@@ -3460,8 +3469,8 @@
\family typewriter
autocombine.py
\family default
- has been run, you should end up with 2 files (or 24 files for full CitComS)
- that resemble these:
+ has been run, you should end up with 2 files (or 24 files for full spherical
+ version of CitComS.py) that resemble these:
\end_layout
\begin_layout LyX-Code
@@ -3523,12 +3532,12 @@
\end_layout
\begin_layout Standard
-OpenDX modules designed for CitComS can be found in the directory called
+OpenDX modules designed for CitComS.py can be found in the directory called
\family typewriter
PREFIX/share/CitcomS/visual
\family default
-, where PREFIX is the directory under which you installed CitcomS (default
+, where PREFIX is the directory under which you installed CitcomS.py (default
\family typewriter
/usr/local
@@ -4297,11 +4306,7 @@
\family typewriter
cookbook3
\family default
-), and the Rayleigh number (
-\begin_inset Formula $10^{\text{6}}$
-\end_inset
-
-).
+), and the Rayleigh number (10^6).
\end_layout
\begin_layout LyX-Code
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