[cig-commits] r5215 - in mc/3D/CitcomS/trunk/doc/manual: . graphics
sue at geodynamics.org
sue at geodynamics.org
Thu Nov 9 11:37:42 PST 2006
Author: sue
Date: 2006-11-09 11:37:41 -0800 (Thu, 09 Nov 2006)
New Revision: 5215
Removed:
mc/3D/CitcomS/trunk/doc/manual/citcoms_cover-layers.pdf
mc/3D/CitcomS/trunk/doc/manual/citcoms_cover.pdf
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
mc/3D/CitcomS/trunk/doc/manual/graphics/c_fig1.eps
Log:
various typos and fixes
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-11-09 14:11:18 UTC (rev 5214)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-11-09 19:37:41 UTC (rev 5215)
@@ -4,10 +4,14 @@
\begin_header
\textclass book
\begin_preamble
+\usepackage{natbib}
+
\usepackage{hyperref}
\let\myUrl\url
\renewcommand{\url}[1]{(\myUrl{#1})}
+
+\raggedbottom
\end_preamble
\language english
\inputencoding auto
@@ -83,7 +87,7 @@
\end_layout
\begin_layout Title
-CitComS.py Manual
+CitComS.py User Manual
\end_layout
\begin_layout Author
@@ -125,24 +129,6 @@
\end_layout
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-raggedbottom
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Part
Preface
\end_layout
@@ -188,7 +174,7 @@
\end_layout
\begin_layout Standard
-Errors and bug fixes in this manual should be directed to
+Errors and bug fixes in this manual should be directed to the
\begin_inset LatexCommand \htmlurl[CIG Mantle Convection Mailing List]{cig-mc at geodynamics.org}
\end_inset
@@ -526,8 +512,8 @@
The second major release of CitComS (2.0) incorporated the software framework
Pyre, free surface modeling methods, and stress boundary conditions on
the top and bottom surfaces.
- In the summer of 2005, as part of the 2.0.1 release, the CIG replaced the
- old build procedure with the GNU Build System.
+ In the summer of 2005, as part of the 2.0.1 release, CIG replaced the old
+ build procedure with the GNU Build System.
A subsequent release, version 2.0.2, could compile and run on 64-bit systems.
\end_layout
@@ -537,7 +523,11 @@
the most important being the use of HDF5 (a parallel version of the Hierarchica
l Data Format).
The HDF5 format allows you to deal with the massive number of files that
- were created for production runs with the del system (see Chapter (TODO: xref)).
+ were created for production runs with the del system (see Chapter
+\series bold
+ (TODO: xref)
+\series default
+).
The new version incorporates
\family typewriter
.cfg
@@ -554,12 +544,17 @@
\end_inset
- (in addition to GMT (TODO: url) and
+ in addition to
+\begin_inset LatexCommand \htmlurl[Generic Mapping Tools (GMT)]{gmt.soest.hawaii.edu}
+
+\end_inset
+
+ and
\begin_inset LatexCommand \htmlurl[OpenDX]{www.opendx.org}
\end_inset
-).
+.
Finally, you will find instructions on using this version as a preinstalled
package on some of the NSF TeraGrid sites.
\end_layout
@@ -640,7 +635,7 @@
\begin_layout Standard
\begin_inset Float figure
-placement h
+placement H
wide false
sideways false
status open
@@ -654,9 +649,11 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Graphics
filename graphics/c_fig1.eps
- width 100col%
+ scale 85
rotateOrigin center
\end_inset
@@ -678,7 +675,7 @@
Developers have created Pyre classes for CitComS.py to facilitate simulation
setup.
However, they are not independent classes in a strict sense.
- They still share the same underlaying data structure and their functionality
+ They still share the same underlying data structure and their functionality
is not divided clearly.
CitComS.py was not designed to be object-oriented and to make it so would
require significant investment of effort with little return.
@@ -895,11 +892,11 @@
\begin_inset Formula $R_{0}$
\end_inset
- is the radius of the earth,
+ is the radius of the Earth,
\begin_inset Formula $\eta_{0}$
\end_inset
- is a reference viscosity,
+ is a reference viscosity, and
\begin_inset Formula $\Delta T$
\end_inset
@@ -1073,7 +1070,7 @@
.
Brick elements are used, such as eight velocity nodes with trilinear shape
functions and one constant pressure node for each element.
- The use of brick elements in 3-D (or rectangular elements in 2-D) is important
+ The use of brick elements in 3D (or rectangular elements in 2D) is important
for accurately determining the pressure, such as dynamic topography, in
incompressible Stokes' flow
\begin_inset LatexCommand \cite{Hughes The Finite Element Method}
@@ -1286,10 +1283,9 @@
\end_layout
\begin_layout Standard
-To install CitComS.py, you will follow the procedure that is commonly used
- with other open source software packages.
- First, you will download the source package (in the form of a compressed
-
+To install CitComS.py, you follow the procedure that is commonly used with
+ other open source software packages.
+ First, download the source package (in the form of a compressed
\family typewriter
tar
\family default
@@ -1299,9 +1295,9 @@
\end_inset
.
- After unpacking the source, you will run a prepackaged shell script to
- configure CitComS for your system.
- Finally, you will use the
+ After unpacking the source, you run a prepackaged shell script to configure
+ CitComS for your system.
+ Finally, you use the
\family typewriter
make
\family default
@@ -1312,13 +1308,12 @@
\begin_layout Standard
Advanced users and software developers may be interested in downloading
the latest CitComS source code directly from the CIG source code repository,
- instead of using the prepared source package.
- See the
+ instead of using the prepared source package; see Section
\begin_inset LatexCommand \ref{sec:Software-Repository}
\end_inset
- section later in this chapter.
+ later in this chapter.
\end_layout
\begin_layout Standard
@@ -1337,8 +1332,9 @@
\end_inset
.
- You can subscribe to the Mailing List and view archived discussion at
-\begin_inset LatexCommand \htmlurl[Geodynamics Mail Lists]{www.geodynamics.org/cig/lists}
+ You can subscribe to the Mailing List and view archived discussion at the
+
+\begin_inset LatexCommand \htmlurl[Geodynamics Mail Lists web page]{www.geodynamics.org/cig/lists}
\end_inset
@@ -1367,8 +1363,15 @@
\begin_layout Standard
Users familiar with older versions of CitComS may prefer to install only
- the legacy CitComS tools, CitcomSFull and CitcomSRegional (TODO: fixed font), and forgo use
- of the Pyre framework.
+ the legacy CitComS tools,
+\family typewriter
+CitcomSFull
+\family default
+ and
+\family typewriter
+CitcomSRegional
+\family default
+, and forgo use of the Pyre framework.
This process requires only a C compiler.
\end_layout
@@ -1385,25 +1388,19 @@
\end_layout
\begin_layout Itemize
-(Optional) the Parallel HDF5 library
-(TODO: move this bullet after MPI)
+An MPI library
\end_layout
\begin_layout Itemize
-An MPI library
+(Optional) the Parallel HDF5 library
\end_layout
\begin_layout Standard
-For more information, see the subsection
+For more information, see Section
\begin_inset LatexCommand \ref{sec:Installing-without-Pyre}
\end_inset
- on page
-\begin_inset LatexCommand \pageref{sec:Installing-without-Pyre}
-
-\end_inset
-
.
\end_layout
@@ -1413,7 +1410,7 @@
\begin_layout Standard
On all supported systems, C and C++ compilers are readily available.
- If you using GCC, you will need version 3 or later.
+ If you are using GCC, you need version 3 or later.
\end_layout
\begin_layout Subsection
@@ -1430,34 +1427,9 @@
.
\end_layout
-\begin_layout Subsection
-Python
-\end_layout
-
-\begin_layout Standard
-You can download Python from the
-\begin_inset LatexCommand \htmlurl[Python website]{www.python.org}
-
-\end_inset
-
-.
- If your system is running a recent release of Linux or Mac OS X, chances
- are you already have a suitable Python interpreter installed.
- To check, type the 'python' command:
-\end_layout
-
-\begin_layout LyX-Code
-$ python -V
-\end_layout
-
-\begin_layout LyX-Code
-Python 2.3.4
-\end_layout
-
\begin_layout Quote
\series bold
-(TODO: move this section after MPI)
Note for Mac OS X Users
\series default
: You will need Xcode, which is freely available from
@@ -1485,6 +1457,34 @@
$ fink install lammpi lammpi-dev
\end_layout
+\begin_layout Subsection
+Python
+\end_layout
+
+\begin_layout Standard
+You can download Python from the
+\begin_inset LatexCommand \htmlurl[Python website]{www.python.org}
+
+\end_inset
+
+.
+ If your system is running a recent release of Linux or Mac OS X, chances
+ are you already have a suitable Python interpreter installed.
+ To check, type the 'python' command:
+\end_layout
+
+\begin_layout LyX-Code
+$ python -V
+\end_layout
+
+\begin_layout LyX-Code
+Python 2.3.4
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
\begin_layout Section
Downloading and Unpacking Source
\end_layout
@@ -1787,13 +1787,15 @@
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1in">
+<column alignment="center" valignment="top" leftline="true" width="1in">
<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
<row topline="true" bottomline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
+
+\series bold
Variable
\end_layout
@@ -1803,6 +1805,8 @@
\begin_inset Text
\begin_layout Standard
+
+\series bold
Description
\end_layout
@@ -1936,7 +1940,7 @@
These variables collectively specify how to build MPI programs.
The variables MPICC and MPICXX specify compiler commands; MPIINCLUDES specifies
preprocessor flags, and MPILIBS specifies linker flags.
- See
+ See Section
\begin_inset LatexCommand \ref{sec:MPI-Configuration}
\end_inset
@@ -1990,7 +1994,7 @@
\end_layout
\begin_layout Subsection
-Manually specifying MPI wrappers
+Manually Specifying MPI Wrappers
\end_layout
\begin_layout LyX-Code
@@ -2035,7 +2039,7 @@
\end_layout
\begin_layout Subsection
-Manually specifying MPI
+Manually Specifying MPI
\family typewriter
include
\family default
@@ -2043,7 +2047,7 @@
\family typewriter
lib
\family default
- directories
+ Directories
\end_layout
\begin_layout LyX-Code
@@ -2063,7 +2067,7 @@
\end_layout
\begin_layout Subsection
-Manually specifying MPI
+Manually Specifying MPI
\family typewriter
include
\family default
@@ -2071,7 +2075,7 @@
\family typewriter
lib
\family default
- directories, and an alternative compiler
+ Directories and an Alternative Compiler
\end_layout
\begin_layout LyX-Code
@@ -2301,14 +2305,14 @@
\end_layout
\begin_layout Standard
-In order to import HDF5 file into OpenDX, you will need the OpenDXutils
- package from the Cactus project.
+In order to import HDF5 files into OpenDX, you need the OpenDXutils package
+ from the Cactus project.
Go to the
\begin_inset LatexCommand \url[OpenDXutils package website]{www.cactuscode.org/Visualization/openDX}
\end_inset
- and follow the instuction in the webpage to download and install the package.
+ and follow the instructions to download and install the package.
Note that you will need to set both
\family typewriter
DXMODULES
@@ -2542,12 +2546,6 @@
svn
\family default
; it should return a usage message.
- For more information on Subversion, visit the
-\begin_inset LatexCommand \htmlurl[Subversion website]{subversion.tigris.org}
-
-\end_inset
-
-.
\end_layout
\begin_layout LyX-Code
@@ -2559,6 +2557,15 @@
\end_layout
\begin_layout Standard
+For more information on Subversion, visit the
+\begin_inset LatexCommand \htmlurl[Subversion website]{subversion.tigris.org}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
Second, you must have the GNU tools Autoconf, Automake, and Libtool installed.
To check, enter the following commands:
\end_layout
@@ -2606,21 +2613,31 @@
Like the release version, the development version depends upon Pythia v0.8.
In addition, the development version also depends upon a package called
Exchanger.
- Unless you plan to build only the legacy CitComS tools (see
+ Unless you plan to build only the legacy CitComS tools (see Section
\begin_inset LatexCommand \ref{sec:Installing-without-Pyre}
\end_inset
earlier in this chapter), you will need to check out the Pythia and Exchanger
packages as well.
- Like CitComS, Exchanger is available from the geodynamics.org server.
- For convenience, Pythia is also available from geodynamics.org.
+ Like CitComS, Exchanger is available from the
+\begin_inset LatexCommand \htmlurl[Geodynamics website]{www.geodynamics.org}
+
+\end_inset
+
+.
+ For convenience, Pythia is also available from the
+\begin_inset LatexCommand \htmlurl[Geodynamics website]{www.geodynamics.org}
+
+\end_inset
+
+.
To check out Pythia and Exchanger, use the following commands:
\end_layout
\begin_layout LyX-Code
-(TODO: update this description)
-$ svn checkout svn://geodynamics.org/cig/vendor/pythia/v0.8 pythia-0.8
+(TODO: update this description)$ svn checkout svn://geodynamics.org/cig/vendor/py
+thia/v0.8 pythia-0.8
\end_layout
\begin_layout LyX-Code
@@ -2781,7 +2798,7 @@
\end_layout
\begin_layout Section
-Using CitComS.py Without Pyre
+Using CitComS.py without Pyre
\end_layout
\begin_layout Standard
@@ -2815,8 +2832,8 @@
\end_layout
\begin_layout Standard
-Two inputfile examples, one for regional spherical model and one for full
- spherical model, are provided in the
+Two input file examples, one for a regional spherical model and one for
+ a full spherical model, are provided in the
\family typewriter
examples/Regional
\family default
@@ -2838,7 +2855,7 @@
\end_layout
\begin_layout Standard
-If you build CitComS.py with Pyre framework, a program
+If you build CitComS.py with the Pyre framework, a program
\family typewriter
citcoms
\family default
@@ -2862,8 +2879,8 @@
\family default
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
+ It can also run a full spherical model if the correct parameters are set
+ (see Section
\begin_inset LatexCommand \vref{sec:Cookbook-1:-Global}
\end_inset
@@ -2890,7 +2907,7 @@
\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 Appendix
-\begin_inset LatexCommand \vref{cha:Appendix-A:-Input}
+\begin_inset LatexCommand \ref{cha:Appendix-A:-Input}
\end_inset
@@ -2902,18 +2919,18 @@
\end_layout
\begin_layout Standard
-There are several methods to set the input parameters for CitComS.py, which
- will be discussed in this section.
- The command line input will override the input from the .cfg file, which
- will in turn override the input from the .pml file.
+There are several methods to set the input parameters for CitComS.py: via
+ the command line or by using a .cfg or .pml file.
+ Command line input will override any input contained in a .cfg file, which
+ will in turn override input in a .pml file.
\end_layout
\begin_layout Subsection
-From the Command Line
+Using the Command Line
\end_layout
\begin_layout Standard
-Pyre has the following syntax to change properties from the command lines.
+Pyre uses the following syntax to change properties from the command lines.
To change the value of a property of a component, use:
\end_layout
@@ -2940,7 +2957,7 @@
\end_layout
\begin_layout Subsection
-In a
+Using a
\family typewriter
.cfg
\family default
@@ -2950,16 +2967,14 @@
\begin_layout Standard
Entering all those parameters via the command line involves the risk of
typographical errors, which can lead to undesired results.
- So, you may find it easier to write a brief input file that contains the
- parameters.
+ You may find it easier to write a brief input file that contains the parameters.
Since v2.1, the input parameters can be saved in a
\family typewriter
.cfg
\family default
file.
- The file has a format similar to a Windows INI file.
- The file is composed of one or more sections.
- Each section looks like this:
+ This file has a format similar to a Windows INI file.
+ The file is composed of one or more sections which are formatted as follows:
\end_layout
\begin_layout LyX-Code
@@ -2988,7 +3003,7 @@
\end_layout
\begin_layout Subsection
-In a
+Using a
\family typewriter
CitcomS.pml
\family default
@@ -3003,8 +3018,7 @@
file is an XML file that assigns values to properties, components, and
facilities in an application, allowing a user to override the default values
assigned in the respective inventories.
- The file is composed of nested sections.
- Each section is like:
+ The file is composed of nested sections which are formatted as follows:
\end_layout
\begin_layout LyX-Code
@@ -3066,12 +3080,12 @@
\family typewriter
CitcomS.pml
\family default
- in different directories.
+ files in different directories.
The
\family typewriter
CitcomS.pml
\family default
- in 3 beats the others, 2 beats 1, and 1 beats whatever the default is.
+ in 3 will override all the others, 2 overrides 1, and 1 verrides the default.
\end_layout
@@ -3268,13 +3282,12 @@
\family default
directory.
CitComS.py has been extensively used on both environments, using up to several
- hundred of processors.
+ hundred processors.
How to run a multiprocessor CitComS.py model depends on your hardware and
- software settings.
- For example, whether a batch system is used, what are the names of the
- computers in a cluster, and how is the filesystem organized.
- This section will lead you thorough the different settings of parallel
- environment.
+ software settings, e.g., whether a batch system is used, what the names of
+ the computers in a cluster are, and how the file system is organized.
+ This section will lead you through the different settings of parallel environme
+nt.
\end_layout
@@ -3321,12 +3334,12 @@
\begin_layout Standard
This example uses 2 processors in colatitude (x-coordinate), 2 in longitude
- (y-direction), and 1 in the radial (z-direction), i.
- e., it uses 4 processors in total.
+ (y-direction), and 1 in the radial (z-direction), i.e., it uses 4 processors
+ in total.
In addition, there will be 17 nodes in x (theta), 17 nodes in y (fi), and
9 nodes in z (radius_inner).
- The model will run for 71 time steps and the code outputs the results every
- 10 time steps.
+ The model will run for 71 time steps and the code will output the results
+ every 10 time steps.
\end_layout
\begin_layout Standard
@@ -3351,11 +3364,19 @@
\begin_layout Standard
These quantities refer to the total number of FEM nodes in a given direction
for the complete problem, and for the example it works out that within
- a given processor there will be 9 x 9 x 9 nodes.
+ a given processor there will be 9
+\begin_inset Formula $\times$
+\end_inset
+
+ 9
+\begin_inset Formula $\times$
+\end_inset
+
+ 9 nodes.
Note that in the x-direction (or y) that for the entire problem there are
17 nodes and there is one node shared between two processors.
This shared node is duplicated in two adjacent processors.
- Unfortunately, "nodes" sometimes also refers to the individual computers
+ Unfortunately, "nodes" sometimes also refer to the individual computers
which make up a Beowulf cluster or supercomputer.
In the example scripts, this is indicated with:
\end_layout
@@ -3401,7 +3422,7 @@
\end_layout
\begin_layout Standard
-CitComS.py will potentially output a large number of ASCII files.
+CitComS.py potentially generates a large number of ASCII files.
This means that you will have to organize your directories carefully when
running CitComS.py so that you can find your way through these files as
well as use a post-processing program contained with this distribution.
@@ -3428,12 +3449,12 @@
\family typewriter
/scratch/username
\family default
- (you should subsitute
+ (you should substitute
\family typewriter
username
\family default
- to your own username) exists on all local hard disks, you can run the example
- script with:
+ with your own username) exists on all local hard disks, you can run the
+ example script with:
\end_layout
\begin_layout LyX-Code
@@ -3454,11 +3475,9 @@
\family typewriter
/scratch/username
\family default
- with a filename prefix
+ on each individual machine with a filename prefix
\family typewriter
-example1
-\family default
- on each individual machine.
+example1.
\end_layout
\begin_layout Standard
@@ -3545,7 +3564,7 @@
\begin_layout Standard
The last choice is the most powerful one.
- Instead of writing many ASCII files, CitComS.py can write its result in
+ Instead of writing many ASCII files, CitComS.py can write its result into
a single HDF5 (Hierarchical Data Format) file.
The HDF5 file takes less disk space than the ASCII files in total and doesn't
require additional post-processing to be visualized in OpenDX.
@@ -3595,7 +3614,7 @@
mpirun
\family default
requires several command line options to launch a parallel job.
- Or if you have used one of the batch system, you will know that the batch
+ Or if you have used one of the batch systems, you will know that the batch
system requires you to write a script to launch a job.
Fortunately, launching a parallel CitComS.py job is simplified by the
\family typewriter
@@ -3632,7 +3651,7 @@
\family typewriter
launcher.nodegen
\family default
- property is a print-style format string, used in conjunction with
+ property is a printf-style format string, used in conjunction with
\family typewriter
launcher.nodelist
\family default
@@ -3645,7 +3664,7 @@
\end_layout
\begin_layout Standard
-If you are using MPICH, you will notice that a machine file
+If you use MPICH, you will notice that a machine file
\family typewriter
mpirun.nodes
\family default
@@ -3655,7 +3674,7 @@
\end_layout
\begin_layout Standard
-If you are using LAM/MPI, there is no machine file generated.
+If you use LAM/MPI, no machine file is generated.
In addition, you can pass additional environment variables to LAM/MPI via:
\end_layout
@@ -3694,7 +3713,7 @@
In any case, the progress is always saved in a log file.
The log file contains the convergence progress of the computation and,
if an error occurs, debugging output.
- The time file contains the elapsed model time (in non-dimensional unit)
+ The time file contains the elapsed model time (in non-dimensional units)
and CPU time (in seconds) of every time step.
The format of the time file can be found in Appendix
\begin_inset LatexCommand \vref{cha:Appendix-C:-CitComS,}
@@ -3725,13 +3744,13 @@
The TeraGrid is an open scientific discovery infrastructure combining leadership
class resources at eight partner sites to create an integrated, persistent
computational resource.
- The TeraGrid takes its name from two concepts from high-end computing.
+ The TeraGrid takes its name from two concepts from high-end computing:
"Tera" is the metric prefix for "trillions" as in teraflops (trillions
of calculations per second) and terabytes (trillions of bytes) and reflects
- the scale of the computing power provided by the TeraGrid.
- The "Grid" portion of TeraGrid reflects the idea of harnessing and using
- distributed computers, data storage systems, networks, and other resources
- as if they were a single massive system.
+ the scale of the computing power provided by the TeraGrid; the "Grid" portion
+ of TeraGrid reflects the idea of harnessing and using distributed computers,
+ data storage systems, networks, and other resources as if they were a single
+ massive system.
In other words, Grid computing uses software technologies to allow researchers
to create "virtual supercomputers" far larger than individual hardware
components.
@@ -3741,10 +3760,10 @@
\begin_layout Standard
Although the TeraGrid is a high-end resource, it was developed to be accessible
to the general community of scientists and engineers as a production facility.
- Since the TeraGrid software is based on commodity clusters, Linux/Unix,
- and Globus, it should be easier to scale from a laboratory development
- environment to a high-end environment in a straightforward manner which
- promotes application performance.
+ Since TeraGrid software is based on commodity clusters, Linux/Unix, and
+ Globus, it should be easier to scale from a laboratory development environment
+ to a high-end environment in a straightforward manner which promotes applicatio
+n performance.
\end_layout
\begin_layout Standard
@@ -3848,7 +3867,7 @@
\shape italic
hyperslabs
\shape default
-, which consists of a subarray or strided subarray of the multi-dimensional
+, which consist of a subarray or strided subarray of the multi-dimensional
dataset.
The selection is performed in the file dataspace for the dataset.
HDF5 also supports parallel I/O.
@@ -4542,7 +4561,10 @@
\end_layout
+\begin_deeper
\begin_layout Standard
+
+\family roman
To control the size of the buffer used in collective I/O
\end_layout
@@ -4561,6 +4583,8 @@
\end_layout
\begin_layout Standard
+
+\family roman
To change the size of the buffer used by the sieve algorithm
\end_layout
@@ -4575,6 +4599,8 @@
\end_layout
\begin_layout Standard
+
+\family roman
To change the data alignment parameters
\end_layout
@@ -4593,6 +4619,8 @@
\end_layout
\begin_layout Standard
+
+\family roman
To change the size of the raw data chunk cache
\end_layout
@@ -4610,14 +4638,15 @@
cache_rdcc_nbytes=1048576
\end_layout
+\end_deeper
\begin_layout LyX-Code
\end_layout
\begin_layout Standard
-For more details, refer to (TODO:insert reference to chapter) in the HDF5 documentati
-on, the (TODO:insert reference to chapter) in the MPI-2 reference book, and the
- documentation for your parallel file system.
+For more details, refer to (TODO:insert reference to chapter) in the HDF5
+ documentation, the (TODO:insert reference to chapter) in the MPI-2 reference
+ book, and the documentation for your parallel file system.
\end_layout
\begin_layout Section
@@ -4645,8 +4674,6 @@
$ h5tocap file.h5 [frame1 [frame2 [...]]]
\end_layout
-(TODO: output of h5tocap)
-
\begin_layout Subsection
Python
\end_layout
@@ -4659,14 +4686,14 @@
provides a good example for using PyTables to access the data in an HDF5
file.
In PyTables, datasets can be retrieved from disk as NumPy arrays through
- an array interface that avoids unecessary copying of data by using hyperslabs,
+ an array interface that avoids unnecessary copying of data by using hyperslabs,
and which takes advantage of Python's powerful array slice-indexing.
\end_layout
\begin_layout Standard
For example, obtaining the node coordinates, temperature, and topography
- values over the entire surface of the sphere for all timesteps can be done
- easily with the following code snippet.
+ values over the entire surface of the sphere for all time steps can be
+ done easily with the following code snippet:
\end_layout
\begin_layout LyX-Code
@@ -4695,9 +4722,17 @@
0:12
\family default
refers to all caps explicitly, while the empty slice
+\begin_inset Quotes srd
+\end_inset
+
+
\family typewriter
:
\family default
+
+\begin_inset Quotes sld
+\end_inset
+
refers to the entire extent of the corresponding dimension.
The values of
\family typewriter
@@ -4714,8 +4749,8 @@
\end_layout
\begin_layout Standard
-For more details, refer to the documentation for PyTables (TODO:insert link here)
- and NumPy (TODO:insert link here).
+For more details, refer to the documentation for PyTables (TODO:insert link
+ here) and NumPy (TODO:insert link here).
\end_layout
\begin_layout Subsection
@@ -4750,7 +4785,7 @@
Once you have run CitComS.py, you should have a series of output files (potential
ly spread throughout the file systems of your Beowulf or on a set of directories
on your parallel file system).
- You will have to retrieve and combine the data for the time step (or age)
+ You now 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
Open Visualization Data Explorer, better known as OpenDX.
@@ -4760,7 +4795,7 @@
\end_inset
.
- If you are uisng Linux, OpenDX is usually available as package
+ If you are using Linux, OpenDX is usually available as package
\family typewriter
dx
\family default
@@ -4825,12 +4860,12 @@
\family typewriter
2
\family default
- corresponds to the processor number (so it is output by the 2nd processor)
- , and
+ corresponds to the processor number (so it is output by the 2nd processor),
+ and
\family typewriter
10
\family default
- corresponds to the time-step.
+ corresponds to the time step.
\end_layout
@@ -4860,8 +4895,8 @@
\family default
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.
- This file will be referred as the
+ archiving and postprocessing.
+ This file will be referred to as the
\family typewriter
pidfile
\family default
@@ -4886,7 +4921,7 @@
\family typewriter
autocombine.py
\family default
-, you can retrieve and combine data of time-step 10 by:
+, retrieve and combine data of time-step 10:
\end_layout
\begin_layout LyX-Code
@@ -4898,7 +4933,7 @@
\family typewriter
mpirun.nodes
\family default
-) and CitComS.py pidfile (
+) and the CitComS.py pidfile (
\family typewriter
pid12345.cfg
\family default
@@ -4924,7 +4959,7 @@
\family typewriter
PREFIX/bin/batchpaste.sh
\family default
- and replace 'rsh' to 'ssh' in the script.
+ and replace 'rsh' with 'ssh' in the script.
\end_layout
@@ -4933,8 +4968,13 @@
\family typewriter
/scratch/username
\family default
-) on a parallel file system, you can post-process your output files by following
- the instructions in the next section.
+) on a parallel file system, you can postprocess your output files by following
+ the instructions in Section
+\begin_inset LatexCommand \ref{sec:Postprocessing-in-a}
+
+\end_inset
+
+.
\end_layout
@@ -4943,8 +4983,8 @@
\family typewriter
autocombine.py
\family default
- has been run, you should end up with 2 files (or 24 files for full spherical
- version of CitComS.py) that resemble these:
+ has been run, you should end up with 2 files (or 24 files for the full
+ spherical version of CitComS.py) that resemble these:
\end_layout
\begin_layout LyX-Code
@@ -4963,10 +5003,14 @@
\end_inset
.
- The later file is the OpenDX header for the data.
+ The latter file is the OpenDX header for the data.
\end_layout
\begin_layout Section
+\begin_inset LatexCommand \label{sec:Postprocessing-in-a}
+
+\end_inset
+
Postprocessing in a Non-Cluster Environment
\end_layout
@@ -5486,8 +5530,6 @@
The fourth tab (unconnected, default to 0) specifies which cap(s) to import.
\end_layout
-(TODO: GMT scripts)
-
\begin_layout Chapter
Cookbooks
\end_layout
@@ -5586,8 +5628,8 @@
\end_layout
\begin_layout Standard
-The second set of parameters specifies the number of time steps (101),
- how often full outputs of the computation are created (25), and the prefix
+The second set of parameters specifies the number of time steps (101), how
+ often full outputs of the computation are created (25), and the prefix
of output filenames (cookbook1).
\end_layout
Deleted: mc/3D/CitcomS/trunk/doc/manual/citcoms_cover-layers.pdf
===================================================================
(Binary files differ)
Deleted: mc/3D/CitcomS/trunk/doc/manual/citcoms_cover.pdf
===================================================================
(Binary files differ)
Modified: mc/3D/CitcomS/trunk/doc/manual/graphics/c_fig1.eps
===================================================================
(Binary files differ)
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