[cig-commits] r14607 - doc/CitcomS/manual

[tan2 at geodynamics.org]

Author: tan2
Date: 2009-04-06 11:30:35 -0700 (Mon, 06 Apr 2009)
New Revision: 14607

Modified:
   doc/CitcomS/manual/citcoms.lyx
Log:
Going through chapter 4 and 5. 


Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx	2009-04-06 18:13:12 UTC (rev 14606)
+++ doc/CitcomS/manual/citcoms.lyx	2009-04-06 18:30:35 UTC (rev 14607)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 276
 \begin_document
 \begin_header
@@ -5261,25 +5261,11 @@
 The TeraGrid is a set of parallel supercomputer facilities at eight partner
  sites in the U.S.
  which creates an integrated, persistent computational resource.
- 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.
- In other words, Grid computing uses software technologies to allow researchers
- to create ``virtual supercomputers'' far larger than individual hardware
- components.
  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
-Although the TeraGrid is a high-end resource, it was developed to be accessible
+ 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.
  TeraGrid accounts for small allocations are available directly from CIG
  for investigators in the U.S.
@@ -5332,7 +5318,7 @@
  Since the v2.1 release, CitcomS solves this problem when running the software
  on computers that have parallel file systems by assembling a binary HDF5
  file in parallel I/O mode.
- 
+ You can skip this chapter if you are not using the HDF5 output format.
 \end_layout
 
 \begin_layout Section
@@ -5360,7 +5346,15 @@
 \begin_layout Standard
 HDF5 files are organized in a hierarchical structure, similar to a Unix
  file system.
- Two types of primary objects, groups and datasets, are stored in this structure.
+ Two types of primary objects, 
+\shape italic
+groups
+\shape default
+ and 
+\shape italic
+datasets
+\shape default
+, are stored in this structure.
  A group contains instances of zero or more groups or datasets, while a
  dataset stores a multi-dimensional array of data elements.
  Both kinds of objects are accompanied by supporting metadata.
@@ -5468,7 +5462,7 @@
  The optimal values for these parameters may vary from file system to file
  system.
  Ideally, before compiling CitcomS, the build procedure would configure
- these parameters based on your platform.
+ these parameters based on your platform, but this is not implemented currently.
  
 \end_layout
 
@@ -5477,8 +5471,7 @@
  a variety of parallel file systems such as GPFS, PVFS, IBRIX FusionFS,
  etc., you can specify the following parameters in the CitcomS input file.
  You may use these parameters to tune the performance of the parallel I/O
- on your system, although in future versions of CitcomS this step may become
- unnecessary for supported file systems.
+ on your system.
 \end_layout
 
 \begin_layout Standard
@@ -5693,9 +5686,9 @@
 test-case.100.h5
 \family default
 \size default
- contains data of time step 10).
+ contains data of time step 100).
  Most of the output data from CitcomS is specified at the nodes of a logically
- cartesian grid and is therefore well represented by multi-dimensional arrays.
+ Cartesian grid and is therefore well represented by multi-dimensional arrays.
  A cap dimension is defined for addressing each of the CitcomS caps, followed
  by three spatial indices 
 \begin_inset Formula $(i,j,k)$
@@ -6383,7 +6376,7 @@
 \family default
  provides a good example of using the PyTables extension module to access
  the data contained in the CitcomS HDF5 files.
- In PyTables, datasets can be retrieved from disk as NumPy arrays.
+ Using PyTables, datasets can be retrieved from disk as NumPy arrays.
  The retrieval avoids unnecessary copying of data by using hyperslabs, which
  take advantage of Python's powerful array slice-indexing.
 \end_layout
@@ -6466,7 +6459,7 @@
 \end_layout
 
 \begin_layout Standard
-NCSA HDFView is a visual tool written for accessing HDF files.
+NCSA HDFView is a visual tool for accessing HDF files.
  You can use it for viewing the internal file hierarchy in a tree structure,
  creating new files, adding or deleting groups and datasets, and modifying
  existing datasets.
@@ -6550,9 +6543,9 @@
 \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 or in a set of directories
- on your parallel file system).
+Once you have run CitcomS, you would have a series of output files (potentially
+ spread throughout the file systems of your Beowulf cluster or in a set
+ of directories on your parallel file system).
  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
@@ -6708,7 +6701,7 @@
 \family typewriter
 current age
 \family default
- field that lists the time-step numbers and their corresponding times.
+ line that lists the time-step numbers and their corresponding times.
  To choose an age to export for postprocessing, you have to determine which
  time step corresponds to the age that interests you by looking at the log
  file.
@@ -6790,7 +6783,7 @@
 \family default
 ) to access the computation nodes, you must manually edit 
 \family typewriter
-batchpaste.sh
+visual/batchpaste.sh
 \family default
  and replace `rsh' with `ssh' in the script.
  
@@ -7039,7 +7032,7 @@
 placement H
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Standard
 \align center
@@ -7082,7 +7075,10 @@
 \family default
 \series default
  can increase or reduce the resolution of the velocity vectors and grids.
- 
+ Reducing resolution is often necessary for visualizing large dataset interactiv
+ely.
+ Note that the resolution of other fields (e.g., temperature and viscosity)
+ is not reduced.
 \end_layout
 
 \begin_layout Itemize
@@ -7266,7 +7262,10 @@
 \family default
 \series default
  can increase or reduce the resolution of the velocity vectors and grids.
- 
+ Reducing resolution is often necessary for visualizing large dataset interactiv
+ely.
+ Note that the resolution of other fields (e.g., temperature and viscosity)
+ is not reduced.
 \end_layout
 
 \begin_layout Itemize
@@ -7636,7 +7635,7 @@
 placement H
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Standard
 \noindent
@@ -7769,7 +7768,7 @@
 placement H
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Standard
 \noindent
@@ -7847,7 +7846,7 @@
 placement H
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Standard
 \noindent