[cig-commits] r5357 - mc/3D/CitcomS/trunk/doc/manual

[tan2 at geodynamics.org]

Author: tan2
Date: 2006-11-27 19:34:23 -0800 (Mon, 27 Nov 2006)
New Revision: 5357

Modified:
   mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
Chapter 3 updated

Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-11-28 03:29:32 UTC (rev 5356)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-11-28 03:34:23 UTC (rev 5357)
@@ -520,11 +520,13 @@
 This release of CitComS (2.1) incorporates new features and functionality,
  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
-\series bold
- (TODO: xref)
-\series default
+ The HDF5 format allows you to deal with the massive data output that were
+ created for production runs (see Chapter
+
+\begin_inset LatexCommand \ref{cha:Working-with-HDF5}
+
+\end_inset
+
 ).
  The new version incorporates 
 \family typewriter
@@ -3459,28 +3461,35 @@
 \begin_layout LyX-Code
 [CitcomS]
 \newline
-steps = 10
+steps = 5
 \newline
 
 \newline
 [CitcomS.controller]
 \newline
-monitoringFrequency = 5
+monitoringFrequency = 1
 \newline
 
 \newline
 [CitcomS.solver]
 \newline
-data
-file = example0
+dataf
+ile = example0
 \newline
 
 \newline
 [CitcomS.solver.mesher]
 \newline
-nodex = 17
+nprocx = 1
 \newline
-nodey = 17
+nprocy = 1
+\newline
+nodex =  9
+\newline
+nodey =
+  9
+\newline
+nodez =  9
 \end_layout
 
 \begin_layout Section
@@ -3636,7 +3645,7 @@
 \end_layout
 
 \begin_layout Subsection
-File Systems and Output Formats
+Output Directory and Output Formats
 \end_layout
 
 \begin_layout Standard
@@ -3664,14 +3673,9 @@
  to have a common directory structure for all of the local hard disks.
  For example, if the directory 
 \family typewriter
-/scratch/username
+/scratch
 \family default
- (you should substitute 
-\family typewriter
-username
-\family default
- with your own username) exists on all local hard disks, you can run the
- example script with:
+ exists on all local hard disks, you can run the example script with:
 \end_layout
 
 \begin_layout LyX-Code
@@ -3679,18 +3683,18 @@
 \family typewriter
 example1.cfg
 \family default
- --solver.datafile=/scratch/username/example1
+ --solver.datadir=/scratch
 \end_layout
 
 \begin_layout Standard
 The additional command line option will override the 
 \family typewriter
-datafile
+datadir
 \family default
- property in the input file.
+ property, which specifies the output directory.
  Then, the output files would be placed in 
 \family typewriter
-/scratch/username
+/scratch
 \family default
  on each individual machine with a filename prefix 
 \family typewriter
@@ -3698,9 +3702,67 @@
 \end_layout
 
 \begin_layout Standard
+Another example, if the output directory name on each local hard disk depends
+ on the machine hostname.
+ You can run the example script with:
+\end_layout
+
+\begin_layout LyX-Code
+$ citcoms 
+\family typewriter
+example1.cfg
+\family default
+ --solver.datadir=/scratch_%HOSTNAME
+\end_layout
+
+\begin_layout Standard
+The specail string %HOSTNAME will be substituted by the hostname of each
+ machine.
+ As the final example for local file system, you can specify arbitrary output
+ directory for each machine.
+ To do so, you should write a program, which will be executed on each machine
+ and print the output directory.
+ The programe must be named 
+\family typewriter
+citcoms_datadir
+\family default
+ and is on your path.
+ An example of 
+\family typewriter
+citcoms_datadir
+\family default
+ can be found in the 
+\family typewriter
+visual/
+\family default
+ directory.
+ Then you can run the example script with:
+\end_layout
+
+\begin_layout LyX-Code
+$ citcoms 
+\family typewriter
+example1.cfg
+\family default
+ --solver.datadir=%DATADIR
+\end_layout
+
+\begin_layout Standard
+The specail string %DATADIR will be substituted by the output of 
+\family typewriter
+citcoms_datadir
+\family default
+ for each machine.
+\end_layout
+
+\begin_layout Standard
 If you want CitComS.py write its output to the parallel file system, you
  have several choices.
- You can run the example script with:
+ You can run the example script with (you should subsutitute 
+\family typewriter
+username
+\family default
+ with your own username):
 \end_layout
 
 \begin_layout LyX-Code
@@ -3708,7 +3770,7 @@
 \family typewriter
 example1.cfg
 \family default
- --solver.datafile=/home/username/example1
+ --solver.datadir=/home/username
 \end_layout
 
 \begin_layout Standard
@@ -3734,15 +3796,12 @@
 \family typewriter
 example1.cfg
 \family default
- --solver.datadir=/home/username 
-\backslash
-
-\newline
---solver.output.output_format=ascii
+ --solver.datadir=/home/username/%RANK
 \end_layout
 
 \begin_layout Standard
-You will see four new directories 
+The specail string %RANK will be substituted by the MPI rank of each processor.
+ You will see four new directories 
 \family typewriter
 /home/username/0
 \family default
@@ -3813,7 +3872,7 @@
 /home/username/example1.h5
 \family default
 .
- See Chapter 
+ (TODO: update for the new hdf5 scheme...) See Chapter 
 \begin_inset LatexCommand \ref{cha:Working-with-HDF5}
 
 \end_inset
@@ -4234,24 +4293,26 @@
  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
  to the general community of scientists and engineers as a production facility.
- 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.
+ TeraGrid accounts for small allocations are available directly from CIG.
 \end_layout
 
 \begin_layout Standard
-CitComS.py has already been tested on several NSF TeraGrid platforms.
- Accounts for small allocations are available directly from CIG.
+CitComS.py has already been installed and tested on several NSF TeraGrid
+ platforms, includes NCSA, SDSC and TACC.
+ To use CitComS.py on these machines, please log in your TeraGrid account
+ and read $TG_COMMUNITY/CIG/CitcomS/TG_README and follow the instruction
+ inside.
  
-\series bold
-(TODO: description of CSA)
 \end_layout
 
 \begin_layout Chapter