[cig-commits] r14583 - doc/CitcomS/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Fri Apr 3 15:01:53 PDT 2009
Author: tan2
Date: 2009-04-03 15:01:53 -0700 (Fri, 03 Apr 2009)
New Revision: 14583
Modified:
doc/CitcomS/manual/citcoms.lyx
Log:
Go through Chapter 2 and 3, and Section 6.1.
* Mentioned LAM/MPI and Open MPI in the installation of MPI library
* Updated the download link
* Using Exchanger-1.0.1
* Update the version number of GNU autotools
* Explained the difference of C and Pyre version
* Shrunk the .pml section
* Fixed inconsistent code listing in Section 3.4
* Added brief introduction of each cookbook.
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2009-04-03 20:10:27 UTC (rev 14582)
+++ doc/CitcomS/manual/citcoms.lyx 2009-04-03 22:01:53 UTC (rev 14583)
@@ -1901,7 +1901,7 @@
file) available at the
\begin_inset LatexCommand htmlurl
name "Geodynamics Software Packages web page"
-target "geodynamics.org/cig/software/packages"
+target "geodynamics.org/cig/software/packages/mc/citcoms"
\end_inset
@@ -1912,7 +1912,7 @@
\family typewriter
make
\family default
- utility to build and install CitcomS from source.
+ utility to build and, optionally, install CitcomS from source.
\end_layout
@@ -2129,12 +2129,31 @@
\end_inset
.
- Installing MPICH from source involves walking through the standard GNU
- build procedure (
+ Other choices include
+\begin_inset LatexCommand htmlurl
+name "LAM/MPI"
+target "www.lam-mpi.org"
+
+\end_inset
+
+ and
+\begin_inset LatexCommand htmlurl
+name "Open MPI"
+target "www.open-mpi.org"
+
+\end_inset
+
+.
+ Installing MPI from source involves walking through the standard GNU build
+ procedure (
\family typewriter
configure && make && make install
\family default
-).
+) while logged in as
+\family typewriter
+root
+\family default
+.
\end_layout
\begin_layout Standard
@@ -2196,7 +2215,7 @@
\end_layout
\begin_layout LyX-Code
-Python 2.3.4
+Python 2.5.2
\end_layout
\begin_layout Standard
@@ -2221,7 +2240,7 @@
\family default
) in addition to the core Python package -- even if you don't plan on doing
any Python software development.
- The development package contains the Python include files, which are necessary
+ The development package contains the Python header files, which are necessary
for building CitcomS.
\end_layout
@@ -2279,6 +2298,10 @@
\end_layout
\begin_layout LyX-Code
+$ export PATH=$HOME/bin:$PATH
+\end_layout
+
+\begin_layout LyX-Code
$ cd
\end_layout
@@ -2325,30 +2348,14 @@
\end_layout
\begin_layout Standard
-Download CitcomS from the
+To obtain CitcomS, go to the
\begin_inset LatexCommand htmlurl
-name "Geodynamics website"
-target "geodynamics.org"
+name "Geodynamics Software Packages web page"
+target "geodynamics.org/cig/software/packages/mc/citcoms"
\end_inset
-.
- Click the
-\family sans
-software
-\family default
- tab at the top of the page.
- Then click
-\family sans
-Software Packages
-\family default
-, then
-\family sans
-Mantle Convection
-\family default
-.
- Once you click the CitcomS link, download the source archive and unpack
- it using the
+, download the source archive and unpack it using the
\family typewriter
tar
\family default
@@ -2459,7 +2466,7 @@
\end_layout
\begin_layout Subsection
-Installing to a Secondary Location
+Installing to a Secondary Location (Optional)
\end_layout
\begin_layout Standard
@@ -2699,7 +2706,7 @@
\end_layout
\begin_layout Standard
-CitcomS 3.0 requires Pythia v0.8.1 or higher, which
+(TODO) CitcomS 3.0 requires Pythia v0.8.1 or higher, which
\family typewriter
configure
\family default
@@ -2861,7 +2868,7 @@
\InsetSpace ~
\InsetSpace ~
\InsetSpace ~
-PYTHON=/opt/python2.3/bin/python
+PYTHON=/opt/python2.5/bin/python
\family default
\end_layout
@@ -2896,8 +2903,33 @@
\begin_layout Standard
C compiler command.
- This is usually set to the name of an MPI wrapper command.
- See Section
+ This is usually set to the name of an MPI wrapper command, e.g.,
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\InsetSpace ~
+\InsetSpace ~
+./configure
+\backslash
+
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+\InsetSpace ~
+CC=/opt/mpich-1.2.6/bin/mpicc
+\end_layout
+
+\begin_layout Standard
+See Section
\begin_inset LatexCommand vref
reference "sec:MPI-Configuration"
@@ -3189,7 +3221,7 @@
\end_layout
\begin_layout LyX-Code
-$ cd Exchanger-1.0.0/
+$ cd Exchanger-1.0.1/
\end_layout
\begin_layout LyX-Code
@@ -3216,7 +3248,7 @@
\end_layout
\begin_layout LyX-Code
-$ export PYTHONPATH=$HOME/cig/lib/python2.3/site-packages:$PYTHONPATH
+$ export PYTHONPATH=$HOME/cig/lib/python2.5/site-packages:$PYTHONPATH
\end_layout
\begin_layout LyX-Code
@@ -3451,6 +3483,14 @@
\family default
is invoked directly from the batch script.
On others, a special wrapper is used instead.
+ If you need help to configure Pyre for your cluster, you can contact
+\begin_inset LatexCommand htmlurl
+name "CIG Mantle Convection Mailing List"
+target "cig-mc at geodynamics.org"
+
+\end_inset
+
+ for assistance.
\end_layout
\begin_layout Standard
@@ -3494,8 +3534,7 @@
\end_layout
\begin_layout Standard
-To build just the CitcomS tools (or ``drivers'') from the legacy C code,
- give
+To build CitcomS binaries just from the C code, give
\family typewriter
configure
\family default
@@ -3623,8 +3662,8 @@
\end_inset
.
- The CitcomS v3.0.3 source package was created with Autoconf 2.59, Automake
- 1.9.2, and Libtool 1.5.6.
+ The CitcomS v3.0.3 source package was created with Autoconf 2.61, Automake
+ 1.9.6, and Libtool 1.5.26.
\end_layout
\begin_layout Subsection
@@ -3844,7 +3883,8 @@
\end_layout
\begin_layout Standard
-When you build CitcomS, two binary executables,
+No matter you build CitcomS with or without Pyre, two binary executables,
+
\family typewriter
CitcomSRegional
\family default
@@ -3852,13 +3892,13 @@
\family typewriter
CitcomSFull
\family default
-, are placed under the
+, are always placed under the
\family typewriter
bin
\family default
directory.
- These programs do not use Python or the Pyre framework (even if CitcomS
- was configured to use the Pyre framework).
+ These programs are compiled from pure C code and do not use Python or the
+ Pyre framework.
Each program has the same usage:
\end_layout
@@ -3889,6 +3929,20 @@
.
\end_layout
+\begin_layout Standard
+The pure C version, compared to the Pyre version, shares the same input
+ parameters and functionality, but is less flexible in changing parameters
+ and in launching parallel jobs.
+ Users are encouraged to use the Pyre version if possible.
+ In the following sections and Chapter
+\begin_inset LatexCommand ref
+reference "cha:Cookbooks"
+
+\end_inset
+
+, we will concentrate on the Pyre version only.
+\end_layout
+
\begin_layout Section
Using CitcomS with Pyre
\end_layout
@@ -3945,8 +3999,8 @@
\begin_layout Standard
Most of the properties you will set using CitcomS have names which are identical
- to the parameters for the old CitcomS, which are described in Appendix
-
+ to the parameters for CitcomS in pure C version, which are described in
+ Appendix
\begin_inset LatexCommand ref
reference "cha:Appendix-A:-Input"
@@ -3965,10 +4019,6 @@
\family typewriter
.cfg
\family default
- or
-\family typewriter
-.pml
-\family default
format.
\end_layout
@@ -4097,28 +4147,6 @@
generated by another program, e.g., a GUI, web application, or a high-level
structured editor.
This file fomat will not be discussed further here.
- But if you are interested in using
-\family typewriter
-.pml
-\family default
- files, note that
-\family typewriter
-.pml
-\family default
- files and
-\family typewriter
-.cfg
-\family default
- files can be used interchangeably; in the following discussion, a file
- with a
-\family typewriter
-.pml
-\family default
- extension can be substituted anywhere a
-\family typewriter
-.cfg
-\family default
- file can be used.
\end_layout
\begin_layout Subsection
@@ -4126,11 +4154,12 @@
\end_layout
\begin_layout Standard
-Configuration files may be specified on the command line:
+One or more onfiguration files and command line options may be specified
+ on the command line:
\end_layout
\begin_layout LyX-Code
-$ citcoms example.cfg
+$ citcoms a.cfg b.cfg --foo.bar=baz
\end_layout
\begin_layout Standard
@@ -4171,7 +4200,13 @@
\begin_layout Standard
Parameters given directly on the command line will override any input contained
in a configuration file.
- Configuration files given on the command line override all others.
+ If more than one configurations files are given on the command line, the
+ later one override the former ones.
+ Configuration files given on the command line override all other
+\family typewriter
+CitcomS.cfg
+\family default
+ files.
The
\family typewriter
CitcomS.cfg
@@ -4210,6 +4245,11 @@
\end_inset
9 nodal points.
+ Since we did not provide the parameter
+\family typewriter
+solver.mesher.nodez
+\family default
+, the default value 9 is used.
The model results are written to files
\family typewriter
example0.*
@@ -4289,16 +4329,9 @@
\newline
[CitcomS.solver.mesher]
\newline
-nprocx = 1
+nodex = 17
\newline
-nprocy = 1
-\newline
-nodex = 9
-\newline
-nodey =
- 9
-\newline
-nodez = 9
+nodey = 17
\end_layout
\begin_layout Section
@@ -4569,7 +4602,11 @@
%HOSTNAME
\family default
will be substituted by the hostname of each machine.
- As the final example for a local file system, you can specify an arbitrary
+
+\end_layout
+
+\begin_layout Standard
+As the final example for a local file system, you can specify an arbitrary
output directory for each machine.
To do so, you must write a program to be executed on each machine which
will print the output directory.
@@ -5180,11 +5217,21 @@
Usually, the stderr is directed to your terminal so that you can monitor
the progress.
On some system, the stderr is redirected to a file.
- In any case, the progress is always saved in a log file.
+ In any case, the progress is always saved in a log file (e.g.
+
+\family typewriter
+example1.log
+\family default
+).
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 units)
- and CPU time (in seconds) of every time step.
+ The time file (e.g.
+
+\family typewriter
+example1.time
+\family default
+) 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
reference "cha:Appendix-C:-CitComS,"
@@ -7864,6 +7911,12 @@
\begin_layout Chapter
Cookbooks
+\begin_inset LatexCommand label
+name "cha:Cookbooks"
+
+\end_inset
+
+
\end_layout
\begin_layout Section
@@ -7890,6 +7943,21 @@
for more information).
\end_layout
+\begin_layout Standard
+Cookbook 1 to 4 introduces the basic parameters and are suitable for all
+ users.
+ Cookbook 5 introduces time-dependent velocity boundary conditions and tuning
+ of the advection solver.
+ Cookbook 6 introduces the pseudo-free-surface formulation for studying
+ short wavelength dynamics topography.
+ Cookbook 7 introduces thermo-chemical convection problem and tuning of
+ the Conjugate Gradient velocity solver.
+ Cookbook 8 introduces compressible convection problem, checkpointing/restarting
+, geoid and tuning of the Multigrid and Uzawa velocity solver.
+ Cookbook 10 introduces embedding one CitcomS domain within another CitcomS
+ domain, and further tuning of the advection solver.
+\end_layout
+
\begin_layout Section
\begin_inset LatexCommand label
name "sec:Cookbook-1:-Global"
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