[cig-commits] r4677 - mc/3D/CitcomS/trunk/doc/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Mon Oct 2 15:43:46 PDT 2006
Author: tan2
Date: 2006-10-02 15:43:45 -0700 (Mon, 02 Oct 2006)
New Revision: 4677
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
Slightly updated postprocessing chapter. Revised Cookbook 1.
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-02 20:55:51 UTC (rev 4676)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-02 22:43:45 UTC (rev 4677)
@@ -2727,7 +2727,7 @@
\end_layout
\begin_layout Paragraph
-Example: Uniprocessor CitComS.py, example0.cfg
+Example: Uniprocessor, example0.cfg
\end_layout
\begin_layout LyX-Code
@@ -2758,6 +2758,10 @@
\end_layout
\begin_layout Section
+\begin_inset LatexCommand \label{sec:Multiprocessor-Example}
+
+\end_inset
+
Multiprocessor Example
\end_layout
@@ -2781,7 +2785,7 @@
\end_layout
\begin_layout Paragraph
-Example: Multiprocessor CitComS.py, example1.cfg
+Example: Multiprocessor, example1.cfg
\end_layout
\begin_layout LyX-Code
@@ -3202,20 +3206,17 @@
\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).
- You will have to retrieve and combine the data for the time-step (age)
+ You will have to retrieve and combine the data for the time step (or age)
of interest.
-\end_layout
-
-\begin_layout Standard
-To visualize your results, it is recommended that you use the open source
+ To visualize your results, it is recommended that you use the open source
Open Visualization Data Explorer, better known as OpenDX.
- Both the software and tutorials are available from the
+ The software is available from the
\begin_inset LatexCommand \htmlurl[OpenDX website]{http://www.opendx.org/}
\end_inset
.
- If you are using Mac OS X, a free version OpenDX is available via
+ If you are using Mac OS X, OpenDX is available via
\begin_inset LatexCommand \htmlurl[Fink]{http://fink.sourceforge.net/}
\end_inset
@@ -3232,14 +3233,22 @@
\end_layout
\begin_layout Section
-Processing on a Beowulf Cluster
+Postprocessing on a Beowulf Cluster
\end_layout
\begin_layout Standard
Generally, the results from your CitComS 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 your datafile in the input file.
+ specified as the
+\family typewriter
+datafile
+\family default
+ property (and maybe
+\family typewriter
+datadir
+\family default
+ property) in the input file.
To examine those files, login to a node and change directories to the one
you specified with a prefix.
For example, if you selected your datafile to be called
@@ -3304,13 +3313,13 @@
When you execute a CitComS run, your input parameters will be saved in a
file
\family typewriter
-PID.parameters
+pidxxxxx.cfg
\family default
-, where
+ where
\family typewriter
-PID
+xxxxx
\family default
- is a five-digit number for the process ID.
+ 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)
@@ -3378,13 +3387,12 @@
\end_layout
\begin_layout Standard
-If your cluster uses a parallell file system and all of your data resides
- in one directory (e.g.,
+If all of your data resides in one directory (e.g.,
\family typewriter
/scratch/username
\family default
-) in the 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 post-process your output files by following
+ the instructions in the next section.
\end_layout
@@ -3687,6 +3695,18 @@
of problems CitComS.py can solve.
Cookbook examples range from regional to full spherical shell problems
that address traditional convection problems.
+ These cookbook examples are distributed with the package under
+\family typewriter
+the examples
+\family default
+ directory.
+ However, you might need to edit these example scripts slightly to launch
+ the job on your cluster (see
+\begin_inset LatexCommand \vref{sec:Multiprocessor-Example}
+
+\end_inset
+
+for more information.)
\end_layout
\begin_layout Section
@@ -3704,9 +3724,9 @@
\begin_layout Standard
You would like to solve for thermal convection within a full spherical shell
domain.
- One of the versions of CitComS.py is designed to run on a cluster that decompose
-s the shell into 12 equal "caps" and then distributes the calculation for
- caps onto separate processors.
+ The full spherical versions of CitComS.py is designed to run on a cluster
+ that decomposes the spherical shell into 12 equal "caps" and then distributes
+ the calculation for caps onto separate processors.
To run CitComS.py with the full solver parameter set, it is recommended
that you have a minimum of 12 processors available on your cluster.
@@ -3733,9 +3753,7 @@
\end_inset
-Global\InsetSpace ~
-Model\InsetSpace ~
-"Caps": Left (A): Three-dimensional perspective image showing
+Global Model "Caps": Left (A): Three-dimensional perspective image showing
the 12 spherical caps used in a full CitComS.py run.
Right (B): The temperature field at 1081 km depth from a Cookbook 1 run.
\end_layout
@@ -3750,246 +3768,98 @@
\end_layout
\begin_layout Standard
-You will be running
-\family sans
-cookbook1.sh
+You will be using
+\family typewriter
+cookbook1.cfg
\family default
- which calls the script
-\family sans
-citcomsfull.sh
-\family default
.
- The first set of parameters specifies the number of nodes (12) and their
- names on your cluster through Pyre's
-\family sans
-launcher
-\family default
- facility.
+ The first set of parameters specifies that you are going to use the full
+ spherical version of solver.
\end_layout
\begin_layout LyX-Code
---launcher.nodes=12
-\backslash
-
+solver = full
\end_layout
-\begin_layout LyX-Code
---launcher.nodegen="n%03d"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodelist=[101-106,101-106]
-\backslash
-
-\end_layout
-
\begin_layout Standard
-The second set of parameters specifies the number of time steps (101), and
- how often the computation should be monitored (25).
+The second set of parameters specifies the number of time steps (101), how
+ often to montior the computation (25), the prefix of output filenames (cookbook
+1).
\end_layout
\begin_layout LyX-Code
---steps=101
-\backslash
-
+steps = 101
+\newline
+monitoringFrequency = 25
+\newline
+datafile = cookbook1
\end_layout
-\begin_layout LyX-Code
---controller.monitoringFrequency=25
-\backslash
-
-\end_layout
-
\begin_layout Standard
-The last set of parameters includes
-\end_layout
-
-\begin_layout Itemize
-the prefix of the output filenames, e.g.,
+The last set of parameters includes the number of perturbations to the initial
+ temperature (1), the number of nodal lines of the perturbation in the longitudi
+nal direction, e.g., spherical harmonic order (3), and the number of nodal
+ lines in the latitudinal direction, e.g., spherical harmonic degree (2).
+ Note that although the number of perturbations is assigned here as
\family typewriter
- cookbook1
-\end_layout
-
-\begin_layout Itemize
-the number of perturbations (1)
-\end_layout
-
-\begin_layout Itemize
-the number of nodal lines in the longitudinal direction (4), e.g., spherical
- harmonic in terms of time-step order or
-\family typewriter
-perturbm=2
-\family default
-,
-\end_layout
-
-\begin_layout Itemize
-the number of nodal lines in the latitudinal direction, e.g., spherical harmonic
- degree
-\family typewriter
-perturbl=3
-\end_layout
-
-\begin_layout Quote
-Note that although the number of perturbations is assigned here as
-\family typewriter
solver.ic.num_perturbations=1
\family default
, that is actually the default value.
\end_layout
\begin_layout LyX-Code
---solver.datafile="cookbook1"
-\backslash
-
+num_perturbations=1
+\newline
+perturbl=3
+\newline
+perturbm=2
\end_layout
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.num_perturbations=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.perturbl=3
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.perturbm=2
-\end_layout
-
\begin_layout Standard
-Assuming your script is named
-\family typewriter
-cookbook1.sh
-\family default
-, it is run by typing
+This example is run by typing
\end_layout
\begin_layout LyX-Code
-$ ./cookbook1.sh
+$ citcoms cookbook1.cfg
\end_layout
-\begin_layout Subsection
-Cookbook 1: Global Model
+\begin_layout Paragraph*
+Example: Global Model, cookboo1.cfg
\end_layout
\begin_layout LyX-Code
-#!/bin/sh
+[CitcomS]
\newline
+solver = full
+\newline
+steps = 101 ; number of time steps
+\newline
\newline
-../../tests/citcomsfull.sh
-\backslash
+[CitcomS.
+controller]
+\newline
+monitoringFrequency = 25 ; how often to monitor the computation
+\newline
-\end_layout
+\newline
+[Ci
+tcomS.solver]
+\newline
+datafile = cookbook1 ; prefix of output filenames
+\newline
-\begin_layout LyX-Code
-
-\backslash
-
+\newline
+[CitcomS.solv
+er.ic]
+\newline
+num_perturbations = 1
+\newline
+perturbl = 3
+\newline
+perturbm = 2
\end_layout
-\begin_layout LyX-Code
---launcher.nodes=12
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodegen="n%03d"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodelist=[141-146,141-146]
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---steps=101
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---controller.monitoringFrequency=25
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.datafile="cookbook1"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.num_perturbations=1
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.perturbl=3
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.ic.perturbm=2
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---solver.rayleigh=5.0e+4
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-# End of file
-\end_layout
-
\begin_layout Standard
Once you have run the model, you can visualize it using OpenDX, described
in the previous chapter.
@@ -4011,6 +3881,7 @@
\begin_layout Standard
\begin_inset Graphics
filename graphics/cookbook1.2.jpg
+ lyxscale 50
\end_inset
@@ -4033,7 +3904,7 @@
\end_layout
\begin_layout Standard
-You have generated a simple example of the full CitComS model, with minimal
+You have generated a simple example of the full CitComS.py model, with minimal
parameter alterations.
With a default Rayleigh number of
\begin_inset Formula $10^{5}$
@@ -4047,28 +3918,19 @@
\begin_layout Standard
As a note, it is not required that 12 processors, with one spherical cap
per processor, be used.
- As an end-member possibility, 12 different jobs could be run on a single
- computer by invoking:
+ As an end-member possibility, for example, 12 different jobs could be run
+ on a single computer (
+\family typewriter
+n001
+\family default
+ in this example) by invoking:
\end_layout
\begin_layout LyX-Code
---launcher.node=12
-\backslash
-
+$ citcoms cookbook1.cfg --launcher.nodegen="n%03d" --launcher.nodelist=[1,1,1,1,1,1
+,1,1,1,1,1,1]
\end_layout
-\begin_layout LyX-Code
---launcher.node="n%03d"
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
---launcher.nodelist=[101,101,101,101,101,101,101,101,101,101,101,101]
-\backslash
-
-\end_layout
-
\begin_layout Standard
This is not particularly efficient, but it does illustrate the flexibility
of both
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