[cig-commits] r5362 - mc/3D/CitcomS/trunk/doc/manual
sue at geodynamics.org
sue at geodynamics.org
Tue Nov 28 11:26:21 PST 2006
Author: sue
Date: 2006-11-28 11:26:20 -0800 (Tue, 28 Nov 2006)
New Revision: 5362
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
various edits to 3.6.1 and 3.7
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-11-28 07:33:41 UTC (rev 5361)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-11-28 19:26:20 UTC (rev 5362)
@@ -520,9 +520,8 @@
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 data output that were
- created for production runs (see Chapter
-
+ The HDF5 format allows you to deal with the massive data output created
+ for production runs (see Chapter
\begin_inset LatexCommand \ref{cha:Working-with-HDF5}
\end_inset
@@ -3645,23 +3644,25 @@
\end_layout
\begin_layout Subsection
-Output Directory and Output Formats
+Output Directories and Output Formats
\end_layout
\begin_layout Standard
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.
+ running CitComS.py so that you can manage these files as well as use a post-proc
+essing program contained in this distribution.
\end_layout
\begin_layout Standard
-You might have a local hard disk on every machine (node) on a Beowulf cluster.
- Each hard disk is mounted locally to the machine.
- This scenario is referred to as a local file system in this section.
- Or you might be using some kind of parallel file system on your computer
- (e.g., NFS, GPFS, PVFS, to name a few), which is mounted on all of the nodes.
+How to best manage this large output depends on whether you will use a local
+ file system or a parallel file system.
+ For example, if you have a local hard disk on every machine (node) on a
+ Beowulf cluster, with each hard disk mounted locally to the machine, this
+ scenario is referred to as a local file system in this section.
+ Or you might use some kind of parallel file system on your computer (e.g.,
+ NFS, GPFS, PVFS, to name a few), which is mounted on all of the nodes.
Usually your home directory is mounted on the parallel file system.
The local file system is usually more cost- and time-efficient than the
parallel file system.
@@ -3670,7 +3671,7 @@
\begin_layout Standard
If you want CitComS.py to write its output to the local hard disks, you need
- to have a common directory structure for all of the local hard disks.
+ to have a common directory structure on all of the local hard disks.
For example, if the directory
\family typewriter
/scratch
@@ -3692,7 +3693,7 @@
datadir
\family default
property, which specifies the output directory.
- Then, the output files would be placed in
+ The output files are then placed in
\family typewriter
/scratch
\family default
@@ -3702,9 +3703,8 @@
\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:
+However, 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
@@ -3716,17 +3716,17 @@
\end_layout
\begin_layout Standard
-The specail string %HOSTNAME will be substituted by the hostname of each
+The special 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
+ 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.
+ The program must be named
\family typewriter
citcoms_datadir
\family default
- and is on your path.
+ and must reside on your path.
An example of
\family typewriter
citcoms_datadir
@@ -3748,20 +3748,26 @@
\end_layout
\begin_layout Standard
-The specail string %DATADIR will be substituted by the output of
+The special string
\family typewriter
+%DATADIR
+\family default
+ 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
+If you want CitComS.py to write its output to a parallel file system, you
have several choices.
- You can run the example script with (you should subsutitute
+ You can run the example script as follows (substitute
\family typewriter
+\emph on
username
\family default
+\emph default
with your own username):
\end_layout
@@ -3770,11 +3776,13 @@
\family typewriter
example1.cfg
\family default
- --solver.datadir=/home/username
+ --solver.datadir=/home/
+\emph on
+username
\end_layout
\begin_layout Standard
-Then, the output files would be placed in your home directory with a filename
+The output files are then placed in your home directory with a filename
prefix
\family typewriter
example1
@@ -3782,10 +3790,14 @@
.
A potential problem with this approach is that the directory
\family typewriter
-/home/username
+/home/
+\emph on
+username
\family default
- will be flooded with hundreds or tens of thousands files if you are running
- a model using several tens of processors for thousands of time steps.
+\emph default
+ will be flooded with hundreds of files, perhaps even tens of thousands
+ of files if you are running a model using several tens of processors for
+ thousands of time steps.
Alternatively you can have each machine write its output to its own directory,
according to its MPI rank.
You can run the example script with:
@@ -3796,31 +3808,59 @@
\family typewriter
example1.cfg
\family default
- --solver.datadir=/home/username/%RANK
+ --solver.datadir=/home/
+\emph on
+username
+\emph default
+/%RANK
\end_layout
\begin_layout Standard
-The specail string %RANK will be substituted by the MPI rank of each processor.
+The special string
+\family typewriter
+%RANK
+\family default
+ will be substituted by the MPI rank of each processor.
You will see four new directories
\family typewriter
-/home/username/0
+/home/
+\emph on
+username
+\emph default
+/0
\family default
,
\family typewriter
-/home/username/1
+/home/
+\emph on
+username
+\emph default
+/1
\family default
,
\family typewriter
-/home/username/2
+/home/
+\emph on
+username
+\emph default
+/2
\family default
, and
\family typewriter
-/home/username/3
+/home/
+\emph on
+username
+\emph default
+/3
\family default
.
The processor of MPI rank 0 will write its output in
\family typewriter
-/home/username/0
+/home/
+\emph on
+username
+\emph default
+/0
\family default
with a filename prefix
\family typewriter
@@ -3842,9 +3882,9 @@
The last choice is the most powerful one.
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.
- In order to use this feature, you need to compile CitComS.py with the parallel
+ The HDF5 file takes less disk space than all the ASCII files combined and
+ doesn't require additional post-processing to be visualized in OpenDX.
+ In order to use this feature, you must compile CitComS.py with the parallel
HDF5 library if you haven't done so already (see Section
\begin_inset LatexCommand \vref{sec:HDF5-Configuration}
@@ -3859,7 +3899,11 @@
\family typewriter
example1.cfg
\family default
- --solver.datafile=/home/username/example1
+ --solver.datafile=/home/
+\emph on
+username
+\emph default
+/example1
\backslash
\newline
@@ -3867,9 +3911,13 @@
\end_layout
\begin_layout Standard
-Then, the output file will be
+The output file will be
\family typewriter
-/home/username/example1.h5
+/home/
+\emph on
+username
+\emph default
+/example1.h5
\family default
.
(TODO: update for the new hdf5 scheme...) See Chapter
@@ -3877,7 +3925,7 @@
\end_inset
- for more information on how to work with HDF5 output.
+ for more information on how to work with the HDF5 output.
\end_layout
\begin_layout Subsection
@@ -4309,9 +4357,12 @@
\begin_layout Standard
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 $TG_COMMUNITY/CIG/CitcomS/TG_README and follow the instruction
- inside.
+ To use CitComS.py on these machines, please log in to your TeraGrid account
+ and read the instructions at
+\family typewriter
+$TG_COMMUNITY/CIG/CitcomS/TG_README
+\family default
+.
\end_layout
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