[cig-commits] r4777 - mc/3D/CitcomS/trunk/doc/manual

[sue at geodynamics.org]

Author: sue
Date: 2006-10-10 13:37:07 -0700 (Tue, 10 Oct 2006)
New Revision: 4777

Modified:
   mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
added hdf5 install and addt tools chapters

Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-10-10 20:03:32 UTC (rev 4776)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-10-10 20:37:07 UTC (rev 4777)
@@ -1,4 +1,4 @@
-#LyX 1.4.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
 \lyxformat 245
 \begin_document
 \begin_header
@@ -512,7 +512,7 @@
  In the summer of 2005, as part of the 2.0.1 release, the CIG replaced the
  old build procedure with the GNU Build System.
  A subsequent release, version 2.0.2, could compile and run on 64-bit systems.
- (TODO: histroy of v2.1)
+ (TODO: history of v2.1)
 \end_layout
 
 \begin_layout Section
@@ -1339,11 +1339,11 @@
 \family typewriter
 tar
 \family default
- command: (TODO: update version numbers).
+ command: 
 \end_layout
 
 \begin_layout LyX-Code
-$ tar xzf CitcomS-2.0.2.tar.gz
+$ tar xzf CitcomS-2.1.0.tar.gz
 \end_layout
 
 \begin_layout Standard
@@ -1351,7 +1351,7 @@
 \end_layout
 
 \begin_layout LyX-Code
-$ gunzip -c CitcomS-2.0.2.tar.gz | tar xf -
+$ gunzip -c CitcomS-2.1.0.tar.gz | tar xf -
 \end_layout
 
 \begin_layout Section
@@ -1377,7 +1377,7 @@
 \newline
 
 \family typewriter
-$ cd CitcomS-2.0.2
+$ cd CitcomS-2.1.0
 \family default
 
 \newline
@@ -1439,7 +1439,7 @@
 \end_layout
 
 \begin_layout LyX-Code
-$ cd CitcomS-2.0.2
+$ cd CitcomS-2.1.0
 \end_layout
 
 \begin_layout LyX-Code
@@ -1968,14 +1968,124 @@
  problem for you.
 \end_layout
 
+\begin_layout Section
+HDF5 Configuration (optional)
+\end_layout
+
 \begin_layout Standard
-TODO: HDF5 Configuration here
-\newline
-TODO: Additional Tools section here (or somewhere
- in this chapter).
+CitcomS requires parallel HDF5 (PHDF5) for writing its output in binary
+ format.
+ In turn, PHDF5 requires an MPI compiler with MPI-IO support and a parallel
+ filesystem.
+ If an existing installation of the PHDF5 library is not available on your
+ cluster, you can compile it from source by following the instructions in
+ the file release docs/INSTALL parallel under the HDF5 source tree.
+ Under Debian Linux, you may simply install the libhdf5-mpich, libhdf5-mpich-dev
+ and hdf5-tools packages.
 \end_layout
 
+\begin_layout Standard
+By default, CitcomS will attempt to auto-detect your PHDF5 installation,
+ and will disable HDF5 support if it is not found.
+ You may explicitly specify the location of your PHDF5 installation by setting
+ the PHDF5 HOME environment variable to the appropriate installation prefix.
+\end_layout
+
+\begin_layout LyX-Code
+$ export PHDF5_HOME=/opt/phdf5/1.6.5
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --with-hdf5 --prefix=$HOME/cig [...]
+\end_layout
+
 \begin_layout Section
+Additional Tools
+\end_layout
+
+\begin_layout Standard
+While the following software is not necessary for the normal operation of
+ CitcomS, you may find it useful for accessing CitcomS data in HDF5 files.
+\end_layout
+
+\begin_layout Subsection
+NumPy
+\end_layout
+
+\begin_layout Standard
+NumPy is an extension to Python which adds support for multi-dimensional
+ arrays for use in scientific computing.
+ You may download NumPy at the 
+\begin_inset LatexCommand \htmlurl[Numby home page]{http://numpy.scipy.org/}
+
+\end_inset
+
+.
+ To compile and install this extension, download it and issue the following
+ commands:
+\end_layout
+
+\begin_layout LyX-Code
+$ cd numpy-1.0.x
+\end_layout
+
+\begin_layout LyX-Code
+$ python setup.py install --prefix=$HOME/cig
+\end_layout
+
+\begin_layout Standard
+Alternatively, under Debian Linux you can install the python-numpy package.
+ On Gentoo Linux, NumPy is available in the dev-python/numpy ebuild.
+\end_layout
+
+\begin_layout Subsection
+PyTables
+\end_layout
+
+\begin_layout Standard
+PyTables is an extension to Python which is able to expose HDF5 array datasets
+ as Python NumPy arrays.
+ It is available at 
+\begin_inset LatexCommand \htmlurl[PyTables]{http://www.pytables.org}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
+To compile and install this extension, download it and issue the following
+ commands:
+\end_layout
+
+\begin_layout LyX-Code
+$ cd pytables-2.0.x
+\end_layout
+
+\begin_layout LyX-Code
+$ python setup.py install --prefix=$HOME/cig
+\end_layout
+
+\begin_layout Standard
+To install on Debian Linux, you may use the python-tables package instead.
+ On Gentoo Linux, it is available in the dev-python/pytables ebuild.
+\end_layout
+
+\begin_layout Subsection
+HDFView
+\end_layout
+
+\begin_layout Standard
+HDFView is a visual tool for browsing and editing HDF5 files.
+ You may download it from 
+\begin_inset LatexCommand \htmlurl[HDF Java Products]{http://hdf.ncsa.uiuc.edu/hdf-java-html/hdfview/}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Section
 \begin_inset LatexCommand \label{sec:Batch-System-Configuration}
 
 \end_inset
@@ -2243,7 +2353,7 @@
 \end_inset
 
 .
- The CitComS v2.0.2 source package was created with Autoconf 2.59, Automake
+ The CitComS v2.1.0 source package was created with Autoconf 2.59, Automake
  1.9.2, and Libtool 1.5.6.
 \end_layout