[cig-commits] r7632 - cs/cigma/branches/cigma-0.9b1/doc/manual
sue at geodynamics.org
sue at geodynamics.org
Tue Jul 10 10:49:28 PDT 2007
Author: sue
Date: 2007-07-10 10:49:28 -0700 (Tue, 10 Jul 2007)
New Revision: 7632
Modified:
cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx
Log:
linkified URLs, other format and minor content edits, added citsoms's intro to hdf5
Modified: cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx
===================================================================
--- cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx 2007-07-10 17:46:59 UTC (rev 7631)
+++ cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx 2007-07-10 17:49:28 UTC (rev 7632)
@@ -135,8 +135,8 @@
The CIG Model Analyzer (Cigma) consists of a suite of tools intended to
facilitate the comparison of numerical models.
CIG has developed Cigma in response to demand from the short-term tectonics
- community, who desired for a simple tool that can perform rigorous error
- analysis on their FEM codes.
+ community for a simple tool that can perform rigorous error analysis on
+ their FEM codes.
\end_layout
@@ -159,9 +159,8 @@
\begin_layout Standard
Cigma can do analysis in two ways.
It can take a random sampling of points inside a domain of interest and
- analyze the pointwise differences between physical fields.
- A second way it can operate is to perform an integration of the errors
- over a discretized version of the domain.
+ analyze the pointwise differences between physical fields, or it can perform
+ an integration of the errors over a discretized version of the domain.
\end_layout
\begin_layout Standard
@@ -235,8 +234,11 @@
\end_layout
\begin_layout Standard
-This will create several binaries inside the (TODO: typewriter font) bin/
- directory under the project root.
+This will create several binaries inside the
+\family typewriter
+bin/
+\family default
+directory under the project root.
\end_layout
\begin_layout Section
@@ -249,8 +251,14 @@
\begin_layout Standard
The primary dependency for Cigma is the Hierarchical Data Format (HDF5)
- library, which can be obtained from.
- HDF5 is available for download from http://hdf.ncsa.uiuc.edu/HDF5 (TODO)
+ library, which can be obtained from [TODO: what did you wish here? URL
+ that follows?].
+ HDF5 is available for download from
+\begin_inset LatexCommand \htmlurl[The HDF Group]{hdf.ncsa.uiuc.edu/HDF5}
+
+\end_inset
+
+.
\end_layout
\begin_layout Subsection
@@ -259,7 +267,12 @@
\begin_layout Standard
PyTables is a python extension module that builds on top of the HDF5 library.
- It is available from http://www.pytables.org (TODO: linkify)
+ It is available from
+\begin_inset LatexCommand \htmlurl[PyTables]{www.pytables.org}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -267,11 +280,11 @@
and issue the following commands
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ cd pytables-2.x.x
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ python setup.py install --prefix=$HOME
\end_layout
@@ -284,8 +297,12 @@
HDF5 files.
You can use it for viewing the internal file hierarchy in a tree structure,
adding new datasets, and modifying or deleting existing datasets.
- You can download it from the HDFView home page at http://hdf.ncsa.uiuc.edu/hdf-jav
-a-html/hdfview (TODO: linkify)
+ You can download it from the
+\begin_inset LatexCommand \htmlurl[HDFView home page]{hdf.ncsa.uiuc.edu/hdf-java-html/hdfview}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -430,18 +447,19 @@
Cigma was designed with the following use cases in mind:
\end_layout
-\begin_layout Itemize
-Error Analysis: To assist scientists in comparing two different codes, possibly
+\begin_layout Description
+Error\InsetSpace ~
+Analysis To assist scientists in comparing two different codes, possibly
on the same mesh
\end_layout
-\begin_layout Itemize
-Benchmarking: To help the geodynamics community agree on a standard solution
+\begin_layout Description
+Benchmarking To help the geodynamics community agree on a standard solution
to a specific problem
\end_layout
-\begin_layout Itemize
-Verification: For developers to test software changes so as to ensure that
+\begin_layout Description
+Verification For developers to test software changes so as to ensure that
those changes don't affect the consistency of the results
\end_layout
@@ -467,9 +485,87 @@
\end_layout
\begin_layout Standard
-(TODO: yank part of intro-to-hdf5 chapter from CitcomS manual)
+(TODO: edit following part of intro-to-hdf5 chapter from CitcomS manual)
\end_layout
+\begin_layout Subsection
+About HDF5
+\end_layout
+
+\begin_layout Standard
+The Hierarchical Data Format (HDF) is a portable file format developed at
+ the
+\begin_inset LatexCommand \htmlurl[National Center for Supercomputing Applications (NCSA)]{hdf.ncsa.uiuc.edu/HDF5}
+
+\end_inset
+
+.
+ It is designed for storing, retrieving, analyzing, visualizing, and converting
+ scientific data.
+ The current and most popular version is HDF5, which stores multi-dimensional
+ arrays together with ancillary data in a portable self-describing format.
+ It uses a hierarchical structure that provides application programmers
+ with a host of options for organizing how data is stored in HDF5 files.
+\end_layout
+
+\begin_layout Standard
+HDF5 files are organized in a hierarchical structure, similar to a UNIX
+ file system.
+ Two types of primary objects, groups and datasets, are stored in this structure.
+ A group contains instances of zero or more groups or datasets, while a
+ dataset stores a multi-dimensional array of data elements.
+ Both kinds of objects are accompanied by supporting metadata.
+\end_layout
+
+\begin_layout Standard
+A dataset is physically stored in two parts: a header and a data array.
+ The header contains miscellaneous metadata describing the dataset as well
+ as information that is needed to interpret the array portion of the dataset.
+ Essentially, it includes the name, datatype, dataspace, and storage layout
+ of the dataset.
+ The name is a text string identifying the dataset.
+ The datatype describes the type of the data array elements.
+ The dataspace defines the dimensionality of the dataset, i.e., the size and
+ shape of the multi-dimensional array.
+ The dimensions of a dataset can be either fixed or unlimited (extensible).
+ The storage layout specifies how the data arrays are arranged in the file.
+\end_layout
+
+\begin_layout Standard
+The data array contains the values of the array elements and can be either
+ stored together in a contiguous file space or split into smaller
+\shape italic
+chunks
+\shape default
+ stored at any allocated location.
+ Chunks are defined as equally-sized multi-dimensional subarrays (blocks)
+ of the whole data array and each chunk is stored in a separate contiguous
+ file space.
+ Extensible datasets whose dimensions can grow are required to be stored
+ in chunks.
+ One dimension is increased by allocating new chunks at the end of the file
+ to cover the extension.
+\end_layout
+
+\begin_layout Standard
+HDF5 also supports access to portions (or selections) of a dataset by
+\shape italic
+hyperslabs
+\shape default
+, which consist of a subarray or strided subarray of the multi-dimensional
+ dataset.
+ The selection is performed in the file dataspace for the dataset.
+ HDF5 also supports parallel I/O.
+ Parallel access is supported through MPI-IO.
+ The file and datasets are collectively created/opened by all participating
+ processes.
+ Each process accesses part of a dataset by defining its own file dataspace
+ for that dataset.
+ When accessing data, the data transfer property specifies whether each
+ process will perform independent I/O or all processes will perform collective
+ I/O.
+\end_layout
+
\begin_layout Section
Field Metadata
\end_layout
@@ -479,17 +575,17 @@
interpret the meaning of the field data
\end_layout
-\begin_layout Itemize
-MeshID: a universally unique identifier (uuid) assigned to the mesh
+\begin_layout Description
+MeshID a universally unique identifier (uuid) assigned to the mesh
\end_layout
-\begin_layout Itemize
-MeshLocation: the HDF5 group which contains the appropriate coordinates
- and connectivity datasets.
+\begin_layout Description
+MeshLocation the HDF5 group which contains the appropriate coordinates and
+ connectivity datasets.
\end_layout
-\begin_layout Itemize
-FunctionSpace: identifies which shape functions for interpolating values
+\begin_layout Description
+FunctionSpace identifies which shape functions for interpolating values
inside the element.
\end_layout
@@ -502,7 +598,7 @@
\end_layout
\begin_layout Standard
-The data flow in Cigma is decoupled to the extent.
+The data flow in Cigma is decoupled to the extent [TODO: more to this sentence?].
\end_layout
@@ -757,7 +853,7 @@
\begin_layout Standard
\begin_inset Graphics
filename figures/cigma-abcd-triangle.jpg
- lyxscale 50
+ lyxscale 25
scale 25
\end_inset
@@ -2046,7 +2142,7 @@
\begin_layout Bibliography
-\bibitem {key-12}
+\bibitem {key-3}
Uesu, D., L.
Bavoil, S.
Fleishman, J.
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