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Contents of /release/4.0/doc/user/changes.tex

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2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3 % Copyright (c) 2003-2014 by University of Queensland
4 % http://www.uq.edu.au
5 %
6 % Primary Business: Queensland, Australia
7 % Licensed under the Open Software License version 3.0
8 % http://www.opensource.org/licenses/osl-3.0.php
9 %
10 % Development until 2012 by Earth Systems Science Computational Center (ESSCC)
11 % Development 2012-2013 by School of Earth Sciences
12 % Development from 2014 by Centre for Geoscience Computing (GeoComp)
13 %
14 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
16 \chapter{Changes from previous releases}
17 \label{app:changes}
19 \subsection*{3.4.2 to 4.0}
20 \begin{itemize}
21 \item New spectral element domain, \speckley
22 \item CUDA-based solvers and block-diagonal system matrices in \ripley
23 \item DC Resistivity forward modeling
24 \item New build options:
25 \begin{itemize}
26 \item 'domains': allows only the specified domains to be built
27 \item 'prelaunch', 'launcher', 'postlaunch': allows build-time
28 customization of escript launcher
29 \item 'cuda', 'nvcc', 'nvccflags', 'thrust_prefix': path and flags for
30 CUDA compiler and thrust headers
31 \end{itemize}
32 \item Gmsh reader now \MPI parallelised
33 \item cycle and timestamp support for saveSilo and saveVTK
34 \item PDEs using \ripley now have per-PDE assemblers to allow domains to have
35 multiple PDEs of different types without conflict
36 \item General documentation updates, both guides and code commenting
37 \item Test framework compatible with older versions of Python
38 \item Removed BASHisms from \escript launcher
39 \item Data objects now have hasNaN() and replaceNaN() methods
40 \item readBinaryGrid() now supports scaling and 64-bit floats in non-native
41 byte order
42 \item Now compiles with Cray compiler
43 \item Wave models corrected
44 \item Equality checks on Data objects now throw exceptions
45 \item General changes to help compilers with \OPENMP parallelisation
46 \item Intel-based \OPENMP flavours now have proper thread binding
47 \item \ripley dirac points no longer get lost in domains with enormous
48 elements
49 \item lots of improvements in inversion toolbox \downunder and symbolic
50 toolbox
51 \end{itemize}
53 \subsection*{3.4.1 to 3.4.2}
54 \begin{itemize}
55 \item Changes to SolverOptions: Most of this is under the hood at this point
56 but any code which accesses parameters from a SolverOptions object like this:
57 \begin{python}
58 variable.getSolverOptions().DIRECT
59 \end{python}
60 will need to be modified to:
61 \begin{python}
62 SolverOptions.DIRECT
63 \end{python}
65 \item Data objects can be created using smoothed random data.
66 \item Support for OSX10.9
67 \item Support for additional problem types in downunder.
68 \item More efficient ripley domains for large compute clusters
69 \item Added symbolic toolbox and associated documentation
70 \item Ripley now supports Dirac delta functions.
71 \item Improved reading of netCDF files
72 \item Paso is now in its own namespace
73 \item Examples have been updated to use Python 3 behaviour (with future imports for Python 2).
74 \item Ripley supports reading from gzipped files.
75 \item Fixed fault in documentation generation
76 \item Fixes to keep clang++ happy
77 \end{itemize}
80 \subsection*{3.4 to 3.4.1}
81 \begin{itemize}
82 \item Renamed design.Design to design.AbstractDesign as a more explicit/descriptive name, {\bf this will break any existing custom implementation} until changed to match.
84 \item Efficiency improvements in esys.downunder inversions.
85 \item Implemented more CF conventions for the netCDF datasource and added GDAL support.
86 \item Strongly coupled joint inversion added.
87 \item Preliminary work on seismic modelling.
88 \item Added support for more input data types in ER Mapper files.
89 \item Improved stability for long MPI runs.
90 \item Added timeStepFormat option to \texttt{esys.escript.saveESD}.
91 \item Document generation process more stable.
92 \item Added support for smoothed random 2D data.
93 \item Documentation updated.
94 \item Improved read support for grid-reading.
95 \item Removed last usages of C compiler.
96 \item Efficiency improvements in \texttt{esys.downunder}.
97 \item Removed support for VSL random (\texttt{boost::random} is sufficient).
98 \item Fixes related to compatibility with Intel compiler.
99 \item Simplified module structure.
100 \item Various code cleanup and bug fixes.
101 \end{itemize}
103 \subsection*{3.3.1 to 3.4}
104 \begin{itemize}
105 \item This release does not use the support bundles from $3.0$ so building from source will be required in more cases.
106 \item In Debian and Ubuntu, there are now two packages. One containing escript itself and the other containing documentation.
107 This fits better with the way Debian does things.
108 \item esys.weipa can now write Voxet files for data on ripley.
109 \item All support for OpenDX has been dropped.
110 \item Improved documentation HTML API documentation.
111 \item Improvements to inversion module.
112 \end{itemize}
115 \subsection*{3.3 to 3.3.1}
116 \begin{itemize}
117 \item Source packages for Debian and Ubuntu can now be made directly by dpkg-source from the source tree\footnote{For this to work, you will need to place a file called \texttt{svn_version} containing the revision number in the root of the source.}.
118 \item non-uniform 1D interpolation (see Section~\ref{sec:interpolation}).
119 \item The minimum version of python required for escript is now $2.6$.
120 \item saveVTK and saveDX (previously deprecated) have been removed from the main escript module.
121 Please see the \module{weipa} documentation for export functionality.
122 \item The \module{downunder} inversion module is included.
123 \begin{itemize}
124 \item The documentation includes an inversion cookbook to get you started.
125 \item Most operations are possible with \escript's existing dependencies but some \emph{may} require \module{pyproj} or \module{gdal}
126 but \escript will let you know if that happens.
127 \end{itemize}
129 \end{itemize}
132 \subsection*{3.2.1 to 3.3}
133 \begin{itemize}
134 \item Experimental support for \pythonthree.
135 \item Parameter order for the table interpolation methods has changed to be consistent.
136 Please test your scripts if you use these functions.
137 \item setX on \finley and \dudley domains will now only accept coordinates from ContinuousFunction spaces.
138 This is to avoid some potentially nasty behaviour when using periodic boundary conditions.
139 You can still use setX, just make sure that you interpolate first.
140 \end{itemize}
143 \subsection*{3.1 to 3.2}
144 \begin{itemize}
145 \item The deprecated name for the launcher has been removed. To run scripts use
146 \emph{run-escript} not \emph{escript}.
147 \item \escript is no longer automatically imported by importing \finley.
148 You will need to import escript explicitly. (All of our example scripts do this anyway.)
149 \item An experimental version of the new Dudley domain is now available.
150 \item Various bug fixes and optimisations.
151 \item New algorithms for gmsh support.
152 \item Improvements to the AMG solver. AMG is the recommended solver for symmetric problems.
153 \item Fixed compilation issues using netcdf.
154 \item Redesigned configuration files to make it easier to compile from source
155 without finding the locations of all your libraries.
156 \item Faster rendering of documentation.
157 \item Documentation is now hyperlinked.
158 \item New data export module \weipa. The \texttt{saveVTK} functionality has
159 been moved into this module, and while calling \texttt{saveVTK} from the
160 \escript module still works it is discouraged and will be removed in a
161 future release.
162 \item New \texttt{esys.escript.DataManager} class for convenient checkpointing
163 and exporting of escript data.
164 \item \VisIt simulation interface for online data access and visualization.
165 \item Simpler interpolation and support for interpolation from 3D vectors.
166 \item HRZ lumping has been added and some clarification on how to use it.
167 \item Data objects populated with ``random'' values can be created.
168 \end{itemize}
170 \subsection*{3.0 to 3.1}
171 \begin{itemize}
172 \item The \emph{escript} launcher has been renamed to \emph{run-escript}. The
173 old name will still work in this version but will be removed in the future.
174 \item Lazy evaluation features have been improved and documented (see \Sec{sec:lazy}).
175 \item The \emph{escript} documentation now includes a new Cookbook which
176 demonstrates how to solve sample problems using escript.
177 \item Macro elements have been introduced.
178 \item The \var{saveDataCSV} method allows one or more \Data objects to be
179 exported in CSV format (see \Sec{sec:savedatacsv}).
180 \item \Data objects can be populated by interpolating from values in a table.
181 \item The new \var{getInfLocator} and \var{getSupLocator} functions in
182 \pdetools return Locators to a minimal/maximal point over the
183 data.
184 \item There is a new class to model fault systems (\var{esys.escript.faultsystems.FaultSystem}).
185 \item A beta version of an Algebraic Multigrid (AMG) solver is included.
186 \item Inverting square matrices larger than 3x3 is now permitted if escript is
187 compiled with Lapack support.
188 \item If escript is compiled with a modern compiler, then inf/sup/Lsup will now
189 report NaN, +/-inf as appropriate if those values appear in the data.
190 \item Data.setTags will take tag names as well as tag numbers.
191 \item The Scalar, Vector, Tensor, Tensor3, Tensor4 factory methods can now take
192 arrays/nested sequence like objects as their initial values.
193 \item escript.util.mkDir can now take a list of directories to create.
194 \item Behind the scenes, \PYTHON docstrings have been rewritten from epydoc to
195 restructured text.
196 \item Various other bug fixes and performance tweaks.
197 \end{itemize}
199 \subsection*{2.0 to 3.0}
200 \begin{itemize}
201 \item The major change here was replacing \module{numarray} with \numpy.
202 For general instructions on converting scripts to use numpy see \url{http://www.stsci.edu/resources/software_hardware/numarray/numarray2numpy.pdf}.
203 The specific changes to \escript are:
204 \begin{itemize}
205 \item getValueOfDataPoint() which returned a \module{numarray}.array has been
206 replaced by getTupleForDataPoint() which returns a \PYTHON tuple
207 containing the components of the data point. In the case of matrices or
208 higher ranked data, the tuples will be nested.
209 Use \numpy.array(data.getTupleForDataPoint()) if a \numpyNDA object is
210 required.
211 \item getValueOfGlobalDataPoint() has similarly been replaced by
212 getTupleForGlobalDataPoint().
213 \item \code{integrate(data)} now returns a \numpyNDA instead of a
214 \module{numarray}.array.
215 \end{itemize}
216 Any python methods which previously accepted \module{numarray} objects now
217 accept \numpy objects instead.
219 \item The way to define solver options for \LinearPDE objects has changed.
220 There is now a \SolverOptions object attached to the \LinearPDE
221 object which handles the options of solvers used to solve the PDE.
222 The following changes apply:
223 \begin{itemize}
224 \item The \method{setTolerance} and \method{setAbsoluteTolerance} methods
225 have been removed. Instead use \method{setTolerance} and
226 \method{setAbsoluteTolerance} on the \SolverOptions object. For example:
227 \method{getSolverOptions().setTolerance(\ldots)}
228 \item The \method{setSolverPackage} and \method{setSolverMethod} methods have
229 been removed. Instead use the methods \method{setPackage},
230 \method{setSolverMethod} and \method{setPreconditioner}. For example:
231 getSolverOptions().setPackage(\ldots).
232 \item The static class variables defining packages, solvers and
233 preconditioners have been removed and are now accessed via the
234 corresponding static class variables in \SolverOptions.
235 For instance use \method{SolverOptions.PCG} instead of
236 \method{LinearPDE.PCG} to select the preconditioned conjugate gradient
237 method.
238 \item The \method{getSolution} now takes no argument. Use the corresponding
239 methods of the \SolverOptions object returned by
240 \method{getSolverOptions()} to set values,\\ e.g. use
241 \method{getSolverOptions().setVerbosityOn()} instead of argument
242 \code{verbose=True} and \method{getSolverOptions().setIterMax(1000)}
243 instead of argument \code{iter_max=1000}.
244 \end{itemize}
245 \end{itemize}

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