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manual.bib
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% This file was created with JabRef 2.9.
% Encoding: MacRoman
@MANUAL{hennenfent08MNrap,
title = {Repro: a {Python} package for automating reproducible research in scientific computing},
author = {Gilles Hennenfent and Sean Ross-Ross},
year = {2008},
abstract = {Repro is a Python package for automating reproducible
research in scientific computing. Repro works in
combination with SCons, a next-generation build
tool. The package is freely available over the
Internet. Downloading and installation instructions
are provided in this gui de. The repro package is
documented in various ways (many comments in source
code, this guide{\textendash}-written using repro
itself!{\textendash}-and a reference guide). In this
user{\textquoteright}s guide, we present a few
pedagogical examples that uses Matlab, Python,
Seismic Unix (SU), and Madagascar. We also include
demo pa pers. These papers are written in LaTeX and
compiled using repro. The figures they contain are
automatically generated from the source codes prov
ided. In that sense, the demo papers are a model of
self-contained documents that are fully
reproducible. The repro package is largely inspired
by some parts of Madagascar, a geophysical software
package for reproducible research. However, the
repro package is intended for a broad audience co
ming from a wide spectrum of interest areas.},
keywords = {SLIM},
month = {08},
url = {http://repro.sourceforge.net/Site/Home.html}
}
@MANUAL{rossross07MNsda,
title = {{SLIMpy} development and programming interface for seismic processing},
author = {Sean Ross-Ross and Henryk Modzelewski and Cody R. Brown and Felix J. Herrmann},
year = {2007},
abstract = {Inverse problems in (exploration) seismology are known
for their large to very large scale. For instance,
certain sparsity-promoting inversion techniques
involve vectors that easily exceed unknowns while
seismic imaging involves the construction and
application of matrix-free discretized operators
where single matrix-vector evaluations may require
hours, days or even weeks on large compute
clusters. For these reasons, software development in
this field has remained the domain of highly
technical codes programmed in low-level languages
with little eye for easy development, code reuse and
integration with (nonlinear) programs that solve
inverse problems.Following ideas from the
Symes{\textquoteright} Rice Vector Library and
Bartlett{\textquoteright}s C++ object-oriented
interface, Thyra, and Reduction/Transformation
operators (both part of the Trilinos software
package), we developed a software-development
environment based on overloading. This environment
provides a pathway from in-core prototype
development to out-of-core and MPI
{\textquoteright}production{\textquoteright} code
with a high level of code reuse. This code reuse is
accomplished by integrating the out-of-core and MPI
functionality into the dynamic object-oriented
programming language Python. This integration is
implemented through operator overloading and allows
for the development of a coordinate-free solver
framework that (i) promotes code reuse; (ii)
analyses the statements in an abstract syntax tree
and (iii) generates executable statements. In the
current implementation, we developed an interface to
generate executable statements for the out-of-core
unix-pipe based (seismic) processing package
RSF-Madagascar (rsf.sf.net). The modular design
allows for interfaces to other seismic processing
packages and to in-core Python packages such as
numpy. So far, the implementation overloads linear
operators and element-wise reduction/transformation
operators. We are planning extensions towards
nonlinear operators and integration with existing
(parallel) solver frameworks such as Trilinos.},
keywords = {SLIM, software},
url = {https://slim.gatech.edu/Software/SLIM/SLIMpy/}
}
@MANUAL{rossross08MNsai,
title = {{SLIMPy}: a python interface for unix-pipe based coordinate-free scientific computing},
author = {Sean Ross-Ross and Henryk Modzelewski and Felix J. Herrmann},
year = {2008},
abstract = {SLIMpy is a Python interface that exposes the
functionality of seismic data processing packages,
such as MADAGASCAR, through oper ator overloading.
SLIMpy provides a concrete coordinate-free
implementation of classes for out-of-core linear
(implicit matrix-vector), and element-wise
operations, including calculation of norms and other
basic vector operations. The library is intended to
provide the user with an abstract sc ripting
language to program iterative algorithms from
numerical linear algebra. These algorithms require
repeated evaluation of operators that were initially
designed to be run as part of batch-oriented
processing flows. The current implementation
supports a plugin for Madagascar{\textquoteright}s
out-of-core UNIX pipe-based applications and is
extenable to pipe-based collections of programs such
as Seismic Unix, SEPLib, and FreeUSP. To optimize
perform ance, SLIMpy uses an Abstract Syntax Tree
that parses the algorithm and optimizes the pipes.},
month = {07},
url = {https://slim.gatech.edu/Software/SLIM/SLIMpy/}
}
@MANUAL{vandenberg07MNsat,
title = {{SPARCO}: a toolbox for testing sparse reconstruction algorithms},
author = {Ewout {van den Berg} and Michael P. Friedlander},
year = {2007},
abstract = {Sparco is a suite of problems for testing and
benchmarking algorithms for sparse signal
reconstruction. It is also an environment for
creating new test problems, and a suite of standard
linear operators is provided from which new problems
can be assembled. Sparco is implement ed entirely in
Matlab and is self contained. (A few optional test
problems are based on the CurveLab toolbox, which
can be installed separately.) At the core of the
sparse recovery problem is the linear system
$Ax+r=b$, where $A$ is an $m$-by-$n$ linear operator
and the $m$-vector $b$ is the observed signal. The
goal is to find a sparse $n$-vector $x$ such that
$r$ is small in norm.},
keywords = {SLIM},
month = {10},
url = {http://www.cs.ubc.ca/labs/scl/sparco/}
}