Useful resources for Computational Geomechanics Research

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Finite Element Systems

• The Real ESSI (Earthquake-Soil-Structure Interaction) Simulator (pronunciation of ESSI is similar to EASY) is a software, hardware and documentation system for high fidelity, high performance, time domain, nonlinear, 3D, finite element modeling and simulation of earthquake-soil/rock-structure interaction of Nuclear Power Plants (NPPs). It is developed in collaboration and with financial support of the US-NRC. The NRC ESSI Simulator consists of NRC ESSI Simulator Program (software, aka NRC-ESSI-Program), NRC ESSI Simulator Computer (hardware, aka NRC-ESSI-Computer), and NRC ESSI Simulator Notes (documentation, aka NRC-ESSI-Notes).
• Z_SOIL.PC 2007 Soil, rock and underground structures mechanics on microcomputers using plasticity theory, a software package for geotechnical engineering.
• Getfem++ is a project focusing on the development of a generic and efficient C++ library for finite element methods elementary computations.
• CASTEM, An Object oriented Finite Element Method framework.
• CESAR-LCPC is a software of the Laboratoire Central des Ponts et Chaussees, and is distributed by Itech SARL.
• OpenFOAM(Field Operation and Manipulation) software package can simulate anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options.
• FreeFEM++ is an implementation of a language dedicated to the finite element method.
• OpenSees is a software framework (actually turned to be just a program) for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes.
• deal.II (A Finite Element Differential Equations Analysis Library)is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements. It uses state-of-the-art programming techniques to offer you a modern interface to the complex data structures and algorithms required.
• The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling.
• OpenFEM is an open-source software freely distributed under the terms of the "GNU Lesser Public License" (LGPL). It is a general purpose multi-physic FEM environment.
• Tahoe is a research-oriented, open source platform for the development of numerical methods and material models. The goal of the work surrounding Tahoe is the simulation of stresses and deformations for situations that cannot be treated by standard continuum simulation techniques. These situations include material fracture or failure, interfacial adhesion and debonding, shear banding, length-scale dependent elasticity and plasticity, and deformation in small-scale structures. Aside from a collection of standard finite elements, Tahoe includes meshfree simulation capability and particle methods. Tahoe includes a number of "cohesive" approaches for modeling fracture. These include both surface and bulk constitutive models that incorporate cohesive behavior. Tahoe is capable of performing static and transient dynamic coupled-physics analysis in two and three dimensions. Many capabilities support parallel execution.
• OOFEM is free finite element code with object oriented architecture for solving mechanical, transport and fluid mechanics problems that operates on various platforms. The aim of this project is to develop efficient and robust tool for FEM computations as well as to provide modular and extensible environment for future development. OOFEM is released under GNU General Public License (GPL).
• Rheolef, A finite element environment, i.e. some C++ classes and unix commands
• Code_Aster provides, well beyond the standard function of any other thermo-mechanic calculation code, a whole array of analysis methods and multi-physic models. Its application domain extends from seismic analysis, to porous medium, without forgetting acoustics, fatigue, stochastic dynamics\u2026 Its models, its algorithms and its solvers have improved in robustness and thoroughness (1000000 lines of code, 200 operators). Completely open, it is chained, coupled and encapsulated in thousands of ways. All in all, the user has complete freedom of choice.
• Elmer is an open source multiphysical simulation software developed by CSC. Elmer development was started 1995 in collaboration with Finnish Universities, research institutes and industry.
• Kratos is a framework for building multi-disciplinary finite element programs. It provides several tools for easy implementation of finite element applications and a common platform for natural interaction of the same in different ways.

Software Database is a comprehensive online database of software for Architecture, Engineering and Construction.

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Reading material

• Bibliography collected over years on different subjects: Computational Mechanics, Computer Sciences, Education.
• Useful Readings related to Computational Geomechanics Research and Education.

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The science, art and technology of writing, presenting:

• HandBrake is a tool for converting video from nearly any format to a selection of modern, widely supported codecs.
• CALIBRE, e-book management. calibre is a free and open source e-book library management application developed by users of e-books for users of e-books.
• TeX Catalogue Online.
• Powerdot is a presentation class for TeX that allows for the quick and easy development of professional presentations. It comes with many tools that enhance presentations and aid the presenter. Examples are automatic overlays, personal notes and a handout mode. To view a presentation, DVI, PS or PDF output can be used. A powerful template system is available to easily develop new styles.
• Animate Create PDF animations from graphics files and inline graphics.
• Sébastien's Latex Tricks.
• Useful Tips and Tricks in LaTeX.
• LaTeX2rtf is a translator program which is intended to translate a LaTeX document (precisely: the text and a limited subset of LaTeX tags) into the RTF format which can be imported by several textprocessors (including Microsoft Word for Windows and Word for Macintosh).
• code_swarm shows the history of commits in a software project. Google code repository is available also, while discussion group is here
• H^EV^EA is a quite complete and fast L^AT_EX to HTML translator.
• Scott Meyers advice to prospective book authors.
• Tim Love's help pages on online movies at University of Cambridge.
• Nvu is a complete Web Authoring System.
• Word2x is a GPLed program for converting word documents to plain text, LaTeX and HTML.
• The Beamer class is a LaTeX class that allows you to create a beamer presentation.
• hyperref-FAQ.
• Effective Scientific Electronic Publishing makes it easy by Markus G. Kuhn, University of Cambridge.
• PDFpages makes it easy top insert pages of external PDF documents. It works only with pdflatex!).
• Mathematical Writing by Donald E. Knuth, Tracy Larrabee, and Paul M. Roberts.
• A (Not So) Short Introduction to LaTeX2e by Tobias Oetiker.
• pdfTeX and in particular:
  • users manual,
  • FAQ,
• PDF reference Fourth Edition, from Adobe specifications site.
• Creating Presentations in PDFLaTeX by Matt Welsh.
• Local (UCD CG) PDFLaTeX examples.
• Local (UCD CG) LaTeX examples.
• Internet Resources for POSTSCRIPT and GHOSTSCRIPT.
• Customised BibTeX styles.
• PPower4 P^4, Pdf Presentation Post Processor.
• W3Schools A collection of free HTML, CSS, JavaScript, DHTML, XML, XHTML, WAP, ASP, SQL tutorials with lots of working examples and source code.

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Visualization related links:

• OpendTect, a free open source seismic iterpretation Platform
• ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.
• VISIT is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms.
• CGAL: The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.
• Vis5D is a free OpenGL-based volumetric visualization program for scientific datasets in 3+ dimensions.
• Java 3D is the extension to Java for displaying three dimensional graphics.
• FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
• VTK The Visualization ToolKit.
• Rocketeer is a powerful tool for visualizing 3 dimensional scientific data sets.
• Qt is a multiplatform, C++ framework for GUI applications with ``write once, compile anywhere'' approach.
• Coin is a high-level 3D graphics library with a C++ Application Programming Interface.
• OpenInventor is an object-oriented 3D toolkit for interactive graphics programming.
• Tensor Visualization at UCSC.

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Mesh Generation related links:

• Paul Heckbert's Collection of Mesh Generation Links.
• A very comprehensive LIST of public domain mesh generation software.
• CUBIT Tool Suite (mesh generators)
• Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities.
• GID The personal pre and post processor.
• the Delaunay Triangulation.
• the GNU Triangulated Surface Library.
• TetGen A Quality Tetrahedral Mesh Generator and Three-Dimensional Delaunay Triangulator.
• TrueGrid High Quality Hexahedral Grid and Mesh Generation for Fluids and Structures.

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High Performance - Parallel Computing, Hardware and Software links:

• The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners.
• Building a simple Beowulf cluster with Ubuntu
• The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
• LTensor is a high performance C++ Tensor Library based on indicial notation.
• JOSTLE is a software package designed to partition unstructed meshes (for example, finite element or finite volume meshes) for use on distributed memory parallel computers.
• SCOTCH Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
• GPGPU stands for General-Purpose computation on GPUs. With the increasing programmability of commodity graphics processing units (GPUs), these chips are capable of performing more than the specific graphics computations for which they were designed. They are now capable coprocessors, and their high speed makes them useful for a variety of applications. The goal of this page is to catalog the current and historical use of GPUs for general-purpose computation.
• ggcov is a GTK+ GUI for exploring test coverage data produced by C and C++ programs compiled with gcc -fprofile-arcs -ftest-coverage.
• LCOV is a graphical front-end for GCC's coverage testing tool gcov.
• Breakin is Advanced Clustering's stress-test and hardware diagnostics tool.
• COVTOOL is an open source test coverage analyzer for C++ programs.
• On comparing floating point numbers, since floating point math is not exact.
• memtest86 is thorough, stand alone memory test for x86 architecture computers.
• MPFRCPP is free object oriented interface to the MPFR library.
• The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
• SystemImager is software which automates Linux installs, software distribution, and production deployment.
• IEEE 754 standard governs binary floating-point arithmetic.
• KAOS: A high-performance computing system is not created by accident, but by the careful design and implementation of interactions between Compilers, Hardware Architectures, and Operating Systems.
• The Aggregate refers to a collection of researchers and the technologies that they use to make the components of a computing system work better together.
• GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. There is no practical limit to the precision except the ones implied by the available memory in the machine GMP runs on. GMP has a rich set of functions, and the functions have a regular interface.
library which allows to estimate the round-off error propagation on every scientific code written in FORTRAN or C/C++ language.
• Omega is a tool that works with Valgrind and shows where the block of memory was leaked.
• GotoBLAS codes are currently the fastest implementations of the Basic Linear Algebra Subroutines.
• SmartHeap is a fast (3X-100X faster than compiler-supplied libraries), portable (Windows, Linux, Solaris, HP-UX, IBM-AIX, Dec OSF Tru64, SGI Irix), reliable, ANSI-compliant malloc/operator new library. SmartHeap supports multiple memory pools, includes a fixed-size allocator, and is thread-safe. SmartHeap also includes comprehensive memory debugging APIs to detect leakage, overwrites, double-frees, wild pointers, out of memory, references to previously freed memory, and other memory errors.
• Valkyrie is an open-source graphical user interface for the Valgrind 3.X line.
• C++ Reference Guide by Danny Kalev.
• OProfile is a system-wide profiler for Linux systems, capable of profiling all running code at low overhead.
• Alleyoop is a graphical front-end to the increasingly popular Valgrind memory checker for x86 GNU/ Linux using the Gtk+ widget set and other GNOME libraries for the X-Windows environment.
• Valgui a GPL front-end for Valgrind.
• Stream: Sustainable Memory Bandwidth in High Performance Computers.
• SPEC, the Standard Performance Evaluation Corporation is a non-profit corporation formed to establish, maintain and endorse a standardized set of relevant benchmarks that can be applied to the newest generation of high-performance computers.
• Acovea (Analysis of Compiler Options via Evolutionary Algorithm) implements a genetic algorithm to find the "best" options for compiling programs with the GNU Compiler Collection (GCC) C and C++ compilers. "Best", in this context, is defined as those options that produce the fastest executable program from a given source code. Acovea is a C++ framework that can be extended to test other programming languages and non-GCC compilers.
• FTEnsor is a high performance tensor library written in C++.
• GCOV is a test coverage program.
• The Paradyn project develops technology that aids tool and application developers in their pursuit of high-performance, scalable, parallel and distributed software.
• TBCI Temporary Base Class Idiom, a templated library of numerical base classes which implement basic data structures like complex numbers, dynamic vectors, static vectors, different types of matrices like full matrices, band matrices, sparse matrices, etc. and also included a representation for Tensors and its typical operations like contraction, direct product and multiplication with contraction. Further-on, some standard matrix solvers like gauss-jordan LU-decomposition or iterative solvers have been implemented as well as several interfaces to libraries as CLAPACK or SuperLU. .
• Boost Timer Library supplies a timer class for measuring elapsed time, a progress_timer class for reporting elapsed time, and a progress_display class for displaying an indication of progress toward a goal.
• The Linux Clusters Institute.
• The Cornell Theory Center.
• OSCAR Open Source Cluster Application Resources.
• Rocks Cluster Distribution An Open Source High Performance Linux Cluster Solution.
• The Warewulf Cluster Project The Distributed Linux Distribution.
• WebCT-HPC is the web-based training site for High Performance Computing sponsored by the National Center for Supercomputing Applications (NCSA).
• Brahma The Duke Physics Department's Beowulf Compute Cluster (lots of good links).
• Techniques for Scientific C++ by Todd Veldhuizen.
• PAPI Performance Application Programming Interface.
• Vector arithmetic speed.
• METIS is a family of programs for partitioning unstructured graphs and hypergraphs and computing fill-reducing orderings of sparse matrices.
• Zoltan Data-Management Services for Parallel Applications.
• SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. The library is written in C and is callable from either C or Fortran.
• Tiny Vector Matrix library using Expression Templates (TVMET): Project Page and Home Page by Olaf Petzold.
• Blitz++ at OONUMERICS.
• Run time program performance profiling: OProfile, and PAPI.
• WSMP Watson Sparse Matrix Package (including an MPICH-based parallel WSMP library for IA32 Linux clusters).
• etLAP expression template Linear Algebra Package (aka "excessively templated LAP") Extremely lightweight C++ library providing real and complex Matrices and Vectors with simple and intuitive operations offering ultimate speed.
• ATLAS Automatically Tuned Linear Algebra Software.
• Benchmark for Templated Libraries project.
• CADNA library which allows to estimate the round-off error propagation on every scientific code written in FORTRAN or C/C++ language.
• Valgrind is a GPL'd system for debugging and profiling x86-Linux programs.
• KCachegrind is a visualisation tool for the profiling data generated by Cachegrind.
• Debugging PARALLEL programs by Norm Matloff of UCD.
• MPICH A Portable Implementation of MPI.
• MPICH FAQ .
• Configuring MPICH with ssh .
• Rogue Wave Totalview: debugger .
• Allinea DDT: parallel debugger .

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Compiler, interpreter, programming language and programming systems related links:

• Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
• Ch is an embeddable C/C++ interpreter for cross-platform scripting, shell programming, 2D/3D plotting, numerical computing, and embedded scripting. Ch is a free and user-friendly alternative to C/C++ compilers for beginners to learn C/C++.
• The C++ Virtual Library
• C++ Annotations Version 5.0.0: This document is intended for knowledgeable users of C who would like to make the transition to C++. It is a guide for Frank's C++ programming courses, which are given yearly at the University of Groningen. As such, this document is not a complete C++ handbook. Rather, it serves as an addition to other documentation sources. If you want a hard-copy version of the C++ annotations: hard copies are available in postscript, pdf and other formats in ftp://ftp.icce.rug.nl/pub/documents
• ViewVC is a browser interface for CVS and Subversion version control repositories. It generates templatized HTML to present navigable directory, revision, and change log listings. It can display specific versions of files as well as diffs between those versions. Basically, ViewVC provides the bulk of the report-like functionality you expect out of your version control tool, but much more prettily than the average textual command-line program output.
• Boost Tools: Boost developers, testers, and maintainers have developed various tools to help with the administration of the Boost Libraries.
• Jam is a software build tool that makes building simple things simple and building complicated things manageable.
  • Jambase is a base set of Jam rules which provide roughly make(1)-like functionality for jam, the Jam executable program.
• CVMLCPP, Common Versatile Multi-purpose Library for C++.
• Clang: Clang: a C language front-end for LLVM
• Elsa: The Elkhound-based C/C++ Parser
• The C++ Tutorial
• Bruce Eckel's books online: Free Electronic Book Volume 1 & Volume 2
• Programming Tutorials
• WWW C++ Information
• C++ Language Tutorial
• SAX is the Simple API for XML.
• The Document Object Model (DOM), is a platform- and language-neutral interface that will allow programs and scripts to dynamically access and update the content, structure and style of documents.
• The Meta Programming System (MPS), is a new programming environment which makes it easy to define your own specialized languages, and use them together with any other language, as you see fit.
• GIT, Tree History Storage Tool. GIT is a "directory content manager" designed to handle absolutely massive projects with speed and efficiency. Replacement for BitKeeper on linux kernel project.
• BitKeeper is a scalable configuration management system.
• TRAC is an enhanced wiki and issue tracking system for software development projects.
• Open Software License v. 2.1.
• Doc++ is a documentation system for C/C++ and Java generating both, LaTeX output for high quality hardcopies and HTML output for sophisticated online browsing of your documentation.
• CodeViz - A call graph generation utility for C/C++.
• Graphviz - Graph Visualization Software.
• Doxygen is a documentation system for C++, C, Java, Objective-C, IDL (Corba and Microsoft flavors) and to some extent PHP, C# and D.
• Doxywizard is a GUI front-end for configuring and running doxygen.
• Boost Regression Test User Documentation, and example of Boost CVS health summary for developers.
• OOtips: Object Oriented Tips, a free service devoted to object oriented technologies.
• TUT: C++ Unit Test Framework.
• Front Page, for the PortlandPatternRepository and WikiWikiWeb.
• Extreme Programming Roadmap, from C2.
• New User Pages, Wiki from C2.
• Testing Framework, from C2.
• Inspect Tools, for BOOST.
• ++ FAQ Lite, by Marshall Cline.
• Parsing Techniques - A Practical Guide, is a 320-page book that treats parsing in its own right, in greater depth than is found in most computer science and linguistics books.
• Spirit is an object oriented recursive descent parser generator framework implemented using template meta-programming techniques. Related references are here. Quick Start. Spirit Application Repository.
• Boost Pool Library is a memory allocation scheme that is very fast, but limited in its usage.
• The Boost MPL library is a C++ template metaprogramming framework of compile-time algorithms, sequences and metafunction classes.
• BOOST WIKI.
• BOOST provides free peer-reviewed portable C++ source libraries.
• CINT is a C/C++ interpreter aimed at processing C/C++ scripts.
• Free C/C++ Compilers; Compilers, cross-compilers, interpreters for ANSI C and ANSI C++.
• OpenTop Cross-Platform C++.
• JavaCC Java Compiler Compiler [tm] (JavaCC [tm]) - The Java Parser Generator. BUILD your own language with JavaCC.
• Examples for Creating Your Own Tcl Interpreter in C or C++ (from Eric Foster-Johnson).
• Catalog of Free Compilers and Interpreters.
• djgpp -> gcc DOS compiler.
• gcc -> DOS cross compiler. More info, and yet more here.
• Python Language; Python is an OO scripting language that does all the things that you can do with Perl or TCL - only better (sic) , since it was designed from the ground up as an OO language. Lots of Python documentation is available at http://www.python.org, as well as source code and binaries for UNIX, Macintosh, Win95/NT, DOS, etc.
• PHP is a widely-used general-purpose scripting language that is especially suited for Web development and can be embedded into HTML.
• ActiveState Tcl.
• Incr Tcl.
• The 11 rules of the Tcl syntax.
• The Tcler's Wiki.
• Tcl/Tk headquarters.
• Tcl/Tk man pages.
• Visual Tcl.
• XSLT for libxml2.

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Other useful links awaiting categorization

• bibtex2endnote converter.
• diskscrub overwrites hard disks, files, and other devices with repeating patterns intended to make recovering data from these devices more difficult. Although physical destruction is unarguably the most reliable method of destroying sensitive data, it is inconvenient and costly. For certain classes of data, organizations may be willing to do the next best thing which is scribble on all the bytes until retrieval would require heroic efforts in a lab.
• Geany is a text editor using the GTK2 toolkit with basic features of an integrated development environment. It was developed to provide a small and fast IDE, which has only a few dependencies from other packages. It supports many filetypes and has some nice features
• Kyoshin Network (K-NET), a data network of the Japanese National Research Institute for Earth Science and Disaster Prevention.
• NAFEMS is an independent not-for-profit body with the sole aim of promoting the effective use of engineering simulation methods such as finite element analysis, multibody system dynamics and computational fluid dynamics.
• Today's Wolfram|Alpha is the first step in an ambitious, long-term project to make all systematic knowledge immediately computable by anyone.
• Cheat Sheets.
• Amanda The Advanced Maryland Automatic Network Disk Archiver.
• Mathematica, an amazing symbolic/computational system.
• The Interactive Data Language (IDL), is the ideal software for data analysis, visualization, and cross-platform application development.
• GNU Octave is a high-level language, primarily intended for numerical computations.
• Matlab is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation.
• Plagiarism in natural and programming languages: an overview of current tools and technologies a paper by Paul Clough.
• SCons is an Open Source software construction tool--that is, a next-generation build tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache.
• Program Development, at linuxlist.
• Scientific Toolworks, understand your software. Reverse engineering, documentation and metrics tools for C, C++, JAVA source code.
• Lint for C/C++ , programe checking and testing.
• CodeCheck, PCyacc, CodeFix, programming language analysis tools.
• Parasoft, automatic testing of C++, C and Java programs.
• MK toolkit, for porting UNIX applications top Windows.
• The Oilfield Glossary, useful solid and fluid mechanics terms and brief explanations (from Schlumberger).
• Procmail mail processing. Also very good Procmail Tips. Also useful is man 5 procmailex.
• Verification and Validation in Computational Mechanics.
• Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc.
• The Globus Alliance is developing fundamental technologies needed to build computational grids.
• 6dof Simulation and Finite Elements web Portal.
• UPX the Ultimate Packer for eXecutables.
• hypersrc a freeware source code browser.
• Subversion, a compelling replacement for CVS. A new book just came out.
• First steps with UNIX by Norm Matloff of UCD.
• Unix Tutorial Center including the elementary C programming by Norm Matloff of UCD.
• Debugging programs by Norm Matloff of UCD.
• The QUAKE project at CMU.
• CVS manuals
• How to setup batch ssh2 jobs, Paul Keck's tutorial.
• Yet another ssh Tutorial at Deadman.org .
• Stochastic Differential Equations.
• Useful Resources for Parsing Tools such as YACC - LEX - Bison - FLEX. Collection maintained by Nima Tafazzoli.

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Interesting People:

• Martin Fowler
• Bjarne Stroustrup
• Andrew Koenig
• Carlos Felippa
• Matt Welsh
• Bruce Fast
• Albert Tarantola
• Ed Wilson
• Tony O'Hagan and the art/science of expert opinions

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Boris Jeremic