Links to AMSC 663-664 Resource Material

Information from Class Lecutres

• Parallel Hardware
  Lecture given by Michael Shay.
  (September 7, 2004)


• Autoconf and Automake
  Lecture given by Bob Shuttleworth.
  (November 1, 2004)


• CVS
  Lecture given by Scott Olsson.
  Another tutorial on CVS
  (November 1, 2004)


• Debuggers (Mainly gdb, dbx, and pdbx)
  Lecture given by Michael Shay
  (November 18, 2004)

Some General Resource Material

Code Development Tools

• make and more importantly, makefile; tutorial
  A complicated example using Michael Shay's two-fluid code
  

• Concurrent Versions System (CVS) Webpage: an example of a version management package.
  

• Configure documentation
  

• DocBook: a general purpose XML and SGML document type particularly well suited to books and papers about computer hardware and software
  

• Doxygen: a code documentation system
  

• Gnuplot documentation
  

• Emacs documentation and FAQ
  

• Vim FAQ
  

Debugging

• Tutorial: debugging techniques and hints
  

• gdb: GNU debugger
  

• TotalView: Etnus debugger (especially good for debugging parallel code)
  

Profilers

• gprof: GNU profiler
  

Recommended Numerical Packages

• Netlib Repository: a useful collection of mathematical software, papers, and databases.
  

• FFTW: the fastest Fourier Transform in the West.
  

Computational Facilities

• Computational Facilities at CSCAMM
  

• Borg Beowolf Cluster in Astronomy: built by Derek Richardson
  

• PC Linux Cluster at UMIACS
  

• Computational Facilities at NERSC
  

High Quality Numerical Projects (Examples)

• Clawpack Webpage: an example of excellent scientific software documentation.
  

• GS2: plasma turbulence
  

• GYRO: plasma turbulence
  

• NWChem: computational chemistry
  

Material from Lectures

• Talk by Dunlavy (PDF)
  

• Code snippets
  

• Notes on some good programming practices by Arnaud Disitter.
  

• Notes on Debugging, Profiling, and Validation by Dave Levermore.
  

• Slides on Debugging by Bill Dorland.

• Slides on Optimizing (.pdf) by Bill Dorland.
  

• Condor Homepage. The link to the presentation by Zoe Leinhardt and Kevin Walsh is at the bottom.
  

Parallelization

• MPI home page
  

• MPI tutorial
  

Compilers

• Lahey Fortran compiler
  

• NAGWare compilers
  

• Intel compilers
  

• IBM compilers
  

Links to Additional Resources

• NERSC links to resources
  

• Notes on good programming practices by Arnaud Disitter.
  

Items Mention in Class

• Unified Modeling Language resources
  

• Vis5d: Visualization of scientific data in 3+ dimensions
  

• IDL: David Fanning's excellent site for IDL resources
  

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