UW AMath High Performance Scientific Computing
AMath 483/583 Class Notes
Spring Quarter, 2013

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Bibliography and further reading

Many other pages in these notes have links not listed below. These are some references that are partiuclarly useful or are cited often elsewhere.


[Lin-Snyder]C. Lin and L. Snyder, Principles of Parallel Programming, 2008.
[Scott-Clark-Bagheri]L. R. Scott, T. Clark, B. Bagheri, Scientific Parallel Computing, Princeton University Press, 2005.
[McCormack-scientific-fortran]D. McCormack, Scientific Software Development in Fortran, Lulu Press, ... ebook ... paperback
[Rauber-Ruenger](1, 2) T. Rauber and G. Ruenger, Parallel Programming For Multicore and Cluster Systems, Springer, 2010 ... book ... ebook
[Chandra-etal-openmp]R. Chandra, L. Dagum, et. al., Parallel Programming in OpenMP, Academic Press, 2001.
[Gropp-Lusk-Skjellum-MPI]W. Gropp, E. Lusk, A. Skjellum, Using MPI, Second Edition, MIT Press, 1999. Google books
[Snir-Dongarra-etal-MPI]M. Snir, J. Dongarra, J. S. Kowalik, S. Huss-Lederman, S. W. Otto, D. W. Walker, MPI: The Complete Reference (2-volume set) , MIT Press, 2000.
[Dive-into-Python]M. Pilgram, Dive Into Python, http://www.diveintopython.org/.
[Python]G. van Rossum, An Introduction to Python, http://www.network-theory.co.uk/docs/pytut/index.html
[Langtangen-scripting]H. P. Langangen, Python Scripting for Computational Science, 3rd edition, Springer, 2008. book and scripts ... lots of slides
[Langtangen-Primer]H. P. Langtangen, A Primer on Scientific Programming with Python, Springer 2009 What’s the difference from the previous one?
[Goedecker-Hoisie-optimization]S. Goedecker and A. Hoisie, Performance Optimization of Numerically intensive Codes, SIAM 2001.
[Matloff-Salzman-debugging]N. Matloff and P. J. Salzman, The Art of Debugging with GDB, DDD, and Eclipse, no starch press, San Francisco, 2008.
[Overton-IEEE]M. Overton, Numerical Computing with IEEE Floating Point Arithmetic, SIAM, 2001.
[Eijkhout]V. Eijkhout, Introduction to High-Performance Scientific Computing, [link to book and slides]

Other courses with useful slides or webpages

[software-carpentry]Greg Wilson, http://software-carpentry.org/ See Software Carpentry for links to some useful sections.
[Reynolds-class]Dan Reynolds, SMU http://dreynolds.math.smu.edu/Courses/Math6370_Spring11/.
[Snyder-UW-CSE524]Larry Snyder, UW CSE 524, Parallel Algorithms
[Gropp-UIUC]William Gropp UIUC Topics in HPC
[Yelick-UCB]Kathy Yelick, Berkeley course on parallel computing
[Demmel-UCB]Jim Demmel, Berkeley course on parallel computing
[Kloekner-Berger-NYU]Andreas Kloeckner and Marsha Berger, NYU course
[Berger-Bindel-NYU]Marsha Berger and David Bindel, NYU course
[LLNL-HPC]Livermore HPC tutorials
[NERSC-tutorials]NERSC tutorials


See also

Downloading and installing software for this class for links to software download pages.

[CosmicProject]links to open source Python software

Virtual machine references



[Python-3.0-tutorial]http://docs.python.org/3.0/tutorial/ (we are not using Python 3.0 in this class!)
[IPython-documentation]http://ipython.org/documentation.html (With lots of links to other documentation and tutorials)
[Python-pdb]Python debugger documentation
[IPython-book]Cyrille Rossant, Learning IPython for Interactive Computing and Data Visualization, Packt Publishing, 2013. http://ipython.rossant.net/.

Version control systems references


Reproducibility references

[sci-code-manifesto]Science Code Manifesto
[icerm-workshop]Links from a recent workshop on the topic
[winter-school]A recent Winter School on the topic in Geilo, Norway:

Fortran references

Many tutorials and references are available online. Search for “fortran 90 tutorial” or “fortran 95 tutorial” to find many others.

[Reynolds-fortran]Dan Reynolds fortran page http://dreynolds.math.smu.edu/Courses/Math6370_Spring11/fortran.html
[Shene-fortran]C.-K. Shene’s Fortran 90 tutorial http://www.cs.mtu.edu/~shene/COURSES/cs201/NOTES/fortran.html
[Dodson-fortran]Zane Dodson’s Fortran 90 tutorial http://www.cisl.ucar.edu/tcg/consweb/Fortran90/F90Tutorial/tutorial.html
[fortran-tutorials]Links to a few other tutorials http://gcc.gnu.org/wiki/Fortran%2095%20tutorials%20available%20online
[advanced-fortran]Kaiser, Advanced Fortran 90 http://www.sdsc.edu/~tkaiser/f90.html

Computer architecture references


Floating point arithmetic

[Arnold-disasters]Doug Arnold’s descriptions of some disasters due to bad numerical computing, http://www.ima.umn.edu/~arnold/disasters/

Languages and compilers


OpenMP references

[Chandra-etal-openmp]R. Chandra, L. Dagum, et. al., Parallel Programming in OpenMP, Academic Press, 2001.
[Chapman-Jost]B. Chapman, G. Jost, R. van der Pas, Using OpenMP: Portable Shared Memory Parallel Programming, MIT Press, 2007
[openmp-RR]Section 6.3 and beyond of [Rauber-Ruenger]
[openmp.org]http://openmp.org/wp/resources contains pointers to many books and tutorials.
[openmp-specs]http://openmp.org/wp/openmp-specifications/ has the latest official specifications
[openmp-llnl]https://computing.llnl.gov/tutorials/openMP/ Livermore tutorials
[openmp-refcard]OpenMP in Fortran Reference card

MPI references

[openmp-RR]Chapter 5 of [Rauber-Ruenger]

See also [Gropp-Lusk-Skjellum-MPI] and [Snir-Dongarra-etal-MPI]

See MPI for more references.