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.

Books

[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

[HPC-University]

http://www.hpcuniv.org/

Other Links

Software

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

[VirtualBox]

http://www.virtualbox.org/

[VirtualBox-documentation]

http://www.virtualbox.org/wiki/Documentation

Sphinx references

[sphinx]

http://sphinx-doc.org

[sphinx-documentation]

http://sphinx-doc.org/contents.html

[sphinx-rst]

http://sphinx-doc.org/rest.html

[rst-documentation]

http://docutils.sourceforge.net/rst.html

[sphinx-cheatsheet]

http://matplotlib.sourceforge.net/sampledoc/cheatsheet.html

[sphinx-examples]

http://sphinx-doc.org/examples.html

[sphinx-sampledoc]

http://matplotlib.sourceforge.net/sampledoc/index.html

Python:

[Python-2.5-tutorial]

http://www.python.org/doc/2.5.2/tut/tut.html

[Python-2.7-tutorial]

http://docs.python.org/tutorial/

[Python-documentation]

http://docs.python.org/2/contents.html

[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)

[IPython-notebook]

http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html

[Python-pdb]

Python debugger documentation

[IPython-book]

Cyrille Rossant, Learning IPython for Interactive Computing and Data Visualization, Packt Publishing, 2013. http://ipython.rossant.net/.

Numerical Python references

[NumPy-tutorial]

http://www.scipy.org/Tentative_NumPy_Tutorial

[NumPy-reference]

http://docs.scipy.org/doc/numpy/reference/

[NumPy-SciPy-docs]

http://docs.scipy.org/doc/

[NumPy-for-Matlab-Users]

http://www.scipy.org/NumPy_for_Matlab_Users

[NumPy-pros-cons]

http://www.scipy.org/NumPyProConPage

[Numerical-Python-links]

http://wiki.python.org/moin/NumericAndScientific

Unix, bash references

[Reynolds-unix]

Dan Reynolds unix page has good links.

[Wikipedia-unix-utilities]

http://en.wikipedia.org/wiki/List_of_Unix_utilities

[Bash-Beginners-Guide]

http://tldp.org/LDP/Bash-Beginners-Guide/html/index.html

[gnu-bash]

http://www.gnu.org/software/bash/bash.html

[Wikipedia-bash]

http://en.wikipedia.org/wiki/Bash(Unix_shell)

[wikipedia-tar]

http://en.wikipedia.org/wiki/Tar_%28file_format%29 (tar files)

Version control systems references

[wikipedia-revision-control]

http://en.wikipedia.org/wiki/Revision_control

[wikipedia-revision-control-software]

http://en.wikipedia.org/wiki/List_of_revision_control_software

Git references

[git-try]

Online interactive tutorial

[git-tutorials]

List of 10 tutorials http://sixrevisions.com/resources/git-tutorials-beginners/

[gitref]

http://gitref.org/index.html

[git-book]

Git Book http://git-scm.com/book/en/Getting-Started-Git-Basics

[github-help]

Github help page: http://help.github.com/

[git-parable]

http://tom.preston-werner.com/2009/05/19/the-git-parable.html

Mercurial references

[hgbook]

http://hgbook.red-bean.com/

[hg-faq]

http://mercurial.selenic.com/wiki/FAQ

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

Makefile references

[carpentry-make]

http://software-carpentry.org/4_0/make/

[gnu-make]

http://www.gnu.org/software/make/manual/make.html

[make-tutorial]

http://mrbook.org/tutorials/make/

[Wikipedia-make]

http://en.wikipedia.org/wiki/Make_%28software%29

Computer architecture references

[wikipedia-computer-architecture]

http://en.wikipedia.org/wiki/Computer_architecture

[wikipedia-memory-hierachy]

http://en.wikipedia.org/wiki/Memory_hierarchy

[wikipedia-moores-law]

http://en.wikipedia.org/wiki/Moore%27s_law.

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

[wikipedia-machine-code]

http://en.wikipedia.org/wiki/Machine_code

[wikipedia-assembly]

http://en.wikipedia.org/wiki/Assembly_language

[wikipedia-compilers]

http://en.wikipedia.org/wiki/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-gfortran]

http://gcc.gnu.org/onlinedocs/gfortran/OpenMP.html

[openmp-gfortran2]

http://sites.google.com/site/gfortransite/

[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.

Exa-scale computing

[exascale-doe]

Modeling and Simulation at the Exascale for Energy and the Environment, DOE Town Hall Meetings Report

[exascale-sc08]

http://www.lbl.gov/CS/html/SC08ExascalePowerWorkshop/index.html

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