Bibliography and further reading

See also

Links from 2009 seminar

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 (A copy is on reserve in the Engineering Library)

[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

[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. (A copy is on reserve in the Engineering Library)

[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.

Other courses with useful slides or webpages

[software-carpentry]

Greg Wilson, http://software-carpentry.org/.

[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-Simon-UCB]

Jim Demmel and Horst Simon, Berkeley course on parallel computing

[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/resources/list/

Other Links

Software

See also

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

[CosmicProject]

links to open source software

Virtual machine:

[VirtualBox]

http://www.virtualbox.org/

[VirtualBox-documentation]

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

Sphinx:

[sphinx]

http://sphinx.pocoo.org

[sphinx-documentation]

http://sphinx.pocoo.org/contents.html

[sphinx-rst]

http://sphinx.pocoo.org/rest.html

[rst-documentation]

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

[sphinx-cheatsheet]

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

[sphinx-examples]

http://sphinx.pocoo.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-2.6-tutorial]

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

[Python-3.0-tutorial]

http://docs.python.org/dev/3.0/tutorial/ (we are not using Python 3.0 in this class!)

[IPython-documentation]

http://ipython.scipy.org/doc/stable/html/

[IPython-links]

http://ipython.scipy.org/moin/Documentation

[Python-pdb]

Python debugger documentation

[IPython-pdb]

Using pdb from IPython

Numerical Python

[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:

[Reynolds-unix]

D. 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

[wikipedia-tar]

http://en.wikipedia.org/wiki/Tar_%28file_format%29

Mercurial and other version control systems:

[hgbook]

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

[Bitbucket-hg-intro]

http://bitbucket.org/help/GettingStartedWithMercurial

[hg-faq]

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

[hg-hgrc]

http://www.selenic.com/mercurial/hgrc.5.html

[wikipedia-revision-control]

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

[wikipedia-revision-control-software]

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

Fortran

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

[Reynolds-fortran]

D. Reynolds fortran page has good links.

[Shene-fortran]

C.-K. Shene’s Fortran 90 tutorial

[Dodson-fortran]

Zane Dodson’s Fortran 90 tutorial

[fortran-tutorials]

Links to a few other tutorials

[advanced-fortran]

Kaiser, `Advanced Fortran 90 <http://www.sdsc.edu/~tkaiser/f90.html>1_

Makefiles:

[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

[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:

[openmp-RR]

Section 6.3 and beyond of [Rauber-Ruenger]

[openmp.org]

http://openmp.org/wp/

[openmp-gfortran]

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

[openmp-gfortran2]

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

[openmp-api3.0]

http://www.openmp.org/mp-documents/spec30.pdf

[openmp-refcard]

OpenMP in Fortran Reference card

[openmp-fort90-examples]

http://people.sc.fsu.edu/~burkardt/f_src/open_mp/open_mp.html

MPI:

[openmp-RR]

Chapter 5 of [Rauber-Ruenger]

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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