.. _biblio:
=============================================================
Bibliography and further reading
=============================================================
.. seealso:: `Links from 2009 seminar
<http://kingkong.amath.washington.edu/trac/hpsc09/wiki/links>`_
Many other pages in these notes have links not listed below. These are some
references that are partiuclarly useful or are cited often elsewhere.
.. _biblio_books:
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 <http://www.lulu.com/product/download/scientific-software-development-in-fortran/6208176>`_ ...
`paperback <http://www.lulu.com/product/paperback/scientific-software-development-in-fortran/6208175>`_
**(A copy is on reserve in the Engineering Library)**
.. [Rauber-Ruenger] T. Rauber and G. Ruenger,
*Parallel Programming For Multicore and Cluster Systems*,
Springer, 2010 ... `book <http://www.springer.com/computer/swe/book/978-3-642-04817-3>`_
... `ebook <http://www.springerlink.com/content/978-3-642-04817-3#section=675480&page=1&locus=0>`_
.. [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
<http://books.google.com/books?id=xpBZ0RyRb-oC&printsec=frontcover&dq=Gropp+lusk+skjellum+mpi&source=bl&ots=u9fzi2MK9Z&sig=GvK20XXrv9xMgYSyJ3JXKt45fhY&hl=en&ei=zpOlS-6HIIOeswPPwu3YAw&sa=X&oi=book_result&ct=result&resnum=1&ved=0CAYQ6AEwAA#v=onepage&q=&f=false>`_
.. [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 <http://folk.uio.no/hpl/scripting/>`_ ...
`lots of slides <http://heim.ifi.uio.no/~hpl/scripting/all-nosplit/>`_
.. [Langtangen-Primer] H. P. Langtangen, *A Primer on Scientific Programming
with Python*, Springer 2009 `What's the difference from the previous
one? <http://folk.uio.no/hpl/scripting/book_comparison.html>`_
.. [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:
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
<http://www.cs.washington.edu/education/courses/524/08wi/>`_
.. [Gropp-UIUC] William Gropp `UIUC Topics in HPC <http://www.cs.uiuc.edu/homes/wgropp/cs598/index.htm>`_
.. [Yelick-UCB] Kathy Yelick, `Berkeley course on parallel computing
<http://www.cs.berkeley.edu/~yelick/cs267/>`_
.. [Demmel-Simon-UCB] Jim Demmel and Horst Simon,
`Berkeley course on parallel computing <http://www.cs.berkeley.edu/~demmel/cs267_Spr09/>`_
.. [Berger-Bindel-NYU] Marsha Berger and David Bindel,
`NYU course <http://www.cs.nyu.edu/courses/fall08/G22.2945-001/index.html>`_
.. [LLNL-HPC] `Livermore HPC tutorials <https://computing.llnl.gov/?set=training&page=index>`_
.. [NERSC-tutorials] `NERSC tutorials <http://www.nersc.gov/nusers/help/tutorials/>`_
.. [HPC-University] `<http://www.hpcuniv.org/resources/list/>`_
.. _biblio_links:
Other Links
-----------
Software
^^^^^^^^^^^^^^^^
.. seealso:: :ref:`software_installation` for links to software download pages.
.. [CosmicProject] `links to open source software <http://cosmicproject.org/links.html>`_
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>`_
.. _biblio_python:
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 <http://docs.python.org/library/pdb.html>`_
.. [IPython-pdb] `Using pdb from IPython <http://ipython.scipy.org/doc/stable/html/interactive/tutorial.html?highlight=pdb>`_
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 <http://dreynolds.math.smu.edu/Courses/Math6370_Spring11/unix.html>`_ 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>`_
.. _biblio_hg:
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>`_
.. _biblio_fortran:
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 <http://dreynolds.math.smu.edu/Courses/Math6370_Spring11/fortran.html>`_ has good links.
.. [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] T. H. Kaiser, `Advanced Fortran 90 <http://www.sdsc.edu/~tkaiser/f90.html>1_
.. _biblio_make:
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>`_
.. _biblio_computer_arch:
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>`_
.. _biblio_openmp:
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 <http://openmp.org/mp-documents/OpenMP3.0-FortranCard.pdf>`_
.. [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 <http://www.er.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf>`_
.. [exascale-sc08] `<http://www.lbl.gov/CS/html/SC08ExascalePowerWorkshop/index.html>`_
--------------
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