.. _biblio:

=============================================================
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.

.. _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>`_

.. [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>`_

.. [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 <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.

.. [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] <http://tacc-web.austin.utexas.edu/veijkhout/public_html/istc/istc.html>`_

.. _other_courses:

Other courses with useful slides or webpages
---------------------------------------------


.. [software-carpentry] Greg Wilson, `<http://software-carpentry.org/>`_
   See :ref:`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 
   <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-UCB] Jim Demmel, 
   `Berkeley course on parallel computing <http://www.cs.berkeley.edu/~demmel/cs267_Spr12/>`_

.. [Kloekner-Berger-NYU] Andreas Kloeckner and Marsha Berger,
   `NYU course <http://wiki.tiker.net/Teaching/HPCFall2012/>`_

.. [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/>`_

.. _biblio_links:

Other Links
-----------

Software
-----------------------------------

.. seealso:: :ref:`software_installation` for links to software download pages.

.. [CosmicProject] `links to open source Python software <http://cosmicproject.org/links.html>`_

.. _biblio_vm:

Virtual machine references
-----------------------------------

.. [VirtualBox] `<http://www.virtualbox.org/>`_

.. [VirtualBox-documentation] `<http://www.virtualbox.org/wiki/Documentation>`_

.. _biblio_sphinx:

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>`_

.. _biblio_python:

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 <http://docs.python.org/2/library/pdb.html>`_

.. [IPython-book] Cyrille Rossant,
   *Learning IPython for Interactive Computing and Data Visualization*,
   Packt Publishing, 2013. `<http://ipython.rossant.net/>`_.


.. _biblio_numpy:

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>`_

.. _biblio_unix:

Unix, bash references
-----------------------------------

.. [Reynolds-unix] `Dan 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(Unix_shell)>`_

.. [wikipedia-tar] `<http://en.wikipedia.org/wiki/Tar_%28file_format%29>`_
   (tar files)

.. _biblio_vcs:

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>`_


.. _biblio_git:

Git references
-----------------------------------

.. [git-try] `Online interactive tutorial <http://try.github.com/>`_

.. [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>`_

.. _biblio_repro:

Reproducibility references
-----------------------------------


.. [sci-code-manifesto]  `Science Code Manifesto <http://sciencecodemanifesto.org/>`_

.. [icerm-workshop] `Links from a recent workshop on the topic
  <http://icerm.brown.edu/tw12-5-rcem-wiki.php>`_

.. [winter-school]  `A recent Winter School on the topic in Geilo, Norway:
  <http://www.sintef.no/Projectweb/eVITA/Winter-Schools/2013/>`_


.. _biblio_fortran:

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>`_

.. _biblio_make:

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>`_

.. _biblio_computer_arch:

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>`_

.. _biblio_openmp:

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 <http://openmp.org/mp-documents/OpenMP3.0-FortranCard.pdf>`_

.. _biblio_mpi:

MPI references
-----------------------------------

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

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

See :ref:`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 <http://www.er.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf>`_

.. [exascale-sc08] `<http://www.lbl.gov/CS/html/SC08ExascalePowerWorkshop/index.html>`_

--------------

**More will be added, check back later**