Contents of class notes for UW HPSC – Coursera Edition

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Condensed Table of Contents without subsections

Course materials

• Notes on the Coursera Edition
• About these notes – important disclaimers
  • License
• Overview and syllabus
  • Some topics
• Homework
  • Homework solutions
• Downloading and installing software for this class
  • Versions
  • Individual packages
  • Software available through apt-get
  • Software available through easy_install
• Virtual Machine for this class
  • System requirements
  • Setting up the VM in VirtualBox
  • Starting the VM
  • Running programs
  • Fixing networking issues
  • Shutting down
  • Cutting and pasting
  • Shared Folders
  • Enabling more processors
  • Problems enabling multiple processors...
  • Changing guest resolution/VM window size
  • Setting the host key
  • Guest Additions
  • How This Virtual Machine was made
  • About the VM
  • Further reading
• Amazon Web Services EC2 AMI
  • Launching an instance with the uwhpsc AMI
  • Logging on to your instance
  • Transferring files to/from your instance
  • Stopping your instance
  • Creating your own AMI
  • Viewing webpages directly from your instance
• Software Carpentry

Technical Topics

• Shells
  • Unix shells
  • IPython shell
  • Further reading
• Unix, Linux, and OS X
  • pwd and cd
  • ls
  • more, less, cat, head, tail
  • removing, moving, copying files
  • background and foreground jobs
  • nice and top
  • killing jobs
  • sudo
  • The bash shell
  • .bashrc file
  • Environment variables
  • PATH and other search paths
  • which
  • Setting the prompt
  • Further reading
• Unix top command
  • Running top
  • Summary area
  • Task area
  • Interactive commands
  • Further reading
• Using ssh to connect to remote computers
  • X-window forwarding
  • scp
• Text editors
  • Leafpad
  • gedit
  • NEdit
  • XCode
  • TextWrangler
  • vi or vim
  • emacs
• Reproducibility
  • Scripting vs. using a shell or GUI
  • IPython history command
• Version Control Software
  • Client-server systems
  • Distributed systems
  • Further reading
• Git
  • Instructions for cloning the class repository
  • Updating your clone
  • Creating your own Bitbucket repository
  • Further reading
• Bitbucket repositories: viewing changesets, issue tracking
• More about Git
  • Using git to stay synced up on multiple computers
• Sphinx documentation
  • Using Sphinx for your own project
  • Using Sphinx to create these webpages
  • Making a pdf version
  • Further reading
• Binary/metric prefixes for computer size, speed, etc.
  • Prefixes
  • Units of memory, storage
  • Units of speed
  • Flops
• Computer Architecture
  • Moore’s Law
  • Further reading
• Storing information in binary
  • Integers
  • Real numbers
  • Text
  • Colors
  • Hexidecimal numbers
  • Machine instructions
• Punch cards
• Python and Fortran
  • Further reading

Python

• Python
  • Interactive Python
  • Indentation
  • Wrapping lines
  • Comments
  • Strings
  • Docstrings
  • Running Python scripts
  • Python objects
  • Declaring variables?
  • Lists
  • Copying objects
  • Mutable and Immutable objects
  • Tuples
  • Iterators
  • range
  • enumerate
  • Further reading
• Python scripts and modules
  • Writing scripts for ease of importing
  • Reloading modules
  • Command line arguments
  • Importing modules
  • The Python Path
  • Other forms of import
  • Further reading
• Python functions
  • Defining functions in modules
  • Lambda functions
  • Further reading
• Python strings
  • String formatting
  • Further reading
• Numerics in Python
  • Vectors and Matrices
  • Component-wise operations
  • Further reading
• IPython_notebook
• Sage
• Plotting with Python
  • matplotlib and pylab
  • Mayavi and mlab
  • VisIt
  • ParaView
• Python debugging
  • Python IDEs
  • Reloading modules
  • Print statements
  • pdb debugger
  • Debugging after an exception occurs
  • Using pdb from IPython
  • Other pdb commands

Fortran

• Fortran
  • General References:
  • History
  • Fortran 77
  • Fortran 90/95
  • Compilers
  • File extensions
  • Compiling, linking, and running a Fortran code
  • Sample codes
  • Intrinsic functions
  • Default 8-byte real numbers
  • Fortran Arrays
  • Loops
  • if-then-else
  • Booleans
  • Further reading
• Useful gfortran flags
  • Output flags
  • Warning flags
  • Fortran dialect flags
  • Debugging flags
  • Optimization flags
  • Further reading
• Fortran subroutines and functions
  • Functions
  • Modifying arguments
  • The use of intent
  • Subroutines
  • Subroutine in a module
  • Further reading
• Fortran examples: Taylor series
• Array storage in Fortran
  • Passing rank 1 arrays to subroutines, Fortran 77 style
  • Fortran arrays of higher rank
  • Why do we care how arrays are stored?
• Fortran modules
  • Some reasons to use modules
  • Compiling modules
  • Circles module example
  • Module variables
• Fortran Input / Output
  • Formats vs. unformatted
  • Writing to a file
  • Reading input
• Fortran debugging
  • Print statements
  • Compiling with various gfortran flags
  • The gdb debugger
  • Totalview
• Fortran example for Newton’s method

Parallel computing

• OpenMP
  • Sample codes
  • Other directives
  • Fine-grain vs. coarse-grain paralellism
  • Further reading
• MPI
  • MPI implementations
  • MPI on the class VM
  • Test code
  • Reduction example
  • Send-Receive example
  • Master-worker examples
  • Sample codes
  • Further reading

Miscellaneous

• Makefiles
  • Further reading
• Special functions
  • Taylor series expansions
  • Newton’s method for the square root
• Timing code
  • Unix time command
  • Fortran timing utilities
  • Timing OpenMP code
• Linear Algebra software
  • The BLAS
  • LAPACK
  • Direct methods for sparse systems
  • Other references
• Random number generators

Applications

• Numerical methods for the Poisson problem
  • Iterative methods for the Poisson problem
  • Monte Carlo methods for the steady state diffusion equation
• Jacobi iteration using OpenMP with parallel do constructs
• Jacobi iteration using OpenMP with coarse-grain parallel block
• Jacobi iteration using MPI

References

• Bibliography and further reading
  • Books
  • Other courses with useful slides or webpages
  • Other Links
  • Software
  • Virtual machine references
  • Sphinx references
  • Python:
  • Numerical Python references
  • Unix, bash references
  • Version control systems references
  • Git references
  • Mercurial references
  • Reproducibility references
  • Fortran references
  • Makefile references
  • Computer architecture references
  • Floating point arithmetic
  • Languages and compilers
  • OpenMP references
  • MPI references
  • Exa-scale computing
• Software Carpentry