Contents of class notes for AMath 483/583

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Condensed Table of Contents without subsections

Course materials

• About these notes – important disclaimers
• Overview and syllabus
  • Outline and schedule
• Slides from lectures
• Homework
  • Assignments
• 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
  • Changing guest resolution/VM window size
  • Setting the host key
  • Shutting down
  • About the VM
  • Guest Additions
  • Further reading
• Bibliography and further reading
  • Books
  • Other courses with useful slides or webpages
  • Other Links

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
  • sftp
• Text editors
  • gedit
  • NEdit
  • XCode
  • TextWrangler
  • vi or vim
  • emacs
  • Further reading
• Version Control Software
  • Client-server systems
  • Distributed systems
• Mercurial (hg)
  • Instructions for cloning the class repository
  • Updating your clone
  • Creating your own Bitbucket repository
  • Further reading
• More commands in hg
  • Reverting to a previous version
  • Further reading
• Bitbucket repositories: viewing changesets, issue tracking
  • Further reading
• Mercurial examples
  • Examples for Lecture 3
  • hg init
  • hg revert
  • hgignore
  • hg diff
  • hg serve
  • Cloning this repository
  • Removing .hg
  • Making a copy of a directory
• 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
• Computer Architecture
  • Moore’s Law
  • Further reading
• Computer Memory and Storage
  • Integers
  • Real numbers
  • Text
  • Colors
  • Hexidecimal numbers
  • Machine instructions
• Punch cards
• Machine code and assembly language
  • Further reading
• Programming languages
  • Interpreted languages
  • Compiled languages
  • Object oriented languages
  • Further reading
• Python and Fortran
  • Further reading
• Makefiles
  • Further reading

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
• Fortran Input / Output
  • Formats vs. unformatted
  • Writing to a file
  • Reading input
• Optimizing code
  • Further reading
• Optimizing Fortran
  • Further reading
• Debugging and debuggers
  • Further reading
• Fortran debugging
  • Print statements
  • Compiling with various gfortran flags
  • The gdb debugger
  • Totalview
• Fortran Software Packages
  • zeroin software
• Linear Algebra software
• Installing LAPACK and BLAS
• LAPACK examples

Parallel Computing

• Parallel Computing
• OpenMP
  • Sample codes
  • Fine-grain vs. coarse-grain paralellism
  • Further reading
• MPI
  • MPI implementations
  • MPI on the class VM
  • Sample codes
  • Further reading
• MPI with subroutine calls
• Installing MPI on a Mac

Python

• Python
  • Interactive Python
  • Indentation
  • Wrapping lines
  • Comments
  • Strings
  • Docstrings
  • Running Python scripts
  • Importing modules
  • Python objects
  • Declaring variables?
  • Lists
  • Copying objects
  • Mutable and Immutable objects
  • Tuples
  • Iterators
  • range
  • enumerate
  • Further reading
• Numerics in Python
  • Vectors and Matrices
  • Component-wise operations
  • Further reading
• Python functions
  • Defining functions in modules
  • Lambda functions
  • Further reading
• Python Namespaces
  • Further reading
• Python scripts and modules
  • Writing scripts for ease of importing
  • Reloading modules
  • Command line arguments
• Python strings
  • String formatting
  • Further reading
• Python dictionaries
  • Dictionary methods
  • Further reading
• Allocating memory in Python
• Python vectorization
  • Booleans for NumPy arrays
• Python debugging
  • Python IDEs
  • Reloading modules
  • Print statements
  • pdb debugger
  • Debugging after an exception occurs
  • Using pdb from IPython
  • Other pdb commands
• Timing and profiling computer codes
  • Unix time command
  • Python time module
  • Python cProfile module
  • Timing Fortran codes
  • Profiling Fortran codes

Visualization

• Visualization and graphics
• Plotting with Python
  • matplotlib and pylab
  • Mayavi and mlab
  • VisIt
  • ParaView

Applications

• Special functions
  • Taylor series expansions
  • Newton’s method for the square root
• Particle methods
  • Rotating particles
  • Cosmology
  • Granular flow and molecular dynamics
• Rotating particles and Python efficiency
  • A poorly written code
  • Eliminating repeated computations
  • Vectorizing code and eliminating loops
  • Linear algebra version
• Rotating particles and Fortran efficiency
  • A poorly written code
  • Eliminating repeated computations
  • Array operations
  • Linear algebra version
• 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