MSC321 Scientific Programming for Atmospheric Science

• Instructor Mohamed Iskandarani Office MSC 320, tel: x 4045
  
• Course web site http://www.rsmas.miami.edu/personal/miskandarani/Courses/MSC321/index.htm
• Teaching Assistant Changheng Chen MSC 234A, tel: (305)794-6592
  
• Grades
  • 30% Homework (involve programming)
  • 40% 2-Mid term
  • 30% Term project or Final

• The syllabus
• The textbooks and references can be downloaded in pdf format.
• Lectures notes
  1. Lecture 1
  2. Lecture 2-3
  3. More on Intrinsic data types
  4. Flow Control
  5. Subroutines
  6. Arrays
  7. I/O operations
  8. Coding and RK4
  9. Derived data types and modules
  10. Parallel Computing
  11. MPI
  12. Parallel Performance
• Numerical Methods
  1. Taylor Series
  2. Trapezoidal integration
  3. Iterative solution of nonlinear equations
  4. Finite Difference Approximations
  5. Ordinary Differential Equations
  6. Finite Volume
  7. Von Neumann Stability Analysis
  8. Finite Volume in 2D
  9. The Boundary Element Method
  10. Vortex Methods in 2D
• Homeworks
  1. Intrinsic data types and expressions
  2. Flow control
  3. Procedures, Functions and subroutines
  4. Manipulating arrays
  5. Numerical Differentiation
  6. Numerical Integration of ODE
  7. Finite Volume Reconstruction
  8. Von Neumann Stability analysis
  9. Finite Volume Advection in 1D
  10. Finite Volume Advection in 2D
  11. Projects Volume Advection in 2D
• Final Projects
  1. Final Projects

1. Branching
   1. if statement
   2. select case statement
2. Loops
   1. indexed-do loops
   2. do while loops
   3. infinite loops
   4. cycling versus exiting loops
3. Subroutines and functions in modules
   1. function in a module
   2. subroutine in a module
   3. variable scoping in procedures
4. Arrays
   1. 1D arrays
   2. Passing Arrays to Subroutines
   3. Array inquiry functions
   4. Array allocation
5. Derived data types
   1. derived data type in a module
6. File I/O
   1. Module fileio.f90 is very useful for doing array-oriented I/O in Fortran. It encapsulates the essential of opening and closing files, and doing input and output of Fortran arrays in both ASCII and binary formats. The code testio.f90 illustrates how the module fileio can be used. Currently it is coded to deal with double precision arrays, but that can be easily extended. If all arrays written in binary are of the same shape, then reading and writing the data in fortran, and passing it to matlab are straightforward operations, see matlab script fortread.m.
7. Timing
   1. timing module to perform manual profiling on code segments.
8. Source code file management
   Makefile to manage the creation of executables from source codes. The following commands are useful:
   1. make example will create executable example from source code example.f90
   2. "make clean" to delete all module and object files

Useful Software and Tools

1. Student who want to install Linux software on Mac laptops should visit Mac Ports. It greatly simplified installing open-source software on Macs. The web page guides through installing MacPorts and using it to install packages.
2. Unix Primer These notes a crash course in navigating UNIX file systems, editing with emacs, and compiling. Other web resources can also be handy:
   1. UNIX Tutorial for Beginners
   2. A Basic UNIX Tutorial
   3. INTRODUCTION TO UNIX
3. Editors for text editing.
   1. vim/gvim
      a vim graphical cheat sheet
      vim graphical help
      
   2. emacs
      emacs reference card
      emacs_cheat
   3. gedit
   All these editors are installed on metofis. All of them have a graphical user interface that make them easy to learn while getting useful work done. Finally, vim and emac can be run on Linux, Windows and Macs, they have a context sensitive editor to help in programming (they highlights the C/C++/Fortran statements which helps you identify problems quickly).
4. gfortran is a fortran compiler that is available through gcc (for Macs visit hpc.sourceforge.net) . You can install it on your laptop if you want to program when no internet connection is available. If you have installed a recent version of gcc, chances are that gfortran is already available on your system. A final note is that if the software is installed in a non-standard directory tree, e.g. /usr/local, then you have to make sure that the executables are in your path, and the shared libraries are in your load library paths. The following are the commands you have to include in your .bashrc file:

   #modify the PATH to find the new executable
    export PATH=$PATH:/home/username/softdir/bin
   #modify the LD_LIBRARY_PATH to find the new shared libraries
    export LD_LIBRARY_PATH=$PATH:/home/username/softdir/lib
   #modify the MANPATH to find the new manual pages
    export MANPATH=$MANPATH:/home/username/softdir/man
   

   Here /home/username/softdir is the root directory where the softwarre has been installed. At the command line issue the command source .bashrc.
5. Cygwin is an application interface and a collection of tools which provide a Linux environment and commands for WINDOWS. In addition it has a free implementation of the X Window system which will allow you seemless access to the UNIX server. Installion is pretty easy but can take a little while depending on available bandwidth. Although the unix commands are useful, it is Cygwin/X that is the most valuable to allow you access to Unix/Linux servers; make sure it is installed.
6. Octave is a high-level language, primarily intended for numerical computations and visualization. Its language is mostly compatible with Matlab. It is available for all platforms (Windows, MacOS, and Linux).
7. Debugging for weeding out programming bugs.
8. Make for compiling executables with multiple source files.