Introduction to scientific programming in Earth's Sciences

1
Introduction to scientific programming in Earth's
Sciences
J.W. Goethe University. Frankfurt

• Dr Guillaume RICHARD
• Institüt für Geowissenchaften 1.232
• richard_at_geophysik.uni-frankfurt.de

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Overview

• 12 x 45min Lectures / 45min training classes
  (praktical)
• Basics (Hardware, OS, editor, etc.. )
• Basics 2 (Linux commands, Compile,Visualize )
• Languages Fortran (FORmula TRANslation)
• Languages Fortran (2)
• Languages Fortran (3)
• Languages Fortran (4)
• Languages C/C
• Languages Matlab (1)
• Languages Matlab (2)
• Languages Maple
• Introduction to Finite difference / Finite Volume
  method
• Introduction to Finite difference / Finite Volume
  method (2)

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Basics
1. Problem. Clearly and unambiguously identify
the problem to be solved.
2. Model. Use simplification and abstraction to
arrive at a mathematical model for the problem.
3. Method. Identify a computational method for
solving the model.
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Basics
4. Implementation. Implement the method in the
appropriate language.
5. Assessment. Concurrently with the other four
steps, actively assess the problem-solving
process to identify mistakes and unwarranted
assumptions.
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Basics
6. Visualisation.
7. Optimisation. Parallelization. Vectorization.
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Basics
Hardware
CPU - Central Processor Unit RAM - Random Access
Memory VRAM - Video RAM ROM -Read Only Member
IO Input/Output. HD Hard Disk CDROM Compact
Disk Read-only-memory CD-RW DVD Read/Write
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Basics
Jargon and Fundamentals of Computer

• Computers have only 2 fingers. A bit 0 or
  1(false/true)
• CPU basically only knows how to perform AND,
  OR, XOR (exclusive OR) operations
• AND returns true if both same
• OR returns true if either true
• XOR returns true if different
• CPU is a massive collection of AND and OR gates
  (transistors)
• A specific CPU has a set of instructions it can
  execute (usually small 50-100) (Machine language)

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Basics
Jargon and Fundamentals of Computer

• theclock speed the number of instructions
  per seconds. e.g, 500 MHz
• a cycle One clock tick. Modern CPUs can
  execute more than one instruction per cycle
• All programming ultimately ends up as a set of
  instructions to executed by the CPU
  (compiling/linking or interpreter do this for
  you).
• flops unit to mesure Floating point speed
  floating point operations per seconds.
• byte group of 8 bits
• word group of 2/4/8 bytes (depends on the
  CPU). New machines have 64 bits (8bytes)
  architecture.

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Basics
Jargon and Fundamentals of Computer
Number of unique values that can be represented
depends on number of bits. ex For n bits,
unique values are 0 to 2n-1 Grouped into larger
units to represent different things ex ASCII
(American Standard Code for Information
Interchange) Basic version is 7 bit (128
characters) A-Z, a-z, 0-9 and special
characters Values lt32 are control characters
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Basics
Jargon and Fundamentals of Computer

• Numbers representation depends on the base system
  used
• Binary base 2 (0-1), Octal base 8 (0-7)
• Hexadecimal base 16 (0-15, with A-F representing
  10-15)
• ex 543666110110
• Prefixes kilo 1024 mega1048576giga107377418
  24 (approximately 103,106,109)
• integer (2/4-bytes)
• Real (floating point) IEEE 4-byte floating
  point is 8bit exponent, 24bit mantissa (1 sign
  bit for each), 7 significant digits, range 1038

ex 541036166681101102
ex 2-byte unsigned 0-65535, signed 32767
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Basics
Jargon and Fundamentals of Computer
BIOS (Basic Input/Output System) A program
built into every PC for setting up very basic
things (ex how many hard and floppy disks) the
first thing that loads when you start your PC.
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Basics
Operating System (OS)

• Windows (3.0, 3.1, NT, 95, 98, Millenium, 2000,
  XP, Vista, etc)

• Macintosh ( System sofware (1-7), Classic Mac
  OS 8-9 , Mac OS X)

• UNIX (Bourne shell, the (T)C shell, Kornshell,
  Z-shell, etc)

• Linux (bash Debian, RedHat/Fedora, Suze, Ubuntu,
  etc)

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Basics
Operating System (OS)

• Controls everything in the way the computer
  works.
• Not Specific to a CPU type but often some OSs are
  associated with specific CPU
• OS controls IO and memory management (latter is
  important in multi-tasking OS).
• Specific program implementations are often
  dependent on OS

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Basics
Editors

• Text editor (Notepad) vs word processor (Word,
  open office)
• UNIX (Vi(m), (X)emacs, E, Nedit, TextEdit, gedit)
• Specific editors
• HyperTextMarkupLanguage (HTML) DreamWeaver,
  Frontpage, Seamonkey, Mozzila composer, GoLive
• Java Eclispse
• Fortran Xemacs, Kedit, Tidy (Clean up Fortran
  77 code), Melite, Magic Editor, Neoxen,
  Understand for FORTRAN (Scitools), Visual
  Fortran, etc
• Integrated Development Environment (IDE), Matlab,
  scilab, IDL, etc

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Programming Languages

• Fortran 77/90/95/2003
• C/C
• Pascal, TurboPascal
• Matlab, IDL, Scilab
• Maple, Mathematica
• Perl, Python
• Htlm, Java
• Excel ??