 |
Intro to Scientific Computing |
 |
The Scientific Computing Environment
By scientific computing environment, we mean the hardware, software, operating system, and customary tools, with which you will carry out the computations described in the previous page. Thus the environment can be quite extensive. However for our purposes it is possible to set up a very nice scientific computing environment on a personal computer.
Scientific Computing Hardware
There is a wide range of machines upon which good science is done. These range from graphing calculators up to multi-million dollar computing facilities which house the fastest and most advanced computers in the world.Let's first look at perhaps the simplest scientific computing environment, the handheld graphing calculator. If you (or your friend) has a TI-8X (a Texas Instruments 82, 83, 84, or 86, etc.) calculator, you can do a significant number of the items described under scientific computing tasks on the previous page. As an example (and particularly if you yourself have one of these little pocket pals), visit The Quick and Dirty TI Guide to see a list of these features.
For example, my TI-86 does:
- Data visualization
- Curve fitting
- Linear algebra (solving several linear equations)
- Statistical computations
- Scientific programming
This is pretty good for something that fits in your pocket (or at
least can hang from your belt)!
High Performance Computing
At the other end, consider the Earth Simulator, one of the world's fastest computers (in 2005) located in Japan.
This computer takes up an entire two story building that is a bit smaller than a football field. The bottom floor is cooling, power, and cabling, and the top floor houses thousands of CPUs wired together to work as one single system. As its name implies, the Earth Simulator was built for global climate modeling.
An example visualization of some of its output is here (an El Nino event):
The Operating System
We all are familiar with the two major operating systems running on 90% of the personal computers we see everyday. Many of you will also be familiar with the third mjor OS, Unix (or its PC version, Linux). Some of you will be VERY familiar with this jargon, being computer science or computer engineering majors, however I review if for those new to the broader computer world.
- Unix
The unix operating system was developed before both Windows and Mac OS for large computers called "Mainframes" of the 1970s (i.e. "back in the Day!). One interacted with these machines by "logging on" via a text terminal, usually in another office, at a place like a bank or an airport where there were many people working simultaneously. These mainframes managed many simultaneous users--they were the original "servers". Thus the unix operating system, developed at Bell Laboratories, was originally designed to be "multitasking" from the beginning, something that personal computers only developed in the very late 1980s, after the appearance of the 80386 Intel processor (this is the precursor to the Pentium, the 80586). Also in the 1980s, unix workstations became quite popular among scientists and engineers, and a number of tools were developed for to aid scientists in their work.
Many different computer vendors such as IBM, Sun Microsystems, Silicon Graphics, and Hewlett-Packard have developed their own forms of unix to run on their specific hardware. These versions of unix go by the names: AIX, Solaris, Ultrix, and HPUX. The development history, evolution, and relationship of these different versions is shown below.
The University of the Pacific maintains a powerful central mainframe unix system called the Sun Ray System, developed by Sun Microsystems, which is available all over campus. At some point we will login to this system and try out Sun's version of unix called Solaris.
I've always thought "Solaris" was an odd name for an operating system. It originates in the classic scifi novel "Solaris" by Stanislaw Lem, where a sentient ocean covering a distant planet drives explorers mad who are sent to study it.
- Sun Rays at Pacific
If you are living on campus and are a Physics or Engineering major, your professors will be familiar with the Sun Rays. There are labs with Sun Ray terminals available in these departments. The scientific computing environment on the Sun Rays is briefly listed here. Note that most links describing the software are broken at the moment. But you can see what software is there.
Later in the course we will log on to the Pacific unix system to try some applications.
- Unix on a PC: Linux
With the introduction of the 80386 CPU chip by Intel in the 1980s, PCs
became able to multitask allowing the development of a form of unix
which would run on the PC architecture. This version was developed by
Linus Torvalds, a Finnish graduate student and the GNU Free Software
Foundation developed by Richard Stallman. The name of this version is
Linux which is extremely
popular, powerful, and free
While I use Linux on my own PC, most students who take this course are not familiar with Unix. Thus we will begin our course by installing the tools we need on a PC or Mac. If you are already familiar with Linux and wish to use it, let me know. All of the tools that I will introduce to you in this course come with the standard Linux distributions, but it is beyond the scope of this course to have all students install Linux on their particular computers.
Many people run Linux in dual boot mode which means that one has the choice to boot to Windows or Linux upon startup.
- Windows
As we all know, for better or worse, Microsoft Windows dominates the world market in Operating Systems, which has made Bill Gates the richest man in the world. Windows has been developed largely to do the things listed on the Introduction page under Non-Scientific Computing: email, office work, word processing, calendars, games, etc.; these are the things most of people in the world do with their personal computers.
We will use an application called Cygwin which provides much of the environment that Unix/Linux users are used to.
- Cygwin
Cygwin is kind of a bridge between windows and unix. It installs with a graphical user interface (GUI) which allows you to install the basic system, then select packages you wish to install. The packages include all the tools we will use in this course, in addition to many more. It provides almost a full unix environment running under the Windows OS. We will use Cygwin in this course for those that have Windows computers.
From the Cygwin website:
What Is Cygwin? Cygwin is a Linux-like environment for Windows. It consists of two parts:
- A DLL (cygwin1.dll) which acts as a Linux API emulation layer providing substantial Linux API functionality.
- A collection of tools which provide Linux look and feel.
What Isn't Cygwin?
- Cygwin is not a way to run native linux apps on Windows. You have to rebuild your application from source if you want it to run on Windows.
- Cygwin is not a way to magically make native Windows apps aware of UNIX ® functionality, like signals, ptys, etc. Again, you need to build your apps from source
- Macintosh
The Mac was developed to make the computer easier to use. It featured one of the first popular mouse based interaction systems (Graphical User Interfaces, or GUI). It did many of the same things that MS Windows did, but originally tended to focus on games, educational programs, and artistic programs (music and art in particular).
Since the 10th vesion of the Mac operating system, OSX, Apple has moved to a unix based OS with a large layer of user friendly applications over the top. One of the reasons that makes Macs very smooth in operation (fewer driver problems, conflicts, etc.) is that Apple controls both the software and hardware, as opposed to Microsoft which produces the software only, but controls hardware through coersion.
If you are using a Mac, you already have a basic unix system beneath OSX. we will install scientific software using an application called Fink. Fink is very much like Cygwin. More on this later.
NEXT: Summary