Science the GNU Way, Part I
In my past several articles, I've looked at various packages to do all kinds of science. Sometimes, however, there just isn't a tool to solve a particular problem. That's the great thing about science. There is always something new to discover and study. But, this means it's up to you to develop the software tools you need to do your analysis. This article takes a look at the GNU Scientific Library, or GSL. This library is the Swiss Army library of routines that you will find useful in your work.
First, you need to to get a copy of GSL and install it on your system. Because it is part of the GNU Project, it is hosted at http://www.gnu.org/s/gsl. You always can download and build from the source code, but all major distributions should have packages available. For example, on Debianbased systems, you need to install the package libgsl0dev to develop your code and gslbin to run that code. GSL is meant for C and C++, so you also need a compiler. Most of you probably already are familiar with GCC, so I stick with that here.
The next step is actually the last step. I'm looking at compiling now so that I can focus on all the tools available in GSL. All the header files for GSL are stored in a subdirectory named gsl. So, for example, if you wanted to include the math header file, you would use:
#include <gsl/gsl_math.h>
All the functions are stored in a single library file called libgsl.a or libgsl.so. You also need a library to handle basic linear algebra. GSL provides one (in the file libgslcblas.so), but you can use your own. Additionally, you need to link in the math library. So, the final compile and link command should look like this: Garrick, one line below.
gcc o hello_world hello_world.c lgsl lgslcblas lm
There are optional inline versions for some of the performancecritical
functions in GSL. To use these, you need to include
DHAVE_INLINE
with
your compile command. To try to help with portability issues, GSL offers
some functions that exist only on certain platforms (and not others). As an
example, the BSD math library has a function called
hypot
. GSL offers
its own version, called gsl_hypot
, that you can use on nonBSD
platforms. Some functions have both a general algorithm as well
as optimized versions for specific platforms. This way, if you are running
on a SPARC, for example, you can select a version optimized for SPARC if it
exists.
One of the first things you likely will want to do is check
whether you are getting correct results from your code or if there were
errors. GSL has a number of functions and data structures available in the
header file named gsl_errno.h. Functions return a value of zero if everything
is fine. If there were any problems in trying to complete the requested
action, a nonzero value is returned. This could be an actual error
condition, like a wrong data type or memory error, or it could be a
condition like not being able to converge to within the requested accuracy
in the function call. This is why you always need to check the return value
for all GSL function calls. The actual values returned in an error
condition are error codes, defined in the file gsl_errno.h. They are
defined as macros that start with GSL_
. Examples
include the following:

GSL_EDOM
— domain error, used by functions when an argument doesn't fall into the domain over which the function is defined. 
GSL_ERANGE
— range error, either an overflow or underflow. 
GSL_ENOMEM
— no memory available.
The library will use values only up to 1024. Values above this are available
for use in your own code. There also are string versions of these error
codes available. You can translate the error code to its text value with
the function gsl_errno()
.
Now that you know how to compile your program and what to do with errors,
let's start looking at what kind of work you can do with GSL. Basic
mathematical functions are defined in the file gsl_math.h. The set of
mathematical constants from the BSD math library are provided by this part
of GSL. All of the constants start with M_
. Here are
a few of them:

M_PI
— pi. 
M_SQRT2
— the square root of 2. 
M_EULER
— Euler's constant.
There also are capabilities for dealing with infinities and nonnumbers. Three macros define the values themselves:

GSL_POSINF
— positive infinity. 
GSL_NEGINF
— negative infinity. 
GSL_NAN
— not a number.
There also are functions to test variables:

gsl_isnan
— is it not a number? 
gsl_isinf
— is it infinite? 
gsl_finite
— is it finite?
There is a macro to find the sign of a number.
GSL_SIGN(x)
returns the
sign of x: 1 if it is positive and –1 if it is negative. If you are
interested in seeing whether a number is even or odd, two macros
are defined: GSL_IS_ODD(x)
and
GSL_IS_EVEN(x)
. These return 1 if the
condition is true and 0 if it is not.
A series of elementary functions are part of the BSD math library. GSL provides versions of these for platforms that don't have native versions, including items like:

gsl_hypot
— calculate hypotenuse. 
gsl_asinh
,gsl_acosh
,gsl_atanh
— the arc hyperbolic trig functions.
If you are calculating the power of a number, you would use
gsl_pow_int(x,n)
, which gives you x to the power of n. There are
specific versions for powers less than 10. So if you wanted to find the
cube of a number, you would use gsl_pow_3
. These are very efficient and
highly optimized. You even can inline these specialized functions when
HAVE_INLINE
is defined.
Several macros are defined to help you find
the maximum or minimum of numbers, based on data type. The basic
GSL_MAX(a,b)
and GSL_MIN(a,b)
simply return either the maximum or
minimum of the two numbers a and b. GSL_MAX_DBL
and
GSL_MIN_DBL
find
the maximum and minimum of two doubles using an inline function.
GSL_MAX_INT
and GSL_MIN_INT
do the same for integer arguments.
When you
do any kind of numerical calculation on a computer, errors
always are introduced by roundoff and truncation. This is because you can't exactly
reproduce numbers on a finite binary system. But, what if you want to
compare two numbers and see whether they are approximately the same? GSL
provides the function gsl_fcmp(x,y,epsilon)
. This function compares the
two doubles x and y, and checks to see if they are within epsilon of each
other. If they are within this range, the function returns 0. If x < y, it
returns –1, and it returns 1 if x > y.
Complex numbers are used in many scientific fields. Within GSL, complex data
types are defined in the header file gsl_complex.h, and relevant functions
are defined in gsl_complex_math.h. To store complex numbers, the data
type gsl_complex
is defined. This is a struct that stores the two
portions. You can set the values with the functions
gsl_complex_rect(x,y)
or gsl_complex_polar(x,y)
. In the first, this
represents x+iy; whereas
in the second, x is the radius, and y is the angle in a polar representation.
You can pull out the real and imaginary parts of a complex number with the
macros GSL_REAL
and GSL_IMAG
. There is a function available to find the
absolute value of a complex number,
gsl_complex_abs(x)
, where x is of
type gsl_complex. Because complex numbers actually are built up of two
parts, even basic arithmetic is not simple. To do basic math, you can use
the following:

gsl_complex_add(a,b)

gsl_complex_sub(a,b)

gsl_complex_mul(a,b)

gsl_complex_div(a,b)
You can calculate the conjugate with
gsl_complex_conjugate(a)
and the
inverse with gsl_complex_inverse(a)
.
There are functions for basic
mathematical functions. To calculate the square root, you would use
gsl_complex_sqrt(x)
. To calculate the logarithm, you would use
gsl_complex_log(x)
. Several others are available too.
Trigonometric functions are provided, like
gsl_complex_sin(x)
. There also
are functions for hyperbolic trigonometric functions, along with the relevant
inverse functions.
Now that you have the basics down, my next article will explore all the actual scientific calculations you can do. I'll look at statistics, linear algebra, random numbers and many other topics.
Science image via Shutterstock.com.
Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.
Linux has become a key foundation for supporting today's rapidly growing IT environments. Linux is being used to deploy business applications and databases, trading on its reputation as a lowcost operating environment. For many IT organizations, Linux is a mainstay for deploying Web servers and has evolved from handling basic file, print, and utility workloads to running missioncritical applications and databases, physically, virtually, and in the cloud. As Linux grows in importance in terms of value to the business, managing Linux environments to high standards of service quality — availability, security, and performance — becomes an essential requirement for business success.
Sponsored by Red Hat
If you already use virtualized infrastructure, you are well on your way to leveraging the power of the cloud. Virtualization offers the promise of limitless resources, but how do you manage that scalability when your DevOps team doesn’t scale? In today’s hypercompetitive markets, fast results can make a difference between leading the pack vs. obsolescence. Organizations need more benefits from cloud computing than just raw resources. They need agility, flexibility, convenience, ROI, and control.
Stackato private PlatformasaService technology from ActiveState extends your private cloud infrastructure by creating a private PaaS to provide ondemand availability, flexibility, control, and ultimately, faster timetomarket for your enterprise.
Sponsored by ActiveState
Trending Topics
Great Scott! It's Version 13!  Jul 21, 2014 
Adminer—Better Than Awesome!  Jul 17, 2014 
It Actually Is Rocket Science  Jul 16, 2014 
Android Candy: Repix, Not Just Another Photo App  Jul 14, 2014 
Wanted: Your Embedded Linux Projects  Jul 10, 2014 
Linux Kernel Testing and Debugging  Jul 10, 2014 
 Great Scott! It's Version 13!
 Adminer—Better Than Awesome!
 It Actually Is Rocket Science
 NSA: Linux Journal is an "extremist forum" and its readers get flagged for extra surveillance
 Divx# Watch The Other Woman Full HD Online Streaming Viooz
 RSS Feeds
 Tech Tip: Really Simple HTTP Server with Python
 Linux Kernel Testing and Debugging
 Android Candy: Repix, Not Just Another Photo App
 Linux Systems Administrator
Featured Jobs
Linux Systems Administrator  Houston and Austin, Texas  Host Gator 
Senior Perl Developer  Austin, Texas  Host Gator 
Technical Support Rep  Houston and Austin, Texas  Host Gator 
UX Designer  Austin, Texas  Host Gator 
Web & UI Developer (JavaScript & j Query)  Austin, Texas  Host Gator 
Comments
Superb article. The way you
Superb article. The way you explained this is superb. Thanks for sharing this.
find command in unix and linux
Awesome
In my past several articles, I've looked at various packages to do all kinds of science. Sometimes, however, there just isn't a tool to solve a particular problem. That's the great thing about science.
telefonkatalogen.biz
Thanks for sharing this
Thanks for sharing this information with us. I am very impressed with this article. Your blog is very interesting. I appreciate your work. click jogos jogos jogos click jogos jogos de tiro jogos de sinuca jogos de futebol jogos jogos de meninas jogos do ben 10 jogos de vestir jogos da barbie
gsl_strerror() instead of
gsl_strerror() instead of gsl_errno() ?
"You can translate the error code to its text value with the function gsl_errno(). "
jogos online jogos de futebol
Great Post
Great PostSchools In Review.
Thanks for your sharing so
Thanks for your sharing so important ideas, the function of the GNU is good, but
fell the library is a little complicated to most. jogos do mario jogos de carros
nice site
Sometimes, however, there just isn't a tool to solve a particular problem.Jobs in the UK
Awesome..
This post is so informative and makes a very nice image on the topic in my mind. It is the first time I visit your blog, but I was extremely impressed. Keep posting as I am gonna come to read it everyday! Truss Display
Awesome..
This post is so informative and makes a very nice image on the topic in my mind. It is the first time I visit your blog, but I was extremely impressed. Keep posting as I am gonna come to read it everyday! Truss Display
Your article is very exciting
Your article is very exciting and informational. I am trying to decide on a career move and this has helped me with one aspect. Thank you so much!
كيف تعرف شخصيتك
science gnu
Undoubtedly one of the best articles I read here in LinuxJournal, you are the best at what they do, congratulations jogos de vestir
jogos da barbie
Awesome
I think this is one of the most significant information for me. And i am glad reading your article. But should remark on few general things, The site style is ideal, the articles is really nice : D. Good job, cheers.
solar panels.
Good one
I really appreciate the site for having such nice articles and good collections of information provided here.the article on mental health is very informative which would help many peoples.< ahref="http://www.backlinktime.com/" rel="follow">seo backlinks
Good...
Thanks for your sharing so important ideas, the function of the GNU is good, but fell the library is a little complicated to most, anyway can put the tool more simple and easy install, that's will be fine, thanks! jogos de meninas
jogos do ben 10
GNU
great article. But I wonder if there is another address with a copy of the GSL? When I tried to me was dead. Gstei very stepbystep. Once you manage to enter the site will realize it ... News send to my site, since already grateful! jogos
Awesome
Thanks for sharing this information with us. I am very impressed with this article. Your blog is very interesting. I appreciate your work.Visual Search Technology
Great
Thanks for it...Autonoleggio Creta.
gnu thes best way
I agree with you on finding new situations is never enough. I speak from experience. I program in C and C + +, and I confess that I never know quite where I lack knowledge, and when that happens nothing better than hooking up with people who now have a better than how our.
It has a website where I am always looking for new codes for my developments Ver Tv Online
This GNU is a little complicated to most
Thanks for your sharing so important ideas, the function of the GNU is good, but fell the library is a little complicated to most, anyway can put the tool more simple and easy install, that's will be fine, thanks!costume jewelry rings, rings for sale
Nice One...
Very well written post. It will be valuable to everyone who utilizes it, including myself. Keep doing what you are doing for sure I will check out more posts. There is a macro to find the sign of a number. GSL_SIGN(x) returns the sign of x: 1 if it is positive and –1 if it is negative. If you are interested in seeing whether a number is even or odd, two macros are defined: GSL_IS_ODD(x) and GSL_IS_EVEN(x). These return 1 if the condition is true and 0 if it is not.linkkei
science gnu
Undoubtedly one of the best articles I read here in LinuxJournal, you are the best at what they do, congratulations spc serasa
gsl_strerror() instead of
gsl_strerror() instead of gsl_errno() ?
"You can translate the error code to its text value with the function gsl_errno(). "
Common form in many
Common form in many libraries. gsl_strerror(gsl_errno()) gives you a nice text representation of an error. Users would rather see explanatory text than a numeric value.
Waiting for your next
Waiting for your next article. :)