Using the Library¶

This chapter describes how to compile programs that use GSL, and introduces its conventions.

An Example Program¶

The following short program demonstrates the use of the library by computing the value of the Bessel function $J_0(x)$ for $x=5$ :

#include <stdio.h>
#include <gsl/gsl_sf_bessel.h>

int
main (void)
{
  double x = 5.0;
  double y = gsl_sf_bessel_J0 (x);
  printf ("J0(%g) = %.18e\n", x, y);
  return 0;
}

The output is shown below, and should be correct to double-precision accuracy 1,

J0(5) = -1.775967713143382642e-01

The steps needed to compile this program are described in the following sections.

Compiling and Linking¶

The library header files are installed in their own gsl directory. You should write any preprocessor include statements with a gsl/ directory prefix thus:

#include <gsl/gsl_math.h>

If the directory is not installed on the standard search path of your compiler you will also need to provide its location to the preprocessor as a command line flag. The default location of the gsl directory is /usr/local/include/gsl. A typical compilation command for a source file example.c with the GNU C compiler gcc is:

$ gcc -Wall -I/usr/local/include -c example.c

This results in an object file example.o. The default include path for gcc searches /usr/local/include automatically so the -I option can actually be omitted when GSL is installed in its default location.

Linking programs with the library¶

The library is installed as a single file, libgsl.a. A shared version of the library libgsl.so is also installed on systems that support shared libraries. The default location of these files is /usr/local/lib. If this directory is not on the standard search path of your linker you will also need to provide its location as a command line flag.

To link against the library you need to specify both the main library and a supporting CBLAS library, which provides standard basic linear algebra subroutines. A suitable CBLAS implementation is provided in the library libgslcblas.a if your system does not provide one. The following example shows how to link an application with the library:

$ gcc -L/usr/local/lib example.o -lgsl -lgslcblas -lm

The default library path for gcc searches /usr/local/lib automatically so the -L option can be omitted when GSL is installed in its default location.

The option -lm links with the system math library. On some systems it is not needed. 2

For a tutorial introduction to the GNU C Compiler and related programs, see “An Introduction to GCC” (ISBN 0954161793). 3

Linking with an alternative BLAS library¶

The following command line shows how you would link the same application with an alternative CBLAS library libcblas.a:

$ gcc example.o -lgsl -lcblas -lm

For the best performance an optimized platform-specific CBLAS library should be used for -lcblas. The library must conform to the CBLAS standard. The ATLAS package provides a portable high-performance BLAS library with a CBLAS interface. It is free software and should be installed for any work requiring fast vector and matrix operations. The following command line will link with the ATLAS library and its CBLAS interface:

$ gcc example.o -lgsl -lcblas -latlas -lm

If the ATLAS library is installed in a non-standard directory use the -L option to add it to the search path, as described above.

For more information about BLAS functions see BLAS Support.

Shared Libraries¶

To run a program linked with the shared version of the library the operating system must be able to locate the corresponding .so file at runtime. If the library cannot be found, the following error will occur:

$ ./a.out
./a.out: error while loading shared libraries:
libgsl.so.0: cannot open shared object file: No such file or directory

To avoid this error, either modify the system dynamic linker configuration 4 or define the shell variable LD_LIBRARY_PATH to include the directory where the library is installed.

For example, in the Bourne shell (/bin/sh or /bin/bash), the library search path can be set with the following commands:

$ LD_LIBRARY_PATH=/usr/local/lib
$ export LD_LIBRARY_PATH
$ ./example

In the C-shell (/bin/csh or /bin/tcsh) the equivalent command is:

% setenv LD_LIBRARY_PATH /usr/local/lib

The standard prompt for the C-shell in the example above is the percent character %, and should not be typed as part of the command.

To save retyping these commands each session they can be placed in an individual or system-wide login file.

To compile a statically linked version of the program, use the -static flag in gcc:

$ gcc -static example.o -lgsl -lgslcblas -lm

ANSI C Compliance¶

The library is written in ANSI C and is intended to conform to the ANSI C standard (C89). It should be portable to any system with a working ANSI C compiler.

The library does not rely on any non-ANSI extensions in the interface it exports to the user. Programs you write using GSL can be ANSI compliant. Extensions which can be used in a way compatible with pure ANSI C are supported, however, via conditional compilation. This allows the library to take advantage of compiler extensions on those platforms which support them.

When an ANSI C feature is known to be broken on a particular system the library will exclude any related functions at compile-time. This should make it impossible to link a program that would use these functions and give incorrect results.

To avoid namespace conflicts all exported function names and variables have the prefix gsl_, while exported macros have the prefix GSL_.

Inline functions¶

The inline keyword is not part of the original ANSI C standard (C89) so the library does not export any inline function definitions by default. Inline functions were introduced officially in the newer C99 standard but most C89 compilers have also included inline as an extension for a long time.

To allow the use of inline functions, the library provides optional inline versions of performance-critical routines by conditional compilation in the exported header files. The inline versions of these functions can be included by defining the macro HAVE_INLINE when compiling an application:

$ gcc -Wall -c -DHAVE_INLINE example.c

If you use autoconf this macro can be defined automatically. If you do not define the macro HAVE_INLINE then the slower non-inlined versions of the functions will be used instead.

By default, the actual form of the inline keyword is extern inline, which is a gcc extension that eliminates unnecessary function definitions. If the form extern inline causes problems with other compilers a stricter autoconf test can be used, see Autoconf Macros.

When compiling with gcc in C99 mode (gcc -std=c99) the header files automatically switch to C99-compatible inline function declarations instead of extern inline. With other C99 compilers, define the macro GSL_C99_INLINE to use these declarations.

Long double¶

In general, the algorithms in the library are written for double precision only. The long double type is not supported for actual computation.

One reason for this choice is that the precision of long double is platform dependent. The IEEE standard only specifies the minimum precision of extended precision numbers, while the precision of double is the same on all platforms.

However, it is sometimes necessary to interact with external data in long-double format, so the vector and matrix datatypes include long-double versions.

It should be noted that in some system libraries the stdio.h formatted input/output functions printf and scanf are not implemented correctly for long double. Undefined or incorrect results are avoided by testing these functions during the configure stage of library compilation and eliminating certain GSL functions which depend on them if necessary. The corresponding line in the configure output looks like this:

checking whether printf works with long double... no

Consequently when long double formatted input/output does not work on a given system it should be impossible to link a program which uses GSL functions dependent on this.

If it is necessary to work on a system which does not support formatted long double input/output then the options are to use binary formats or to convert long double results into double for reading and writing.

Portability functions¶

To help in writing portable applications GSL provides some implementations of functions that are found in other libraries, such as the BSD math library. You can write your application to use the native versions of these functions, and substitute the GSL versions via a preprocessor macro if they are unavailable on another platform.

For example, after determining whether the BSD function hypot() is available you can include the following macro definitions in a file config.h with your application:

/* Substitute gsl_hypot for missing system hypot */

#ifndef HAVE_HYPOT
#define hypot gsl_hypot
#endif

The application source files can then use the include command #include <config.h> to replace each occurrence of hypot() by gsl_hypot() when hypot() is not available. This substitution can be made automatically if you use autoconf, see Autoconf Macros.

In most circumstances the best strategy is to use the native versions of these functions when available, and fall back to GSL versions otherwise, since this allows your application to take advantage of any platform-specific optimizations in the system library. This is the strategy used within GSL itself.

Alternative optimized functions¶

The main implementation of some functions in the library will not be optimal on all architectures. For example, there are several ways to compute a Gaussian random variate and their relative speeds are platform-dependent. In cases like this the library provides alternative implementations of these functions with the same interface. If you write your application using calls to the standard implementation you can select an alternative version later via a preprocessor definition. It is also possible to introduce your own optimized functions this way while retaining portability. The following lines demonstrate the use of a platform-dependent choice of methods for sampling from the Gaussian distribution:

#ifdef SPARC
#define gsl_ran_gaussian gsl_ran_gaussian_ratio_method
#endif
#ifdef INTEL
#define gsl_ran_gaussian my_gaussian
#endif

These lines would be placed in the configuration header file config.h of the application, which should then be included by all the source files. Note that the alternative implementations will not produce bit-for-bit identical results, and in the case of random number distributions will produce an entirely different stream of random variates.

Support for different numeric types¶

Many functions in the library are defined for different numeric types. This feature is implemented by varying the name of the function with a type-related modifier—a primitive form of C++ templates. The modifier is inserted into the function name after the initial module prefix. The following table shows the function names defined for all the numeric types of an imaginary module gsl_foo with function fn():

gsl_foo_fn               double
gsl_foo_long_double_fn   long double
gsl_foo_float_fn         float
gsl_foo_long_fn          long
gsl_foo_ulong_fn         unsigned long
gsl_foo_int_fn           int
gsl_foo_uint_fn          unsigned int
gsl_foo_short_fn         short
gsl_foo_ushort_fn        unsigned short
gsl_foo_char_fn          char
gsl_foo_uchar_fn         unsigned char

The normal numeric precision double is considered the default and does not require a suffix. For example, the function gsl_stats_mean() computes the mean of double precision numbers, while the function gsl_stats_int_mean() computes the mean of integers.

A corresponding scheme is used for library defined types, such as gsl_vector and gsl_matrix. In this case the modifier is appended to the type name. For example, if a module defines a new type-dependent struct or typedef gsl_foo it is modified for other types in the following way:

gsl_foo                  double
gsl_foo_long_double      long double
gsl_foo_float            float
gsl_foo_long             long
gsl_foo_ulong            unsigned long
gsl_foo_int              int
gsl_foo_uint             unsigned int
gsl_foo_short            short
gsl_foo_ushort           unsigned short
gsl_foo_char             char
gsl_foo_uchar            unsigned char

When a module contains type-dependent definitions the library provides individual header files for each type. The filenames are modified as shown in the below. For convenience the default header includes the definitions for all the types. To include only the double precision header file, or any other specific type, use its individual filename:

#include <gsl/gsl_foo.h>               All types
#include <gsl/gsl_foo_double.h>        double
#include <gsl/gsl_foo_long_double.h>   long double
#include <gsl/gsl_foo_float.h>         float
#include <gsl/gsl_foo_long.h>          long
#include <gsl/gsl_foo_ulong.h>         unsigned long
#include <gsl/gsl_foo_int.h>           int
#include <gsl/gsl_foo_uint.h>          unsigned int
#include <gsl/gsl_foo_short.h>         short
#include <gsl/gsl_foo_ushort.h>        unsigned short
#include <gsl/gsl_foo_char.h>          char
#include <gsl/gsl_foo_uchar.h>         unsigned char

Compatibility with C++¶

The library header files automatically define functions to have extern "C" linkage when included in C++ programs. This allows the functions to be called directly from C++.

To use C++ exception handling within user-defined functions passed to the library as parameters, the library must be built with the additional CFLAGS compilation option -fexceptions.

Aliasing of arrays¶

The library assumes that arrays, vectors and matrices passed as modifiable arguments are not aliased and do not overlap with each other. This removes the need for the library to handle overlapping memory regions as a special case, and allows additional optimizations to be used. If overlapping memory regions are passed as modifiable arguments then the results of such functions will be undefined. If the arguments will not be modified (for example, if a function prototype declares them as const arguments) then overlapping or aliased memory regions can be safely used.

Thread-safety¶

The library can be used in multi-threaded programs. All the functions are thread-safe, in the sense that they do not use static variables. Memory is always associated with objects and not with functions. For functions which use workspace objects as temporary storage the workspaces should be allocated on a per-thread basis. For functions which use table objects as read-only memory the tables can be used by multiple threads simultaneously. Table arguments are always declared const in function prototypes, to indicate that they may be safely accessed by different threads.

There are a small number of static global variables which are used to control the overall behavior of the library (e.g. whether to use range-checking, the function to call on fatal error, etc). These variables are set directly by the user, so they should be initialized once at program startup and not modified by different threads.

Deprecated Functions¶

From time to time, it may be necessary for the definitions of some functions to be altered or removed from the library. In these circumstances the functions will first be declared deprecated and then removed from subsequent versions of the library. Functions that are deprecated can be disabled in the current release by setting the preprocessor definition GSL_DISABLE_DEPRECATED. This allows existing code to be tested for forwards compatibility.

Code Reuse¶

Where possible the routines in the library have been written to avoid dependencies between modules and files. This should make it possible to extract individual functions for use in your own applications, without needing to have the whole library installed. You may need to define certain macros such as GSL_ERROR and remove some #include statements in order to compile the files as standalone units. Reuse of the library code in this way is encouraged, subject to the terms of the GNU General Public License.

Footnotes

1: The last few digits may vary slightly depending on the compiler and platform used—this is normal
2: It is not needed on MacOS X
3: http://www.network-theory.co.uk/gcc/intro/
4: /etc/ld.so.conf on GNU/Linux systems