GNU Scientific Library -- Reference Manual - Using the library

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# Using the library

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

## ANSI C Compliance

The library is written in ANSI C and is intended to conform to the ANSI C standard. 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_`.

## 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 ``app.c'` with the GNU C compiler `gcc` is,

    gcc -I/usr/local/include -c app.c

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

The library is installed as a single file, ``libgsl.a'`. A shared version of the library is also installed on systems that support shared libraries. The default location of these files is ``/usr/local/lib'`. 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 app.o -lgsl -lgslcblas -lm

The following command line shows how you would link the same application with an alternative blas library called ``libcblas'`,

    gcc app.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 app.o -lgsl -lcblas -latlas -lm

For more information see section BLAS Support.

The program `gsl-config` provides information on the local version of the library. For example, the following command shows that the library has been installed under the directory ``/usr/local'`,

    bash$ gsl-config --prefix
    /usr/local

Further information is available using the command `gsl-config --help`.

## Shared Libraries

To run a program linked with the shared version of the library it may be necessary to define the shell variable `LD_LIBRARY_PATH` to include the directory where the library is installed. For example,

    LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH ./app

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

    gcc -static app.o -lgsl -lgslcblas -lm

## Autoconf macros

For applications using `autoconf` the standard macro `AC_CHECK_LIB` can be used to link with the library automatically from a `configure` script. The library itself depends on the presence of a CBLAS and math library as well, so these must also be located before linking with the main `libgsl` file. The following commands should be placed in the ``configure.in'` file to perform these tests,

    AC_CHECK_LIB(m,main)
    AC_CHECK_LIB(gslcblas,main)
    AC_CHECK_LIB(gsl,main)

Assuming the libraries are found the output during the configure stage looks like this,

    checking for main in -lm... yes
    checking for main in -lgslcblas... yes
    checking for main in -lgsl... yes

If the library is found then the tests will define the macros `HAVE_LIBGSL`, `HAVE_LIBGSLCBLAS`, `HAVE_LIBM` and add the options `-lgsl -lgslcblas -lm` to the variable `LIBS`.

The tests above will find any version of the library. They are suitable for general use, where the versions of the functions are not important. An alternative macro is available in the file ``gsl.m4'` to test for a specific version of the library. To use this macro simply add the following line to your ``configure.in'` file instead of the tests above:

    AM_PATH_GSL(GSL_VERSION,
               [action-if-found],
               [action-if-not-found])

The argument `GSL_VERSION` should be the two or three digit MAJOR.MINOR or MAJOR.MINOR.MICRO version number of the release you require. A suitable choice for `action-if-not-found` is,

    AC_MSG_ERROR(could not find required version of GSL)

Then you can add the variables `GSL_LIBS` and `GSL_CFLAGS` to your Makefile.am files to obtain the correct compiler flags. `GSL_LIBS` is equal to the output of the `gsl-config --libs` command and `GSL_CFLAGS` is equal to `gsl-config --cflags` command. For example,

    libgsdv_la_LDFLAGS =    \
            $(GTK_LIBDIR) \
            $(GTK_LIBS) -lgsdvgsl $(GSL_LIBS) -lgslcblas

Note that the macro `AM_PATH_GSL` needs to use the C compiler so it should appear in the ``configure.in'` file before the macro `AC_LANG_CPLUSPLUS` for programs that use C++.

## Inline functions

The `inline` keyword is not part of ANSI C and the library does not export any inline function definitions by default. However, the library provides optional inline versions of performance-critical functions by conditional compilation. The inline versions of these functions can be included by defining the macro `HAVE_INLINE` when compiling an application.

    gcc -c -DHAVE_INLINE app.c

If you use `autoconf` this macro can be defined automatically. The following test should be placed in your ``configure.in'` file,

    AC_C_INLINE

    if test "$ac_cv_c_inline" != no ; then
      AC_DEFINE(HAVE_INLINE,1)
      AC_SUBST(HAVE_INLINE)
    fi

and the macro will then be defined in the compilation flags or by including the file ``config.h'` before any library headers. If you do not define the macro `HAVE_INLINE` then the slower non-inlined versions of the functions will be used instead.

Note that the actual usage of the inline keyword is `extern inline`, which eliminates unnecessary function definitions in GCC. If the form `extern inline` causes problems with other compilers a stricter autoconf test can be used, see section Autoconf Macros.

## Long double

The extended numerical type `long double` is part of the ANSI C standard and should be available in every modern compiler. However, the precision of `long double` is platform dependent, and this should be considered when using it. The IEEE standard only specifies the minimum precision of extended precision numbers, while the precision of `double` is the same on all platforms.

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. The substitution can be made automatically if you use `autoconf`. For example, to test whether the BSD function `hypot` is available you can include the following line in the configure file ``configure.in'` for your application,

    AC_CHECK_FUNCS(hypot)

and place the following macro definitions in the file ``config.h.in'`,

    /* 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 substitute `gsl_hypot` for each occurrence of `hypot` when `hypot` is not available.

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 alternate 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, or any other specific type, file 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.

## 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.

## 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.

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