GNU Scientific Library (GSL) - bwHPC Wiki GNU Scientific Library (GSL) - bwHPC Wiki

GNU Scientific Library (GSL)

From bwHPC Wiki
Jump to: navigation, search
Description Content
module load numlib/gsl
License GNU General Public License (GPL)
Citing
The recommended way is to cite the reference manual,
e.g. M. Galassi et al, GNU Scientific Library Reference Manual
(3rd Ed.), ISBN 0954612078.
Links GSL-GNU Scientific Library Homepage | Online-Documentation
Graphical Interface No


1 Description

The GNU Scientific Library (or GSL) is a software library for numerical computations in applied mathematics and science. The GSL is written in the C programming language, but bindings exist for other languages as well.
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

The complete range of subject areas covered by the library includes
• Complex Numbers • Roots of Polynomials • Special Functions • Vectors and Matrices • Permutations • Sorting • BLAS Support • Linear Algebra • Eigensystems • Fast Fourier Transforms • Quadrature • Random Numbers • Quasi-Random Sequences • Random Distributions • Statistics • Histograms • N-Tuples • Monte Carlo Integration • Simulated Annealing • Differential Equations • Interpolation • Numerical Differentiation • Chebyshev Approximation • Series Acceleration • Discrete Hankel Transforms • Root-Finding • Minimization • Least-Squares Fitting • Physical Constants • IEEE Floating-Point • Discrete Wavelet Transforms • Basis splines • Running Statistics • Sparse Matrices and Linear Algebra

2 Versions and Availability

A list of versions currently available on the bwForCluster Chemistry can be obtained from the
Cluster Information System CIS
Show a list of available versions using 'module avail numlib/gsl' on any HPC-C5 cluster.

: EXAMPLE bwUniCluster
$ module avail numlib/gsl
--------------------- /opt/bwhpc/common/modulefiles -----------------------
numlib/gsl/1.16-gnu-4.4             numlib/gsl/1.16-intel-14.0
numlib/gsl/1.16-intel-13.1(default)


3 Documentation

3.1 Online

3.2 Local

  • info gsl
  • man gsl
  • man gsl-config


4 Loading the module

You can load the default version of the GSL library with the command
'module load numlib/gsl'.
The module will try to load modules it needs to function. If loading the module fails, check if you have already loaded one of those modules with the command 'module list'.
If you wish to load a specific (older) version (if available), you can do so using e.g. ' module load numlib/gsl/'version' to load the version you desires.

$ module avail numlib/gsl
---------------------- /opt/bwhpc/common/modulefiles -----------------------
numlib/gsl/1.16-gnu-4.4             numlib/gsl/1.16-intel-14.0
numlib/gsl/1.16-intel-13.1(default)
$ module load numlib/gsl/1.16-gnu-4.4
$ module list
Currently Loaded Modulefiles:
  1) numlib/gsl/1.16-gnu-4.4


5 GSL-Specific Environments

To see a list of all GSL environments set by the 'module load'-command use 'env | grep GSL'.
Or use the command 'module show numlib/gsl'.

$ module show numlib/gsl
-----------------------------------------------------------------
/opt/bwhpc/common/modulefiles/numlib/gsl/1.16-intel-13.1:
GSL_VERSION = 1.16 
GSL_HOME = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1 
GSL_BIN_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/bin 
GSL_INC_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/include 
GSL_LIB_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/lib 
GSL_STA_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/lib 
GSL_SHA_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/lib 
GSL_MAN_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/man 
GSL_INF_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/info 
GSL_DOC_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/doc 
GSL_EXA_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/doc/examples 
GSL_WWW http://www.gnu.org/software/gsl/ 
PATH = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/bin:$PATH
MANPATH = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/man:$MANPATH
INFOPATH = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/info:$INFOPATH
LD_LIBRARY_PATH = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/lib:$LD_LIBRARY_PATH
INCLUDE = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/include:$INCLUDE
[...] 


6 How To Use the Library

6.1 Includes

Your source code should contain preprocessor include statements with a gsl/ prefix, such as

#include <gsl/gsl_math.h>

6.2 Compile

A typical compilation command for a source file example.c with the Intel C compiler icc is

 $ icc -Wall -I$GSL_INC_DIR  -c example.c 

The $GSL_INC_DIR environment variable points to location of the include path for the gsl header files.

6.3 Link

The following command can be used to link the application with the gsl libraries.

 $ icc -L$GSL_LIB_DIR -o example example.o -lgsl -lgslcblas -lm 

The $GSL_LIB_DIR environment variable points to the location of the gsl libraries.
Also make sure to have the GSL-module loaded before running applications build with this library.

7 Example C-Source Code

7.1 Create source code file 'intro.c'

#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;
}

Bessel-Functions and more

7.2 Compile and Link

Load the GSL module for the Intel compiler, compile, link and run the program

$ module load numlib/gsl/1.16-intel-13.1
Loading module dependency 'compiler/intel/13.1'.
$ icc -Wall -I$GSL_INC_DIR  -c intro.c
$ icc -L$GSL_LIB_DIR -o intro intro.o -lgsl -lgslcblas -lm
$ ./intro
J0(5) = -1.775967713143382642e-01