Difference between revisions of "Development/GSL"

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{{Softwarepage|numlib/gsl}}
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| module load
  
| module load
 
| numlib/gsl
  
| numlib/gsl
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|-
  
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| Availability
  
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| [[bwUniCluster_2.0]] | [[BwForCluster_JUSTUS_2]]
  
 
|-
  
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| License
  
| License
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|-
  
|-
 
|Citing
  
|Citing
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| <small><small><pre>M. Galassi et al., GNU Scientific Library Reference Manual (3rd Ed.), ISBN 0954612078.</pre></small></small>
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| <pre>M. Galassi et al., GNU Scientific Library Reference Manual (3rd Ed.), ISBN 0954612078.</pre>
 
|-
  
|-
 
| Links
  
| Links
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<br>
  
<br>
 
<br>
  
<br>
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== How to use GSL ==
   
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A man page is available and can be accessed by typing
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= Availability =
  
−  
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GSL is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].
  
−  
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In order to check which versions of GSL are installed on the compute cluster, run the following command:
  
 
<pre>
  
<pre>
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$ module avail numlib/gsl
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$ man gsl
 
</pre>
  
</pre>
   
  +
=== Includes ===
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= Documentation =
  
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=== Online ===
  
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* [http://www.gnu.org/software/gsl/ Online-Documentation]
  
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=== Local ===
  
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* info gsl
  
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* man gsl
  
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* man gsl-config
  
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<br>
  
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= Usage =
  
   
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Your source code should contain preprocessor include statements with a gsl/prefix such as
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== Loading the module ==
  
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<source lang="c">#include <gsl/gsl_math.h></source>
   
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=== Compile ===
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You can load the default version of GSL with the following command:
  
−
<pre>
  
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$ module load numlib/gsl
  
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</pre>
  
   
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A typical compilation command for a source file 'example.c' using the Intel C compiler icc is
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The module will try to load all modules it needs to function (e.g., compiler, mpi, ...). If loading the module fails, check if you have already loaded one of those modules, but not in the version required by GSL.
  
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<pre> $ icc -Wall -I$GSL_INC_DIR -c example.c </pre>
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The <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$GSL_INC_DIR</span> environment variable points to the location of the include path for the GSL header files.
   
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=== Link ===
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If you wish to load another (older) version of GSL, you can do so using
  
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<pre>
  
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$ module load numlib/gsl/<version>
  
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</pre>
  
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with <version> specifying the desired version.
  
   
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The following command can be used to link the application with the GSL libraries:
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= GSL-Specific Environments =
  
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To see a list of all GSL environments set by the 'module load'-command use 'env | grep GSL'.
  
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<br>
  
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Or use the command 'module show numlib/gsl'.
  
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<pre>
  
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$ module show numlib/gsl
  
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-----------------------------------------------------------------
  
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/opt/bwhpc/common/modulefiles/numlib/gsl/1.16-intel-13.1:
  
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GSL_VERSION = 1.16
 
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GSL_HOME = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1
 
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GSL_BIN_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/bin
 
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GSL_INC_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/include
 
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GSL_LIB_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/lib
 
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GSL_STA_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/lib
 
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GSL_SHA_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/lib
 
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GSL_MAN_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/man
 
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GSL_INF_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/info
 
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GSL_DOC_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/doc
 
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GSL_EXA_DIR = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/doc/examples
 
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GSL_WWW http://www.gnu.org/software/gsl/
 
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PATH = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/bin:$PATH
  
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MANPATH = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/man:$MANPATH
  
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INFOPATH = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/share/info:$INFOPATH
  
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LD_LIBRARY_PATH = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/lib:$LD_LIBRARY_PATH
  
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INCLUDE = /opt/bwhpc/common/numlib/gsl/1.16-intel-13.1/include:$INCLUDE
  
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[...]
 
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</pre>
  
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<br>
  
−  
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= How To Use the Library =
  
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== Includes ==
  
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Your source code should contain preprocessor include statements with a gsl/ prefix, such as
  
−
<source lang="c">#include <gsl/gsl_math.h></source>
  
−
== Compile ==
  
−
A typical compilation command for a source file example.c with the
 
−
Intel C compiler icc is
  
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<pre> $ icc -Wall -I$GSL_INC_DIR -c example.c </pre>
  
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The [[#GSL-Specific Environments|$GSL_INC_DIR environment variable]] points to location of
 
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the include path for the gsl header files.
  
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<br>
  
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== Link ==
  
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The following command can be used to link the application with the gsl libraries.
  
 
<pre> $ icc -L$GSL_LIB_DIR -o example example.o -lgsl -lgslcblas -lm </pre>
  
<pre> $ icc -L$GSL_LIB_DIR -o example example.o -lgsl -lgslcblas -lm </pre>
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The [[#GSL-Specific Environments|$GSL_LIB_DIR environment]] variable points to the location
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The <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$GSL_LIB_DIR</span> 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.
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of the gsl libraries.
  
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<br>
  
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Also make sure to have the GSL-module loaded before running applications build
  
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with this library.
  
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<br><br>
  
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= Example C-Source Code =
 
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== Create source code file 'intro.c' ==
  
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<source lang="c">
  
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#include <stdio.h>
  
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#include <gsl/gsl_sf_bessel.h>
  
   
  +
= Useful links =
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int main (void)
  
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{
  
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double x = 5.0;
  
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double y = gsl_sf_bessel_J0 (x);
  
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printf ("J0(%g) = %.18e\n", x, y);
  
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return 0;
  
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}
  
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</source>
  
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<small>[https://www.gnu.org/software/gsl/manual/html_node/Special-Functions.html Bessel-Functions and more]</small>
  
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<br>
  
   
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* [https://www.gnu.org/software/gsl/doc/html/index.html Documentation (english)]
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== Compile and Link ==
  
  +
* [https://de.wikipedia.org/wiki/GNU_Scientific_Library Wikipedia article (german)]
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Load the GSL module for the Intel compiler, compile, link and run the program
  
  +
* [https://en.wikipedia.org/wiki/GNU_Scientific_Library Wikipedia article (english)]
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<pre>
  
−
$ module load numlib/gsl/1.16-intel-13.1
  
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Loading module dependency 'compiler/intel/13.1'.
  
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$ icc -Wall -I$GSL_INC_DIR -c intro.c
  
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$ icc -L$GSL_LIB_DIR -o intro intro.o -lgsl -lgslcblas -lm
  
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$ ./intro
  
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J0(5) = -1.775967713143382642e-01
  
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</pre>
  
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<br>
  
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[[Category: Numerical libraries]][[Category:BwUniCluster]][[Category:BwUniCluster_2.0]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]
  

Latest revision as of 00:03, 15 March 2023

The main documentation is available via module help numlib/gsl on the cluster. Most software modules for applications provide working example batch scripts.


Description Content
module load numlib/gsl
License GNU General Public License (GPL)
Citing 
M. Galassi et al., GNU Scientific Library Reference Manual (3rd Ed.), ISBN 0954612078.
Links Homepage | Documentation
Graphical Interface No


1 Description

The GNU Scientific Library (GSL) is a software library for numerical computations in applied mathematics and science. GSL is written in C, but bindings exist for other programming languages as well. 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:

• 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

1.1 How to use GSL

A man page is available and can be accessed by typing 

$ man gsl

1.1.1 Includes

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

#include <gsl/gsl_math.h>

1.1.2 Compile

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

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

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

1.1.3 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.

2 Useful links

Retrieved from "https://wiki.bwhpc.de/wiki/index.php?title=Development/GSL&oldid=11853"