Updated 2019-02-14

Use GSL on the Cluster

Overview

  • This guide will cover how to load and run the GNU Scientific Library
  • To use GSL in a C program, you must first load the GSL module with module load gsl in your PBS script.
  • After loading the module in your PBS script, you must add to the PBS script the necessary commands for compilation and execution of your C program.
  • Submit the job with qsub <.pbs filename>

Walkthrough : Use GSL on the Cluster

  • This walkthrough will use GSL to calculate the value of a Bessel function with an input of 5.
  • This example C program is from the GSL documentation
  • C program: gslExample.c
  • PBS Script: gsl.pbs
  • To follow along, manually copy these files into the same directory in your account on the cluster, or transfer them to your account (again put them in the same folder).

Part 1: The PBS Script

#PBS -N gslTest
#PBS -l nodes=1:ppn=2
#PBS -l pmem=2gb
#PBS -l walltime=1:00
#PBS -q iw-shared-6
#PBS -j oe
#PBS -o gsl.out

cd $PBS_O_WORKDIR
module load gcc
module load gsl
gcc -o gslExample gslExample.c `gsl-config --cflags --libs`
./gslExample
  • The #PBS directives are standard, requesting just 1 minute of walltime and 1 node with 2 cores. More on #PBS directives can be found in the PBS guide
  • $PBS_O_WORKDIR is simply a variable that represents the directory you submit the PBS script from. Make sure the .c file you want to run is in the same directory you put the PBS script. Otherwise, the C program wont be found when the job is run.
  • Output Files, such as the resulting executable, will also show up in the same directory as the PBS script
  • The module load lines load gcc (compiler) and gsl.
  • The gcc line links the GSL library and compiles the C program into an executable called gslExample .
  • ./gslExample runs the program

Part 2: Submit Job and Check Status

  • Make sure you're in the directory that contains the PBS script and the .c file
  • Submit as normal, with qsub <pbs script name>. In this case qsub gsl.pbs
  • Check job status with qstat -u username3 -n, replacing "username3" with your gtusername
  • You can delete the job with qdel 22182721, replacing the number with the jobid returned after running qsub

Part 3: Collecting Results

  • In the directory where you submitted the PBS script, you should see a couple of newly generated files, including gslExample and gsl.out
  • gslExample is the executable file created
  • gsl.out contains the results of the job
  • Open gsl.out with vim gsl.out (you can use any text editor).
  • The output should contain the result of the computation:
Job name:   gslTest
Queue:      iw-shared-6
End PBS Prologue Wed Nov 14 12:59:43 EST 2018
---------------------------------------
J0(5) = -1.775967713143382642e-01
---------------------------------------
Begin PBS Epilogue Wed Nov 14 12:59:44 EST 2018
Job ID:     22899130.shared-sched.pace.gatech.edu
  • After the result files are produced, you can move the out file as well as any other files off the cluster. Refer to the file transfer guide for help.
  • Congratulations! You successfully used GSL on the cluster.