Run Octave in Batch Mode¶
- Octave is a powerful math focused programming language. It includes :
- An interactive terminal version
- A GUI version which can be used to run the interactive terminal
- Batch Mode (scripting)
- This guide will focus on batch mode, but if you want to run the interactive modes check out the Octave Interactive guide
- In the
PBSscript, load octave with
module load octave.
You can use
module avail octave to see what versions of octave are available.
- The line to run an octave script is
octave <filename>.m. Add this to the computation part of your
PBSscript to run.
Walkthrough: Run Octave on the Cluster¶
- This walkthrough will use a simple Octave script that calculates the sqrt(3^2 + 4^2).
- Octave script: octaveTest.m
- PBS script: octave.pbs
- You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.
Part 1: The PBS Script¶
#PBS -N octaveTest #PBS -l nodes=1:ppn=2 #PBS -l pmem=2gb #PBS -l walltime=1:00 #PBS -q inferno #PBS -j oe #PBS -o octaveTest.out cd $PBS_O_WORKDIR module load octave octave octaveTest.m
#PBSdirectives are standard, requesting just 1 minute of walltime and 1 node with 2 cores. More on
#PBSdirectives can be found in the PBS guide
$PBS_O_WORKDIRis simply a variable that represents the directory you submit the PBS script from.
Make sure the octave script you want to run (in this case, octaveTest.m) is in the same directory you put the PBS script.
module load octaveloads octave. To see what octave versions are available, run
module avail octave, and load the one you want
Part 2: Submit Job and Check Status¶
- Make sure you're in the dir that contains the
- Submit as normal, with
qsub <pbs script name>. In this case
- Check job status with
qstat -u <gtusername3> -n, replacing "gtusername3" with your gt username.
- 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
PBSscript, you should see a
octaveTest.outfile, which contains the results of the job. Use
cat octaveTest.outor open the file in a text editor to take a look.
octaveTest.outshould look something like this:
Job name: octaveTest Queue: inferno End PBS Prologue Thu Oct 4 09:20:23 EDT 2018 --------------------------------------- octave: X11 DISPLAY environment variable not set octave: disabling GUI features x = 5 Sqrt of 3^2 + 4^2 = 5.0000 Elapsed time: 0.0004 seconds --------------------------------------- Begin PBS Epilogue Thu Oct 4 09:20:24 EDT 2018 Job ID: 22612013.shared-sched.pace.gatech.edu User ID: shollister7 Job name: octaveTest Resources: neednodes=1:ppn=2,nodes=1:ppn=2,pmem=2gb,walltime=00:01:00
- After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
- Congratulations! You successfully ran an Octave script on the cluster.
Run Octave Interactively on the Cluster¶
- Running Octave interactively is very similar to any other interactive program. The steps are as follows:
- Set up VNC session
- Load Octave from terminal (within VNC Session)
- Run Octave (again from terminal)
Set up Interactive (VNC) Session¶
- Please see the VNC guide for instructions on how to set up the Interactive VNC session
Load and Start Octave on VNC¶
- Open terminal in the vnc window by clicking top left
System Tools> scroll down to
- all commands here on will be typed in terminal in VNC
module avail octave #see what versions are available module load octave #load default version octave #launch interactive gui
Run an Octave Script in Interactive Mode¶
- Simply type the script name without the
.mfile type, and add a semicolon