Using X11 Virtual Frame Buffer (Xvfb) in a submission script

Blog post edited by Nicholas Anthony Rahme

Some programs require access to a display in order to run properly. For example, MATLAB will provide an error if you try to create an AVI file from a image frame in -nodisplay mode. This can be an annoying problem on the HPCC because all of our batch compute nodes do not have displays attached. Fortunately, the X virtual Frame Buffer (Xvfb) is a program that simulates an attached display and can allow programs that require Graphical User Interfaces (X11) displays to run.

The following is a typical submission script for running a MATLAB program :

makeAVI.qsub

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#!/bin/bash
#PBS -l nodes=1:ppn=1,mem=2gb,feature=gbe
#PBS -l walltime=01:00:00
#PBS -j oe
#PBS -W x=gres:MATLAB

#Change directory to the qsub submission directory
cd ${PBS_O_WORKDIR}

#Run matlab script (replace this with your X11 code)
matlab -nodisplay -r "makeAVI"

#Print out job usage
qstat -f ${PBS_JOBID}

Running this script will give me an error that says "Display not found." The following script is modified to start Xvfb at the beginning, run the same basic command and then terminate Xvfb at the end:

makeAVI.qsub

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#!/bin/bash
#PBS -l nodes=1:ppn=1,mem=2gb,feature=gbe
#PBS -l walltime=01:00:00
#PBS -j oe
#PBS -W x=gres:MATLAB

#Change directory to the qsub submission directory
cd ${PBS_O_WORKDIR}

##### Specify the display, start the Xvfb server, and save the process ID.
export DISPLAY=":1"
rm -f /tmp/.X11-unix
rm -f /tmp/.X11-lock
Xvfb $DISPLAY -auth /dev/null/ &
XVFB_PID=$!

#Give system time to spin up X11 display (Probably not needed)
sleep 5
####

#Run matlab script
matlab -r "makeAVI"

##### Stop the Xvfb server and remove the files it created.
kill -9 $XVFB_PID
rm -rf /tmp/.X11-unix
rm -f  /tmp/.X11-lock
####

#Print out job usage
qstat -f ${PBS_JOBID}

Please note that the -nodisplay option was removed from the MATLAB command line in the second script

An working example of this script can be downloaded on the HPCC using the getexample command. Type the following on any development node to run the example:

module load powertools
getexample
getexample MATLAB_movie
cd MATLAB_movie
qsub makeAVI.qsub

• Dirk

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