How-To: Use Matlab¶
Note
This information is outdated and will soon be removed.
GNU Octave as Matlab alternative
Note that GNU Octave is an Open Source alternative to Matlab. While both packages are not 100% compatible, Octave is an alternative that does not require any license management. Further, you can easily install it yourself using Conda.
Want to use the Matlab GUI?
Make sure you understand X forwarding as outline in this FAQ entry.
You can also use Open OnDemand Portal to run Matlab.
Pre-requisites¶
You have to register with hpc-helpdesk@bih-charite.de for requesting access to the Matlab licenses.
Afterwards, you can connect to the High-Memory using the license_matlab_r2016b resource (see below).
How-To Use¶
BIH has a license of Matlab R2016b for 16 seats and various licensed packages (see below). To display the available licenses:
hpc-login-1:~$ scontrol show lic
LicenseName=matlab_r2016b
Total=16 Used=0 Free=16 Remote=no
Matlab is installed on all of the compute nodes:
# The following is VITAL so the scheduler allocates a license to your session.
hpc-login-1:~$ srun -L matlab_r2016b:1 --pty bash -i
med0127:~$ scontrol show lic
LicenseName=matlab_r2016b
Total=16 Used=1 Free=15 Remote=no
med0127:~$ module avail
----------------- /usr/share/Modules/modulefiles -----------------
dot module-info null
module-git modules use.own
----------------------- /opt/local/modules -----------------------
cmake/3.11.0-0 llvm/6.0.0-0 openmpi/3.1.0-0
gcc/7.2.0-0 matlab/r2016b-0
med0127:~$ module load matlab/r2016b-0
Start matlab without GUI: matlab -nosplash -nodisplay -nojvm
Start matlab with GUI (requires X forwarding (ssh -X)): matlab
med0127:~$ matlab -nosplash -nodisplay -nojvm
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016b (9.1.0.441655) 64-bit (glnxa64)
September 7, 2016
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.
Non-Degree Granting Education License -- for use at non-degree granting, nonprofit,
educational organizations only. Not for government, commercial, or other organizational use.
>> ver
--------------------------------------------------------------------------------------------
MATLAB Version: 9.1.0.441655 (R2016b)
MATLAB License Number: 1108905
Operating System: Linux 3.10.0-862.3.2.el7.x86_64 #1 SMP Mon May 21 23:36:36 UTC 2018 x86_64
Java Version: Java is not enabled
--------------------------------------------------------------------------------------------
MATLAB Version 9.1 (R2016b)
Bioinformatics Toolbox Version 4.7 (R2016b)
Global Optimization Toolbox Version 3.4.1 (R2016b)
Image Processing Toolbox Version 9.5 (R2016b)
Optimization Toolbox Version 7.5 (R2016b)
Parallel Computing Toolbox Version 6.9 (R2016b)
Partial Differential Equation Toolbox Version 2.3 (R2016b)
Signal Processing Toolbox Version 7.3 (R2016b)
SimBiology Version 5.5 (R2016b)
Statistics and Machine Learning Toolbox Version 11.0 (R2016b)
Wavelet Toolbox Version 4.17 (R2016b)
>> exit
Running MATLAB UI¶
For starting the Matlab with GUI, make sure that your client is running a X11 server and you connect with X11 forwarding enabled (e.g., ssh -X hpc-login-1.cubi.bihealth.org from the Linux command line).
Then, make sure to use srun -L matlab_r2016b:1 --pty --x11 bash -i for connecting to a node with X11 forwarding enabled.
client:~$ ssh -X hpc-login-1.cubi.bihealth.org
[...]
hpc-login-1:~ $ srun -L matlab_r2016b:1 --pty --x11 bash -i
[...]
med0203:~$ module load matlab/r2016b-0
Start matlab without GUI: matlab -nosplash -nodisplay -nojvm
Start matlab with GUI (requires X forwarding (ssh -X)): matlab
med0203:~$ matlab
[UI will start]
For forcing starting in text mode can be done (as said after module load): matlab -nosplash -nodisplay -nojvm.
Also see this FAQ entry.
See Available Matlab Licenses¶
You can use scontrol show lic to see the currently available MATLAB license.
E.g., here I am running an interactive shell in which I have requested 1 of the 16 MATLAB licenses, so 15 more remain.
$ scontrol show lic
LicenseName=matlab_r2016b
Total=16 Used=1 Free=15 Remote=no
A Working Example¶
Get a checkout of our MATLAB example. Then, look around at the contents of this repository.
hpc-login-1:~$ git clone https://github.com/bihealth/bih-cluster-matlab-example.git
hpc-login-1:~$ cd bih-cluster-matlab-example
hpc-login-1:~$ cat job_script.sh
#!/bin/bash
# Logging goes to directory sge_log
#SBATCH -o slurm_log/%x-%J.log
# Keep current environment variables
#SBATCH --export=ALL
# Name of the script
#SBATCH --job-name MATLAB-example
# Allocate 4GB of RAM per core
#SBATCH --mem 4G
# Maximal running time of 2 hours
#SBATCH --time 02:00:00
# Allocate one Matlab license
#SBATCH -L matlab_r2016b:1
module load matlab/r2016b-0
matlab -r example
$ cat example.m
% Example Hello World script for Matlab.
disp('Hello world!')
disp('Thinking...')
pause(10)
disp(sprintf('The square root of 2 is = %f', sqrt(2)))
exit
For submitting the script, you can do the following
hpc-login-1:~$ sbatch job_script.sh
This will submit a job with one Matlab license requested. If you were to submit 17 of these jobs, then at least one of them would have to wait until all licenses are free.
Matlab License Server
Note that there is a Matlab license server running on the server that will check whether 16 or less Matlab sessions are currently running.
If a Matlab session is running but this is not made known to the scheduler via -L matlab_r2016b then this can lead to scripts crashing as not enough licenses are available.
If this happens to you, double-check that you have specified the license requirements correctly and notify hpc-helpdesk@bih-charite.de in case of any problems.
We will try to sort out the situation then.