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Overview
MATLAB is a programming and numeric computing platform used by millions of engineers and scientists to analyze data, develop algorithms, and create models. Simulink is a dynamic simulation environment to design and simulate systems for model development. Together these flagship platforms contain thousands of pre-written and validated functions to accelerate your workflows across multiple CPU and GPU cores.
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If you know your Matlab application is neither computation nor data intensive, please see the advice in the section 'Running Single-core Jobs'. |
Once get the access to the matlab license on Gadi, please confirm with your institution that whether the license comes with either of the features 'Parallel Computing Toolbox' and 'Distributed Computing Server'. Although some linear algebra and numerical functions, such as matrix products, fft, eig, sort, are implicitly multi-threaded and make use of all the cores available to the job without any extra programming efforts, see an incomplete list provided by Mathworks Support Team here, the majority of the functions provided by matlab runs only on a single core and users need to explicitly use the functionalities provided by these two features to enable the utilisation of multi-cores and multi-compute nodes, respectively. As of 30 Oct 2020, the majority of NCI-hosted matlab licenses provides only the feature Parallel Computing Toolbox, therefore, supports jobs running only within a single compute node.
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To load the specific version of R2019b, please run
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$ module load matlab/R2019b |
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To load the license module for your own matlab software group, please run
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$ module load matlab_licence/<institution> |
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#!/bin/bash #PBS -q normal #PBS -l walltime=02:00:00 #PBS -l ncpus=48 #PBS -l mem=190GB #PBS -l jobfs=400GB #PBS -l software=matlab_<institution> #PBS -l wd # Load modules, always specify version number. module load matlab/R2019b module load matlab_licence/<institution> # Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job # needs access to `/scratch/ab12/` and `/g/data/yz98/`. Details on: # https://opus.nci.org.au/display/Help/PBS+Directives+Explained. # Run matlab application matlab -nodisplay -nosplash -r "outputDir='$PBS_JOBFS',numberOfWorkers=$PBS_NCPUS, mfile, quit" > $PBS_JOBID.log |
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Once the job submission script is saved to the same directory in which the matlab script mfile.m is located, run
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$ qsub matlabjob.sh |
inside that directory to submit your job to the PBS scheduler.
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#!/bin/bash #PBS -q normal #PBS -l ncpus=1 #PBS -l walltime=00:02:00 #PBS -l mem=250MB #PBS -l software=matlab_<institution> #PBS -l wd # Load modules, always specify version number. module load matlab/R2019b module load matlab_licence/<iname><institution> # Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job # needs access to `/scratch/ab12/` and `/g/data/yz98/`. Details on: # https://opus.nci.org.au/display/Help/PBS+Directives+Explained. # Run matlab application matlab -nosplash -nojvm -singleCompThread < mfile.m > $PBS_JOBID.log |
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To get access to your own institution provided Matlab licence, join the corresponding software group in the table below on my.nci.org.au first. Once your group membership request is approved, the corresponding licence module becomes visible to use. Run `module avail matlab` to see the license modulefile name. Jobs need to load the license module together with the application module to run Matlab.
| Institution | PBS Directive `-lsoftware=` | software group |
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| The Australian National University | matlab_anu | matlab_anu |
| CSIRO* | matlab_csiro | matlab_csiro |
| Flinders University | matlab_flinders | matlab_flinders |
| The University of Newcastle | matlab_newcastle | matlab_newcastle |
| Latrobe University | matlab_latrobe | matlab_latrobe |
| Macquarie University | matlab_macquarie | matlab_mq |
| The University of Melbourne | matlab_melbourne | matlab_melbourne |
| Monash University | matlab_monash | matlab_monash |
| Royal Melbourne Institute of Technology | matlab_rmit | matlab_rmit |
| The University of New South Wales | matlab_unsw | matlab_unsw |
| The University of Wollongong | matlab_wollongong | matlab_wollongong |
| The University of Sydney | matlab_usyd | matlab_usyd |
| Victoria University | matlab_vu | matlab_vu |
| University of South Australia | matlab_unisa | matlab_unisa |
| University of Tasmania | matlab_utas | matlab_utas |
* CSIRO has a special arrangement with NCI that allows only a specific group of users to use their license. Please contact CSIRO licensing service to discuss the access. We can only add users to the group on their approval.
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