MATLAB

A high-level language and interactive environment for numerical computing. MATLAB Homepage

Warning

MATLAB is proprietary software. Make sure you meet the requirements for it's usage.

Available Modules¶

module load MATLAB/2021b

Warning

Licences¶

The following network licence servers can be accessed from the NeSI cluster.

Institution	Uptime
University of Waikato	98%
National Institute of Water and Atmospheric Research	0%
Institute of Geological and Nuclear Sciences	99%
Massey University	13%
University of Auckland	98%
University of Otago	100%
Victoria University of Wellington	100%
Auckland University of Technology	12%
University of Canterbury	12%
Plant & Food Research	13%

If you do not have access, or want a server connected Contact our Support Team.

No Licence?

If you want to run MATLAB code on the cluster, but are not a member of an institution without access to floating licences, MATLAB code can still be run on the cluster using MCR.

Example scripts¶

Info

When developing MATLAB code on your local machine, take measures to ensure it will be platform independent. Use relative paths when possible and not avoid using '\s see here.

ScriptFunction

#!/bin/bash -e
#SBATCH --job-name   MATLAB_job     # Name to appear in squeue 
#SBATCH --time       01:00:00       # Max walltime 
#SBATCH --mem        512MB          # Max memory

module load MATLAB/2021b

# Run the MATLAB script MATLAB_job.m 
matlab -nodisplay < MATLAB_job.m

#!/bin/bash -e

#SBATCH --job-name       MATLAB_job    # Name to appear in squeue
#SBATCH --time           06:00:00      # Max walltime
#SBATCH --mem            2048MB        # Max memory
#SBATCH --cpus-per-task  4             # 2 physical cores.
#SBATCH --output         %x.log        # Location of output log

module load MATLAB/2021b 

matlab -batch "addpath(genpath('.'));myFunction(5,20)"
# For versions older than 2019a, use '-nodisplay -r' instead of '-batch'

Command Line

When using matlab on command line, all flag options use a single '-' e.g. -nodisplay, this differs from the GNU convention of using -- for command line options of more than one character.

Tip

Using the prefix ! will allow you to run bash commands from within MATLAB. e.g. !squeue -u $USER will print your currently queued slurm jobs.

Parallelism¶

MATLAB does not support MPI therefore #SBATCH --ntasks should always be 1, but if given the necessary resources some MATLAB functions can make use of multiple threads (--cpus-per-task) or GPUs (--gpus-per-node).

Implicit parallelism¶

Implicit parallelism requires no changes to be made in your code. By default MATLAB will utilise multi-threading for a wide range of operations, scalability will vary but generally you will not be able to utilise more than a 4-8 CPUs this way.

Explicit parallelism¶

Tip

If your code is explicitly parallel at a high level it is preferable to use SLURM job arrays as there is less computational overhead and the multiple smaller jobs will queue faster and therefore improve your throughput.

Explicit parallelism is when you write your code specifically to make use of multiple CPU's. This can be done using MATLABs parpool-based language constructs, MATLAB assigns each thread a 'worker' that can be assigned sections of code.

MATLAB will make temporary files under your home directory (in ~/.matlab/local/<cluster>/jobs) for communication with worker processes. To prevent simultaneous parallel MATLAB jobs from interfering with each other you should tell them to each use their own job-specific local directories:

pc = parcluster('local')
pc.JobStorageLocation = getenv('TMPDIR')
parpool(pc, str2num(getenv('SLURM_CPUS_PER_TASK')))

Tip

Parpool will throw a warning when started due to a difference in how time zone is specified. To fix this, add the following line to your SLURM script: export TZ="Pacific/Auckland'

The main ways to make use of parpool are;

parfor¶

Executes each iteration of a loop on a different worker. e.g.

parfor i=1:100

   %Your operation here.

end

parfor operates similarly to a SLURM job array and must be embarrassingly parallel. Therefore all variables either need to be defined locally (used internally within one iteration of the loop), or static (not changing during execution of loop).

More info here.

parfeval¶

parfeval is used to assign a particular function to a thread, allowing it to be run asynchronously. e.g.

my_coroutine=parfeval(@my_async_function,2,in1,in2);

% Do something that doesn't require outputs from 'my_async_function'

[out1, out2]=fetchOutputs(my_coroutine); % If 'my_coroutine' has not finished execution will pause.

function [out1,out2]=my_async_function(in1,in2)

%Your operation here.

end

fetchOutputs is used to retrieve the values.

More info here.

Tip

When killed (cancelled, timeout, etc), job steps utilising parpool may show state OUT_OF_MEMORY, this is a quirk of how the steps are ended and not necessarily cause to raise total memory requested.

Determining which of these categories your variables fall under is a good place to start when attempting to parallelise your code.

Using GPUs¶

As with standard parallelism, some MATLAB functions will work implicitly on GPUs while other require setup. More info on using GPUs with MATLAB here, and writing code for GPUs here.

MATLAB uses NVIDIA CUDA toolkit. Depending on the version of MATLAB, a different version of CUDA is needed, see GPU Support by Release in MATLAB documentation. Use module spider CUDA to list all available CUDA modules and select the appropriate one. For example, for MATLAB R2021a, use module load CUDA/11.0.2 before launching MATLAB.

If you want to know more about how to access the different type of available GPUs on NeSI, check the GPU use on NeSI support page.

Support for A100 GPUs

To use MATLAB with a A100 or a A100-1g.5gb GPU, you need to use a version of MATLAB supporting the Ampere architecture (see GPU Support by Release). We recommend that you use R2021a or a more recent version.

GPU cost

A GPU device-hour costs more than a core-hour, depending on the type of GPU. You can find a comparison table in our What is an allocation? support page.

GPU Example¶

#!/bin/bash -e
#SBATCH --job-name       MATLAB_GPU    # Name to appear in squeue
#SBATCH --time           01:00:00      # Max walltime
#SBATCH --mem            10G           # 10G per GPU
#SBATCH --cpus-per-task  4             # 4 CPUs per GPU
#SBATCH --output         %x.%j.log     # Location of output log
#SBATCH --gpus-per-node  1             # Number of GPUs to use (max 2)

module load MATLAB/2021a
module load CUDA/11.0.2  # Drivers for using GPU

matlab -batch "gpuDevice()"

Adding Support Packages¶

If you have X-11 set up you can install additional package through the GUI. You can also install manually if you already have the files by copying them into your Support Package root directory..

Support packages are usually saved in your home directory, you can see the path using the MATLAB command matlabshared.supportpkg.getSupportPackageRoot if it is unset, you can specify it with matlabshared.supportpkg.setSupportPackageRoot("<path>")

mexopencv¶

mexopencv is mex wrapper MATLAB wrapper for the openCV library.

Some of the internal MATLAB libraries clash with those used by OpenCV, to avoid problems cause by this

Use a version of OpenCV built using GCC (as opposed to gimkl).
Compile using the -DWITH_OPENCL=OFF flag.

Please contact support if you have any issues.

Improving performance with mexing¶

Like other scripting languages, MATLAB code will generally run slower than compiled code since every MATLAB instruction needs to be parsed and interpreted. Instructions inside large MATLAB loops are often performance hotspots due to the interpreter's overhead, which consumes CPU time at every iteration.

Fortunately MATLAB lets programmers extend their scripts with C/C++ or Fortran, which is referred to as mexing.

more info about compiling software on NeSI here.

Writing mex functions¶

This involves the following steps (using C++ as an example):

Focus on a loop to extend, preferably a nested set of loops.
Identify the input and output variables of the section of code to extend.
Write C++ code. The name of the C++ file should match the name of the function to call from MATLAB, e.g. myFunction.cpp for a function named myFunction.
Compile the extension using the MATLAB command mex myFunction.cpp

At the minimum, the C++ extension should contain:

#include <mex.h>
#include <matrix.h>

void mexFunction(int nlhs, mxArray *plhs[],
                 int nrhs, const mxArray *prhs[]) {
    // implementation goes here
}

Note that the above function should always be called mexFunction and its signature be int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]. Here, nlhs and nrhs refer to the number of output and input arguments respectively. Access each dummy argument with index i = 0 ... nlhs-1 and j = 0 ... nrhs-1 respectively. Regardless of the type of argument, whether it is a number, a matrix or an object, its type is mxArray. Often you will need to cast the argument into a corresponding C++ type, e.g.

// cast as a double, note the asterisk in front of mxGetPr
double x = (double) *mxGetPr(prhs[0]);

// cast as an array of doubles
double* arr = (double*) mxGetPr(prhs[0]);

Use mxCreateDoubleMatrix and mxCreateDoubleScalar to create a matrix and a number, respectively. For example:

// function returns [plhs[0], plhs[1]]
plhs[0] = mxCreateDoubleMatrix(3, 2, mxREAL);  // 3 by 2 matrix
plhs[1] = mxCreateDoubleScalar(2);  // number

All numbers are doubles. Use flat array indexing a[i + n*j - 1] in C++ to access elements of a MATLAB matrix a(i, j) of size n x m.

MATLAB will take care of destroying matrices and other object so you should feel free to create objects inside C++ code (required for functions that have return values).

Some mex function source code examples can be found in the table here.

Compilation¶

MATLAB supports the following compilers.


C++	up to GCC 6.3.x
C	up to GCC 6.3.x
FORTRAN	up to GNU gfortran 6.3.x

The most up to date compilers supported by MATLAB can be loaded on NeSI using module load gimkl/2017a

If no GCC module is loaded, the default system version of these compilers will be used.

Further configuration can be done within MATLAB using the command mex -setup

mex <file_name> will then compile the mex function.

Default compiler flags can be overwritten with by setting the appropriate environment variables. The COMPFLAGS variable is ignored as it is Windows specific.


C++	`CXXFLAGS`
C	`CFLAGS`
FORTRAN	`FFLAGS`
Linker	`LDFLAGS`

For example, adding OpenMP flags for a fortran compile:

Compiler Version

Using an 'unsupported' compiler with versions of MATLAB 2020b onward will result in an Error (previously was a 'Warning').

Known Bugs¶

When using versions of MATLAB more recent than 2021a you may notice the following warning.

ldd

This is due to our operating system being too old.

With the exception of a few commands that directly make requests of the OS, your code should run fine.

If you believe this bug is causing problems, running on our newer hardware will fix it.