Difference between revisions of "Applications/Matlab"
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=== Application Details === | === Application Details === | ||
| − | * Description: MATLAB is a numerical computing environment and programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, and implementation of algorithms. A range of toolboxes | + | * Description: MATLAB is a numerical computing environment and programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, and implementation of algorithms. A range of toolboxes is available to extend functionality. |
| − | * Versions: 2016a, 2016b | + | * Versions: 2016a, 2016b, 2017a, 2018a, 2019a, 2020a |
| − | * Module names: matlab/2016a matlab/2016b | + | * Module names: matlab/2016a matlab/2016b matlab/2017a matlab/2018a matlab/2019a matlab/2020a |
| − | * License: University of Hull Total Academic Headcount license, available to members of the university for research use | + | * License: University of Hull Total Academic Headcount license, available to members of the university for research use |
==== Toolboxes ==== | ==== Toolboxes ==== | ||
| − | {| class="wikitable" style="background-color:#f5f5dc;" | + | Matlab on our HPC has the following toolboxes available: |
| + | {| class="wikitable mw-collapsible mw-collapsed" style="background-color:#f5f5dc;" | ||
| + | |- | ||
| + | ! Toolbox | ||
| + | ! Toolbox | ||
| + | ! Toolbox | ||
| + | ! Toolbox | ||
| + | |- | ||
| MATLAB | | MATLAB | ||
| Filter Design HDL Coder | | Filter Design HDL Coder | ||
| Line 75: | Line 82: | ||
== Usage Examples == | == Usage Examples == | ||
| − | === Executables === | + | {| |
| + | |style="width:5%; border-width: 0;cellpadding=0" | [[File:icon_exclam3.png]] | ||
| + | |style="width:95%; border-width: 0;cellpadding=0" | By default Matlab will make use of multithreading for certain functions, with the maximum number of computational threads equal to the number of computational cores on the node. If a job or session hasn't requested an appropriate resource, this multithreading can cause contention for CPU resources and negatively impact other users. For this reason when using the standard '''matlab''' command please make sure you request appropriate resources by either: | ||
| + | * Using an exclusive session, e.g. use '''interactive --exclusive''' or submit a task with the '''#SBATCH --exclusive''' option | ||
| + | * Starting matlab using '''matlab ‑singleCompThread''' which limits Matlab to using a single CPU core | ||
| + | |- | ||
| + | |} | ||
| + | |||
| + | <!--=== Executables === | ||
{| class="wikitable" style="background-color:#f5f5dc;" | {| class="wikitable" style="background-color:#f5f5dc;" | ||
! Executable | ! Executable | ||
! Description | ! Description | ||
|- | |- | ||
| − | | | + | | MatLab |
| − | | By default Matlab will make use of multithreading for certain functions, with the maximum number of computational threads equal to the number of computational cores on the node. If a job or session hasn't requested appropriate resource, this multithreading can cause contention for CPU | + | | By default Matlab will make use of multithreading for certain functions, with the maximum number of computational threads equal to the number of computational cores on the node. If a job or session hasn't requested an appropriate resource, this multithreading can cause contention for CPU resources and negatively impact other users. For this reason when using the standard '''matlab''' command please make sure you request appropriate resources by either using an exclusive session with '''interactive --exclusive''' or submitting a task with the '''#SBATCH --exclusive'''. See [[Applications/Matlab#Parallel_Matlab | Parallel Matlab]] |
|- | |- | ||
| − | | matlab - | + | | matlab ‑singleCompThread ## need to replace matlab ‑singleCompThread with a non-breaking space followed by a non-breaking hyphen otherwise this looks rubbish cc 2018-09-25 ## |
| − | | If you do not require the possible performance benefits provided by using multiple cores, please run Matlab with | + | | If you do not require the possible performance benefits provided by using multiple cores, please run Matlab with ‑singleCompThread option and it will only use a single CPU core. See [[Applications/Matlab#Parallel_Matlab | Parallel Matlab]] |
|} | |} | ||
| − | + | --> | |
=== Interactive === | === Interactive === | ||
| − | Interactive with full graphical interface (note the - | + | Interactive with full graphical interface (note the use of --exclusive when starting the interactive session): |
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ interactive | + | [username@login01 ~]$ interactive --exclusive |
salloc: Granted job allocation 289663 | salloc: Granted job allocation 289663 | ||
Job ID 289663 connecting to c170, please wait... | Job ID 289663 connecting to c170, please wait... | ||
Last login: Thu Jan 26 12:59:11 2017 from 10.254.5.246 | Last login: Thu Jan 26 12:59:11 2017 from 10.254.5.246 | ||
| − | [username@c170 ~]$ module add matlab/ | + | [username@c170 ~]$ module add matlab/2020a |
| − | [username@c170 ~]$ matlab | + | [username@c170 ~]$ matlab |
</pre> | </pre> | ||
Interactive with command line only: | Interactive with command line only: | ||
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@c170 ~]$ matlab -nodisplay | + | [username@c170 ~]$ matlab -nodisplay |
< M A T L A B (R) > | < M A T L A B (R) > | ||
| − | Copyright 1984- | + | Copyright 1984-2020 The MathWorks, Inc. |
| − | + | R2020a Update 4 (9.8.0.1417392) 64-bit (glnxa64) | |
| − | + | June 24, 2020 | |
To get started, type one of these: helpwin, helpdesk, or demo. | To get started, type one of these: helpwin, helpdesk, or demo. | ||
| Line 116: | Line 131: | ||
=== Batch Submission === | === Batch Submission === | ||
| + | To submit a batch job for Matlab, put your code in a .m script file and refer to this in your batch submission script, as shown below in the example MATLABtest.job job script. Remember to leave the .m extension from the script name in the Matlab command line. | ||
<pre style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;"> | <pre style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;"> | ||
#!/bin/bash | #!/bin/bash | ||
| − | #SBATCH -J MATLAB | + | #SBATCH -J MATLAB |
| − | #SBATCH -N 1 | + | #SBATCH -N 1 |
| − | #SBATCH -o %N.%j.out | + | #SBATCH -o %N.%j.out |
| − | #SBATCH -e %N.%j.err | + | #SBATCH -e %N.%j.err |
| − | #SBATCH -p compute | + | #SBATCH -p compute |
#SBATCH --exclusive | #SBATCH --exclusive | ||
module purge | module purge | ||
| − | module add matlab/ | + | module add matlab/2020a |
| − | matlab -nodisplay | + | matlab -nodisplay -r my_matlab_m_file |
</pre> | </pre> | ||
| − | Matlab | + | |
| + | To submit the Matlab job, use sbatch as shown below: | ||
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| Line 138: | Line 155: | ||
== Parallel Matlab == | == Parallel Matlab == | ||
| − | By default Matlab on Viper will run on a single core as multi-threading conflicts with the schedulers resource management, however there are | + | By default Matlab on Viper will run on a single core as multi-threading conflicts with the schedulers resource management, however, there are two ways in which Matlab can utilize multiple processors: |
=== Multi-threading === | === Multi-threading === | ||
| − | Matlab can use multiple threads for certain built in functions for example linear algebra and numerical functions such as fft, \ (mldivide), eig, svd, and sort. These functions automatically execute on multiple computational threads in a single MATLAB session, allowing them to execute faster on multicore-enabled machines. Additionally, many functions in Image Processing Toolbox are multithreaded. | + | Matlab can use multiple threads for certain built-in functions for example linear algebra and numerical functions such as fft, \ (mldivide), eig, svd, and sort. These functions automatically execute on multiple computational threads in a single MATLAB session, allowing them to execute faster on multicore-enabled machines. Additionally, many functions in the Image Processing Toolbox are multithreaded. |
Firstly, using the '''matlab''' command with the -singleCompThread option: | Firstly, using the '''matlab''' command with the -singleCompThread option: | ||
| Line 187: | Line 204: | ||
</pre> | </pre> | ||
| − | When using Matlab with multicore enabled, please ensure you have exclusive access to the node, see [[ | + | When using Matlab with multicore enabled, please ensure you have exclusive access to the node, see [[Quickstart/Interactive#Exclusive_interactive_session | Exclusive interactive]] or [[Quickstart/Batch Jobs#Exclusive Batch Jobs|Exclusive batch jobs]]. |
=== Parallel Computing Toolbox === | === Parallel Computing Toolbox === | ||
| Line 208: | Line 225: | ||
</pre> | </pre> | ||
| − | When using Matlab with the Parallel Computing Toolbox, please ensure you have exclusive access to the node, see [[ | + | When using Matlab with the Parallel Computing Toolbox, please ensure you have exclusive access to the node, see [[Quickstart/Interactive#Exclusive_interactive_session | Exclusive interactive]] or [[Quickstart/Batch Jobs#Exclusive_Batch_Jobs|Exclusive batch jobs]]. |
| − | === | + | ==Next Steps== |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
* [https://www.mathworks.com/products/matlab.html Matlab website] | * [https://www.mathworks.com/products/matlab.html Matlab website] | ||
* [http://www.mathworks.com/academia/student_center/tutorials.html Useful Matlab tutorials] | * [http://www.mathworks.com/academia/student_center/tutorials.html Useful Matlab tutorials] | ||
* [https://uk.mathworks.com/discovery/matlab-multicore.html Matlab multicore] | * [https://uk.mathworks.com/discovery/matlab-multicore.html Matlab multicore] | ||
| − | + | ||
| − | + | {{Modulepagenav}} | |
Latest revision as of 11:15, 23 March 2023
Contents
Application Details
- Description: MATLAB is a numerical computing environment and programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, and implementation of algorithms. A range of toolboxes is available to extend functionality.
- Versions: 2016a, 2016b, 2017a, 2018a, 2019a, 2020a
- Module names: matlab/2016a matlab/2016b matlab/2017a matlab/2018a matlab/2019a matlab/2020a
- License: University of Hull Total Academic Headcount license, available to members of the university for research use
Toolboxes
Matlab on our HPC has the following toolboxes available:
| Toolbox | Toolbox | Toolbox | Toolbox |
|---|---|---|---|
| MATLAB | Filter Design HDL Coder | MATLAB Report Generator | SimRF |
| Simulink | Financial Instruments Toolbox | Model Predictive Control Toolbox | Simscape |
| Aerospace Blockset | Financial Toolbox | Neural Network Toolbox | Simscape Electronics |
| Bioinformatics Toolbox | Fixed-Point Designer | Optimization Toolbox | Simscape Multibody |
| Communications System Toolbox | Fuzzy Logic Toolbox | Parallel Computing Toolbox | Simscape Power Systems |
| Computer Vision System Toolbox | Global Optimization Toolbox | Partial Differential Equation Toolbox | Simulink Coder |
| Control System Toolbox | Image Acquisition Toolbox | Phased Array System Toolbox | Simulink Control Design |
| Curve Fitting Toolbox | Image Processing Toolbox | RF Toolbox | Simulink Design Optimization |
| DSP System Toolbox | Instrument Control Toolbox | Robotics System Toolbox | Stateflow |
| Database Toolbox | LTE System Toolbox | Robust Control Toolbox | Statistics and Machine Learning Toolbox |
| Datafeed Toolbox | MATLAB Coder | Signal Processing Toolbox | Symbolic Math Toolbox |
| Econometrics Toolbox | MATLAB Compiler | SimBiology | System Identification Toolbox |
| Embedded Coder | MATLAB Compiler SDK | SimEvents | Wavelet Toolbox |
Usage Examples
|
By default Matlab will make use of multithreading for certain functions, with the maximum number of computational threads equal to the number of computational cores on the node. If a job or session hasn't requested an appropriate resource, this multithreading can cause contention for CPU resources and negatively impact other users. For this reason when using the standard matlab command please make sure you request appropriate resources by either:
|
Interactive
Interactive with full graphical interface (note the use of --exclusive when starting the interactive session):
[username@login01 ~]$ interactive --exclusive salloc: Granted job allocation 289663 Job ID 289663 connecting to c170, please wait... Last login: Thu Jan 26 12:59:11 2017 from 10.254.5.246 [username@c170 ~]$ module add matlab/2020a [username@c170 ~]$ matlab
Interactive with command line only:
[username@c170 ~]$ matlab -nodisplay
< M A T L A B (R) >
Copyright 1984-2020 The MathWorks, Inc.
R2020a Update 4 (9.8.0.1417392) 64-bit (glnxa64)
June 24, 2020
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Academic License
>>
Batch Submission
To submit a batch job for Matlab, put your code in a .m script file and refer to this in your batch submission script, as shown below in the example MATLABtest.job job script. Remember to leave the .m extension from the script name in the Matlab command line.
#!/bin/bash #SBATCH -J MATLAB #SBATCH -N 1 #SBATCH -o %N.%j.out #SBATCH -e %N.%j.err #SBATCH -p compute #SBATCH --exclusive module purge module add matlab/2020a matlab -nodisplay -r my_matlab_m_file
To submit the Matlab job, use sbatch as shown below:
[username@login01 ~]$ sbatch MATLABtest.job Submitted batch job 289522
Parallel Matlab
By default Matlab on Viper will run on a single core as multi-threading conflicts with the schedulers resource management, however, there are two ways in which Matlab can utilize multiple processors:
Multi-threading
Matlab can use multiple threads for certain built-in functions for example linear algebra and numerical functions such as fft, \ (mldivide), eig, svd, and sort. These functions automatically execute on multiple computational threads in a single MATLAB session, allowing them to execute faster on multicore-enabled machines. Additionally, many functions in the Image Processing Toolbox are multithreaded.
Firstly, using the matlab command with the -singleCompThread option:
[username@c170 ~]$ matlab -singleCompThread -nodisplay -nojvm -nodesktop -nosplash -r "maxNumCompThreads , exit"
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016a (9.0.0.341360) 64-bit (glnxa64)
February 11, 2016
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.
Academic License
Warning: maxNumCompThreads will be removed in a future release. Please remove any instances of this function from your code.
> In maxNumCompThreads (line 26)
ans =
1
Using the standard matlab command, on Viper this starts Matlab with multithreading support enabled:
[username@c170 ~]$ matlab -nodisplay -nojvm -nodesktop -nosplash -r "maxNumCompThreads , exit"
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016a (9.0.0.341360) 64-bit (glnxa64)
February 11, 2016
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.
Academic License
Warning: maxNumCompThreads will be removed in a future release. Please remove any instances of this function from your code.
> In maxNumCompThreads (line 26)
ans =
28
When using Matlab with multicore enabled, please ensure you have exclusive access to the node, see Exclusive interactive or Exclusive batch jobs.
Parallel Computing Toolbox
The Parallel Computing Toolbox allows you to open a number of workers (separate Matlab engines) on the local node, up to the number of cores on that node (28 for standard nodes in an exclusive session).
>> parpool('local',28)
Starting parallel pool (parpool) using the 'local' profile ... connected to 28 workers.
ans =
Pool with properties:
Connected: true
NumWorkers: 28
Cluster: local
AttachedFiles: {}
IdleTimeout: 30 minute(s) (30 minutes remaining)
SpmdEnabled: true
When using Matlab with the Parallel Computing Toolbox, please ensure you have exclusive access to the node, see Exclusive interactive or Exclusive batch jobs.