Difference between revisions of "Applications/Matlab"
(→Change Log) |
(→Batch Submission) |
||
| Line 122: | Line 122: | ||
#SBATCH -o %N.%j.out # Standard output will be written here | #SBATCH -o %N.%j.out # Standard output will be written here | ||
#SBATCH -e %N.%j.err # Standard error will be written here | #SBATCH -e %N.%j.err # Standard error will be written here | ||
| − | #SBATCH -p compute # Slurm partition, where you want the job to be queued | + | #SBATCH -p compute # Slurm partition, where you want the job to be queued |
| + | #SBATCH --exclusive | ||
module purge | module purge | ||
| Line 129: | Line 130: | ||
matlab -nodisplay -nojvm -nodesktop -nosplash -r my_matlab_m_file | matlab -nodisplay -nojvm -nodesktop -nosplash -r my_matlab_m_file | ||
</pre> | </pre> | ||
| − | |||
Matlab | Matlab | ||
Revision as of 08:31, 9 April 2018
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 are available to extend functionality.
- Versions: 2016a, 2016b
- Module names: matlab/2016a matlab/2016b
- License: University of Hull Total Academic Headcount license, available to members of the university for research use
Toolboxes
| 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
Executables
| Executable | 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 resource and negatively impact other users. For this reason the standard matlab command has been aliased so it runs with -singleCompThread option and will only use a single CPU core. See Parallel Matlab |
| matlab-mt | To access standard matlab that supports multithreading, please use the matlab-mt command and request appropriate resource by either using an exclusive session with interactive --exclusive or submiting a task with the #SBATCH --exclusive. See Parallel Matlab |
Interactive
Interactive with full graphical interface:
[username@login01 ~]$ interactive 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/2016a [username@c170 ~]$ matlab
Interactive with command line only:
[username@c170 ~]$ matlab -nodisplay
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016a (9.0.0.341360) 64-bit (glnxa64)
February 11, 2016
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Academic License
>>
Batch Submission
#!/bin/bash #SBATCH -J MATLAB # Job name, you can change it to whatever you want #SBATCH -N 1 # Number of nodes (for Matlab should be always one) #SBATCH -o %N.%j.out # Standard output will be written here #SBATCH -e %N.%j.err # Standard error will be written here #SBATCH -p compute # Slurm partition, where you want the job to be queued #SBATCH --exclusive module purge module add matlab/2016a matlab -nodisplay -nojvm -nodesktop -nosplash -r my_matlab_m_file
Matlab
[username@login01 ~]$ sbatch MATLABtest.job Submitted batch job 289522
Parallel Matlab
By default Matlab on Viper will run on a single core as mutli-threading conflicts with the schedulers resource management, however there are three ways in which Matlab can utilise 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 Image Processing Toolbox are multithreaded.
Using the standard matlab command, on Viper this is aliased to matlab -singleCompThread to limit to one thread:
[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 =
1
Using the matlab-mt command, on Viper this starts Matlab with multithreading support enabled:
[username@c170 ~]$ matlab-mt -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 (using the matlab-mt command), 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.
Matlab Distributed Computing Server
The Matlab Distributed Computing Server is not currently supported on Viper.
Change Log
[2017-06-09] Matlab 2016b installed
[2017-02-22] Changed default Matlab launch command in module to matlab -singleCompThread to disable multi-threading