Difference between revisions of "Matlab"

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==Installation==
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{|align=right
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Currently matlab is located here:
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  |__TOC__
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  |}
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__NOEDITSECTION__
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[[Category:Software]][[Category:Language]][[Category:Math]]
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{|<!--Main settings - REQUIRED-->
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|{{#vardefine:app|matlab}}
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|{{#vardefine:url|http://www.mathworks.com/}}
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
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|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
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|{{#vardefine:job|1}} <!--Enable job script wiki page link-->
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|{{#vardefine:policy|}} <!--Enable policy section -->
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|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
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|{{#vardefine:faq|}} <!--Enable FAQ section -->
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|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
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|}
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<!-- ########  Template Body ######## -->
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<!--Description-->
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{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 +
 
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MATLAB is a programming environment for algorithm development, data analysis, visualization, and numerical computation. Using MATLAB, you can solve technical computing problems faster than traditional programming languages, such as C, C++, and Fortran.
 +
 
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You can use MATLAB in various applications, including signal and image processing, communications, control design, test and measurement, financial modeling and analysis, and computational biology. MATLAB is the language of technical computing for a million engineers and scientists in industry and academia.
 +
<!--Modules-->
 +
==Environment Modules==
 +
Run <code>module spider matlab</code> or <code>module spider mcr</code> to find out what environment modules are available for the MATLAB GUI and for the MATLAB Compiler Runtime. Use Matlab to compile your code and mcr to run it. The mcr does not consume MATLAB licenses.
 +
 
 +
==Restrictions==
 +
The MATLAB install on HiPerGator is restricted to the toolboxes available under the UF license. The complete list of ineligible toolboxes is on the MATLAB website: [https://www.mathworks.com/support/requirements/product-requirements-platform-availability-list.html MATLAB Add-On Availability]
 +
 
 +
Run <code>matlab_show_license_use</code> after loading a Matlab module to see what licenses are available and how many are in use.
 +
 
 +
==System Variables==
 +
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 +
<!--Additional-->
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{{#if: {{#var: conf}}|==Configuration==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
 +
|}}
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{{#if: {{#var: policy}}|==Usage Policy==
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WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 +
|}}
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{{#if: {{#var: testing}}|==Performance==
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WRITE PERFORMANCE TESTING RESULTS HERE|}}
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{{#if: {{#var: faq}}|==FAQ==
 +
*'''Q:''' **'''A:'''
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|}}
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{{#if: {{#var: citation}}|==Citation==
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If you publish research that uses {{#var: app}} you have to cite it as follows:
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X. Yang, K. Dorman and S. Aluru, “Reptile: Representative tiling for short read error correction”, Bioinformatics, 26(20), 2526-2533, 2010.
 +
|}}
 +
==Policies==
 +
# You may not interactively run Matlab or compiled MATLAB executables on the login servers.
 +
# Long running (more than 10 minutes) MATLAB jobs must be in compiled form and submitted to the batch system.
 +
# UF Research Computing has no budget for application software and licensing. All MATLAB licenses (including the compiler) come from and are shared with the entire UF campus. For this reason, it is sometimes difficult to obtain a license, or MATLAB may take a long time to start. If your research depends on MatLab and you do not want to be delayed by licensing issues, you should consider purchasing a MATLAB license for your personal or group use.
 +
 
 +
==Available components==
 +
See the [[Matlab add-ons]] for a full list of licensed MATLAB components.
 +
 
 +
==Compiling MatLab Programs==
 +
MATLAB programs must be compiled via the MATLAB compiler before they can be run in batch mode on HiPerGator. To compile MATLAB programs, you should
 +
 
 +
# See [[Development and Testing]] page to learn how to get an interactive developmental session on HiPerGator under SLURM.
 +
# Set up your environment so that the libraries needed by the compiler can be found.
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#*<pre>module load matlab</pre>
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#*'''Note:''' The module load command should also be included in your batch submission script since your compiled Matlab executable must also find the appropriate dynamically loaded libraries.
 +
# Compile your MATLAB program (.m) files using the MatLab compiler.
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#*<pre>mcc -R -singleCompThread -m some_prog.m</pre>
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#*'''Note:'''  The "<code>-R -singleCompThread</code>" options on the mcc command line will result in a '''single-threaded''' executable. By default, multithreading is enabled in executables produced by mcc.  One computational thread will be started for each processor in a machine that runs your executable. That's not usually what you want. Unless you know what you are doing and intend to take advantage of multithreading (including requesting the appropriate resources in your submission script), you should use these options and generate a '''single-threaded''' executable.
 +
===Example===
 +
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
 +
''Expand this section to view MATLAB example.''
 +
<div class="mw-collapsible-content" style="padding: 5px;">
 +
Let us say we have a program like that below in a source file named houdini.m
 +
<pre>
 +
function [m,t] = houdini();
 +
% Doc example, chapter 3.
 +
 
 +
% Copyright 1997 The MathWorks, Inc.
 +
% $Revision: 1.1.6.1 $
 +
 
 +
m = magic(2); % Assign 2x2 matrix to m.
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t = m .^ 3;  % Cube each element of m.
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disp(t);      % Display the value of t.
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</pre>
 +
Since we already have the environment set, we can compile this program. It is recommended that this be done in a separate directory as several files are produced.
 +
<pre>
 +
mkdir tmp
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cd tmp
 +
cp ../houdini.m .
 +
module load matlab
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mcc -R -singleCompThread -m houdini.m
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ls -l
 +
total 124
 +
-rwxr-xr-x  1 root root 12299 Apr  3 10:08 houdini
 +
-rw-r--r--  1 root root 63146 Apr  3 10:08 houdini.ctf
 +
-rw-r--r--  1 root root  239 Apr  3 10:06 houdini.m
 +
-rw-r--r--  1 root root  2900 Apr  3 10:08 houdini_main.c
 +
-rw-r--r--  1 root root  6328 Apr  3 10:08 houdini_mcc_component_data.c
 +
-rw-r--r--  1 root root  5461 Apr  3 10:08 houdini.prj
 +
-rw-r--r--  1 root root  1010 Apr  3 10:08 mccExcludedFiles.log
 +
-rw-r--r--  1 root root  6757 Apr  3 10:08 readme.txt
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-rwxr--r--  1 root root  1446 Apr  3 10:08 run_houdini.sh
 +
</pre>
 +
The MATLAB executable '''houdini''' has been generated and can be run by typing ./houdini, or by putting that command in a batch submission script.
 +
</div></div>
 +
----
 +
[http://www.mathworks.com/access/helpdesk/help/toolbox/compiler MATLAB Compiler Documentation] can be found on the MatLab Website.
 +
 
 +
==MATLAB GUI use on HiPerGator==
 +
 
 +
If you must use the Graphical User Interface for MATLAB, use [[Open OnDemand|Open on Demand]]
 +
 
 +
==MATLAB online training==
 +
 
 +
Mathworks also has several free [https://www.mathworks.com/services/training.html online training resources].
 +
 
 +
 
 +
==Compiled DLL==
 +
If you have compiled a MATLAB DLL to use as an executable, it will not run on the cluster. DLL's are Microsoft Windows based dynamically linked libraries that will only work under the Windows operating system.
 +
 
 +
==Setting a Command Path==
 +
To set a command path in your MATLAB program, should add the following code.
 
<pre>
 
<pre>
−
/apps/matlab/bin
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path(path, '/path/to/matlab/binaries')
 
</pre>
 
</pre>
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==Policy==
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This will add the specified directory to the MATLAB search path. For more information, see the [http://www.mathworks.com/access/helpdesk/help/techdoc/index.html?/access/helpdesk/help/techdoc/ref/path.html&http://www.google.com/search?hl=en&q=matlab+set+path&btnG=Google+Search&aq=f&oq= Matlab] web site.
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Please remember that the HPC Center resources are not to be used interactively! Matlab jobs should be submitted via Torque submission scripts with no user interaction.
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==Frequently Asked Questions==
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==Known Issues==
−
Dear Sirs,
+
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
 +
''Expand this section to view common troubleshooting steps.''
 +
<div class="mw-collapsible-content" style="padding: 5px;">
 +
===No Licenses Available===
 +
You may run into an error when using the MATLAB compiler, such as
 +
 
 +
'''Licensed number of users already reached.'''
 +
 
 +
If so, the number of licenses available for the MATLAB compiler has been exceeded. Only two are shared among the entire university, so you should expect to see this problem occasionally if you use the MATLAB compiler frequently. If the problem persists for over a few hours, please open a [https://support.rc.ufl.edu support request].
  
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I have a basic question about what can be run on the cluster. I have a
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===MCR_CACHE_ROOT Directory===
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standalone C application file generated by the Matlab compiler. Is it
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'''Could not access the MCR component cache'''
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possible to run it (after porting/copying the required libraries) as an
 
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external application on a particular node of the cluster. This is
 
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because it is not possible for me to compile the C source files on the
 
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cluster itself?
 
−
 
 
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OK... from what I gather here, I think you have the following:
 
  
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# A compiled executable, most likely in linux x86 format.
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This error message means that MATLAB cannot access the MCR cache directory. When you load the MATLAB module, MCR_CACHE_ROOT is set for you, and you should not encounter this error. If you do, please open a [https://support.rc.ufl.edu support request]. For batch jobs, <code>module load matlab</code> uses the $TMPDIR variable, and MCR_CACHE_ROOT is set to $TMPDIR/mcr_cache. For non-batch jobs, MCR_CACHE_ROOT is set to /scratch/local/$USER/mcr_cache
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#: This executable obviously requires specific libraries to run, and if we don't have them installed they won't work. From what I remember of the matlab compiler suite, it is possible for the matlab compiler to actually generate a full set of files that include your executable and the libraries it needs to support it such that the whole suite is portable. This is what you really want to look for, and I know it has been done before.
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−
# Possibly the source code.
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===Older Versions===
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#: If you have the C source code, you should be able to compile that source code on our systems with out any trouble, unless it requires some sort of library provided by matlab. If this is the case, then option 1 above is your best bet.
+
To use older versions of MATLAB that are installed on the cluster, you can list them via the following command:
 +
<pre>
 +
$ module spider matlab
 +
</pre>
 +
If you were to see that an older version of MATLAB is available, such as version r2012a, you would then load the appropriate module for that version:
 +
<pre>
 +
$ module load matlab/2012a
 +
</pre>
 +
</div></div>

Latest revision as of 16:06, 28 November 2023

Description

matlab website  

MATLAB is a programming environment for algorithm development, data analysis, visualization, and numerical computation. Using MATLAB, you can solve technical computing problems faster than traditional programming languages, such as C, C++, and Fortran.

You can use MATLAB in various applications, including signal and image processing, communications, control design, test and measurement, financial modeling and analysis, and computational biology. MATLAB is the language of technical computing for a million engineers and scientists in industry and academia.

Environment Modules

Run module spider matlab or module spider mcr to find out what environment modules are available for the MATLAB GUI and for the MATLAB Compiler Runtime. Use Matlab to compile your code and mcr to run it. The mcr does not consume MATLAB licenses.

Restrictions

The MATLAB install on HiPerGator is restricted to the toolboxes available under the UF license. The complete list of ineligible toolboxes is on the MATLAB website: MATLAB Add-On Availability

Run matlab_show_license_use after loading a Matlab module to see what licenses are available and how many are in use.

System Variables

  • HPC_MATLAB_DIR - installation directory



Policies

  1. You may not interactively run Matlab or compiled MATLAB executables on the login servers.
  2. Long running (more than 10 minutes) MATLAB jobs must be in compiled form and submitted to the batch system.
  3. UF Research Computing has no budget for application software and licensing. All MATLAB licenses (including the compiler) come from and are shared with the entire UF campus. For this reason, it is sometimes difficult to obtain a license, or MATLAB may take a long time to start. If your research depends on MatLab and you do not want to be delayed by licensing issues, you should consider purchasing a MATLAB license for your personal or group use.

Available components

See the Matlab add-ons for a full list of licensed MATLAB components.

Compiling MatLab Programs

MATLAB programs must be compiled via the MATLAB compiler before they can be run in batch mode on HiPerGator. To compile MATLAB programs, you should

  1. See Development and Testing page to learn how to get an interactive developmental session on HiPerGator under SLURM.
  2. Set up your environment so that the libraries needed by the compiler can be found. 
    • module load matlab
    • Note: The module load command should also be included in your batch submission script since your compiled Matlab executable must also find the appropriate dynamically loaded libraries.
  3. Compile your MATLAB program (.m) files using the MatLab compiler. 
    • mcc -R -singleCompThread -m some_prog.m
    • Note: The "-R -singleCompThread" options on the mcc command line will result in a single-threaded executable. By default, multithreading is enabled in executables produced by mcc. One computational thread will be started for each processor in a machine that runs your executable. That's not usually what you want. Unless you know what you are doing and intend to take advantage of multithreading (including requesting the appropriate resources in your submission script), you should use these options and generate a single-threaded executable.

Example

Expand this section to view MATLAB example.

Let us say we have a program like that below in a source file named houdini.m 

function [m,t] = houdini();
% Doc example, chapter 3.

% Copyright 1997 The MathWorks, Inc.
% $Revision: 1.1.6.1 $

m = magic(2); % Assign 2x2 matrix to m. 
t = m .^ 3;   % Cube each element of m. 
disp(t);      % Display the value of t.

Since we already have the environment set, we can compile this program. It is recommended that this be done in a separate directory as several files are produced. 

 mkdir tmp
 cd tmp
 cp ../houdini.m .
 module load matlab
 mcc -R -singleCompThread -m houdini.m 
 ls -l
total 124
-rwxr-xr-x  1 root root 12299 Apr  3 10:08 houdini
-rw-r--r--  1 root root 63146 Apr  3 10:08 houdini.ctf
-rw-r--r--  1 root root   239 Apr  3 10:06 houdini.m
-rw-r--r--  1 root root  2900 Apr  3 10:08 houdini_main.c
-rw-r--r--  1 root root  6328 Apr  3 10:08 houdini_mcc_component_data.c
-rw-r--r--  1 root root  5461 Apr  3 10:08 houdini.prj
-rw-r--r--  1 root root  1010 Apr  3 10:08 mccExcludedFiles.log
-rw-r--r--  1 root root  6757 Apr  3 10:08 readme.txt
-rwxr--r--  1 root root  1446 Apr  3 10:08 run_houdini.sh

The MATLAB executable houdini has been generated and can be run by typing ./houdini, or by putting that command in a batch submission script.

MATLAB Compiler Documentation can be found on the MatLab Website.

MATLAB GUI use on HiPerGator

If you must use the Graphical User Interface for MATLAB, use Open on Demand

MATLAB online training

Mathworks also has several free online training resources.


Compiled DLL

If you have compiled a MATLAB DLL to use as an executable, it will not run on the cluster. DLL's are Microsoft Windows based dynamically linked libraries that will only work under the Windows operating system.

Setting a Command Path

To set a command path in your MATLAB program, should add the following code. 

path(path, '/path/to/matlab/binaries')

This will add the specified directory to the MATLAB search path. For more information, see the Matlab web site.

Known Issues

Expand this section to view common troubleshooting steps.

No Licenses Available

You may run into an error when using the MATLAB compiler, such as

Licensed number of users already reached.

If so, the number of licenses available for the MATLAB compiler has been exceeded. Only two are shared among the entire university, so you should expect to see this problem occasionally if you use the MATLAB compiler frequently. If the problem persists for over a few hours, please open a support request.

MCR_CACHE_ROOT Directory

Could not access the MCR component cache

This error message means that MATLAB cannot access the MCR cache directory. When you load the MATLAB module, MCR_CACHE_ROOT is set for you, and you should not encounter this error. If you do, please open a support request. For batch jobs, module load matlab uses the $TMPDIR variable, and MCR_CACHE_ROOT is set to $TMPDIR/mcr_cache. For non-batch jobs, MCR_CACHE_ROOT is set to /scratch/local/$USER/mcr_cache

Older Versions

To use older versions of MATLAB that are installed on the cluster, you can list them via the following command: 

$ module spider matlab

If you were to see that an older version of MATLAB is available, such as version r2012a, you would then load the appropriate module for that version: 

$ module load matlab/2012a
Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Matlab&oldid=28252"