Difference between revisions of "Matlab"

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==Installation==
+
__TOC__
Currently matlab is located here:
+
__NOEDITSECTION__
<pre>
+
[[Category:Software]][[Category:Language]][[Category:Math]]
Version 2009b: /apps/matlab/2009b/
+
{|<!--Main settings - REQUIRED-->
</pre>
+
|{{#vardefine:app|matlab}}
 +
|{{#vardefine:url|http://www.mathworks.com/}}
 +
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 +
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 +
|{{#vardefine:job|1}} <!--Enable job script wiki page link-->
 +
|{{#vardefine:policy|}} <!--Enable policy section -->
 +
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 +
|{{#vardefine:faq|}} <!--Enable FAQ section -->
 +
|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
 +
|}
 +
<!-- ########  Template Body ######## -->
 +
<!--Description-->
 +
{{#if: {{#var: url}}|
 +
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
==Policies==
+
MATLAB is a programming environment for algorithm development, data analysis, visualization, and numerical computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran.
# You may not run MatLab nor compiled MatLab executables interactively on submit1 or submit2.
 
# You must use the test nodes (test01 - test05) to test and compile your MatLab programs.
 
# Long running (more than 30 minutes) MatLab jobs must be submitted to the batch system.
 
# Large numbers of jobs must not be run on the test nodes but must be submitted to the batch system.
 
# The UF HPC Center has no budget for application software and licensing.   All MatLab licenses (including the compiler) come from, and are shared with, all of campus.  For this reason it is sometimes difficult to obtain a license.  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.
 
  
==Compiling MatLab Programs==
+
You can use MATLAB in a wide range of applications, including signal and image processing, communications, control design, test and measurement, financial modeling and analysis, and computational biology. For a million engineers and scientists in industry and academia, MATLAB is the language of technical computing.
 +
<!--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 for compiling your code and mcr for running it. The mcr does not consume matlab licenses.
  
MatLab programs must be compiled via the MatLab compiler before they can be run in batch mode on the HPC Center cluster.
+
==Restrictions==
In order to compile MatLab programs you should
+
MatLab install on HiPerGator is restricted to the toolboxes available under the UF license. The full list of ineligible toolboxes is on the MATLAB website:
  
1. Once on submit1 or submit2, log into one of the test nodes (test01 - test05) via ssh.  Due to user memory constraints on submit1 and submit2, the MatLab compiler cannot be used on them.
+
[https://www.mathworks.com/support/requirements/product-requirements-platform-availability-list.html MATLAB Add-On Availability]
<pre>
 
submit1% ssh test05
 
</pre> 
 
2. Set up your environment so that the libraries needed by the compiler can be found.
 
<pre>
 
test05% export LD_LIBRARY_PATH=/apps/matlab/2009b/bin/glnxa64:/apps/matlab/2009b/sys/os/glnxa64
 
test05% export PATH=${PATH}:/apps/matlab/2009b/bin
 
</pre>
 
  
'''Note:''' These environment settings should be included in your batch submission script since they will also be needed by the resulting MatLab executable.  
+
Run <code>matlab_show_license_use</code> after loading a matlab module to see what licenses are available and how many are in use.
  
3a. For batch jobs, you should also set the MCR_CACHE_ROOT environment variable in your PBS job script.
+
==System Variables==
<pre>
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
test05% export MCR_CACHE_ROOT=${TMPDIR}
+
<!--Additional-->
</pre>
+
{{#if: {{#var: conf}}|==Configuration==
 +
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
 +
|}}
 +
{{#if: {{#var: policy}}|==Usage Policy==
 +
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 +
|}}
 +
{{#if: {{#var: testing}}|==Performance==
 +
WRITE PERFORMANCE TESTING RESULTS HERE|}}
 +
{{#if: {{#var: faq}}|==FAQ==
 +
*'''Q:''' **'''A:'''
 +
|}}
 +
{{#if: {{#var: citation}}|==Citation==
 +
If you publish research that uses {{#var: app}} you have to cite it as follows:
 +
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 run MatLab nor compiled MatLab executables interactively on the login servers.
 +
# Long running (more than 30 minutes) MatLab jobs need to be in compiled form and must be 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, all of 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.
  
Please see the [[PBS Sample Job Scripts]] for a sample MatLab submission script.
+
==Available components==
 +
See the [[Matlab add-ons]] for a full list of licensed Matlab components.
  
3b. For an interactive run (only on the test nodes), you should set MCR_CACHE_ROOT to a directory /scratch/local.
+
==Compiling MatLab Programs==
 +
MatLab programs must be compiled via the MatLab compiler before they can be run in batch mode on HiPerGator.
  
<pre>
+
In order to compile MatLab programs you should
test05% mkdir -p /scratch/local/$USER/mcr_cache
 
test05% export MCR_CACHE_ROOT=/scratch/local/$USER/mcr_cache
 
</pre>
 
  
4. Compile your matlab program (.m) files using the MatLab compiler ([[mcc]]).
+
# See [[Development and Testing]] page to learn how to get an interactive developmental session on HiPerGator under SLURM.
<pre>
+
# Set up your environment so that the libraries needed by the compiler can be found.
  test05% mcc -R -singleCompThread -m some_prog.m
+
module load matlab
</pre>
+
'''Note:''' The module load command should be included in your batch submission script as well since your compiled matlab executable will also need to find the appropriate dynamically loaded libraries.
 +
# Compile your matlab program (.m) files using the MatLab compiler ([[mcc]]).
 +
  mcc -R -singleCompThread -m some_prog.m
  
 
===Example===
 
===Example===
Line 63: Line 85:
 
Since we already have the environment setup, we can compile this program. It is recommended that this be done in a separate directory as a number of files are produced.
 
Since we already have the environment setup, we can compile this program. It is recommended that this be done in a separate directory as a number of files are produced.
 
<pre>
 
<pre>
  test05% mkdir tmp
+
  mkdir tmp
  test05% cd tmp
+
  cd tmp
  test05% cp ../houdini.m .
+
  cp ../houdini.m .
  test05% ls
+
  module load matlab
houdini.m
+
  mcc -R -singleCompThread -m houdini.m  
test05% export LD_LIBRARY_PATH=/apps/matlab/2009b/bin/glnxa64:/apps/matlab/2009b/sys/os/glnxa64
+
  ls -l
test05% export PATH=${PATH}:/apps/matlab/2009b/bin
 
  test05% mcc -R -singleCompThread -m houdini.m  
 
Warning: Unable to open display , MATLAB is starting without a display.
 
  You will not be able to display graphics on the screen.
 
  test05% ls -l
 
 
total 124
 
total 124
 
-rwxr-xr-x  1 root root 12299 Apr  3 10:08 houdini
 
-rwxr-xr-x  1 root root 12299 Apr  3 10:08 houdini
Line 85: Line 102:
 
-rwxr--r--  1 root root  1446 Apr  3 10:08 run_houdini.sh
 
-rwxr--r--  1 root root  1446 Apr  3 10:08 run_houdini.sh
 
</pre>
 
</pre>
The MatLab executable '''houdini''' has been generated.
+
The MatLab executable '''houdini''' has been generated, and can be run by typing ./houdini, or by putting that command in a batch submission script.  
  
'''Note:'''  The "<code>-R -singleCompThread</code>" options on the mcc command line will result in a '''single-threaded''' executable.  By default, multi-threading is enabled in executables produced by mcc.  The result is that 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.  Otherwise, your MatLab jobs will oversubscribe the compute nodes and interfere with other users' programs.
+
'''Note:'''  The "<code>-R -singleCompThread</code>" options on the mcc command line will result in a '''single-threaded''' executable.  By default, multi-threading is enabled in executables produced by mcc.  The result is that 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.
 
----
 
----
Documentation for the MatLab compiler can be viewed on the [http://www.mathworks.com/access/helpdesk/help/toolbox/compiler MatLab Website].
+
[http://www.mathworks.com/access/helpdesk/help/toolbox/compiler MatLab Compiler Documentation] can be found on the MatLab Website.
 
 
  
===Where is the Distributed Computing Toolbox?===
+
==MATLAB GUI use on HiPerGator==
It hasn't been added because we do not have a license for the distributed computing toolbox. The University of Florida has not purchased a license for that product.  The HPC Center has no budget for application software and licensing.  Users and/or groups must purchase commercial software on their own.
 
  
===Compiled DLL===
+
If you must use the Graphical User Interface for MatLab follow the [[Matlab GUI Example]] documentation, or options in [[GUI Programs]]
If you have compiled a DLL to use as an executable, it will not work on the cluster. DLL's are Microsoft Windows based dynamically linked libraries that matlab would be able to run on a Windows machine in a faster method because it would not have to do any compiling of its own. Basically it is the same thing as a matlab byte-compiled package. A number of different software packages and languages out there use the same methodology, such as Java and emacs-lisp.
 
===Setting a Path===
 
In order to set a path, in your matlab script you would put the following:
 
<pre>
 
path(path, '/path/to/wherever/you/want')
 
</pre>
 
This would add a search path to the matlab system. This is also detailed on 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] website.
 
  
You can also set a path for the compiler to look at via the command line:
+
==MATLAB online training==
-a <pathname>
+
Please see the Pre-recorded [https://training.it.ufl.edu/training/items/running-matlab-on-hipergator.html MATLAB on HiPerGator Training session] for information on using MATLAB on HiPerGator.
  
==Troubleshooting==
+
Mathworks also has a number of free [https://www.mathworks.com/services/training.html online training resources].
===2008a===
 
When version 2008a was installed on our system, it installed fine but when run it would complain about glibc being too old. The error message given my matlab looked like the following:
 
<pre>
 
****************************************************************************************************
 
Error: The MATLAB script returned a bad status while determining
 
      environment variables. There appears to be a problem
 
      with your MATLAB installation. You must fix the problem
 
      before mcc can work. Any messages from the script
 
      follow . . .  
 
  
  
----------------------------------------------------------------------------
+
==Compiled DLL==
Warning: glibc 2.3.4      - Unsupported version
+
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.
        glibc 2.3.6      - MATLAB built using this version
 
----------------------------------------------------------------------------
 
-> Your configuration APPEARS to be too OLD to run this MATLAB program!
 
----------------------------------------------------------------------------
 
  For system requirements consult http://www.mathworks.com ...
 
  
***************************************************************************
+
==Setting a Command Path==
 +
To set a command path in your MatLab program, should add the following code.
 +
<pre>
 +
path(path, '/path/to/matlab/binaries')
 
</pre>
 
</pre>
In order to fix this problem, we first searched on the web to find that there was a patch available from Mathworks if you asked them for it. We did just this, and the fix turned out to be very simple. Unfortunately it appears that no one else has bothered to publish this fix, so here it is:
+
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.
<pre>
 
--- oscheck.sh    2008-05-28 09:48:55.000000000 -0400
 
+++ oscheck.sh.old    2007-12-02 01:34:35.000000000 -0500
 
@@ -102,7 +102,7 @@
 
#                  of the data. Set oscheck_debug=0 for shipping.
 
#
 
# Copyright 1996-2007 The MathWorks, Inc.
 
-# $Revision: 1.1.12.1 $  $Date: 2008/03/24 17:59:41 $
 
+# $Revision: 1.1.6.4 $  $Date: 2007/12/03 21:53:17 $
 
#----------------------------------------------------------------------------
 
#
 
  
@@ -153,8 +153,8 @@ else
+
==Known Issues==
#                  arch  OSprefix minimum_ver release_ver future_ver
+
===No Licenses Available===
#
+
You may run into an error when using the MatLab compiler such as
oslist="        sol64  SunOS    5.10        5.10        -"
 
-        oslist="$oslist glnx86  glibc    2.3.4      2.3.4      -"
 
-        oslist="$oslist glnxa64 glibc    2.3.4      2.3.4      -"
 
+        oslist="$oslist glnx86  glibc    2.3.6      2.3.6      -"
 
+        oslist="$oslist glnxa64 glibc    2.3.6      2.3.6      -"
 
oslist="$oslist mac    Darwin  8.7.0      8.7.0      -"
 
oslist="$oslist maci    Darwin  8.7.0      8.7.0      -"
 
oslist="$oslist maci64  Darwin  9.0.0      9.0.0      -"
 
</pre>
 
====Compiler Issues====
 
You may run into an error when using the matlab compiler that looks something like this:
 
  
 
'''Licensed number of users already reached.'''
 
'''Licensed number of users already reached.'''
  
In this case what is probably happening is that the number of licenses for the matlab compiler has been exhausted. The University only has two licenses, and if they are currently being used then this is the error that will be issued.
+
If so, the number of licenses available for the MatLab compiler has been exceeded. There are only two shared among the entire university so you should expect to see this problem from time to time if you use the MatLab compiler frequently. If the problem persists for more than a few hours, please open a [https://support.rc.ufl.edu support request].
  
'''"Could not access the MCR component cache." error message'''
+
===MCR_CACHE_ROOT Directory===
 +
'''Could not access the MCR component cache'''
  
What is happening here is that matlab is not able to access the MCE cache directory, which it expects to be in your home directory. The reason this is happening is that we have found that when a large number of these programs are running at the same time, the load on the home area file system is too great, and we start having problems with the filesystem.
+
This error message means that MatLab is not able to 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, module load matlab makes use of 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
 +
 +
===Interactive Use===
 +
See the GUI section above for information on running the MATLAB GUI on HiPerGator.
  
In order to solve this problem, you just need to do the following:
+
Some Windows users running Xming have reported problems with MATLAB becoming unresponsive, especially after saving a new file. If you run into this problem, we suggest using an alternate X11 server, such as [http://mobaxterm.mobatek.net/ MobaXterm]. Please open a  [http://support.rc.ufl.edu support request] if you continue to experience problems.
export MCR_CACHE_ROOT=$TMPDIR
 
  
This redirects the cache to a temp directory that is able to handle the traffic.
+
===Older Versions===
 
+
In order to use older versions of Matlab that are installed on the cluster, you can list them via the following command:
==Installation Notes==
+
<pre>
===Licensing===
+
$ module spider matlab
The matlab license is a floating license provided to us from the University. As such, we cannot be using hundreds if not thousands of licenses from this provision, as we would completely wipe out the ability of the rest of the university to use the software.
+
</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:
As such, matlab licenses can only be used from select machines, typically submit and test nodes.
+
<pre>
 
+
$ module load matlab/2012a
This is done by copying ''/etc/matlab.dat'' from submit to whatever nodes need to have the license. The software installation of matlab in /apps has a symbolic link to this file, so if the file is there it can read the license, and if not the software will not work.
+
</pre>
===Installation Notes===
 
See [[matlab installation]] for more details.
 

Latest revision as of 21:34, 24 October 2022

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 with traditional programming languages, such as C, C++, and Fortran.

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

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 for compiling your code and mcr for running it. The mcr does not consume matlab licenses.

Restrictions

MatLab install on HiPerGator is restricted to the toolboxes available under the UF license. The full 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 run MatLab nor compiled MatLab executables interactively on the login servers.
  2. Long running (more than 30 minutes) MatLab jobs need to be in compiled form and must be 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, all of 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.

In order 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 be included in your batch submission script as well since your compiled matlab executable will also need to find the appropriate dynamically loaded libraries.

  1. Compile your matlab program (.m) files using the MatLab compiler (mcc).
mcc -R -singleCompThread -m some_prog.m

Example

Let us say that we have a program such as 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 setup, we can compile this program. It is recommended that this be done in a separate directory as a number of 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.

Note: The "-R -singleCompThread" options on the mcc command line will result in a single-threaded executable. By default, multi-threading is enabled in executables produced by mcc. The result is that 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.


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 follow the Matlab GUI Example documentation, or options in GUI Programs

MATLAB online training

Please see the Pre-recorded MATLAB on HiPerGator Training session for information on using MATLAB on HiPerGator.

Mathworks also has a number of 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

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. There are only two shared among the entire university so you should expect to see this problem from time to time if you use the MatLab compiler frequently. If the problem persists for more than 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 is not able to 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 makes use of 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

Interactive Use

See the GUI section above for information on running the MATLAB GUI on HiPerGator.

Some Windows users running Xming have reported problems with MATLAB becoming unresponsive, especially after saving a new file. If you run into this problem, we suggest using an alternate X11 server, such as MobaXterm. Please open a support request if you continue to experience problems.

Older Versions

In order 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