MATLAB DCS: Difference between revisions

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{{Matlab_deprecated}}
Cheaha now has a 128 node license for the [http://www.mathworks.com/products/distriben/ Distributed Computing Server] component of Matlab.


In order to use DCS on Cheaha, you will have to use your own Matlab and [http://www.mathworks.com/products/parallel-computing/ Parallel Computing Toolbox] license.


== Overview ==
The [http://www.mathworks.com/products/distriben MATLAB Distributed Computing Server (MATLAB DCS)] is a parallel computing extension to MATLAB that enables processing to be spread across a large number of worker nodes, accelerating the speed at which compute intensive operations can complete.
The following is an overview of the process to run Matlab jobs on cheaha using the Distributed Computing Server:
* Obtain your own Matlab client license
* Obtain your own Parallel Computing Toolbox license
* Install and license both Matlab client and Parallel Computing Toolbox on your Windows / Linux / Mac workstation
* Configure SSH on your workstation (see the section on 'SSH Keys' below)
* Download and extract the Matlab submission functions to your Matlab PATH
* Add Cheaha to the Parallel Computing Toolbox configuration
* Write, test and debug your parallel code on your local workstation
* Once the code is ready for production, run it on Cheaha using the Parallel Computing Toolbox
* After the job completes (you will receive an email), retrieve the results
* Destroy the job related content on cheaha to clean up


== SSH Keys ==
UAB IT Research Computing maintains a 128 worker node license for the the [[Cheaha]] computing platform. In order to use DCS on Cheaha, you will need to [[MATLAB#Using_MATLAB|use a MATLAB instance]] with the Parallel Computing Toolbox installed.
The Matlab Parallel Toolbox uses SSH authentication via public-private key-pair to connect to the Matlab Distributed Computing Server on the cluster head node.


The process of configuring SSH keys differs depending on your client operating system. Linux and Mac should already have the appropriate SSH client software installed, Windows will require the installation of [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html PuTTY].
In order to leverage the MATLAB worker nodes on [[Cheaha]] the Parallel Computing Toolbox will need to be configured to submit compute tasks to [[Cheaha]] by following the steps in this document.


=== Windows ===
{{MatlabAppPage}}
This section documents the steps to install and configure PuTTY on Windows computers. This software provides the utilities that Matlab uses to communicate with the head node.


==== PuTTY ====
== Overview ==
If PuTTY is installed, skip to the next section "Generate an SSH Key Pair".
 
If PuTTY isn't already installed on your system, download the tools from the [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html PuTTY Downloads page].
 
Download and run [http://the.earth.li/~sgtatham/putty/latest/x86/putty-0.60-installer.exe this file] to install PuTTY using the graphical installation tool.
 
Alternatively, you can download the individual components to a directory of your choosing. This install approach does not require Windows Administrator privileges:
* [http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe putty.exe]
* [http://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink.exe]
* [http://the.earth.li/~sgtatham/putty/latest/x86/pageant.exe pageant.exe]
* [http://the.earth.li/~sgtatham/putty/latest/x86/puttygen.exe puttygen.exe]
* [http://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe pscp.exe]
* [http://the.earth.li/~sgtatham/putty/latest/x86/psftp.exe psftp.exe]
 
Using the individual component install approach requires that you add the install directory to your PATH. See this [http://support.microsoft.com/kb/310519 Microsoft Support] page for details on altering the PATH environment variable.
 
===== Generate an SSH Key Pair =====
 
Generate a public-private key pair by running the puttygen command.
 
Start PuTTYgen by either:
* Clicking Start -> All Programs -> PuTTY --> PuTTYgen
* Opening Windows Explorer / My Computer, browse to the PuTTY directory and double click 'puttygen'
 
This will bring up a window to manage your key pair.
 
[[Image:puttygen-window.png|400px]]
 
Press the "Generate" button to start the process.  You will be requested to move your mouse around in the blank are of that window to help generate a good random number.  The progress bar will fill in as you do so letting you know when the process is complete.  Once complete, the PuTTY Gen window will display your public key and offer you various options to work with that key. 
 
[[Image:puttygen-savekey2.png|400px]]
 
# Change the "Key Comment" to your Windows host name (run 'hostname' at the command prompt to discover the name of your Windows system)
# Set a passphrase for your private key, filling in both the "Key passphrase" and "Confirm passphrase" text boxes with the same passphrase.  The passphrase is a '''local''' password for this private key.  It doesn't have anything to do with any other passwords.  It is strictly about protecting the private key that you just generated. Please refer to the UAB IT page for instructions on [http://main.uab.edu/Sites/it/faqs/49118/ creating a strong password]. You need to remember this passphrase because you will be prompted for it whenever you use this key-pair.
# Press the "Save private key" button. The save button, will by default save the private key to your "My Documents" folder.  This is fine, and you can give any file name you like.  Just remember the name and where you saved it, so you can load it in the next steps. 
# Keep your PuTTY Key Generator window open so we can use below when we register you public key with the SSH server.
#'''Remember your passphrase.'''
 
===== Create a Session Definition =====
 
The PuTTY tools that Matlab Parallel Toolbox leverages are configured by creating "Saved Sessions" PuTTY.
 
To create a PuTTY session for cheaha.uabgrid.uab.edu, follow these steps.
 
Start PuTTY by either:
* Clicking Start -> All Programs -> PuTTY --> PuTTY
* Opening Windows Explorer / My Computer, browse to the PuTTY directory and double click 'putty'
 
# This brings up the following dialog that has a collection of configuration categories in the "Category:" window on the left, and a context sensitive set of actions on the right.  That is, if you change the category on the left you will change what you see on the right. The default category that you see is the Session, which is the main focus of our work here. <br>[[Image:putty-session-dialog.png|400px]]
# In the default "Session" category, fill in the "Host Name (or IP address)" text box with "cheaha.uabgrid.uab.edu", and fill in the "Saved Sessions" text box with "cheaha.uabgrid.uab.edu".  Press the "Save" button <br>[[Image:putty-session-dialog-filled-cheaha.png|400px]]
# Select the "Data" sub-category under the "Connection" category from the left-side Category browser.  Fill in the "Auto-login username" text box with the username for your account on cheaha.
# Select the "Session" category, and press "Save" again.  You now have a saved session ready for use.
# Press the "Open" button at the bottom on the dialog. This will bring up a login window with a login prompt for your password.  Provide your cheaha password to login.  Keep this session open, as you will use it in the next section.
 
===== Register Your Public Key =====
 
In order to use your public-private key-pair to start an SSH session, you need to register you public key with cheaha by adding your public key to the list of authorized keys for that SSH server.
 
# Use the SSH connection established in the previous step
# In the PuTTYgen window text area labeled "Public key for pasting into OpeSSH authorized_keys file:", select the public key by right clicking the key and clicking "Select All". Copy the key by right clicking again and selecting "Copy"
# In the SSH session window, enter the command <pre>vi $HOME/.ssh/authorized_keys</pre>
# Press the '''SHIFT''' and '''o''' keys (in other words, a capital letter O), and the press your '''right''' mouse button over this window. This will paste your public key onto a new line.  Press the '''Escape''' (Esc) key, press the key sequence colon-w-q-enter (:wq Enter)
# Fix the file permissions using the command <pre>chmod u=rw $HOME/.ssh/authorized_keys</pre>
# End the session. Type the command <pre>exit</pre>
 
You can close the PuTTY Configuration and PuTTY Key Generator windows now if you haven't already done so.
 
===== Load Your Private Key =====
 
Loading your private key is the first step you will take prior to using Matlab to submit jobs to cheaha.  This step essentially activates your key so that all PuTTY-based tools can use it in their operations.
 
Start PuTTYagent by either:
* Clicking Start -> All Programs -> PuTTY --> PuTTYagent
* Opening Windows Explorer / My Computer, browse to the PuTTY directory and double click 'pagent'
 
This will place the "Pageant" icon (a computer wearing a tilted hat: [[Image:pageant-icon.png]]) in you shortcuts toolbar in the lower-right of our screen.
# Click on the icon to bring up the Pageant Key List dialog <br> [[Image:pageant-dialog.png|300px]]
# Press the "Add Key" button.  From the file dialog, select the private key created above (in My Documents by default)
# Press "Open" on the file dialog, you will be prompted for the passphrase to load your private key. Enter in the passphrase and click OK
 
The private key should now be loaded and ready for use with all PuTTY-based tools. Click the close button to minimize PuTTYagent.
 
Warning: While Pagent is running and has your private key loaded, anyone else using your computer can access your account on Cheaha. Please LOCK your workstation when unattended!
 
You are now ready to begin using the Matlab Parallel Toolbox.
 
=== Linux ===
If you don't already have an RSA key-pair generated for your user account on your workstation, do so by running the following command (choose a good passphrase)
<pre>$ ssh-keygen -t rsa
 
Enter file in which to save the key (~/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again: </pre>
Copy the public key to cheaha (change USERID to your cheaha login id). You will be prompted for your cheaha password.
<pre>
$ ssh-copy-id -i $HOME/.ssh/id_rsa.pub USERID@cheaha.uabgrid.uab.edu
</pre>
Run ssh-agent to load the key on your Linux workstation
<pre>
$ ssh-agent
Enter passphrase for ~/.ssh/id_rsa:
Identity added: ~/.ssh/id_rsa (~/.ssh/id_rsa)
</pre>
Now test that you can connect to cheaha without entering a password (again change USERID to your login name)
<pre>
$ ssh USERID@cheaha.uabgrid.uab.edu uptime
 
15:34:10 up 9 days,  5:11, 14 users,  load average: 0.25, 0.34, 0.50
</pre>
 
=== Mac ===
This section will be updated shortly. In the mean time, the steps in the Linux section should be very close, if not the same.
 
== Matlab from Your Desktop ==
Once SSH has been successfully configured, you are ready to continue setting up the Matlab client.
 
Matlab Parallel Toolbox enables you to submit your Matlab code to the cluster without leaving the graphical interface.
 
This section discusses the following steps:
# Download and extract the Matlab submission functions
# Start the Matlab client
# Add the cheaha parallel computing toolbox configuration
# Perform the validation tests
 
=== Matlab Submit Functions ===
In order for Parallel Toolbox to work with our cluster, you will have to copy the special submit functions to your Matlab PATH.
 
Download the appropriate zipped file and extract it to a directory in your Matlab PATH (note that both Linux and Mac use the 'unix' submit functions)
* [http://projects.uabgrid.uab.edu/matlab/browser/trunk/distributables/matlab-windows-nonshared.zip Windows Matlab Submit Functions] - '''Updated 04/28/2010'''
* [http://projects.uabgrid.uab.edu/matlab/browser/trunk/distributables/matlab-unix-nonshared.zip Linux Matlab Submit Functions] - '''Updated 04/28/2010'''
* [http://projects.uabgrid.uab.edu/matlab/browser/trunk/distributables/matlab-unix-nonshared.zip Mac Matlab Submit Functions] - '''Updated 04/28/2010'''
 
Typical Matlab PATH locations:
* Windows:    My Documents\MATLAB
* Linux:      $HOME/Documents/MATLAB
* Mac:        ???
* All Systems: $MATLABROOT/toolbox/local
 
Once the files have been unzipped / extracted to your Matlab PATH, you can start the Matlab client.
 
=== Parallel Computing Toolbox Configuration ===
In this section we will add the cheaha configuration to the Parallel Computing Toolbox followed by a quick validation test.
 
Prior to continuing, make sure that you've completed the following:
* Configured SSH and successfully tested passwordless authentication to Cheaha
* Loaded your SSH key
** Windows users - means starting PuTTY Pagent and loading your SSH key
** Linux users - means running ssh-agent to load the SSH key
** Mac users - ???
* Downloaded and extracted the latest Matlab submission scripts to your Matlab PATH
 
Start the Matlab client on your workstation (Windows users should have a Matlab icon on the desktop), Linux and Mac may have to use the command line.
 
# Click the Parallel menu
# Click Manage Configurations
# Click File -> New -> Generic
 
You should now have a window titled "Generic Scheduler Configuration Properties"


Make the following changes (please adjust DataLocation to an appropriate directory and substitute R2010a with R2009b or 2009a to match your client version):
The following outline highlights the steps involved to configure your MatLab install and write programs that submit tasks to the worker nodes of the Distributed Computing Server on Cheaha:
* Configuration name: '''cheaha'''
* Description: '''cheaha.uabgrid.uab.edu'''
* Scheduler Tab
** Root directory of MATLAB installation for workers (ClusterMatlabRoot): '''/share/apps/mathworks/R2010a'''
** Number of workers available to scheduler (ClusterSize): '''8'''
** Directory where job data is stored (DataLocation): '''C:\jobs\matlab'''
** Function called when submitting parallel jobs (ParallelSubmitFcn): '''{@sgeNonSharedParallelSubmitFcn, 'cheaha.uabgrid.uab.edu', '$UABGRID_SCRATCH/jobs/matlab/ptbx'}'''
** Function called when submitting distributed jobs (SubmitFcn): '''{@sgeNonSharedSimpleSubmitFcn, 'cheaha.uabgrid.uab.edu', '$UABGRID_SCRATCH/jobs/matlab/ptbx'}'''
** Function called when canceling a job (CancelJobFcn):
** Function called when canceling a task (CancelTaskFcn):
** Cluster nodes' OS (ClusterOSType): '''unix'''
** Function called when destroying a job (DestroyJobFcn): '''@sgeDestroyJob'''
** Function called when destroying a task (DestroyTaskFcn):
** Function called when getting the job state (GetJobStateFcn): '''@sgeGetJobState'''
** Job data location is accessible from both client and cluster nodes (HasSharedFilesystem): '''False'''
* Jobs Tab: Do not change
* Tasks Tab: Do not change


The configuration should look similar to this screen shot
* Configure the Task Submit Environment (One-time Setup)
[[Image:cheaha-parallel-config.jpg]]
** [[MatLab|Install MatLab]] with the Parallel Computing Toolbox on your Windows / Linux / Mac workstation
** Download and extract the MatLab task submission functions to your workstation MatLab environment
** Define the "cheaha" parallel configuration in your workstation MatLab environment to submit tasks to Cheaha
** Run the validation tests to ensure your "cheaha" parallel configuration works
* Develop and Run Parallel Computing Applications
** Write, test and debug your parallel code on your local workstation using the default "local" parallel configuration
** Once your code works, select the "cheaha" parallel configuration to submit tasks to the Cheaha cluster. Note: your workstation MatLab application does not need to keep running after the tasks are submitted.
** You will receive an email when the tasks you submitted are complete
** Use your workstation MatLab application to retrieve the results
** When you are finished with your job contexts, clean up the job related content to free disk space


== Matlab from the Command Line ==
== Using MATLAB DCS ==


=== Matlab Versions ===
The MATLAB Distributed Computing Services (DCS) are accessed via the Parallel Computing Toolbox (PCT) which is installed as part of your desktop [[MATLAB|MATLAB installation]]. The PCT allows MATLAB running on your workstation to send MATLAB code and data (tasks) to the cluster directly from the comfort of your familiar MATLAB environment on your desktop. This makes the expanded compute power of [[Cheaha]] available to processes work loads that exceed the capabilities of your desktop computer.  Once your tasks are submitted to [[Cheaha]], your desktop MATLAB is also free to move on to other tasks or be closed completely, freeing your desktop or laptop for your other activities.
Use the 'module' command to view a list of available Matlab versions. If the version that you require isn't listed, please open a help desk ticket to request the installation.


The following is an example output of the command and doesn't necessarily represent the currently installed versions:
Configuring the Parallel Computing Toolbox involves three steps documented below:
<pre>
# install MATLAB submit functions on your workstation
$ module avail mathworks
# configure the "cheaha" parallel computing target to which PCT tasks can be submitted
# run the validation tests to confirm a working installation.


------------------------------------ /etc/modulefiles -------------------------------------
This page documents the DCS configuration for MATLAB 2010b and later.  For DCS configuration instructions on previous versions of MATLAB, please see the page [[MatLab DCS R2010a and Earlier]]
mathworks/R2009b
mathworks/R2009a


</pre>
Using MATLAB DCS requires you have a cluster account on [[Cheaha]].  Please request an account by sending an email to [[mailto:support@listserv.uab.edu]] and include your campus affiliation and a brief statement of your research interests for using the cluster.
=== Simple Matlab Test ===
A simple test to verify that the Matlab client on Cheaha can check out a license from your server.


Set up your environment with the command:
=== MATLAB DCS from Your Desktop ===
<pre>
$ module load mathworks/R2010a
</pre>
As a test, you can run MatLab and access your license server with
<pre>
$ matlab -c port@license-server -nodesktop -nojvm -r 'rand, pause(0), exit'
</pre>
For example:
<pre>
$ module load mathworks/R2010a
$ matlab -c 27000@licserver -nodesktop -nojvm -r 'rand, pause(0), exit'


                                    < M A T L A B (R) >
==== MATLAB Submit Functions ====
                          Copyright 1984-2010 The MathWorks, Inc.
                        Version 7.10.0.499 (R2010a) 64-bit (glnxa64)
                                      February 5, 2010


The MATLAB submit functions create a cluster job context for your code and are responsible for transferring your code and the data it analyzes to the cluster for processing.
  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.
>>
ans =


    0.8147
These submit functions must be installed on your computer and must be accessible to MATLAB via the MATLAB PATH environment.  The easiest way to accomplish this is to copy the submit functions to the default directory created for by MATLAB.  These directories on the respective operating systems are listed below.


</pre>
All operating systems (Windows, Linux and Mac) are supported by the same set of submit functions. The functions are written in MATLAB making them cross-platform and only dependent on the version of MATLAB in use.
This will start matlab without a graphical display and without Java support.  This is good just to
verify things work, but do not run any significant computations on the Cheaha head node!


MatLab computational work must be run on the compute nodes by submitting a job submission script to the SGE scheduler
# Download the MATLAB submit functions
#* [http://projects.uabgrid.uab.edu/matlab/browser/trunk/distributables/matlab-R2013a-nonshared.zip?format=raw Submit Functions for MATLAB R2013a] -(updated 09/04/2013)
#* [http://projects.uabgrid.uab.edu/matlab/browser/trunk/distributables/matlab-R2012a-nonshared.zip?format=raw Submit Functions for MATLAB R2012a] -(updated 03/07/2012)
#* [http://projects.uabgrid.uab.edu/matlab/browser/trunk/distributables/matlab-R2011b-nonshared.zip?format=raw Submit Functions for MATLAB R2010b, R2011a, R2011b] -(updated 02/21/2011)
# Unzip the files to a directory included in your MATLAB PATH setting. Recommended locations are:
#* Windows:  <pre>My Documents\MATLAB</pre>
#* Linux:    <pre>$HOME/Documents/MATLAB</pre>
#* Mac:      <pre>$HOME/Documents/MATLAB</pre>


=== Serial Matlab ===
Once the submit function files have been downloaded and unzipped in the above paths, restart MATLAB to ensure they are properly loaded in your environment.
Serial Matlab jobs have the following characteristics:
* Consumes one of your client licenses for the duration of the job
* Does not use the distributed licenses available on cheaha
* Does not require the parallel computing toolbox
* Restricted to a single CPU core (slot)


See the next section for an example using the distributed computing license.
NOTE: If you choose not to use the above path recommendations, your MATLAB PATH may be viewed/altered by starting the MATLAB client on your workstation and clicking File -> Set Path and adding the path in which you unpacked the submit functions.


Create a job script "matlabtest.qsub" making sure to change:
==== Parallel Computing Toolbox Configuration ====
* YOUR_EMAIL_ADDRESS
* h_rt and s_rt to appropriate hard and soft runtime limits
* h_vmem to the maximum amount of memory that your job will use
<pre>
$ mkdir -p $UABGRID_SCRATCH/jobs/matlab/serial01/output
$ cd $UABGRID_SCRATCH/jobs/matlab/serial01
</pre>
<pre>
#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#
#$ -N serialMatlab
#$ -l h_rt=00:10:00,s_rt=00:08:00,h_vmem=2G
#$ -j y
#
#$ -M YOUR_EMAIL_ADDRESS
#$ -m eas
#
module load mathworks/R2010a
#$ -V
matlab -c port@license-server -nodisplay -nojvm < matlab-script
</pre>
Then submit the script to the scheduler with
<pre>
$ cd $UABGRID_SCRATCH/jobs/matlab/serial01
$ qsub matlabtest.qsub
</pre>


Check on it with qstat.
The Parallel Computing Toolbox (PCT) enables language extensions in MATLAB that support dividing your application into tasks that can be executed in parallel.  By default, all of these tasks will run on your local workstation using the pre-defined "local" PCT configuration.
<pre>
$ qstat -u $USER
</pre>


=== Distributed Matlab ===
To run these tasks on the Cheaha compute cluster, a new configuration for the PCT must be defined.  In this section we will create the "cheaha" configuration and run a quick validation test to confirm its operation.
These instructions provide an example of how to create and submit a distributed Matlab job on cheaha.


Distributed Matlab jobs use the following licenses:
'''Prior to continuing''', make sure you:
* Your own Matlab client license with the Parallel Computing Toolbox
* can establish an SSH connection to Cheaha
* The Cheaha Distributed Computing license
* have followed the steps in the previous section


The client license will only be needed for as long as it takes Matlab to start the job on the compute nodes (unless you keep the client open, for example using "waitForState(job)" in your Matlab script).
===== Create the "cheaha" PCT Configuration =====
Download and save the Cheaha cluster configuration file for your MATLAB version
# [http://projects.uabgrid.uab.edu/matlab/browser/trunk/parallel-configs/cheaha-R2011b.mat?format=raw R2010b, R2011a, R2011b] cluster configuration file
#* Start MATLAB on your workstation
#* Click the "Parallel" menu
#* Click "Manage Configurations"
#* In the "Configurations Manager" window, click "File -> Import"
#* Browse to the location where you saved the '''cheaha-R2011b.mat''' file, select it, and click "Open"
# [http://projects.uabgrid.uab.edu/matlab/browser/trunk/parallel-configs/cheaha-R2012a.settings?format=raw R2012a] cluster configuration file
#* Start MATLAB R2012a on your workstation
#* Click the "Parallel" menu
#* Click "Manage Cluster Profiles"
#* In the "Cluster Profile Manager" window, click the "Import" button on the toolbar
#* Browse to the location where you saved the '''cheaha-R2012a.settings''' file, select it, and click "Open"


The instructions are a work in progress, so please contact Research Computing support with any questions or corrections.
The Configuration Manager for R2011b and prior should now list a new entry named "cheaha" as shown in the following image, R2012a and later will also have a new entry in the Cluster Profile list:
[[Image:2011_config_mngr.png|none|x400px]]


First, create the working directory for the job
===== Personalize the "cheaha" PCT Configuration -2011b and earlier =====
<pre>
$ mkdir -p $UABGRID_SCRATCH/jobs/matlab/distrib01/output
$ cd $UABGRID_SCRATCH/jobs/matlab/distrib01


</pre>
#Double click on cheaha in the Configuration Manager window to open the configuration editor. (Note: stretch the "Generic Scheduler Configuration Properties" window to the right so that you can view all of the text in the fields making it easier to read and edit correctly.)
# Edit the following fields to use your personal data directories
#* '''ClusterMatlabRoot''': Make sure that the Root directory of MATLAB installation for workers matches the exact version of MATLAB you are using on your workstation. In this example '''/share/apps/mathworks/R2011a''' matches a MATLAB R2011a workstation install.  Change the "R2011a" to match your workstation MATLAB version.
#* '''DataLocation'''    : Change the directory path where job data is stored to an existing directory on your workstation where MATLAB can stage job files.
#* '''ParallelSubmitFcn''': Change the text "YOURUSERID" to your login id on Cheaha
#* '''SubmitFcn'''        : Change the text "YOURUSERID" to your login id on Cheaha
# Click 'OK'to save the configuration
# SSH to cheaha and make sure to create the $USER_SCRATCH/matlab directory. If this directory does not exist, the parallel computing toolbox jobs will fail.


Next, create a simple 2 task distributed Matlab script called "sharedDistrib01.m" make sure to change:
The initial configuration will look similar to this screen shot.  You will need to edit the fields as describe in the preceding steps before you can use the configuration. '''NOTE: be sure to replace the template user name settings "YOURUSERNAME" with the appropriate settings for your desktop and cluster account.'''
  * email to your email address
  * s_rt to an appropriate soft wall time limit
* h_rt to the maximum wall time for your job
* mem_free to the maximum memory needed for each task
* outputDirectory to the directory where results should be stored


Don't make any changes to the section labeled "Configure the scheduler"
[[Image:Cheaha_parallel_config.png|none|x650px]]
<pre>
% Always set these variables
matlab_ver      = 'R2010a';    % (Matlab release supported by your license) R2009a R2009b R2010a
email          = 'YOUREMAIL'; % your email address
email_opt      = 'eas';      % qsub email options
s_rt            = '00:05:00';  % soft wall time
h_rt            = '00:07:00';  % hard wall time
mem_free        = '1G';        % Amount of memory need per task
scratch        = getenv('UABGRID_SCRATCH');
outputDirectory  = [scratch, '/jobs/matlab/distrib01/output'];


% Configure the scheduler
===== Personalize the "cheaha" PCT Configuration -2012a  =====
sched = findResource('scheduler', 'type', 'generic');
set(sched, 'DataLocation'      , outputDirectory);
set(sched, 'ClusterMatlabRoot', ['/share/apps/mathworks/', matlab_ver]);
set(sched, 'HasSharedFilesystem',  true);
set(sched, 'ClusterOsType'      , 'unix');
set(sched, 'SubmitFcn', {@sgeSubmitFcn});
set(sched, 'DestroyJobFcn', {@sgeDestroyJob});
set(sched, 'GetJobStateFcn', {@sgeGetJobState});
sge_options = ['-pe matlab 1 -l matlab_dcs=1,mem_free=', mem_free, ',h_rt=', h_rt, ',s_rt=', s_rt, ' -m ', email_opt, ' -M ', email];
get(sched)
job = createJob(sched);


% start of user specific commands
#Double click on cheaha in the Configuration Manager window to open the configuration editor. (Note: stretch the "Generic Scheduler Configuration Properties" window to the right so that you can view all of the text in the fields making it easier to read and edit correctly.)
createTask(job, @rand, 1, {3,3});
# Edit the following fields to use your personal data directories
createTask(job, @rand, 1, {3,3});
#* '''ClusterMatlabRoot''': Make sure that the Root directory of MATLAB installation for workers matches the exact version of MATLAB you are using on your workstation. In this example '''/share/apps/mathworks/R2012a''' matches a MATLAB R2012a workstation install.  Change the "R2012a" to match your workstation MATLAB version.
#* '''DataLocation'''    : Change the directory path where job data is stored to an existing directory on your workstation where MATLAB can stage job files.
#* '''independentSubmitFcn''': Change the text "YOURUSERID" to your login id on Cheaha
#* '''communicatingSubmitFcn'''        : Change the text "YOURUSERID" to your login id on Cheaha
# Click 'OK'to save the configuration
# SSH to cheaha and make sure to create the $USER_SCRATCH/matlab directory. If this directory does not exist, the parallel computing toolbox jobs will fail.


submit(job)
The initial configuration will look similar to this screen shot.  You will need to edit the fields as describe in the preceding steps before you can use the configuration.  '''NOTE: be sure to replace the template user name settings "YOURUSERNAME" and "YOURUSERID" with the appropriate settings for your desktop and cluster account.'''
</pre>


Running the Matlab script will submit 2 SGE single slot (CPU) jobs, one for each task. The Parallel Computing Toolbox requires Java VM, so notice that for this job we do not include the "-nojvm" switch!
[[Image:MATLAB_R2012a_configuration.png|none|x650px]]
<pre>
$ module load mathworks/R2010a
$ matlab -c port@license-server -nodisplay < sharedDistrib01.m
</pre>


Check qstat to see that the scheduler now has 2 jobs running, one for each task
===== Validate the "cheaha" PCT Configuration =====
<pre>
$ qstat -u $USER


job-ID  prior  name      user        state submit/start at    queue                          slots ja-task-ID
# Before starting validation please make sure the directory 'lustre/scratch/YOURUSERID/matlab' (please convert all settings to point to the new preferred location) or ''''/scratch/user/YOURUSERID/matlab'''' (preferred)  exists on the  scratch space on the Cheaha. If it does not please SSH into Cheaha and create the directory before proceeding.
-----------------------------------------------------------------------------------------------------------------
# Select Cheaha on the configuration manager page and click 'Start Validation'
110839 0.50167 Job1.1    jdoe        r    03/10/2010 16:32:37 all.q@compute-0-12.local          1
# Wait for the validation to complete. This might take a few minutes and you ask for User credentials on Cheaha. All tests other than 'Matlabpool' validate on the Cheaha and the output is as shown.
110840 0.50083 Job1.2    jdoe        r    03/10/2010 16:32:37 all.q@compute-0-12.local          1
</pre>


The job output can be found in the "output" directory
[[Image:Validation.png|none|x400px]]


=== Parallel Matlab ===
===== Begin Using MATLAB DCS from your Desktop =====
These instructions provide an example of how to create and submit a parallel Matlab job on cheaha. Parallel Matlab jobs require two separate licenses:
* Your own client license that includes the Parallel Computing Toolbox
* The Cheaha 128 node Distributed Computing license


The client license will only be needed for as long as it takes Matlab to start the job on the compute nodes (unless you keep the client open, for example using "waitForState(job)" in your Matlab script).
The MATLAB DCS is now configured for Desktop usage. A simple parallel wave job "rParforWave" to test the configuration is described in [[MatLab_DCS_Examples]].


Check out this [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/brjw1e5-1.html Matlab Help Page] for a quick overview of using parallel code in your Matlab scripts.
A summary of the above steps is available at [[MATLAB_workshop_2011]] with additional examples and submit scripts available in the [[MATLAB_workshop_2011#Workshop_Demo.27s | workshop demo ]] section.


First, create the working directory for the job
=== MATLAB DCS from Cheaha ===
<pre>
$ mkdir -p $UABGRID_SCRATCH/jobs/matlab/paralle01/output
$ cd $UABGRID_SCRATCH/jobs/matlab/parallel01


</pre>
MATLAB can be started interactively from [[Cheaha]] via an SSH session using the [[MatLab CLI|command line]], X windows forwarding, or VNC.  This is very similar to using MATLAB from your desktop: in order to leverage the compute power of the cluster the Parallel Computing Toolbox must be configured to send tasks to the cluster scheduler.


Next, create a simple 4 slot parallel Matlab script called "parjob.m" make sure to change:
If you do not follow these configuration steps, parallel tasks will be executed locally on the cluster log in node (head node).  This will negatively impact your own and others interactive use of this log in node and may lead to your computations being stopped administratively.
  * email to your email address
* s_rt to an appropriate soft wall time limit
* h_rt to the maximum wall time for your job
* mem_free to the maximum memory needed for each task
* outputDirectory to the directory where results should be stored


Don't make any changes to the section labeled "Configure the scheduler"
==== MATLAB Submit Functions ====
<pre>
% Always set these variables
email          = 'YOUR_EMAIL_ADDRESS';
s_rt            = '00:05:00';
h_rt            = '00:07:00';
mem_free        = '2G';
clusterHost    = 'cheaha.uabgrid.uab.edu';
scratch        = getenv('UABGRID_SCRATCH');
outputDirectory = [scratch, '/jobs/matlab/parallel01/output'];


% Configure the scheduler
The MATLAB submit functions create a cluster job context for your code. When running MATLAB from Cheaha, the submit functions are already installed and no additional actions are required by the user for this step.
sched = findResource('scheduler', 'type', 'generic');
set(sched, 'DataLocation'      , outputDirectory);
set(sched, 'ClusterMatlabRoot', '/share/apps/mathworks/R2009b');
set(sched, 'HasSharedFilesystem', true              );
set(sched, 'ClusterOsType'      , 'unix'            );
set(sched, 'ParallelSubmitFcn', {@sgeParallelSubmitFcn, h_rt, s_rt, mem_free, email});
set(sched, 'DestroyJobFcn', {@sgeDestroyJob});
set(sched, 'GetJobStateFcn', {@sgeGetJobState});
get(sched)
pjob = createParallelJob(sched);


% start of user specific commands
==== Parallel Computing Toolbox Configuration ====
createTask(pjob, 'rand', 1, {4});
set(pjob, 'MinimumNumberOfWorkers', 4);
set(pjob, 'MaximumNumberOfWorkers', 4);


submit(pjob)
The Parallel Computing Toolbox (PCT) for your copy of MATLAB running in your cluster account must be configured to submit tasks to the compute nodes of the cluster.  Keep in mind that running MATLAB interactively on the cluster is the same as running it from your own desktop: MATLAB runs all tasks on the machine on which it is running unless it is told to send the work to another computer.  This condition holds even "inside" the Cheaha cluster: the cluster compute nodes are physically separate computers and MATLAB must request access via the scheduler just like any other job running on the cluster.
</pre>


Running the Matlab script will submit 1 SGE job requesting 4 slots (cpu cores). The Parallel Computing Toolbox requires Java VM, so notice that for this job we do not include the "-nojvm" switch!
Configuring the PCT when running MATLAB interactively from Cheaha is just like the configuration when running MATLAB from your desktop with two exceptions:
<pre>
* you must transfer any code or data to your Cheaha account explicitly outside of MATLAB using standard cluster procedures, aka SSH.
$ module load mathworks/R2009b
* when MATLAB submits your tasks to the compute nodes, it benefits from the shared storage on the cluster and does not need to further copy your code and data to the compute nodes
$ matlab -c port@license-server -nodisplay < parjob.m
</pre>


Check qstat to see that the scheduler now has 2 jobs running, one for each task
To address these differences, follow the [[#Parallel Computing Toolbox Configuration|PCT instructions above]] and when [[#Personalize the "cheaha" PCT Configuration|editing the "cheaha" configuration]] modify the steps for the following fields:
<pre>
# '''Folder where job data is stored (DataLocation)''': specify a directory in your personal Cheaha account
$ qstat -u $USER
# '''Function called when submitting parallel jobs (ParallelSubmitFnc)''': change the value to "{@ParallelSubmitFnc}"
# '''Function called when submitting distributed jobs (DistributedSubmitFnc)''': change the value to "{@DistributedSubmitFnc}"
# '''Job data location is accessible from both client and cluster nodes''': change this value to "True"


job-ID prior  name   user        state submit/start at    queue                          slots ja-task-ID
Now save the "cheaha" configuring by clicking OK and proceeding to the [[#Validate the "cheaha" PCT Configuration|validation tests described above]]. Note: when running MATLAB interactively on Cheaha MatlabPool works and the validation tests are expected to pass (you'll see a green checkmark).
-----------------------------------------------------------------------------------------------------------------
110857 0.00000 Job1   jdoe        r    03/10/2010 17:20:08                                    4


</pre>
== References ==
* [http://www.mathworks.com/help/toolbox/distcomp/ Parallel Computing Toolbox on-line documentation]
* [http://www.mathworks.com/access/helpdesk/help/pdf_doc/distcomp/distcomp.pdf Parallel Computing Toolbox User's Guide (pdf)] - The 655 page MATLAB User Guide for the Parallel Computing Toolbox and is recommended reading!


The job output can be found in the "output" directory
{{MATLAB Support}}


=== ParFor Parallel Example ===
[[Category:MATLAB]][[Category:MATLAB installation]]
This example will utilize the parfor parallel loop as [http://www.mathworks.com/products/parallel-computing/parallel/accelerate.html defined here].

Latest revision as of 19:41, 11 February 2019

Ambox important.png

This page is Deprecated
To Use MATLAB with the SLURM scheduler on Cheaha please click the link below

MATLAB with SLURM


The MATLAB Distributed Computing Server (MATLAB DCS) is a parallel computing extension to MATLAB that enables processing to be spread across a large number of worker nodes, accelerating the speed at which compute intensive operations can complete.

UAB IT Research Computing maintains a 128 worker node license for the the Cheaha computing platform. In order to use DCS on Cheaha, you will need to use a MATLAB instance with the Parallel Computing Toolbox installed.

In order to leverage the MATLAB worker nodes on Cheaha the Parallel Computing Toolbox will need to be configured to submit compute tasks to Cheaha by following the steps in this document.

Please see the MATLAB application page for more information and a general overview of MATLAB and its use at UAB.

Overview

The following outline highlights the steps involved to configure your MatLab install and write programs that submit tasks to the worker nodes of the Distributed Computing Server on Cheaha:

  • Configure the Task Submit Environment (One-time Setup)
    • Install MatLab with the Parallel Computing Toolbox on your Windows / Linux / Mac workstation
    • Download and extract the MatLab task submission functions to your workstation MatLab environment
    • Define the "cheaha" parallel configuration in your workstation MatLab environment to submit tasks to Cheaha
    • Run the validation tests to ensure your "cheaha" parallel configuration works
  • Develop and Run Parallel Computing Applications
    • Write, test and debug your parallel code on your local workstation using the default "local" parallel configuration
    • Once your code works, select the "cheaha" parallel configuration to submit tasks to the Cheaha cluster. Note: your workstation MatLab application does not need to keep running after the tasks are submitted.
    • You will receive an email when the tasks you submitted are complete
    • Use your workstation MatLab application to retrieve the results
    • When you are finished with your job contexts, clean up the job related content to free disk space

Using MATLAB DCS

The MATLAB Distributed Computing Services (DCS) are accessed via the Parallel Computing Toolbox (PCT) which is installed as part of your desktop MATLAB installation. The PCT allows MATLAB running on your workstation to send MATLAB code and data (tasks) to the cluster directly from the comfort of your familiar MATLAB environment on your desktop. This makes the expanded compute power of Cheaha available to processes work loads that exceed the capabilities of your desktop computer. Once your tasks are submitted to Cheaha, your desktop MATLAB is also free to move on to other tasks or be closed completely, freeing your desktop or laptop for your other activities.

Configuring the Parallel Computing Toolbox involves three steps documented below:

  1. install MATLAB submit functions on your workstation
  2. configure the "cheaha" parallel computing target to which PCT tasks can be submitted
  3. run the validation tests to confirm a working installation.

This page documents the DCS configuration for MATLAB 2010b and later. For DCS configuration instructions on previous versions of MATLAB, please see the page MatLab DCS R2010a and Earlier

Using MATLAB DCS requires you have a cluster account on Cheaha. Please request an account by sending an email to [[1]] and include your campus affiliation and a brief statement of your research interests for using the cluster.

MATLAB DCS from Your Desktop

MATLAB Submit Functions

The MATLAB submit functions create a cluster job context for your code and are responsible for transferring your code and the data it analyzes to the cluster for processing.

These submit functions must be installed on your computer and must be accessible to MATLAB via the MATLAB PATH environment. The easiest way to accomplish this is to copy the submit functions to the default directory created for by MATLAB. These directories on the respective operating systems are listed below.

All operating systems (Windows, Linux and Mac) are supported by the same set of submit functions. The functions are written in MATLAB making them cross-platform and only dependent on the version of MATLAB in use.

  1. Download the MATLAB submit functions
  2. Unzip the files to a directory included in your MATLAB PATH setting. Recommended locations are:
    • Windows: 
      My Documents\MATLAB
    • Linux: 
      $HOME/Documents/MATLAB
    • Mac: 
      $HOME/Documents/MATLAB

Once the submit function files have been downloaded and unzipped in the above paths, restart MATLAB to ensure they are properly loaded in your environment.

NOTE: If you choose not to use the above path recommendations, your MATLAB PATH may be viewed/altered by starting the MATLAB client on your workstation and clicking File -> Set Path and adding the path in which you unpacked the submit functions.

Parallel Computing Toolbox Configuration

The Parallel Computing Toolbox (PCT) enables language extensions in MATLAB that support dividing your application into tasks that can be executed in parallel. By default, all of these tasks will run on your local workstation using the pre-defined "local" PCT configuration.

To run these tasks on the Cheaha compute cluster, a new configuration for the PCT must be defined. In this section we will create the "cheaha" configuration and run a quick validation test to confirm its operation.

Prior to continuing, make sure you:

  • can establish an SSH connection to Cheaha
  • have followed the steps in the previous section
Create the "cheaha" PCT Configuration

Download and save the Cheaha cluster configuration file for your MATLAB version

  1. R2010b, R2011a, R2011b cluster configuration file
    • Start MATLAB on your workstation
    • Click the "Parallel" menu
    • Click "Manage Configurations"
    • In the "Configurations Manager" window, click "File -> Import"
    • Browse to the location where you saved the cheaha-R2011b.mat file, select it, and click "Open"
  2. R2012a cluster configuration file
    • Start MATLAB R2012a on your workstation
    • Click the "Parallel" menu
    • Click "Manage Cluster Profiles"
    • In the "Cluster Profile Manager" window, click the "Import" button on the toolbar
    • Browse to the location where you saved the cheaha-R2012a.settings file, select it, and click "Open"

The Configuration Manager for R2011b and prior should now list a new entry named "cheaha" as shown in the following image, R2012a and later will also have a new entry in the Cluster Profile list:

2011 config mngr.png
Personalize the "cheaha" PCT Configuration -2011b and earlier
  1. Double click on cheaha in the Configuration Manager window to open the configuration editor. (Note: stretch the "Generic Scheduler Configuration Properties" window to the right so that you can view all of the text in the fields making it easier to read and edit correctly.)
  2. Edit the following fields to use your personal data directories
    • ClusterMatlabRoot: Make sure that the Root directory of MATLAB installation for workers matches the exact version of MATLAB you are using on your workstation. In this example /share/apps/mathworks/R2011a matches a MATLAB R2011a workstation install. Change the "R2011a" to match your workstation MATLAB version.
    • DataLocation  : Change the directory path where job data is stored to an existing directory on your workstation where MATLAB can stage job files.
    • ParallelSubmitFcn: Change the text "YOURUSERID" to your login id on Cheaha
    • SubmitFcn  : Change the text "YOURUSERID" to your login id on Cheaha
  3. Click 'OK'to save the configuration
  4. SSH to cheaha and make sure to create the $USER_SCRATCH/matlab directory. If this directory does not exist, the parallel computing toolbox jobs will fail.

The initial configuration will look similar to this screen shot. You will need to edit the fields as describe in the preceding steps before you can use the configuration. NOTE: be sure to replace the template user name settings "YOURUSERNAME" with the appropriate settings for your desktop and cluster account.

Cheaha parallel config.png
Personalize the "cheaha" PCT Configuration -2012a
  1. Double click on cheaha in the Configuration Manager window to open the configuration editor. (Note: stretch the "Generic Scheduler Configuration Properties" window to the right so that you can view all of the text in the fields making it easier to read and edit correctly.)
  2. Edit the following fields to use your personal data directories
    • ClusterMatlabRoot: Make sure that the Root directory of MATLAB installation for workers matches the exact version of MATLAB you are using on your workstation. In this example /share/apps/mathworks/R2012a matches a MATLAB R2012a workstation install. Change the "R2012a" to match your workstation MATLAB version.
    • DataLocation  : Change the directory path where job data is stored to an existing directory on your workstation where MATLAB can stage job files.
    • independentSubmitFcn: Change the text "YOURUSERID" to your login id on Cheaha
    • communicatingSubmitFcn  : Change the text "YOURUSERID" to your login id on Cheaha
  3. Click 'OK'to save the configuration
  4. SSH to cheaha and make sure to create the $USER_SCRATCH/matlab directory. If this directory does not exist, the parallel computing toolbox jobs will fail.

The initial configuration will look similar to this screen shot. You will need to edit the fields as describe in the preceding steps before you can use the configuration. NOTE: be sure to replace the template user name settings "YOURUSERNAME" and "YOURUSERID" with the appropriate settings for your desktop and cluster account.

MATLAB R2012a configuration.png
Validate the "cheaha" PCT Configuration
  1. Before starting validation please make sure the directory 'lustre/scratch/YOURUSERID/matlab' (please convert all settings to point to the new preferred location) or '/scratch/user/YOURUSERID/matlab' (preferred) exists on the scratch space on the Cheaha. If it does not please SSH into Cheaha and create the directory before proceeding.
  2. Select Cheaha on the configuration manager page and click 'Start Validation'
  3. Wait for the validation to complete. This might take a few minutes and you ask for User credentials on Cheaha. All tests other than 'Matlabpool' validate on the Cheaha and the output is as shown.
Validation.png
Begin Using MATLAB DCS from your Desktop

The MATLAB DCS is now configured for Desktop usage. A simple parallel wave job "rParforWave" to test the configuration is described in MatLab_DCS_Examples.

A summary of the above steps is available at MATLAB_workshop_2011 with additional examples and submit scripts available in the workshop demo section.

MATLAB DCS from Cheaha

MATLAB can be started interactively from Cheaha via an SSH session using the command line, X windows forwarding, or VNC. This is very similar to using MATLAB from your desktop: in order to leverage the compute power of the cluster the Parallel Computing Toolbox must be configured to send tasks to the cluster scheduler.

If you do not follow these configuration steps, parallel tasks will be executed locally on the cluster log in node (head node). This will negatively impact your own and others interactive use of this log in node and may lead to your computations being stopped administratively.

MATLAB Submit Functions

The MATLAB submit functions create a cluster job context for your code. When running MATLAB from Cheaha, the submit functions are already installed and no additional actions are required by the user for this step.

Parallel Computing Toolbox Configuration

The Parallel Computing Toolbox (PCT) for your copy of MATLAB running in your cluster account must be configured to submit tasks to the compute nodes of the cluster. Keep in mind that running MATLAB interactively on the cluster is the same as running it from your own desktop: MATLAB runs all tasks on the machine on which it is running unless it is told to send the work to another computer. This condition holds even "inside" the Cheaha cluster: the cluster compute nodes are physically separate computers and MATLAB must request access via the scheduler just like any other job running on the cluster.

Configuring the PCT when running MATLAB interactively from Cheaha is just like the configuration when running MATLAB from your desktop with two exceptions:

  • you must transfer any code or data to your Cheaha account explicitly outside of MATLAB using standard cluster procedures, aka SSH.
  • when MATLAB submits your tasks to the compute nodes, it benefits from the shared storage on the cluster and does not need to further copy your code and data to the compute nodes

To address these differences, follow the PCT instructions above and when editing the "cheaha" configuration modify the steps for the following fields:

  1. Folder where job data is stored (DataLocation): specify a directory in your personal Cheaha account
  2. Function called when submitting parallel jobs (ParallelSubmitFnc): change the value to "{@ParallelSubmitFnc}"
  3. Function called when submitting distributed jobs (DistributedSubmitFnc): change the value to "{@DistributedSubmitFnc}"
  4. Job data location is accessible from both client and cluster nodes: change this value to "True"

Now save the "cheaha" configuring by clicking OK and proceeding to the validation tests described above. Note: when running MATLAB interactively on Cheaha MatlabPool works and the validation tests are expected to pass (you'll see a green checkmark).

References

MATLAB Support / Mailing List

As with any application or computer language, learning to use MATLAB to analyze data or to develop or modify MATLAB applications is an individual responsibility. There is ample application documentation available from the Mathworks website, potential outreach to colleagues who also use MATLAB, and options for consultation with Mathworks. Mathworks also host on-campus training seminars several times a year and provides many on-line learning tutorials.

Installation support for MATLAB at UAB is provided by your local IT support organization and the Docs wiki.

Mathworks Website

Your first and best option for application-specific questions on MATLAB is to refer to the on-line MATLAB documentation. The Mathworks site also provides a a support matrix and an on-line knowledge base.

UAB MATLAB Wiki

The MATLAB page on the Docs wiki is the starting point for installing MATLAB at UAB and, optionally, configuring it to use cluster computing. All users are encouraged to contribute to the MATLAB knowledge in this wiki, especially if you see areas where improvements are needed. Remember, this knowledge base is only as good as the people who contribute to it.

Contributing to the wiki is as easy as clicking the login link on the top-right of the page and signing in with your UAB BlazerID. If you are unsure about making an edit, you can make suggestions for improvement on the page's Discussion tab or discuss the proposed improvement in the MATLAB user group.

UAB MATLAB User Group

At UAB, MATLAB installation support is provided by your local IT support group. Support for application specific questions is available from peers in your research group. We realize that some people are not as familiar with MATLAB as others. For this reason, we have established a MATLAB user forum (mailing list) where users of MATLAB at UAB can help answer each others questions.

This is a network of volunteers sharing their knowledge with peers. You are encouraged to reach out to this community for questions on using MATLAB by

Archives of MATLAB user group discussions are available on-line at https://vo.uabgrid.uab.edu/sympa/arc/matlab-user. You may find your question is already answered in these archives.


UAB MATLAB announce mailing list

To receive information about UAB's MATLAB license and announcements please subscribe to the matlab-annc mailing list by

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