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Document under development!

This document is still under development and is being written/edited by RCSG and MathWorks staff.

Table of Contents

Introduction

There are several ways in which to submit MATLAB jobs to a cluster.  This document will cover the various ways to run MATLAB compute jobs on the Shared Research Compute clusters, which will include using the Parallel Computing Toolbox (PCT) and the MATLAB Distributed Compute Server (MDCS) to submit many independent tasks as well as to submit a single task that has parallel components.   Examples are included.

Definitions

Task Parallel Application - The same application that runs independently on several nodes, possibly with different input parameters.  There is no communication, shared data, or synchronization points between the nodes.

Data Parallel Application - The same application that runs on several labs simultaneously, with communication, shared data, or synchronization points between the labs.

Lab - A MATLAB worker in a multicore (Data Parallel) job.  One lab is assigned to one worker (core).  Thus, a job with eight labs has eight processor cores allocated to it and will have eight workers each working together as peers.

MDCS - MATLAB Distributed Compute Server.  This is a component of MATLAB that allows our clusters to run MATLAB jobs that exceed the size of a single compute node (multinode parallel jobs).  It also allows jobs to run even if there are not enough toolbox licenses available for a particular toolbox, so long as the university owns at least one license for the particular toolbox. 

PCT - Parallel Computing Toolbox.

MATLAB Task - One segment of a job to be evaluated by a worker.

MATLAB Job - The complete large-scale operation to perform in MATLAB, composed of a set of tasks.

MATLAB Worker - The MATLAB session that performs the task computations.  If a job needs eight processor cores, then it must have eight workers.

Job - Job submitted via the PBS job scheduler (also called PBS Job).

Data Location

This document assumes that all of your input data files, output files, and MATLAB code files are stored on the cluster's filesystem, not on your desktop.  When you launch the MATLAB GUI and look at your home folder, you will be looking at your home folder on the cluster, not on your desktop.  If your data or code files are stored on your desktop, you will need to transfer them to the cluster first.

Toolbox Licenses

The version of MATLAB installed on our clusters shares a site license with the rest of the campus.  To see which Toolboxes our campus is licensed to use, launch MATLAB interactively on your desktop or on one of our clusters and run the ver command.

Number of Toolbox Licenses

The ver command will show you which Toolboxes we are licensed to use.  However, it will not show you the number of licenses (seats) for each toolbox.  In some cases there might be only a single seat for a given toolbox.  This means only one user can use the toolbox at any given time.

Running MATLAB with the GUI for Code Development

if you need to run MATLAB on one of the clusters to develop your code and run short (30 minutes or less) tests of the code, please follow these instructions.

1.  Login to the Cluster

Login to the cluster using our published instructions

Windows users will need to use Xming in order to run the MATLAB GUI on the cluster and have it displayed on their desktop. 

2.  Load the MATLAB Environment

Load the MATLAB module with the following command:

3.  Run MATLAB

To run MATLAB with our without the GUI as follows:

This will start MATLAB with and without the GUI, respectively.

At this point MATLAB will be running interactively on one of the login nodes, not one of the compute nodes. When you get the matlab prompt, start writing your code as your normally would. This method of running MATLAB is intended for code development and for executing short test runs of your code (30 minutes or less).

Do not run full length compute jobs on the login nodes

Do not run full length compute jobs on the login nodes.  Use one of the methods below for submitting a compute job to a job queue.

Submitting Interactive Jobs

If you need to run a MATLAB compute job interactively, please follow these instructions.

1.  Login to the Cluster

Login to the cluster using our published instructions

Windows users will need to use Xming in order to run the MATLAB GUI on the cluster and have it displayed on their desktop. 

2.  Load the MATLAB Environment

Load the MATLAB module with the following command:

3.  Submit an Interactive PBS Job

Submit an interactive PBS job as follows:

Change the ppn and walltime values to suit your job.

When this job starts executing you will receive a prompt on a compute node. The output will look something like the following:

You will notice that the command prompt has changed from a login node designation to a compute node designation.

Interactive Jobs Might Not Run Immediately

At present this type of job submission will compete with all other jobs on the system for run time. If no nodes are available then the job submission will pause and a command prompt on a compute node will not be presented until an idle node is available. This should not be a problem during periods when cluster utilization is low. When cluster utilization is high, this wait time could be lengthy.

Job Submission Must Satisfy Cluster Queue Policy

Job submissions of this type must satisfy the queue policy on each cluster or the job will not execute.  For example, STIC requires that jobs submitted to the default queue request two or more nodes while jobs on Sugar must be one node only.  Consult the documentation for each cluster for the queue policy.

4.  Launch MATLAB

After you have obtained a command line prompt on a compute node, launch MATLAB with or without the GUI. An example without the GUI is shown below.

From the prompt you can run any MATLAB command that you wish.

MATLAB will terminate when the walltime has been exceeded

Your MATLAB  session will be terminated when its run time (walltime) has been reached.

You must remain logged into the cluster for this job to execute

You will need to remain logged into the cluster for this interactive session to execute. If you terminate your login, MATLAB will also terminate. Therefore, using the interactive method is not a good choice for a job that is going to run for many hours.

To run MATLAB with the GUI, simply run the matlab command on the compute node without the -nodisplay option.  The GUI will perform more slowly than if you were running in on your desktop since the graphics are being transmitted from a compute node to your desktop.

Submitting Jobs with PBS qsub

The recommended method of submitting Task Parallel jobs is to use PCT as described below.  However, if you need to submit one or more single core jobs, and are not encountering problems with the lack of specific toolbox licenses, then you might wish to submit your jobs directly with PBS as described in the following steps.

Multicore Jobs Not Supported

Multicore (parallel) jobs are not supported using this submission method.  If you need to submit a parallel job then please use PCT .

1. Build a MATLAB .m code file

Include all of the MATLAB commands that you need to execute in a MATLAB .m file, such as sample.m and place it somewhere in your home directory or subdirectory. The creation and contents of a .m file are beyond the scope of this document. Consult the MATLAB documentation for information on .m files.

2. Create a PBS batch script

You will need to execute MATLAB from within a PBS batch script, such as sample.pbs as follows. In this example, this file is saved in the same directory as sample.m.

sample.pbs

In this example the sample.pbs script calls matlab with the -r option followed by the MATLAB script name that was created in step #1. Leave off the trailing .m from the script name when calling MATLAB  this way.

For more information about PBS job scripts, please see our FAQ.

Job Submission Must Satisfy Cluster Queue Policy

Job submissions of this type must satisfy the queue policy on each cluster or the job will not execute.  For example, STIC requires that jobs submitted to the default queue request two or more nodes while jobs on Sugar must be one node only.  Consult the documentation for each cluster for the queue policy.

3. Submit the Job

After you have created sample.m and sample.pbs, go to the directory where sample.pbs resides, load the MATLAB module (if you have not already done so) and submit the job to the job scheduler:

You should now be able to see your job in the queue by going to your Linux terminal window and using the showq command.

This type of job submission will compete with all other jobs on the system for run time. If no processors are available then the job submission will wait in the queue until it is able to run.

Possible License Errors

This type of job may fail due to license checkout errors. MATLAB shares a site license with the rest of the campus. If your job is using a toolkit for which there are no licenses available for checkout, the job will fail when it starts to run. You will need to use PCT to avoid this problem.

Submitting multiple MATLAB jobs via PBS

In order to submit multiple MATLAB batch jobs, simply repeat this section for each job.

Submitting Task Parallel and Data Parallel Jobs with PCT

The Parallel Computing Toolbox (PCT) provides an API that allows you to submit a job that has multiple independent tasks (Task Parallel) or submit a job that has a single task that is a multiprocessor, and possibly multinode, task (Data Parallel).  In order to run this type of job you must first configure MATLAB for this type of job submission by following these steps;

One-time Setup

These steps need to be performed only once.  Subsequent sessions of MATLAB do not need to be configured.

Configuring MATLAB

1.  Enable passwordless for your cluster account.

After you have logged into the cluster, follow these instructions to enable passwordless ssh.

2.   In your home directory create the MdcsDataLocation subdirectory.

3.  Load the MATLAB 2011a environment:

4.  Run MATLAB on the login node:

5.  In MATLAB, add the /opt/apps/matlab/2011a/local folder to your MATLAB path so that MATLAB will be able to find the scripts necessary to submit and schedule jobs.

  1. Click File > Set Path
  2. Click Add Folder
  3. Specify the following folder:
    /opt/apps/matlab/2011a/local

    Error saving pathdef.m

    If MATLAB reports that it is unable to save pathdef.m in your current folder, then follow the prompts to select your home folder before saving the file.

6.  Import the cluster configuration for the cluster you are running on:

  1. On the MATLAB Desktop menu bar, click Parallel > Manage Configurations.
  2. Click File > Import
  3. In the Import Configuration dialog box, browse to find the MAT-file for the configuration that you want to import.  Navigate to /opt/apps/matlab/2011a/local and select the configuration for the system you are using, such as sugar.mat, davinci.mat, stic.mat, and so forth.  Select the file and click Import.
  4. Select the configuration you have imported and click Start Validation.
    1. All four stages should pass except as specified below:  Find Resources, Distributed Job, Parallel Job, Matlabpool

      Validation failures

      Validation is expected to fail if any of the following conditions occur:
      1.  If the cluster is busy such that a job submission must wait before it will run then the validation steps will fail.
      2.  Distributed job validation on STIC will always fail due to the system queue policy.
      3.  Parallel job validation appear to take a long time because it will try with the maximum number of workers (currently 128).  A 128 core validation job takes a long time to execute but should not fail unless condition #1 above exists.
      4.  There are insufficient licenses available to run the validation job. 

    2. Select this configuration to be the default configuration.
    3. Close the Configuration Manager window.

If all validation stages succeed, then you are ready to submit jobs to MDCS.

Submitting Task Parallel Jobs

The following is an example of a Task Parallel job.  The task-parallel example code, frontDemo, calculates the risk and return based on historical data from a collection of stock prices. The core of the code, calcFrontier, minimizes the equations for a set of returns. In order to parallelize the code, the for loop is converted into a parfor loop with each iteration of the loop becoming its own independent task. 

To submit the job, copy submitParJobToCluster.m into your working directory, make the necessary modifications for your job environment, and then run the code from within MATLAB. This will submit the job.  An explanation of the code follows:

submitParJobToCluster.m

Code

When you run submitParJobToCluster within MATLAB, the frontDemo code will be submitted to the PBS job scheduler.  Use the showq command from a cluster terminal window to look for your job in the job queue.

Job Submission Best Practice

The above is only an example used to illustrate how to submit a job and retrieve the results from within the same MATLAB session.  In most cases using job.wait will not be desirable because of the length of time it might take for a job to start running (perhaps several hours).  The best practice is to have your MATLAB code write the results to a file, rather than waiting for it to finish and retrieving the results with job.getAllOutputArguments();  The job.wait function and all of the lines below it should not be used unless you intend to keep the MATLAB session open while the job runs.

Maximum and Minimum Number of Workers Per Submission

The maximum and minimum number of workers per job submission is constrained by the queue policy on each cluster, with one worker per processor core.  For example, Sugar will not accept a compute job of more than 8 cores.  Therefore, your MATLAB job must be 8 workers or less.  Further, the number of workers must be n-1 where n is the number of cores you want to use.  If you want to run a single node (8 core) job, you will want to set sz to be 7.   MATLAB will run on one core and the workers will run on the other 7 cores, for a total of 8 cores.   Therefore you can run 7 workers on a single 8 core node.  Further, the maximum number of workers is constrained by our MATLAB MDCS license.  Consult our documentation for a listing of these constraints.

Running Task Parallel Jobs on a Single Core

If you have one or more single core jobs to run then you would simply set the size parameter, sz, to be zero in the above example.  This simply allows the job to offload the work to a single MDCS worker and does not enable parallel capabilities.

Help with batch() command

For more information on the batch() command and all of its input arguments and how to use the diary, please see the MATLAB online help or the MathWorkshttp://www.mathworks.com/help/toolbox/distcomp/batch.html website.

About the CaptureDiary parameter

The above example has the CaptureDiary parameter set to true.   This will allow the job to capture or display the Command Window output of the batch job.  See the diary() function for more information.

Cleanup your job space after the job has finished

Be sure to destroy your job after the job has finished.

Submitting Data Parallel Jobs

The data-parallel example code calculates the area of pi under the curve. The non parallel version, calcPiSerial, calculates with a for loop, looping through discrete points. The parallel version, calcPiSpmd, uses the spmd construct to evaluate a part of the curve on each MATLAB instance. Each MATLAB instances uses its labindex (i.e. rank) to determine which portion of the curve to calculate. The calculations are then globally summed together and broadcasted back out. The code uses higher level routines, rather than lower level MPI calls. Once the summation has been calculated, it’s indexed into and communicated back to the local client MATLAB to calculate the total area.  

To submit the job, copy submitSpmdJobToCluster.m into your working directory, make the necessary modifications for your job environment, and then run the code from within MATLAB.  This will submit the job.   An explanation of the code follows:

submitSpmdJobToCluster.m

 
When you run submitSpmdJobToCluster within MATLAB, the calcPiSpmd code will be submitted to the PBS job scheduler.  Use the showq command from a cluster terminal window to look for your job in the job queue.

Code

Job Submission Best Practice

The above is only an example used to illustrate how to submit a job and retrieve the results from within the same MATLAB session.  In most cases using job.wait will not be desirable because of the length of time it might take for a job to start running (perhaps several hours).  The best practice is to have your MATLAB code write the results to a file, rather than waiting for it to finish and retrieving the results with job.getAllOutputArguments();

Maximum and Minimum Number of Workers Per Submission

The maximum and minimum number of workers per job submission is constrained by the queue policy on each cluster, with one worker per processor core.  For example, Sugar will not accept a compute job of more than 8 cores.  Therefore, your MATLAB job must be 8 workers or less.  Further, the number of workers must be n-1 where n is the number of cores you want to use.  If you want to run a single node (8 core) job, you will want to set sz to be 7.   MATLAB will run on one core and the workers will run on the other 7 cores, for a total of 8 cores.   Therefore you can run 7 workers on a single 8 core node.  Further, the maximum number of workers is constrained by our MATLAB MDCS license.  Consult our documentation for a listing of these constraints.

Help with batch() command

For more information on the batch() command and all of its input arguments and how to use the diary, please see MATLAB's online help or the MathWorks website.

Cleanup your job space after the job has finished

Be sure to destroy your job after the job has finished.

Job Dependencies

In order to run code on the cluster, a job may be dependent on several MATLAB or data files. The batch() function takes two parameters: PathDependencies and FileDependencies. Both can be assigned to a comma separated cell array of filenames and/or folder names. If the MATLAB client shares a file system with the compute nodes, then typically the user will specify the dependencies on the local path (i.e PathDependencies). For example:

If the MATLAB client does not share a file system with the compute nodes, then the user will specify the dependencies on the path (i.e. FileDependencies}, which in turn will be zipped up as part of the job. For example:

In this example, the files myrand.m and random.m will be zipped up (the caller function, myrand, is assumed to be needed and is always included in the ZIP file).

Configuring Cluster Parameters with ClusterInfo

As previously mentioned, configurations are written to describe the scheme of the cluster. However, there are some properties that may need to be set often or at runtime. ClusterInfo provides a mechanism for the user to set additional properties. For example, the user may want to specify that a job should last no longer than 30 minutes.

Or the email address to use to be notified when a job is running

The entire collection of properties can be displayed with the state method

The values persist between jobs as well as between MATLAB sessions, until cleared. They can be cleared by setting a single property empty

Or by clearing the entire set

It is very important to note that properties set with ClusterInfo will persist between MATLAB sessions.

Destroying a Job

When you submit a job with batch, you will notice that each submission is labeled Job1, Job2, and so forth.  Temporary directories associated with each job can be found in ~/MdcsDataLocation as the jobs are running.  When job.destroy is called, these temporary directories are deleted.  The above examples call job.destroy.  If you close your MATLAB session before executing job.destroy, which is likely unless you are using the full example with job.wait, you will need to manually cleanup temporary directories in ~/MdcsDataLocation.

Running a Job on a GPGPU

MATLAB 2011a and higher versions are capable of running jobs on GPGPUs as well as on CPUs.  See our FAQ for details.

Running Locally on a Desktop

In order to run MATLAB code with a parallel component on your desktop locally, you must first start up a MATLAB Pool, as such:

where 8 is the number of MATLAB processes to attach to the job.  At this point you will have access to eight MATLAB workers for use with parallel code, such as code with parfor loops, and so on.

Maximum number of processors assigned to a job

This should not be more than nc-1, where nc is the number of cores on the local machine.  The  maximum number of cores that you can use is 8 with version 2011a, and 12 with version 2011b.  Your ability to run parallel jobs on your desktop will be constrained by the number of PCT licenses that are available for checkout on the campus license server.

After running the code, close the MATLAB Pool:

Calls to matlabpool should not be embedded in in the MATLAB code, but rather called at the MATLAB command prompt.

PCT Resources and Demos

Here are a few resources for getting started with the Parallel Computing Toolbox:

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