R2014a with MDCS

Directory list:

Level of support

This page contains NSC specific documentation about using MDCS on our clusters.

For full documentation about running parallell jobs in Matlab please read Mathworks Parallel Computing Toolbox documentation.

Starting Matlab

Log on to Triolith. To use the Matlab GUI we recommend that you log on using ThinLinc.

Load the Matlab module:

[paran@triolith3 ~]$ module add matlab/R2014a

Start matlab:

[paran@triolith3 ~]$ matlab

Initial setup

The first time you use MDCS you need to create a cluster profile. To do this start Matlab and run the following command:

>> configCluster()
        [1] gamma
        [2] triolith
Select a cluster [1-2]: 2

This will create a cluster profile named triolith_local_r2014a and set as your default.

Matlab will remember your cluster profile, so you only have to run this once.

Configure job parameters

You can now submit jobs using Matlab. To add parameters to the jobs that Matlab will submit to the queue you use ClusterInfo.

All jobs need to specify WallTime, and most will need to specify ProjectName.

Examples:

Reset ClusterInfo state

>> ClusterInfo.clear

Show ClusterInfo state

>> ClusterInfo.state

                   Arch : 
            ClusterHost : 
           EmailAddress : 
            GpusPerNode : 
               MemUsage : 
         PrivateKeyFile : 
           ProcsPerNode : 
            ProjectName : 
              QueueName : 
            Reservation : 
                 UseGpu : 0
     UserDefinedOptions : 
      UserNameOnCluster : 
               WallTime : 

Specify job walltime limit:

>> ClusterInfo.setWallTime('01:00:00')

Specify project name for job:

>> ClusterInfo.setProjectName('snic2014-X-Y')

After running the last four example commands ClusterInfo.state would look like this:

>> ClusterInfo.state                  

                   Arch : 
            ClusterHost : 
           EmailAddress : 
            GpusPerNode : 
               MemUsage : 
         PrivateKeyFile : 
           ProcsPerNode : 
            ProjectName : snic2014-X-Y
              QueueName : 
            Reservation : 
                 UseGpu : 0
     UserDefinedOptions : 
      UserNameOnCluster : 
               WallTime : 01:00:00

Specify reservation to use. For example to use the development reservation for short test jobs:

>> ClusterInfo.setReservation('devel')

Run a batch job

The following small example use MDCS to submit a batch job:

If you have the following Matlab code in a file named rndmat.m:

parfor i=1:524288
  A(i) = rand()
end

You can use the following commands to submit it as a batch using 3 workers. One core will also run the script itself, so in total this job will use 4 cores:

>> job = batch('rndmat','pool',3)

To wait for the job to finish, then load the results A you can run:

>> wait(job)
>> load(job,'A')

Alternatively, in the Matlab GUI you can click on Parallell > Monitor Jobs to monitor your job.