Contents

Minimizing Network Traffic

In this example, we look at how we can reduce the run time of our jobs in the Parallel Computing Toolbox™ by minimizing the network traffic. It is likely that the network bandwidth is severely limited, especially when considered relative to memory transfer speeds, and we therefore have a strong incentive to make the most efficient use of it. Additionally, the Parallel Computing Toolbox has limitations on the sizes of the MATLAB® objects that the tasks can receive and return, and we will look at how we can work around them. In particular, we will discuss how to use the file system and show some of the advantages and the disadvantages of using it.

Prerequisites:

For further reading, see:

Reducing the Amount of Data Returned

If heavy network traffic is causing our jobs to slow down, the first question is whether we really need all the data that is being transmitted. If not, we should write a wrapper task function that drops the redundant data and only returns what is necessary. You can see an example of that in the Writing Task Functions example.

Using the JobData Property of the Job

When using an MJS cluster, it is possible to use the JobData property of the job to minimize the job and the task creation times by reducing the data transfer over our network. If the task input data is large and it is shared between all the tasks in a job, we may benefit from passing it to the task functions through the JobData property of the job rather than as an input argument to all the task functions. This way, the data is only transmitted once to the cluster instead of being passed once for each task.

Let's use a simple example to illustrate the syntax involved. We let the task function consist of calculating x.^p, where x is a fixed vector and p varies. This implies that x will be stored in the JobData property of the job and p will be passed as the input argument to the task function. The task function uses the getCurrentJob function to obtain the job object, and obtains the JobData through that job object.

type pctdemo_task_tutorial_network_traffic;
function y = pctdemo_task_tutorial_network_traffic(p)
%PCTDEMO_TASK_TUTORIAL_NETWORK_TRAFFIC Calculate x.^p.
%   y = pctdemo_task_tutorial_network_traffic(p) uses getCurrentJob to obtain 
%   the JobData property of the current job.  The function then returns 
%   the p-th power of the vector found in the JobData property.
    
%   Copyright 2007 The MathWorks, Inc.
    
    job = getCurrentJob();
    if isempty(job)
        % We are not running on a worker, so we do not have any JobData to 
        % work on.
        y = [];
        return;
    end
    
    x = get(job, 'JobData');
    y = x.^p;
end % End of pctdemo_task_tutorial_network_traffic.

We can now create a job whose JobData property is set to x.

myCluster = parcluster;
job = createJob(myCluster);
x = 0:0.1:10;
job.JobData = x;

We create the tasks in the job, one task for each value of p. Note that the tasks' function only has p as its input argument.

pvec = [0.1, 0.2, 0.3, 0.4, 0.5];
for p = pvec
    createTask(job, @pctdemo_task_tutorial_network_traffic, 1, {p});
end
submit(job);

We can now return to the MATLAB prompt and continue working while waiting for the job to finish. Alternatively, we can block the prompt until the job has finished:

wait(job);

Since we have finished using the job object, we delete it.

delete(job);

When to Use a Shared File System

If we want the workers to process data that already exists on a shared file system, we use the AdditionalPaths property of the job. All the folder names that we put into that cell array are added to the path on the workers, thereby making them easy for us to access. The user that the workers run as must have the permissions required to read from those folders.

Regarding the question of when it is appropriate to write data to the shared file system in the MATLAB client to make it available to the workers, or vice versa, we have to keep in mind that shared file systems often have high latency. Consequently, if we have followed the advice given above and we are transferring only objects that are a few hundred kilobytes in size, we are probably better off not using the file system explicitly, but instead relying on the transfer mechanism that is built into the Parallel Computing Toolbox. However, when using an MJS cluster, it is probably better to use the file system when transferring objects that are tens of megabytes in size or larger.

Handling Delayed Updates of a Shared File System

Some network file systems trade off latency for network efficiency through delayed updates. Delayed updates can cause problems if the client computer expects files generated on the workers to be immediately available. For this reason, we recommend avoiding reading task output files in the task finished callback functions. As a rule of thumb, we should not expect files written on one computer to be immediately available on all other computers.

Writing to a Shared File System on a Homogeneous Cluster

It is easy to communicate through a shared filesystem on a homogeneous cluster by using the load and save functions in MATLAB. Of course, the client and the workers must have permission to read and write the input and output files. If the cluster consists of Windows® machines, we also have to remember to use only UNC paths and not the names of mapped network drives. That is, we can only use full filenames of the form

f = '\\mycomputer\user\subdir\myfile.mat';

and not

f = 'h:\subdir\myfile.mat';

because network mappings, such as that of \\mycomputer\user to h:, may only work on the client machine and MATLAB may not have access to those mappings on the workers.

Writing to a Shared File System on a Heterogeneous Cluster

Using a shared file system can be more difficult if it does not look the same from the workers and the clients. The Parallel Computing Toolbox examples show one way of solving that problem in the case of a mixed environment of Windows and UNIX® computers. Let's assume that the path names

windowsdir = '\\mycomputer\user\subdir';
unixdir = '/home/user/subdir';

refer to the same directory on the file server, and that the former is valid on all of our Windows computers and the latter is valid on all of our UNIX computers. We can tell the Parallel Computing Toolbox examples about this association and allow it to use this directory for writing temporary files by issuing the command

orgconf = paralleldemoconfig();
paralleldemoconfig('NetworkDir', ...
    struct('windows', windowsdir, 'unix', unixdir));

When the examples need to write a file to the file system, they look at the NetworkDir field of the paralleldemoconfig structure:

conf = paralleldemoconfig();
netDir = conf.NetworkDir;
disp( netDir )
    windows: '\\mycomputer\user\subdir'
       unix: '/home/user/subdir'

Given a filename, such as 'myfile.mat' from above, the examples pass the netDir structure and 'myfile.mat' to the workers. The workers can then choose whether to use

fullfile(netDir.windows, 'myfile.mat')

or

fullfile(netDir.unix, 'myfile.mat')

according on what platform they are on. This platform-dependent choice has been wrapped into the example function pctdemo_helper_fullfile:

type pctdemo_helper_fullfile;
function filename = pctdemo_helper_fullfile(networkDir, file)
%PCTDEMO_HELPER_FULLFILE Build full filename from parts.
%   PCTDEMO_HELPER_FULLFILE(networkDir, file) returns 
%   FULLFILE(networkDir.windows, file) on the PC Windows platform, and 
%   FULLFILE(networkDir.unix, file) on other platforms.
%
%   networkDir must be a structure with the field names 'windows' and
%   'unix', and the field values must be strings.
%   
%   See also FULLFILE
    
%   Copyright 2007-2012 The MathWorks, Inc.
    
    % Verify the input argument
    narginchk(2, 2);
    tc = pTypeChecker();
    if ~(tc.isStructWithFields(networkDir, 'unix', 'windows') ...
         && iscellstr(struct2cell(networkDir)))
        error('pctexample:helperfullfile:InvalidArgument', ...
              ['Network directory must be a structure with the field names '...
              'windows and unix and the field values must be strings']);
    end
    if ~ischar(file) || isempty(file)
        error('pctexample:helperfullfile:InvalidArgument', ...
              'File must be a non-empty character array');
    end
    
    if ispc
        base = networkDir.windows;
    else
        base = networkDir.unix;
    end
    filename = fullfile(base, file);
end % End of pctdemo_helper_fullfile

so that the workers actually call only

f = pctdemo_helper_fullfile(netDir, 'myfile.mat');

and they will then receive the correct, full filename of myfile.mat.

Restoring the Original Settings

We do not want this tutorial to change the default example settings, so we restore their original values.

paralleldemoconfig(orgconf);
Was this topic helpful?