Basic Examples MDCS 2016

Basic MDCS usage: Example of a task-parallel job

The following example illustrates how to submit a job to the HPC cluster (or CARL and EDDY). After you have entered the batch command and the command returned with no error, you could, e.g., do some other MATLAB computations, close your MATLAB session, or even power down your machine. In the meantime, your MDCS job gets executed "in the background". After it has finished, you can analyse the results, visualize them, etc.

As an elementary example of an "embarrassingly parallel" (or "task-parallel" in MATLAB terminology) problem we use a parameter sweep of a 2^nd order ODE (the damped Harmonic Oscillator). The parameters varied are the spring constant (or equivalently, the eigenfrequency) and the damping. For each pair of parameter values and fixed initial condition, the solution of the ODE is calculated (up to a certain maximum time) and the peak value of the amplitude is calculated and stored in an array.

The parameter sweep is achieved in a for loop. This can easily be parallelized using parfor instead. The total execution time of the parfor loop is measured with the tic and toc commands.

Please download the following zip-file containing the definition of the ODE system and the MATLAB script for the parameter sweep: [MEDIA:ode_matlabscript.zip | Download]

One way to run this code in parallel is to open a Matlabpool of the cluster and then executing the script that performs the parameter sweep. MATLAB then automatically distributes the independent loop iterations across the available workers (or "labs" in this case). Define a "scheduler object" sched which describes your cluster configuration (in the above example setup, the configuration named HERO), and submit the job to the cluster using the batch command:

sched = parcluster('HERO');
job = batch(sched, 'paramSweep_batch', 'Pool', 7, 'AttachedFiles', {'odesystem.m'});

The first time you submit a job to the cluster in a MATLAB session, you will be prompted for your credentials (username, password). Please enter your usual cluster account data. The number of "labs" is 1 + the number specified after the 'Pool' keyword. Thus in the above example, the job would run on eight workers. The specification of the file dependencies by the 'AttachedFiles' keyword is necessary since the script paramSweep_batch.m depends on odesystem.m and thus the latter must be copied to the cluster such that the script can run there (that is one of the purposes of the local and remote "job data" directories that must be specified in the configuration of the scheduler).

Check the state of the job with the Job Monitor (from the Main menue: Parallel -> Job Monitor), or in the command window:

job.State

By typing

job

you get additional useful information like, e.g., the start time of the job (if it has already started running), the current runtime, etc. Another useful command is

sched.getJobClusterData(job)

which will return, among other information, the job-ID from the cluster manager which can be used in turn to get more information later on (with the qacct command).

In order to analyze results after the job has finished, load the job data into the workspace:

jobData=load(job);

Check the runtime of the job:

jobData.t1

You can visualize the results by:

figure;
f=surf(jobData.bVals, jobData.kVals, jobData.peakVals);
set(f,'LineStyle','none');
set(f,'FaceAlpha',0.5);
xlabel('Damping'); ylabel('Stiffness'); zlabel('Peak Displacement');
view(50, 30);

If you no longer need the job, clean up (includes deletion of all files related to the job in the local job data directory):

delete(job);

The following table shows the runtime measured on the HERO cluster as a function of the number of workers:

Number of workers	Runtime
1 (serial job)	220s
2	196s
4	69s
8	35s
16	17s
32	8.5s

Obviously, the simple parallelization strategy using the parfor loop leads to a significant speed-up in this case.

Advanced usage: Specifying resources

Any job running on the cluster must specify certain resources (e.g., runtime, memory, disk space) which are passed to SGE as options to the qsub command. If you submit jobs to the cluster via MDCS, you do not directly access SGE and, usually, do not have to care at all about these resource requests. MATLAB has been configured to choose reasonable default values (e.g., a runtime of 24 hours, 1.5 GB memory per worker, 50 GB disk space) and to correctly pass them to SGE. The default values for runtime, memory, and disk space are printed when you submit a MATLAB job via MDCS.

However, it is possible to modify these resource requirements for an MDCS jobs from within the MATLAB session if necessary (e.g., if your job runs longer than 24 hours, needs more memory, etc.). That also makes sense if the requirements are significantly lower than the default values (e.g., the runtime is only one hour, the memory requirements much lower, etc.), since that would avoid unnecessary blocking of resources and also increase the chance that the job starts earlier if the cluster is under heavy load. In principle, everything that one would usually write into an SGE job submission script could also be specified from within a MATLAB session when one submits an MDCS job.

The following resource specifications have been implemented:

runtime
memory
diskspace

These correspond, in SGE language, to the h_rt, h_vmem, and h_fsize resource attributes, respectively. The runtime must be specified in the format hh:mm:ss (hours, minutes, seconds), and must not be longer than 8 days. The other resources as a positive (integer) number followed by K (for Kilobyte), M (for Megabyte), or G (for Gigabyte). If you want to change any of these resources from its defaults, you have to add optional arguments to one of the functions distributedSubmitFcn or parallelSubmitFcn, depending on whether it is a distributed or parallel job (e.g., if you open a Matlabpool, it is by definition always a "parallel" job).

Example (modifying runtime and memory)

Your parallel (Pool) job has a runtime of at most 3 days (with a suitable safety margin) and needs 4 GB of memory per worker. If you are a HERO user, you would then first define a "scheduler" object, and then modify the CommunicatingSubmitFcn (supply additional parameters) of that object:

sched = parcluster('HERO');
set(sched, 'CommunicatingSubmitFcn', cat(2, sched.CommunicatingSubmitFcn, {'runtime','72:0:0','memory','4G'}));

The job can be submitted, e.g., via the batch command, but you also have to specify the scheduler object as first argument since otherwise the default configuration would be chosen:

job = batch(sched, 'paramSweep_batch', 'Pool', 7, 'AttachedFiles', {'odesystem.m'});

You will see the modified values of the resources from the messages printed when you submit the job.