Parallelising with Job Arrays

Estimated time: 20 minutes

Overview

Questions

• What are job arrays?
• What benefits do job arrays bring?
• What type of jobs would benefit from job arrays?

Objectives

• Prepare a job submission script for an array job.
• Launch a job to be executed in parallel over several nodes

Parallel computing allows multiple computational tasks to execute simultaneously in order to reduce execution time for a task, or increase throughput for multiple tasks. Depending on the application, the workload may be divided into cooperating subtasks that communicate with one another, or into independent tasks that execute separately.

One common approach to parallel computing is to distribute computation across multiple processes that cooperate by exchanging information during execution using the Message Passing Interface. This is the “MPI” that we saw as a dependency of the amdahl application.

Not all workloads require processes to cooperate. Many scientific workflows are made up of independent jobs. For these cases, Slurm provides Job Arrays, allowing many similar jobs to be submitted and managed together.

For instance, you might need to run the same task on several independent input files, or you may have multiple serial tasks that take some parameter, and you need to explore several values of the parameter. Workflows made up of these independent elements are also sometimes called “high-throughput” computing.

Operationally speaking, a Job Array is a collection of related batch jobs submitted using a single job script.

Challenge

Challenge

What distinguishes workloads that are suitable for job arrays from those that require traditional parallel programming? Describe some examples.

Show me the solution

Tasks appropriate for array jobs are “high-throughput”, where the same thing needs to be done many times, possibly over a set of parameters, but where each task is independent of the others.

For example, running the same statistical analysis on a large number of independent input files is a good candidate for an array solution.

Parallel tasks which have interactions between the various parallel processes need to communicate between processes at run-time, and are not appropriate for job arrays.

For example, most parallel scientific codes that run in parallel have a requirement to communicate between parallel elements at run-time, and are not appropriate for job arrays.

Similarly, serial tasks which only need to be run once do not benefit from parallelism. Aggregating unrelated tasks into an array merely for the sake of grouping does not make sense.

We have already seen how to submit a single serial job to the Slurm scheduler.

Array jobs differ in character, but are specified in a similar manner. The batch file describes the array to the system, and at submission time, all of the array elements are submitted together. They may dispatch at different times, and may or may not run concurrently.

Within the execution environment of an array element, a number of environment variables will be set, which can be used at run-time by the array elements to identify the size of the array, and their position within it, allowing them to select the correct input file. These jobs will be dispatched as their resource requirements and priorities are met, and they may or may not run concurrently.

By way of review, we will construct a job submission script that runs the amdahl executable with the default arguments.

Using nano, create a script called job_single_amdahl.sh containing the following:

BASH

#!/bin/bash
#SBATCH --partition=cpubase_bycore_b1
#SBATCH --job-name=amdahl_defaults
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=00:05:00

echo "Run the Amdahl executable with default arguments."
amdahl
echo "Finished Amdahl."

Challenge

Challenge

How would you submit the script to Slurm for execution?

Show me the solution

BASH

sbatch job_single_amdahl.sh

Array Job Syntax

---

To specify an array job, you only need to add a single directive to your batch file, and then adapt your run command to take advantage of the information provided by the environment variables.

The relevant array directive has this format:

BASH

#SBATCH --array=<array-spec>

The <array-spec> above is a place-holder for specifying the size and extent of the array. The specification will resolve to set of integers, which will index the job array elements.

For a simple example, an array specification of 1-4 means the system should create four array elements, numbered consecutively from one through four.

You can also specify a comma-separated set of numbers, such as 1,3,5, or you can specify a stride, for example by specifying 1-10:2 (which is equivalent to 1,3,5,7,9).

In addition to these, you can also specify a limit on the number of array elements that will run concurrently, using the % sign. An example of this, building on what we saw before, would be to specify 1-10:2%4, which will create five array elements with indices 1, 3, 5, 7, and 9, and run at most four of them at a time until they are all complete.

When an array element job is running, the run-time environment will include some special environment variables, the most important of which is SLURM_ARRAY_TASK_ID, which specifies the index of the current instance. There are other environment variables which tell you the full size of the array, and the starting and ending indices. As we have seen, because there is a fairly rich syntax for specifying arrays, it is not straightforward to infer the size of the array from the high and low indices.

There are also some file-name patterns you can use to control where your executable reads and writes data. The most important of these is the %a pattern, which corresponds to the index of the current array element, similarly to SLURM_ARRAY_TASK_ID.

Challenge

Challenge

Write a batch script to run the amdahl program as an array job with 4 independent jobs, to examine the effects of jitter.

Use the directives discussed above to specify the array elements, and to direct the output of each array element to a separate file.

Show me the solution

BASH

#!/bin/bash
#SBATCH --partition=cpubase_bycore_b1
#SBATCH --job-name=amdahl-array
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --array=1-4
#SBATCH --time=00:05:00
#SBATCH --output=amdahl-%A-%a

# Run the Amdahl executable several times independently.

echo "Starting the Amdahl array script."
amdahl 
echo "Finished Amdahl array script."

Key Points

• Parallel programming allows applications to take advantage of parallel hardware.
• The queuing system facilitates executing parallel tasks.
• Parallel computing allows applications to distribute the workload over several CPUs or nodes
• There are multiple parallelization strategies that are generally supported by resource managers.
• Array parallel jobs are suitable for independent runs of the same executable with varying inputs or outputs.