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Further Job Options

Processor Types

BlueBEAR is made up of nodes with different processors. By default, your job will be allocated to use any of the available processor types, but a single job will not be split across multiple different processor types. It is not normally necessary to choose a processor type, but if your job has particular performance or processor instruction needs (see below) then you may wish to do so.

Note

Some of the memory a node has is for running system processes and will be unavailable to jobs.

Ice Lake

In 2021 we launched water-cooled nodes with Ice Lake CPUs:

#SBATCH --constraint=icelake

Each of these nodes has 2x 36 core Intel® Xeon® Platinum 8360Y and 512GB memory.

Cascade Lake

In 2019 we launched water-cooled nodes with Cascade Lake CPUs:

#SBATCH --constraint=cascadelake

Each of these nodes has 2x 20 core Intel® Xeon® Gold 6248 and 192GB memory.

Use Local Disk Space

If a job uses significant I/O (Input/Output) then files should be created using the local disk space and only written back to the final directory when the job is completed. This is particularly important if a job makes heavy use of disk for scratch or work files. Heavy I/O to the network file-stores such as the home directories or /rds can cause problems for other users. There is a directory /scratch which is local to each node that can be used for temporary files that are associated with a job.

For jobs that are running on a single node, this file-store can also be used for input and output files for a job. Since /scratch is not shared across nodes it cannot be used for parallel jobs that use multiple nodes where all of the processes need to be able to read from or write to a shared file-store; but it can be used for multi-core jobs on a single node.

To use scratch space, include the following lines at the start of your job script (after the #SBATCH headers):

BB_WORKDIR=$(mktemp -d /scratch/${USER}_${SLURM_JOBID}.XXXXXX)
export TMPDIR=${BB_WORKDIR}

These two lines will create a directory for you based on your username (USER), the ID of the job you are running (SLURM_JOBID) followed by a period and six random letters. The use of random letters is recommended for security reasons. This is then exported to the environment as TMPDIR. Many applications utilise TMPDIR for temporary storage while it is running. If you want to copy your files back to the current directory at the end, insert this line:

test -d ${BB_WORKDIR} && /bin/cp -r ${BB_WORKDIR} .

This checks that the directory still exists (using test -d) then copies it and everything in it (using -r, for recursive copy) to the current directory (.) if it does. Then, at the end of your job script, insert the line:

test -d ${BB_WORKDIR} && /bin/rm -rf ${BB_WORKDIR}

This checks that the directory still exists (using test -d) then removes it if it does.

Multi-core Jobs

There are several ways to run a multi-core job using Slurm but the methods we recommend are to use the options --ntasks and --nodes. For most people, it is enough to specify only --ntasks. This is because Slurm is sophisticated enough to take your job and spread it across as many nodes as necessary to meet the number of cores that the job requires. This is practical for MPI jobs and means that cluster is used more efficiently (as multiple users can share nodes). For example, adding the following line will request a job with 20 cores on an undefined number of nodes:

#SBATCH --ntasks=20

For jobs that require multiple cores but must remain on a certain number of nodes (e.g. OpenMP jobs which can only run on a single node), the option --nodes can be specified with a minimum and maximum number of nodes. For example, the first example here specifies that between 3 and 5 nodes should be used; and the second example that a single node should be used:

#SBATCH --nodes=3-5
#SBATCH --nodes=1

The environment variable SLURM_NTASKS is set to the number of tasks requested. For single node, multi-core jobs this can be used directly to make the software fit the resources assigned to the job. For example:

./my_application --my-threads=${SLURM_NTASKS}

It is important to note that not all jobs scale well over multiple cores and sadly just doubling will often not double the speed. Software must be written to use extra cores so make sure the application you wish to run can make use of the cores you request. Useful advice if you are not certain is to submit some short runs of your jobs and see whether they perform as well as they should.

Note that requesting more cores will probably mean that you need to queue for longer before the job can start. Also, using the --nodes option will often lengthen the queue time.

An efficient way to parallelise your work without needing to know whether your application supports multi-threading is to use array jobs. See the following section for more details on this.

Array Jobs

Array jobs are an efficient way of submitting many similar jobs that perform the same work using the same script but on different data. Sub-jobs are the jobs created by an array job and are identified by an array job ID and an index. For example, if 55620_1 is an identifier, the number 55620 is a job array ID, and 1 is the sub-job.

Example array job

#!/bin/bash
#SBATCH --time=5:0
#SBATCH --qos=bbshort
#SBATCH --array=2-5

set -e
module purge; module load bluebear 
echo "${SLURM_JOB_ID}: Job ${SLURM_ARRAY_TASK_ID} of ${SLURM_ARRAY_TASK_MAX} in the array"

In Slurm, there are different environment variables that can be used to dynamically keep track of these identifiers.

  • #SBATCH --array=2-5 tells Slurm that this job is an array job and that it should run 4 sub jobs (with IDs 2, 3, 4, 5). You can specify up to 4,096 array tasks in a single job (e.g. --array 1-4096).
  • SLURM_ARRAY_TASK_COUNT will be set to the number of tasks in the job array, so in the example this will be 4.
  • SLURM_ARRAY_TASK_ID will be set to the job array index value, so in the example there will be 4 sub-jobs, each with a different value (from 2 to 5).
  • SLURM_ARRAY_TASK_MIN will be set to the lowest job array index value, so in the example this will be 2.
  • SLURM_ARRAY_TASK_MAX will be set to the highest job array index value, son in the example this will be 5.
  • SLURM_ARRAY_JOB_ID will be set to the job ID provided by running the sbatch command.

The above job is similar to the one that can be found in the Job Script Options section above. Visit that section for a detailed explanation of the workings of a script similar to the one above. Visit the Job Array Support section of the Slurm documentation for more details on how to carry out an array job.