An introduction to batch processing

An introduction to batch processing

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When running jobs on Legion or Grace, users need to interact with the batch system. For users unfamiliar with HPC environments, this can be a way of working which is unfamiliar to them.

What is a batch system?

On a large, multi-user machine like Legion many users compete for relatively limited resources. There are two possible ways of organising access to this resource: Either allow everyone to run anything they want when they want but run the risk of people’s jobs interfering with each other or else construct a system where users are allocated resources in turn. This is called a "batch" system. In a batch system, users submit their programs with a script to run them and a list of requirements and these jobs are run when resources are available. On Legion, the order jobs are run in is subject to a fair use policy which is discussed in the scheduling policy section. On other sites, users may be billed for their usage and most batch systems provide features for managing accounting in this scenario.

When a user uses a batch system, they need to remember a number of important things. The first is that (with some exceptions) their jobs are not interactive. This means that a user must provide their application with inputs in advance (and if they are a developer design their program to operate in this manner). This means that some applications are not suitable for running in a batch system (visualisation for example). In most systems, each job is given a unique ID by the scheduler and this ID is used when interacting with jobs once they have been submitted. Once jobs have been submitted, users can log out and their jobs will execute even though they are not logged in.

The second important thing to remember is that once a job has been submitted, a user has little control of when the job is actually run, because the time to completion (from submission) depends on how busy the machine is. It is therefore necessary for users to plan ahead and submit their jobs in a timely manner, rather than waiting until the last minute.

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Basic commands

There are three basic commonly used commands in any batch system - one for submitting jobs, one for checking the status of jobs and one for deleting jobs. On Sun Grid Engine, these are qsub, qstat and qdel.

qsub

The qsub command submits your job to the batch queue.

qsub myscript.sh

You can override the settings in your script by specifying them on the command-line, so for example if you want to change the name of the job for this one instance of the job you can submit your script with:

qsub -N NewName myscript.sh

Or if you want to increase the wall-clock time to 24 hours:

qsub -l h_rt=24:0:0 myscript.sh

You can submit jobs with dependencies by using the -hold_jid option. For example, the command below submits a job that won't run until job 12345 has finished:

qsub -hold_jid 12345 myscript.sh

You may specify node type (see Resource Allocation section for more details) with the "-ac allow=" flags as below:

qsub -ac allow=XYZ myscript.sh

The example above would restrict the job to running on the older nodes.

Note that for debugging purposes, it helps us if you have these options inside your jobscript rather than passed in on the command line, if possible. We can see your jobscript but not what command line you submitted with.

qstat

The qstat command shows the status of your jobs. By default, if you run it with no options, it shows only your jobs (and no-one else’s). This makes it easier to keep track of your jobs. If you want to get more information on a particular job, note its job ID and then use the -f and -j flags to get full output about that job

qstat -f -j 12345

If you see that your job is in Eqw state then an error occurred before your job could begin. You can see a truncated version of the error in the output of qstat -j - this is often enough to tell what the problem is if it is a file or directory not found.

You can get the full error with qexplain.

qexplain 12345

qdel

The qdel command lets you delete a job from the queue. You need to provide qdel with a job ID like so:

qdel 12345

You can delete all your jobs with qdel '*'

If you wish to learn about additional commands, please run the command "man qstat" and take note of the commands shown in the "SEE ALSO" section of the manual page. Exit the manual page and then run the "man" command on those.

If you cannot find the information you need in the man pages, then contact us at | rc-support@ucl.ac.uk for assistance.

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