Writing pbs files

Once you have written a PBS command file, you can schedule it to be run from the command line via. By default, Torque runs your PBS command file from your home directory after executing your profile. Torque populates a multitude of environment variables that you can use from within your PBS command file.

You can find a description of some of these and some we don't have in the Torque docs. Page tree. Browse pages. JIRA links. See also: Queue policies for a detailed description of the queues that can be used on CyberLAMP Torque documentation on job submission and generic info about allocating resources, etc.

Here, we describe the qsub command as it pertains to CyberLAMP, how to schedule a single-command job, how to schedule an interactive job, and finally how to write PBS command files and schedule them to be run. MSU and NYU documentation is at least partly applicable since they also use Torque though possibly different versions and certainly with different resources. Commonly-used options and all those that are particular to CyberLAMP and hence not described sufficiently--or at all--in the man page for the qsub command are described here.

See the qsub man page for other options. If a resource is not specified, a default value will be used based on the account and queue requested. Common resource specs include the following:. Use one of these to specify the Nvidia compute mode in which to set the GPU s ; optional, but do not specify more than one. Specify all job resources to qsub at the command line, and specify -I capital-eye for interactive and optionally -X to forward X In this example, it determines whether the job executes Python code using MPI or if it executes it without parallelization.

More information on passing arguments to job scripts can be found in the Running Jobs document. Main Menu Main Menu. Introduction In the context of the cluster, job scripts submit non-interactive batch jobs to the scheduler for execution. Scripting Fundamentals To understand how job scripts work, you should generally understand how a script itself works.

All three arguments can be provided. PBS -n Instructs the interpreter to schedule this job as node-exclusive. The job will consume an entire node rather than sharing it with other jobs. Refer to Table 3. Supply the variables in a comma-delimited format. At the time of this writing, only the batch and debug queues are available to users. Job arrays execute the same job with multiple runs. The -t option accepts a single integer e.

For multinode jobs, this option must be used with a valid ppn value. If a ppn value is not specified, the job will be rejected. By default, users will receive one core for their jobs if they do not specify a ppn value. QoS values influence the maximum amount of time available to jobs. For more information, review the Running Jobs document.

Separate multiple partitions with colons :. Review the Running Jobs document for the list of available partitions. Review the Running Jobs document for more information.

Review the Running Jobs document for the list of QoS attributes. If you wish to run your job in a private condo, specify the condo QoS attribute.

Click here to see the examples of different scenarios in which a job using a specific project account and QoS attribute can be submitted to land it on a private or institutional condo. Jobs should always be submitted from within Lustre space. Defines the interpreter that will parse the job script. Everything after the program name are called the arguments. The [] bracketed arguments above are more likely to be optional, and [] is the general convention for indicating optional arguments.

In the example above, the program bwa has a sub-function index. However, note that not all programs are consistent! Its good practice but not essential for software developers. Manual pages and help commands are generally alike. The contribution of resource usage to your fair share count depends on the queue your job runs in. More on this in Episode 4. Toggle navigation Artemis Series. Submitting and monitoring Artemis Jobs Break! Introduction to Artemis HPC.

Teaching: 30 min Exercises: 10 min. Questions How do we communicate with the HPC scheduler? Objectives Learn how to write job submission scripts.

Usually a select: or walltime: block. Receive notification on a bort, b egin, or e nd of jobs. Integers; indices will be i to j in steps of k. See manual page for more info: man qsub.