Cardinal

Batch System Concepts

The only access to significant resources on the HPC machines is through the batch process.

Why use a batch system?

Access to the OSC clusters is through a system of login nodes. These nodes are reserved solely for the purpose of managing your files and submitting jobs to the batch system. Acceptable activities include editing/creating files, uploading and downloading files of moderate size, and managing your batch jobs. You may also compile and link small-to-moderate size programs on the login nodes.

Batch-Related Command Summary

This section summarizes two groups of batch-related commands: commands that are run on the login nodes to manage your jobs and commands that are run only inside a batch script. Only the most common options are described here.

Many of these commands are discussed in more detail elsewhere in this document. All have online manual pages (example: man sbatch ) unless otherwise noted.

In describing the usage of the commands we use square brackets [like this] to indicate optional arguments. The brackets are not part of the command.

FFTW

FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. It is portable and performs well on a wide variety of platforms.

BLAST

The BLAST programs are widely used tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence. While often referred to as just "BLAST", this can really be thought of as a set of programs: blastp, blastn, blastx, tblastn, and tblastx.

Getting Connected

There are two ways to connect to our systems. The traditional way will require you to install some software locally on your machine, including an SSH client, SFTP client, and optionally an X Windows server. The alternative is to use our zero-client web portal, OnDemand.

ANSYS

ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires. Supports are provided by ANSYS, Inc. 

AMBER

The Assisted Model Building with Energy Refinement (AMBER) package, which includes AmberTools, contains many molecular simulation programs targeted at biomolecular systems. A wide variety of modelling techniques are available. It generally scales well on modest numbers of processors, and the GPU enabled CUDA programs are very efficient.

CUDA

CUDA™ (Compute Unified Device Architecture) is a parallel computing platform and programming model developed by Nvidia that enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).

Job Submission

Job scripts are submitted to the batch system using the sbatch command.  Be sure to submit your job on the system you want your job to run on, or use the --cluster=<system> option to specify one.

Standard batch job

Most jobs on our system are submitted as scripts with no command-line options. If your script is in a file named myscript:

sbatch myscript

In response to this command you’ll see a line with your job ID:

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