Pitzer

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.

Slurm Directives Summary

Slurm directives may appear as header lines in a batch script or as options on the sbatch command line. They specify the resource requirements of your job and various other attributes. Many of the directives are discussed in more detail elsewhere in this document. The online manual page for sbatch (man sbatch) describes many of them.

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.

Monitoring and Managing Your Job

Several commands allow you to check job status, monitor execution, collect performance statistics or even delete your job, if necessary.

Status of queued jobs

There are many possible reasons for a long queue wait — read on to learn how to check job status and for more about how job scheduling works.

squeue

Use the squeue command to check the status of your jobs, including whether your job is queued or running and information about requested resources. If the job is running, you can view elapsed time and resources used.

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).

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