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Bioperl

Bioperl offers a set of perl modules which can be used for sequence manipulation. Knowledge of PERL programming is required.

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.

HPC Basics

Overview

Using the HPC or “supercomputer” is a little different from running programs on your desktop. When you login you’ll be connected to one of the system’s “login nodes”. These nodes serve as a staging area for you to marshal your data and submit jobs to the batch scheduler. Your job will then wait in a queue along with other researchers' jobs. Once the resources it requires become available, the batch scheduler will then run your job on a subset of our hundreds of “compute nodes”. You can see the overall structure in the diagram below.

 

Managing Your Account

Once your account is set-up you will receive a welcome letter from us containing your username and default password, which will allow you to register your ARMSTRONG account.

The ARMSTRONG portal provides many services to OSC users, including:

ANSYS

ANSYS is an engineering package and support routine for general-purpose finite-element analysis: statics, heat transfer, mode frequency, stability analysis, magnetostatics, coupled field analysis, etc. Supports are provided by ANSYS, Inc.

AMBER

The Assisted Model Building with Energy Refinement (AMBER) package 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 programs are very efficient.

Altair HyperWorks

HyperWorks is a high-performance, comprehensive toolbox of CAE software for engineering design and simulation.

Scheduling Policies and Limits

The batch scheduler is configured with a number of scheduling policies to keep in mind. The policies attempt to balance the competing objectives of reasonable queue wait times and efficient system utilization. The details of these policies differ slightly on Oakley and Glenn. Exceptions to the limits can be made under certain circumstances; contact oschelp@osc.edu for details.

Monitoring and Managing Your Job

There are several commands available that allow you to check the status of your job, monitor execution of a running job, and collect performance statistics for your job. You can also delete a job if necessary.

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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