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Getting Started on the Newton cluster

If you are unfamiliar with computing in a distributed memory environment, you will want to take a few steps to prepare yourself for cluster computing.

1. Logging into Newton

To use the cluster, you will first need to obtain an account by submitting an account application. Once you have received the verification email, you will be able to log into the primary interactive node,, via SSH:

2. Using the Shell

Once logged into the cluster, you will be presented with a bash shell running under the Scientific Linux 5.5 operating system. If you are unfamiliar with bash, you should read Introduction to using Bash (external source).

3. Editing files

In order to create and modify files on Newton, you will need to familiarize yourself with one or more of the following text editors:

4. Loading Modules

Many of the software packages and development libraries you will want to use are accessed via the module system, which provides a convenient interface for managing the shell environment as needed to access each package. Modules are explained in more detail in Managing Your Environment With Modules.

5. Where to Store Files

There are three classes of disk storage on the cluster: home directory, scratch, and project-associated mass storage. The most appropriate choice for which type of storage to use varies from one task to another. To learn more about the different storage types, read Cluster Storage.

6. Installing Software

Most software is installed and Newton by compiling the code from source. You may request installation of packages; these requests will be fulfilled when the system maintainers deem the software in question to have a sufficiently wide user base. Software for personal use should be installed in your home directory. For more details on this procedure, read Compiling and Installing Software.

7. Using the Batch System

All compute jobs are executed Using the Grid Engine batch queue system. The batch queue is tasked with distributing your compute jobs to the worker nodes of the cluster. The newton cluster supports both serial jobs (one instance of a program running on one CPU of the cluster) and parallel jobs (a program which runs over more than one CPU of the cluster). Parallel jobs can use the low latency Infiniband interconnect for inter-process message passing.

For further details please consult the Documentation.