Quick Start Tutorial
This Quick Start Tutorial
demonstrates each of the steps for porting a workflow from a desktop computer to the HPC cluster, Henry2. The user is led through the various steps using the existing website documentation.
The Tutorial covers:
- Gaining access to Henry2
- A set of essential Linux commands
- Software requirements and instructions for logging in and transferring files
- How to run an existing application in several ways, using R as an example. Includes methods for running in batch, command-line interactive, and GUI interactive.
- The basics of running parallel jobs
HPC at NC State: Basic use of the Henry2 cluster
The Quick Start is now available as a series of videos and quizzes, with class content delivered through Moodle.
Basic HPC usage
- Review the procedure for gaining HPC access, and read the Acceptable Use Policy.
- Henry2 is a Linux cluster. See the following recommended links for learning Linux, click the box to expand the learning paths, and choose a set of learning materials based on use case. Alternatively, go straight to this Linux tutorial.
- Connect to the cluster from a local machine by logging in.
- Review the details for the available storage on HPC, including directory locations, size limits, and backup policies.
- Learn various methods of transferring files between Henry2 and a local machine.
- To run an existing application on Henry2, locate the application on the software page.
After looking at the examples for suggested use, check the documentation on running programs to further inform job submissions.
- Learn how to submit batch jobs and run parallel programs.
- Read this before submitting parallel jobs
To install software or compile a research application
- Applications will generally not fit in a home directory. Request a space for user maintained software.
- Read the README, FAQ, and tutorials provided by the software. Software may not be installed using automatic installers that require sudo permissions, so users must spend time understanding the software requirements such as compiler types and library dependencies.
- Automatic package installers require sudo because they write to system directories. Often the only necessary modification to an auto-installer is for the user is to specify an alternate installation directory prefix.
- A successful compilation often requires an understanding of the compute environment on Henry2. Sometimes the compile requirements are a matter of locating the correct library or setting the proper path on Henry2, but other times a user may have to install their own custom compiled libraries.
See the R documentation for examples of setting the compute environment to install R packages.
- There are descriptions and instructions for using the compilers available on Henry2.
- Here is some general guidance for installing software.
The HPC center has various hardware and software resources. See the available hardware and storage options, monitor the cluster status, or investigate the system installed software.