A Quick Guide to getting started with SCINet
What is SCINet?
SCINet is the USDA-ARS’s initiative for scientific computing. It consists of:
- High performance computer clusters for running command-line and graphical programs. There are currently two clusters: Ceres cluster in Ames IA and Atlas cluster in Starkville MS. SCINet also offers AWS cloud computing. See SCINet HPC Systems for more detail.
- Network improvements across ARS.
- Support for computing through the Virtual Research Support Core (VRSC). See VRSC Support for more detail.
- Training and workshop opportunities in multiple areas of scientific computing. See our event calendar for more information.
Users who are new to the HPC environment may benefit from the SCINet/Ceres onboarding video which covers most of the material contained in this guide. Note that /KEEP storage discussed in the video at 16:20 is no longer available. Instead data that cannot be easily reproduced should be manually backed up to Juno. The instructional video at https://www.youtube.com/watch?v=I3lnsCAfx3Q demonstrates how to transfer files between local computer, Ceres, Atlas and Juno using Globus.
Use the navgation options or select one of the guides below to get started with SCINet
SCINet HPC Resources
HPC Clusters on SCINet
Cluster name Location Login Nodes Transfer Nodes Ceres Ames, IA ceres.scinet.usda.gov ceres-dtn.scinet.usda.gov Atlas Starkville, MS atlas-login.hpc.msstate.edu atlas-dtn.hpc.msstate.edu TBD Beltsville, MD TBD TBD
For security, SCINet requires multifactor authentication. Use these instructions to get set up.
All users should have received their login credentials in an email. If you have not, please email the Virtual Research Support Core at scinet_vrsc@USDA.GOV.
Before accessing various SCINet resources, new users need to ssh either to Ceres or Atlas cluster and change the temporary password. Note that home directories on Atlas are not created right away, so it is recommended to wait a day after receiving email with the credentials before logging to Atlas cluster.
A video demonstration for changing your password can be found here. Please keep in mind that due to the recent password requirement change, the video is out of date. It will list more password requirements than necessary. The current requirements are found below:
- AT LEAST 14 characters long
- Your last 24 passwords cannot be reused.
This document provides detailed information about the storage options provided by SCINet and how to use them. For a simpler overview of suggested procedures for managing data on SCINet, please see Managing Data on ARS HPC and Storage Infrastructure.
There are multiple places to store data on the Ceres and Atlas clusters that all serve different purposes.
Data Transfer best practices.
Globus Online is the recommended method for transferring data to and from the HPC clusters.
SoftwareThe login node provides access to a wide variety of scientific software tools that users can access and use via the module system. These software tools were compiled and optimized for use on SCINet by members of the Virtual Research Support Core (VRSC) team. Most users will find the software tools they need for their research among the provided packages and thus will not need to compile their own software packages.
To learn more about graphical software such as Galaxy, CSC, Geneious, RStudio, and Juptyer, please select the Software Preinstalled on Ceres guide
Open OnDemand Interface
Open OnDemand is an intuitive, innovative, and interactive interface to remote computing resources. The key benefit for SCINet users is that they can use any web browser, including browsers on a mobile phone, to access Ceres.