This document is intented for faculty at institutions using the RCDS's Umbrella HPC service.
First log into our accounts management webpage to create your own account and accounts for students you supervise. Click the green 'New User' button and fill out the form on the next page. Next, click the blue 'add service' button and choose the account type under the 'New Service Request' heading. The various account types available are:
A temporary password will be emailed to the address you enter. If you need to create many users at once, email us and we can do this in a batch process.
RCDS offers High Performance Compute resources and common data analysis software on a linux platform. A description of the hardware resources available is here. You can access web-based IDE's such as JupyterHub and RStudio on our standalone servers. You can also SSH in to the standalone servers for command line interface (CLI) access. The web-based IDE's are at:
JupyterHub : https://standalone_server_name.ibest.uidaho.edu:8000 Rstudio : https://standalone_server_name.ibest.uidaho.edu
The JupyterHub web application also allows you to interact with the CLI through a terminal session hosted in a web page (click New -> Terminal).
We have a large variety of bioinformatics and general research software installed, when logged in the 'module avail' command will show you what is available.
The cluster is available only through the CLI. We have a workshop that is a good introduction to cluster computing.
With the exception of onyx.ibest.uidaho.edu (sandbox accounts), all our servers share a distributed file storage system which means that it doesn't matter which server you upload data to - it will end up in the same place.
To download data directly from the internet, use
wget from a terminal session, for example:
wget -nc http://www.hpc.uidaho.edu/example-data/Myco.tb.fasta
If your data is on your local computer, can upload it through the JupyterHub IDE, or you can
scp the data to the server:
scp /path/to/local/data email@example.com:/path/to/destination
Note: SCP does not deal well with spaces in paths or filenames.
Other graphical SFTP client options: