Working in a High-Performance Clusters (HPC) environment requires users to learn command line since these resources generally don’t have a user interface to help navigate through the files on the system (like Mac and Windows we are used to). Research Technologies (RT) (more information on RT, click here) team developed Research Desktop (RED) a graphical interface for novice users working on HPC Carbonate (for more information on Carbonate, click here). The goal is to shorten the learning curve required to work with HPC systems and improve the accessibility of these resources to a wider user base. For more information on RED click here. Just as the name suggests, this is the desktop to Carbonate, with access to all the file stored on Carbonate and dc2 space (both scratch and project space).
Getting access to RED
- Get a carbonate account
If you don’t have a carbonate account – fill out this survey here to receive an IU affiliate account with NCGAS. You will receive an email within 24 to 48 hours with instructions on setting up an IU affiliate account.
If you already have an IU affiliate account or IU account, but not sure if you have access to carbonate
Go to one.iu/Accounts, login using IU/IU affiliate credentials
Look under the list of accounts and verify if Carbonate is listed.
If not, then click on “Create Computing Account”, and select “Carbonate” to create a Carbonate account
- Using a browser- Type in the URL https://red.uits.iu.edu, log in with your IU credentials, start working on Carbonate.
- Download ThinLinc, the links to download are here
Once ThinLinc is installed, configure ThinLinc options as suggested in the link here, and login to the machine “red.uits.iu.edu” with IU credentials.
Advantages of RED
Here is a list of some reasons why RED is great (complete list of its features are listed here),
- Similar to a desktop, you can click on the Desktop icons to browse the internet (Firefox), access terminal to script/submit jobs, File browser to access files on carbonate and scratch space
- All the bioinformatics programs installed on Carbonate system-wide is accessible from RED
- Rstudio, MATLAB, SAS available on RED
- Configure Thinlinc to mount your drives and directories on (or connected to) your personal computer
- Visualization tools- Cytoscape, Integrative Genomics Viewer
- HPC Slack Channel – to message the IU HPC team to get a quick response
- IU box cloud is also mounted on RED to access files saved on box or move files to box for long-term storage
- SDA, move files on carbonate to SDA using Filezilla on RED or use Globus (blog post on Globus, click here)
- You have the ability to disconnect and reconnect to a session. In other words, you can start a long-running task for testing, disconnect from the session, and come back at a later time to check on how things are going or simply pick up where you left off.
RED is a great resource in helping new users start working with HPC resources. Since this is also an HPC resource (but with a Dekstop), remember not to run scripts that require large memory or CPUs here. This is a great place to write your scripts and test them (using Rstudio or Jupyter notebooks), but once you have a working script, always run these scripts as an interactive job or submit them as job. For more information on submitting jobs, go here.