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Supercomputing for Everyone Series

Carbonate at IU (Intro to High Performance Computing)

Started Jan 1, 2019

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Full course description

About This Training

Carbonate at Indiana University is a large memory computer cluster configured to support high-performance, data-intensive computing. Carbonate can handle computing tasks for researchers using genome assembly software, large-scale phylogenetic software, and other genome analysis applications that require large amounts of computer memory.

Length: 1-2 weeks

Certificate: Yes

Audience: IU students, faculty, staff, and non-IU collaborators with IU guest account


This course will introduce the operation of IU High Performance Computing Systems and Carbonate including the data storage option, sensitive data management, carbonate basic operation, file transmission, job execution, and Carbonate deep learning node. There are some practice questions that can help you to practice the Carbonate opreating skills.


Research Technologies at

Additional Information

To enroll in the course:

  1. Click “Enroll”
  2. Login to Expand if you have not already done so. (You will either use your IU credentials to login, or take steps to create a guest login if you do not have IU credentials.)
  3. Click “Enroll in Course”
  4. Select “Go to Your Dashboard”
  5. Locate the proper course under “In Progress” then select “Begin Course"

Course Modules

1. Preparation - Pathfinder Quiz
- Apply for an Account
- Knowledge Base (KB)
- Status.IU
- Command-line Interface

2. Storage Options
- Storage Options at IU
- Storage Option - Home Directory
- Storage Option - Scholarly Data Archive
- Storage Option - Slate

3. Work with Sensitive Data
- About Sensitive Data at IU
- Your Legal Responsibilities for Protecting Data
- About Protected Health Information
- About HIPAA

4. Getting Start with Carbonate
- Introduction to Carbonate
- Install the Support Software (SSH)
- Install the Support Software (SFTP)
- Install the Support Software (X)

5. Carbonate Operation
- Connect to Carbonate
- Connect to Carbonate with X
- Transfer Files to Carbonate by SFTP

6. Executing Jobs in Carbonate
- Available Packages in Carbonate
- Run Jobs on Carbonate
- Create Job Script in Carbonate
- Sample Job Scripts in Carbonate
- Submit Your Job in Carbonate
- Manage Your Job in Carbonate

7. Deep Learning Nodes on Carbonate
- Deep Learning Nodes Overview
- Run Jobs on Deep Learning Nodes
- Software and Partition Information

8. Specific Job Practice (Optional)
- Run MATLAB in Karst or Carbonate
- Run Python in Karst or Carbonate
- Run Stata in Karst or Carbonate