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Supercomputing for Everyone Series (SC4E): Carbonate at IU is a Course

Supercomputing for Everyone Series (SC4E): Carbonate at IU

Dec 17 - Sep 12, 2020


Full course description

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. Accounts are available to IU students, faculty, and staff. Carbonate also serves as a "condominium cluster" environment for IU researchers, research labs, departments, and schools.

Carbonate has 72 general-purpose compute nodes, each with 256 GB of RAM, and eight large-memory compute nodes, each with 512 GB of RAM. Each node is a Lenovo NeXtScale nx360 M5 server equipped with two 12-core Intel Xeon E5-2680 v3 CPUs and four 480 GB solid-state drives. Carbonate also features 12 GPU-accelerated Lenovo ThinkSystem SD530 deep learning (DL) nodes, each equipped with two Intel Xeon Gold 6126 12-core CPUs, two NVIDIA GPU accelerators (eight with Tesla P100s; four with Tesla V100s), four 1.92 TB solid-state drives, and 192 GB of RAM.

Course Module

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

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