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  • Overview
    • Why move to the cloud?
      • Remove technical barriers
        • Software
        • Compute
        • Data
      • Open new research opportunities
        • Massive Earth observation data
    • External resources on cloud computing for science
  • Beginner tutorials
    • Quick start guide for new users
      • Step 1: Sign up an Amazon Web Service (AWS) account
      • Step 2: Launch a server with GEOS-Chem pre-installed
      • Step 3: Log into the server and run GEOS-Chem
      • Step 4: Analyze output data with Python
      • Step 5: Shut down the server (Very important!!)
    • Overview of basic AWS compute and storage services
      • Core AWS concepts for scientific computing
    • Set up AWS Command Line Interface (AWS-CLI)
      • Install AWSCLI
      • Try to configure AWSCLI
      • Obtaining security credentials
        • With root account
        • With IAM user account
      • Finish AWSCLI configuration
      • Additional notes
    • Use S3 as major storage
      • Use S3 from the console
      • Working with S3 using AWSCLI
      • Access NASA-NEX data in S3 (Optional but recommended)
      • Access GEOS-Chem input data repository in S3
    • Use EBS volumes as temporary disk storage
      • Viewing existing EBS volumes
      • Choose volume size at launch time
      • Attach new volumes after EC2 launch (Optional)
        • Launch and attach a volume
        • Make that volume usable
      • Save volumes into snapshots (Optional)
    • Use Spot Instances to reduce EC2 cost
      • What are spot instances and why they exist
      • Use spot instances for big computing
      • Deal with spot instance interruptions
    • Notes on security groups (EC2 firewall)
    • Put everything together: a complete workflow
      • General comments on cloud vs local computer
      • A reference workflow
      • Launch EC2 instance with custom configuration
      • Set up your own model configuration
        • Get source code and checkout model version
        • Generate run directory
      • Tweak run-time configurations as needed
      • Get more input data from S3
      • Perform long-term simulation
      • Analyze output data
      • Save your files to S3
      • Terminate server, start over whenever needed
  • Advanced tutorials
    • Enable S3 access from EC2 by IAM role
      • What is Identity and Access Management (IAM)
      • Grant S3 permission to EC2
        • Create a new IAM role
        • Assign that role to EC2
    • More advanced usages of AWSCLI
      • Launch on-demand instances
      • Request spot instances
      • Other use cases
    • Use containers for platform-independent deployment
      • Containers and scientific reproducibility
      • The container landscape
      • Installing the container software
        • Install on your own machine
        • Testing pre-installed container on the cloud
      • Using GEOS-Chem container image
        • Using Docker
        • Using Singularity
        • Using CharlieCloud
      • Using custom GEOS-Chem source code
      • Using GCHP container image
      • Getting GEOS-Chem input data to your local machine
    • Overview of HPC cluster options on AWS
      • Why do you need an HPC cluster
      • HPC cluster management tools
        • AWS ParallelCluster
        • AlcesFlight
        • ElasticCluster
        • StarCluster
  • Developer guide
    • Install compilers and commonly-used libraries
      • Start with a fresh operating system
      • C, C++, and Fortran compilers
      • NetCDF library
        • Install NetCDF with package manager
        • Test sample NetCDF code
        • (Optional) Build NetCDF from source
      • MPI library
        • Install MPI with package manager
        • Test sample MPI code
        • (Optional) Build MPI from source
      • Install scientific Python environment
      • Additional tools
    • Save your system and share with others
    • Building an MPI cluster from scratch
    • Set up GEOS-Chem environment from scratch
      • Building GEOS-Chem AMI
      • Building GEOS-Chem Docker image
  • AWS concepts and services in detail
    • Common AWS concepts (but often confuse non-IT people)
      • Regions and Availability Zones
      • Virtual Private Clouds (VPCs) and Subnets
      • IAM users and IAM roles
      • Security groups
    • Monitoring AWS cost
  • Appendix
    • List of public AWS resources for GEOS-Chem
    • Simplify SSH login with config file
      • Set up SSH config file
      • Enable port forwarding
      • For multiple servers
      • Additional notes
    • Keep a program running after logoff
      • Use nohup command (not recommended)
      • Use GNU Screen
      • Use tmux (recommended)
    • Sample Python code to plot GEOS-Chem data
      • GEOS-Chem netCDF diagnostics
      • GEOS-FP met field
    • Sample Python code to analyze NASA-NEX data
GEOS-Chem on cloud
  • »
  • Appendix
  • Edit on GitHub

Appendix¶

This chapter provides additional resources that don’t fit into the main tutorials.

  • List of public AWS resources for GEOS-Chem
  • Simplify SSH login with config file
    • Set up SSH config file
    • Enable port forwarding
    • For multiple servers
    • Additional notes
  • Keep a program running after logoff
    • Use nohup command (not recommended)
    • Use GNU Screen
    • Use tmux (recommended)
  • Sample Python code to plot GEOS-Chem data
    • GEOS-Chem netCDF diagnostics
    • GEOS-FP met field
  • Sample Python code to analyze NASA-NEX data
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© Copyright 2018, Jiawei Zhuang. Revision 03161e23.

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