GEOS-Chem on cloud
Overview
Why move to the cloud
Remove technical barriers
Software
Compute
Data
Open new research opportunities
Massive Earth observation data
Machine learning and deep learning
Status of cloud for scientific computing
Atmospheric models
Relavant applications
University Classes
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 (Optional)
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
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)
Final word on research workflow on cloud
Advanced tutorials
Use containers to enhance research reproducibility
What are containers?
Run GEOS-Chem inside Singularity container
Overview of HPC cluster options on AWS
Why do you need an HPC cluster
HPC cluster management tools
Use CfnCluster to manage HPC clusters
Use AlcesFlight to manage HPC clusters
Developer guide
Install compilers and NetCDF libraries
GCC and gfortran compilers
Install NetCDF library with package manager
Test NetCDF sample code
(Optional) Install NetCDF from source code
Share your AMI with others
Set up GEOS-Chem environment
Environment variables
Source code and run directory
Test compile
Prepare input data
Test run
Install scientific Python environment
Build your own containers
Install MPI libraries
AWS services in detail
AWS services in human language
Monitoring AWS cost
EC2 configuration details
Appendix
List of public AWS resources for GEOS-Chem
Keep a program running after logoff
Use nohup command (not recommended)
Use GNU Screen
Use tmux (recommended)
Sample Python code to analyze GEOS-Chem data
GEOS-Chem NetCDF diagnostics
GEOS-FP metfield
Sample Python code to analyze NASA-NEX data
GEOS-Chem on cloud
Docs
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Advanced tutorials
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Use AlcesFlight to manage HPC clusters
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Use AlcesFlight to manage HPC clusters
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