NEON Data Science Institute 2018¶
Moving Geospatial Data Analysis onto hybrid Cloud & HPC¶
The purpose of this tutorial is to set up a linux-based Virtual Machine running on CyVerse Atmosphere or XSEDE Jetstream to do interactive geospatial analyses in Jupyter Notebooks and RStudio-Server.
The VM(s) can also be run in any other number of ways that the user sees fit.
Contents¶
Prerequisites¶
Downloads, access, and services¶
In order to complete this tutorial you will need access to the following services/software
| Prerequisite | Preparation/Notes | Link/Download |
|---|---|---|
| CyVerse account | You will need a CyVerse account to complete this exercise | Register |
| Atmosphere access | You must have access to Atmosphere | Request Access |
| CyVerse Data Store allocation increase (Optional) | You must be registered for CyVerse | Request Increase (form #2) |
| Jetstream access (Optional) | You must have registered with XSEDE | Request Access |
| Cyberduck (Optional) | Standalone program for uploading/downloading data to Data Store | Download |
| Windows 10 Linux Subsystem (Optional) | Install Ubuntu Bash on a Windows OS | Installation Instructions |
Platform(s)¶
We will use the following CyVerse platform(s):
| Platform | Interface | Link | Platform Documentation | Quick Start |
|---|---|---|---|---|
| Data Store | GUI/Command line | Data Store | Data Store Manual | Guide |
| Discovery Environment | Jupyter Notebooks / non-interactive Docker jobs | Discovery Environment | DE Manual | Guide |
| Atmosphere | Command line (ssh) and/or Desktop (VNC) | Atmosphere | Atmosphere Manual | Guide |
Application(s) used¶
Discovery Environment App(s):
| Name | Version | Location | App Link | Notes/other |
|---|---|---|---|---|
| Jupyter Notebooks | 0.1 | TBA | TBA | TBA |
Atmosphere Image(s):
Here are the tested Ubuntu images.
Warning: The latest version of Ubuntu (18.04) may not have current packages for some software.
| Image Name | Version | Description | Link |
|---|---|---|---|
| Ubuntu 18.04 GUI | 1.0 | Ubuntu 18.04 GUI XFCE Base | Image |
| Ubuntu 18.04 non-GUI | 1.0 | Ubuntu 18.04 non-GUI Base | Image |
| Ubuntu 16.04 GUI | 2.1 | Ubuntu 16.04 GUI XFCE Base | Image |
| Ubuntu 16.04 non-GUI | 1.6 | Ubuntu 16.04 non-GUI Base | Image |
Jetstream Image(s):
Input and example data¶
In order to complete this tutorial you will need to have the following inputs prepared
| Input File(s) | Format | Preparation/Notes | Example Data |
|---|---|---|---|
| Discrete lidar | *.laz, *.las, *.xyz, *.bin | classified | Data Portal |
| Orthophotography | *.tif | ||
| Hyperspectral | *.hdf |
Fix or improve this documentation
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- Report an issue or submit a change: |Github Repo Link|
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