Geospatial

Here is a guide on setting up an environment for geospatial analysis on the Midway3 cluster at the University of Chicago. This guide is divided into sections that detail the steps for connecting to the cluster, and using software and containers relevant to geospatial analysis.

Section I: Connecting to Midway Cluster

1. GUI-based Access

For geovisualization, a GUI-based approach is preferred. ThinLinc is recommended due to its seamless working environment which supports features like a shared clipboard. ThinLinc can be accessed in two ways:

ThinLinc Client: Download and install the ThinLinc client from ThinLinc Download Page. It is available for all major operating systems.
Web Access: You can also access ThinLinc through a browser by navigating to https://midway3.rcc.uchicago.edu. This method does not require any client installation.

2. Command Line Access and X Forwarding

For users who prefer or require command-line access, especially for scripting and automation:

Using SSH with X Forwarding:
- Xshell and VcXsrv: Xshell is preferred for academic and home use as it is free and has a smaller memory footprint compared to other tools like MobaXterm. However, it requires the installation of an X11 client such as Xming or VcXsrv.
- Connect via SSH with X forwarding enabled:
```
ssh -Y <user>@midway3.rcc.uchicago.edu
```
  Replace <user> with your actual username on the Midway3 cluster.

Section II: Software

1. Using Software Packages

Key geospatial libraries and tools are available on Midway3, including GDAL for geospatial data manipulation and analysis, as well as spatial libraries for R and Python:

For R:
Load the R module and start R:
```
module load R
R
```
For Python:
Python and its libraries can be accessed via Anaconda modules, which support virtual environments:
```
module load python
source activate <env_name>
```

2. Loading QGIS

QGIS can be loaded and used directly on Midway3 by activating the appropriate Python environment and loading the software module:

module load python
source activate qgis
qgis

3. Using Containers

Containers provide a reproducible environment for more complex or customized setups. Singularity is used on Midway3 to manage containers:

How to Use Singularity:

Load the Singularity module and interact with a container:

ml singularity
singularity shell -B $HOME/code:<mount_point> -B $SCRATCH/$USER:/data <image_path>

For example, to load an OTBTF (Orfeo Toolbox with TensorFlow) image:

singularity shell -B $HOME/code/cook -B $SCRATCH/$USER:/data otbtf_6.3.1-cpu.sif

export SINGULARITY_TMPDIR="/software/src/tmp" export SINGULARITY_CACHEDIR="/software/src/cache" This guide covers the basic setup for geospatial analysis on Midway3. Depending on specific project requirements, additional configurations or software packages might be necessary.