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Working with Docker and Singularity

CyVerse recently taught a Container BootCamp with in depth instructions for working with Docker and Singularity.

In these examples we’ll use Singularity to launch both Docker and Singularity containers.

Description: Run CLI and GUI programs on VMs using Docker & Singularity Containers

If you’re running on Windows OS you can set up the Windows-Linux subsystem to access a real Linux terminal. This will enable you to run secure shell connections to your VM.

Another option is to use the Atmosphere Web Desktop, which is running an XFCE Desktop.

Build a Singularity Container yourself

If you want to develop your own containers you can download the example Singularity file from my Github repository and make your own changes

EZ Install Singularity on Atmosphere or Jetstream

To install Singularity on linux follow these instructions.

As of early May 2018, Singularity is version 2.5.1

VERSION=2.5.1
wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz
tar xvf singularity-$VERSION.tar.gz
cd singularity-$VERSION
./configure --prefix=/usr/local
make
sudo make install
cd ..
sudo rm -rf singularity-$VERSION.tar.gz

Singularity build dependencies:

Get the Singularity file from terminal:

  1. Clone github repository onto the VM (e.g. /home/user/)
git clone https://github.com/tyson-swetnam/osgeo-singularity
cd osgeo-singularity
  1. Select Singularity file and view it if you like, make any changes you wish.
  2. Build the container locally:
sudo singularity build osgeo.simg Singularity

Download the Container from Singularity-Hub

The container image is hosted on Singularity Hub and can be downloaded from there.

  1. Pull the image from Singularity-Hub
singularity pull --name osgeo.simg shub://tyson-swetnam/osgeo-singularity

Running CLI scripts

To run the container from the CLI:

singularity shell osgeo.simg

Running a container from your Jupyter Notebook (Python3)

Run GUI Applications

Run the container with the singularity exec command to use the GUI applications, the interface for GRASS:

singularity exec osgeo.simg grass74

GRASS 7.4 has a problem with its environment variables not being set within the container. You can do this by hand while the container is running:

singularity shell osgeo.simg

GISBASE=/opt/osgeo/grass-7.4.0
GRASS_PROJSHARE=/usr/share/proj
LD_LIBRARY_PATH=/opt/osgeo/lib:/opt/osgeo/grass-7.4.0/lib
PATH=/opt/osgeo/bin:/opt/osgeo/grass-7.4.0/bin:$PATH
PYTHONPATH=/opt/osgeo/lib/python3.6/site-packages
export GISBASE GRASS_PROJSHARE LD_LIBRARY_PATH PATH PYTHONPATH

grass74

For QGIS:

singularity exec osgeo.simg qgis

For Saga-GIS:

singularity exec osgeo.simg saga_gui

Note

Running the GUI applications requires a stable, fast, internet connection, else loading large raster layers may be very slow.

You must use the Atmosphere Web Shell or ssh -X in the terminal to access the Container’s GUI applications.

ssh -X <USERNAME>@<IP-ADDRESS>

If you are using the Web Desktop, you can resize the screen by opening the terminal emulator and typing xrandr

 SZ:    Pixels          Physical       Refresh
 0   1024 x 768    ( 260mm x 195mm )   0
 1    800 x 600    ( 203mm x 152mm )   0
 2   1280 x 800    ( 325mm x 203mm )   0
 3   1280 x 960    ( 325mm x 244mm )   0
 4   1280 x 1024   ( 325mm x 260mm )   0
 5   1680 x 1050   ( 427mm x 267mm )   0
 6   1920 x 1080   ( 488mm x 274mm )   0
*7   1920 x 1200   ( 488mm x 305mm )  *0
 8   3360 x 1050   ( 853mm x 267mm )   0
 9   1024 x 700    ( 260mm x 178mm )   0
 10  1200 x 740    ( 305mm x 188mm )   0
 11  1600 x 1000   ( 406mm x 254mm )   0
 12  1600 x 1200   ( 406mm x 305mm )   0
 13  3200 x 1000   ( 813mm x 254mm )   0
 14  3200 x 1200   ( 813mm x 305mm )   0
Current rotation - normal
Current reflection - none
Rotations possible - normal
Reflections possible - none

This will show you the list of possible screen resolutions. To reset the screen resolution to HD (1920x1080):

xrandr -s 6

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