JIVE Wiki

On this page you find instructions for optional software

Installing the infrastructure to run the Jupyter Notebooks is optional.

For parts of the tutorials we have developed Jupyter Notebooks based on the Jupyter CASA environment. This requires singularity or a docker container to run. For MacOS there is only a beta-version of singularity available, so the instructions below are based on docker. This installation is optional, all tutorials can also be done using the stand-alone version of CASA.

These instructions are verified to work on MacOS 10.14 and 10.15. For installation on a Linux system you can follow the same steps, as the docker platform should work the same way.

1. Install Docker for your preferred OS.
2. Open a terminal window
3. On the command line of the terminal type docker pull penngwyn/jupytercasa
4. Go to the directory where you want to do your data processing, or generate a new one
5. Move your data here and any notebook you already have
6. Run docker command: docker run -p 8888:8888 -i -t -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=$DISPLAY -v <absolute path to your data processing directory>:/home/jupyter/data penngwyn/jupytercasa
7. Copy the URL displayed in the terminal, paste it into a browser and edit it such that the section between brackets displays only the IP address. It should look something like: http://127.0.0.1:888/?token<loads of characters>.
8. You can generate a new notebook by clicking the “New” button on the top right in the notebook server page.
9. If you downloaded the tutorial notebook you should see it in the list on your browser and can launch it by clicking on the link once.

There is a known issue with X11-forwarding on MacOS. The workaround for this is to slightly modify step 6 above. You first launch the docker, inside the docker you launch the notebook. You can than proceed with step 7 above.

1. Start the docker with docker run -p 8888:8888 -i -t -e DISPLAY=$DISPLAY -v <absolute path to your data processing directory>:/home/jupyter/data penngwyn/jupytercasa
2. Inside the same terminal window launch the notebook xvfb-run jupyter notebook

If you launch the docker image with the -rm option (as it suggested in the Github readme), everything in the docker virtual drives will be removed upon shutdown. You probably don't want this to happen after a long day of work, so make sure the mirroring works.

The option -v mirrors a local directory on your laptop to a directory in the docker image. This is required to make the docker environment see your data and to store your notebooks on your local disk for future use. Upon shutdown of the container or notebook your local disks will not be touched.

The tutorial notebook is based on the VLA tutorial and requires the dataset you can download from this page. You can also follow the tutorial in a CASA5.7 installation on your laptop.

The notebook runs CASA5.6, but this should not impact the basic functionality used in the tutorials.

For the VLA tutorial there is a version of the notebook available in the examples. To get this to your laptop, in a terminal type wget https://github.com/aardk/jupyter-casa/raw/master/examples/vla-cont-tutorial.ipynb

There is a beta version of the EVN pipeline notebook and an example notebook based on the DARA and EVN tutorials. These will be linked here later.