Workshop materials for a 4h course on Dask Jobqueue

Dask Jobqueue Docs: https://jobqueue.dask.org

Recorded version

There's a recorded version of this workshop here:

• Part 1: https://training.e-cam2020.eu/files/5d244ed9e4b0920ffce61cd4
• Part 2: https://training.e-cam2020.eu/files/5d244edde4b0920ffce62116

Requirements

Depending on what type of a learner you are, you might want to learn more about Dask itself before diving in here. The https://examples.dask.org website and especially this binder with all the examplpes to be run interactively are a great place to start.

Topics covered in the course

• 00_A_brief_tour_of_the_docs.ipynb : A brief overview of the Dask-Jobqueue docs and of other relevant places to get help from.

• 01_local_cluster_monte_carlo_estimate_of_pi.ipynb : A short recap of LocalClusters that runs a Monte Carlo estimate of the number pi that is explained here.

• 02_slurm_cluster_monte_carlo_estimate_of_pi.ipynb : An intro to a basic deployment of a SLURMCluster that shows hot to manually scale a cluster.

• 03_tuning_adaptive_clusters.ipynb : Different ways of tuning adaptive SLURMClusters in order for them to automatically grow / shrink depending on the work load.

• 04_resilient_clusters.ipynb : An example with a fraction of the workers disapparing suddenly that shows how Dask is resilient to disappearing workers.

• 05_cluster_size_and_distributed_IO.ipynb : An example with Dask clusters spanning different numbers of HPC cluster nodes that shows how IO bandwidth in a distributed file system increases with cluster size.

• 10_scale_out_with_numba.ipynb : An example of scaling out JIT compiled code with Numba. (WIP)

• 99_Outlook.ipynb : An outlook on things not covered in this workshop and on possible future additions to Dask and Dask-Jobqueue.

Setup and Requirements

This workshop uses Jupyter Notebooks for all hands-on computations. To start working, please ask your cluster admins if they already offer a way of using Jupyter on their machine and what is the best way to use / install Python packages on their system.

If they cannot help, you can find info on how to set up and use a basic Python installation on HPC systems with Miniconda here: https://git.geomar.de/python/jupyter_on_HPC_setup_guide

An environment containing all dependencies necessary to follow the workshop, is defined in environment.yaml.

If you followed the guide above, you can set up all the dependencies by first activating the base environment of your Anaconda or Miniconda installation and then running:

conda env create -f <path-to-the-workshop-materials>/environment.yaml