Introduction  

Dask Gateway  is a service which manages Dask  clusters for users. On JASMIN, it creates a Dask cluster in LOTUS, our batch computing cluster. It automatically creates a Dask for you, scheduling Slurm jobs to create Dask schedulers and workers as appropriate.

Prerequisites  

Before using Dask Gateway on JASMIN, you will need:

1. An existing JASMIN account and valid jasmin-login access role: Apply here     
2. Subsequently (once jasmin-login has been approved and completed), the dask access role: Apply here     

The jasmin-login access role ensures that your account is set up with access to the LOTUS batch processing cluster, while the dask role grants access to the special LOTUS partition used by the Dask Gateway service.

Creating a Dask cluster  

In the JASMIN Notebooks service  

In the JASMIN notebooks service  , authentication to dask-gateway happens automatically. You can use the snippet below to create a cluster and get a Dask client which you can use:

import dask_gateway

# Create a connection to dask-gateway.
gw = dask_gateway.Gateway("https://dask-gateway.jasmin.ac.uk", auth="jupyterhub")

# Inspect and change the options if required before creating your cluster.
options = gw.cluster_options()
options.worker_cores = 2

# Create a Dask cluster, or, if one already exists, connect to it.
# This stage creates the scheduler job in Slurm, so it may take some
# time while your job queues.
clusters = gw.list_clusters()
if not clusters:
    cluster = gw.new_cluster(options, shutdown_on_close=False)
else:
    cluster = gw.connect(clusters[0].name)

# Create at least one worker, and allow your cluster to scale to three.
cluster.adapt(minimum=1, maximum=3)

# Get a Dask client.
client = cluster.get_client()

#########################
### DO DASK WORK HERE ###
#########################

# When you are done and wish to release your cluster:
cluster.shutdown()

Elsewhere on JASMIN  

The following explains how to use the Dask Gateway elsewhere on JASMIN, for example, on the sci machines.

At the current time, it is still necessary to use the notebooks service to generate an API token to allow you to connect to the gateway server.

Setup  

1. Make a Dask configuration folder in your home directory

   mkdir -p ~/.config/dask

2. Create a configuration file for dask-gateway

   touch ~/.config/dask/gateway.yaml

3. Change the permissions on the file so that only you can read it

   chmod 600 ~/.config/dask/gateway.yaml

4. Head to the API token generator page  , put a note in the box to remind yourself what this token is for, press the big orange button, then copy the token.

5. Paste the following snippet into ~/.config/dask/gateway.yaml, replace the entry on the final line with the API token you just created.

   gateway:
     address: https://dask-gateway.jasmin.ac.uk
     auth:
       type: jupyterhub
       kwargs:
         api_token: replaceWithYourSecretAPIToken

6. You’re done. You can now use dask-gateway from the command line.

Access the Dask dashboard  

To get the link to your Dask dashboard, run the following:

print(client.dashboard_link)

Currently the Dask dashboard is not accessible from a browser outside the JASMIN firewall. If your browser fails to load the dashboard link returned, please use our graphical desktop service to run a Firefox browser inside the firewall to view your dashboard.

Use a custom Python environment  

By default the JASMIN Notebooks service and Dask Gateway use the latest version of the jaspy software environment. However, often users would like to use their own software environments.

Understanding the problem  

When Dask Gateway creates a dask cluster for a user, it runs a setup command to activate a conda environment or python venv. To have Dask use your packages, you need to create a custom environment which you can pass to dask-gateway to activate.

However, for technical reasons, it is not currently possible to use the same virtual environment in both the notebook service and on JASMIN. So you will need to make two environments, one for your notebook to use and one for Dask to use.

If you use a self-contained conda environment this is not a problem, and you can use this as a kernel in the notebooks service and on the sci machines. You can skip to Putting it all together below.

Creating a virtual environment for Dask  

• Login to one of the JASMIN sci machines.
• Activate jaspy

module load jaspy

• Create your environment in the normal way

python -m venv name-of-environment

• Activate the environment

source name-of-environment/bin/activate

• Install dask and dask gateway and dependencies: without this step your environment will not work with dask.

pip install dask-gateway dask lz4

Creating a virtual environment for the notebooks service  

• Follow the instructions here to create a virtual environment.
• Install Dask and Dask Gateway and dependencies: without this step your environment will not work with Dask.

pip install dask-gateway dask lz4

Putting it all together  

• Set your notebook virtual environment as the kernel for the notebook in question as shown in the instructions linked above.
• Set options.worker_setup to a command which will activate your Dask virtual environment. For example

options.worker_setup = "source /home/users/example/name-of-environment/bin/activate"

• If you have an existing Dask cluster, close it and ensure all LOTUS jobs are stopped before recreating it using the new environment.

Code Examples  

Examples of code and notebooks which can be used to test the JASMIN Dask Gateway service are available on GitHub  .