Examples not working?

Log in to Wynton JupyterHub (JHub) #

As of now JHub can be accessed either by connecting to VPN or from campus network using JupyterHub Login.

Please set up your own environment before getting started. The base environment on JupyterHub is installed locally on the server and won’t be accessible from the cluster.

There are several ways one can set up an environment, we recommend using virtualenv. See Installing packages to a virtual environment for instructions.

Creating an IPython kernel for virtual environment #

To create an IPython kernel that you can access from JHub follow the steps below. First, activate the virtual environment, i.e.

[alice@dev1 ~]$ cd my_project
[alice@dev1 my_project]$ . bin/activate
(my_project) [alice@dev1 my_project]$

Second, install the ipykernel package and create an IPython kernel:

(my_project) [alice@dev1 my_project]$ python3 -m pip install ipykernel
(my_project) [alice@dev1 my_project]$ python3 -m ipykernel install --user --name=<my_project>

Refresh JHub page and you should see the new IPython kernel.

Interactive Data Science on SGE with Dask #

Dask can scale Python natively by distributing the job to compute nodes. You would have to use Dask-specific libraries to be able to leverage this.

from dask_jobqueue import SGECluster
from dask.distributed import Client

cluster = SGECluster(queue = "short.q",
                     cores = 1,
                     memory = "1GB",
                     walltime = "00:10:00",
                     death_timeout = 60,
                     local_directory = "/wynton/scratch/$USER",
                     log_directory = "~/dask_logs",
                     
                     # Python for Dask worker to use, visible to the grid nodes
                     python = "/wynton/group/jhadmin/base-clone/bin/python",
                     
                     # Increment the port up from 40000 if it's taken. 
                     # Needed for the Dask workers to communicate back
                     # to the scheduler on the app server
                     scheduler_options = {
                         "host": "jhub.wynton.ucsf.edu:40000"
                     })

import os

# Set environment variables
os.environ["SGE_ROOT"] = "/opt/sge"
os.environ["SGE_CLUSTER_NAME"]="wynton_cluster"
os.environ["SGE_CELL"]="wynton"
os.environ["SGE_ARCH"]="lx-amd64"

cluster.scale(2) # number of workers needed for your job
client = Client(cluster)
client

You can check if the workers are assigned, by running the qstat command from the Python prompt as:

!qstat

To print the assigned SGE parameters, call:

print(cluster.job_script())