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Quest and Kellogg Linux Cluster Downtime, December 14 - 18.
Quest, including the Quest Analytics Nodes, the Genomics Compute Cluster (GCC), the Kellogg Linux Cluster (KLC), and Quest OnDemand, will be unavailable for scheduled maintenance starting at 8 A.M. on Saturday, December 14, and ending approximately at 5 P.M. on Wednesday, December 18. During the maintenance window, you will not be able to login to Quest, Quest Analytics Nodes, the GCC, KLC, or Quest OnDemand submit new jobs, run jobs, or access files stored on Quest in any way including Globus. For details on this maintenance, please see the Status of University IT Services page.
Quest RHEL8 Pilot Environment - November 18.
Starting November 18, all Quest users are invited to test and run their workflows in a RHEL8 pilot environment to prepare for Quest moving completely to RHEL8 in March 2025. We invite researchers to provide us with feedback during the pilot by contacting the Research Computing and Data Services team at quest-help@northwestern.edu. The pilot environment will consist of 24 H100 GPU nodes and seventy-two CPU nodes, and it will expand with additional nodes through March 2025. Details on how to access this pilot environment will be published in a KB article on November 18.
Overview
Jupyter Notebook can be launched and run on a Quest compute node through an interactive job on Quest.
To schedule the interactive job from the command line on Quest, ssh into a login node and type:
srun -A <allocation_name> -p <queue_name> -N 1 --ntasks-per-node=1 --mem-per-cpu=4G --time=04:00:00 --pty bash -l
This example requests a single core for a 4 hour job. Substitute an active allocation name and queue name, for example if using allocation p12345 this might be:
srun -A p12345 -p short -N 1 --ntasks-per-node=1 --mem-per-cpu=4G --time=04:00:00 --pty bash -l
Note that the more cores requested, the longer the wait for the interactive session to start. Do not request more than 1 node for Jupyter notebook sessions.
Once the session begins, get the name of the compute node the session has landed on:
hostname
Load the version of python that you require for the session. For example, to load Python 3.7 use module load python-anaconda3/2019.10. Once the correct Python module has loaded, type:
jupyter notebook --port=8899 --no-browser
This example uses port 8899, but a please specify a different port as this example port is likely already in use.
Once jupyter notebook is running on the compute node, open a new terminal window on your local computer, and type:
ssh -L 8899:localhost:8899 <your_netID>@quest.northwestern.edu ssh -N -L 8899:localhost:8899 qnode<number>
If using a different port number, substitute it for the number "8899" in the command. Be sure and use your netID, and at the end replace qnode<number> with the name of the compute node. You will be prompted for your Quest password, which will not return a prompt.
On your local computer, open up your browser and connect to http://localhost:8899/. If not using port 8899, change the address to use the port specified when you launched jupyter notebook. Your browser is now connected to the jupyter notebook session running on Quest.
Note that your jupyter notebook session will quit abruptly when the walltime of the interactive job comes to an end. Save often and be aware of walltime to avoid losing your work.
Accessing Conda Environments in Jupyter
By default, jupyter will use the "root" environment of the Anaconda module you have loaded. If you are using a conda environment, for example to be able to install specific versions of software or because you are sharing an environment with other people in your group, you will need to manually install the environment into your jupyter configuration. This can only be done from the command line, not within the jupyter notebook. First, load whichever Anaconda module you are using and activate your environment, for example:
Create a iPython Kernel
module purge all
module load python-miniconda3/4.12.0
conda create --name jupyter-kernel-py38 -c conda-forge python=3.8 numpy pandas matplotlib ipykernel --yes
source activate jupyter-kernel-py38
python -m ipykernel install --user --name jupyter-kernel-py38 --display-name "Python (jupyter-kernel-py38)"
The last command adds the environment to your list of available environments in Jupyter, and once you have done this it will be available for you under the "New" menu.
Create a R Kernel
module purge all
module load python-miniconda3/4.12.0
conda create -c conda-forge --name r-kernel r-irkernel r=4.1 jupyterlab
source activate r-kernel
R -e "IRkernel::installspec(name = 'ir41', displayname = 'R4.1')"
The last command adds the environment to your list of available environments in Jupyter, and once you have done this it will be available for you under the "New" menu.
Then, when you launch jupyter using the commands given above, you will have the option of launching a notebook using your newly installed environment as the kernel:
