Jupyter Notebook on UIowa's HPCs: An Example of Using Argon

I have been working a lot with our university’s high performance computing resources lately. The new system, Argon, is a very cool and exciting resource, each of whose node has 56 cores! It enables parallelization of data analysis, especially for those embarrassingly parallel tasks. I myself needs a lot of cores for data preprocessing and preliminary analyses and Argon really helps a lot.

However, in the past semesters, I found it not as convenient if I need to submit jobs all the time. Interactive is what I wanted. Therefore, I wanted to run Jupyter notebooks on the computing nodes. On asking the HPC admins (and thanks to them), I got to know that port forwarding can enable us access the notebook from the login node. However, this is not enough for me because login node can hardly handle heavy computing. With a bit of explorations, I find that running a Jupyter notebook from computing nodes are indeed possible by doing port forwarding twice!

Interactive sessions

To get Jupyter notebook run on the compute nodes, we need to use qlogin to start interactive sessions. A simple usage (that fits my own need) is

$ qlogin -q QUEUE_NAME -pe smp CORE_NUMBER

where QUEUE_NAME is the queue to submit to; CORE_NUMBER is the number of cores requested. Without the second argument -pe, a full node will be used (i.e., 56 cores).

After qlogin, nothing will be changed except the host name, which will be the name of the compute node (e.g., argon-mm-compute-4-06). Once we are on the compute node, we can start the notebook server, without prompting the browser, simply because no user interface is avaiable on HPC systems:

$ nohup jupyter notebook --no-browser --port 9898 > jupyter.log &

I like to use nohup, along with > jupyter.log & to make it run in the background and log any outputs into a specified file. One can specify any eligible port number. I like to stick with one choice so that I do not noeed to change it every time.

Port forwarding

Once we get Jupyter notebook to run on the compute node, we first forward the port number to the login node. My way is to run the following:

$ nohup ssh -L 9898:localhost:9898 COMPUTE-NODE -N > port_forward.log &

where 9898 is the port number I choose to use for both the compute and login node, just to make it simple. One can actually use different port numbers; COMPUTE-NODE is the host name of the compute node. Again, I make it run in the background for convenience.

The final step is just to repeat the above step on your own computer. The only change is to replace COMPUTE-NODE by LOGIN-NODE host name. This can be found in the terminal. In Argon, there are two login nodes: argon-login-1.hpc.uiowa.edu or argon-login-2.hpc.uiowa.edu.

Access the notebook on your local browser

Now, to access the notebooks, we need to find out the full URL on the compute node, where we start the notebook server. I usually use less to quickly look at the log and get the address. For example:

$ less jupyter.log

Then we can copy the line similar to the address below and open it in our own browser:

Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:

Finally we can enjoy both the interactive notebooks with the amazing computing resources of our HPC systems!

Stop the port fowarding

To kill the processes, we can use the following to find out the PID of the port forwarding processes and kill it:

$ ps aux | grep ssh | grep HAWKID
$ kill -9 PID

where HAWKID is the hawk id so that we can filter out processes related to ourselves; PID is in the number in the second column. We can find out the PID for Jupyter notebook in a similar way.

Zhiya Zuo

Zhiya Zuo

Filet-O-Fish 🍔 is the BEST!

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