Difference between revisions of "Jupyter on Euler and Leonhard Open"

Revision as of 14:34, 6 May 2022

Introduction

Jupyter notebooks and Jupyter Lab are becoming more widely used among the scientific community at ETH. We therefore developed a script that you can run on your local computer to start Jupyter notebooks or Jupyter lab on Euler. The shell script starts a Jupyter in a batch job on Euler and connects your local browser with it.

The script runs on Linux, macOS and Windows (using WSL/WSL2 or git bash).

Please note, that with this script we are addressing beginners that start to use Jupyter notebooks on the cluster. It is not addressing advanced users that need a wide range of additional features going beyond simple Jupyter notebooks. Advanced users can take the script and adapt it, such that it can be used with other Python versions (centrally installed, or local installations) and add support for GPU, adding new kernels etc.

Installation

Download the repository with the commnad

git clone https://gitlab.ethz.ch/sfux/Jupyter-on-Euler-or-Leonhard-Open

Mac OS X:

git clone https://gitlab.ethz.ch/sfux/Jupyter-on-Euler-or-Leonhard-Open.git

After downloading the script from gitlab.ethz.ch, you need to change its permissions to make it executable cd Jupyter-on-Euler-or-Leonhard-Open/ chmod 755 start_jupyter_nb.sh

Prerequisites

In order to use this script, users need to make sure, that they have set up SSH keys for passwordless access to the cluster:

https://scicomp.ethz.ch/wiki/Accessing_the_clusters#SSH_keys

Please make sure that xdg-open is installed. This package is used to automatically start your default browser. You can install it with the following command:

CentOS:

yum install xdg-utils

Ubuntu:

apt-get install xdg-utils

Further more, the script requires that there is a Python installation available, which is usually included in the Linux distribution or Mac OS.

Download and setup

The script is available on the Gitlab instance of ETH Zurich:

https://gitlab.ethz.ch/sfux/Jupyter-on-Euler-or-Leonhard-Open

Download the repository with the command

git clone https://gitlab.ethz.ch/sfux/Jupyter-on-Euler-or-Leonhard-Open

Mac OS X:

git clone https://gitlab.ethz.ch/sfux/Jupyter-on-Euler-or-Leonhard-Open.git

After downloading the script from gitlab.ethz.ch, you need to change its permissions to make it executable

chmod 755 start_jupyter_nb.sh

Software stack

Please note that currently the old software stack is still set a default (this will change). The script is using the new software stack (unless you explicitly request the old software stack with the option -s old (or --softwarestack old). Therefore please make sure that you set the new software stack as permanent default by using the command

set_software_stack.sh new

You can find more information about this script on our wiki:

https://scicomp.ethz.ch/wiki/Setting_permanent_default_for_software_stack_upon_login

Using SSH keys with non-default names

Since the reopening of Euler and Leonhard Open after the cyber attack in May 2020, we recommend to the cluster users to use SSH keys. We recommend to use different keys for Euler and Leonhard Open, with according names

$HOME/.ssh/id_ed25519_euler

In order to use this keys with the jupyter script, then there are two options. You can configure your ssh client to use this option automatically by adding the following lines in the $HOME/.ssh/config file on your local computer:

Host euler.ethz.ch
IdentityFile ~/.ssh/id_ed25519_euler

Both options work and are equivalent.

Installing additional Python packages locally

When starting a Jupyter notebook with this script, then it will use a central Python installation:

• New software stack: module load gcc/6.3.0 python/3.8.5
• Old software stack: module load new gcc/4.8.2 python/3.6.1

Therefore you can only use packages that are centrally installed out-of-the-box. But you have the option to install additional packages locally in your home directory, which can afterwards be used.

For installing a Python package from inside a Jupyter notebook, you would need to run the following command:

!pip install --user package_name

This will install package_name into $HOME/.local, as described on our wiki page about Python:

https://scicomp.ethz.ch/wiki/Python#Installing_a_Python_package.2C_using_PIP

Running the script

The start_jupyer_nb.sh script needs to be executed on your local computer. Please find below the list of options that can be used with the script:

$ ./start_jupyter_nb.sh -h
./start_jupyter_nb.sh: Script to start jupyter notebook/lab on Euler from a local computer
Usage: start_jupyter_nb.sh [options]

Options:

        -u | --username       USERNAME         ETH username for SSH connection to Euler
        -n | --numcores       NUM_CPU          Number of CPU cores to be used on the cluster
        -W | --runtime        RUN_TIME         Run time limit for jupyter notebook/lab in hours and minutes HH:MM
        -m | --memory         MEM_PER_CORE     Memory limit in MB per core

Optional arguments:

        -c | --config         CONFIG_FILE      Configuration file for specifying options
        -e | --environment    ENV              Python virtual environment
        -g | --numgpu         NUM_GPU          Number of GPUs to be used on the cluster
        -h | --help                            Display help for this script and quit
        -i | --interval       INTERVAL         Time interval for checking if the job on the cluster already started
        -k | --key            SSH_KEY_PATH     Path to SSH key with non-standard name
        -l | --lab                             Start jupyter lab instead of a jupyter notebook
        -s | --softwarestack  SOFTWARE_STACK   Software stack to be used (old, new)
        -v | --version                         Display version of the script and exit
        -w | --workdir        WORKING_DIR      Working directory for the jupyter notebook/lab

Examlples:

        ./start_jupyter_nb.sh -u sfux -n 4 -W 04:00 -m 2048 -w /cluster/scratch/sfux

        ./start_jupyter_nb.sh --username sfux --numcores 2 --runtime 01:30 --memory 2048 --softwarestack new

        ./start_jupyter_nb.sh -c $HOME/.jnb_config

Format of configuration file:

JNB_USERNAME=""             # ETH username for SSH connection to Euler
JNB_NUM_CPU=1               # Number of CPU cores to be used on the cluster
JNB_NUM_GPU=0               # Number of GPUs to be used on the cluster
JNB_RUN_TIME="01:00"        # Run time limit for jupyter notebook/lab in hours and minutes HH:MM
JNB_MEM_PER_CPU_CORE=1024   # Memory limit in MB per core
JNB_WAITING_INTERVAL=60     # Time interval to check if the job on the cluster already started
JNB_SSH_KEY_PATH=""         # Path to SSH key with non-standard name
JNB_SOFTWARE_STACK="new"    # Software stack to be used (old, new)
JNB_WORKING_DIR=""          # Working directory for jupyter notebook/lab
JNB_ENV=""                  # Path to virtual environment
JNB_JLAB=""                 # "lab" -> start jupyter lab; "" -> start jupyter notebook

Example for running a Jupyter notebook on the Euler cluster

Reconnect to a Jupyter notebook

When running the script, it creates a local file called reconnect_info in the installation directory, which contains all information regarding the used ports, the remote IP address, the command for the SSH tunnel and the URL for the browser. This information should be sufficient to reconnect to a Jupyter notebook if connection was lost.

Terminate the Jupyter session

Please note that when you finish working with the jupyter notebook, you need to click on the "Quit" or "Logout" button in your Browser. "Quit" will stop the batch job running on Euler, "Logout" will just log you out from the session but not stop the batch job (in this case you need to login to the cluster, identify the job with bjobs and then kill it with the bkill command, using the jobid as parameter). Afterwards you also need to clean up the SSH tunnel that is running in the background.

Example:

samfux@bullvalene:~/Jupyter-on-Euler-or-Leonhard-Open$ ps -u | grep -m1 -- "-L" | grep -- "-N"
samfux    8729  0.0  0.0  59404  6636 pts/5    S    13:46   0:00 ssh sfux@euler.ethz.ch -L 51339:10.205.4.122:8888 -N
samfux@bullvalene:~/jupyter-on-Euler-or-Leonhard-Open$ kill 8729

Troubleshooting

Logs

If the script does not work, then we recommend to check the logs. There is on one hand the file $HOME/jnbinfo which contains logs, and on the other hand there is the lsf.o* logfile of the job that was running the jupyter notebook.

Mismatch of software stacks

In many cases it turns out that there are issues when the software stack used in the script does not match the default software stack that you have set. You can check which software stack is set as default by running the command

set_software_stack.sh -i

The script has an option (-s/--softwarestack) for which you can specify either "old" or "new". Please either adapt the software stack that you are requesting for the script or change the default setting for the software stack that you use on the cluster.

Conflict with locally installed Python packages

When the jnbinfo contains a Python error with a backtrace, then it could be that some of the Python packages that you installed locally in $HOME/.local are conflicting with the centrally provided Jupyter installation.

Jupyter in VSCode

Another possibility to work with jupyter notebooks on Euler is to run them in VSCode (https://code.visualstudio.com/docs/datascience/jupyter-notebooks). You can run VSCode (actually code-server) on Euler using the script:

https://scicomp.ethz.ch/wiki/VSCode