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How to connect to the Linux machines

  1. Putty connect to mp-linux-2
  2. (One time only) install pyenv (see below)
  3. Start the correct python environment
  4. Launch Jupiter lab
  5. Connect Jupyter lab from a browser (on Windows or anywhere else)

Typical setup for a new user account

Shell and general configuration files


Accessing AFS and EOS

AFS and EOS are mounted automatically:

ls /afs ls /eos

For convenience it is easy to create symbolic links in your home directory:

ln -s /afs/ afs
ln -s /eos/home-c/chernal Eos

Python environments

Instead of relying on the system Python installation (e.g. installed from yum) it is best to use a Python version management system such as pyenv.

First, install pyenv:

git clone ~/.pyenv
cd ~/.pyenv && src/configure && make -C src
echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bash_profile
echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bash_profile
echo -e 'if command -v pyenv 1>/dev/null 2>&1; then\n  eval "$(pyenv init -)"\nfi' >> ~/.bash_profile

Also use a virtualenv manager in the form of a plugin for peen:

git clone (pyenv root)/plugins/pyenv-virtualenv echo 'eval "(pyenv virtualenv-init -)"' >> ~/.bash_profile

You can then install some Python versions

pyenv install 3.8.8 pyenv virtualenv 3.8.8 my-virtual-env-3.8.8

That way one can maintain a clean environment for each project.

pyenv shell 3.8.8 Or pyenv shell my-virtual-env-3.8.8

Using Jupyter Lab or Jupyter Notebook

Two strategies: - install Jupiter lab in your project environment (easier) - install an environment specifically for Jupiter lab and add multiple kernels (more elegant)

A Jupyter service as been added for firewalls, the ports in the range 8888 to 8899 are open. See

Installing Jupyter lab in the project environment

pip install jupyterlab

Do not forget to change the configuration file to allow connection from any IP, not just localhost.

Git and gitlab


Upload your public key to Gitlab (via the web interface in your settings).

ssh-keygen -t ed25519 -C ""

And test it at the end:

ssh -T


Git submodule update --init --recursive

Plugin for Jupyter lab for plotly

(As root) curl -fsSL | bash - Sudo yum install nodejs

jupyter labextension install jupyterlab-plotly@4.14.3

jupyter labextension install @jupyter-widgets/jupyterlab-manager plotlywidget@4.14.3

Need to install node first

Sudo ym install npm