Overview

Teaching: min
Exercises: min

Questions

Objectives

1. Setting up individual Jupyter kernel for using Libra on the OOD (Open On Demand)

1. Add this in your .bashrc:

module use /projects/academic/cyberwksp21/MODULES
module load libra_ava/devel

Restart your terminal or reload your .bashrc:

source ~/.bashrc

2. Activate libra environment and install jupyter kernel in user location:

conda activate libra 
python -m ipykernel install     --user     --name libra     --display-name "Python (libra)"

3. Update the kernel.json file in /user/<your username>/.local/share/jupyter/kernels/libra to be like this:

{
 "argv": [
  "/user/<your username>/.local/share/jupyter/kernels/libra/launcher.sh",
  "-f",
  "{connection_file}"
 ],
 "display_name": "Python (libra)",
 "language": "python",
 "metadata": {
  "debugger": true
 }
}

Note: Replace <your username> with your actual user name e.g. alexeyak

4. Create the file launcher.sh in /user/<your username>/.local/share/jupyter/kernels/libra to be like this:

#!/bin/bash
# ======================================================
# HARD CLEAN (CRITICAL on CCR)
# ======================================================
unset PYTHONPATH
unset PYTHONHOME
unset EBPYTHONPREFIXES
# Prevent user site leakage
export PYTHONNOUSERSITE=1
# ======================================================
# Load module environment (ONLY ONE layer)
# ======================================================
module use /projects/academic/cyberwksp21/MODULES
module load libra_ava/devel
# ======================================================
# Activate Conda environment (must match module!)
# ======================================================
source /projects/academic/cyberwksp21/SOFTWARE/Conda/etc/profile.d/conda.sh
conda activate libra
# ======================================================
# Libra runtime libraries
# ======================================================
export LD_LIBRARY_PATH=/projects/academic/cyberwksp21/SOFTWARE/libra/_build/src:$LD_LIBRARY_PATH
# ======================================================
# Launch kernel
# ======================================================
exec /projects/academic/cyberwksp21/SOFTWARE/Conda/envs/libra/bin/python \
     -m ipykernel_launcher "$@"

And make it executable:

chmod +x .local/share/jupyter/kernels/libra/launcher.sh

5. Launch Jupyter on the OOD without any additional modules load needed

6. In the started Jupyter select “Python (libra)” kernel

2. Starting tutorials

The Libra tutorials are available at https://github.com/compchem-cybertraining/Tutorials_Libra

it is advisable that you just clone this repository to your local working directory and go from there.

1. Go to your working directory, e.g.:

cd /projects/academic/cyberwksp21/Students/alexeyak/libra_examples`

or go to your home directory:

cd

2. Clone the Tutorials_Libra repository:

git clone https://github.com/compchem-cybertraining/Tutorials_Libra.git

3. Start your Jupyter app on the OOD and open the desired tutorial/example

4. Keep in mind that Jupyter app run on the OOD can “see” only your home directory.

If you keep your examples elsewhere, e.g. on the /projects/academic/cyberwksp21/Students/alexeyak,

you need to create a symlink (symbolic link) to that directory in your home directory, e.g.:

cd
ln -s /projects/academic/cyberwksp21/Students/<my working folder> workshop

Note: replace <my working folder> with the actual name

This will create a link (that would appear as a folder) in your home directory called workshop. It will point to the actual folder located at /projects/academic/cyberwksp21/Students/<my working folder>

WARNING: Link behaves the same way as the actual folder, so if you try to delete the link like this rm -r workshop, it will delete your actual tutorials folder. If you no longer need the link, use rm workshop (no -r option!)

3. Lesson plan

To be added

Key Points