Exercises

Isolated

Create a virtual environment with a requirements file below

Create a virtual environment with Python 3.11.X (check what is available on your cluster) with the name analysis.
Install packages defined by the requirements.txt file (save it).

numpy==1.22.3
matplotlib==3.5.2
pandas==1.4.2

Check that the packages were installed.
Don’t forget to deactivate afterwards.

Solution for UPPMAX

    $ module load python/3.11.8
    $ python -m venv --system-site-packages /proj/naiss2024-22-107/<user>/python/analysis

Activate it.

.. code-block:: sh

   $ source /proj/naiss2024-22-107/<user>/python/analysis/bin/activate

- Note that your prompt is changing to start with (analysis) to show that you are within an environment.
- Install the packages from the file::

  pip install -r requirements.txt

.. code-block:: sh

   $ pip list
   $ deactivate

Solution for HPC2N

    $ module load GCC/12.3.0 Python/3.11.3
    $ virtualenv --system-site-packages /proj/nobackup/hpc2n2024-025/<your-directory>/analysis

Activate it.

.. code-block:: sh

   $ source /proj/nobackup/hpc2n2024-025/<your-directory>/analysis/bin/activate

- Note that your prompt is changing to start with (analysis) to show that you are within an environment.
- Install the packages from the file::

  pip install -r requirements.txt

.. code-block:: sh

   $ pip list
   $ deactivate

Conda (UPPMAX)

UPPMAX: Create a conda environment and install some packages

Be sure to deactivate any virtual environment.
First check the current installed packages while having python/3.11.8 loaded
Open a new terminal and have the old one available for later comparison
Use the conda module on Rackham and create an environment with name HPC-python24 with python 3.11 and numpy 1.22
- Use your a path for CONDA_ENVS_PATH of your own choice or /proj/naiss2024-22-107/<user>/python
- (It may take a minute or so)
Activate!
Check with pip list what is there. Compare with the environment given from the python module in the first terminal window.
- Which version of Python did you get?
Don’t forget to deactivate the Conda environment before doing other exercises!

Solution for UPPMAX

Write this in the terminal

$ module load conda
$ export CONDA_ENVS_PATH=/proj/naiss2024-22-107/<user>/python
$ conda create --name HPC-python24 python=3.11 numpy=1.22
$ source activate HPC-python24
$ pip list
$ python -V
$ source deactivate

Batch

Run the first serial example script from further up on the page for this short Python code (sum-2args.py)

import sys

x = int(sys.argv[1])
y = int(sys.argv[2])

sum = x + y

print("The sum of the two numbers is: {0}".format(sum))

Remember to give the two arguments to the program in the batch script.

Solution for HPC2N

This batch script is for Kebnekaise. Adding the numbers 2 and 3.

#!/bin/bash
#SBATCH -A hpc2n2024-025 # Change to your own after the course
#SBATCH --time=00:05:00 # Asking for 5 minutes
#SBATCH -n 1 # Asking for 1 core

# Load any modules you need, here for Python 3.11.3
module load GCC/12.3.0  Python/3.11.3

# Run your Python script
python sum-2args.py 2 3

Solution for UPPMAX

This batch script is for UPPMAX. Adding the numbers 2 and 3.

#!/bin/bash
#SBATCH -A naiss2024-22-107 # Change to your own after the course
#SBATCH --time=00:05:00 # Asking for 5 minutes
#SBATCH -n 1 # Asking for 1 core

# Load any modules you need, here for Python 3.11.8
module load python/3.11.8

# Run your Python script
python sum-2args.py 2 3