Summary

Keypoints

  • Load and run and pre-installed packages

    • Use python from module system

    • Start a Python shell session either with python or ipython

    • run scripts with python3 <script.py>

    • Check for preinstalled packages

      • from the Python shell with the import command

      • from BASH shell with the

        • pip list command at both centers

        • ml help python/3.9.5 at UPPMAX

        • module -r spider '.*Python.*' at HPC2N

  • Install packages and use isolated environments

    • With a virtual environment you can tailor an environment with specific versions for Python and packages, not interfering with other installed python versions and packages.

    • Make it for each project you have for reproducibility.

    • There are different tools to create virtual environemnts.
      • virtualenv and venv

        • install packages with pip.

        • the flag --system-site-packages includes preinstalled packages as well

    • (At UPPMAX Conda is also available)
      • Conda is an installer of packages but also bigger toolkits

        • Conda creates isolated environments as well - requires that you install all packages needed.

      • Rackham: Pip or secondary conda

      • Bianca: conda and secondary wharf + (pip or conda)

  • Batch mode

    • The SLURM scheduler handles allocations to the calculation nodes

    • Batch jobs runs without interaction with user

    • A batch script consists of a part with SLURM parameters describing the allocation and a second part describing the actual work within the job, for instance one or several Python scripts.

    • Remember to include possible input arguments to the Python script in the batch script.

  • Interactive work on calculation nodes
    • Start an interactive session on a calculation node by a SLURM allocation (similar flags)

      • At HPC2N: salloc …

      • At UPPMAX: interactive …

    • Follow the same procedure as usual by loading the Python module and possible prerequisites.

  • Parallel

    • You deploy cores and nodes via SLURM, either in interactive mode or batch

    • In Python, threads, distributed and MPI parallelization and DASK can be used.

  • GPUs

    • You deploy GPU nodes via SLURM, either in interactive mode or batch

    • In Python the numba package is handy

  • Machine Learning

    • At all clusters you will find PyTorch, TensorFlow, Scikit-learn

    • The loading are slightly different at the clusters

      • UPPMAX: All tools are available from the module python_ML_packages

      • HPC2N: module load GCC/10.3.0  OpenMPI/4.1.1 TensorFlow/2.6.0-CUDA-11.3.1

See also

Note