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Docs: NERSC ipympl Work-Around #2815

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Feb 2, 2022
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Docs: NERSC ipympl Work-Around #2815

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8 changes: 7 additions & 1 deletion Docs/source/install/hpc/cori.rst
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Expand Up @@ -320,11 +320,17 @@ In this manual, we often use this ``conda create`` line over the officially docu

.. code-block:: bash

conda create -n myenv -c conda-forge python mamba ipykernel ipympl matplotlib numpy pandas yt openpmd-viewer openpmd-api h5py fast-histogram
conda create -n myenv -c conda-forge python mamba ipykernel ipympl==0.8.1 matplotlib numpy pandas yt openpmd-viewer openpmd-api h5py fast-histogram

We then follow the `Customizing Kernels with a Helper Shell Script <https://docs.nersc.gov/services/jupyter/#customizing-kernels-with-a-helper-shell-script>`__ section to finalize the setup of using this conda-environment as a custom Jupyter kernel.

When opening a Jupyter notebook, just select the name you picked for your custom kernel on the top right of the notebook.

Additional software can be installed later on, e.g., in a Jupyter cell using ``!mamba install -c conda-forge ...``.
Software that is not available via conda can be installed via ``!python -m pip install ...``.

.. warning::

Jan 6th, 2022 (NERSC-INC0179165 and `ipympl #416 <https://github.com/matplotlib/ipympl/issues/416>`__):
Above, we fixated the ``ipympl`` version to *not* take the latest release of `Matplotlib Jupyter Widgets <https://github.com/matplotlib/ipympl>`__.
This is an intentional work-around; the ``ipympl`` version needs to exactly fit the version pre-installed on the Jupyter base system.
3 changes: 2 additions & 1 deletion Docs/source/install/hpc/perlmutter.rst
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Expand Up @@ -107,7 +107,8 @@ Post-Processing

For post-processing, most users use Python via NERSC's `Jupyter service <https://jupyter.nersc.gov>`__ (`Docs <https://docs.nersc.gov/services/jupyter/>`__).

Please follow the same guidance as for :ref:`NERSC Cori post-processing <post-processing-cori>`.
Please follow the same process as for :ref:`NERSC Cori post-processing <post-processing-cori>`.
**Important:** The *environment + Jupyter kernel* must separate from the one you create for Cori.

The Perlmutter ``$PSCRATCH`` filesystem is currently not yet available on Jupyter.
Thus, store or copy your data to Cori's ``$SCRATCH`` or use the Community FileSystem (CFS) for now.