diff options
| -rw-r--r-- | Docs/source/install/hpc/cori.rst | 22 | ||||
| -rw-r--r-- | Docs/source/install/hpc/perlmutter.rst | 13 | ||||
| -rw-r--r-- | Docs/source/install/hpc/spock.rst | 10 | ||||
| -rw-r--r-- | Docs/source/install/hpc/summit.rst | 35 |
4 files changed, 80 insertions, 0 deletions
diff --git a/Docs/source/install/hpc/cori.rst b/Docs/source/install/hpc/cori.rst index f1aeec351..c901500e6 100644 --- a/Docs/source/install/hpc/cori.rst +++ b/Docs/source/install/hpc/cori.rst @@ -313,3 +313,25 @@ A multi-node batch script template can be found below: .. literalinclude:: ../../../../Tools/BatchScripts/batch_cori_gpu.sh :language: bash + + +.. _post-processing-cori: + +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/>`__). + +As a one-time preparatory setup, `create your own Conda environment as described in NERSC docs <https://docs.nersc.gov/services/jupyter/#conda-environments-as-kernels>`__. +In this manual, we often use this ``conda create`` line over the officially documented one: + +.. conda-block:: bash + + conda create -n myenv -c conda-forge python mamba ipykernel ipympl 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 ...``. diff --git a/Docs/source/install/hpc/perlmutter.rst b/Docs/source/install/hpc/perlmutter.rst index 3efd44cbf..0901bf3b3 100644 --- a/Docs/source/install/hpc/perlmutter.rst +++ b/Docs/source/install/hpc/perlmutter.rst @@ -125,3 +125,16 @@ To run a simulation, copy the lines above to a file ``batch_perlmutter.sh`` and sbatch batch_perlmutter.sh to submit the job. + + +.. _post-processing-perlmutter: + +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>`. + +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. diff --git a/Docs/source/install/hpc/spock.rst b/Docs/source/install/hpc/spock.rst index e28daeb25..78bb08361 100644 --- a/Docs/source/install/hpc/spock.rst +++ b/Docs/source/install/hpc/spock.rst @@ -104,3 +104,13 @@ Or in non-interactive runs: :language: bash We can currently use up to ``4`` nodes with ``4`` GPUs each (maximum: ``-N 4 -n 16``). + + +.. _post-processing-spock: + +Post-Processing +--------------- + +For post-processing, most users use Python via OLCFs's `Jupyter service <https://jupyter.olcf.ornl.gov>`__ (`Docs <https://docs.olcf.ornl.gov/services_and_applications/jupyter/index.html>`__). + +Please follow the same guidance as for :ref:`OLCF Summit post-processing <post-processing-summit>`. diff --git a/Docs/source/install/hpc/summit.rst b/Docs/source/install/hpc/summit.rst index 794ec6bb0..55f0c7697 100644 --- a/Docs/source/install/hpc/summit.rst +++ b/Docs/source/install/hpc/summit.rst @@ -289,3 +289,38 @@ Known System Issues For instance, if you compile large software stacks with Spack, make sure to register ``libfabric`` with that exact version as an external module. If you load the documented ADIOS2 module above, this problem does not affect you, since the correct ``libfabric`` version is chosen for this one. + +.. warning:: + + Oct 12th, 2021 (OLCFHELP-4242): + There is currently a problem with the pre-installed Jupyter extensions, which can lead to connection splits at long running analysis sessions. + + Work-around this issue by running in a single Jupyter cell, before starting analysis: + + .. code-block:: bash + + !jupyter serverextension enable --py --sys-prefix dask_labextension + + +.. _post-processing-summit: + +Post-Processing +--------------- + +For post-processing, most users use Python via OLCFs's `Jupyter service <https://jupyter.olcf.ornl.gov>`__ (`Docs <https://docs.olcf.ornl.gov/services_and_applications/jupyter/index.html>`__). + +We usually just install our software on-the-fly on Summit. +When starting up a post-processing session, run this in your first cells: + +.. conda-block:: bash + + # work-around for OLCFHELP-4242 + !jupyter serverextension enable --py --sys-prefix dask_labextension + + # next Jupyter cell: install a faster & better conda package manager + !conda install -c conda-forge -y mamba + + # next cell: the software you want + !mamba install -c conda-forge -y openpmd-api openpmd-viewer ipympl ipywidgets fast-histogram yt + + # restart notebook |