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Docs: Cori PICMI Instructions
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Too tricky to get right to just cross-link - add documentation how to
build & run PICMI interfaces on Cori.
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ax3l committed Aug 20, 2021
1 parent 04b7c5c commit 9b699a0
Showing 1 changed file with 21 additions and 7 deletions.
28 changes: 21 additions & 7 deletions Docs/source/install/hpc/cori.rst
Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,15 @@ If you want to run on either of the three partitions of Cori, open a new termina
# GPU:
#source $HOME/gpu_warpx.profile
.. warning::

Consider that all three Cori partitions are *incompatible*.

Do not *source* multiple ``...warpx.profile`` files in the same terminal session.
Open a new terminal and log into Cori again, if you want to switch the targeted Cori partition.

If you re-submit an already compiled simulation that you ran on another day or in another session, *make sure to source* the corresponding ``...warpx.profile`` again after login!

Then, ``cd`` into the directory ``$HOME/src/warpx`` and use the following commands to compile:

.. code-block:: bash
Expand All @@ -153,16 +162,19 @@ Then, ``cd`` into the directory ``$HOME/src/warpx`` and use the following comman
cmake -S . -B build -DWarpX_OPENPMD=ON -DWarpX_DIMS=3
cmake --build build -j 16
The general :ref:`cmake compile-time options and instructions for Python (PICMI) bindings <building-cmake>` apply as usual.
The general :ref:`cmake compile-time options and instructions for Python (PICMI) bindings <building-cmake>` apply as usual:

.. warning::

Consider that all three Cori partitions are *incompatible*.
.. code-block:: bash
Do not *source* multiple ``...warpx.profile`` files in the same terminal session.
Open a new terminal and log into Cori again, if you want to switch the targeted Cori partition.
# PICMI build
cd $HOME/src/warpx
If you re-submit an already compiled simulation that you ran on another day or in another session, *make sure to source* the corresponding ``...warpx.profile`` again after login!
# update Python dependencies
python3 -m pip install --user -U pip
CFLAGS="$(CC --cray-print-opts=cflags)" LDFLAGS="$(CC --cray-print-opts=libs)" python3 -m pip install -U --user mpi4py
# compile parallel PICMI interfaces with openPMD support and 3D, 2D and RZ
WarpX_MPI=ON WarpX_OPENPMD=ON BUILD_PARALLEL=16 python3 -m pip install --force-reinstall -v --user .
.. _running-cpp-cori:

Expand All @@ -178,6 +190,8 @@ The batch script below can be used to run a WarpX simulation on 2 KNL nodes on
the supercomputer Cori at NERSC. Replace descriptions between chevrons ``<>``
by relevant values, for instance ``<job name>`` could be ``laserWakefield``.

For PICMI Python runs, the ``<path/to/executable>`` has to read ``python3`` and the ``<input file>`` is the path to your PICMI input script.

.. literalinclude:: ../../../../Tools/BatchScripts/batch_cori.sh
:language: bash

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