Documentation fixes by glesur · Pull Request #248 · idefix-code/idefix · GitHub
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Documentation fixes #248

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Merged
glesur merged 5 commits into from
Jun 19, 2024
Merged

Documentation fixes #248

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f011d36
directly ask kokkos for its execution space
glesur Jun 18, 2024
0dbcf5d
remove replace source files, as this doesn't work with header files
glesur Jun 18, 2024
6dcb5e7
add proper readme
glesur Jun 19, 2024
83670ef
clean up hdf5 mess in readme (is already in the full doc)
glesur Jun 19, 2024
78394ec
add Async malloc option to JZ configuration
glesur Jun 19, 2024
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33 changes: 30 additions & 3 deletions README.md
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24 changes: 5 additions & 19 deletions doc/source/reference/makefile.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -146,15 +146,16 @@ We recommend the following modules and environement variables on Jean Zay:

.. code-block:: bash

-DKokkos_ENABLE_CUDA=ON -DKokkos_ENABLE_VOLTA70=ON
-DKokkos_ENABLE_CUDA=ON -DKokkos_ENABLE_VOLTA70=ON -DKokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC=OFF

While Ampere A100 GPUs are enabled with

.. code-block:: bash

-DKokkos_ENABLE_CUDA=ON -DKokkos_ENABLE_AMPERE80=ON
-DKokkos_ENABLE_CUDA=ON -DKokkos_ENABLE_AMPERE80=ON -DKokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC=OFF

MPI (multi-GPU) can be enabled by adding ``-DIdefix_MPI=ON`` as usual.
MPI (multi-GPU) can be enabled by adding ``-DIdefix_MPI=ON`` as usual. The malloc async option is here to prevent a bug when using PSM2 with async
cuda malloc possibly leading to openmpi crash or hangs on the Jean Zay machine.

.. _setupSpecificOptions:

Expand All @@ -176,7 +177,7 @@ explicitely the options as they are required, using the functions ``set_idefix_p

.. _customSourceFiles:

Add/replace custom source files
Add custom source files
+++++++++++++++++++++++++++++++

It is possible to add custom source files to be compiled and linked against *Idefix*. This can be useful
Expand All @@ -191,21 +192,6 @@ say you want to add source files for an analysis, your ``CMakeLists.txt`` should
add_idefix_source(analysis.hpp)


*Idefix* also allows one to replace a source file in `$IDEFIX_DIR` by your own implementation. This is useful when developping new functionnalities without touching
the main directory of your *Idefix* repository. For instance, say one wants to replace the implementation of viscosity in `$IDEFIX_SRC/src/hydro/viscosity.cpp`,
with a customised `myviscosity.cpp` in the problem directory, one should add a ``CMakeLists.txt`` in the problem directory reading

.. code-block::
:caption: CMakeLists.txt

replace_idefix_source(hydro/viscosity.cpp myviscosity.cpp)


Note that the first parameter of ``replace_idefix_source`` is used as a search pattern in `$IDEFIX_DIR`. Hence it is possible to ommit the parent directory
of the file being replaced if there is only one file with that name in the *Idefix* source directory, which is not guaranteed (some classes may implement
methods with the same name). It is therefore recommended to add the parent directory in the first argument of ``replace_idefix_source``.


.. tip::

Don't forget to delete `CMakeCache.txt` before attempting to reconfigure the code when adding a problem-specific
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15 changes: 6 additions & 9 deletions src/input.cpp
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