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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 8a52a628f3013f125a864dec409fdbfe
+tags: 645f666f9bcd5a90fca523b33c5a78b7

952-sparse_advection-format-string-incorrect/_sources/index.rst.txt

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+.. Spiner Documentation master file, created by
+   sphinx-quickstart on Tue Nov 2 16:56:44 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Parthenon: A Performance Portable Block-Structured Adaptive Mesh Refinement Framework
+=====================================================================================
+
+`Parthenon`_ is a performance portable block-structured adaptive mesh refinement framework.
+
+.. _Parthenon: https://github.com/parthenon-hpc-lab/parthenon
+
+Key Features
+^^^^^^^^^^^^^
+
+* Device first/device resident approach (work data only in device memory to prevent expensive transfers between host and device)
+* Transparent packing of data across blocks (to reduce/hide kernel launch latency)
+* Direct device-to-device communication via asynchronous, one-sided  MPI communication
+* Intermediate abstraction layer to hide complexity of device kernel launches
+* Flexible, plug-in package system
+* Abstract variables controlled via metadata flags
+* Support for particles
+* Multi-stage drivers/integrators with support for task-based parallelism
+
+Community
+^^^^^^^^^^
+
+* `Chat room on matrix.org`_
+
+.. _`Chat room on matrix.org`: https://app.element.io/#/room/#parthenon-general:matrix.org
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+   :glob:
+
+   src/*
+   src/interface/*
+   src/mesh/*
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`

952-sparse_advection-format-string-incorrect/_sources/src/README.rst.txt

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+Overview
+========
+
+This file provides an overview of different (not necessarily all)
+features in Parthenon and how to use them.
+
+Building parthenon
+------------------
+
+See the :ref:`build doc <building>` for details on building Parthenon
+for specific systems.
+
+Description of examples
+-----------------------
+
+-  `Calculate π <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/example/calculate_pi>`_
+-  `Average face-centered variables to cell
+   centers <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/example/face_fields>`_
+-  `Stochastic subgrid <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/example/stochastic_subgrid>`_ Performs a
+   random amount of work per cell (drawn from a power law distribution)
+
+Short feature descriptions
+--------------------------
+
+Automated tests
+~~~~~~~~~~~~~~~
+
+Regression and convergence tests that cover the majority of features are
+based on the `Advection example <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/example/advection-example>`__ and
+defined in the
+`advection-convergence <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/tst/regression/test_suites/advection_convergence>`__
+and `output_hdf5 <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/tst/regression/test_suites/output_hdf5>`__ test
+suites.
+
+The tests currently cover
+
+- advection of wave in x, y, and z direction
+  as well oblique to the *static* grid for different resolutions to
+  demonstrate first order convergence (see
+  ``tst/regression/outputs/advection_convergence/advection-errors.png``
+  file in the build directory after running the test)
+- Advection of a smoothed sphere at an angle on a *static* grid, on a *static* grid a
+  twice the resolution, and with *AMR* covering the sphere at the
+  effective higher resolution
+- Advection of a sharp sphere at an angle
+  with *AMR* writing hdf5 output and comparing against a gold standard output.
+
+To execute the tests run, e.g.,
+
+.. code:: bash
+
+   # from within the build directory (add -V fore more detailed output)
+   ctest -R regression
+
+The gold standard files (reference solutions) used in the regression
+tests should automatically be downloaded during the configure phase.
+Alternatively, you can download them as a release from
+`GitHub <https://github.com/parthenon-hpc-lab/parthenon/releases/>`__ and extract the
+contents of the archive to
+``PARTHENON_ROOT/tst/regression/gold_standard`` directory. Make sure to
+get the correct version matching your source (stored in the
+``REGRESSION_GOLD_STANDARD_VER`` CMake variable). Note: If you results
+are (slightly) different, that may stem from using different
+compiler/optimization options.
+
+In case you adds new tests that require reference data just put all file
+in the ``PARTHENON_ROOT/tst/regression/gold_standard`` directory and
+either
+
+- increase the version integer by one (both in the
+  ``PARTHENON_ROOT/tst/regression/gold_standard/current_version`` file and
+  in the ``PARTHENON_ROOT/CMakeLists.txt`` file), or
+- configure with
+  ``REGRESSION_GOLD_STANDARD_SYNC=OFF``. The former is considered the
+  safer option as it prevents accidental overwriting of those files during
+  configure (as ``REGRESSION_GOLD_STANDARD_SYNC`` is ``ON`` by default).
+  In the pull request of the suggested changes we will then update the
+  official gold standard release file and appropriate hash prior to
+  merging.
+
+Usage in downstream codes
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The easiest/recommended way to reuse the ``Parthenon`` regression test
+infrastructure in downstream codes is to adapt a similar directory
+structure. The following steps have been tested to work when
+``Parthenon`` is built from source in the downstream project
+(specifically, the ``Parthenon`` source is expected to be located in the
+``external/parthenon`` folder in the project’s root directory) :
+
+1. Add the following to the downstream root ``CMakeLists.txt`` after
+   ``Parthenon`` has been included:
+
+::
+
+   include(CTest)
+   add_subdirectory(tst/regression)
+
+.. note::
+   If the ``Parthenon`` regression tests should also be integrated
+   in the downstream testing, the binary output directory should only be
+   changed (e.g., via the ``CMAKE_RUNTIME_OUTPUT_DIRECTORY`` variable)
+   *after* ``Parthenon`` has been included. Otherwise the paths to the
+   ``Parthenon`` regression test binaries will be wrong.
+
+2. Create the following directories and files in the project folder (for an example
+   ``my_first_test`` test):
+
+::
+
+   tst/
+       regression/
+           CMakeLists.txt
+           test_suites/
+               __init__.py  # <-- empty file
+               my_first_test/
+                   __init.py__  # <-- empty file
+                   my_first_test.py
+
+3. Contents of ``tst/regression/CMakeLists.txt``
+
+::
+
+
+   # import Parthenon setup_test_serial and setup_test_parallel
+   include(${PROJECT_SOURCE_DIR}/external/parthenon/cmake/TestSetup.cmake)
+
+   setup_test_serial("my_first_test" "--driver /path/to/downstream_binary \
+     --driver_input ${PROJECT_SOURCE_DIR}/inputs/test_input_file.in --num_steps 3" "my_custom_test_label")
+
+The same options for ``setup_test_serial`` and ``setup_test_parallel``
+as described in Parthenon `here <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/tst/regression/CMakeLists.txt>`__
+and `here <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/cmake/TestSetup.cmake>`__ apply.
+
+4. ``my_first_test.py`` contains the same logic as any other test in Parthenon, see a
+   `simple <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/tst/egression/test_suites/advection_outflow/advection_outflow.py>`__
+   or more
+   `complicated <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/tst/egression/test_suites/advection_outflow/advection_outflow.py>`__
+   example.
+
+5. Now ``my_first_test`` should be automatically executed when
+   running ``ctest`` from the build directory.
+
+ParthenonManager
+~~~~~~~~~~~~~~~~
+
+This class provides a streamlined capability to write new applications
+by providing a simple interface to initialize and finalize a simulation.
+It’s usage is straightforward and demonstrated in the π
+`example <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/example/calculate_pi/calculate_pi.cpp>`__.
+
+Initialization is mandatory and takes care of (including sanity checks)
+
+1. initializing MPI (if enabled)
+2. initializing Kokkos (including device setup)
+3. parsing command line arguments and parameter input file
+4. ``ProcessPackages`` Constructs and returns a ``Packages_t`` object
+   that contains a listing of all the variables and their metadata
+   associated with each package.
+
+Application can chose between a single and double stage initialization:
+
+- Single stage: ``ParthenonInit(int argc, char *argv[])`` includes steps 1-5 above.
+- Double stage: ``ParthenonInitEnv(int argc, char *argv[])``
+  includes steps 1-3 and ``ParthenonInitPackagesAndMesh()`` includes steps
+  4 and 5. This double stage setup allows, for example, to control the
+  package's behavior at runtime by setting the problem generator based on
+  a variable in the input file.
+
+User-specified internal functions
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+During a simulation, Parthenon calls a number of default internal
+functions whose behavior can be redefined by an application. Currently,
+these functions are, by class:
+
+Mesh
+^^^^
+
+-  ``InitUserMeshData``
+-  ``PreStepUserWorkInLoop``
+-  ``PostStepUserWorkInLoop``
+-  ``UserWorkAfterLoop``
+
+MeshBlock
+^^^^^^^^^
+
+-  ``InitApplicationMeshBlockData``
+-  ``InitMeshBlockUserData``
+-  ``ProblemGenerator``
+-  ``UserWorkBeforeOutput``
+
+To redefine these functions, the user sets the respective function
+pointers in the ApplicationInput member app_input of the
+ParthenonManager class prior to calling ``ParthenonInit``. This is
+demonstrated in the ``main()`` functions in the examples.
+
+Note that the ``ProblemGenerator``\ s of ``Mesh`` and ``MeshBlock`` are
+mutually exclusive. Moreover, the ``Mesh`` one requires
+``parthenon/mesh/pack_size=-1`` during initialization, i.e., all blocks
+on a rank need to be in a single pack. This allows to use MPI reductions
+inside the function, for example, to globally normalize quantities. The
+``parthenon/mesh/pack_size=-1`` exists only during problem
+inititalization, i.e., simulations can be restarted with an arbitrary
+``pack_size``. For an example of the ``Mesh`` version, see the `Poisson
+example <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/example/poisson/parthenon_app_inputs.cpp>`__.
+
+Error checking
+~~~~~~~~~~~~~~
+
+Macros for causing execution to throw an exception are provided
+`here <https://github.com/parthenon-hpc-lab/parthenon/blob/develop/src/utils/error_checking.hpp>`__
+
+- ``PARTHENON_REQUIRE(condition, message)`` exits if the condition does not evaluate to true.
+- ``PARTHENON_REQUIRE_THROWS(condition, message)`` throws a ``std::runtime_error`` exception if the condition does not evaluate to true.
+- ``PARTHENON_FAIL(message)`` always exits.
+- ``PARTHENON_THROW(message)`` throws a runtime error.
+- ``PARTHENON_DEBUG_REQUIRE(condition, message)`` exits if the condition does not evaluate to true when in debug mode.
+- ``PARTHENON_DEBUG_REQUIRE_THROWS(condition, message)`` throws if the condition does not evaluate to true when in debug mode.
+- ``PARTHENON_DEBUG_FAIL(message)`` always exits when in debug mode.
+- ``PARTHENON_DEBUG_THROW(message)`` throws a runtime error when in debug mode.
+
+All macros print the message, and filename and line number where the
+macro is called. PARTHENON_REQUIRE also prints the condition. The macros
+take a ``std::string``, a ``std::stringstream``, or a C-style string. As
+a rule of thumb:
+
+- Use the exception throwing versions in non-GPU,
+  non-performance critical code.
+- On GPUs and in performance-critical
+  sections, use the non-throwing versions and give them C-style strings.
+
+Developer guide
+~~~~~~~~~~~~~~~
+
+Please see the :ref:`full development guide <development>` on how to use
+Kokkos-based performance portable abstractions available within
+Parthenon and how to write performance portable code.
+
+State Management
+~~~~~~~~~~~~~~~~
+
+:ref:`Full Documentation <state>`
+
+Parthenon provides a convenient means of managing simulation data.
+Variables can be registered with Parthenon to have the framework
+automatically manage the field, including updating ghost cells,
+prolongation, restriction, and I/O.
+
+Application Drivers
+~~~~~~~~~~~~~~~~~~~
+
+A description of the Parthenon-provided classes that facilitate
+developing the high-level functionality of an application (e..g. time
+stepping) can be found :ref:`here <driver>`.
+
+Adaptive Mesh Refinement
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+A description of how to enable and extend the AMR capabilities of
+Parthenon is provided :ref:`here <amr>`.
+
+Tasks
+~~~~~
+
+The tasking capabilities in Parthenon are documented
+:ref:`here <tasks>`.
+
+Outputs
+~~~~~~~
+
+Check :ref:`here <outputs>` for a description of how to get data out of
+Parthenon and how to visualize it.
+
+MeshBlockDatas and MeshBlockData Iterators
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+See :ref:`here <containers>` for a description of containers,
+container iterators, and variable packs.
+
+Index Shape and Index Range
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+A description of mesh indexing classes :ref:`here <domain>`.
+
+Coordinates
+~~~~~~~~~~~
+
+Accessing coordinate information on each block is described
+:ref:`here <coordinates>`. Currently only uniform Cartesian coordinates
+are supported in Parthenon but uniform Spherical and cylindrical
+coordinates specified at compile time are forthcoming.
+
+Input file parameter
+~~~~~~~~~~~~~~~~~~~~
+
+An overview of input file parameters :ref:`here <inputs>`
+
+Note that all parameters can be overridden (or new parameters added)
+through the command line by appending the parameters to the launch
+command. For example, the ``refine_tol`` parameter in the
+``<parthenon/refinement0>`` block in the input file can be changed by
+appending ``parthenon/refinement0/refine_tol=my_new_value`` to the
+launch command (e.g.,
+``srun ./myapp -i my_input.file parthenon/refinement0/refine_tol=my_new_value``).
+This similarly applies to simulations that are restarted.
+
+Global reductions
+~~~~~~~~~~~~~~~~~
+
+Global reductions are a common need for downstream applications and can
+be accomplished within Parthenon’s task-based execution as described
+:ref:`here <reductions>`.
+
+Solvers
+~~~~~~~
+
+Solvers are still a work in progress in Parthenon, but some basic
+building blocks are described :ref:`here <solvers>`.