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docs: add in-situ analysis (#586)
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### Description
Adds documentation for enabling *in-situ* analysis of simulations.

Also: updates the documentation on how to read a time series of
plotfiles with VisIt.

### Related issues
N/A

### Checklist
_Before this pull request can be reviewed, all of these tasks should be
completed. Denote completed tasks with an `x` inside the square brackets
`[ ]` in the Markdown source below:_
- [x] I have added a description (see above).
- [x] I have added a link to any related issues see (see above).
- [x] I have read the [Contributing
Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
- [ ] I have added tests for any new physics that this PR adds to the
code.
- [ ] I have tested this PR on my local computer and all tests pass.
- [ ] I have manually triggered the GPU tests with the magic comment
`/azp run`.
- [x] I have requested a reviewer for this PR.
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@BenWibking
BenWibking authored Apr 4, 2024
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3 changes: 2 additions & 1 deletion docs/index.rst
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running_on_hpc_clusters
tests/index
parameters
analysis
insitu_analysis
postprocessing
instability

Developer Guide
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141 changes: 141 additions & 0 deletions docs/insitu_analysis.rst
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.. insitu_analysis
In-situ analysis
=====

*In-situ analysis* refers to analyzing the simulations as they are running.
There are two options: using the *runtime diagnostics* that are built-in to Quokka, and using *Ascent*, a third-party library.

Diagnostics
-----------------------
Most of Quokka's diagnostics are adapted from the implementation included in the *Pele* suite of AMReX-based combustion codes.
(See the documentation for `PeleLMeX diagnostics <https://amrex-combustion.github.io/PeleLMeX/manual/html/LMeXControls.html#run-time-diagnostics>`_ for an explanation of the original implementation.)

There are three built-in diagnostics that can be configured to output at periodic intervals while the simulation is running:

* axis-aligned 2D projections
* axis-aligned 2D slices, and
* N-dimensional probability distribution functions (PDFs).

2D Projections
^^^^^^^^^^^^^^^^^^^^^^^
This diagnostic outputs 2D axis-aligned projections as AMReX plotfiles prefixed with `proj`.

Currently, using this diagnostic requires implementing a custom function in the problem generator for your simulation.
(In the future, this diagnostic may be improved so that it can be configured entirely with runtime parameters.)

The problem generator must call `computePlaneProjection(F const &user_f, const int dir)`
where `user_f` is a lambda function that returns the value to project and `dir` is the axis along which the projection is taken.

*Example problem generator implementation:* ::

template <> auto RadhydroSimulation<ShockCloud>::ComputeProjections(const int dir) const -> std::unordered_map<std::string, amrex::BaseFab<amrex::Real>>
{
// compute density projection
std::unordered_map<std::string, amrex::BaseFab<amrex::Real>> proj;
proj["nH"] = computePlaneProjection<amrex::ReduceOpSum>(
[=] AMREX_GPU_DEVICE(int i, int j, int k, amrex::Array4<const Real> const &state) noexcept {
Real const rho = state(i, j, k, HydroSystem<ShockCloud>::density_index);
return (quokka::cooling::cloudy_H_mass_fraction * rho) / m_H;
},
dir);
return proj;
}

*Example input file configuration:* ::

projection_interval = 200
projection.dirs = x z

2D Slices
^^^^^^^^^^^^^^^^^^^^^^^
.. note:: This is based on the *DiagFramePlane* diagnostic from PelePhysics, and the same
runtime parameters should apply here without modification. The output format is also the
same as that produced by the *Pele* codes.

This outputs 2D slices of the simulation as AMReX plotfiles that can be further examined using, e.g., VisIt or yt.

*Example input file configuration:* ::

quokka.diagnostics = slice_z # Space-separated name(s) of diagnostics (arbitrary)
quokka.slice_z.type = DiagFramePlane # Diagnostic type (others may be added in the future)
quokka.slice_z.file = slicez_plt # Output file prefix (should end in "plt")
quokka.slice_z.normal = 2 # Plane normal (0 == x, 1 == y, 2 == z)
quokka.slice_z.center = 2.4688e20 # Coordinate in the normal direction
quokka.slice_z.int = 10 # Output interval (in number of coarse steps)
quokka.slice_z.interpolation = Linear # Interpolation type: Linear or Quadratic (default: Linear)

# The problem must output these derived variable(s)
derived_vars = temperature
# List of variables to include in output
quokka.slice_z.field_names = gasDensity gasInternalEnergy temperature

Histograms/PDFs
^^^^^^^^^^^^^^^^^^^^^^^
.. note:: This is based on the *DiagPDF* diagnostic from PelePhysics, but significant changes
have been made to both the runtime parameters and the output format in order to support
N-dimensional histograms, log-spaced binning, and histogramming by mass.

This adds histogram outputs (as fixed-width text files) at fixed timestep intervals as the simulation evolves.
The quantity accumulated in each bin is the total mass, volume, or cell count summed over all cells not covered by refined grids over all AMR levels. If unspecified in the input parameters, the default is to accumulate the volume in each bin.

By default, the bins extend over the full range of the data at a given timestep. The *range* parameter can instead specify the minimum and maximum extent for the bins. Bins can be optionally log-spaced by setting *log_spaced_bins = 1*.

Normalization of the output is left up to the user.

*Example input file configuration:* ::

quokka.hist_temp.type = DiagPDF # Diagnostic type
quokka.hist_temp.file = PDFTempDens # Output file prefix
quokka.hist_temp.int = 10 # Output cadence (in number of coarse steps)
quokka.hist_temp.weight_by = mass # (Optional, default: volume) Accumulate: mass, volume, cell_counts
quokka.hist_temp.var_names = temperature gasDensity # Variable(s) of interest (compute a N-D histogram)

quokka.hist_temp.temperature.nBins = 20 # temperature: Number of bins
quokka.hist_temp.temperature.log_spaced_bins = 1 # temperature: (Optional, default: 0) Use log-spaced bins
quokka.hist_temp.temperature.range = 1e3 1e7 # temperature: (Optional, default: data range) Specify min/max of bins

quokka.hist_temp.gasDensity.nBins = 5 # gasDensity: Number of bins
quokka.hist_temp.gasDensity.log_spaced_bins = 1 # gasDensity: (Optional, default: 0) Use log-spaced bins
quokka.hist_temp.gasDensity.range = 1e-29 1e-23 # gasDensity: (Optional, default: data range) Specify min/max of bins


*Filters (based on any variables, not necessary those used for the histogram) can be optionally added:* ::

quokka.hist_temp.filters = dense # (Optional) List of filters
quokka.hist_temp.dense.field_name = gasDensity # Filter field
quokka.hist_temp.dense.value_greater = 1e-25 # Filters: value_greater, value_less, value_inrange

Ascent (deprecated)
-----------------------
.. warning:: Due to correctness and performance issues, **using Ascent is not recommended**. Support for Ascent will be removed in a future version of Quokka.

Ascent allows you to generate visualizations (as PNG images) while the simulation is running, without any extra effort.

.. note:: On Setonix, Ascent is already built.
In your job script, add the line:
``export Ascent_DIR=/software/projects/pawsey0807/bwibking/ascent_06082023/install/ascent-develop/lib/cmake/ascent``.

Compiling Ascent via Spack
^^^^^^^^^^^^^^^^^^^^^^^
1. Run ``spack external find``.
2. Make sure there are entries listed for ``hdf5``, ``cuda``, and ``openmpi`` in your ``~/.spack/packages.yaml`` file.
3. Add `buildable: False <https://spack.readthedocs.io/en/latest/build_settings.html#external-packages>`_ to each entry.
4. Run ``spack fetch --dependencies ascent@develop+cuda+vtkh~fortran~shared cuda_arch=70 ^conduit~parmetis~fortran``
5. On a dedicated compute node, run ``spack install ascent@develop+cuda+vtkh~fortran~shared cuda_arch=70 ^conduit~parmetis~fortran``

For A100 GPUs, change the above lines to `cuda_arch=80`.
Currently, it's not possible to `build for both GPU models at the same time <https://github.com/Alpine-DAV/ascent/issues/950#issuecomment-1153243232>`_.

Compiling Quokka with Ascent support
^^^^^^^^^^^^^^^^^^^^^^^
1. Load Ascent: ``spack load ascent``
2. Add ``-DAMReX_ASCENT=ON -DAMReX_CONDUIT=ON`` to your CMake options.
3. Compile your problem, e.g.: ``ninja -j4 test_hydro3d_blast``

Customizing the visualization
^^^^^^^^^^^^^^^^^^^^^^^
Add an `ascent_actions.yaml file <https://ascent.readthedocs.io/en/latest/Actions/Actions.html>`_ to the simulation working directory.
This file can even be edited while the simulation is running!

.. warning:: Volume renderings do not correctly handle ghost cells (`GitHub issue <https://github.com/Alpine-DAV/ascent/issues/955>`_).
50 changes: 13 additions & 37 deletions docs/analysis.rst → docs/postprocessing.rst
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.. Analysis
.. Postprocessing
Analyzing simulations
Postprocessing
=====

There are several ways to analyze Quokka simulations. One method (Ascent) allows you to run the analysis in memory as the simulation is running.
The other methods (AMReX PlotfileTools, yt, VisIt) allow you to analyze the outputs after they are written to disk.

Ascent
-----------------------
Ascent allows you to generate visualizations (as PNG images) while the simulation is running, without any extra effort.

.. note:: On Setonix, Ascent is already built.
In your job script, add the line:
``export Ascent_DIR=/software/projects/pawsey0807/bwibking/ascent_06082023/install/ascent-develop/lib/cmake/ascent``.

Compiling Ascent via Spack
^^^^^^^^^^^^^^^^^^^^^^^
1. Run ``spack external find``.
2. Make sure there are entries listed for ``hdf5``, ``cuda``, and ``openmpi`` in your ``~/.spack/packages.yaml`` file.
3. Add `buildable: False <https://spack.readthedocs.io/en/latest/build_settings.html#external-packages>`_ to each entry.
4. Run ``spack fetch --dependencies ascent@develop+cuda+vtkh~fortran~shared cuda_arch=70 ^conduit~parmetis~fortran``
5. On a dedicated compute node, run ``spack install ascent@develop+cuda+vtkh~fortran~shared cuda_arch=70 ^conduit~parmetis~fortran``

For A100 GPUs, change the above lines to `cuda_arch=80`.
Currently, it's not possible to `build for both GPU models at the same time <https://github.com/Alpine-DAV/ascent/issues/950#issuecomment-1153243232>`_.

Compiling Quokka with Ascent support
^^^^^^^^^^^^^^^^^^^^^^^
1. Load Ascent: ``spack load ascent``
2. Add ``-DAMReX_ASCENT=ON -DAMReX_CONDUIT=ON`` to your CMake options.
3. Compile your problem, e.g.: ``ninja -j4 test_hydro3d_blast``

Customizing the visualization
^^^^^^^^^^^^^^^^^^^^^^^
Add an `ascent_actions.yaml file <https://ascent.readthedocs.io/en/latest/Actions/Actions.html>`_ to the simulation working directory.
This file can even be edited while the simulation is running!

.. warning:: Volume renderings do not correctly handle ghost cells (`GitHub issue <https://github.com/Alpine-DAV/ascent/issues/955>`_).
There are several ways to post-process the output of Quokka simulations.
AMReX PlotfileTools, yt, and VisIt all allow you to analyze the outputs after they are written to disk.

AMReX PlotfileTools
-----------------------
Expand Down Expand Up @@ -80,7 +48,15 @@ For details, see the `yt documentation on reading AMReX data <https://yt-project

VisIt
-----------------------
VisIt can read AMReX plotfiles. You have to select the ``plt00000/Header`` file in VisIt's Open dialog box.
VisIt can read cell-centered output variables from AMReX plotfiles. Currently, there is no support for reading either face-centered variables or particles. (However, by default, cell-centered averages of face-centered variables are included in Quokka plotfiles.)

In order to read an individual plotfile, you can select the ``plt00000/Header`` file in VisIt's Open dialog box.

If you want to read a timeseries of plotfiles, you can create a file with a `.visit` extension that lists the `plt*/Header` files, one per line, with the following command: ::

ls -1 plt*/Header | tee plotfiles.visit

Then select `plotfiles.visit` in VisIt's Open dialog box.

.. warning:: There are rendering bugs with unscaled box dimensions. Slices generally work.
However, do not expect volume rendering to work when using, e.g. parsec-size boxes with cgs units.

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