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 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

Run spack external find.
Make sure there are entries listed for hdf5, cuda, and openmpi in your ~/.spack/packages.yaml file.
Add buildable: False to each entry.
Run spack fetch --dependencies ascent@develop+cuda+vtkh~fortran~shared cuda_arch=70 ^conduit~parmetis~fortran
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.

Compiling Quokka with Ascent support

Load Ascent: spack load ascent
Add -DAMReX_ASCENT=ON -DAMReX_CONDUIT=ON to your CMake options.
Compile your problem, e.g.: ninja -j4 test_hydro3d_blast

Customizing the visualization

Add an ascent_actions.yaml file 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).