Execution Environment for Testing Divergence Free Interpolation in Flash-X + AMReX

Overview of steps to get this lab notebook running.

1. Install Jobrunner, pip install pyjobrunner==2023.8 --user, make sure ~/.local/bin is in your path.

2. Create a new sites folder for you machine see sites/<site-name>

3. Copy sites/sedona/environment.sh and sites/sedona/Makefile.h to sites/<site-name>.

4. Edit sites/<site-name>/environment.sh to set MPI_HOME and HDF5_HOME. If HDF5 is not installed on your machine do step 7.

5. Run configure:

./configure -s <site-name>

This will create config.sh

6. Setup software stack:

jobrunner setup software/amrex
jobrunner setup software/flashx
jobrunner setup software/flashkit

7. If HDF5 is not available on your local machine do:

jobrunner setup  software/hdf5

8. Setup a test simulation:

jobrunner setup simulation/DeformingBubble/DivFreeTest2D

9. Run the simulation

jobrunner submit simulation/DeformingBubble/DivFreeTest2D

Console output can be viewed in file simulation/DeformingBubble/DivFreeTest2D/job.output

10. Postprocessing:

cd simulation/DeformingBubble/DivFreeTest2D
flashkit create xdmf --auto

This will create INS_Deforming_Bubble.xmf that can be opened in paraview.