Broken ParaView export for DiffusionGrid

[TobiasDuswald]

Description

Exporting the DiffusionGrid to ParaView leads to unexpected behavior, e.g. I see empty slices, sometimes filled with more or less random data. See images (yet to follow).

Work Log

• Identified that the ParaView export works fine for certain combinations of DiffusionGrid::resolution and OMP_NUM_THREADS. For others it did not work as expected. E.g. resolution = 20 did work well for 4 threads but did not work for 8 threads.
• @Senui observed the same problem and verified on macOS i386
• The current setup always exports a certain number of slices 1 .. N, the error always appears for the first layer of slide N.
• Double checked the entire export pipe line could not find an error.
• Test case resolution = 20 with 4 and 8 threads. 4 threads export 4 * 5 slices. 8 threads export (5*3 + 5), e.g. the last slice should be equivalent. The diff tool shows no difference between the slice N=4 and N=6 for 4 and 8 threads respectively.
• Restructured export in a hopefully more load balanced way using all threads if possible, ⭐ current believe: fixes the problem (:zap: Test fail, not sure if important or why)

To Reproduce

Simply have a diffusion grid and export to PV. Choose resolution%num_threads!=0.
Reproducer to follow.

Expected behavior

No empty space.

Setup (please complete the following information):

• OS: macOS (i386, arm64); Linux (not clear yet)
• BioDynaMo version v1.05.0-137fdb15

[TobiasDuswald]

Often observed:

Expected

[TobiasDuswald]

Reproducer
diffusion.zip

Reproducer is written for resolution 20, if you have 8 threads, you should see strange behavior. Using the branch pv-export should hopefully solve this problem

[TobiasDuswald]

💻 Task for assignees

• Verify bug
• Stress test solution
• Next steps: address failing ParaView tests and Performance

[TobiasDuswald]

discussion with @LukasBreitwieser

• Bug reproducible on Ubuntu 20.04
• Fix works (visually) on Ubuntu 20.04
• Unit tests actually pass; not on macOS
• Explained test

Conclusion: fix tests, hopefully good to go