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verified publisher icon BioDynaMo

Broken ParaView export for `DiffusionGrid`

Open TobiasDuswald opened this issue 3 years ago • 4 comments

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 avatar Oct 13 '22 14:10 TobiasDuswald

Often observed: image

Expected image

TobiasDuswald avatar Oct 13 '22 14:10 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 avatar Oct 13 '22 14:10 TobiasDuswald

💻 Task for assignees

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

TobiasDuswald avatar Oct 13 '22 15:10 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

TobiasDuswald avatar Oct 14 '22 13:10 TobiasDuswald