Out-of-bounds, overflow and incorrect outputs in gmx spatial - Redmine #3214
Archive from user: Shun Sakuraba
While using gmx spatial I encountered multiple problems. After reading the source I also found multiple problems that corrupts the results of the analysis (especially the wrong number of grid counts and incorrect coordinates are problematic ones).
- Out-of-bound memory writes
- Confusing error message when the coordinate is exactly on the boundary (happens with .xtc files)
- Norm may become negative due to overflow
- Having negative iIGNOREOUTER (default –1) led to incorrect number of grid points
- The coordinates of the grid points were incorrect especially when iIGNOREOUTER is non-zero
- Norm calculation was incorrect
Attached patches should solve the problems.
(from redmine: issue id 3214, created on 2019-11-25 by gmxdefault)
- Uploads:
- 0001-Fixed-out-of-bound-access-in-gmx-spatial.patch Fixes (1)
- 0003-Fixed-multiple-issues-with-gmx-spatial.patch Fixes (3)-(6)
- 0002-Fixed-incorrect-boundary-conditions-in-gmx-spatial.patch Fixes (1), (2)