[petsc-users] Crash caused by strange error in KSPSetUp

[Richard Beare]

Hi Everyone,
I am experimenting with the Simlul at trophy tool (
https://github.com/Inria-Asclepios/simul-atrophy) that uses petsc to
simulate brain atrophy based on segmented MRI data. I am not the author. I
have this running on most of a dataset of about 50 scans, but experience
crashes with several that I am trying to track down. However I am out of
ideas. The problem images are slightly bigger than some of the successful
ones, but not substantially so, and I have experimented on machines with
sufficient RAM. The error happens very quickly, as part of setup - see the
valgrind report below. I haven't managed to get the sgcheck tool to work
yet. I can only guess that the ksp object is somehow becoming corrupted
during the setup process, but the array sizes that I can track (which
derive from image sizes), appear correct at every point I can check. Any
suggestions as to how I can check what might go wrong in the setup of the
ksp object?
Thankyou.

valgrind tells me:

==18175== Argument 'size' of function memalign has a fishy (possibly
negative) value: -17152038144
==18175==    at 0x4C320A6: memalign (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==18175==    by 0x4F0F1F2: PetscMallocAlign(unsigned long, int, char
const*, char const*, void**) (mal.c:28)
==18175==    by 0x56B43CA: MatSeqAIJSetPreallocation_SeqAIJ (aij.c:3595)
==18175==    by 0x56B39BD: MatSeqAIJSetPreallocation (aij.c:3539)
==18175==    by 0x59A9B44: DMCreateMatrix_DA_3d_MPIAIJ(_p_DM*, _p_Mat*)
(fdda.c:1085)
==18175==    by 0x59A4C71: DMCreateMatrix_DA(_p_DM*, _p_Mat**) (fdda.c:759)
==18175==    by 0x58BBD29: DMCreateMatrix (dm.c:956)
==18175==    by 0x5E509D5: KSPSetUp (itfunc.c:262)
==18175==    by 0x40A3DE: PetscAdLemTaras3D::solveModel(bool)
(PetscAdLemTaras3D.hxx:269)
==18175==    by 0x42413F: AdLem3D<3u>::solveModel(bool, bool, bool)
(AdLem3D.hxx:552)
==18175==    by 0x41C25C: main (PetscAdLemMain.cxx:349)
==18175==

-- 
--
A/Prof Richard Beare
Imaging and Bioinformatics, Peninsula Clinical School
orcid.org/0000-0002-7530-5664
Richard.Beare at monash.edu
+61 3 9788 1724



Geospatial Research:
https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis
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