Richard,
It is likely that for these problems some of the integers become too large
for the int variable to hold them, thus they overflow and become negative.
You should make a new PETSC_ARCH configuration of PETSc that uses the
configure option --with-64-bit-indices, this will change PETSc to use 64 bit
integers which will not overflow.
Good luck and let us know how it works out
Barry
Probably the code is built with an older version of PETSc; the later
versions should produce a more useful error message.
> On Feb 13, 2020, at 11:43 PM, Richard Beare via petsc-users
> <[email protected]> wrote:
>
> Hi Everyone,
> I am experimenting with the Simlul@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
> [email protected]
> +61 3 9788 1724
>
>
>
> Geospatial Research:
> https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis
