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

[Richard Beare]

No luck - exactly the same error after including the
--with-64-bit-indicies=yes --download-mpich=yes options

==8674== Argument 'size' of function memalign has a fishy (possibly
negative) value: -17152036540
==8674==    at 0x4C320A6: memalign (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8674==    by 0x4F0CFF2: PetscMallocAlign(unsigned long, int, char const*,
char const*, void**) (mal.c:28)
==8674==    by 0x4F0F716: PetscTrMallocDefault(unsigned long, int, char
const*, char const*, void**) (mtr.c:188)
==8674==    by 0x569AF3E: MatSeqAIJSetPreallocation_SeqAIJ (aij.c:3595)
==8674==    by 0x569A531: MatSeqAIJSetPreallocation (aij.c:3539)
==8674==    by 0x599080A: DMCreateMatrix_DA_3d_MPIAIJ(_p_DM*, _p_Mat*)
(fdda.c:1085)
==8674==    by 0x598B937: DMCreateMatrix_DA(_p_DM*, _p_Mat**) (fdda.c:759)
==8674==    by 0x58A2BF2: DMCreateMatrix (dm.c:956)
==8674==    by 0x5E377B3: KSPSetUp (itfunc.c:262)
==8674==    by 0x409FFC: PetscAdLemTaras3D::solveModel(bool)
(PetscAdLemTaras3D.hxx:255)
==8674==    by 0x4239FB: AdLem3D<3u>::solveModel(bool, bool, bool)
(AdLem3D.hxx:551)
==8674==    by 0x41BD17: main (PetscAdLemMain.cxx:344)
==8674==
On Fri, 14 Feb 2020 at 17:07, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:

>
>    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 <
> petsc-users at mcs.anl.gov> wrote:
> >
> > 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
>
>

-- 
--
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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