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

Fri Feb 14 15:03:49 CST 2020

I will see if I can build with master. The docs for simulatrophy say
3.6.3.1.

On Sat, 15 Feb 2020 at 02:47, Junchao Zhang <jczhang at mcs.anl.gov> wrote:

> Which petsc version do you use? In aij.c of the master branch, I saw Barry
> recently added a useful check to catch number of nonzero overflow, ierr =
> PetscIntCast(nz64,&nz);CHKERRQ(ierr);  But you mentioned using 64-bit
> indices did not solve the problem, it might not be the reason.  You should
> try the master branch if feasible. Also, vary number of MPI ranks to see if
> error stack changes.
>
> --Junchao Zhang
>
>
> On Fri, Feb 14, 2020 at 5:12 AM Richard Beare via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
>> 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
>>
>

-- 
--
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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