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 <[email protected]> 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 < > [email protected]> 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. <[email protected]> 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 < >>> [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 >>> >>> >> >> -- >> -- >> 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 >> > -- -- 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
