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
